vEmbryo In Silico Models: Predicting Vascular Developmental Toxicity

EPA Science Inventory

The cardiovascular system is the first to function in the vertebrate embryo, reflecting the critical need for nutrient delivery and waste removal during organogenesis. Blood vessel development occurs by complex interacting signaling networks, including extra-cellular matrix remod...

Getting Personalization Right!

ERIC Educational Resources Information Center

DeWaters, Carrie

2017-01-01

In today's differentiated classroom, each individual student receives from their teacher student-centered instruction and customized assignments to reflect their skills and knowledge. Teachers differentiate their assignments so each of their students may access the Common Core State Standards, interact with complex nonfiction texts, integrate…

The BioPlex Network: A Systematic Exploration of the Human Interactome.

PubMed

Huttlin, Edward L; Ting, Lily; Bruckner, Raphael J; Gebreab, Fana; Gygi, Melanie P; Szpyt, John; Tam, Stanley; Zarraga, Gabriela; Colby, Greg; Baltier, Kurt; Dong, Rui; Guarani, Virginia; Vaites, Laura Pontano; Ordureau, Alban; Rad, Ramin; Erickson, Brian K; Wühr, Martin; Chick, Joel; Zhai, Bo; Kolippakkam, Deepak; Mintseris, Julian; Obar, Robert A; Harris, Tim; Artavanis-Tsakonas, Spyros; Sowa, Mathew E; De Camilli, Pietro; Paulo, Joao A; Harper, J Wade; Gygi, Steven P

2015-07-16

Protein interactions form a network whose structure drives cellular function and whose organization informs biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7,668 proteins with 86% previously undocumented. BioPlex accurately depicts known complexes, attaining 80%-100% coverage for most CORUM complexes. The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins. More generally, network architecture reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. Network structure also reveals associations among thousands of protein domains, suggesting a basis for examining structurally related proteins. Finally, BioPlex, in combination with other approaches, can be used to reveal interactions of biological or clinical significance. For example, mutations in the membrane protein VAPB implicated in familial amyotrophic lateral sclerosis perturb a defined community of interactors. Copyright © 2015 Elsevier Inc. All rights reserved.

The BioPlex Network: A Systematic Exploration of the Human Interactome

PubMed Central

Huttlin, Edward L.; Ting, Lily; Bruckner, Raphael J.; Gebreab, Fana; Gygi, Melanie P.; Szpyt, John; Tam, Stanley; Zarraga, Gabriela; Colby, Greg; Baltier, Kurt; Dong, Rui; Guarani, Virginia; Vaites, Laura Pontano; Ordureau, Alban; Rad, Ramin; Erickson, Brian K.; Wühr, Martin; Chick, Joel; Zhai, Bo; Kolippakkam, Deepak; Mintseris, Julian; Obar, Robert A.; Harris, Tim; Artavanis-Tsakonas, Spyros; Sowa, Mathew E.; DeCamilli, Pietro; Paulo, Joao A.; Harper, J. Wade; Gygi, Steven P.

2015-01-01

SUMMARY Protein interactions form a network whose structure drives cellular function and whose organization informs biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7,668 proteins with 86% previously undocumented. BioPlex accurately depicts known complexes, attaining 80-100% coverage for most CORUM complexes. The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins. More generally, network architecture reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. Network structure also reveals associations among thousands of protein domains, suggesting a basis for examining structurally-related proteins. Finally, BioPlex, in combination with other approaches can be used to reveal interactions of biological or clinical significance. For example, mutations in the membrane protein VAPB implicated in familial Amyotrophic Lateral Sclerosis perturb a defined community of interactors. PMID:26186194

Brain signal complexity rises with repetition suppression in visual learning.

PubMed

Lafontaine, Marc Philippe; Lacourse, Karine; Lina, Jean-Marc; McIntosh, Anthony R; Gosselin, Frédéric; Théoret, Hugo; Lippé, Sarah

2016-06-21

Neuronal activity associated with visual processing of an unfamiliar face gradually diminishes when it is viewed repeatedly. This process, known as repetition suppression (RS), is involved in the acquisition of familiarity. Current models suggest that RS results from interactions between visual information processing areas located in the occipito-temporal cortex and higher order areas, such as the dorsolateral prefrontal cortex (DLPFC). Brain signal complexity, which reflects information dynamics of cortical networks, has been shown to increase as unfamiliar faces become familiar. However, the complementarity of RS and increases in brain signal complexity have yet to be demonstrated within the same measurements. We hypothesized that RS and brain signal complexity increase occur simultaneously during learning of unfamiliar faces. Further, we expected alteration of DLPFC function by transcranial direct current stimulation (tDCS) to modulate RS and brain signal complexity over the occipito-temporal cortex. Participants underwent three tDCS conditions in random order: right anodal/left cathodal, right cathodal/left anodal and sham. Following tDCS, participants learned unfamiliar faces, while an electroencephalogram (EEG) was recorded. Results revealed RS over occipito-temporal electrode sites during learning, reflected by a decrease in signal energy, a measure of amplitude. Simultaneously, as signal energy decreased, brain signal complexity, as estimated with multiscale entropy (MSE), increased. In addition, prefrontal tDCS modulated brain signal complexity over the right occipito-temporal cortex during the first presentation of faces. These results suggest that although RS may reflect a brain mechanism essential to learning, complementary processes reflected by increases in brain signal complexity, may be instrumental in the acquisition of novel visual information. Such processes likely involve long-range coordinated activity between prefrontal and lower order visual areas. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

Greater than the sum of its parts? Modelling population contact and interaction of cultural repertoires

PubMed Central

Kolodny, Oren; Feldman, Marcus W.

2017-01-01

Evidence for interactions between populations plays a prominent role in the reconstruction of historical and prehistoric human dynamics; these interactions are usually interpreted to reflect cultural practices or demographic processes. The sharp increase in long-distance transportation of lithic material between the Middle and Upper Palaeolithic, for example, is seen as a manifestation of the cultural revolution that defined the transition between these epochs. Here, we propose that population interaction is not only a reflection of cultural change but also a potential driver of it. We explore the possible effects of inter-population migration on cultural evolution when migrating individuals possess core technological knowledge from their original population. Using a computational framework of cultural evolution that incorporates realistic aspects of human innovation processes, we show that migration can lead to a range of outcomes, including punctuated but transient increases in cultural complexity, an increase of cultural complexity to an elevated steady state and the emergence of a positive feedback loop that drives ongoing acceleration in cultural accumulation. Our findings suggest that population contact may have played a crucial role in the evolution of hominin cultures and propose explanations for observations of Palaeolithic cultural change whose interpretations have been hotly debated. PMID:28468920

Collaborative Reflection Under the Microscope: Using Conversation Analysis to Study the Transition From Case Presentation to Discussion in GP Residents' Experience Sharing Sessions.

PubMed

Veen, Mario; de la Croix, Anne

2016-01-01

PHENOMENON: In higher education, reflection sessions are often used when participants learn in the workplace. In the Netherlands, all General Practitioner training programs include regular meetings called Exchange of Experiences, in which General Practitioner trainees are expected to learn collaboratively from their own and one another's experiences. Despite this being common practice, we found little research into the structure and process of these sessions. The purpose of this study is to describe the structure and characteristics of group reflection by describing transitions in interactions. We aim to describe the tutor's role in some detail, as this could lead to faculty development. In medical education, reflection is often approached from a cognitive perspective. However, learning in a group is also an interactional achievement. It is therefore relevant to study the sequential nature of group interaction in collaborative reflective practice. We have used conversation analysis to study the reflection meetings, zooming in on the transition between case presentation and discussion, focusing on the role of each of the participants in these transitions. The transitions were conversationally complex. Three interactional aspects recurred in the meetings. First, the transitions can be characterized as ambiguous, as there is ambiguity about what will happen next and the floor is open. Second, transitions are an arena for negotiations between case presenter, participants, and tutors, in which knowledge and the right to take the floor (epistemics) play an important part. Third, the tutor can have different interactional roles, namely, that of teacher, expert, facilitator, and active participant. The role of the tutor is important as the tutor's interactional behavior is part of the hidden curriculum. Insights: Conversation analysis focuses on the interaction in group learning and shows how the interaction is part of what is learned and how learning takes place. Transitions are the "messy" moments in interaction yet can tell a lot about the way in which group participants relate to one another. Being conscious of how the floor is taken, the tutor's roles, and the way negotiations take place could help medical educators in the way they shape collaborative learning sessions.

Structure-wise discrimination of adenine and guanine by proteins on the basis of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2015-01-01

We have analyzed the nonbonded interactions of the structurally similar moieties, adenine and guanine forming complexes with proteins. The results comprise (a) the amino acid-ligand atom preferences, (b) solvent accessibility of ligand atoms before and after complex formation with proteins, and (c) preferred amino acid residue atoms involved in the interactions. We have observed that the amino acid preferences involved in the hydrogen bonding interactions vary for adenine and guanine. The structural variation between the purine atoms is clearly reflected by their burial tendency in the solvent environment. Correlation of the mean amino acid preference values show the variation that exists between adenine and guanine preferences of all the amino acid residues. All our observations provide evidence for the discriminating nature of the proteins in recognizing adenine and guanine.

Silicon supported lipid-DNA thin film structures at varying temperature studied by energy dispersive X-ray diffraction and neutron reflectivity.

PubMed

Domenici, F; Castellano, C; Dell'Unto, F; Albinati, A; Congiu, A

2011-11-01

Non-viral gene transfection by means of lipid-based nanosystems, such as solid supported lipid assemblies, is often limited due to their lack of stability and the consequent loss of efficiency. Therefore not only a detailed thermo-lyotropic study of these DNA-lipid complexes is necessary to understand their interaction mechanisms, but it can also be considered as a first step in conceiving and developing new transfection biosystems. The aim of our study is a structural characterization of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC)-dimethyl-dioctadecyl-ammonium bromide (DDAB)-DNA complex at varying temperature using the energy dispersive X-ray diffraction (EDXD) and neutron reflectivity (NR) techniques. We have shown the formation of a novel thermo-lyotropic structure of DOPC/DDAB thin film self-organized in multi-lamellar planes on (100)-oriented silicon support by spin coating, thus enlightening its ability to include DNA strands. Our NR measurements indicate that the DOPC/DDAB/DNA complex forms temperature-dependent structures. At 65°C and relative humidity of 100% DNA fragments are buried between single lamellar leaflets constituting the hydrocarbon core of the lipid bilayers. This finding supports the consistency of the hydrophobic interaction model, which implies that the coupling between lipid tails and hypo-hydrated DNA single strands could be the driving force of DNA-lipid complexation. Upon cooling to 25°C, EDXD analysis points out that full-hydrated DOPC-DDAB-DNA can switch in a different metastable complex supposed to be driven by lipid heads-DNA electrostatic interaction. Thermotropic response analysis also clarifies that DOPC has a pivotal role in promoting the formation of our observed thermophylic silicon supported lipids-DNA assembly. Copyright © 2011 Elsevier B.V. All rights reserved.

A laboratory investigation of the variability of cloud reflected radiance fields

NASA Technical Reports Server (NTRS)

Mckee, T. B.; Cox, S. K.

1986-01-01

A method to determine the radiative properties of complex cloud fields was developed. A Cloud field optical simulator (CFOS) was constructed to simulate the interaction of cloud fields with visible radiation. The CFOS was verified by comparing experimental results from it with calculations performed with a Monte Carlo radiative transfer model. A software library was developed to process, reduce, and display CFOS data. The CFSOS was utilized to study the reflected radiane patterns from simulated cloud fields.

Eu(III)-Fulvic Acid Complexation: Evidence of Fulvic Acid Concentration Dependent Interactions by Time-Resolved Luminescence Spectroscopy.

PubMed

Kouhail, Yasmine Z; Benedetti, Marc F; Reiller, Pascal E

2016-04-05

Europium speciation is investigated by time-resolved luminescence spectroscopy (TRLS) in the presence of Suwannee River fulvic acid (SRFA). From complexation isotherms built at different total Eu(III) concentrations, pH values, ionic strength, and SRFA concentrations, it appears that two luminescence behaviors of Eu(III) are occurring. The first part, at the lowest CSRFA values, is showing the typical luminescence evolution of Eu(III) complexed by humic substances--that is, the increase of the asymmetry ratio between the (5)D0 → (7)F2 and (5)D0 → (7)F1 transitions up to a plateau--, and the occurrence of a biexponential decay--the first decay being faster than free Eu(3+). At higher CSRFA, a second luminescence mode is detected as the asymmetry ratio is increasing again after the previous plateau, and could correspond to the formation of another type of complex, and/or it can reflect a different spatial organization of complexed europium within the SRFA structure. The luminescence decay keeps on evolving but link to hydration number is not straightforward due to quenching mechanisms. The Eu(III) chemical environment evolution with CSRFA is also ionic strength dependent. These observations suggest that in addition to short-range interactions--intraparticulate complexation--, there might be interactions at longer range--interparticulate repulsion--between particles that are complexing Eu(III) at high CSRFA. These interactions are not yet accounted by the different complexation models.

Evolutionary Agent-Based Simulation of the Introduction of New Technologies in Air Traffic Management

NASA Technical Reports Server (NTRS)

Yliniemi, Logan; Agogino, Adrian K.; Tumer, Kagan

2014-01-01

Accurate simulation of the effects of integrating new technologies into a complex system is critical to the modernization of our antiquated air traffic system, where there exist many layers of interacting procedures, controls, and automation all designed to cooperate with human operators. Additions of even simple new technologies may result in unexpected emergent behavior due to complex human/ machine interactions. One approach is to create high-fidelity human models coming from the field of human factors that can simulate a rich set of behaviors. However, such models are difficult to produce, especially to show unexpected emergent behavior coming from many human operators interacting simultaneously within a complex system. Instead of engineering complex human models, we directly model the emergent behavior by evolving goal directed agents, representing human users. Using evolution we can predict how the agent representing the human user reacts given his/her goals. In this paradigm, each autonomous agent in a system pursues individual goals, and the behavior of the system emerges from the interactions, foreseen or unforeseen, between the agents/actors. We show that this method reflects the integration of new technologies in a historical case, and apply the same methodology for a possible future technology.

U.S./Arab Reflections on Our Tolerance for Ambiguity

ERIC Educational Resources Information Center

Bright, Larry K.; Mahdi, Ghada S.

2012-01-01

As the authors, a Midwestern American educational administration professor and a Middle Eastern Iraqi doctoral candidate, have continued to interact over the past 3 years, both have come to appreciate the importance of increasing their tolerance for ambiguity--ambiguities in examining cultural, linguistic, and religious customs and complexities in…

Wave reflection in a reaction-diffusion system: breathing patterns and attenuation of the echo.

PubMed

Tsyganov, M A; Ivanitsky, G R; Zemskov, E P

2014-05-01

Formation and interaction of the one-dimensional excitation waves in a reaction-diffusion system with the piecewise linear reaction functions of the Tonnelier-Gerstner type are studied. We show that there exists a parameter region where the established regime of wave propagation depends on initial conditions. Wave phenomena with a complex behavior are found: (i) the reflection of waves at a growing distance (the remote reflection) upon their collision with each other or with no-flux boundaries and (ii) the periodic transformation of waves with the jumping from one regime of wave propagation to another (the periodic trigger wave).

Wave reflection in a reaction-diffusion system: Breathing patterns and attenuation of the echo

NASA Astrophysics Data System (ADS)

Tsyganov, M. A.; Ivanitsky, G. R.; Zemskov, E. P.

2014-05-01

Formation and interaction of the one-dimensional excitation waves in a reaction-diffusion system with the piecewise linear reaction functions of the Tonnelier-Gerstner type are studied. We show that there exists a parameter region where the established regime of wave propagation depends on initial conditions. Wave phenomena with a complex behavior are found: (i) the reflection of waves at a growing distance (the remote reflection) upon their collision with each other or with no-flux boundaries and (ii) the periodic transformation of waves with the jumping from one regime of wave propagation to another (the periodic trigger wave).

Genetic interactions within inositol-related pathways are associated with longitudinal changes in ventricle size

PubMed Central

Koran, Mary Ellen I.; Hohman, Timothy J.; Meda, Shashwath A.; Thornton-Wells, Tricia A.

2013-01-01

The genetic etiology of late onset Alzheimer disease (LOAD) has proven complex, involving clinical and genetic heterogeneity and gene-gene interactions. Recent genome wide association studies (GWAS) in LOAD have led to the discovery of novel genetic risk factors; however, the investigation of gene-gene interactions has been limited. Conventional genetic studies often use binary disease status as the primary phenotype, but for complex brain-based diseases, neuroimaging data can serve as quantitative endophenotypes that correlate with disease status and closely reflect pathological changes. In the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort, we tested for association of genetic interactions with longitudinal MRI measurements of the inferior lateral ventricles (ILVs), which have repeatedly shown a relationship to LOAD status and progression. We performed linear regression to evaluate the ability of pathway-derived SNP-SNP pairs to predict the slope of change in volume of the ILVs. After Bonferroni correction, we identified four significant interactions in the right ILV (RILV) corresponding to gene-gene pairs SYNJ2-PI4KA, PARD3-MYH2, PDE3A-ABHD12B and OR2L13-PRKG1 and one significant interaction in the left ILV (LILV) corresponding to SYNJ2-PI4KA. The SNP-SNP interaction corresponding to SYNJ2-PI4KA was identical in the RILV and LILV and was the most significant interaction in each (RILV: p=9.10×10−12; LILV: p=8.20×10−13). Both genes belong to the inositol phosphate signaling pathway which has been previously associated with neurodegeneration in AD and we discuss the possibility that perturbation of this pathway results in a down-regulation of the Akt cell survival pathway and, thereby, decreased neuronal survival, as reflected by increased volume of the ventricles. PMID:24077433

Tonal synchrony in mother-infant interaction based on harmonic and pentatonic series.

PubMed

Van Puyvelde, Martine; Vanfleteren, Pol; Loots, Gerrit; Deschuyffeleer, Sara; Vinck, Bart; Jacquet, Wolfgang; Verhelst, Werner

2010-12-01

This study reports the occurrence of 'tonal synchrony' as a new dimension of early mother-infant interaction synchrony. The findings are based on a tonal and temporal analysis of vocal interactions between 15 mothers and their 3-month-old infants during 5 min of free-play in a laboratory setting. In total, 558 vocal exchanges were identified and analysed, of which 84% reflected harmonic or pentatonic series. Another 10% of the exchanges contained absolute and/or relative pitch and/or interval imitations. The total durations of dyads being in tonal synchrony were normally distributed (M=3.71, SD=2.44). Vocalisations based on harmonic series appeared organised around the major triad, containing significantly more simple frequency ratios (octave, fifth and third) than complex ones (non-major triad tones). Tonal synchrony and its characteristics are discussed in relation to infant-directed speech, communicative musicality, pre-reflective communication and its impact on the quality of early mother-infant interaction and child's development. Copyright © 2010 Elsevier Inc. All rights reserved.

Ground state atoms confined in a real Rydberg and complex Rydberg-Scarf II potential

NASA Astrophysics Data System (ADS)

Mansoori Kermani, Maryam

2017-12-01

In this work, a system of two ground state atoms confined in a one-dimensional real Rydberg potential was modeled. The atom-atom interaction was considered as a nonlocal separable potential (NLSP) of rank one. This potential was assumed because it leads to an analytical solution of the Lippmann-Schwinger equation. The NLSPs are useful in the few body problems that the many-body potential at each point is replaced by a projective two-body nonlocal potential operator. Analytical expressions for the confined particle resolvent were calculated as a key function in this study. The contributions of the bound and virtual states in the complex energy plane were obtained via the derived transition matrix. Since the low energy quantum scattering problems scattering length is an important quantity, the behavior of this parameter was described versus the reduced energy considering various values of potential parameters. In a one-dimensional model, the total cross section in units of the area is not a meaningful property; however, the reflectance coefficient has a similar role. Therefore the reflectance probability and its behavior were investigated. Then a new confined potential via combining the complex absorbing Scarf II potential with the real Rydberg potential, called the Rydberg-Scarf II potential, was introduced to construct a non-Hermitian Hamiltonian. In order to investigate the effect of the complex potential, the scattering length and reflectance coefficient were calculated. It was concluded that in addition to the competition between the repulsive and attractive parts of both potentials, the imaginary part of the complex potential has an important effect on the properties of the system. The complex potential also reduces the reflectance probability via increasing the absorption probability. For all numerical computations, the parameters of a system including argon gas confined in graphite were considered.

Alignment and integration of complex networks by hypergraph-based spectral clustering

NASA Astrophysics Data System (ADS)

Michoel, Tom; Nachtergaele, Bruno

2012-11-01

Complex networks possess a rich, multiscale structure reflecting the dynamical and functional organization of the systems they model. Often there is a need to analyze multiple networks simultaneously, to model a system by more than one type of interaction, or to go beyond simple pairwise interactions, but currently there is a lack of theoretical and computational methods to address these problems. Here we introduce a framework for clustering and community detection in such systems using hypergraph representations. Our main result is a generalization of the Perron-Frobenius theorem from which we derive spectral clustering algorithms for directed and undirected hypergraphs. We illustrate our approach with applications for local and global alignment of protein-protein interaction networks between multiple species, for tripartite community detection in folksonomies, and for detecting clusters of overlapping regulatory pathways in directed networks.

Alignment and integration of complex networks by hypergraph-based spectral clustering.

PubMed

Michoel, Tom; Nachtergaele, Bruno

2012-11-01

Complex networks possess a rich, multiscale structure reflecting the dynamical and functional organization of the systems they model. Often there is a need to analyze multiple networks simultaneously, to model a system by more than one type of interaction, or to go beyond simple pairwise interactions, but currently there is a lack of theoretical and computational methods to address these problems. Here we introduce a framework for clustering and community detection in such systems using hypergraph representations. Our main result is a generalization of the Perron-Frobenius theorem from which we derive spectral clustering algorithms for directed and undirected hypergraphs. We illustrate our approach with applications for local and global alignment of protein-protein interaction networks between multiple species, for tripartite community detection in folksonomies, and for detecting clusters of overlapping regulatory pathways in directed networks.

A computational interactome for prioritizing genes associated with complex agronomic traits in rice (Oryza sativa).

PubMed

Liu, Shiwei; Liu, Yihui; Zhao, Jiawei; Cai, Shitao; Qian, Hongmei; Zuo, Kaijing; Zhao, Lingxia; Zhang, Lida

2017-04-01

Rice (Oryza sativa) is one of the most important staple foods for more than half of the global population. Many rice traits are quantitative, complex and controlled by multiple interacting genes. Thus, a full understanding of genetic relationships will be critical to systematically identify genes controlling agronomic traits. We developed a genome-wide rice protein-protein interaction network (RicePPINet, http://netbio.sjtu.edu.cn/riceppinet) using machine learning with structural relationship and functional information. RicePPINet contained 708 819 predicted interactions for 16 895 non-transposable element related proteins. The power of the network for discovering novel protein interactions was demonstrated through comparison with other publicly available protein-protein interaction (PPI) prediction methods, and by experimentally determined PPI data sets. Furthermore, global analysis of domain-mediated interactions revealed RicePPINet accurately reflects PPIs at the domain level. Our studies showed the efficiency of the RicePPINet-based method in prioritizing candidate genes involved in complex agronomic traits, such as disease resistance and drought tolerance, was approximately 2-11 times better than random prediction. RicePPINet provides an expanded landscape of computational interactome for the genetic dissection of agronomically important traits in rice. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Research in Reading in English as a Second Language.

ERIC Educational Resources Information Center

Devine, Joanne, Ed.; And Others

This collection of essays, most followed by comments, reflect some aspect of the general theme: reading is a multifacted, complex, interactive process that involves many subskills and many types of reader, as well as text, variables. Papers include: "The Eclectic Synergy of Methods of Reading Research" (Ulla Connor); "A View of…

Planning Effective Educational Programs for Adult Learners

ERIC Educational Resources Information Center

Shi, Hong

2017-01-01

Educational program planning is a complex ongoing process and planners should reflect on and consider for all of the involved factors, context, and people. The purpose of this study is to analyze how to plan effective educational programs for adult learners. Adult education is a developmental process and interacts with broad social events. Adult…

External Mandates and Instructional Leadership: School Leaders as Mediating Agents

ERIC Educational Resources Information Center

Louis, Karen Seashore; Robinson, Viviane M.

2012-01-01

Purpose: The purpose of this paper is to examine how US school leaders make sense of external mandates, and the way in which their understanding of state and district accountability policies affects their work. It is posited that school leaders' responses to external accountability are likely to reflect a complex interaction between their…

Closing the water balance with cosmic-ray soil moisture measurements and assessing their relation to evapotranspiration in two semiarid watersheds

USDA-ARS?s Scientific Manuscript database

Soil moisture dynamics reflect the complex interactions of meteorological conditions with soil, vegetation and terrain properties. In this study, intermediate-scale soil moisture estimates from the cosmic-ray neutron sensing (CRNS) method are evaluated for two semiarid ecosystems in the southwestern...

The utility of vignettes to stimulate reflection on professionalism: theory and practice.

PubMed

Bernabeo, E C; Holmboe, E S; Ross, K; Chesluk, B; Ginsburg, S

2013-08-01

Professionalism remains a substantive theme in medical literature. There is an emerging emphasis on sociological and complex adaptive systems perspectives that refocuses attention from just the individual role to working within one's system to enact professionalism in practice. Reflecting on responses to professional dilemmas may be one method to help practicing physicians identify both internal and external factors contributing to (un) professional behavior. We present a rationale and theoretical framework that supports and guides a reflective approach to the self assessment of professionalism. Guided by principles grounded in this theoretical framework, we developed and piloted a set of vignettes on professionally challenging situations, designed to stimulate reflection in practicing physicians. Findings show that participants found the vignettes to be authentic and typical, and reported the group experience as facilitative around discussions of professional ambiguity. Providing an opportunity for physicians to reflect on professional behavior in an open and safe forum may be a practical way to guide physicians to assess themselves on professional behavior and engage with the complexities of their work. The finding that the focus groups led to reflection at a group level suggests that effective reflection on professional behavior may require a socially interactive process. Emphasizing both the behaviors and the internal and external context in which they occur can thus be viewed as critically important for understanding professionalism in practicing physicians.

Structural insights into the p97-Ufd1-Npl4 complex

PubMed Central

Pye, Valerie E.; Beuron, Fabienne; Keetch, Catherine A.; McKeown, Ciaran; Robinson, Carol V.; Meyer, Hemmo H.; Zhang, Xiaodong; Freemont, Paul S.

2007-01-01

p97/VCP (Cdc48 in yeast) is an essential and abundant member of the AAA+ family of ATPases and is involved in a number of diverse cellular pathways through interactions with different adaptor proteins. The two most characterized adaptors for p97 are p47 and the Ufd1 (ubiquitin fusion degradation 1)-Npl4 (nuclear protein localization 4) complex. p47 directs p97 to membrane fusion events and has been shown to be involved in protein degradation. The Ufd1-Npl4 complex directs p97 to an essential role in endoplasmic reticulum-associated degradation and an important role in mitotic spindle disassembly postmitosis. Here we describe the structural features of the Ufd1-Npl4 complex and its interaction with p97 with the aid of EM and other biophysical techniques. The Ufd1-Npl4 heterodimer has an elongated bilobed structure that is ≈80 × 30 Å in dimension. One Ufd1-Npl4 heterodimer is shown to interact with one p97 hexamer to form the p97-Ufd1-Npl4 complex. The Ufd1-Npl4 heterodimer emanates from one region on the periphery of the N-D1 plane of the p97 hexamer. Intriguingly, the p97-p47 and the p97-Ufd1-Npl4 complexes are significantly different in stoichiometry, symmetry, and quaternary arrangement, reflecting their specific actions and their ability to interact with additional cofactors that cooperate with p97 in diverse cellular pathways. PMID:17202270

Social learning: medical student perceptions of geriatric house calls.

PubMed

Abbey, Linda; Willett, Rita; Selby-Penczak, Rachel; McKnight, Roberta

2010-01-01

Bandura's social learning theory provides a useful conceptual framework to understand medical students' perceptions of a house calls experience at Virginia Commonwealth University School of Medicine. Social learning and role modeling reflect Liaison Committee on Medical Education guidelines for "Medical schools (to) ensure that the learning environment for medical students promotes the development of explicit and appropriate professional attributes (attitudes, behaviors, and identity) in their medical students." This qualitative study reports findings from open-ended survey questions from 123 medical students who observed a preceptor during house calls to elderly homebound patients. Their comments included reflections on the medical treatment as well as interactions with family and professional care providers. Student insights about the social learning process they experienced during house calls to geriatric patients characterized physician role models as dedicated, compassionate, and communicative. They also described patient care in the home environment as comprehensive, personalized, more relaxed, and comfortable. Student perceptions reflect an appreciation of the richness and complexity of details learned from home visits and social interaction with patients, families, and caregivers.

Categorizing Biases in High-Confidence High-Throughput Protein-Protein Interaction Data Sets*

PubMed Central

Yu, Xueping; Ivanic, Joseph; Memišević, Vesna; Wallqvist, Anders; Reifman, Jaques

2011-01-01

We characterized and evaluated the functional attributes of three yeast high-confidence protein-protein interaction data sets derived from affinity purification/mass spectrometry, protein-fragment complementation assay, and yeast two-hybrid experiments. The interacting proteins retrieved from these data sets formed distinct, partially overlapping sets with different protein-protein interaction characteristics. These differences were primarily a function of the deployed experimental technologies used to recover these interactions. This affected the total coverage of interactions and was especially evident in the recovery of interactions among different functional classes of proteins. We found that the interaction data obtained by the yeast two-hybrid method was the least biased toward any particular functional characterization. In contrast, interacting proteins in the affinity purification/mass spectrometry and protein-fragment complementation assay data sets were over- and under-represented among distinct and different functional categories. We delineated how these differences affected protein complex organization in the network of interactions, in particular for strongly interacting complexes (e.g. RNA and protein synthesis) versus weak and transient interacting complexes (e.g. protein transport). We quantified methodological differences in detecting protein interactions from larger protein complexes, in the correlation of protein abundance among interacting proteins, and in their connectivity of essential proteins. In the latter case, we showed that minimizing inherent methodology biases removed many of the ambiguous conclusions about protein essentiality and protein connectivity. We used these findings to rationalize how biological insights obtained by analyzing data sets originating from different sources sometimes do not agree or may even contradict each other. An important corollary of this work was that discrepancies in biological insights did not necessarily imply that one detection methodology was better or worse, but rather that, to a large extent, the insights reflected the methodological biases themselves. Consequently, interpreting the protein interaction data within their experimental or cellular context provided the best avenue for overcoming biases and inferring biological knowledge. PMID:21876202

Complexity and dynamics of topological and community structure in complex networks

NASA Astrophysics Data System (ADS)

Berec, Vesna

2017-07-01

Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

Understanding, creating, and managing complex techno-socio-economic systems: Challenges and perspectives

NASA Astrophysics Data System (ADS)

Helbing, D.; Balietti, S.; Bishop, S.; Lukowicz, P.

2011-05-01

This contribution reflects on the comments of Peter Allen [1], Bikas K. Chakrabarti [2], Péter Érdi [3], Juval Portugali [4], Sorin Solomon [5], and Stefan Thurner [6] on three White Papers (WP) of the EU Support Action Visioneer (www.visioneer.ethz.ch). These White Papers are entitled "From Social Data Mining to Forecasting Socio-Economic Crises" (WP 1) [7], "From Social Simulation to Integrative System Design" (WP 2) [8], and "How to Create an Innovation Accelerator" (WP 3) [9]. In our reflections, the need and feasibility of a "Knowledge Accelerator" is further substantiated by fundamental considerations and recent events around the globe. newpara The Visioneer White Papers propose research to be carried out that will improve our understanding of complex techno-socio-economic systems and their interaction with the environment. Thereby, they aim to stimulate multi-disciplinary collaborations between ICT, the social sciences, and complexity science. Moreover, they suggest combining the potential of massive real-time data, theoretical models, large-scale computer simulations and participatory online platforms. By doing so, it would become possible to explore various futures and to expand the limits of human imagination when it comes to the assessment of the often counter-intuitive behavior of these complex techno-socio-economic-environmental systems. In this contribution, we also highlight the importance of a pluralistic modeling approach and, in particular, the need for a fruitful interaction between quantitative and qualitative research approaches. newpara In an appendix we briefly summarize the concept of the FuturICT flagship project, which will build on and go beyond the proposals made by the Visioneer White Papers. EU flagships are ambitious multi-disciplinary high-risk projects with a duration of at least 10 years amounting to an envisaged overall budget of 1 billion EUR [10]. The goal of the FuturICT flagship initiative is to understand and manage complex, global, socially interactive systems, with a focus on sustainability and resilience.

Decoding the Heart through Next Generation Sequencing Approaches.

PubMed

Pawlak, Michal; Niescierowicz, Katarzyna; Winata, Cecilia Lanny

2018-06-07

: Vertebrate organs develop through a complex process which involves interaction between multiple signaling pathways at the molecular, cell, and tissue levels. Heart development is an example of such complex process which, when disrupted, results in congenital heart disease (CHD). This complexity necessitates a holistic approach which allows the visualization of genome-wide interaction networks, as opposed to assessment of limited subsets of factors. Genomics offers a powerful solution to address the problem of biological complexity by enabling the observation of molecular processes at a genome-wide scale. The emergence of next generation sequencing (NGS) technology has facilitated the expansion of genomics, increasing its output capacity and applicability in various biological disciplines. The application of NGS in various aspects of heart biology has resulted in new discoveries, generating novel insights into this field of study. Here we review the contributions of NGS technology into the understanding of heart development and its disruption reflected in CHD and discuss how emerging NGS based methodologies can contribute to the further understanding of heart repair.

Playful and mindful interactions in the recursive adaptations of the zone of proximal development: a critical complexity science approach

NASA Astrophysics Data System (ADS)

Raia, Federica; Deng, Mario C.

2011-12-01

We discuss Konstantinos Alexakos, Jayson Jones and Victor Rodriguez's hermeneutic study of formation and function of kinship-like relationships among inner city male students of color in a college physics classroom. From our Critical Complexity Science framework we first discuss the reading erlebnisse of students laughing at and with each other as something that immediately captured our attention in being transformative of the classroom. We continue by exploring their classroom and research experience as an emergent structure modifying their collective as well as their individual experiences. As we analyze both the classroom and the research space as a complex system, we reflect on the instructor/students interactions characterized by an asymmetrical "power" relationship. From our analysis we propose to consider the zone of proximal development as the constantly emerging and transforming person experience ( erlebnisse and erfahrung).

A New Theoretical Foundation for Relationship-centered Care

PubMed Central

Suchman, Anthony L

2006-01-01

Relationship-centered care (RCC) is a clinical philosophy that stresses partnership, careful attention to relational process, shared decision-making, and self-awareness. A new complexity-inspired theory of human interaction called complex responsive processes of relating (CRPR) offers strong theoretical confirmation for the principles and practices of RCC, and thus may be of interest to communications researchers and reflective practitioners. It points out the nonlinear nature of human interaction and accounts for the emergence of self-organizing patterns of meaning (e.g., themes or ideas) and patterns of relating (e.g., power relations). CRPR offers fresh new perspectives on the mind, self, communication, and organizations. For observers of interaction, it focuses attention on the nature of moment-to-moment relational process, the value of difference and diversity, and the importance of authentic and responsive participation, thus closely corresponding to and providing theoretical support for RCC. PMID:16405709

What experimental approaches (eg, in vivo, in vitro, tissue retrieval) are effective in investigating the biologic effects of particles?

PubMed Central

Bostrom, Mathias; O'Keefe, Regis

2009-01-01

Understanding the complex cellular and tissue mechanisms and interactions resulting in periprosthetic osteolysis requires a number of experimental approaches, each of which has its own set of advantages and limitations. In vitro models allow for the isolation of individual cell populations and have furthered our understanding of particle-cell interactions; however, they are limited because they do not mimic the complex tissue environment in which multiple cell interactions occur. In vivo animal models investigate the tissue interactions associated with periprosthetic osteolysis, but the choice of species and whether the implant system is subjected to mechanical load or to unloaded conditions are critical in assessing whether these models can be extrapolated to the clinical condition. Rigid analysis of retrieved tissue from clinical cases of osteolysis offers a different approach to studying the biologic process of osteolysis, but it is limited in that the tissue analyzed represents the end-stage of this process and, thus, may not reflect this process adequately. PMID:18612016

What experimental approaches (eg, in vivo, in vitro, tissue retrieval) are effective in investigating the biologic effects of particles?

PubMed

Bostrom, Mathias; O'Keefe, Regis

2008-01-01

Understanding the complex cellular and tissue mechanisms and interactions resulting in periprosthetic osteolysis requires a number of experimental approaches, each of which has its own set of advantages and limitations. In vitro models allow for the isolation of individual cell populations and have furthered our understanding of particle-cell interactions; however, they are limited because they do not mimic the complex tissue environment in which multiple cell interactions occur. In vivo animal models investigate the tissue interactions associated with periprosthetic osteolysis, but the choice of species and whether the implant system is subjected to mechanical load or to unloaded conditions are critical in assessing whether these models can be extrapolated to the clinical condition. Rigid analysis of retrieved tissue from clinical cases of osteolysis offers a different approach to studying the biologic process of osteolysis, but it is limited in that the tissue analyzed represents the end-stage of this process and, thus, may not reflect this process adequately.

Direct interaction enables cross-talk between ionotropic and group I metabotropic glutamate receptors.

PubMed

Perroy, Julie; Raynaud, Fabrice; Homburger, Vincent; Rousset, Marie-Claude; Telley, Ludovic; Bockaert, Joël; Fagni, Laurent

2008-03-14

Functional interplay between ionotropic and metabotropic receptors frequently involves complex intracellular signaling cascades. The group I metabotropic glutamate receptor mGlu5a co-clusters with the ionotropic N-methyl-d-aspartate (NMDA) receptor in hippocampal neurons. In this study, we report that a more direct cross-talk can exist between these types of receptors. Using bioluminescence resonance energy transfer in living HEK293 cells, we demonstrate that mGlu5a and NMDA receptor clustering reflects the existence of direct physical interactions. Consequently, the mGlu5a receptor decreased NMDA receptor current, and reciprocally, the NMDA receptor strongly reduced the ability of the mGlu5a receptor to release intracellular calcium. We show that deletion of the C terminus of the mGlu5a receptor abolished both its interaction with the NMDA receptor and reciprocal inhibition of the receptors. This direct functional interaction implies a higher degree of target-effector specificity, timing, and subcellular localization of signaling than could ever be predicted with complex signaling pathways.

Storytelling as Academic Discourse: Bridging the Cultural-Linguistic Divide in the Era of the Common Core

ERIC Educational Resources Information Center

Lin, Ching Ching

2014-01-01

Bakhtin's dialogism provides a sociocultural approach that views language as a social practice informed by the complex interaction between discourse and meaning. Drawing on this theoretical framework, I argue that a dialogized version of storytelling can be helpful in creating a reflective form of academic discourse that bridges the gap between…

Advancing Understanding of Affordability in Washington State: An Interactive Model Exploring Student Higher Education Financing

ERIC Educational Resources Information Center

Fridley, James L.; Sharpe, Rachelle E.

2016-01-01

Higher education affordability is a complex concept that reflects resources available from multiple parties, the remaining cost of education, and the ability of students and families to pay the balance. States play a key role in determining the affordability of higher education for students attending public institutions. Yet decisions are made…

Classroom Conversation Analysis and Critical Reflective Practice: Self-Evaluation of Teacher Talk Framework in Focus

ERIC Educational Resources Information Center

Ghafarpour, Hajar

2017-01-01

The uniqueness of the Language Classroom and its complexity raises a need for foreign language teachers to develop necessary skills and knowledge to observe, analyse and evaluate their classroom discourse. Hence, interactional awareness of language teachers is an integral part of pedagogical and practical knowledge. In this article, the…

Developing Family Psychoeducational Treatments for Patients with Bipolar and Other Severe Psychiatric Disorders: A Pathway from Basic Research to Clinical Trials.

ERIC Educational Resources Information Center

Miklowitz, David J.; Hooley, Jill M.

1998-01-01

Describes the development pathway of family treatments for patients with severe and persistent psychiatric disorders in a population for whom family attributes have prognostic importance. The methodological complexities of psychosocial treatment studies are many. Moreover, the results of these studies often reflect interactions between treatment,…

Multiplex PageRank.

PubMed

Halu, Arda; Mondragón, Raúl J; Panzarasa, Pietro; Bianconi, Ginestra

2013-01-01

Many complex systems can be described as multiplex networks in which the same nodes can interact with one another in different layers, thus forming a set of interacting and co-evolving networks. Examples of such multiplex systems are social networks where people are involved in different types of relationships and interact through various forms of communication media. The ranking of nodes in multiplex networks is one of the most pressing and challenging tasks that research on complex networks is currently facing. When pairs of nodes can be connected through multiple links and in multiple layers, the ranking of nodes should necessarily reflect the importance of nodes in one layer as well as their importance in other interdependent layers. In this paper, we draw on the idea of biased random walks to define the Multiplex PageRank centrality measure in which the effects of the interplay between networks on the centrality of nodes are directly taken into account. In particular, depending on the intensity of the interaction between layers, we define the Additive, Multiplicative, Combined, and Neutral versions of Multiplex PageRank, and show how each version reflects the extent to which the importance of a node in one layer affects the importance the node can gain in another layer. We discuss these measures and apply them to an online multiplex social network. Findings indicate that taking the multiplex nature of the network into account helps uncover the emergence of rankings of nodes that differ from the rankings obtained from one single layer. Results provide support in favor of the salience of multiplex centrality measures, like Multiplex PageRank, for assessing the prominence of nodes embedded in multiple interacting networks, and for shedding a new light on structural properties that would otherwise remain undetected if each of the interacting networks were analyzed in isolation.

Unpacking the Complex Relationship Between Beliefs, Practice, and Change Related to Inquiry-Based Instruction of One Science Teacher

NASA Astrophysics Data System (ADS)

Lebak, Kimberly

2015-12-01

This case study examines the complex relationship between beliefs, practice, and change related to inquiry-based instruction of one science teacher teaching in a high-poverty urban school. This study explores how video-supported collaboration with peers can provide the catalyst for change. Transcribed collaborative dialogue sessions, written self-reflections, and videotapes of lessons were used to identify and isolate the belief systems that were critical to the teacher's decision making. The Interconnected Model of Professional Growth was then used to trace the trajectories of change of the individual belief systems. Analysis of the data revealed the relationship between beliefs and practices was complex in which initially espoused beliefs were often inconsistent with enacted practice and some beliefs emerged as more salient than others for influencing practice. Furthermore, this research indicates change in both beliefs and practice was an interactive process mediated by collaborative and self-reflection through participation in the video-supported process.

Neutron Reflectivity as a Tool for Physics-Based Studies of Model Bacterial Membranes.

PubMed

Barker, Robert D; McKinley, Laura E; Titmuss, Simon

2016-01-01

The principles of neutron reflectivity and its application as a tool to provide structural information at the (sub-) molecular unit length scale from models for bacterial membranes are described. The model membranes can take the form of a monolayer for a single leaflet spread at the air/water interface, or bilayers of increasing complexity at the solid/liquid interface. Solid-supported bilayers constrain the bilayer to 2D but can be used to characterize interactions with antimicrobial peptides and benchmark high throughput lab-based techniques. Floating bilayers allow for membrane fluctuations, making the phase behaviour more representative of native membranes. Bilayers of varying levels of compositional accuracy can now be constructed, facilitating studies with aims that range from characterizing the fundamental physical interactions, through to the characterization of accurate mimetics for the inner and outer membranes of Gram-negative bacteria. Studies of the interactions of antimicrobial peptides with monolayer and bilayer models for the inner and outer membranes have revealed information about the molecular control of the outer membrane permeability, and the mode of interaction of antimicrobials with both inner and outer membranes.

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

Mehta, Y.; Neal, C.; Salari, K.

Propagation of a strong shock through a bed of particles results in complex wave dynamics such as a reflected shock, a transmitted shock, and highly unsteady flow inside the particle bed. In this paper we present three-dimensional numerical simulations of shock propagation in air over a random bed of particles. We assume the flow is inviscid and governed by the Euler equations of gas dynamics. Simulations are carried out by varying the volume fraction of the particle bed at a fixed shock Mach number. We compute the unsteady inviscid streamwise and transverse drag coefficients as a function of time formore » each particle in the random bed as a function of volume fraction. We show that (i) there are significant variations in the peak drag for the particles in the bed, (ii) the mean peak drag as a function of streamwise distance through the bed decreases with a slope that increases as the volume fraction increases, and (iii) the deviation from the mean peak drag does not correlate with local volume fraction. We also present the local Mach number and pressure contours for the different volume fractions to explain the various observed complex physical mechanisms occurring during the shock-particle interactions. Since the shock interaction with the random bed of particles leads to transmitted and reflected waves, we compute the average flow properties to characterize the strength of the transmitted and reflected shock waves and quantify the energy dissipation inside the particle bed. Finally, to better understand the complex wave dynamics in a random bed, we consider a simpler approximation of a planar shock propagating in a duct with a sudden area change. We obtain Riemann solutions to this problem, which are used to compare with fully resolved numerical simulations.« less

An Analysis Method for Superconducting Resonator Parameter Extraction with Complex Baseline Removal

NASA Technical Reports Server (NTRS)

Cataldo, Giuseppe

2014-01-01

A new semi-empirical model is proposed for extracting the quality (Q) factors of arrays of superconducting microwave kinetic inductance detectors (MKIDs). The determination of the total internal and coupling Q factors enables the computation of the loss in the superconducting transmission lines. The method used allows the simultaneous analysis of multiple interacting discrete resonators with the presence of a complex spectral baseline arising from reflections in the system. The baseline removal allows an unbiased estimate of the device response as measured in a cryogenic instrumentation setting.

Theoretical Study on the Photoelectron Spectra of Ln(COT)2-: Lanthanide Dependence of the Metal-Ligand Interaction.

PubMed

Nakajo, Erika; Masuda, Tomohide; Yabushita, Satoshi

2016-12-08

We have performed a theoretical analysis of the recently reported photoelectron (PE) spectra of the series of sandwich complex anions Ln(COT) 2 - (Ln = La-Lu, COT = 1,3,5,7-cyclooctatetraene), focusing on the Ln dependence of the vertical detachment energies. For most Ln, the π molecular orbitals, largely localized on the COT ligands, have the energy order of e 1g < e 1u < e 2g < e 2u as in the actinide analogues, reflecting the substantial orbital interaction with the Ln 5d and 5p orbitals. Thus, it would be expected that the lanthanide contraction would increase the orbital interaction so that the overlaps between the COT π and Ln atomic orbitals tend to increase across the series. However, the PE spectra and theoretical calculations were not consistent with this expectation, and the details have been clarified in this study. Furthermore, the energy level splitting patterns of the anion and neutral complexes have been studied by multireference ab initio methods, and the X peak splittings observed in the PE spectra only for the middle-range Ln complexes were found to be due to the specific interaction between the Ln 4f and ligand π orbitals of the neutral complexes in e 2u symmetry. Because the magnitude of this 4f-ligand interaction depends critically on the final state 4f electron configuration and the spin state, a significant Ln dependence in the PE spectra is explained.

Musical rhythm and pitch: A differential effect on auditory dynamics as revealed by the N1/MMN/P3a complex.

PubMed

Lelo-de-Larrea-Mancera, E Sebastian; Rodríguez-Agudelo, Yaneth; Solís-Vivanco, Rodolfo

2017-06-01

Music represents a complex form of human cognition. To what extent our auditory system is attuned to music is yet to be clearly understood. Our principal aim was to determine whether the neurophysiological operations underlying pre-attentive auditory change detection (N1 enhancement (N1e)/Mismatch Negativity (MMN)) and the subsequent involuntary attentional reallocation (P3a) towards infrequent sound omissions, are influenced by differences in musical content. Specifically, we intended to explore any interaction effects that rhythmic and pitch dimensions of musical organization may have over these processes. Results showed that both the N1e and MMN amplitudes were differentially influenced by rhythm and pitch dimensions. MMN latencies were shorter for musical structures containing both features. This suggests some neurocognitive independence between pitch and rhythm domains, but also calls for further address on possible interactions between both of them at the level of early, automatic auditory detection. Furthermore, results demonstrate that the N1e reflects basic sensory memory processes. Lastly, we show that the involuntary switch of attention associated with the P3a reflects a general-purpose mechanism not modulated by musical features. Altogether, the N1e/MMN/P3a complex elicited by infrequent sound omissions revealed evidence of musical influence over early stages of auditory perception. Copyright © 2017 Elsevier Ltd. All rights reserved.

­Understanding Information Flow Interaction along Separable Causal Paths in Environmental Signals

NASA Astrophysics Data System (ADS)

Jiang, P.; Kumar, P.

2017-12-01

Multivariate environmental signals reflect the outcome of complex inter-dependencies, such as those in ecohydrologic systems. Transfer entropy and information partitioning approaches have been used to characterize such dependencies. However, these approaches capture net information flow occurring through a multitude of pathways involved in the interaction and as a result mask our ability to discern the causal interaction within an interested subsystem through specific pathways. We build on recent developments of momentary information transfer along causal paths proposed by Runge [2015] to develop a framework for quantifying information decomposition along separable causal paths. Momentary information transfer along causal paths captures the amount of information flow between any two variables lagged at two specific points in time. Our approach expands this concept to characterize the causal interaction in terms of synergistic, unique and redundant information flow through separable causal paths. Multivariate analysis using this novel approach reveals precise understanding of causality and feedback. We illustrate our approach with synthetic and observed time series data. We believe the proposed framework helps better delineate the internal structure of complex systems in geoscience where huge amounts of observational datasets exist, and it will also help the modeling community by providing a new way to look at the complexity of real and modeled systems. Runge, Jakob. "Quantifying information transfer and mediation along causal pathways in complex systems." Physical Review E 92.6 (2015): 062829.

Historical Reflections on the Ascendancy of ADHD in North America, c. 1980 - c. 2005

ERIC Educational Resources Information Center

Neufeld, Paul; Foy, Michael

2006-01-01

An ecological niche framework (Hacking, 1998) is utilised to examine the growth of ADHD in North America. The analysis suggests ADHD flourishes, at least in part, due to a complex and historically situated interaction of factors that created a niche within which a particular kind of explanation and treatment for the troubling behaviours of…

Quantifying covalent interactions with resonant inelastic soft X-ray scattering: Case study of Ni 2+ aqua complex

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

Kunnus, K.; Josefsson, I.; Schreck, S.

We analyze the effects of covalent interactions in Ni 2p3d resonant inelastic X-ray scattering (RIXS) spectra from aqueous Ni 2+ ions and find that the relative RIXS intensities of ligand-to-metal charge-transfer final states with respect to the ligand-field final states reflect the covalent mixing between Ni 3d and water orbitals. Specifically, the experimental intensity ratio at the Ni L 3-edge allows to determine that the Ni 3d orbitals have on average 5.5% of water character. Here, we propose that 2p3d RIXS at the Ni L 3-edge can be utilized to quantify covalency in Ni complexes without the use of externalmore » references or simulations.« less

Quantifying covalent interactions with resonant inelastic soft X-ray scattering: Case study of Ni 2+ aqua complex

DOE PAGES

Kunnus, K.; Josefsson, I.; Schreck, S.; ...

2016-12-23

We analyze the effects of covalent interactions in Ni 2p3d resonant inelastic X-ray scattering (RIXS) spectra from aqueous Ni 2+ ions and find that the relative RIXS intensities of ligand-to-metal charge-transfer final states with respect to the ligand-field final states reflect the covalent mixing between Ni 3d and water orbitals. Specifically, the experimental intensity ratio at the Ni L 3-edge allows to determine that the Ni 3d orbitals have on average 5.5% of water character. Here, we propose that 2p3d RIXS at the Ni L 3-edge can be utilized to quantify covalency in Ni complexes without the use of externalmore » references or simulations.« less

Graph distance for complex networks

NASA Astrophysics Data System (ADS)

Shimada, Yutaka; Hirata, Yoshito; Ikeguchi, Tohru; Aihara, Kazuyuki

2016-10-01

Networks are widely used as a tool for describing diverse real complex systems and have been successfully applied to many fields. The distance between networks is one of the most fundamental concepts for properly classifying real networks, detecting temporal changes in network structures, and effectively predicting their temporal evolution. However, this distance has rarely been discussed in the theory of complex networks. Here, we propose a graph distance between networks based on a Laplacian matrix that reflects the structural and dynamical properties of networked dynamical systems. Our results indicate that the Laplacian-based graph distance effectively quantifies the structural difference between complex networks. We further show that our approach successfully elucidates the temporal properties underlying temporal networks observed in the context of face-to-face human interactions.

Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns.

PubMed

Lezon, Timothy R; Banavar, Jayanth R; Cieplak, Marek; Maritan, Amos; Fedoroff, Nina V

2006-12-12

We describe a method based on the principle of entropy maximization to identify the gene interaction network with the highest probability of giving rise to experimentally observed transcript profiles. In its simplest form, the method yields the pairwise gene interaction network, but it can also be extended to deduce higher-order interactions. Analysis of microarray data from genes in Saccharomyces cerevisiae chemostat cultures exhibiting energy metabolic oscillations identifies a gene interaction network that reflects the intracellular communication pathways that adjust cellular metabolic activity and cell division to the limiting nutrient conditions that trigger metabolic oscillations. The success of the present approach in extracting meaningful genetic connections suggests that the maximum entropy principle is a useful concept for understanding living systems, as it is for other complex, nonequilibrium systems.

The `What is a system' reflection interview as a knowledge integration activity for high school students' understanding of complex systems in human biology

NASA Astrophysics Data System (ADS)

Tripto, Jaklin; Ben-Zvi Assaraf, Orit; Snapir, Zohar; Amit, Miriam

2016-03-01

This study examined the reflection interview as a tool for assessing and facilitating the use of 'systems language' amongst 11th grade students who have recently completed their first year of high school biology. Eighty-three students composed two concept maps in the 10th grade-one at the beginning of the school year and one at its end. The first part of the interview is dedicated to guiding the students through comparing their two concept maps and by means of both explicit and non-explicit teaching. Our study showed that the explicit guidance in comparing the two concept maps was more effective than the non-explicit, eliciting a variety of different, more specific, types of interactions and patterns (e.g. 'hierarchy', 'dynamism', 'homeostasis') in the students' descriptions of the human body system. The reflection interview as a knowledge integration activity was found to be an effective tool for assessing the subjects' conceptual models of 'system complexity', and for identifying those aspects of a system that are most commonly misunderstood.

Hierarchical temporal structure in music, speech and animal vocalizations: jazz is like a conversation, humpbacks sing like hermit thrushes.

PubMed

Kello, Christopher T; Bella, Simone Dalla; Médé, Butovens; Balasubramaniam, Ramesh

2017-10-01

Humans talk, sing and play music. Some species of birds and whales sing long and complex songs. All these behaviours and sounds exhibit hierarchical structure-syllables and notes are positioned within words and musical phrases, words and motives in sentences and musical phrases, and so on. We developed a new method to measure and compare hierarchical temporal structures in speech, song and music. The method identifies temporal events as peaks in the sound amplitude envelope, and quantifies event clustering across a range of timescales using Allan factor (AF) variance. AF variances were analysed and compared for over 200 different recordings from more than 16 different categories of signals, including recordings of speech in different contexts and languages, musical compositions and performances from different genres. Non-human vocalizations from two bird species and two types of marine mammals were also analysed for comparison. The resulting patterns of AF variance across timescales were distinct to each of four natural categories of complex sound: speech, popular music, classical music and complex animal vocalizations. Comparisons within and across categories indicated that nested clustering in longer timescales was more prominent when prosodic variation was greater, and when sounds came from interactions among individuals, including interactions between speakers, musicians, and even killer whales. Nested clustering also was more prominent for music compared with speech, and reflected beat structure for popular music and self-similarity across timescales for classical music. In summary, hierarchical temporal structures reflect the behavioural and social processes underlying complex vocalizations and musical performances. © 2017 The Author(s).

Ultrasonic monitoring of pitting corrosion

NASA Astrophysics Data System (ADS)

Jarvis, A. J. C.; Cegla, F. B.; Bazaz, H.; Lozev, M.

2013-01-01

Exposure to corrosive substances in high temperature environments can cause damage accumulation in structural steels, particularly in the chemical and petrochemical industries. The interaction mechanisms are complex and varied; however initial damage propagation often manifests itself in the form of localized areas of increased material loss. Recent development of an ultrasonic wall thickness monitoring sensor capable of withstanding temperatures in excess of 500°C has allowed permanent monitoring within such hostile environments, providing information on how the shape of a pulse which has reflected from a corroding surface can change over time. Reconstructing localized corrosion depth and position may be possible by tracking such changes in reflected pulse shape, providing extra information on the state of the backwall and whether process conditions should be altered to increase plant life. This paper aims to experimentally investigate the effect certain localized features have on reflected pulse shape by `growing' artificial defects into the backwall while wall thickness is monitored using the sensor. The size and complexity of the three dimensional scattering problem lead to the development of a semi-analytical simulation based on the distributed point source method (DPSM) which is capable of simulating pulse reflection from complex surfaces measuring approximately 17×10λ Comparison to experimental results show that amplitude changes are predicted to within approximately 1dB and that pulse shape changes are accurately modelled. All experiments were carried out at room temperature, measurements at high temperature will be studied in the future.

Body sway reflects leadership in joint music performance.

PubMed

Chang, Andrew; Livingstone, Steven R; Bosnyak, Dan J; Trainor, Laurel J

2017-05-23

The cultural and technological achievements of the human species depend on complex social interactions. Nonverbal interpersonal coordination, or joint action, is a crucial element of social interaction, but the dynamics of nonverbal information flow among people are not well understood. We used joint music making in string quartets, a complex, naturalistic nonverbal behavior, as a model system. Using motion capture, we recorded body sway simultaneously in four musicians, which reflected real-time interpersonal information sharing. We used Granger causality to analyze predictive relationships among the motion time series of the players to determine the magnitude and direction of information flow among the players. We experimentally manipulated which musician was the leader (followers were not informed who was leading) and whether they could see each other, to investigate how these variables affect information flow. We found that assigned leaders exerted significantly greater influence on others and were less influenced by others compared with followers. This effect was present, whether or not they could see each other, but was enhanced with visual information, indicating that visual as well as auditory information is used in musical coordination. Importantly, performers' ratings of the "goodness" of their performances were positively correlated with the overall degree of body sway coupling, indicating that communication through body sway reflects perceived performance success. These results confirm that information sharing in a nonverbal joint action task occurs through both auditory and visual cues and that the dynamics of information flow are affected by changing group relationships.

Body sway reflects leadership in joint music performance

PubMed Central

Livingstone, Steven R.; Bosnyak, Dan J.; Trainor, Laurel J.

2017-01-01

The cultural and technological achievements of the human species depend on complex social interactions. Nonverbal interpersonal coordination, or joint action, is a crucial element of social interaction, but the dynamics of nonverbal information flow among people are not well understood. We used joint music making in string quartets, a complex, naturalistic nonverbal behavior, as a model system. Using motion capture, we recorded body sway simultaneously in four musicians, which reflected real-time interpersonal information sharing. We used Granger causality to analyze predictive relationships among the motion time series of the players to determine the magnitude and direction of information flow among the players. We experimentally manipulated which musician was the leader (followers were not informed who was leading) and whether they could see each other, to investigate how these variables affect information flow. We found that assigned leaders exerted significantly greater influence on others and were less influenced by others compared with followers. This effect was present, whether or not they could see each other, but was enhanced with visual information, indicating that visual as well as auditory information is used in musical coordination. Importantly, performers’ ratings of the “goodness” of their performances were positively correlated with the overall degree of body sway coupling, indicating that communication through body sway reflects perceived performance success. These results confirm that information sharing in a nonverbal joint action task occurs through both auditory and visual cues and that the dynamics of information flow are affected by changing group relationships. PMID:28484007

Interferometric synthetic aperture radar: Building tomorrow's tools today

USGS Publications Warehouse

Lu, Zhong

2006-01-01

A synthetic aperture radar (SAR) system transmits electromagnetic (EM) waves at a wavelength that can range from a few millimeters to tens of centimeters. The radar wave propagates through the atmosphere and interacts with the Earth’s surface. Part of the energy is reflected back to the SAR system and recorded. Using a sophisticated image processing technique, called SAR processing (Curlander and McDonough, 1991), both the intensity and phase of the reflected (or backscattered) signal of each ground resolution element (a few meters to tens of meters) can be calculated in the form of a complex-valued SAR image representing the reflectivity of the ground surface. The amplitude or intensity of the SAR image is determined primarily by terrain slope, surface roughness, and dielectric constants, whereas the phase of the SAR image is determined primarily by the distance between the satellite antenna and the ground targets, slowing of the signal by the atmosphere, and the interaction of EM waves with ground surface. Interferometric SAR (InSAR) imaging, a recently developed remote sensing technique, utilizes the interaction of EM waves, referred to as interference, to measure precise distances. Very simply, InSAR involves the use of two or more SAR images of the same area to extract landscape topography and its deformation patterns.

Mechanisms and behavioural functions of structural coloration in cephalopods

PubMed Central

Mäthger, Lydia M.; Denton, Eric J.; Marshall, N. Justin; Hanlon, Roger T.

2008-01-01

Octopus, squid and cuttlefish are renowned for rapid adaptive coloration that is used for a wide range of communication and camouflage. Structural coloration plays a key role in augmenting the skin patterning that is produced largely by neurally controlled pigmented chromatophore organs. While most iridescence and white scattering is produced by passive reflectance or diffusion, some iridophores in squid are actively controlled via a unique cholinergic, non-synaptic neural system. We review the recent anatomical and experimental evidence regarding the mechanisms of reflection and diffusion of light by the different cell types (iridophores and leucophores) of various cephalopod species. The structures that are responsible for the optical effects of some iridophores and leucophores have recently been shown to be proteins. Optical interactions with the overlying pigmented chromatophores are complex, and the recent measurements are presented and synthesized. Polarized light reflected from iridophores can be passed through the chromatophores, thus enabling the use of a discrete communication channel, because cephalopods are especially sensitive to polarized light. We illustrate how structural coloration contributes to the overall appearance of the cephalopods during intra- and interspecific behavioural interactions including camouflage. PMID:19091688

Integration of Quartz Crystal Microbalance-Dissipation and Reflection-Mode Localized Surface Plasmon Resonance Sensors for Biomacromolecular Interaction Analysis.

PubMed

Ferhan, Abdul Rahim; Jackman, Joshua A; Cho, Nam-Joon

2016-12-20

The combination of label-free, surface-sensitive measurement techniques based on different physical principles enables detailed characterization of biomacromolecular interactions at solid-liquid interfaces. To date, most combined measurement systems have involved experimental techniques with similar probing volumes, whereas the potential of utilizing techniques with different surface sensitivities remains largely unexplored, especially for data interpretation. Herein, we report a combined measurement approach that integrates a conventional quartz crystal microbalance-dissipation (QCM-D) setup with a reflection-mode localized surface plasmon (LSPR) sensor. Using this platform, we investigate vesicle adsorption on a titanium oxide-coated sensing substrate along with the amphipathic, α-helical (AH) peptide-induced structural transformation of surface-adsorbed lipid vesicles into a supported lipid bilayer (SLB) as a model biomacromolecular interaction. While the QCM-D and LSPR signals both detected mass uptake arising from vesicle adsorption, tracking the AH peptide-induced structural transformation revealed more complex measurement responses based on the different surface sensitivities of the two techniques. In particular, the LSPR signal recorded an increase in optical mass near the sensor surface which indicated SLB formation, whereas the QCM-D signals detected a significant loss in net acoustic mass due to excess lipid and coupled solvent leaving the probing volume. Importantly, these measurement capabilities allowed us to temporally distinguish the process of SLB formation at the sensor surface from the overall structural transformation process. Looking forward, these label-free measurement capabilities to simultaneously probe adsorbates at multiple length scales will provide new insights into complex biomacromolecular interactions.

PRIC320, a transcription coactivator, isolated from peroxisome proliferator-binding protein complex.

PubMed

Surapureddi, Sailesh; Viswakarma, Navin; Yu, Songtao; Guo, Dongsheng; Rao, M Sambasiva; Reddy, Janardan K

2006-05-05

Ciprofibrate, a potent peroxisome proliferator, induces pleiotropic responses in liver by activating peroxisome proliferator-activated receptor alpha (PPARalpha), a nuclear receptor. Transcriptional regulation by liganded nuclear receptors involves the participation of coregulators that form multiprotein complexes possibly to achieve cell and gene specific transcription. SDS-PAGE and matrix-assisted laser desorption/ionization reflection time-of-flight mass spectrometric analyses of ciprofibrate-binding proteins from liver nuclear extracts obtained using ciprofibrate-Sepharose affinity matrix resulted in the identification of a new high molecular weight nuclear receptor coactivator, which we designated PRIC320. The full-length human cDNA encoding this protein has an open-reading frame that codes for a 320kDa protein containing 2882 amino acids. PRIC320 contains five LXXLL signature motifs that mediate interaction with nuclear receptors. PRIC320 binds avidly to nuclear receptors PPARalpha, CAR, ERalpha, and RXR, but only minimally with PPARgamma. PRIC320 also interacts with transcription cofactors CBP, PRIP, and PBP. Immunoprecipitation-immunoblotting as well as cellular localization studies confirmed the interaction between PPARalpha and PRIC320. PRIC320 acts as a transcription coactivator by stimulating PPARalpha-mediated transcription. We conclude that ciprofibrate, a PPARalpha ligand, binds a multiprotein complex and PRIC320 cloned from this complex functions as a nuclear receptor coactivator.

Balance of Interactions Determines Optimal Survival in Multi-Species Communities.

PubMed

Choudhary, Anshul; Sinha, Sudeshna

2015-01-01

We consider a multi-species community modelled as a complex network of populations, where the links are given by a random asymmetric connectivity matrix J, with fraction 1 - C of zero entries, where C reflects the over-all connectivity of the system. The non-zero elements of J are drawn from a Gaussian distribution with mean μ and standard deviation σ. The signs of the elements Jij reflect the nature of density-dependent interactions, such as predatory-prey, mutualism or competition, and their magnitudes reflect the strength of the interaction. In this study we try to uncover the broad features of the inter-species interactions that determine the global robustness of this network, as indicated by the average number of active nodes (i.e. non-extinct species) in the network, and the total population, reflecting the biomass yield. We find that the network transitions from a completely extinct system to one where all nodes are active, as the mean interaction strength goes from negative to positive, with the transition getting sharper for increasing C and decreasing σ. We also find that the total population, displays distinct non-monotonic scaling behaviour with respect to the product μC, implying that survival is dependent not merely on the number of links, but rather on the combination of the sparseness of the connectivity matrix and the net interaction strength. Interestingly, in an intermediate window of positive μC, the total population is maximal, indicating that too little or too much positive interactions is detrimental to survival. Rather, the total population levels are optimal when the network has intermediate net positive connection strengths. At the local level we observe marked qualitative changes in dynamical patterns, ranging from anti-phase clusters of period 2 cycles and chaotic bands, to fixed points, under the variation of mean μ of the interaction strengths. We also study the correlation between synchronization and survival, and find that synchronization does not necessarily lead to extinction. Lastly, we propose an effective low dimensional map to capture the behavior of the entire network, and this provides a broad understanding of the interplay of the local dynamical patterns and the global robustness trends in the network.

The GSTome Reflects the Chemical Environment of White-Rot Fungi

PubMed Central

Deroy, Aurélie; Saiag, Fanny; Kebbi-Benkeder, Zineb; Touahri, Nassim; Hecker, Arnaud; Morel-Rouhier, Mélanie; Colin, Francis; Dumarcay, Stephane; Gérardin, Philippe; Gelhaye, Eric

2015-01-01

White-rot fungi possess the unique ability to degrade and mineralize all the different components of wood. In other respects, wood durability, among other factors, is due to the presence of extractives that are potential antimicrobial molecules. To cope with these molecules, wood decay fungi have developed a complex detoxification network including glutathione transferases (GST). The interactions between GSTs from two white-rot fungi, Trametes versicolor and Phanerochaete chrysosporium, and an environmental library of wood extracts have been studied. The results demonstrate that the specificity of these interactions is closely related to the chemical composition of the extracts in accordance with the tree species and their localization inside the wood (sapwood vs heartwood vs knotwood). These data suggest that the fungal GSTome could reflect the chemical environment encountered by these fungi during wood degradation and could be a way to study their adaptation to their way of life. PMID:26426695

Cavitation-induced fragmentation of an acoustically-levitated droplet

NASA Astrophysics Data System (ADS)

Gonzalez Avila, Silvestre Roberto; Ohl, Claus-Dieter

2015-12-01

In this paper we investigate the initial sequence of events that lead to the fragmentation of a millimetre sized water droplets when interacting with a focused ns-laser pulse. The experimental results show complex processes that result from the reflection of an initial shock wave from plasma generation with the soft boundary of the levitating droplet; furthermore, when the reflected waves from the walls of the droplet refocus they leave behind a trail of microbubbles that later act as cavitation inception regions. Numerical simulations of a shock wave impacting and reflecting from a soft boundary are also reported; the simulated results show that the lowest pressure inside the droplet occurs at the equatorial plane. The results of the numerical model display good agreement with the experimental results both in time and in space.

Reduction of short wavelength reflectance of multi-wall carbon nanotubes through ultraviolet laser irradiation

NASA Astrophysics Data System (ADS)

Stephens, Michelle S.; Simonds, Brian J.; Yung, Christopher S.; Conklin, Davis; Livigni, David J.; Oliva, Alberto Remesal; Lehman, John H.

2018-05-01

Multi-wall carbon nanotube coatings are used as broadband, low-reflectance absorbers for bolometric applications and for stray light control. They are also used as high emittance blackbody radiators. Irradiation of single wall carbon nanotubes with ultraviolet (UV) laser light has been shown to remove amorphous carbon debris, but there have been few investigations of the interaction of UV light with the more complex physics of multi-wall carbon nanotubes. We present measurements of reflectance and surface morphology before and after exposure of multi-wall carbon nanotube coatings to 248 nm UV laser light. We show that UV exposure reduces the reflectivity at wavelengths below 600 nm and present modeling of the thermal cycling the UV exposure causes at the surface of the carbon nanotubes. This effect can be used to flatten the spectral shape of the reflectivity curve of carbon nanotube absorber coatings used for broadband applications. Finally, we find that the effect of UV exposure depends on the nanotube growth process.

Biclustering Protein Complex Interactions with a Biclique FindingAlgorithm

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

Ding, Chris; Zhang, Anne Ya; Holbrook, Stephen

2006-12-01

Biclustering has many applications in text mining, web clickstream mining, and bioinformatics. When data entries are binary, the tightest biclusters become bicliques. We propose a flexible and highly efficient algorithm to compute bicliques. We first generalize the Motzkin-Straus formalism for computing the maximal clique from L{sub 1} constraint to L{sub p} constraint, which enables us to provide a generalized Motzkin-Straus formalism for computing maximal-edge bicliques. By adjusting parameters, the algorithm can favor biclusters with more rows less columns, or vice verse, thus increasing the flexibility of the targeted biclusters. We then propose an algorithm to solve the generalized Motzkin-Straus optimizationmore » problem. The algorithm is provably convergent and has a computational complexity of O(|E|) where |E| is the number of edges. It relies on a matrix vector multiplication and runs efficiently on most current computer architectures. Using this algorithm, we bicluster the yeast protein complex interaction network. We find that biclustering protein complexes at the protein level does not clearly reflect the functional linkage among protein complexes in many cases, while biclustering at protein domain level can reveal many underlying linkages. We show several new biologically significant results.« less

A pairwise maximum entropy model accurately describes resting-state human brain networks

PubMed Central

Watanabe, Takamitsu; Hirose, Satoshi; Wada, Hiroyuki; Imai, Yoshio; Machida, Toru; Shirouzu, Ichiro; Konishi, Seiki; Miyashita, Yasushi; Masuda, Naoki

2013-01-01

The resting-state human brain networks underlie fundamental cognitive functions and consist of complex interactions among brain regions. However, the level of complexity of the resting-state networks has not been quantified, which has prevented comprehensive descriptions of the brain activity as an integrative system. Here, we address this issue by demonstrating that a pairwise maximum entropy model, which takes into account region-specific activity rates and pairwise interactions, can be robustly and accurately fitted to resting-state human brain activities obtained by functional magnetic resonance imaging. Furthermore, to validate the approximation of the resting-state networks by the pairwise maximum entropy model, we show that the functional interactions estimated by the pairwise maximum entropy model reflect anatomical connexions more accurately than the conventional functional connectivity method. These findings indicate that a relatively simple statistical model not only captures the structure of the resting-state networks but also provides a possible method to derive physiological information about various large-scale brain networks. PMID:23340410

Thermodynamics of T cell receptor – peptide/MHC interactions: progress and opportunities

PubMed Central

Armstrong, Kathryn M.; Insaidoo, Francis K.; Baker, Brian M.

2013-01-01

αβ T cell receptors (TCR) recognize peptide antigens presented by class I or class II major histocompatibility complex molecules (pMHC). Here we review the use of thermodynamic measurements in the study of TCR-pMHC interactions, with attention to the diversity in binding thermodynamics and how this is related to the variation in TCR-pMHC interfaces. We show that there is no enthalpic or entropic signature for TCR binding; rather, enthalpy and entropy changes vary in a compensatory manner that reflects a narrow free energy window for the interactions that have been characterized. Binding enthalpy and entropy changes do not correlate with structural features such as buried surface area or the number of hydrogen bonds within TCR-pMHC interfaces, possibly reflecting the myriad of contributors to binding thermodynamics, but likely also reflecting a reliance on van’t Hoff over calorimetric measurements and the unaccounted influence of equilibria linked to binding. TCR-pMHC binding heat capacity changes likewise vary considerably. In some cases the heat capacity changes are consistent with conformational differences between bound and free receptors, but there is little data indicating these conformational differences represent the need to organize commonly disordered CDR loops. In this regard, we discuss how thermodynamics may provide additional insight into conformational changes occurring upon TCR binding. Finally, we highlight opportunities for the further use of thermodynamic measurements in the study of TCR-pMHC interactions, not only for understanding TCR binding in general, but for understanding specifics of individual interactions and the engineering of T cell receptors with desired molecular recognition properties. PMID:18496839

Exploring the application of an evolutionary educational complex systems framework to teaching and learning about issues in the science and technology classroom

NASA Astrophysics Data System (ADS)

Yoon, Susan Anne

Understanding the world through a complex systems lens has recently garnered a great deal of interest in many knowledge disciplines. In the educational arena, interactional studies, through their focus on understanding patterns of system behaviour including the dynamical processes and trajectories of learning, lend support for investigating how a complex systems approach can inform educational research. This study uses previously existing literature and tools for complex systems applications and seeks to extend this research base by exploring learning outcomes of a complex systems framework when applied to curriculum and instruction. It is argued that by applying the evolutionary dynamics of variation, interaction and selection, complexity may be harnessed to achieve growth in both the social and cognitive systems of the classroom. Furthermore, if the goal of education, i.e., the social system under investigation, is to teach for understanding, conceptual knowledge of the kind described in Popper's (1972; 1976) World 3, needs to evolve. Both the study of memetic processes and knowledge building pioneered by Bereiter (cf. Bereiter, 2002) draw on the World 3 notion of ideas existing as conceptual artifacts that can be investigated as products outside of the individual mind providing an educational lens from which to proceed. The curricular topic addressed is the development of an ethical understanding of the scientific and technological issues of genetic engineering. 11 grade 8 students are studied as they proceed through 40 hours of curricular instruction based on the complex systems evolutionary framework. Results demonstrate growth in both complex systems thinking and content knowledge of the topic of genetic engineering. Several memetic processes are hypothesized to have influenced how and why ideas change. Categorized by factors influencing either reflective or non-reflective selection, these processes appear to have exerted differential effects on students' abilities to think and act in complex ways at various points throughout the study. Finally, an analysis of winner and loser memes is offered that is intended to reveal information about the conceptual system---its strengths and deficiencies---that can help educators assess curricular goals and organize and construct additional educational activities.

Synthesis, characterization, antibacterial activity, SOD mimic and interaction with DNA of drug based copper(II) complexes

NASA Astrophysics Data System (ADS)

Patel, Mohan N.; Dosi, Promise A.; Bhatt, Bhupesh S.; Thakkar, Vasudev R.

2011-02-01

Novel metal complexes of the second-generation quinolone antibacterial agent enrofloxacin with copper(II) and neutral bidentate ligands have been prepared and characterized with elemental analysis reflectance, IR and mass spectroscopy. Complexes have been screened for their in-vitro antibacterial activity against two Gram (+ve)Staphylococcus aureus, Bacillus subtilis, and three Gram (-ve)Serratia marcescens, Escherichia coli and Pseudomonas aeruginosa organisms using the double dilution technique. The binding of this complex with CT-DNA has been investigated by absorption titration, salt effect and viscosity measurements. Binding constant is ranging from 1.3 × 10 4-3.7 × 10 4. The cleavage ability of complexes has been assessed by gel electrophoresis using pUC19 DNA. The catalytic activity of the copper(II) complexes towards the superoxide anion (O 2rad -) dismutation was assayed by their ability to inhibit the reduction of nitroblue tetrazolium (NBT).

Genes, communities & invasive species: understanding the ecological and evolutionary dynamics of host-pathogen interactions.

PubMed

Burdon, J J; Thrall, P H; Ericson, L

2013-08-01

Reciprocal interactions between hosts and pathogens drive ecological, epidemiological and co-evolutionary trajectories, resulting in complex patterns of diversity at population, species and community levels. Recent results confirm the importance of negative frequency-dependent rather than 'arms-race' processes in the evolution of individual host-pathogen associations. At the community level, complex relationships between species abundance and diversity dampen or alter pathogen impacts. Invasive pathogens challenge these controls reflecting the earliest stages of evolutionary associations (akin to arms-race) where disease effects may be so great that they overwhelm the host's and community's ability to respond. Viewing these different stabilization/destabilization phases as a continuum provides a valuable perspective to assessment of the role of genetics and ecology in the dynamics of both natural and invasive host-pathogen associations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Molecular complexes of some anthraquinone anti-cancer drugs: experimental and computational study

NASA Astrophysics Data System (ADS)

El-Gogary, Tarek M.

2003-03-01

It is known that anti-cancer drugs target DNA in the cell. The mechanism of interaction of anti-cancer drugs with DNA is not fully understood. It is thought that the forces of interaction have some contribution from charge-transfer (CT) binding. The ability of some anthraquinones (AQs) anti-cancer drugs to form CT complexes with well-known electron donor molecules was investigated by NMR. The NMR spectroscopy has indicated the formation of CT complexes between 1,4-bis{[2-(dimethylamino) ethyl]amino}-5,8-dihydroxyanthracene-9,10-dione, (AQ4), and its des-hydroxylated equivalent 1,4-bis{[2-(dimethylamino) ethyl]amino}anthracene-9,10-dione, (AQ4H), as electron acceptors and pyrene (PY) and hexamethylbenzene (HMB) as electron donors. Association constants of the formed CT complexes were determined from the NMR data. AQ4 showed weaker electron accepting power than AQ4H, which could be easily explained on the basis of the electron donating nature of the two-hydroxyl groups. AQ4 and AQ4H have higher stability constant with PY than with HMB. This reflects the weaker interaction of the AQs with the latter, which is a direct effect of the six bulky methyl groups. Electronic absorption spectroscopy of the studied system was performed in chloroform and showed the absence of new absorption bands. The extent of interaction between AQs and donors has been computed using molecular mechanics and quantum mechanics. The computed values were compared with the experimental results of association constants.

Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns

PubMed Central

Lezon, Timothy R.; Banavar, Jayanth R.; Cieplak, Marek; Maritan, Amos; Fedoroff, Nina V.

2006-01-01

We describe a method based on the principle of entropy maximization to identify the gene interaction network with the highest probability of giving rise to experimentally observed transcript profiles. In its simplest form, the method yields the pairwise gene interaction network, but it can also be extended to deduce higher-order interactions. Analysis of microarray data from genes in Saccharomyces cerevisiae chemostat cultures exhibiting energy metabolic oscillations identifies a gene interaction network that reflects the intracellular communication pathways that adjust cellular metabolic activity and cell division to the limiting nutrient conditions that trigger metabolic oscillations. The success of the present approach in extracting meaningful genetic connections suggests that the maximum entropy principle is a useful concept for understanding living systems, as it is for other complex, nonequilibrium systems. PMID:17138668

Efficient Geometric Sound Propagation Using Visibility Culling

NASA Astrophysics Data System (ADS)

Chandak, Anish

2011-07-01

Simulating propagation of sound can improve the sense of realism in interactive applications such as video games and can lead to better designs in engineering applications such as architectural acoustics. In this thesis, we present geometric sound propagation techniques which are faster than prior methods and map well to upcoming parallel multi-core CPUs. We model specular reflections by using the image-source method and model finite-edge diffraction by using the well-known Biot-Tolstoy-Medwin (BTM) model. We accelerate the computation of specular reflections by applying novel visibility algorithms, FastV and AD-Frustum, which compute visibility from a point. We accelerate finite-edge diffraction modeling by applying a novel visibility algorithm which computes visibility from a region. Our visibility algorithms are based on frustum tracing and exploit recent advances in fast ray-hierarchy intersections, data-parallel computations, and scalable, multi-core algorithms. The AD-Frustum algorithm adapts its computation to the scene complexity and allows small errors in computing specular reflection paths for higher computational efficiency. FastV and our visibility algorithm from a region are general, object-space, conservative visibility algorithms that together significantly reduce the number of image sources compared to other techniques while preserving the same accuracy. Our geometric propagation algorithms are an order of magnitude faster than prior approaches for modeling specular reflections and two to ten times faster for modeling finite-edge diffraction. Our algorithms are interactive, scale almost linearly on multi-core CPUs, and can handle large, complex, and dynamic scenes. We also compare the accuracy of our sound propagation algorithms with other methods. Once sound propagation is performed, it is desirable to listen to the propagated sound in interactive and engineering applications. We can generate smooth, artifact-free output audio signals by applying efficient audio-processing algorithms. We also present the first efficient audio-processing algorithm for scenarios with simultaneously moving source and moving receiver (MS-MR) which incurs less than 25% overhead compared to static source and moving receiver (SS-MR) or moving source and static receiver (MS-SR) scenario.

X-ray Intermolecular Structure Factor (XISF): separation of intra- and intermolecular interactions from total X-ray scattering data

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

Mou, Q.; Benmore, C. J.; Yarger, J. L.

2015-06-01

XISF is a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained. XISF has been optimized for performance and can separate intermolecular structure factors of complex molecules.

X-ray Intermolecular Structure Factor ( XISF ): separation of intra- and intermolecular interactions from total X-ray scattering data

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

Mou, Q.; Benmore, C. J.; Yarger, J. L.

2015-05-09

XISFis a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained.XISFhas been optimized for performance and can separate intermolecular structure factors of complex molecules.

Molecular insight on the non-covalent interactions between carbapenems and uc(l,d)-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study

NASA Astrophysics Data System (ADS)

Ntombela, Thandokuhle; Fakhar, Zeynab; Ibeji, Collins U.; Govender, Thavendran; Maguire, Glenn E. M.; Lamichhane, Gyanu; Kruger, Hendrik G.; Honarparvar, Bahareh

2018-05-01

Tuberculosis remains a dreadful disease that has claimed many human lives worldwide and elimination of the causative agent Mycobacterium tuberculosis also remains elusive. Multidrug-resistant TB is rapidly increasing worldwide; therefore, there is an urgent need for improving the current antibiotics and novel drug targets to successfully curb the TB burden. uc(l,d)-Transpeptidase 2 is an essential protein in Mtb that is responsible for virulence and growth during the chronic stage of the disease. Both uc(d,d)- and uc(l,d)-transpeptidases are inhibited concurrently to eradicate the bacterium. It was recently discovered that classic penicillins only inhibit uc(d,d)-transpeptidases, while uc(l,d)-transpeptidases are blocked by carbapenems. This has contributed to drug resistance and persistence of tuberculosis. Herein, a hybrid two-layered ONIOM (B3LYP/6-31G+(d): AMBER) model was used to extensively investigate the binding interactions of LdtMt2 complexed with four carbapenems (biapenem, imipenem, meropenem, and tebipenem) to ascertain molecular insight of the drug-enzyme complexation event. In the studied complexes, the carbapenems together with catalytic triad active site residues of LdtMt2 (His187, Ser188 and Cys205) were treated at with QM [B3LYP/6-31+G(d)], while the remaining part of the complexes were treated at MM level (AMBER force field). The resulting Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) for all complexes showed that the carbapenems exhibit reasonable binding interactions towards LdtMt2. Increasing the number of amino acid residues that form hydrogen bond interactions in the QM layer showed significant impact in binding interaction energy differences and the stabilities of the carbapenems inside the active pocket of LdtMt2. The theoretical binding free energies obtained in this study reflect the same trend of the experimental observations. The electrostatic, hydrogen bonding and Van der Waals interactions between the carbapenems and LdtMt2 were also assessed. To further examine the nature of intermolecular interactions for carbapenem-LdtMt2 complexes, AIM and NBO analysis were performed for the QM region (carbapenems and the active residues of LdtMt2) of the complexes. These analyses revealed that the hydrogen bond interactions and charge transfer from the bonding to anti-bonding orbitals between catalytic residues of the enzyme and selected ligands enhances the binding and stability of carbapenem-LdtMt2 complexes.

Understanding the Complexity of Teacher Reflection in Action Research

ERIC Educational Resources Information Center

Luttenberg, Johan; Meijer, Paulien; Oolbekkink-Marchand, Helma

2017-01-01

Reflection in action research is a complex matter, as is action research itself. In recent years, complexity science has regularly been called upon in order to more thoroughly understand the complexity of action research. The present article investigates the benefits that complexity science may yield for reflection in action research. This article…

Authentication via wavefront-shaped optical responses

NASA Astrophysics Data System (ADS)

Eilers, Hergen; Anderson, Benjamin R.; Gunawidjaja, Ray

2018-02-01

Authentication/tamper-indication is required in a wide range of applications, including nuclear materials management and product counterfeit detection. State-of-the-art techniques include reflective particle tags, laser speckle authentication, and birefringent seals. Each of these passive techniques has its own advantages and disadvantages, including the need for complex image comparisons, limited flexibility, sensitivity to environmental conditions, limited functionality, etc. We have developed a new active approach to address some of these short-comings. The use of an active characterization technique adds more flexibility and additional layers of security over current techniques. Our approach uses randomly-distributed nanoparticles embedded in a polymer matrix (tag/seal) which is attached to the item to be secured. A spatial light modulator is used to adjust the wavefront of a laser which interacts with the tag/seal, and a detector is used to monitor this interaction. The interaction can occur in various ways, including transmittance, reflectance, fluorescence, random lasing, etc. For example, at the time of origination, the wavefront-shaped reflectance from a tag/seal can be adjusted to result in a specific pattern (symbol, words, etc.) Any tampering with the tag/seal would results in a disturbance of the random orientation of the nanoparticles and thus distort the reflectance pattern. A holographic waveplate could be inserted into the laser beam for verification. The absence/distortion of the original pattern would then indicate that tampering has occurred. We have tested the tag/seal's and authentication method's tamper-indicating ability using various attack methods, including mechanical, thermal, and chemical attacks, and have verified our material/method's robust tamper-indicating ability.

Characterizing the physical-basis of orographic rainfall retrieval errors due to terrain artifacts on GPM-DPR reflectivity profiles

NASA Astrophysics Data System (ADS)

Arulraj, M.; Barros, A. P.

2017-12-01

GPM-DPR reflectivity profiles in mountainous regions are severely handicapped by low level ground-clutter artifacts which have different error characteristics depending on landform (upwind slopes of high mountains versus complex topography in middle-mountains) and precipitation regime. These artifacts result in high detection and estimation errors especially in mid-latitude and tropical mountain regions where low-level light precipitation and complex multi-layer clouds interact with incoming storms. Here, we present results assessment studies in the Southern Appalachian Mountains (SAM) and preliminary results over the eastern slopes of the Andes using ground-based observations from the long-term hydrometeorological networks and model studies toward developing a physically-based framework to systematically identify and attribute measurement errors. Specifically, the focus is on events when GPM-DPR Ka- and Ku- Band precipitation radar misses low-level precipitation with vertical altitude less than 2 km AGL (above ground level). For this purpose, ground-based MRR and Parsivel disdrometer observations near the surface are compared with the reflectivity profiles observed by the GPM-DPR overpasses, the raindrop-size spectra are used to classify the precipitation regime associated with different classes of detection and estimation errors. This information will be used along with a coupled rainfall dynamics and radar simulator model to 1) merge the low-level GPM-DPR measured reflectivity with the MRR reflectivities optimally under strict physically-based constraints and 2) build a library of reflectivity profile corrections. Finally, preliminary 4D analysis of the organization of reflectivity correction modes, microphysical regimes, topography and storm environment will be presented toward developing a general physically-based error model.

Energetic neutral atom emissions from Titan interaction with Saturn's magnetosphere.

PubMed

Mitchell, D G; Brandt, P C; Roelof, E C; Dandouras, J; Krimigis, S M; Mauk, B H

2005-05-13

The Cassini Magnetospheric Imaging Instrument (MIMI) observed the interaction of Saturn's largest moon, Titan, with Saturn's magnetosphere during two close flybys of Titan on 26 October and 13 December 2004. The MIMI Ion and Neutral Camera (INCA) continuously imaged the energetic neutral atoms (ENAs) generated by charge exchange reactions between the energetic, singly ionized trapped magnetospheric ions and the outer atmosphere, or exosphere, of Titan. The images reveal a halo of variable ENA emission about Titan's nearly collisionless outer atmosphere that fades at larger distances as the exospheric density decays exponentially. The altitude of the emissions varies, and they are not symmetrical about the moon, reflecting the complexity of the interactions between Titan's upper atmosphere and Saturn's space environment.

Complexation-induced supramolecular assembly drives metal-ion extraction.

PubMed

Ellis, Ross J; Meridiano, Yannick; Muller, Julie; Berthon, Laurence; Guilbaud, Philippe; Zorz, Nicole; Antonio, Mark R; Demars, Thomas; Zemb, Thomas

2014-09-26

Combining experiment with theory reveals the role of self-assembly and complexation in metal-ion transfer through the water-oil interface. The coordinating metal salt Eu(NO3)3 was extracted from water into oil by a lipophilic neutral amphiphile. Molecular dynamics simulations were coupled to experimental spectroscopic and X-ray scattering techniques to investigate how local coordination interactions between the metal ion and ligands in the organic phase combine with long-range interactions to produce spontaneous changes in the solvent microstructure. Extraction of the Eu(3+)-3(NO3(-)) ion pairs involves incorporation of the "hard" metal complex into the core of "soft" aggregates. This seeds the formation of reverse micelles that draw the water and "free" amphiphile into nanoscale hydrophilic domains. The reverse micelles interact through attractive van der Waals interactions and coalesce into rod-shaped polynuclear Eu(III) -containing aggregates with metal centers bridged by nitrate. These preorganized hydrophilic domains, containing high densities of O-donor ligands and anions, provide improved Eu(III) solvation environments that help drive interfacial transfer, as is reflected by the increasing Eu(III) partitioning ratios (oil/aqueous) despite the organic phase approaching saturation. For the first time, this multiscale approach links metal-ion coordination with nanoscale structure to reveal the free-energy balance that drives the phase transfer of neutral metal salts. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of Non-Covalent Interactions of Aflatoxins (B1, B2, G1, G2, and M1) with Serum Albumin

PubMed Central

Poór, Miklós; Bálint, Mónika; Hetényi, Csaba; Gődér, Beatrix; Kunsági-Máté, Sándor; Lemli, Beáta

2017-01-01

Aflatoxins are widely spread mycotoxins produced mainly by Aspergillus species. Consumption of aflatoxin-contaminated foods and drinks causes serious health risks for people worldwide. It is well-known that the reactive epoxide metabolite of aflatoxin B1 (AFB1) forms covalent adducts with serum albumin. However, non-covalent interactions of aflatoxins with human serum albumin (HSA) are poorly characterized. Thus, in this study the complex formation of aflatoxins was examined with HSA applying spectroscopic and molecular modelling studies. Our results demonstrate that aflatoxins form stable complexes with HSA as reflected by binding constants between 2.1 × 104 and 4.5 × 104 dm3/mol. A binding free energy value of −26.90 kJ mol−1 suggests a spontaneous binding process between AFB1 and HSA at room-temperature, while the positive entropy change of 55.1 JK−1 mol−1 indicates a partial decomposition of the solvation shells of the interacting molecules. Modeling studies and investigations with site markers suggest that Sudlow’s Site I of subdomain IIA is the high affinity binding site of aflatoxins on HSA. Interaction of AFB1 with bovine, porcine, and rat serum albumins was also investigated. Similar stabilities of the examined AFB1-albumin complexes were observed suggesting the low species differences of the albumin-binding of aflatoxins. PMID:29068381

Encoding complexity within supramolecular analogues of frustrated magnets

NASA Astrophysics Data System (ADS)

Cairns, Andrew B.; Cliffe, Matthew J.; Paddison, Joseph A. M.; Daisenberger, Dominik; Tucker, Matthew G.; Coudert, François-Xavier; Goodwin, Andrew L.

2016-05-01

The solid phases of gold(I) and/or silver(I) cyanides are supramolecular assemblies of inorganic polymer chains in which the key structural degrees of freedom—namely, the relative vertical shifts of neighbouring chains—are mathematically equivalent to the phase angles of rotating planar (‘XY’) spins. Here, we show how the supramolecular interactions between chains can be tuned to mimic different magnetic interactions. In this way, the structures of gold(I) and/or silver(I) cyanides reflect the phase behaviour of triangular XY magnets. Complex magnetic states predicted for this family of magnets—including collective spin-vortices of relevance to data storage applications—are realized in the structural chemistry of these cyanide polymers. Our results demonstrate how chemically simple inorganic materials can behave as structural analogues of otherwise inaccessible ‘toy’ spin models and also how the theoretical understanding of those models allows control over collective (‘emergent’) phenomena in supramolecular systems.

Single-Molecule Interactions of a Monoclonal Anti-DNA Antibody with DNA

PubMed Central

Nevzorova, Tatiana A.; Zhao, Qingze; Lomakin, Yakov A.; Ponomareva, Anastasia A.; Mukhitov, Alexander R.; Purohit, Prashant K.; Weisel, John W.; Litvinov, Rustem I.

2017-01-01

Interactions of DNA with proteins are essential for key biological processes and have both a fundamental and practical significance. In particular, DNA binding to anti-DNA antibodies is a pathogenic mechanism in autoimmune pathology, such as systemic lupus erythematosus. Here we measured at the single-molecule level binding and forced unbinding of surface-attached DNA and a monoclonal anti-DNA antibody MRL4 from a lupus erythematosus mouse. In optical trap-based force spectroscopy, a microscopic antibodycoated latex bead is trapped by a focused laser beam and repeatedly brought into contact with a DNA-coated surface. After careful discrimination of non-specific interactions, we showed that the DNA-antibody rupture force spectra had two regimes, reflecting formation of weaker (20–40 pN) and stronger (>40 pN) immune complexes that implies the existence of at least two bound states with different mechanical stability. The two-dimensional force-free off-rate for the DNA-antibody complexes was ~2.2 × 10−3 s−1, the transition state distance was ~0.94 nm, the apparent on-rate was ~5.26 s−1, and the stiffness of the DNA-antibody complex was characterized by a spring constant of 0.0021 pN/nm, suggesting that the DNA-antibody complex is a relatively stable, but soft and deformable macromolecular structure. The stretching elasticity of the DNA molecules was characteristic of single-stranded DNA, suggesting preferential binding of the MRL4 antibody to one strand of DNA. Collectively, the results provide fundamental characteristics of formation and forced dissociation of DNA-antibody complexes that help to understand principles of DNA-protein interactions and shed light on the molecular basis of autoimmune diseases accompanied by formation of anti-DNA antibodies. PMID:29104846

Cultivating Reflective Practitioners in Technology Preparation: Constructing TPACK through Reflection

ERIC Educational Resources Information Center

Lu, Liangyue

2014-01-01

Teaching is a complex profession, which is further complicated by the integration of technology into classrooms. Reflection can help teachers unpack the complexity in their practice. Reflection can be an effective instructional strategy in helping preservice teachers develop technological pedagogical content knowledge (TPACK), the complex and…

Supervision for superheroes: the case for reflective professional supervision for senior doctors.

PubMed

Austin, Helen

2016-05-06

The practice of medicine is inherently stressful with regular exposure to trauma and the distress of others. There is a culture in medicine that doctors should not be affected by such things, although it is well recognised that doctors have higher rates of depression, anxiety, suicide, and substance abuse than the general public. Reflective professional supervision is a forum where the complexities of the interpersonal interactions that underpin the provision of healthcare can be explored in a supportive and confidential setting. It is argued that this is a process that should continue for the duration of a doctor's career, with potential benefits including enhanced job satisfaction and resilience, better workplace communication and improved interpersonal skills.

Optical micromanipulation of nanoparticles and cells inside living zebrafish.

PubMed

Johansen, Patrick Lie; Fenaroli, Federico; Evensen, Lasse; Griffiths, Gareth; Koster, Gerbrand

2016-03-21

Regulation of biological processes is often based on physical interactions between cells and their microenvironment. To unravel how and where interactions occur, micromanipulation methods can be used that offer high-precision control over the duration, position and magnitude of interactions. However, lacking an in vivo system, micromanipulation has generally been done with cells in vitro, which may not reflect the complex in vivo situation inside multicellular organisms. Here using optical tweezers we demonstrate micromanipulation throughout the transparent zebrafish embryo. We show that different cells, as well as injected nanoparticles and bacteria can be trapped and that adhesion properties and membrane deformation of endothelium and macrophages can be analysed. This non-invasive micromanipulation inside a whole-organism gives direct insights into cell interactions that are not accessible using existing approaches. Potential applications include screening of nanoparticle-cell interactions for cancer therapy or tissue invasion studies in cancer and infection biology.

Structure of a Yeast Dyn2-Nup159 Complex and Molecular Basis for Dynein Light Chain-Nuclear Pore Interaction*

PubMed Central

Romes, Erin M.; Tripathy, Ashutosh; Slep, Kevin C.

2012-01-01

The nuclear pore complex gates nucleocytoplasmic transport through a massive, eight-fold symmetric channel capped by a nucleoplasmic basket and structurally unique, cytoplasmic fibrils whose tentacles bind and regulate asymmetric traffic. The conserved Nup82 complex, composed of Nsp1, Nup82, and Nup159, forms the unique cytoplasmic fibrils that regulate mRNA nuclear export. Although the nuclear pore complex plays a fundamental, conserved role in nuclear trafficking, structural information about the cytoplasmic fibrils is limited. Here, we investigate the structural and biochemical interactions between Saccharomyces cerevisiae Nup159 and the nucleoporin, Dyn2. We find that Dyn2 is predominantly a homodimer and binds arrayed sites on Nup159, promoting the Nup159 parallel homodimerization. We present the first structure of Dyn2, determined at 1.85 Å resolution, complexed with a Nup159 target peptide. Dyn2 resembles homologous metazoan dynein light chains, forming homodimeric composite substrate binding sites that engage two independent 10-residue target motifs, imparting a β-strand structure to each peptide via antiparallel extension of the Dyn2 core β-sandwich. Dyn2 recognizes a highly conserved QT motif while allowing sequence plasticity in the flanking residues of the peptide. Isothermal titration calorimetric analysis of the comparative binding of Dyn2 to two Nup159 target sites shows similar affinities (18 and 13 μm), but divergent thermal binding modes. Dyn2 homodimers are arrayed in the crystal lattice, likely mimicking the arrayed architecture of Dyn2 on the Nup159 multivalent binding sites. Crystallographic interdimer interactions potentially reflect a cooperative basis for Dyn2-Nup159 complex formation. Our data highlight the determinants that mediate oligomerization of the Nup82 complex and promote a directed, elongated cytoplasmic fibril architecture. PMID:22411995

Distributed mixed-integer fuzzy hierarchical programming for municipal solid waste management. Part I: System identification and methodology development.

PubMed

Cheng, Guanhui; Huang, Guohe; Dong, Cong; Xu, Ye; Chen, Xiujuan; Chen, Jiapei

2017-03-01

Due to the existence of complexities of heterogeneities, hierarchy, discreteness, and interactions in municipal solid waste management (MSWM) systems such as Beijing, China, a series of socio-economic and eco-environmental problems may emerge or worsen and result in irredeemable damages in the following decades. Meanwhile, existing studies, especially ones focusing on MSWM in Beijing, could hardly reflect these complexities in system simulations and provide reliable decision support for management practices. Thus, a framework of distributed mixed-integer fuzzy hierarchical programming (DMIFHP) is developed in this study for MSWM under these complexities. Beijing is selected as a representative case. The Beijing MSWM system is comprehensively analyzed in many aspects such as socio-economic conditions, natural conditions, spatial heterogeneities, treatment facilities, and system complexities, building a solid foundation for system simulation and optimization. Correspondingly, the MSWM system in Beijing is discretized as 235 grids to reflect spatial heterogeneity. A DMIFHP model which is a nonlinear programming problem is constructed to parameterize the Beijing MSWM system. To enable scientific solving of it, a solution algorithm is proposed based on coupling of fuzzy programming and mixed-integer linear programming. Innovations and advantages of the DMIFHP framework are discussed. The optimal MSWM schemes and mechanism revelations will be discussed in another companion paper due to length limitation.

Assessment of DNA complexation onto polyelectrolyte-coated magnetic silica nanoparticles.

PubMed

Dávila-Ibáñez, Ana B; Buurma, Niklaas J; Salgueiriño, Verónica

2013-06-07

The polyelectrolyte-DNA complexation method to form magnetoplexes using silica-coated iron oxide magnetic nanoparticles as inorganic substrates is an attractive and promising process in view of the potential applications including magnetofection, DNA extraction and purification, and directed assembly of nanostructures. Herein, we present a systematic physico-chemical study that provides clear evidence of the type of interactions established, reflects the importance of the DNA length, the nanoparticle size and the ionic strength, and permits the identification of the parameters controlling both the stability and the type of magnetoplexes formed. This information can be used to develop targeted systems with properties optimized for the various proposed applications of magnetoplexes.

Culture & Cognition in a Complex Megaorganization: Implications for Military Leadership

DTIC Science & Technology

2010-01-01

human constructs~ such as self - esteem , introversion and extraversion are made known through actions related in some manner to one’s interactions...Ross, 1977). This error is closely linked to egocentricism or Southern Business Review what is known as the Self - Serving Bias whereby one is more...process of selective percep- tion, a U.S. General Officer or Colonel must be self - reflective about the way culture implicitly and explicitly

"My Tribe is the Hessequa. I'm Khoisan. I'm African": Language, Desire and Performance among Cape Town's Khoisan Language Activists

ERIC Educational Resources Information Center

Brown, Justin; Deumert, Ana

2017-01-01

In this article we provide a discussion of present-day Khoisan activism in Cape Town, South Africa. The main actors in this movement are people whose heritage is complex: their history can be traced back to the early days of the colonial settlement, reflecting the interactions and cohabitation of the indigenous Khoisan, slaves and the European…

WAVE2 serves a functional partner of IRSp53 by regulating its interaction with Rac.

PubMed

Miki, Hiroaki; Takenawa, Tadaomi

2002-04-26

We previously reported that IRSp53 binds both Rac and WAVE2, inducing formation of Rac/IRSp53/WAVE2 complex that is important for membrane ruffling. However, recent reports noted a specific interaction between IRSp53 and Cdc42 but not Rac, which led us to re-examine the binding of IRSp53 to Rac. Immunoprecipitation analysis and pull-down assay reveal that full-length IRSp53 binds Rac much less efficiently than the N-terminal fragment, which may be caused by intramolecular interaction. Interestingly, the intramolecular interaction is interrupted by the binding of WAVE2 and full-length IRSp53 associates with Rac in the presence of WAVE2. We also report that IRSp53 induces spreading and neurite formation of N1E-115 cells, which presumably reflect functional cooperation with Rac.

Efficient anomalous reflection through near-field interactions in metasurfaces

NASA Astrophysics Data System (ADS)

Chalabi, H.; Ra'di, Y.; Sounas, D. L.; Alù, A.

2017-08-01

Gradient metasurfaces have been extensively used in the past few years for advanced wave manipulation over a thin surface. These metasurfaces have been mostly designed based on the generalized laws of reflection and refraction. However, it was recently revealed that metasurfaces based on this approach tend to suffer from inefficiencies and complex design requirements. We have recently proposed a different approach to the problem of efficient beam steering using a surface, based on bianisotropic particles in a periodic array. Here, we show highly efficient reflective metasurfaces formed by pairs of isotropic dielectric rods, which can offer asymmetrical scattering of normally incident beams with unitary efficiency. Our theory shows that moderately broadband anomalous reflection can be achieved with suitably designed periodic arrays of isotropic nanoparticles. We also demonstrate practical designs using TiO2 cylindrical nanorods to deflect normally incident light toward a desired direction. The proposed structures may pave the way to a broader range of light management opportunities, with applications in energy harvesting, signaling, and communications.

Single functional group interactions with individual carbon nanotubes

NASA Astrophysics Data System (ADS)

Friddle, Raymond W.; Lemieux, Melburne C.; Cicero, Giancarlo; Artyukhin, Alexander B.; Tsukruk, Vladimir V.; Grossman, Jeffrey C.; Galli, Giulia; Noy, Aleksandr

2007-11-01

Carbon nanotubes display a consummate blend of materials properties that affect applications ranging from nanoelectronic circuits and biosensors to field emitters and membranes. These applications use the non-covalent interactions between the nanotubes and chemical functionalities, often involving a few molecules at a time. Despite their wide use, we still lack a fundamental understanding and molecular-level control of these interactions. We have used chemical force microscopy to measure the strength of the interactions of single chemical functional groups with the sidewalls of vapour-grown individual single-walled carbon nanotubes. Surprisingly, the interaction strength does not follow conventional trends of increasing polarity or hydrophobicity, and instead reflects the complex electronic interactions between the nanotube and the functional group. Ab initio calculations confirm the observed trends and predict binding force distributions for a single molecular contact that match the experimental results. Our analysis also reveals the important role of molecular linkage dynamics in determining interaction strength at the single functional group level.

Jet and Vortex Projectile Flows in Shock/bubble-on-wall Configuration

NASA Astrophysics Data System (ADS)

Peng, Gaozhu; Zabusky, Norman

2001-11-01

We observe intense coaxial upstream and radial flow structures from a shock in air interacting with a SF6 half-bubble placed against an ideally reflecting wall. Our axisymmetric numerical simulations were done with PPM and models a spherical bubble struck symmetrically by two identical approaching shocks . A "dual" vorticity deposition arises at early time and a coaxial upstream moving primary jet and radial vortex ring flow appears. A coherent vortex ring or vortex projectile (VP), with entrained shocklets originates from the vortex layer produced at the Mach stem (which arises from the primary reflected shock). This VP moves ahead of the jet. The original transmitted wave and other trapped waves in the expanding axial jet causes a collapsing and expanding cavity and other instabilities on the complex bubble interface. We present and analyze our results with different diagnostics: vorticity, density, divergence of velocity, and numerical shadowgraph patterns; global quantification of circulation, enstrophy and r-integrated vorticity; etc. We also discuss data projection and filtering for quantifying and validating complex flows.

;Host-guest; interactions in Captisol®/Coumestrol inclusion complex: UV-vis, FTIR-ATR and Raman studies

NASA Astrophysics Data System (ADS)

Venuti, Valentina; Stancanelli, Rosanna; Acri, Giuseppe; Crupi, Vincenza; Paladini, Giuseppe; Testagrossa, Barbara; Tommasini, Silvana; Ventura, Cinzia Anna; Majolino, Domenico

2017-10-01

The ability of Captisol® (sulphobutylether-β-cyclodextrin, SBE-β-CD), to form inclusion complexes, both in solution and in the solid state, has been tested in order to improve some unfavorable chemical-physical characteristics, such as poor solubility in water, of a bioflavonoid, Coumestrol (Coum), well known for its anti-oxidant, anti-inflammatory, anti-fungal and anti-viral activity. In pure water, a phase-solubility study was carried out to evaluate the enhancement of the solubility of Coum and, therefore, the occurred complexation with the macrocycle. The stoichiometry and the stability constant of the SBE-β-CD/Coum complex were calculated with the phase solubility method and through the Job's plot. After that, the solid SBE-β-CD/Coum complex was prepared utilizing a kneading method. The spectral changes induced by complexation on characteristic vibrational band of Coum were complementary investigated by Fourier transform infrared spectroscopy in attenuated total reflectance geometry (FTIR-ATR) and Raman spectroscopy, putting into evidence the guest chemical groups involved in the "host-guest" interactions responsible of the formation and stabilization of the complex. Particular attention was paid to the Cdbnd O and Osbnd H stretching vibrations, whose temperature-evolution respectively furnished the enthalpy changes associated to the binding of host and guest in solid phase and to the reorganization of the hydrogen bond scheme upon complexation. From the whole set of results, an inclusion geometry is also proposed.

Dynamic interactions between Pit-1 and C/EBPalpha in the pituitary cell nucleus.

PubMed

Demarco, Ignacio A; Voss, Ty C; Booker, Cynthia F; Day, Richard N

2006-11-01

The homeodomain (HD) transcription factors are a structurally conserved family of proteins that, through networks of interactions with other nuclear proteins, control patterns of gene expression during development. For example, the network interactions of the pituitary-specific HD protein Pit-1 control the development of anterior pituitary cells and regulate the expression of the hormone products in the adult cells. Inactivating mutations in Pit-1 disrupt these processes, giving rise to the syndrome of combined pituitary hormone deficiency. Pit-1 interacts with CCAAT/enhancer-binding protein alpha (C/EBPalpha) to regulate prolactin transcription. Here, we used the combination of biochemical analysis and live-cell microscopy to show that two different point mutations in Pit-1, which disrupted distinct activities, affected the dynamic interactions between Pit-1 and C/EBPalpha in different ways. The results showed that the first alpha-helix of the POU-S domain is critical for the assembly of Pit-1 with C/EBPalpha, and they showed that DNA-binding activity conferred by the HD is critical for the final intranuclear positioning of the metastable complex. This likely reflects more general mechanisms that govern cell-type-specific transcriptional control, and the results from the analysis of the point mutations could indicate an important link between the mislocalization of transcriptional complexes and disease processes.

An autoethnographic exploration of the use of goal oriented feedback to enhance brief clinical teaching encounters.

PubMed

Farrell, Laura; Bourgeois-Law, Gisele; Ajjawi, Rola; Regehr, Glenn

2017-03-01

Supervision in the outpatient context is increasingly in the form of single day interactions between students and preceptors. This creates difficulties for effective feedback, which often depends on a strong relationship of trust between preceptor and student. Building on feedback theories focusing on the relational and dialogic aspects of feedback, this study explored the use of goal-oriented feedback in brief encounters with learners. This study used autoethnography to explore one preceptor's feedback interactions over an eight-month period both in the ambulatory setting and on the wards. Data included written narrative reflections on feedback interactions with twenty-three learners informed by discussions with colleagues and repeated reading of feedback literature. Thematic and narrative analyses of data were performed iteratively. Data analysis emphasized four recurrent themes. (1) Goal discussions were most effective when initiated early and integrated throughout the learning experience. (2) Both learner and preceptor goals were multiple and varied, and feedback needed to reflect this complexity. (3) Negotiation or co-construction of goals was important when considering the focus of feedback discussions in order to create safer, more effective interactions. (4) Goal oriented interactions offer potential benefits to the learner and preceptor. Goal oriented feedback promotes dialogue as it requires both preceptor and learner to acknowledge and negotiate learning goals throughout their interaction. In doing so, feedback becomes an explicit component of the preceptor-learner relationship. This enhances feedback interactions even in relatively brief encounters, and may begin an early educational alliance that can be elaborated with longer interactions.

Wavelet multiresolution complex network for decoding brain fatigued behavior from P300 signals

NASA Astrophysics Data System (ADS)

Gao, Zhong-Ke; Wang, Zi-Bo; Yang, Yu-Xuan; Li, Shan; Dang, Wei-Dong; Mao, Xiao-Qian

2018-09-01

Brain-computer interface (BCI) enables users to interact with the environment without relying on neural pathways and muscles. P300 based BCI systems have been extensively used to achieve human-machine interaction. However, the appearance of fatigue symptoms during operation process leads to the decline in classification accuracy of P300. Characterizing brain cognitive process underlying normal and fatigue conditions constitutes a problem of vital importance in the field of brain science. We in this paper propose a novel wavelet decomposition based complex network method to efficiently analyze the P300 signals recorded in the image stimulus test based on classical 'Oddball' paradigm. Initially, multichannel EEG signals are decomposed into wavelet coefficient series. Then we construct complex network by treating electrodes as nodes and determining the connections according to the 2-norm distances between wavelet coefficient series. The analysis of topological structure and statistical index indicates that the properties of brain network demonstrate significant distinctions between normal status and fatigue status. More specifically, the brain network reconfiguration in response to the cognitive task in fatigue status is reflected as the enhancement of the small-worldness.

Membrane association of the PTEN tumor suppressor: Neutron scattering and MD simulations reveal the structure of protein-membranes complexes

PubMed Central

Nanda, Hirsh; Heinrich, Frank; Lösche, Mathias

2014-01-01

Neutron reflection (NR) from planar interfaces is an emerging technology that provides unique and otherwise inaccessible structural information on disordered molecular systems such as membrane proteins associated with fluid bilayers, thus addressing one of the remaining challenges of structural biology. Although intrinsically a low-resolution technique, using structural information from crystallography or NMR allows the construction of NR models that describe the architecture of protein-membrane complexes at high resolution. In addition, a combination of these methods with molecular dynamics (MD) simulations has the potential to reveal the dynamics of protein interactions with the bilayer in atomistic detail. We review recent advances in this area by discussing the application of these techniques to the complex formed by the PTEN phosphatase with the plasma membrane. These studies provide insights in the cellular regulation of PTEN, its interaction with PI(4,5)P2 in the inner plasma membrane and the pathway by which its substrate, PI(3,4,5)P3, accesses the PTEN catalytic site. PMID:25461777

An integrative model of evolutionary covariance: a symposium on body shape in fishes.

PubMed

Walker, Jeffrey A

2010-12-01

A major direction of current and future biological research is to understand how multiple, interacting functional systems coordinate in producing a body that works. This understanding is complicated by the fact that organisms need to work well in multiple environments, with both predictable and unpredictable environmental perturbations. Furthermore, organismal design reflects a history of past environments and not a plan for future environments. How complex, interacting functional systems evolve, then, is a truly grand challenge. In accepting the challenge, an integrative model of evolutionary covariance is developed. The model combines quantitative genetics, functional morphology/physiology, and functional ecology. The model is used to convene scientists ranging from geneticists, to physiologists, to ecologists, to engineers to facilitate the emergence of body shape in fishes as a model system for understanding how complex, interacting functional systems develop and evolve. Body shape of fish is a complex morphology that (1) results from many developmental paths and (2) functions in many different behaviors. Understanding the coordination and evolution of the many paths from genes to body shape, body shape to function, and function to a working fish body in a dynamic environment is now possible given new technologies from genetics to engineering and new theoretical models that integrate the different levels of biological organization (from genes to ecology).

Reflecting on the efficacy of cognitive mapping for decision-making in intellectual disability care: a case study.

PubMed

Duryan, Meri; Nikolik, Dragan; van Merode, Godefridus; Curfs, Leopold M G

2015-01-01

The central aspect of this study is a set of reflections on the efficacy of soft operational research techniques in understanding the dynamics of a complex system such as intellectual disability (ID) care providers. Organizations providing services to ID patients are complex and have many interacting stakeholders with often different and competing interests. Understanding the causes for failures in complex systems is crucial for appreciating the multiple perspectives of the key stakeholders of the system. Knowing the factors that adversely affect delivery of a patient-centred care by ID provider organizations offers the potential for identifying more effective resource-allocation solutions. The authors suggest cognitive mapping as a starting point for system dynamics modelling of optimal resource-allocation projects in ID care. The application of the method is illustrated via a case study in one of the ID care providers in the Netherlands. The paper discusses some of the practical implications of applying problem-structuring methods that support gathering feedback from vulnerable service users and front-line workers. The authors concluded that cognitive mapping technique can assist the management of healthcare organizations in strategic decision-making. Copyright © 2013 John Wiley & Sons, Ltd.

Understanding global health governance as a complex adaptive system.

PubMed

Hill, Peter S

2011-01-01

The transition from international to global health reflects the rapid growth in the numbers and nature of stakeholders in health, as well as the constant change embodied in the process of globalisation itself. This paper argues that global health governance shares the characteristics of complex adaptive systems, with its multiple and diverse players, and their polyvalent and constantly evolving relationships, and rich and dynamic interactions. The sheer quantum of initiatives, the multiple networks through which stakeholders (re)configure their influence, the range of contexts in which development for health is played out - all compound the complexity of this system. This paper maps out the characteristics of complex adaptive systems as they apply to global health governance, linking them to developments in the past two decades, and the multiple responses to these changes. Examining global health governance through the frame of complexity theory offers insight into the current dynamics of governance, and while providing a framework for making meaning of the whole, opens up ways of accessing this complexity through local points of engagement.

SAFETY: an integrated clinical reasoning and reflection framework for undergraduate nursing students.

PubMed

Hicks Russell, Bedelia; Geist, Melissa J; House Maffett, Jenny

2013-01-01

Nurse educators can no longer focus on imparting to students knowledge that is merely factual and content specific. Activities that provide students with opportunities to apply concepts in real-world scenarios can be powerful tools. Nurse educators should take advantage of student-patient interactions to model clinical reasoning and allow students to practice complex decision making throughout the entire curriculum. In response to this change in nursing education, faculty in a pediatric course designed a reflective clinical reasoning activity based on the SAFETY template, which is derived from the National Council of State Boards of Nursing RN practice analysis. Students were able to prioritize key components of nursing care, as well as integrate practice issues such as delegation, Health Insurance Portability and Accountability Act violations, and questioning the accuracy of orders. SAFETY is proposed as a framework for integration of content knowledge, clinical reasoning, and reflection on authentic professional nursing concerns. Copyright 2012, SLACK Incorporated.

Experimental investigation of microwave interaction with magnetoplasma in miniature multipolar configuration using impedance measurements

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

Dey, Indranuj, E-mail: indranuj@aees.kyushu-u.ac.jp; Toyoda, Yuji; Yamamoto, Naoji

2014-09-15

A miniature microwave plasma source employing both radial and axial magnetic fields for plasma confinement has been developed for micro-propulsion applications. Plasma is initiated by launching microwaves via a short monopole antenna to circumvent geometrical cutoff limitations. The amplitude and phase of the forward and reflected microwave power is measured to obtain the complex reflection coefficient from which the equivalent impedance of the plasma source is determined. Effect of critical plasma density condition is reflected in the measurements and provides insight into the working of the miniature plasma source. A basic impedance calculation model is developed to help in understandingmore » the experimental observations. From experiment and theory, it is seen that the equivalent impedance magnitude is controlled by the coaxial discharge boundary conditions, and the phase is influenced primarily by the plasma immersed antenna impedance.« less

Casimir-Polder shifts on quantum levitation states

NASA Astrophysics Data System (ADS)

Crépin, P.-P.; Dufour, G.; Guérout, R.; Lambrecht, A.; Reynaud, S.

2017-03-01

An ultracold atom above a horizontal mirror experiences quantum reflection from the attractive Casimir-Polder interaction, which holds it against gravity and leads to quantum levitation states. We analyze this system by using a Liouville transformation of the Schrödinger equation and a Langer coordinate adapted to problems with a classical turning point. Reflection on the Casimir-Polder attractive well is replaced by reflection on a repulsive wall, and the problem is then viewed as an ultracold atom trapped inside a cavity with gravity and Casimir-Polder potentials acting, respectively, as top and bottom mirrors. We calculate numerically Casimir-Polder shifts of the energies of the cavity resonances and propose an approximate treatment which is precise enough to discuss spectroscopy experiments aimed at tests of the weak-equivalence principle on antihydrogen. We also discuss the lifetimes by calculating complex energies associated with cavity resonances.

The SCEC 3D Community Fault Model (CFM-v5): An updated and expanded fault set of oblique crustal deformation and complex fault interaction for southern California

NASA Astrophysics Data System (ADS)

Nicholson, C.; Plesch, A.; Sorlien, C. C.; Shaw, J. H.; Hauksson, E.

2014-12-01

Southern California represents an ideal natural laboratory to investigate oblique deformation in 3D owing to its comprehensive datasets, complex tectonic history, evolving components of oblique slip, and continued crustal rotations about horizontal and vertical axes. As the SCEC Community Fault Model (CFM) aims to accurately reflect this 3D deformation, we present the results of an extensive update to the model by using primarily detailed fault trace, seismic reflection, relocated hypocenter and focal mechanism nodal plane data to generate improved, more realistic digital 3D fault surfaces. The results document a wide variety of oblique strain accommodation, including various aspects of strain partitioning and fault-related folding, sets of both high-angle and low-angle faults that mutually interact, significant non-planar, multi-stranded faults with variable dip along strike and with depth, and active mid-crustal detachments. In places, closely-spaced fault strands or fault systems can remain surprisingly subparallel to seismogenic depths, while in other areas, major strike-slip to oblique-slip faults can merge, such as the S-dipping Arroyo Parida-Mission Ridge and Santa Ynez faults with the N-dipping North Channel-Pitas Point-Red Mountain fault system, or diverge with depth. Examples of the latter include the steep-to-west-dipping Laguna Salada-Indiviso faults with the steep-to-east-dipping Sierra Cucapah faults, and the steep southern San Andreas fault with the adjacent NE-dipping Mecca Hills-Hidden Springs fault system. In addition, overprinting by steep predominantly strike-slip faulting can segment which parts of intersecting inherited low-angle faults are reactivated, or result in mutual cross-cutting relationships. The updated CFM 3D fault surfaces thus help characterize a more complex pattern of fault interactions at depth between various fault sets and linked fault systems, and a more complex fault geometry than typically inferred or expected from projecting near-surface data down-dip, or modeled from surface strain and potential field data alone.

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.

Evaluating the Spatio-Temporal Factors that Structure Network Parameters of Plant-Herbivore Interactions

PubMed Central

López-Carretero, Antonio; Díaz-Castelazo, Cecilia; Boege, Karina; Rico-Gray, Víctor

2014-01-01

Despite the dynamic nature of ecological interactions, most studies on species networks offer static representations of their structure, constraining our understanding of the ecological mechanisms involved in their spatio-temporal stability. This is the first study to evaluate plant-herbivore interaction networks on a small spatio-temporal scale. Specifically, we simultaneously assessed the effect of host plant availability, habitat complexity and seasonality on the structure of plant-herbivore networks in a coastal tropical ecosystem. Our results revealed that changes in the host plant community resulting from seasonality and habitat structure are reflected not only in the herbivore community, but also in the emergent properties (network parameters) of the plant-herbivore interaction network such as connectance, selectiveness and modularity. Habitat conditions and periods that are most stressful favored the presence of less selective and susceptible herbivore species, resulting in increased connectance within networks. In contrast, the high degree of selectivennes (i.e. interaction specialization) and modularity of the networks under less stressful conditions was promoted by the diversification in resource use by herbivores. By analyzing networks at a small spatio-temporal scale we identified the ecological factors structuring this network such as habitat complexity and seasonality. Our research offers new evidence on the role of abiotic and biotic factors in the variation of the properties of species interaction networks. PMID:25340790

Compressible Vortex Ring

NASA Astrophysics Data System (ADS)

Elavarasan, Ramasamy; Arakeri, Jayawant; Krothapalli, Anjaneyulu

1999-11-01

The interaction of a high-speed vortex ring with a shock wave is one of the fundamental issues as it is a source of sound in supersonic jets. The complex flow field induced by the vortex alters the propagation of the shock wave greatly. In order to understand the process, a compressible vortex ring is studied in detail using Particle Image Velocimetry (PIV) and shadowgraphic techniques. The high-speed vortex ring is generated from a shock tube and the shock wave, which precedes the vortex, is reflected back by a plate and made to interact with the vortex. The shadowgraph images indicate that the reflected shock front is influenced by the non-uniform flow induced by the vortex and is decelerated while passing through the vortex. It appears that after the interaction the shock is "split" into two. The PIV measurements provided clear picture about the evolution of the vortex at different time interval. The centerline velocity traces show the maximum velocity to be around 350 m/s. The velocity field, unlike in incompressible rings, contains contributions from both the shock and the vortex ring. The velocity distribution across the vortex core, core diameter and circulation are also calculated from the PIV data.

Proton NMR spectroscopic characterization of binary and ternary complexes of cobalt(II) carboxypeptidase A with inhibitors

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

Bertini, I.; Luchinat, C.; Messori, L.

The binding of L- and D-phenylalanine and carboxylate inhibitors to cobalt(II)-substituted carboxypeptidase A, Co(II)CPD (E), in the presence and absence of pseudohalogens (X = N/sub 3//sup -/, NCO/sup -/, and NCS/sup -/) has been studied by /sup 1/H NMR spectroscopy. This technique monitors the proton signals of histidine residues bound to cobalt(II) and is therefore sensitive to the interactions of inhibitors that perturb the coordination sphere of the metal. Enzyme-inhibitor complexes, E/times/I, E/times/I/sub 2/, and E/times/I/times/X, each with characteristic NMR features, have been identified. The NMR data suggest that when the carboxylate group of a substrate of inhibitor binds atmore » the active site, a conformational change occurs that allows a second ligand molecule to bind to the metal ion, altering its coordination sphere and thereby attenuating the bidentate behavior of Glu-72. The /sup 1/H NMR signals also reflect alterations in the histidine interactions with the metal upon inhibitor binding. Isotropic shifts in the signals for the C-4 (c) and N protons (a) of one of the histidine ligands are readily observed in all of these complexes. These signals are relatively constant for all E/times/I and E/times/I/times/X complexes, indicating that this ligand is in a relatively fixed or buried conformation. However in the 2:1 carboxylate inhibitor (E/times/I/sub 2/) complexes, both signals are shifted upfield, suggesting a disturbance in the interaction of this histidine with the metal.« less

Influence of chitosan structure on the formation and stability of DNA-chitosan polyelectrolyte complexes.

PubMed

Strand, Sabina P; Danielsen, Signe; Christensen, Bjørn E; Vårum, Kjell M

2005-01-01

The interactions between DNA and chitosans varying in fractional content of acetylated units (FA), degree of polymerization (DP), and degree of ionization were investigated by several techniques, including an ethidium bromide (EtBr) fluorescence assay, gel retardation, atomic force microscopy, and dynamic and electrophoretic light scattering. The charge density of the chitosan and the number of charges per chain were found to be the dominating factors for the structure and stability of DNA-chitosan complexes. All high molecular weight chitosans condensed DNA into physically stable polyplexes; however, the properties of the complexes were strongly dependent on FA, and thereby the charge density of chitosan. By employing fully charged oligomers of constant charge density, it was shown that the complexation of DNA and stability of the polyplexes is governed by the number of cationic residues per chain. A minimum of 6-9 positive charges appeared necessary to provide interaction strength comparable to that of polycations. In contrast, further increase in the number of charges above 9 did not increase the apparent binding affinity as judged from the EtBr displacement assay. The chitosan oligomers exhibited a pH-dependent interaction with DNA, reflecting the number of ionized amino groups. The complexation of DNA and the stability of oligomer-based polyplexes became reduced above pH 7.4. Such pH-dependent dissociation of polyplexes around the physiological pH is highly relevant in gene delivery applications and might be one of the reasons for the high transfection activity of oligomer-based polyplexes observed.

Interprofessional communication training: benefits to practicing pharmacists.

PubMed

Luetsch, Karen; Rowett, Debra

2015-10-01

Interprofessional communication skills are important for pharmacists to build collaborative relationships with other health professionals, integrate into healthcare teams, maximise their effectiveness in patient care in addressing complex care needs and meet the demands of health care reforms. This qualitative study explores clinical pharmacists' experiences and reflections after completing a learning and practice module which introduced them to a framework for successful interprofessional communication. The postgraduate clinical pharmacy program at The University of Queensland and the clinical pharmacy practice environments of forty-eight hospital and seven community based pharmacists. A learning and practice module outlining a framework for successful interprofessional communication was designed and integrated into a postgraduate clinical pharmacy program. Enrolled pharmacists applied newly learnt communication skills in pro-actively initiated, clinical discussions with a health professional in their practice environment. They provided written reflections on their experiences which were analysed using thematic analysis. Pharmacists' perceptions of the impact of applying the communication framework during their interaction with a health professional in their practice setting. Themes which emerged from reflections described pharmacists' confidence and capabilities to successfully conduct a clinical discussion with a health professional after initial apprehension and nervousness about the scheduled interaction. The application of the communication framework enhanced their perception of their professional identity, credibility and ability to build a collaborative working relationship with other health professionals. Pharmacists perceived that a learning and practice module for successful interprofessional practice integrated into a postgraduate clinical pharmacy program enhanced their interprofessional communication skills. The development of pro-active, interprofessional communication skills has the potential to increase interprofessional collaboration and pharmacists' personal role satisfaction. Pharmacists also observed it added value to their professional contribution in health care teams when addressing the demands of increasingly complex health care needs and reforms.

Professionalism and maintenance of certification: using vignettes describing interpersonal dilemmas to stimulate reflection and learning.

PubMed

Bernabeo, Elizabeth C; Reddy, Siddharta G; Ginsburg, Shiphra; Holmboe, Eric S

2014-01-01

Physicians do not always agree on "rules" governing behavior in professionally challenging situations. Little is known about contextual factors that influence physician approaches in these situations. We explored the individual-, social-, and societal-level factors that physicians consider when responding to 2 common professional dilemmas. We were particularly interested in knowing the extent to which physicians engage in self-reflection as a result of responding to the vignettes. A cross-sectional Web-based survey was sent to a random sample of 396 physicians, prompting them to respond to scripted professional dilemmas. A total of 120 physicians responded, yielding a response rate of 32.6%. Physicians responded to these dilemmas in highly variable ways, negotiating a complex array of contextual factors in their decisions. Interacting factors involving individual-level physician (eg, worry, guilt), patient (eg, nature of medical condition or relationship with patient), and social/societal (eg, policy, what peers or colleagues do) were important drivers in physician responses. Qualitative analysis revealed that several interacting themes guide physician approaches to professional dilemmas: patient welfare; types of patients; political, ethical, or legal issues; guiding principles; values; rules; and habits. Physicians negotiate a complex set of individual-, social-, and societal-level factors in response to professional dilemmas. This finding has important implications for the promotion and assessment of professional behavior in practicing physicians. Reflecting on scenarios may be an opportunity for physicians to learn about how and why they make decisions in difficult situations. © 2014 The Alliance for Continuing Education in the Health Professions, the Society for Academic Continuing Medical Education, and the Council on Continuing Medical Education, Association for Hospital Medical Education.

Top-down modulation of visual processing and knowledge after 250 ms supports object constancy of category decisions

PubMed Central

Schendan, Haline E.; Ganis, Giorgio

2015-01-01

People categorize objects more slowly when visual input is highly impoverished instead of optimal. While bottom-up models may explain a decision with optimal input, perceptual hypothesis testing (PHT) theories implicate top-down processes with impoverished input. Brain mechanisms and the time course of PHT are largely unknown. This event-related potential study used a neuroimaging paradigm that implicated prefrontal cortex in top-down modulation of occipitotemporal cortex. Subjects categorized more impoverished and less impoverished real and pseudo objects. PHT theories predict larger impoverishment effects for real than pseudo objects because top-down processes modulate knowledge only for real objects, but different PHT variants predict different timing. Consistent with parietal-prefrontal PHT variants, around 250 ms, the earliest impoverished real object interaction started on an N3 complex, which reflects interactive cortical activity for object cognition. N3 impoverishment effects localized to both prefrontal and occipitotemporal cortex for real objects only. The N3 also showed knowledge effects by 230 ms that localized to occipitotemporal cortex. Later effects reflected (a) word meaning in temporal cortex during the N400, (b) internal evaluation of prior decision and memory processes and secondary higher-order memory involving anterotemporal parts of a default mode network during posterior positivity (P600), and (c) response related activity in posterior cingulate during an anterior slow wave (SW) after 700 ms. Finally, response activity in supplementary motor area during a posterior SW after 900 ms showed impoverishment effects that correlated with RTs. Convergent evidence from studies of vision, memory, and mental imagery which reflects purely top-down inputs, indicates that the N3 reflects the critical top-down processes of PHT. A hybrid multiple-state interactive, PHT and decision theory best explains the visual constancy of object cognition. PMID:26441701

Controls on subglacial patterns and depositional environments in western Ireland

NASA Astrophysics Data System (ADS)

Knight, J.

2009-12-01

In western Ireland, Late Devensian ice flow dynamics and resultant patterns of landforms and sediments reflect the interplay between internal (glaciological) forcing and external forcing by rapid climate changes centred on the adjacent Atlantic Ocean. This interplay can be best demonstrated where ice from climatically-sensitive mountain source regions flowed into surrounding lowlands, such as the Connemara region of west County Galway, western Ireland. Here, a semi-independent ice cap was present over the Twelve Bens mountains, and interacted with ice from the much larger regional ice sheet from central Ireland. Landform and sediment patterns in the flat lowland region (c. 100 km2 below 30 m asl) to the south of the Twelve Bens reflect elements of this ice interaction. In detail, landform and sediment distributions here are highly complex with marked spatial differences in patterns of sediment availability. Across much of the region, sculpted bedrock forms (whaleback and bedrock drumlin ridges, roches mountonnées, striae) reflect subglacial abrasion across the underlying igneous and metamorphic bedrock that forms a relatively flat and lake-dominated landscape. Glacigenic sediments are found only at or around ice-retreat margins, and within isolated bedrock valleys. Here, diamicton drumlins are relatively uncommon but yet must represent depositional conditions that are not reflected elsewhere in this ice sheet sector where subglacial sediments are generally absent. This paper explores the interrelationship between local and regional ice flows through their impact on spatial patterns of glacial landforms and sediments. The paper presents field data on the characteristics of bedrock forms (erosional) and diamicton drumlins (depositional). Subglacial sediments are described from drumlin outcrops at key sites around Connemara, which helps in the understanding of the evolution of the subglacial environment in response to ice interactions from different source regions.

Imbalance between cognitive systems in alcohol-dependence and Korsakoff syndrome: An exploration using the Alcohol Flanker Task.

PubMed

Brion, Mélanie; Dormal, Valérie; Lannoy, Séverine; Mertens, Serge; de Timary, Philippe; Maurage, Pierre

2018-03-06

Alcohol-dependent individuals (ALC) simultaneously present decreased inhibitory control and increased attention towards alcohol-related cues. The dual-process models have proposed that these symptoms reflect an imbalance between prefrontal/reflective and limbic/automatic systems, respectively leading to cognitive dysfunctions in executive processes and to alcohol-related bias. However, most previous research has focused on a separate exploration of these systems among ALC, and the direct measure of their interactions remains to be conducted. Moreover, no study has explored the evolution of this imbalance across the successive stages of alcohol-related disorders, and particularly in Korsakoff syndrome (KS), the most frequent neurological complication of alcohol-dependence. Ten KS, 14 ALC, and 14 matched control participants performed a modified Flanker task, the "Alcohol Flanker Task," based on congruent, incongruent, and neutral conditions with alcohol-related stimuli. This task required inhibitory processing on alcohol-related stimuli and evaluated, through a behavioral approach, the interaction between reflective and automatic systems, as well as its evolution between ALC and KS. ALC and KS both presented high reactivity towards alcohol-related stimuli, confirming the presence of alcohol-related bias. KS showed increased omission rates (related to distractor interference) while ALC showed higher false-alarm rates (related to prepotent response inhibition). These results suggest that different inhibitory subcomponents might be altered at the successive stages of the pathology, and experimentally confirms the crucial role of the interaction between reflective and automatic processes in alcohol-use disorders. The present results reinforce the proposal that alcohol-related cues significantly impact inhibitory control in alcohol-related disorders. However, ALC and KS present different patterns of deficits depending on task complexity (i.e., executive load), thus suggesting a dissociation in inhibitory functions when processing alcohol-related cues.

Optical Neural Classification Of Binary Patterns

NASA Astrophysics Data System (ADS)

Gustafson, Steven C.; Little, Gordon R.

1988-05-01

Binary pattern classification that may be implemented using optical hardware and neural network algorithms is considered. Pattern classification problems that have no concise description (as in classifying handwritten characters) or no concise computation (as in NP-complete problems) are expected to be particularly amenable to this approach. For example, optical processors that efficiently classify binary patterns in accordance with their Boolean function complexity might be designed. As a candidate for such a design, an optical neural network model is discussed that is designed for binary pattern classification and that consists of an optical resonator with a dynamic multiplex-recorded reflection hologram and a phase conjugate mirror with thresholding and gain. In this model, learning or training examples of binary patterns may be recorded on the hologram such that one bit in each pattern marks the pattern class. Any input pattern, including one with an unknown class or marker bit, will be modified by a large number of parallel interactions with the reflection hologram and nonlinear mirror. After perhaps several seconds and 100 billion interactions, a steady-state pattern may develop with a marker bit that represents a minimum-Boolean-complexity classification of the input pattern. Computer simulations are presented that illustrate progress in understanding the behavior of this model and in developing a processor design that could have commanding and enduring performance advantages compared to current pattern classification techniques.

Temporal changes in species interactions in simple aquatic bacterial communities

PubMed Central

2012-01-01

Background Organisms modify their environment and in doing so change the quantity and possibly the quality of available resources. Due to the two-way relationship between organisms and their resource environment, and the complexity it brings to biological communities, measuring species interactions reliably in any biological system is a challenging task. As the resource environment changes, the intensity and even the sign of interactions may vary in time. We used Serratia marcescens and Novosphingobium capsulatum bacteria to study how the interaction between resource environment and organisms influence the growth of the bacterial species during circa 200 generations. We used a sterile-filtering method to measure how changes in resource environment are reflected in growth rates of the two species. Results Changes in the resource environment caused complex time and species composition-dependent effects on bacterial growth performance. Variation in the quality of the growth medium indicated existence of temporally fluctuating within-species facilitation and inhibition, and between-species asymmetric facilitation. Conclusions The interactions between the community members could not be fully predicted based only on the knowledge of the growth performance of each member in isolation. Growth dynamics in sterile-filtered samples of the conditioned growth medium can reveal both biologically meaningful changes in resource availability and temporally changing facilitative resource-mediated interactions between study species. This is the first study we are aware of where the filter-sterilization – growth assay method is applied to study the effect of long-term changes in the environment on species interactions. PMID:22984961

Soil Microbial Forensics.

PubMed

Santiago-Rodriguez, Tasha M; Cano, Raúl J

2016-08-01

Soil microbial forensics can be defined as the study of how microorganisms can be applied to forensic investigations. The field of soil microbial forensics is of increasing interest and applies techniques commonly used in diverse disciplines in order to identify microbes and determine their abundances, complexities, and interactions with soil and surrounding objects. Emerging new techniques are also providing insights into the complexity of microbes in soil. Soil may harbor unique microbes that may reflect specific physical and chemical characteristics indicating site specificity. While applications of some of these techniques in the field of soil microbial forensics are still in early stages, we are still gaining insight into how microorganisms may be more robustly used in forensic investigations.

Segregation of the Anodic Microbial Communities in a Microbial Fuel Cell Cascade

PubMed Central

Hodgson, Douglas M.; Smith, Ann; Dahale, Sonal; Stratford, James P.; Li, Jia V.; Grüning, André; Bushell, Michael E.; Marchesi, Julian R.; Avignone Rossa, C.

2016-01-01

Metabolic interactions within microbial communities are essential for the efficient degradation of complex organic compounds, and underpin natural phenomena driven by microorganisms, such as the recycling of carbon-, nitrogen-, and sulfur-containing molecules. These metabolic interactions ultimately determine the function, activity and stability of the community, and therefore their understanding would be essential to steer processes where microbial communities are involved. This is exploited in the design of microbial fuel cells (MFCs), bioelectrochemical devices that convert the chemical energy present in substrates into electrical energy through the metabolic activity of microorganisms, either single species or communities. In this work, we analyzed the evolution of the microbial community structure in a cascade of MFCs inoculated with an anaerobic microbial community and continuously fed with a complex medium. The analysis of the composition of the anodic communities revealed the establishment of different communities in the anodes of the hydraulically connected MFCs, with a decrease in the abundance of fermentative taxa and a concurrent increase in respiratory taxa along the cascade. The analysis of the metabolites in the anodic suspension showed a metabolic shift between the first and last MFC, confirming the segregation of the anodic communities. Those results suggest a metabolic interaction mechanism between the predominant fermentative bacteria at the first stages of the cascade and the anaerobic respiratory electrogenic population in the latter stages, which is reflected in the observed increase in power output. We show that our experimental system represents an ideal platform for optimization of processes where the degradation of complex substrates is involved, as well as a potential tool for the study of metabolic interactions in complex microbial communities. PMID:27242723

Infrared signature of micro-hydration in the organophosphate sarin: An ab initio study

DOE PAGES

Alam, Todd M.; Pearce, Charles Joseph

2015-06-28

The infrared (IR) spectra of micro-hydrated Sarin•(H 2O) n clusters containing between one and four explicit waters have been studied using ab initio density functional theory (DFT) methods. The phosphate group P=O bond vibration region (~1270 to 1290 cm –1) revealed the largest frequency variation with hydration, with a frequency red shift reflecting the direct hydrogen bond formation between the P=O of Sarin and water. Small variations to the P-F stretch (~810 to 815 cm –1) and the C-O-P vibrational modes (~995 to 1004 cm –1) showed that the water interactions with these functional groups were minor, and that themore » structures of Sarin were not extensively perturbed in the hydrated complexes. Increasing the number of explicit hydration waters produced only small vibrational changes in the lowest free energy complexes. These minor changes were consistent with a single water-phosphate hydrogen bond being the dominant structure, though a second water-phosphate hydrogen bond was observed in some complexes and was identified by an additional red shift of the P=O bond vibration. As a result, the H 2O•H 2O vibrational modes (~3450 to 3660 cm –1) increased in complexity with higher hydration levels and reflect the extended hydrogen bonding networks formed between the explicit waters in the hydrated Sarin clusters.« less

Binding of transducin and transducin-derived peptides to rhodopsin studies by attenuated total reflection-Fourier transform infrared difference spectroscopy.

PubMed Central

Fahmy, K

1998-01-01

Fourier transform infrared difference spectroscopy combined with the attenuated total reflection technique allows the monitoring of the association of transducin with bovine photoreceptor membranes in the dark. Illumination causes infrared absorption changes linked to formation of the light-activated rhodopsin-transducin complex. In addition to the spectral changes normally associated with meta II formation, prominent absorption increases occur at 1735 cm-1, 1640 cm-1, 1550 cm-1, and 1517 cm-1. The D2O sensitivity of the broad carbonyl stretching band around 1735 cm-1 indicates that a carboxylic acid group becomes protonated upon formation of the activated complex. Reconstitution of rhodopsin into phosphatidylcholine vesicles has little influence on the spectral properties of the rhodopsin-transducin complex, whereas pH affects the intensity of the carbonyl stretching band. AC-terminal peptide comprising amino acids 340-350 of the transducin alpha-subunit reproduces the frequencies and isotope sensitivities of several of the transducin-induced bands between 1500 and 1800 cm-1, whereas an N-terminal peptide (aa 8-23) does not. Therefore, the transducin-induced absorption changes can be ascribed mainly to an interaction between the transducin-alpha C-terminus and rhodopsin. The 1735 cm-1 vibration is also seen in the complex with C-terminal peptides devoid of free carboxylic acid groups, indicating that the corresponding carbonyl group is located on rhodopsin. PMID:9726932

The ecologies of community caring.

PubMed

Bent, K N

1999-06-01

Caring has been called the interactive exemplar of nursing in that it relates other foundational concepts of person, health, and environment within the profession and discipline. However, to reflect the dynamic praxis of knowing, being, and doing that is community health nursing, caring must include a focus on communities, the environment, and the global society. The concepts of community and community interventions remain complex and difficult, thus, community caring remains unclear. This article will explore the concept and offer a model of caring praxis in community health nursing.

Indigenous women's voices: marginalization and health.

PubMed

Dodgson, Joan E; Struthers, Roxanne

2005-10-01

Marginalization may affect health care delivery. Ways in which indigenous women experienced marginalization were examined. Data from 57 indigenous women (18 to 65 years) were analyzed for themes. Three themes emerged: historical trauma as lived marginalization, biculturalism experienced as marginalization, and interacting within a complex health care system. Experienced marginalization reflected participants' unique perspective and were congruent with previous research. It is necessary for health care providers to assess the detrimental impact of marginalization on the health status of individuals and/or communities.

Transformations of software design and code may lead to reduced errors

NASA Technical Reports Server (NTRS)

Connelly, E. M.

1983-01-01

The capability of programmers and non-programmers to specify problem solutions by developing example-solutions and also for the programmers by writing computer programs was investigated; each method of specification was accomplished at various levels of problem complexity. The level of difficulty of each problem was reflected by the number of steps needed by the user to develop a solution. Machine processing of the user inputs permitted inferences to be developed about the algorithms required to solve a particular problem. The interactive feedback of processing results led users to a more precise definition of the desired solution. Two participant groups (programmers and bookkeepers/accountants) working with three levels of problem complexity and three levels of processor complexity were used. The experimental task employed required specification of a logic for solution of a Navy task force problem.

Audio-vocal interaction in single neurons of the monkey ventrolateral prefrontal cortex.

PubMed

Hage, Steffen R; Nieder, Andreas

2015-05-06

Complex audio-vocal integration systems depend on a strong interconnection between the auditory and the vocal motor system. To gain cognitive control over audio-vocal interaction during vocal motor control, the PFC needs to be involved. Neurons in the ventrolateral PFC (VLPFC) have been shown to separately encode the sensory perceptions and motor production of vocalizations. It is unknown, however, whether single neurons in the PFC reflect audio-vocal interactions. We therefore recorded single-unit activity in the VLPFC of rhesus monkeys (Macaca mulatta) while they produced vocalizations on command or passively listened to monkey calls. We found that 12% of randomly selected neurons in VLPFC modulated their discharge rate in response to acoustic stimulation with species-specific calls. Almost three-fourths of these auditory neurons showed an additional modulation of their discharge rates either before and/or during the monkeys' motor production of vocalization. Based on these audio-vocal interactions, the VLPFC might be well positioned to combine higher order auditory processing with cognitive control of the vocal motor output. Such audio-vocal integration processes in the VLPFC might constitute a precursor for the evolution of complex learned audio-vocal integration systems, ultimately giving rise to human speech. Copyright © 2015 the authors 0270-6474/15/357030-11$15.00/0.

Modeling of intracerebral interictal epileptic discharges: Evidence for network interactions.

PubMed

Meesters, Stephan; Ossenblok, Pauly; Colon, Albert; Wagner, Louis; Schijns, Olaf; Boon, Paul; Florack, Luc; Fuster, Andrea

2018-06-01

The interictal epileptic discharges (IEDs) occurring in stereotactic EEG (SEEG) recordings are in general abundant compared to ictal discharges, but difficult to interpret due to complex underlying network interactions. A framework is developed to model these network interactions. To identify the synchronized neuronal activity underlying the IEDs, the variation in correlation over time of the SEEG signals is related to the occurrence of IEDs using the general linear model. The interdependency is assessed of the brain areas that reflect highly synchronized neural activity by applying independent component analysis, followed by cluster analysis of the spatial distributions of the independent components. The spatiotemporal interactions of the spike clusters reveal the leading or lagging of brain areas. The analysis framework was evaluated for five successfully operated patients, showing that the spike cluster that was related to the MRI-visible brain lesions coincided with the seizure onset zone. The additional value of the framework was demonstrated for two more patients, who were MRI-negative and for whom surgery was not successful. A network approach is promising in case of complex epilepsies. Analysis of IEDs is considered a valuable addition to routine review of SEEG recordings, with the potential to increase the success rate of epilepsy surgery. Copyright © 2018 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Are Interactional Behaviors Exhibited When the Self-Reported Health Question is Asked Associated with Health Status?*

PubMed Central

Garbarski, Dana; Schaeffer, Nora Cate; Dykema, Jennifer

2011-01-01

The self-reported health question summarizes information about health status across several domains of health and is widely used to measure health because it predicts mortality well. We examine whether interactional behaviors produced by respondents and interviewers during the self-reported health question-answer sequence reflect complexities in the respondent’s health history. We observed more problematic interactional behaviors during question-answer sequences in which respondents reported worse health. Furthermore, these behaviors were more likely to occur when there were inconsistencies in the respondent’s health history, even after controlling for the respondent’s answer to the self-reported health question, cognitive ability, and sociodemographic characteristics. We also found that among respondents who reported “excellent” health, and to a lesser extent among those who reported their health was “very good,” problematic interactional behaviors were associated with health inconsistencies. Overall, we find evidence that the interactional behaviors exhibited during the question-answer sequence are associated with respondents’ health status. PMID:21927518

Linear Elastic Waves - Series: Cambridge Texts in Applied Mathematics (No. 26)

NASA Astrophysics Data System (ADS)

Harris, John G.

2001-10-01

Wave propagation and scattering are among the most fundamental processes that we use to comprehend the world around us. While these processes are often very complex, one way to begin to understand them is to study wave propagation in the linear approximation. This is a book describing such propagation using, as a context, the equations of elasticity. Two unifying themes are used. The first is that an understanding of plane wave interactions is fundamental to understanding more complex wave interactions. The second is that waves are best understood in an asymptotic approximation where they are free of the complications of their excitation and are governed primarily by their propagation environments. The topics covered include reflection, refraction, the propagation of interfacial waves, integral representations, radiation and diffraction, and propagation in closed and open waveguides. Linear Elastic Waves is an advanced level textbook directed at applied mathematicians, seismologists, and engineers. Aimed at beginning graduate students Includes examples and exercises Has application in a wide range of disciplines

Nafion as Cosurfactant: Solubilization of Nafion in Water in the Presence of Pluronics

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

Kelarakis, Antonios; Giannelis, Emmanuel P.

2011-01-18

Incorporation of Nafion to aqueous solutions of Pluronics adversely impacts micellization due to extensive Nafion/copolymer interactions. Light scattering and zeta potential measurements provide evidence for the formation of sizable and stable Nafion/copolymer complexes, in expense of the neat copolymer micelles. At high copolymer concentrations, the overall interaction diagram of Nafion/copolymer reflects the competitive action of the release of packing constraints due to micellar destabilization induced by Nafion on one hand and the gelator nature of the Nafion on the other. Measurements using a quartz crystal microbalance (QCM-D) show that aqueous solutions of Pluronics (even at very low concentration) can dissolvemore » the Nafion coating on the crystal resonator, while typical low molecular weight ionic surfactants fail to induce similar effects. These studies demonstrate that complexation with this class of copolymers is a facile route to impart dispersibility to Nafion in aqueous environments that otherwise can be achieved through tedious and harsh treatments.« less

Heart-Rate Variability—More than Heart Beats?

PubMed Central

Ernst, Gernot

2017-01-01

Heart-rate variability (HRV) is frequently introduced as mirroring imbalances within the autonomous nerve system. Many investigations are based on the paradigm that increased sympathetic tone is associated with decreased parasympathetic tone and vice versa. But HRV is probably more than an indicator for probable disturbances in the autonomous system. Some perturbations trigger not reciprocal, but parallel changes of vagal and sympathetic nerve activity. HRV has also been considered as a surrogate parameter of the complex interaction between brain and cardiovascular system. Systems biology is an inter-disciplinary field of study focusing on complex interactions within biological systems like the cardiovascular system, with the help of computational models and time series analysis, beyond others. Time series are considered surrogates of the particular system, reflecting robustness or fragility. Increased variability is usually seen as associated with a good health condition, whereas lowered variability might signify pathological changes. This might explain why lower HRV parameters were related to decreased life expectancy in several studies. Newer integrating theories have been proposed. According to them, HRV reflects as much the state of the heart as the state of the brain. The polyvagal theory suggests that the physiological state dictates the range of behavior and psychological experience. Stressful events perpetuate the rhythms of autonomic states, and subsequently, behaviors. Reduced variability will according to this theory not only be a surrogate but represent a fundamental homeostasis mechanism in a pathological state. The neurovisceral integration model proposes that cardiac vagal tone, described in HRV beyond others as HF-index, can mirror the functional balance of the neural networks implicated in emotion–cognition interactions. Both recent models represent a more holistic approach to understanding the significance of HRV. PMID:28955705

Heart-Rate Variability-More than Heart Beats?

PubMed

Ernst, Gernot

2017-01-01

Heart-rate variability (HRV) is frequently introduced as mirroring imbalances within the autonomous nerve system. Many investigations are based on the paradigm that increased sympathetic tone is associated with decreased parasympathetic tone and vice versa . But HRV is probably more than an indicator for probable disturbances in the autonomous system. Some perturbations trigger not reciprocal, but parallel changes of vagal and sympathetic nerve activity. HRV has also been considered as a surrogate parameter of the complex interaction between brain and cardiovascular system. Systems biology is an inter-disciplinary field of study focusing on complex interactions within biological systems like the cardiovascular system, with the help of computational models and time series analysis, beyond others. Time series are considered surrogates of the particular system, reflecting robustness or fragility. Increased variability is usually seen as associated with a good health condition, whereas lowered variability might signify pathological changes. This might explain why lower HRV parameters were related to decreased life expectancy in several studies. Newer integrating theories have been proposed. According to them, HRV reflects as much the state of the heart as the state of the brain. The polyvagal theory suggests that the physiological state dictates the range of behavior and psychological experience. Stressful events perpetuate the rhythms of autonomic states, and subsequently, behaviors. Reduced variability will according to this theory not only be a surrogate but represent a fundamental homeostasis mechanism in a pathological state. The neurovisceral integration model proposes that cardiac vagal tone, described in HRV beyond others as HF-index, can mirror the functional balance of the neural networks implicated in emotion-cognition interactions. Both recent models represent a more holistic approach to understanding the significance of HRV.

The interaction between felt touch and tactile consequences of observed actions: an action-based somatosensory congruency paradigm.

PubMed

Deschrijver, Eliane; Wiersema, Jan R; Brass, Marcel

2016-07-01

Action observation leads to a representation of both the motor aspect of an observed action (motor simulation) and its somatosensory consequences (action-based somatosensory simulation) in the observer's brain. In the current electroencephalography-study, we investigated the neuronal interplay of action-based somatosensory simulation and felt touch. We presented index or middle finger tapping movements of a human or a wooden hand, while simultaneously presenting 'tap-like' tactile sensations to either the corresponding or non-corresponding fingertip of the participant. We focused on an early stage of somatosensory processing [P50, N100 and N140 sensory evoked potentials (SEPs)] and on a later stage of higher-order processing (P3-complex). The results revealed an interaction effect of animacy and congruency in the early P50 SEP and an animacy effect in the N100/N140 SEPs. In the P3-complex, we found an interaction effect indicating that the influence of congruency was larger in the human than in the wooden hand. We argue that the P3-complex may reflect higher-order self-other distinction by signaling simulated action-based touch that does not match own tactile information. As such, the action-based somatosensory congruency paradigm might help understand higher-order social processes from a somatosensory point of view. © The Author (2015). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

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.

The Video Interaction Guidance approach applied to teaching communication skills in dentistry.

PubMed

Quinn, S; Herron, D; Menzies, R; Scott, L; Black, R; Zhou, Y; Waller, A; Humphris, G; Freeman, R

2016-05-01

To examine dentists' views of a novel video review technique to improve communication skills in complex clinical situations. Dentists (n = 3) participated in a video review known as Video Interaction Guidance to encourage more attuned interactions with their patients (n = 4). Part of this process is to identify where dentists and patients reacted positively and effectively. Each dentist was presented with short segments of video footage taken during an appointment with a patient with intellectual disabilities and communication difficulties. Having observed their interactions with patients, dentists were asked to reflect on their communication strategies with the assistance of a trained VIG specialist. Dentists reflected that their VIG session had been insightful and considered the review process as beneficial to communication skills training in dentistry. They believed that this technique could significantly improve the way dentists interact and communicate with patients. The VIG sessions increased their awareness of the communication strategies they use with their patients and were perceived as neither uncomfortable nor threatening. The VIG session was beneficial in this exploratory investigation because the dentists could identify when their interactions were most effective. Awareness of their non-verbal communication strategies and the need to adopt these behaviours frequently were identified as key benefits of this training approach. One dentist suggested that the video review method was supportive because it was undertaken by a behavioural scientist rather than a professional counterpart. Some evidence supports the VIG approach in this specialist area of communication skills and dental training. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Purification and characterisation of the fission yeast Ndc80 complex.

PubMed

Matsuo, Yuzy; Maurer, Sebastian P; Surrey, Thomas; Toda, Takashi

2017-07-01

The Ndc80 complex is a conserved outer kinetochore protein complex consisting of Ndc80 (Hec1), Nuf2, Spc24 and Spc25. This complex comprises a major, if not the sole, platform with which the plus ends of the spindle microtubules directly interact. In fission yeast, several studies indicate that multiple microtubule-associated proteins including the Dis1/chTOG microtubule polymerase and the Mal3/EB1 microtubule plus-end tracking protein directly or indirectly bind Ndc80, thereby ensuring stable kinetochore-microtubule attachment. However, the purification of the Ndc80 complex from this yeast has not been achieved, which hampers the in-depth investigation as to how the outer kinetochore attaches to the plus end of the spindle microtubule. Here we report the two-step purification of the fission yeast Ndc80 holo complex from bacteria. First, we purified separately two sub-complexes consisting of Ndc80-Nuf2 and Spc24-Spc25. Then, these two sub-complexes were mixed and applied to size-exclusion chromatography. The reconstituted Ndc80 holo complex is composed of four subunits with equal stoichiometry. The complex possesses microtubule-binding activity, and Total Internal Reflection Fluorescence (TIRF)-microscopy assays show that the complex binds the microtubule lattice. Interestingly, unlike the human complex, the fission yeast complex does not track depolymerising microtubule ends. Further analysis shows that under physiological ionic conditions, the Ndc80 holo complex does not detectably bind Dis1, but instead it interacts with Mal3/EB1, by which the Ndc80 complex tracks the growing microtubule plus end. This result substantiates the notion that the Ndc80 complex plays a crucial role in establishment of the dynamic kinetochore-microtubule interface by cooperating with chTOG and EB1. Copyright © 2017 The Francis Crick Institute. Published by Elsevier Inc. All rights reserved.

Point interactions, metamaterials, and PT-symmetry

NASA Astrophysics Data System (ADS)

Mostafazadeh, Ali

2016-05-01

We express the boundary conditions for TE and TM waves at the interfaces of an infinite planar slab of homogeneous metamaterial as certain point interactions and use them to compute the transfer matrix of the system. This allows us to demonstrate the omnidirectional reflectionlessness of Veselago's slab for waves of arbitrary wavelength, reveal the translational and reflection symmetry of this slab, explore the laser threshold condition and coherent perfect absorption for active negative-index metamaterials, introduce a point interaction modeling phase-conjugation, determine the corresponding antilinear transfer matrix, and offer a simple proof of the equivalence of Veselago's slab with a pair of parallel phase-conjugating plates. We also study the connection between certain optical setups involving metamaterials and a class of PT-symmetric quantum systems defined on wedge-shape contours in the complex plane. This provides a physical interpretation for the latter.

Copper(II) ions interactions in the systems with triamines and ATP. Potentiometric and spectroscopic studies.

PubMed

Hoffmann, S K; Goslar, J; Bregier-Jarzebowska, R; Gasowska, A; Zalewska, A; Lomozik, L

2017-12-01

The mode of interaction and thermodynamic stability of complexes formed in binary and ternary Cu(II)/ATP/triamines systems were studied using potentiometric and spectroscopic (NMR, EPR, UV-Vis) methods. It was found that in binary metal-free systems ATP/H x PA species are formed (PA: Spd=spermidine or 3,3-tri=1,7-diamino-4-azaheptane) where the phosphate groups from nucleotides are preferred negative centers and protonated amine groups of amines are positive centers of reaction. In the ternary systems Cu/ATP/H x (PA) as well as Cu/(ATP)(PA) species are formed. The type of the formed Cu(II) complexes depends on pH of the solution. For a low pH value the complexation appears between Cu(II) and ATP molecules via oxygen atoms of phosphate groups. For a very high pH value, where ATP is hydrolyzed, the Cu(II) ions are bound to the nitrogen atoms of polyamine molecules. We did not detect any direct coordination of the N7 nitrogen atom of adenosine to Cu(II) ions. It means that the CuN7 interaction is an indirect type and can be due to noncovalent interplay including water molecule. EPR studies were performed at glassy state (77K) after a fast freezing both for binary and ternary systems. The glassy state EPR spectra do not reflect species identified in titration studies indicating significant effect of rapid temperature decrease on equilibrium of Cu(II) complexes. We propose the molecular structure of all the studied complexes at the glassy state deduced from EPR and optical spectroscopy results. Copyright © 2017 Elsevier Inc. All rights reserved.

Investigation of Stimulation-Response Relationships for Complex Fracture Systems in Enhanced Geothermal Reservoirs

DOE Data Explorer

Fu, Pengcheng; Johnson, Scott M.; Carrigan, Charles R.

2011-01-01

Hydraulic fracturing is currently the primary method for stimulating low-permeability geothermal reservoirs and creating Enhanced (or Engineered) Geothermal Systems (EGS) with improved permeability and heat production efficiency. Complex natural fracture systems usually exist in the formations to be stimulated and it is therefore critical to understand the interactions between existing fractures and newly created fractures before optimal stimulation strategies can be developed. Our study aims to improve the understanding of EGS stimulation-response relationships by developing and applying computer-based models that can effectively reflect the key mechanisms governing interactions between complex existing fracture networks and newly created hydraulic fractures. In this paper, we first briefly describe the key modules of our methodology, namely a geomechanics solver, a discrete fracture flow solver, a rock joint response model, an adaptive remeshing module, and most importantly their effective coupling. After verifying the numerical model against classical closed-form solutions, we investigate responses of reservoirs with different preexisting natural fractures to a variety of stimulation strategies. The factors investigated include: the in situ stress states (orientation of the principal stresses and the degree of stress anisotropy), pumping pressure, and stimulation sequences of multiple wells.

RMS Spectral Modelling - a powerful tool to probe the origin of variability in Active Galactic Nuclei

NASA Astrophysics Data System (ADS)

Mallick, Labani; Dewangan, Gulab chand; Misra, Ranjeev

2016-07-01

The broadband energy spectra of Active Galactic Nuclei (AGN) are very complex in nature with the contribution from many ingredients: accretion disk, corona, jets, broad-line region (BLR), narrow-line region (NLR) and Compton-thick absorbing cloud or TORUS. The complexity of the broadband AGN spectra gives rise to mean spectral model degeneracy, e.g, there are competing models for the broad feature near 5-7 keV in terms of blurred reflection and complex absorption. In order to overcome the energy spectral model degeneracy, the most reliable approach is to study the RMS variability spectrum which connects the energy spectrum with temporal variability. The origin of variability could be pivoting of the primary continuum, reflection and/or absorption. The study of RMS (Root Mean Square) spectra would help us to connect the energy spectra with the variability. In this work, we study the energy dependent variability of AGN by developing theoretical RMS spectral model in ISIS (Interactive Spectral Interpretation System) for different input energy spectra. In this talk, I would like to present results of RMS spectral modelling for few radio-loud and radio-quiet AGN observed by XMM-Newton, Suzaku, NuSTAR and ASTROSAT and will probe the dichotomy between these two classes of AGN.

The birth of a quasiparticle in silicon observed in time-frequency space.

PubMed

Hase, Muneaki; Kitajima, Masahiro; Constantinescu, Anca Monia; Petek, Hrvoje

2003-11-06

The concept of quasiparticles in solid-state physics is an extremely powerful tool for describing complex many-body phenomena in terms of single-particle excitations. Introducing a simple particle, such as an electron, hole or phonon, deforms a many-body system through its interactions with other particles. In this way, the added particle is 'dressed' or 'renormalized' by a self-energy cloud that describes the response of the many-body system, so forming a new entity--the quasiparticle. Using ultrafast laser techniques, it is possible to impulsively generate bare particles and observe their subsequent dressing by the many-body interactions (that is, quasiparticle formation) on the time and energy scales governed by the Heisenberg uncertainty principle. Here we describe the coherent response of silicon to excitation with a 10-femtosecond (10(-14) s) laser pulse. The optical pulse interacts with the sample by way of the complex second-order nonlinear susceptibility to generate a force on the lattice driving coherent phonon excitation. Transforming the transient reflectivity signal into frequency-time space reveals interference effects leading to the coherent phonon generation and subsequent dressing of the phonon by electron-hole pair excitations.

Demonstrating the saturation of stimulated Brillouin scattering by ion acoustic decay using fully kinetic simulations

DOE PAGES

Chapman, T.; Winjum, B. J.; Brunner, S.; ...

2015-09-01

The saturation of stimulated Brillouin scattering (SBS) by the decay to turbulence of the ion acoustic wave (IAW) that participates in the three-wave SBS interaction is demonstrated using a quasi-noiseless one-dimensional numerical solution to the Vlasov-Maxwell system of equations. This simulation technique permits careful examination of the decay process and its role in the complex evolution of SBS. Here, the IAW decay process is shown to be an effective SBS saturation mechanism. In our example, the instantaneous plasma reflectivity saturates at ~30% and drops to ~0% as a direct consequence of IAW decay. A contrasting example where the reflectivity ismore » controlled by dephasing due to the nonlinear frequency of the IAW is also discussed.« less

Challenging the 'view from nowhere': citizen reflections on specialist expertise in a deliberative process.

PubMed

Davies, Gail; Burgess, Jacquelin

2004-12-01

This paper presents analysis of citizen encounters with specialists in a deliberative process, called Deliberative Mapping, which explored options for addressing the shortage of organs for transplantation in the UK. There is a rich theoretical literature about the extent to which citizens are competent to question the knowledge claims of specialists in complex decision-making processes, suggesting the trustworthiness of scientific expertise will depend on the qualities of social interaction in face-to-face dialogue, but little empirical analysis of specific encounters. This paper presents evidence of how citizens located specialist expertise in making judgements about the legitimacy and credibility of specialist knowledge claims, in ways that reflect differences in epistemic procedures valued by the panels of men and women in this process.

Interactive rendering of acquired materials on dynamic geometry using frequency analysis.

PubMed

Bagher, Mahdi Mohammad; Soler, Cyril; Subr, Kartic; Belcour, Laurent; Holzschuch, Nicolas

2013-05-01

Shading acquired materials with high-frequency illumination is computationally expensive. Estimating the shading integral requires multiple samples of the incident illumination. The number of samples required may vary across the image, and the image itself may have high- and low-frequency variations, depending on a combination of several factors. Adaptively distributing computational budget across the pixels for shading is a challenging problem. In this paper, we depict complex materials such as acquired reflectances, interactively, without any precomputation based on geometry. In each frame, we first estimate the frequencies in the local light field arriving at each pixel, as well as the variance of the shading integrand. Our frequency analysis accounts for combinations of a variety of factors: the reflectance of the object projecting to the pixel, the nature of the illumination, the local geometry and the camera position relative to the geometry and lighting. We then exploit this frequency information (bandwidth and variance) to adaptively sample for reconstruction and integration. For example, fewer pixels per unit area are shaded for pixels projecting onto diffuse objects, and fewer samples are used for integrating illumination incident on specular objects.

Sustainable Deforestation Evaluation Model and System Dynamics Analysis

PubMed Central

Feng, Huirong; Lim, C. W.; Chen, Liqun; Zhou, Xinnian; Zhou, Chengjun; Lin, Yi

2014-01-01

The current study used the improved fuzzy analytic hierarchy process to construct a sustainable deforestation development evaluation system and evaluation model, which has refined a diversified system to evaluate the theory of sustainable deforestation development. Leveraging the visual image of the system dynamics causal and power flow diagram, we illustrated here that sustainable forestry development is a complex system that encompasses the interaction and dynamic development of ecology, economy, and society and has reflected the time dynamic effect of sustainable forestry development from the three combined effects. We compared experimental programs to prove the direct and indirect impacts of the ecological, economic, and social effects of the corresponding deforest techniques and fully reflected the importance of developing scientific and rational ecological harvesting and transportation technologies. Experimental and theoretical results illustrated that light cableway skidding is an ecoskidding method that is beneficial for the sustainable development of resources, the environment, the economy, and society and forecasted the broad potential applications of light cableway skidding in timber production technology. Furthermore, we discussed the sustainable development countermeasures of forest ecosystems from the aspects of causality, interaction, and harmony. PMID:25254225

Sustainable deforestation evaluation model and system dynamics analysis.

PubMed

Feng, Huirong; Lim, C W; Chen, Liqun; Zhou, Xinnian; Zhou, Chengjun; Lin, Yi

2014-01-01

The current study used the improved fuzzy analytic hierarchy process to construct a sustainable deforestation development evaluation system and evaluation model, which has refined a diversified system to evaluate the theory of sustainable deforestation development. Leveraging the visual image of the system dynamics causal and power flow diagram, we illustrated here that sustainable forestry development is a complex system that encompasses the interaction and dynamic development of ecology, economy, and society and has reflected the time dynamic effect of sustainable forestry development from the three combined effects. We compared experimental programs to prove the direct and indirect impacts of the ecological, economic, and social effects of the corresponding deforest techniques and fully reflected the importance of developing scientific and rational ecological harvesting and transportation technologies. Experimental and theoretical results illustrated that light cableway skidding is an ecoskidding method that is beneficial for the sustainable development of resources, the environment, the economy, and society and forecasted the broad potential applications of light cableway skidding in timber production technology. Furthermore, we discussed the sustainable development countermeasures of forest ecosystems from the aspects of causality, interaction, and harmony.

Self-Assembling Peptide Detergents Stabilize Isolated Photosystem Ion a Dry Surface for an Extended Time

PubMed Central

Kiley, Patrick; Zhao, Xiaojun; Vaughn, Michael; Baldo, Marc A; Bruce, Barry D

2005-01-01

We used a class of designed peptide detergents to stabilize photosystem I (PS-I) upon extended drying under N2 on a gold-coated-Ni-NTA glass surface. PS-I is a chlorophyll-containing membrane protein complex that is the primary reducer of ferredoxin and the electron acceptor of plastocyanin. We isolated the complex from the thylakoids of spinach chloroplasts using a chemical detergent. The chlorophyll molecules associated with the PS-I complex provide an intrinsic steady-state emission spectrum between 650 and 800 nm at −196.15 °C that reflects the organization of the pigment-protein interactions. In the absence of detergents, a large blue shift of the fluorescence maxima from approximately 735 nm to approximately 685 nm indicates a disruption in light-harvesting subunit organization, thus revealing chlorophyll−protein interactions. The commonly used membrane protein-stabilizing detergents, N-dodecyl-β-D-maltoside and N-octyl-β-D-glucoside, only partially stabilized the approximately 735-nm complex with approximately 685-nm spectroscopic shift. However, prior to drying, addition of the peptide detergent acetyl- AAAAAAK at increasing concentration significantly stabilized the PS-I complex. Moreover, in the presence of acetyl- AAAAAAK, the PS-I complex is stable in a dried form at room temperature for at least 3 wk. Another peptide detergent, acetyl-VVVVVVD, also stabilized the complex but to a lesser extent. These observations suggest that the peptide detergents may effectively stabilize membrane proteins in the solid-state. These designed peptide detergents may facilitate the study of diverse types of membrane proteins. PMID:15954800

Yeast-yeast interactions revealed by aromatic profile analysis of Sauvignon Blanc wine fermented by single or co-culture of non-Saccharomyces and Saccharomyces yeasts.

PubMed

Sadoudi, Mohand; Tourdot-Maréchal, Raphaëlle; Rousseaux, Sandrine; Steyer, Damien; Gallardo-Chacón, Joan-Josep; Ballester, Jordi; Vichi, Stefania; Guérin-Schneider, Rémi; Caixach, Josep; Alexandre, Hervé

2012-12-01

There has been increasing interest in the use of selected non-Saccharomyces yeasts in co-culture with Saccharomyces cerevisiae. The main reason is that the multistarter fermentation process is thought to simulate indigenous fermentation, thus increasing wine aroma complexity while avoiding the risks linked to natural fermentation. However, multistarter fermentation is characterised by complex and largely unknown interactions between yeasts. Consequently the resulting wine quality is rather unpredictable. In order to better understand the interactions that take place between non-Saccharomyces and Saccharomyces yeasts during alcoholic fermentation, we analysed the volatile profiles of several mono-culture and co-cultures. Candida zemplinina, Torulaspora delbrueckii and Metschnikowia pulcherrima were used to conduct fermentations either in mono-culture or in co-culture with S. cerevisiae. Up to 48 volatile compounds belonging to different chemical families were quantified. For the first time, we show that C. zemplinina is a strong producer of terpenes and lactones. We demonstrate by means of multivariate analysis that different interactions exist between the co-cultures studied. We observed a synergistic effect on aromatic compound production when M. pulcherrima was in co-culture with S. cerevisiae. However a negative interaction was observed between C. zemplinina and S. cerevisiae, which resulted in a decrease in terpene and lactone content. These interactions are independent of biomass production. The aromatic profiles of T. delbrueckii and S. cerevisiae in mono-culture and in co-culture are very close, and are biomass-dependent, reflecting a neutral interaction. This study reveals that a whole family of compounds could be altered by such interactions. These results suggest that the entire metabolic pathway is affected by these interactions. Copyright © 2012 Elsevier Ltd. All rights reserved.

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.

PubMed

Levy, Roie; Carr, Rogan; Kreimer, Anat; Freilich, Shiri; Borenstein, Elhanan

2015-05-17

Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm. NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms' niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds. The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.

[Neuroanatomical, genetic and neurochemical aspects of infantile autism].

PubMed

Gerhant, Aneta; Olajossy, Marcin; Olajossy-Hilkesberger, Luiza

2013-01-01

Infantile autism is a neurodevelopmental disorder characterized by impairments in communication, reciprocal social interaction and restricted repetitive behaviors or interests. Although the cause of these disorders is not yet known, studies strongly suggest a genetic basis with a complex mode of inheritance. The etiopathogenetic processes of autism are extremely complex, which is reflected in the varying course and its symptomatology. Trajectories of brain development and volumes of its structures are aberrant in autistic patients. It is suggested that disturbances in sertotoninergic, gabaergic, glutaminergic, cholinergic and dopaminergic neurotransmission can be responsible for symptoms of autism as well as can disturb the development of the young brain. The objective of this article is to present the results of reasearch on neuroanatomical, neurochemical and genetic aspects of autism.

Invasion complexity at large spatial scales is an emergent property of interactions among landscape characteristics and invader traits

PubMed Central

Jordan, Nicholas R.; Forester, James D.

2018-01-01

Invasion potential should be part of the evaluation of candidate species for any species introduction. However, estimating invasion risks remains a challenging problem, particularly in complex landscapes. Certain plant traits are generally considered to increase invasive potential and there is an understanding that landscapes influence invasions dynamics, but little research has been done to explore how those drivers of invasions interact. We evaluate the relative roles of, and potential interactions between, plant invasiveness traits and landscape characteristics on invasions with a case study using a model parameterized for the potentially invasive biomass crop, Miscanthus × giganteus. Using that model we simulate invasions on 1000 real landscapes to evaluate how landscape characteristics, including both composition and spatial structure, affect invasion outcomes. We conducted replicate simulations with differing strengths of plant invasiveness traits (dispersal ability, establishment ability, population growth rate, and the ability to utilize dispersal corridors) to evaluate how the importance of landscape characteristics for predicting invasion patterns changes depending on the invader details. Analysis of simulations showed that the presence of highly suitable habitat (e.g., grasslands) is generally the strongest determinant of invasion dynamics but that there are also more subtle interactions between landscapes and invader traits. These effects can also vary between different aspects of invasion dynamics (short vs. long time scales and population size vs. spatial extent). These results illustrate that invasions are complex emergent processes with multiple drivers and effective management needs to reflect the ecology of the species of interest and the particular goals or risks for which efforts need to be optimized. PMID:29771923

Optimizing energy functions for protein-protein interface design.

PubMed

Sharabi, Oz; Yanover, Chen; Dekel, Ayelet; Shifman, Julia M

2011-01-15

Protein design methods have been originally developed for the design of monomeric proteins. When applied to the more challenging task of protein–protein complex design, these methods yield suboptimal results. In particular, they often fail to recapitulate favorable hydrogen bonds and electrostatic interactions across the interface. In this work, we aim to improve the energy function of the protein design program ORBIT to better account for binding interactions between proteins. By using the advanced machine learning framework of conditional random fields, we optimize the relative importance of all the terms in the energy function, attempting to reproduce the native side-chain conformations in protein–protein interfaces. We evaluate the performance of several optimized energy functions, each describes the van der Waals interactions using a different potential. In comparison with the original energy function, our best energy function (a) incorporates a much “softer” repulsive van der Waals potential, suitable for the discrete rotameric representation of amino acid side chains; (b) does not penalize burial of polar atoms, reflecting the frequent occurrence of polar buried residues in protein–protein interfaces; and (c) significantly up-weights the electrostatic term, attesting to the high importance of these interactions for protein–protein complex formation. Using this energy function considerably improves side chain placement accuracy for interface residues in a large test set of protein–protein complexes. Moreover, the optimized energy function recovers the native sequences of protein–protein interface at a higher rate than the default function and performs substantially better in predicting changes in free energy of binding due to mutations.

Strontium isotope geochemistry of groundwater in the central part of the Dakota (Great Plains) aquifer, USA

USGS Publications Warehouse

Gosselin, D.C.; Harvey, F.E.; Frost, C.; Stotler, R.; Macfarlane, P.A.

2004-01-01

The Dakota aquifer of the central and eastern Great Plains of the United States is an important source of water for municipal supplies, irrigation and industrial use. Although the regional flow system can be characterized generally as east to northeasterly from the Rocky Mountains towards the Missouri River, locally the flow systems are hydrologically complex. This study uses Sr isotopic data from groundwater and leached aquifer samples to document the complex subsystems within the Dakota aquifer in Nebraska and Kansas. The interaction of groundwater with the geologic material through which it flows has created spatial patterns in the isotopic measurements that are related to: long-term water-rock interaction, during which varying degrees of isotopic equilibrium between water and rock has been achieved; and the alteration of NaCl fluids by water-rock interaction. Specifically, Sr isotopic data distinguish brines from Kansas and western Nebraska from those in eastern Nebraska: the former are interpreted to reflect interaction with Permian rocks, whereas the latter record interaction with Pennsylvanian rocks. The Sr isotopic composition of groundwater from other parts of Nebraska and Kansas are a function of the dynamic interaction between groundwater and unlithified sediments (e.g., glacial till and loess), followed by interaction with oxidized and unoxidized sediments within the Dakota Formation. This study illustrates the power of combining Sr chemistry with more conventional geochemical data to obtain a more complete understanding of groundwater flow systems within regional aquifer systems where extensive monitoring networks do not exist. ?? 2003 Elsevier Ltd. All rights reserved.

Reflections on using biographical approaches in end-of-life care: dignity therapy as example.

PubMed

Lindqvist, Olav; Threlkeld, Guinever; Street, Annette F; Tishelman, Carol

2015-01-01

The therapeutic potential of nonpharmacologic interventions using biographical approaches at the end of life (EoL) is being increasingly recognized, but less attention is paid to processes impeding realization of this potential. In this article, Swedish and Australian researchers reflect on and problematize experiences using one biographical approach, dignity therapy (DT), in EoL care in Sweden. We use this as an example, focusing on critical examination of the process of applying DT in practice, examining frictions experienced in recruiting participants, collecting the data, and creating a biography. We discuss issues regarding agency, which became evident in the recruitment process and choices made about participation, and the power differentials manifested in the interactive process of eliciting stories and crafting them into a final product. We also raise salient questions about how research and practice with biographical approaches in EoL care might better build on and further existing knowledge to better reflect the complexities of everyday life. © The Author(s) 2014.

The "periodic table" of the genetic code: A new way to look at the code and the decoding process.

PubMed

Komar, Anton A

2016-01-01

Henri Grosjean and Eric Westhof recently presented an information-rich, alternative view of the genetic code, which takes into account current knowledge of the decoding process, including the complex nature of interactions between mRNA, tRNA and rRNA that take place during protein synthesis on the ribosome, and it also better reflects the evolution of the code. The new asymmetrical circular genetic code has a number of advantages over the traditional codon table and the previous circular diagrams (with a symmetrical/clockwise arrangement of the U, C, A, G bases). Most importantly, all sequence co-variances can be visualized and explained based on the internal logic of the thermodynamics of codon-anticodon interactions.

Finding Correlation between Protein Protein Interaction Modules Using Semantic Web Techniques

NASA Astrophysics Data System (ADS)

Kargar, Mehdi; Moaven, Shahrouz; Abolhassani, Hassan

Many complex networks such as social networks and computer show modular structures, where edges between nodes are much denser within modules than between modules. It is strongly believed that cellular networks are also modular, reflecting the relative independence and coherence of different functional units in a cell. In this paper we used a human curated dataset. In this paper we consider each module in the PPI network as ontology. Using techniques in ontology alignment, we compare each pair of modules in the network. We want to see that is there a correlation between the structure of each module or they have totally different structures. Our results show that there is no correlation between proteins in a protein protein interaction network.

Evidence for changes in the nucleotide conformation in the active site of H(+)-ATPase as determined by pulsed EPR spectroscopy.

PubMed

Schneider, B; Sigalat, C; Amano, T; Zimmermann, J L

2000-12-19

The conformation of di- and triphosphate nucleosides in the active site of ATPsynthase (H(+)-ATPase) from thermophilic Bacillus PS3 (TF1) and their interaction with Mg(2+)/Mn(2+) cations have been investigated using EPR, ESEEM, and HYSCORE spectroscopies. For a ternary complex formed by a stoichiometric mixture of TF1, Mn(2+), and ADP, the ESEEM and HYSCORE data reveal a (31)P hyperfine interaction with Mn(2+) (|A((31)P)| approximately 5.20 MHz), significantly larger than that measured for the complex formed by Mn(2+) and ADP in solution (|A((31)P)| approximately 4.50 MHz). The Q-band EPR spectrum of the Mn.TF1.ADP complex indicates that the Mn(2+) binds in a slightly distorted environment with |D| approximately 180 x 10(-4) cm(-1) and |E| approximately 50 x 10(-4) cm(-1). The increased hyperfine coupling with (31)P in the presence of TF1 reflects the specific interaction between the central Mn(2+) and the ADP beta-phosphate, illustrating the role of the enzyme active site in positioning the phosphate chain of the substrate for efficient catalysis. Results with the ternary Mn.TF1.ATP and Mn.TF1.AMP-PNP complexes are interpreted in a similar way with two hyperfine couplings being resolved for each complex (|A((31)P(beta))| approximately 4.60 MHz and |A((31)P(gamma))| approximately 5.90 MHz with ATP, and |A((31)P(beta))| approximately 4.20 MHz and |A((31)P(gamma))| approximately 5.40 MHz with AMP-PNP). In these complexes, the increased hyperfine coupling with (31)P(gamma) compared with (31)P(beta) reflects the smaller Mn.P distance with the gamma-phosphate compared with the beta-phosphate as found in the crystal structure of the analogous enzyme from mitochondria [3.53 vs 3.70 A (Abrahams, J. P., Leslie, A. G. W., Lutter, R., and Walker, J. E. (1994) Nature 370, 621-628)] and the different binding modes of the two phosphate groups. The ESEEM and HYSCORE data of a complex formed with Mn(2+), ATP, and the isolated beta subunit show that the (31)P hyperfine coupling is close to that measured in the absence of the protein, indicating a poorly structured nucleotide site in the isolated beta subunit in the presence of ATP. The inhibition data obtained for TF1 incubated in the presence of Mg(2+), ADP, Al(NO(3))(3), and NaF indicate the formation of the inhibited complex with the transition state analogue namely Mg.TF1.ADP.AlF(x) with the equilibrium dissociation constant K(D) = 350 microM and rate constant k = 0.02 min(-1). The ESEEM and HYSCORE data obtained for an inhibited TF1 sample, Mn.TF1.ADP.AlF(x), confirm the formation of the transition state analogue with distinct spectroscopic footprints that can be assigned to Mn.(19)F and Mn.(27)Al hyperfine interactions. The (31)P(beta) hyperfine coupling that is measured in the inhibited complex with the transition state analogue (|A((31)P(beta))| approximately 5.10 MHz) is intermediate between those measured in the presence of ADP and ATP and suggests an increase in the bond between Mn and the P(beta) from ADP upon formation of the transition state.

An experimental investigation of the impingement of a planar shock wave on an axisymmetric body at Mach 3

NASA Technical Reports Server (NTRS)

Brosh, A.; Kussoy, M. I.

1983-01-01

An experimental study of the flow caused by a planar shock wave impinging obliquely on a cylinder is presented. The complex three dimensional shock wave and boundary layer interaction occurring in practical problems, such as the shock wave impingement from the shuttle nose on an external fuel tank, and store carriage interference on a supersonic tactical aircraft were investigated. A data base for numerical computations of complex flows was also investigated. The experimental techniques included pressure measurements and oil flow patterns on the surface of the cylinder, and shadowgraphs and total and static pressure surveys on the leeward and windward planes of symmetry. The complete data is presented in tabular form. The results reveal a highly complex flow field with two separation zones, regions of high crossflow, and multiple reflected shocks and expansion fans.

Respondents, Operants, and Emergents: Toward an Integrated Perspective on Behavior

NASA Technical Reports Server (NTRS)

Rumbaugh, Daune M.; Washburn, David A.; Hillix, William A.

1996-01-01

A triarchic organization of behavior, building on Skinner's description of respondents and operants, is proposed by introducing a third class of behavior called 'emergents.' Emergents are new responses, never specifically reinforced, that require operations more complex than association. Some of these operations occur naturally only in animals above a minimum level of brain complexity, and are developed in an interaction between treatment and organismic variables. (Here complexity is defined in terms of relative levels of hierarchical integration made possible both by the amount of brain, afforded both by brain-body allometric relationships and by encephalization, and, also, the elaboration of dendritic and synaptic connections within the cortex and connections between various parts/regions of the brain.) Examples of emergents are discussed to advance this triarchic view, of behavior. The prime example is language. This triarchic view reflects both the common goals and the cumulative nature of psychological science.

Phase-sensitive terahertz spectroscopy with backward-wave oscillators in reflection mode.

PubMed

Pronin, A V; Goncharov, Yu G; Fischer, T; Wosnitza, J

2009-12-01

In this article we describe a method which allows accurate measurements of the complex reflection coefficient r = absolute value(r) x exp(i phi(R)) of a solid at frequencies of 1-50 cm(-1) (30 GHz-1.5 THz). Backward-wave oscillators are used as sources for monochromatic coherent radiation tunable in frequency. The amplitude of the complex reflection (the reflectivity) is measured in a standard way, while the phase shift, introduced by the reflection from the sample surface, is measured using a Michelson interferometer. This method is particular useful for nontransparent samples, where phase-sensitive transmission measurements are not possible. The method requires no Kramers-Kronig transformation in order to extract the sample's electrodynamic properties (such as the complex dielectric function or complex conductivity). Another area of application of this method is the study of magnetic materials with complex dynamic permeabilities different from unity at the measurement frequencies (for example, colossal-magnetoresistance materials and metamaterials). Measuring both the phase-sensitive transmission and the phase-sensitive reflection allows for a straightforward model-independent determination of the dielectric permittivity and magnetic permeability of such materials.

Phase-sensitive terahertz spectroscopy with backward-wave oscillators in reflection mode

NASA Astrophysics Data System (ADS)

Pronin, A. V.; Goncharov, Yu. G.; Fischer, T.; Wosnitza, J.

2009-12-01

In this article we describe a method which allows accurate measurements of the complex reflection coefficient r̂=|r̂|ṡexp(iφR) of a solid at frequencies of 1-50 cm-1 (30 GHz-1.5 THz). Backward-wave oscillators are used as sources for monochromatic coherent radiation tunable in frequency. The amplitude of the complex reflection (the reflectivity) is measured in a standard way, while the phase shift, introduced by the reflection from the sample surface, is measured using a Michelson interferometer. This method is particular useful for nontransparent samples, where phase-sensitive transmission measurements are not possible. The method requires no Kramers-Kronig transformation in order to extract the sample's electrodynamic properties (such as the complex dielectric function or complex conductivity). Another area of application of this method is the study of magnetic materials with complex dynamic permeabilities different from unity at the measurement frequencies (for example, colossal-magnetoresistance materials and metamaterials). Measuring both the phase-sensitive transmission and the phase-sensitive reflection allows for a straightforward model-independent determination of the dielectric permittivity and magnetic permeability of such materials.

On specular reflectivity measurements in high and low-contrast relativistic laser-plasma interactions

NASA Astrophysics Data System (ADS)

Kemp, G. E.; Link, A.; Ping, Y.; McLean, H. S.; Patel, P. K.; Freeman, R. R.; Schumacher, D. W.; Tiedje, H. F.; Tsui, Y. Y.; Ramis, R.; Fedosejevs, R.

2015-01-01

Using both experiment and 2D3V particle-in-cell (PIC) simulations, we describe the use of specular reflectivity measurements to study relativistic (Iλ2 > 1018 W/cm2ṡμm2) laser-plasma interactions for both high and low-contrast 527 nm laser pulses on initially solid density aluminum targets. In the context of hot-electron generation, studies typically rely on diagnostics which, more-often-than-not, represent indirect processes driven by fast electrons transiting through solid density materials. Specular reflectivity measurements, however, can provide a direct measure of the interaction that is highly sensitive to how the EM fields and plasma profiles, critical input parameters for modeling of hot-electron generation, evolve near the interaction region. While the fields of interest occur near the relativistic critical electron density, experimental reflectivity measurements are obtained centimeters away from the interaction region, well after diffraction has fully manifested itself. Using a combination of PIC simulations with experimentally inspired conditions and an analytic, non-paraxial, pulse propagation algorithm, we calculate reflected pulse properties, both near and far from the interaction region, and compare with specular reflectivity measurements. The experiment results and PIC simulations demonstrate that specular reflectivity measurements are an extremely sensitive qualitative, and partially quantitative, indicator of initial laser/target conditions, ionization effects, and other details of intense laser-matter interactions. The techniques described can provide strong constraints on many systems of importance in ultra-intense laser interactions with matter.

Prospective impact of illness uncertainty on outcomes in chronic lung disease.

PubMed

Hoth, Karin F; Wamboldt, Frederick S; Strand, Matthew; Ford, Dee W; Sandhaus, Robert A; Strange, Charlie; Bekelman, David B; Holm, Kristen E

2013-11-01

To determine which aspect of illness uncertainty (i.e., ambiguity or complexity) has a stronger association with psychological and clinical outcomes over a 2-year period among individuals with a genetic subtype of chronic obstructive pulmonary disease (COPD). Ambiguity reflects uncertainty about physical cues and symptoms, and complexity reflects uncertainty about treatment and the medical system. Four-hundred and 7 individuals with alpha-1 antitrypsin deficiency-associated COPD completed questionnaires at baseline, 1- and 2-year follow-up. Uncertainty was measured using the Mishel Uncertainty in Illness Scale. Outcomes were measured using the Hospital Anxiety and Depression Scale, St. George's Respiratory Questionnaire, and MMRC Dyspnea Scale. Ambiguity and complexity were examined as predictors of depressive symptoms, anxiety, quality of life, and breathlessness using linear mixed models adjusting for demographic and health characteristics. Ambiguity was associated with more depressive symptoms (b = 0.09, SE = 0.02, p < .001) and anxiety (b = 0.13, SE = 0.02, p < .001), worse quality of life (b = 0.57, SE = 0.10, p < .001), and more breathlessness (b = 0.02, SE = 0.006, p < .001). Complexity did not have an independent effect on any outcome. Interactions between ambiguity and time since diagnosis were not statistically significant. Ambiguity was prospectively associated with worse mood, quality of life, and breathlessness. Thus, ambiguity should be targeted in psychosocial interventions. Time since diagnosis did not affect the association between ambiguity and outcomes, suggesting that the impact of ambiguity is equally strong throughout the course of COPD.

Towards terrain interaction prediction for bioinspired planetary exploration rovers.

PubMed

Yeomans, Brian; Saaj, Chakravathini M

2014-03-01

Deployment of a small legged vehicle to extend the reach of future planetary exploration missions is an attractive possibility but little is known about the behaviour of a walking rover on deformable planetary terrain. This paper applies ideas from the developing study of granular materials together with a detailed characterization of the sinkage process to propose and validate a combined model of terrain interaction based on an understanding of the physics and micro mechanics at the granular level. Whilst the model reflects the complexity of interactions expected from a walking rover, common themes emerge which enable the model to be streamlined to the extent that a simple mathematical representation is possible without resorting to numerical methods. Bespoke testing and analysis tools are described which reveal some unexpected conclusions and point the way towards intelligent control and foot geometry techniques to improve thrust generation.

Cryptic diversity and symbiont interactions in rock-posy lichens.

PubMed

Leavitt, Steven D; Kraichak, Ekaphan; Vondrak, Jan; Nelsen, Matthew P; Sohrabi, Mohammad; Perez-Ortega, Sergio; St Clair, Larry L; Lumbsch, H Thorsten

2016-06-01

Identifying factors that influence species interactions is central to research in symbiotic systems. While lichens represent iconic models of symbiosis and play important roles in understanding the biology of symbiotic interactions, patterns of interactions in lichen symbionts and mechanisms governing these relationships are not well characterized. This is due, in part to the fact that current taxonomic approaches for recognizing diversity in lichen symbionts commonly fail to accurately reflect actual species diversity. In this study, we employed DNA-based approaches to circumscribed candidate species-level lineages in rock-posy lichen symbionts (mycobiont=Rhizoplaca s. lat. species; photobiont=Trebouxia species). Our results revealed a high degree of cryptic diversity in both the myco- and photobionts in these lichens. Using the candidate species circumscribed here, we investigated the specificity of the symbionts toward their partners and inferred the relative importance of various factors influencing symbiont interactions. Distinct mycobiont species complexes, ecozones, and biomes are significantly correlated with the occurrence of photobiont OTUs, indicating that complex interactions among mycobiont lineages, ecogeography, and microhabitat determine interactions between photobionts and their mycobionts in lichen symbiosis. One-to-one specificity between mycobiont and photobiont species was not found, with the exception of R. maheui that associated with a single Trebouxia OTU that was not found with other Rhizoplaca s. lat. species. We estimated the most recent common ancestor of the core Rhizoplaca group at c. 62.5Ma, similar in age to the diverse parmelioid core group in the well-studied family Parmeliaceae. However, in contrast to Parmeliaceae, species in Rhizoplaca were found to associate with a narrow range of photobionts. Our study provides important perspectives into species diversity and interactions in iconic lichen symbiotic systems and establishes a valuable framework for continuing research into rock-posy lichens. Copyright © 2016 Elsevier Inc. All rights reserved.

Hyperedge bundling: Data, source code, and precautions to modeling-accuracy bias to synchrony estimates.

PubMed

Wang, Sheng H; Lobier, Muriel; Siebenhühner, Felix; Puoliväli, Tuomas; Palva, Satu; Palva, J Matias

2018-06-01

It has not been well documented that MEG/EEG functional connectivity graphs estimated with zero-lag-free interaction metrics are severely confounded by a multitude of spurious interactions (SI), i.e., the false-positive "ghosts" of true interactions [1], [2]. These SI are caused by the multivariate linear mixing between sources, and thus they pose a severe challenge to the validity of connectivity analysis. Due to the complex nature of signal mixing and the SI problem, there is a need to intuitively demonstrate how the SI are discovered and how they can be attenuated using a novel approach that we termed hyperedge bundling. Here we provide a dataset with software with which the readers can perform simulations in order to better understand the theory and the solution to SI. We include the supplementary material of [1] that is not directly relevant to the hyperedge bundling per se but reflects important properties of the MEG source model and the functional connectivity graphs. For example, the gyri of dorsal-lateral cortices are the most accurately modeled areas; the sulci of inferior temporal, frontal and the insula have the least modeling accuracy. Importantly, we found the interaction estimates are heavily biased by the modeling accuracy between regions, which means the estimates cannot be straightforwardly interpreted as the coupling between brain regions. This raise a red flag that the conventional method of thresholding graphs by estimate values is rather suboptimal: because the measured topology of the graph reflects the geometric property of source-model instead of the cortical interactions under investigation.

Molecular interactions in gelatin/chitosan composite films.

PubMed

Qiao, Congde; Ma, Xianguang; Zhang, Jianlong; Yao, Jinshui

2017-11-15

Gelatin and chitosan were mixed at different mass ratios in solution forms, and the rheological properties of these film-forming solutions, upon cooling, were studied. The results indicate that the significant interactions between gelatin and chitosan promote the formation of multiple complexes, reflected by an increase in the storage modulus of gelatin solution. Furthermore, these molecular interactions hinder the formation of gelatin networks, consequently decreasing the storage modulus of polymer gels. Both hydrogen bonds and electrostatic interactions are formed between gelatin and chitosan, as evidenced by the shift of the amide-II bands of polymers. X-ray patterns of composite films indicate that the contents of triple helices decrease with increasing chitosan content. Only one glass transition temperature (T g ) was observed in composite films with different composition ratios, and it decreases gradually with an increase in chitosan proportion, indicating that gelatin and chitosan have good miscibility and form a wide range of blends. Copyright © 2017 Elsevier Ltd. All rights reserved.

Model colloid system for interfacial sorption kinetics

NASA Astrophysics Data System (ADS)

Salipante, Paul; Hudson, Steven

2014-11-01

Adsorption kinetics of nanometer scale molecules, such as proteins at interfaces, is usually determined through measurements of surface coverage. Their small size limits the ability to directly observe individual molecule behavior. To better understand the behavior of nanometer size molecules and the effect on interfacial kinetics, we use micron size colloids with a weak interfacial interaction potential as a model system. Thus, the interaction strength is comparable to many nanoscale systems (less than 10 kBT). The colloid-interface interaction potential is tuned using a combination of depletion, electrostatic, and gravitational forces. The colloids transition between an entropically trapped adsorbed state and a desorbed state through Brownian motion. Observations are made using an LED-based Total Internal Reflection Microscopy (TIRM) setup. The observed adsorption and desorption rates are compared theoretical predictions based on the measured interaction potential and near wall particle diffusivity. This experimental system also allows for the study of more complex dynamics such as nonspherical colloids and collective effects at higher concentrations.

Flexible and structured survival model for a simultaneous estimation of non-linear and non-proportional effects and complex interactions between continuous variables: Performance of this multidimensional penalized spline approach in net survival trend analysis.

PubMed

Remontet, Laurent; Uhry, Zoé; Bossard, Nadine; Iwaz, Jean; Belot, Aurélien; Danieli, Coraline; Charvat, Hadrien; Roche, Laurent

2018-01-01

Cancer survival trend analyses are essential to describe accurately the way medical practices impact patients' survival according to the year of diagnosis. To this end, survival models should be able to account simultaneously for non-linear and non-proportional effects and for complex interactions between continuous variables. However, in the statistical literature, there is no consensus yet on how to build such models that should be flexible but still provide smooth estimates of survival. In this article, we tackle this challenge by smoothing the complex hypersurface (time since diagnosis, age at diagnosis, year of diagnosis, and mortality hazard) using a multidimensional penalized spline built from the tensor product of the marginal bases of time, age, and year. Considering this penalized survival model as a Poisson model, we assess the performance of this approach in estimating the net survival with a comprehensive simulation study that reflects simple and complex realistic survival trends. The bias was generally small and the root mean squared error was good and often similar to that of the true model that generated the data. This parametric approach offers many advantages and interesting prospects (such as forecasting) that make it an attractive and efficient tool for survival trend analyses.

Interactive effects of an insecticide and a fungicide on different organism groups and ecosystem functioning in a stream detrital food web.

PubMed

Dawoud, Mohab; Bundschuh, Mirco; Goedkoop, Willem; McKie, Brendan G

2017-05-01

Freshwater ecosystems are often affected by cocktails of multiple pesticides targeting different organism groups. Prediction and evaluation of the ecosystem-level effects of these mixtures is complicated by the potential not only for interactions among the pesticides themselves, but also for the pesticides to alter biotic interactions across trophic levels. In a stream microcosm experiment, we investigated the effects of two pesticides targeting two organism groups (the insecticide lindane and fungicide azoxystrobin) on the functioning of a model stream detrital food web consisting of a detritivore (Ispoda: Asellus aquaticus) and microbes (an assemblage of fungal hyphomycetes) consuming leaf litter. We assessed how these pesticides interacted with the presence and absence of the detritivore to affect three indicators of ecosystem functioning - leaf decomposition, fungal biomass, fungal sporulation - as well as detritivore mortality. Leaf decomposition rates were more strongly impacted by the fungicide than the insecticide, reflecting especially negative effects on leaf processing by detritivores. This result most like reflects reduced fungal biomass and increased detritivore mortality under the fungicide treatment. Fungal sporulation was elevated by exposure to both the insecticide and fungicide, possibly representing a stress-induced increase in investment in propagule dispersal. Stressor interactions were apparent in the impacts of the combined pesticide treatment on fungal sporulation and detritivore mortality, which were reduced and elevated relative to the single stressor treatments, respectively. These results demonstrate the potential of trophic and multiple stressor interactions to modulate the ecosystem-level impacts of chemicals, highlighting important challenges in predicting, understanding and evaluating the impacts of multiple chemical stressors on more complex food webs in situ. Copyright © 2017 Elsevier B.V. All rights reserved.

Bioreactor Engineering of Stem Cell Environments

PubMed Central

Tandon, Nina; Marolt, Darja; Cimetta, Elisa; Vunjak-Novakovic, Gordana

2013-01-01

Stem cells hold promise to revolutionize modern medicine by development of new therapies, disease models and drug screening systems. Standard cell culture systems have limited biological relevance because they do not recapitulate the complex 3-dimensional interactions and biophysical cues that characterize the in vivo environment. In this review, we discuss the current advances in engineering stem cell environments using novel biomaterials and bioreactor technologies. We also reflect on the challenges the field is currently facing with regard to translation of stem cell based therapies into the clinic. PMID:23531529

The Hands-On Universe: Making Sense of the Universe with All Your Senses

NASA Astrophysics Data System (ADS)

Trotta, R.

2018-02-01

For the past four years, the Hands-On Universe public engagement programme has explored unconventional, interactive and multi-sensorial ways of communicating complex ideas in cosmology and astrophysics to a wide variety of audiences. The programme lead, Roberto Trotta, has reached thousands of people through food-based workshops, art and science collaborations and a book written using only the 1000 most common words in the English language. In this article, Roberto reflects in first person on what has worked well in the programme, and what has not.

Audio-based, unsupervised machine learning reveals cyclic changes in earthquake mechanisms in the Geysers geothermal field, California

NASA Astrophysics Data System (ADS)

Holtzman, B. K.; Paté, A.; Paisley, J.; Waldhauser, F.; Repetto, D.; Boschi, L.

2017-12-01

The earthquake process reflects complex interactions of stress, fracture and frictional properties. New machine learning methods reveal patterns in time-dependent spectral properties of seismic signals and enable identification of changes in faulting processes. Our methods are based closely on those developed for music information retrieval and voice recognition, using the spectrogram instead of the waveform directly. Unsupervised learning involves identification of patterns based on differences among signals without any additional information provided to the algorithm. Clustering of 46,000 earthquakes of $0.3

Students' perceptions of a community-based service-learning project related to aging in place.

PubMed

Oakes, Claudia E; Sheehan, Nancy W

2014-01-01

This article describes a service-learning project that was designed to help undergraduate health professions students understand the complexities related to aging in place. The service-learning project also incorporated a research component to expose the students to the research process. Students' reflections regarding the benefits that they derived from the experience suggest that they value learning about older adults through one-on-one interactions more than they value the opportunity to participate in the research project. Implications for undergraduate health professional education are discussed.

New doxorubicin nanocarriers based on cyclodextrins.

PubMed

Viale, Maurizio; Giglio, Valentina; Monticone, Massimiliano; Maric, Irena; Lentini, Giovanni; Rocco, Mattia; Vecchio, Graziella

2017-10-01

Polymeric nanoparticles and fibrin gels (FBGs) are attractive biomaterials for local delivery of a variety of biotherapeutic agents, from drugs to proteins. We combined these different drug delivery approaches by preparing nanoparticle-loaded FBGs characterized by their intrinsic features of drug delivery rate and antiproliferative/apoptotic activities. Inclusion complexes of doxorubicin (DOXO) with oligomeric β-cyclodextrins (oCyD) functionalized with different functional groups were studied. These nanocarriers were able to interact with FBGs as shown by a decreased release rate of DOXO. One of these complexes, oCyDNH 2 /DOXO, demonstrated good antiproliferative and apoptotic activity in vitro, reflecting a higher drug uptake by cells. As hypothesized, the nanocarrier/FBG complexes showed a lower drug release rate than similar FBGs loaded with the corresponding non-functionalized oCyD/DOXO. Taken together, our results provide experimental evidence that oCyDNH 2 /DOXO complexes may be useful components in enhanced FBGs and further build support for the great promise these complex molecules hold for clinical use in localized anticancer therapy of inoperable or surgically removable tumors of different histological origin.

Surface complexation of carboxylate adheres Cryptosporidium parvum öocysts to the hematite-water interface

USGS Publications Warehouse

Gao, X.; Metge, D.W.; Ray, C.; Harvey, R.W.; Chorover, J.

2009-01-01

The interaction of viable Cryptosporidium parvum öocysts at the hematite (α-Fe2O3)−water interface was examined over a wide range in solution chemistry using in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. Spectra for hematite-sorbed öocysts showed distinct changes in carboxylate group vibrations relative to spectra obtained in the absence of hematite, indicative of direct chemical bonding between carboxylate groups and Fe metal centers of the hematite surface. The data also indicate that complexation modes vary with solution chemistry. In NaCl solution, öocysts are bound to hematite via monodentate and binuclear bidentate complexes. The former predominates at low pH, whereas the latter becomes increasingly prevalent with increasing pH. In a CaCl2 solution, only binuclear bidentate complexes are observed. When solution pH is above the point of zero net proton charge (PZNPC) of hematite, öocyst surface carboxylate groups are bound to the mineral surface via outer-sphere complexes in both electrolyte solutions.

Modelling the Evolution of Social Structure

PubMed Central

Sutcliffe, A. G.; Dunbar, R. I. M.; Wang, D.

2016-01-01

Although simple social structures are more common in animal societies, some taxa (mainly mammals) have complex, multi-level social systems, in which the levels reflect differential association. We develop a simulation model to explore the conditions under which multi-level social systems of this kind evolve. Our model focuses on the evolutionary trade-offs between foraging and social interaction, and explores the impact of alternative strategies for distributing social interaction, with fitness criteria for wellbeing, alliance formation, risk, stress and access to food resources that reward social strategies differentially. The results suggest that multi-level social structures characterised by a few strong relationships, more medium ties and large numbers of weak ties emerge only in a small part of the overall fitness landscape, namely where there are significant fitness benefits from wellbeing and alliance formation and there are high levels of social interaction. In contrast, ‘favour-the-few’ strategies are more competitive under a wide range of fitness conditions, including those producing homogeneous, single-level societies of the kind found in many birds and mammals. The simulations suggest that the development of complex, multi-level social structures of the kind found in many primates (including humans) depends on a capacity for high investment in social time, preferential social interaction strategies, high mortality risk and/or differential reproduction. These conditions are characteristic of only a few mammalian taxa. PMID:27427758

Gene-Environment Interplay in Common Complex Diseases: Forging an Integrative Model—Recommendations From an NIH Workshop

PubMed Central

Bookman, Ebony B.; McAllister, Kimberly; Gillanders, Elizabeth; Wanke, Kay; Balshaw, David; Rutter, Joni; Reedy, Jill; Shaughnessy, Daniel; Agurs-Collins, Tanya; Paltoo, Dina; Atienza, Audie; Bierut, Laura; Kraft, Peter; Fallin, M. Daniele; Perera, Frederica; Turkheimer, Eric; Boardman, Jason; Marazita, Mary L.; Rappaport, Stephen M.; Boerwinkle, Eric; Suomi, Stephen J.; Caporaso, Neil E.; Hertz-Picciotto, Irva; Jacobson, Kristen C.; Lowe, William L.; Goldman, Lynn R.; Duggal, Priya; Gunnar, Megan R.; Manolio, Teri A.; Green, Eric D.; Olster, Deborah H.; Birnbaum, Linda S.

2011-01-01

Although it is recognized that many common complex diseases are a result of multiple genetic and environmental risk factors, studies of gene-environment interaction remain a challenge and have had limited success to date. Given the current state-of-the-science, NIH sought input on ways to accelerate investigations of gene-environment interplay in health and disease by inviting experts from a variety of disciplines to give advice about the future direction of gene-environment interaction studies. Participants of the NIH Gene-Environment Interplay Workshop agreed that there is a need for continued emphasis on studies of the interplay between genetic and environmental factors in disease and that studies need to be designed around a multifaceted approach to reflect differences in diseases, exposure attributes, and pertinent stages of human development. The participants indicated that both targeted and agnostic approaches have strengths and weaknesses for evaluating main effects of genetic and environmental factors and their interactions. The unique perspectives represented at the workshop allowed the exploration of diverse study designs and analytical strategies, and conveyed the need for an interdisciplinary approach including data sharing, and data harmonization to fully explore gene-environment interactions. Further, participants also emphasized the continued need for high-quality measures of environmental exposures and new genomic technologies in ongoing and new studies. PMID:21308768

Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar.

PubMed

Cárdenas, Constanza; Bidon-Chanal, Axel; Conejeros, Pablo; Arenas, Gloria; Marshall, Sergio; Luque, F Javier

2010-12-01

Knowledge of the 3D structure of the binding groove of major histocompatibility (MHC) molecules, which play a central role in the immune response, is crucial to shed light into the details of peptide recognition and polymorphism. This work reports molecular modeling studies aimed at providing 3D models for two class I and two class II MHC alleles from Salmo salar (Sasa), as the lack of experimental structures of fish MHC molecules represents a serious limitation to understand the specific preferences for peptide binding. The reliability of the structural models built up using bioinformatic tools was explored by means of molecular dynamics simulations of their complexes with representative peptides, and the energetics of the MHC-peptide interaction was determined by combining molecular mechanics interaction energies and implicit continuum solvation calculations. The structural models revealed the occurrence of notable differences in the nature of residues at specific positions in the binding groove not only between human and Sasa MHC proteins, but also between different Sasa alleles. Those differences lead to distinct trends in the structural features that mediate the binding of peptides to both class I and II MHC molecules, which are qualitatively reflected in the relative binding affinities. Overall, the structural models presented here are a valuable starting point to explore the interactions between MHC receptors and pathogen-specific interactions and to design vaccines against viral pathogens.

Visible-to-SWIR wavelength variation of skylight polarization

NASA Astrophysics Data System (ADS)

Dahl, Laura M.; Shaw, Joseph A.

2015-09-01

Knowledge of the polarization state of natural skylight is important to growing applications using polarimetric sensing. We previously published measurements and simulations illustrating the complex interaction between atmospheric and surface properties in determining the spectrum of skylight polarization from the visible to near-infrared (1 μm).1 Those results showed that skylight polarization can trend upward or downward, or even have unusual spectral discontinuities that arise because of sharp features in the underlying surface reflectance. The specific spectrum observed in a given case depended strongly on atmospheric and surface properties that varied with wavelength. In the previous study, the model was fed with actual measurements of highly variable aerosol and surface properties from locations around the world. Results, however, were limited to wavelengths below 1 μm from a lack in available satellite surface reflectance data at longer wavelengths. We now report measurement-driven simulations of skylight polarization from 350 nm to 2500 nm in the short-wave infrared (SWIR) using hand-held spectrometer measurements of spectral surface reflectance. The SWIR degree of linear polarization was found to be highly dependent on the aerosol size distribution and on the resulting relationship between the aerosol and Rayleigh optical depths. Unique polarization features in the modeled results were attributed to the surface reflectance and the skylight DoLP generally decreased as surface reflectance increased.

Volumetric analysis of formation of the complex of G-quadruplex DNA with hemin using high pressure.

PubMed

Takahashi, Shuntaro; Bhowmik, Sudipta; Sugimoto, Naoki

2017-01-01

DNA guanine-quadruplexes (G-quadruplexes) complexed with the Fe-containing porphyrin, hemin (iron(III)-protoporphyrin IX), can catalyze oxidation reactions. This so-called DNAzyme has been widely used in the field of DNA nanotechnology. To improve DNAzyme properties, we sought to elucidate the interaction mechanism between G-quadruplex DNA and hemin. Here, we performed volumetric analyses of formation of the complex between an oligonucleotide with the sequence of human telomeric DNA (h-telo) and hemin. The G-quadruplex DNA alone and the G-quadruplex DNA-hemin complex were destabilized with increasing pressure in Na + buffer. The pressure required to destabilize the h-telo-hemin complex was less in K + -containing buffer than in buffer with Na + , which indicates that there was a smaller volumetric change upon h-telo formation in K + buffer than in Na + buffer. The calculated change in h-telo-hemin binding volume (∆V b ) in the Na + buffer was 2.5mLmol -1 , whereas it was -41.7 in mLmol -1 the K + buffer. The DNAzyme activity in the K + buffer was higher than that in the Na + buffer at atmospheric pressure. Interestingly, the pressure effect on the destabilization of the h-telo-hemin complex in the presence of poly(ethylene glycol)200 (PEG200) was repressed compared to that in the absence of PEG200. These results suggest that differences in volumetric parameters reflect different mechanisms of interaction between hemin and h-telo due to differences in both the fit of hemin into the h-telo structure and hydration. Thus, the pressure-based thermodynamic analysis provided important information about complex formation and could be a useful index to improve function of DNAzymes. Copyright © 2016 Elsevier Inc. All rights reserved.

Movement dynamics reflect a functional role for weak coupling and role structure in dyadic problem solving.

PubMed

Abney, Drew H; Paxton, Alexandra; Dale, Rick; Kello, Christopher T

2015-11-01

Successful interaction requires complex coordination of body movements. Previous research has suggested a functional role for coordination and especially synchronization (i.e., time-locked movement across individuals) in different types of human interaction contexts. Although such coordination has been shown to be nearly ubiquitous in human interaction, less is known about its function. One proposal is that synchrony supports and facilitates communication (Topics Cogn Sci 1:305-319, 2009). However, questions still remain about what the properties of coordination for optimizing communication might look like. In the present study, dyads worked together to construct towers from uncooked spaghetti and marshmallows. Using cross-recurrence quantification analysis, we found that dyads with loosely coupled gross body movements performed better, supporting recent work suggesting that simple synchrony may not be the key to effective performance (Riley et al. 2011). We also found evidence that leader-follower dynamics-when sensitive to the specific role structure of the interaction-impact task performance. We discuss our results with respect to the functional role of coordination in human interaction.

Electronic distributions within protein phenylalanine aromatic rings are reflected by the three-dimensional oxygen atom environments.

PubMed Central

Thomas, K A; Smith, G M; Thomas, T B; Feldmann, R J

1982-01-01

The atomic environments of 170 phenylalanine-residue aromatic rings from 28 protein crystal structures are transformed into a common orientation and combined to calculate an average three-dimensional environment. The spatial distribution of atom types in this environment reveals a preferred interaction between oxygen atoms and the edge of the planar aromatic rings. From the difference in frequency of interaction of oxygen atoms with the edge and the top of the ring, an apparent net free energy difference of interaction favoring the edge of the ring is estimated to be about -1 kcal/mol (1 cal = 4.184 J). Ab initio quantum mechanical calculations, performed on a model consisting of benzene and formamide, indicate that the observed geometry is stabilized by a favorable enthalpic interaction. Although benzene rings are considered to be nonpolar, the electron distribution is a complex multipole with no net dipole moment. The observed interaction orientation frequencies demonstrate that these multipolar electron distributions, when occurring at the short distances encountered in densely packed protein molecules, are significant determinants of internal packing geometries. PMID:6956896

Propagation of acoustic shock waves between parallel rigid boundaries and into shadow zones

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

Desjouy, C., E-mail: cyril.desjouy@gmail.com; Ollivier, S.; Dragna, D.

2015-10-28

The study of acoustic shock propagation in complex environments is of great interest for urban acoustics, but also for source localization, an underlying problematic in military applications. To give a better understanding of the phenomenon taking place during the propagation of acoustic shocks, laboratory-scale experiments and numerical simulations were performed to study the propagation of weak shock waves between parallel rigid boundaries, and into shadow zones created by corners. In particular, this work focuses on the study of the local interactions taking place between incident, reflected, and diffracted waves according to the geometry in both regular or irregular – alsomore » called Von Neumann – regimes of reflection. In this latter case, an irregular reflection can lead to the formation of a Mach stem that can modify the spatial distribution of the acoustic pressure. Short duration acoustic shock waves were produced by a 20 kilovolts electric spark source and a schlieren optical method was used to visualize the incident shockfront and the reflection/diffraction patterns. Experimental results are compared to numerical simulations based on the high-order finite difference solution of the two dimensional Navier-Stokes equations.« less

Interactions of light with rough dielectric surfaces - Spectral reflectance and polarimetric properties

NASA Technical Reports Server (NTRS)

Yon, S. A.; Pieters, C. M.

1988-01-01

The nature of the interactions of visible and NIR radiation with the surfaces of rock and mineral samples was investigated by measuring the reflectance and the polarization properties of scattered and reflected light for slab samples of obsidian and fine-grained basalt, prepared to controlled surface roughness. It is shown that the degree to which radiation can penetrate a surface and then scatter back out, an essential criterion for mineralogic determinations based on reflectance spectra, depends not only upon the composition of the material, but also on its physical condition such as sample grain size and surface roughness. Comparison of the experimentally measured reflectance and polarization from smooth and rough slab materials with the predicted models indicates that single Fresnel reflections are responsible for the largest part of the reflected intensity resulting from interactions with the surfaces of dielectric materials; multiple Fresnel reflections are much less important for such surfaces.

Complexity and diversity.

PubMed

Doebeli, Michael; Ispolatov, Iaroslav

2010-04-23

The mechanisms for the origin and maintenance of biological diversity are not fully understood. It is known that frequency-dependent selection, generating advantages for rare types, can maintain genetic variation and lead to speciation, but in models with simple phenotypes (that is, low-dimensional phenotype spaces), frequency dependence needs to be strong to generate diversity. However, we show that if the ecological properties of an organism are determined by multiple traits with complex interactions, the conditions needed for frequency-dependent selection to generate diversity are relaxed to the point where they are easily satisfied in high-dimensional phenotype spaces. Mathematically, this phenomenon is reflected in properties of eigenvalues of quadratic forms. Because all living organisms have at least hundreds of phenotypes, this casts the potential importance of frequency dependence for the origin and maintenance of diversity in a new light.

Presentation and management of chronic pain.

PubMed

Rajapakse, Dilini; Liossi, Christina; Howard, Richard F

2014-05-01

Chronic pain is an important clinical problem affecting significant numbers of children and their families. The severity and impact of chronic pain on everyday function is shaped by the complex interaction of biological, psychological and social factors that determine the experience of pain for each individual, rather than a straightforward reflection of the severity of disease or extent of tissue damage. In this article we present the research findings that strongly support a biopsychosocial concept of chronic pain, describe the current best evidence for management strategies and suggest a common general pathway for all types of chronic pain. The principles of management of some of the most important or frequently encountered chronic pain problems in paediatric practice; neuropathic pain, complex regional pain syndrome (CRPS), musculoskeletal pain, abdominal pain and headache are also described.

Information-theoretic approach to interactive learning

NASA Astrophysics Data System (ADS)

Still, S.

2009-01-01

The principles of statistical mechanics and information theory play an important role in learning and have inspired both theory and the design of numerous machine learning algorithms. The new aspect in this paper is a focus on integrating feedback from the learner. A quantitative approach to interactive learning and adaptive behavior is proposed, integrating model- and decision-making into one theoretical framework. This paper follows simple principles by requiring that the observer's world model and action policy should result in maximal predictive power at minimal complexity. Classes of optimal action policies and of optimal models are derived from an objective function that reflects this trade-off between prediction and complexity. The resulting optimal models then summarize, at different levels of abstraction, the process's causal organization in the presence of the learner's actions. A fundamental consequence of the proposed principle is that the learner's optimal action policies balance exploration and control as an emerging property. Interestingly, the explorative component is present in the absence of policy randomness, i.e. in the optimal deterministic behavior. This is a direct result of requiring maximal predictive power in the presence of feedback.

Fourier-transform infrared spectroscopy for rapid screening and live-cell monitoring: application to nanotoxicology

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

Sundaram, S. K.; Sacksteder, Colette A.; Weber, T. J.

2013-01-01

A significant challenge to realize the full potential of nanotechnology for therapeutic and diagnostic applications is to understand and evaluate how live-cells interact with an external stimulus, e.g., a nanosized particle (NSP), and the toxicity and broad risk associated with these stimuli. NSPs are increasingly used in medicine with largely undetermined hazards in complex cell dynamics and environments. It is difficult to capture the complexity and dynamics of these interactions by following an omics-based approach exclusively, which are expensive and time-consuming. Additionally, this approach needs destructive sampling methods. Live-cell attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectrometry is well suited tomore » provide noninvasive approach to provide rapid screening of cellular responses to potentially toxic NSPs or any stimuli. Herein we review the technical basis of the approach, the instrument configuration and interface with the biological media, and various effects that impact the data, data analysis, and toxicity. Our preliminary results on live-cell monitoring show promise for rapid screening the NSPs.« less

Inner-outer interactions in a turbulent boundary layer overlying complex roughness

NASA Astrophysics Data System (ADS)

Pathikonda, Gokul; Christensen, Kenneth T.

2017-04-01

Hot-wire measurements were performed in a zero-pressure-gradient turbulent boundary layer overlying both a smooth and a rough wall for the purpose of investigating the details of inner-outer flow interactions. The roughness considered embodies a broad range of topographical scales arranged in an irregular manner and reflects the topographical complexity often encountered in practical flow systems. Single-probe point-wise measurements with a traversing probe were made at two different regions of the rough-wall flow, which was previously shown to be heterogeneous in the spanwise direction, to investigate the distribution of streamwise turbulent kinetic energy and large scale-small scale interactions. In addition, two-probe simultaneous measurements were conducted enabling investigation of inner-outer interactions, wherein the large scales were independently sampled in the outer layer. Roughness-induced changes to the near-wall behavior were investigated, particularly by contrasting the amplitude and frequency modulation effects of inner-outer interactions in the rough-wall flow with well-established smooth-wall flow phenomena. It was observed that the rough-wall flow exhibits both amplitude and frequency modulation features close to the wall in a manner very similar to smooth-wall flow, though the correlated nature of these effects was found to be more intense in the rough-wall flow. In particular, frequency modulation was found to illuminate these enhanced modulation effects in the rough-wall flow. The two-probe measurements helped in evaluating the suitability of the interaction-schematic recently proposed by Baars et al., Exp. Fluids 56, 1 (2015), 10.1007/s00348-014-1876-4 for rough-wall flows. This model was found to be suitable for the rough-wall flow considered herein, and it was found that frequency modulation is a "cleaner" measure of the inner-outer modulation interactions for this rough-wall flow.

Quantum Mechanics for Everybody: An autonomous MOOC on EdX for nonscientists

NASA Astrophysics Data System (ADS)

Freericks, James; Cutler, Dylan; Vieira-Barbosa, Lucas

2017-01-01

We have launched a MOOC for nonscientists that teaches quantum mechanics using the Feynman methodology as outlined in his QED book and in a similar book by Daniel Styer. Using a combination of videos, voice-over powerpoint animations, computer simulations and interactive tutorials, we teach the fundamentals of quantum mechanics employing a minimum of math (high school algebra, square roots, and a little trigonometry) but going into detail on a number of complex quantum ideas. We begin with the Stern-Gerlach experiment, including delayed choice and Bell's inequality variants. Then we focus on light developing the quantum theory for partial reflection and diffraction. At this point we demonstrate the complexity of quantum physics by showing how watched and unwatched two-slit experiments behave differently and how quantum particles interfere. The four week course ends with advanced topics in light where we cover the idea of an interaction free measurement, the quantum Zeno effect and indistinguishable particles via the Hong-Ou-Mandel experiment. We hope this MOOC will reach thousands of students interesting in learning quantum mechanics without any dumbing down or the need to learn complex math. It can also be used with undergraduates to help with conceptual understanding. Funded by the National Science Foundation under grants numbered PHY-1620555 and PHY-1314295 and by Georgetown University.

Functional Connectivity’s Degenerate View of Brain Computation

PubMed Central

Giron, Alain; Rudrauf, David

2016-01-01

Brain computation relies on effective interactions between ensembles of neurons. In neuroimaging, measures of functional connectivity (FC) aim at statistically quantifying such interactions, often to study normal or pathological cognition. Their capacity to reflect a meaningful variety of patterns as expected from neural computation in relation to cognitive processes remains debated. The relative weights of time-varying local neurophysiological dynamics versus static structural connectivity (SC) in the generation of FC as measured remains unsettled. Empirical evidence features mixed results: from little to significant FC variability and correlation with cognitive functions, within and between participants. We used a unified approach combining multivariate analysis, bootstrap and computational modeling to characterize the potential variety of patterns of FC and SC both qualitatively and quantitatively. Empirical data and simulations from generative models with different dynamical behaviors demonstrated, largely irrespective of FC metrics, that a linear subspace with dimension one or two could explain much of the variability across patterns of FC. On the contrary, the variability across BOLD time-courses could not be reduced to such a small subspace. FC appeared to strongly reflect SC and to be partly governed by a Gaussian process. The main differences between simulated and empirical data related to limitations of DWI-based SC estimation (and SC itself could then be estimated from FC). Above and beyond the limited dynamical range of the BOLD signal itself, measures of FC may offer a degenerate representation of brain interactions, with limited access to the underlying complexity. They feature an invariant common core, reflecting the channel capacity of the network as conditioned by SC, with a limited, though perhaps meaningful residual variability. PMID:27736900

Complex free-energy landscapes in biaxial nematic liquid crystals and the role of repulsive interactions: A Wang-Landau study

NASA Astrophysics Data System (ADS)

Kamala Latha, B.; Murthy, K. P. N.; Sastry, V. S. S.

2017-09-01

General quadratic Hamiltonian models, describing the interaction between liquid-crystal molecules (typically with D2 h symmetry), take into account couplings between their uniaxial and biaxial tensors. While the attractive contributions arising from interactions between similar tensors of the participating molecules provide for eventual condensation of the respective orders at suitably low temperatures, the role of cross coupling between unlike tensors is not fully appreciated. Our recent study with an advanced Monte Carlo technique (entropic sampling) showed clearly the increasing relevance of this cross term in determining the phase diagram (contravening in some regions of model parameter space), the predictions of mean-field theory, and standard Monte Carlo simulation results. In this context, we investigated the phase diagrams and the nature of the phases therein on two trajectories in the parameter space: one is a line in the interior region of biaxial stability believed to be representative of the real systems, and the second is the extensively investigated parabolic path resulting from the London dispersion approximation. In both cases, we find the destabilizing effect of increased cross-coupling interactions, which invariably result in the formation of local biaxial organizations inhomogeneously distributed. This manifests as a small, but unmistakable, contribution of biaxial order in the uniaxial phase. The free-energy profiles computed in the present study as a function of the two dominant order parameters indicate complex landscapes. On the one hand, these profiles account for the unusual thermal behavior of the biaxial order parameter under significant destabilizing influence from the cross terms. On the other, they also allude to the possibility that in real systems, these complexities might indeed be inhibiting the formation of a low-temperature biaxial order itself—perhaps reflecting the difficulties in their ready realization in the laboratory.

Influence of polarization characteristic of targets on synthetic aperture imaging ladar

NASA Astrophysics Data System (ADS)

Xu, Qian; Sun, Jianfeng; Lu, Zhiyong; Wang, Lijuan; Hou, Peipei; Lu, Wei; Liu, Liren

2017-09-01

Synthetic aperture imaging ladar (SAIL) is one of the most possible optical active imaging methods to break the diffraction limit and achieve super-resolution in a long distance. Nevertheless, two-dimensional reconstructed images of the natural targets have not been achieved. Polarization state change of the backscattered light, which is always determined by the interaction of the light and the materials on the target plane, will affect the imaging of SAIL. The Mueller matrices can describe the complex polarization features of the target reflection and treat this interaction. In this paper, a measurement of the Mueller matrices for different target materials will be designed, and the influences of polarization characteristic of targets on resolution element imaging in side-looking and down-looking SAILs will be theoretically analyzed.

Effect of drug Piper nigrum on magnesium chloride at varying concentration and temperature through ultrasonic method: A thermoacoustic study

NASA Astrophysics Data System (ADS)

Nalle, Pallavi B.; Deshmukh, S. S.; Dorik, R. G.; Jadhav, K. M.

2016-12-01

The ultrasonic velocity (U), density (ρ), and viscosity (η) of an ethanolic extract of drug Piper nigrum with MgCl2 (metal ions) have been measured as a function of the number of moles n = (0.7009, 1.4018, 2.1027, 2.8036 and 3.5045) at 303.15, 308.15, 313.15 and 318.15 K temperature. Various thermoacoustic and their excess values such as adiabatic compressibilities (β), intermolecular free lengths (Lf), excess adiabatic compressibility (βE), excess intermolecular free length (?) have been computed using values of ultrasonic velocity (U), density (ρ), and viscosity (η). The excess values of ultrasonic velocity, specific acoustic impedance are positive, whereas isentropic compressibility and intermolecular free lengths are negative over the entire composition range of MgCl2 + P. nigrum which indicates the presence of specific interactions between unlike molecules. Molecular association is reflected by ultrasonic investigation. This may be interpreted due to the of complex formation. The chemical interaction may involve the association due to the solute-solvent and ion-solvent interaction and due to the formation of charge-transfer complexes, which is useful to understand the mechanism of their metabolism in living systems. The results obtained from these studies are helpful for pharmacological applications of drugs, transport of drugs across biological membranes.

[Measurement and analysis on complex refraction indices of pear pollen in infrared band].

PubMed

Li, Le; Hu, Yi-hua; Gu, You-lin; Chen, Wei; Zhao, Yi-zheng; Chen, Shan-jing

2015-01-01

Pollen is an important part of bioaerosols, and its complex refractive index is a crucial parameter for study on optical characteristics and detection, identification of bioaerosols. The reflection spectra of pear pollen within the 2. 5 - 15µm waveband were measured by squash method. Based on the measured data, the complex refractive index of pear pollen within the wave-band of 2. 5 to 15 µm was calculated by using Kramers-Kroning (K-K) relation, and calculation deviation about incident angle and different reflectivities at high and low frequencies.were analyzed. The results indicate that 18 degrees angle of incidence and different reflectivities at high and low frequencies have little effect on the results, and it is practicable to calculate the complex refractive index of pollen based on its reflection spectral data. The data of complex refractive index of pollen have some reference value for optical characteristics of pollen, detection and identification of bioaerosols.

Heterogeneity of Purkinje cell simple spike-complex spike interactions: zebrin- and non-zebrin-related variations.

PubMed

Tang, Tianyu; Xiao, Jianqiang; Suh, Colleen Y; Burroughs, Amelia; Cerminara, Nadia L; Jia, Linjia; Marshall, Sarah P; Wise, Andrew K; Apps, Richard; Sugihara, Izumi; Lang, Eric J

2017-08-01

Cerebellar Purkinje cells (PCs) generate two types of action potentials, simple and complex spikes. Although they are generated by distinct mechanisms, interactions between the two spike types exist. Zebrin staining produces alternating positive and negative stripes of PCs across most of the cerebellar cortex. Thus, here we compared simple spike-complex spike interactions both within and across zebrin populations. Simple spike activity undergoes a complex modulation preceding and following a complex spike. The amplitudes of the pre- and post-complex spike modulation phases were correlated across PCs. On average, the modulation was larger for PCs in zebrin positive regions. Correlations between aspects of the complex spike waveform and simple spike activity were found, some of which varied between zebrin positive and negative PCs. The implications of the results are discussed with regard to hypotheses that complex spikes are triggered by rises in simple spike activity for either motor learning or homeostatic functions. Purkinje cells (PCs) generate two types of action potentials, called simple and complex spikes (SSs and CSs). We first investigated the CS-associated modulation of SS activity and its relationship to the zebrin status of the PC. The modulation pattern consisted of a pre-CS rise in SS activity, and then, following the CS, a pause, a rebound, and finally a late inhibition of SS activity for both zebrin positive (Z+) and negative (Z-) cells, though the amplitudes of the phases were larger in Z+ cells. Moreover, the amplitudes of the pre-CS rise with the late inhibitory phase of the modulation were correlated across PCs. In contrast, correlations between modulation phases across CSs of individual PCs were generally weak. Next, the relationship between CS spikelets and SS activity was investigated. The number of spikelets/CS correlated with the average SS firing rate only for Z+ cells. In contrast, correlations across CSs between spikelet numbers and the amplitudes of the SS modulation phases were generally weak. Division of spikelets into likely axonally propagated and non-propagated groups (based on their interspikelet interval) showed that the correlation of spikelet number with SS firing rate primarily reflected a relationship with non-propagated spikelets. In sum, the results show both zebrin-related and non-zebrin-related physiological heterogeneity in SS-CS interactions among PCs, which suggests that the cerebellar cortex is more functionally diverse than is assumed by standard theories of cerebellar function. © 2017 The Authors. The Journal of Physiology © 2017 The Physiological Society.

Using metal-ligand binding characteristics to predict metal toxicity: quantitative ion character-activity relationships (QICARs).

PubMed Central

Newman, M C; McCloskey, J T; Tatara, C P

1998-01-01

Ecological risk assessment can be enhanced with predictive models for metal toxicity. Modelings of published data were done under the simplifying assumption that intermetal trends in toxicity reflect relative metal-ligand complex stabilities. This idea has been invoked successfully since 1904 but has yet to be applied widely in quantitative ecotoxicology. Intermetal trends in toxicity were successfully modeled with ion characteristics reflecting metal binding to ligands for a wide range of effects. Most models were useful for predictive purposes based on an F-ratio criterion and cross-validation, but anomalous predictions did occur if speciation was ignored. In general, models for metals with the same valence (i.e., divalent metals) were better than those combining mono-, di-, and trivalent metals. The softness parameter (sigma p) and the absolute value of the log of the first hydrolysis constant ([symbol: see text] log KOH [symbol: see text]) were especially useful in model construction. Also, delta E0 contributed substantially to several of the two-variable models. In contrast, quantitative attempts to predict metal interactions in binary mixtures based on metal-ligand complex stabilities were not successful. PMID:9860900

Prenatal Nicotine Exposure Disrupts Infant Neural Markers of Orienting.

PubMed

King, Erin; Campbell, Alana; Belger, Aysenil; Grewen, Karen

2018-06-07

Prenatal nicotine exposure (PNE) from maternal cigarette smoking is linked to developmental deficits, including impaired auditory processing, language, generalized intelligence, attention, and sleep. Fetal brain undergoes massive growth, organization, and connectivity during gestation, making it particularly vulnerable to neurotoxic insult. Nicotine binds to nicotinic acetylcholine receptors, which are extensively involved in growth, connectivity, and function of developing neural circuitry and neurotransmitter systems. Thus, PNE may have long-term impact on neurobehavioral development. The purpose of this study was to compare the auditory K-complex, an event-related potential reflective of auditory gating, sleep preservation and memory consolidation during sleep, in infants with and without PNE and to relate these neural correlates to neurobehavioral development. We compared brain responses to an auditory paired-click paradigm in 3- to 5-month-old infants during Stage 2 sleep, when the K-complex is best observed. We measured component amplitude and delta activity during the K-complex. Infants with PNE demonstrated significantly smaller amplitude of the N550 component and reduced delta-band power within elicited K-complexes compared to nonexposed infants and also were less likely to orient with a head turn to a novel auditory stimulus (bell ring) when awake. PNE may impair auditory sensory gating, which may contribute to disrupted sleep and to reduced auditory discrimination and learning, attention re-orienting, and/or arousal during wakefulness reported in other studies. Links between PNE and reduced K-complex amplitude and delta power may represent altered cholinergic and GABAergic synaptic programming and possibly reflect early neural bases for PNE-linked disruptions in sleep quality and auditory processing. These may pose significant disadvantage for language acquisition, attention, and social interaction necessary for academic and social success.

Counselor competence for telephone Motivation Interviewing addressing lifestyle change among Dutch older adults.

PubMed

Mesters, Ilse; Keulen, Hilde M van; de Vries, Hein; Brug, Johannes

2017-12-01

Counselor competence in telephone Motivation Interviewing (MI) to change lifestyle behaviors in a primary care population was assessed using the Motivational Interviewing Treatment Integrity (MITI) rating system. Counselor behavior was evaluated by trained raters. Twenty minutes of a random sample of 336 MI sessions were coded representing 232 counselees. Ninety-four sessions (28%) were double coded to assess inter-rater agreement. The MI fidelity was examined by comparing the MI fidelity scores direction, empathy, spirit, % open questions, % complex reflections, reflections-to-questions ratio, % MI-adherent responses with the matching beginner proficiency MITI threshold. The inter-rater agreements for the MI fidelity summary scores were good (spirit, reflections-to-questions ratio), fair (empathy, % open questions, % MI-adherent responses) or poor (direction, % complex reflection). The MI fidelity scores for direction, empathy, spirit and the percentage of complex reflections exceeded the MITI threshold, but lower scores were found for the percentage of open questions, the reflections-to-questions ratio and the percentage of MI-adherent responses. In conclusion, evidence that MI was implemented was revealed. However, the inter-rater agreements scores and some fidelity scores leave room for improvement indicating that raters and counselors may need more ongoing training and feedback to achieve and maintain adequate competence. These findings apply to more complex skills (as rating complex reflections) in particular. Copyright © 2017 Elsevier Ltd. All rights reserved.

Control of the exercise hyperpnoea in humans: a modeling perspective.

PubMed

Ward, S A

2000-09-01

Models of the exercise hyperpnoea have classically incorporated elements of proportional feedback (carotid and medullary chemosensory) and feedforward (central and/or peripheral neurogenic) control. However, the precise details of the control process remain unresolved, reflecting in part both technical and interpretational limitations inherent in isolating putative control mechanisms in the intact human, and also the challenges to linear control theory presented by multiple-input integration, especially with regard to the ventilatory and gas-exchange complexities encountered at work rates which engender a metabolic acidosis. While some combination of neurogenic, chemoreflex and circulatory-coupled processes are likely to contribute to the control, the system appears to evidence considerable redundancy. This, coupled with the lack of appreciable error signals in the mean levels of arterial blood gas tensions and pH over a wide range of work rates, has motivated the formulation of innovative control models that reflect not only spatial interactions but also temporal interactions (i.e. memory). The challenge is to discriminate between robust competing control models that: (a) integrate such processes within plausible physiological equivalents; and (b) account for both the dynamic and steady-state system response over a range of exercise intensities. Such models are not yet available.

Network Analysis Reveals Putative Genes Affecting Meat Quality in Angus Cattle.

PubMed

Mateescu, Raluca G; Garrick, Dorian J; Reecy, James M

2017-01-01

Improvements in eating satisfaction will benefit consumers and should increase beef demand which is of interest to the beef industry. Tenderness, juiciness, and flavor are major determinants of the palatability of beef and are often used to reflect eating satisfaction. Carcass qualities are used as indicator traits for meat quality, with higher quality grade carcasses expected to relate to more tender and palatable meat. However, meat quality is a complex concept determined by many component traits making interpretation of genome-wide association studies (GWAS) on any one component challenging to interpret. Recent approaches combining traditional GWAS with gene network interactions theory could be more efficient in dissecting the genetic architecture of complex traits. Phenotypic measures of 23 traits reflecting carcass characteristics, components of meat quality, along with mineral and peptide concentrations were used along with Illumina 54k bovine SNP genotypes to derive an annotated gene network associated with meat quality in 2,110 Angus beef cattle. The efficient mixed model association (EMMAX) approach in combination with a genomic relationship matrix was used to directly estimate the associations between 54k SNP genotypes and each of the 23 component traits. Genomic correlated regions were identified by partial correlations which were further used along with an information theory algorithm to derive gene network clusters. Correlated SNP across 23 component traits were subjected to network scoring and visualization software to identify significant SNP. Significant pathways implicated in the meat quality complex through GO term enrichment analysis included angiogenesis, inflammation, transmembrane transporter activity, and receptor activity. These results suggest that network analysis using partial correlations and annotation of significant SNP can reveal the genetic architecture of complex traits and provide novel information regarding biological mechanisms and genes that lead to complex phenotypes, like meat quality, and the nutritional and healthfulness value of beef. Improvements in genome annotation and knowledge of gene function will contribute to more comprehensive analyses that will advance our ability to dissect the complex architecture of complex traits.

The neural correlates of emotion alignment in social interaction.

PubMed

Prehn, Kristin; Korn, Christoph W; Bajbouj, Malek; Klann-Delius, Gisela; Menninghaus, Winfried; Jacobs, Arthur M; Heekeren, Hauke R

2015-03-01

Talking about emotion and sharing emotional experiences is a key component of human interaction. Specifically, individuals often consider the reactions of other people when evaluating the meaning and impact of an emotional stimulus. It has not yet been investigated, however, how emotional arousal ratings and physiological responses elicited by affective stimuli are influenced by the rating of an interaction partner. In the present study, pairs of participants were asked to rate and communicate the degree of their emotional arousal while viewing affective pictures. Strikingly, participants adjusted their arousal ratings to match up with their interaction partner. In anticipation of the affective picture, the interaction partner's arousal ratings correlated positively with activity in anterior insula and prefrontal cortex. During picture presentation, social influence was reflected in the ventral striatum, that is, activity in the ventral striatum correlated negatively with the interaction partner's ratings. Results of the study show that emotional alignment through the influence of another person's communicated experience has to be considered as a complex phenomenon integrating different components including emotion anticipation and conformity. © The Author (2014). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Prospective Impact of Illness Uncertainty on Outcomes in Chronic Lung Disease

PubMed Central

Hoth, Karin F.; Wamboldt, Frederick S.; Strand, Matthew; Ford, Dee W.; Sandhaus, Robert A.; Strange, Charlie; Bekelman, David; Holm, Kristen E.

2014-01-01

Objective To determine which aspect of illness uncertainty (i.e., ambiguity or complexity) has a stronger association with psychological and clinical outcomes over a two year period among individuals with a genetic subtype of chronic obstructive pulmonary disease (COPD). Ambiguity reflects uncertainty about physical cues and symptoms, and complexity reflects uncertainty about treatment and the medical system. Methods 407 individuals with alpha-1 antitrypsin deficiency-associated COPD completed questionnaires at baseline, 1- and 2-year follow-up. Uncertainty was measured using the Mishel Uncertainty in Illness Scale. Outcomes were measured using the Hospital Anxiety and Depression Scale, St. George's Respiratory Questionnaire, and MMRC Dyspnea Scale. Ambiguity and complexity were examined as predictors of depressive symptoms, anxiety, quality of life, and breathlessness using linear mixed models adjusting for demographic and health characteristics. Results Ambiguity was associated with more depressive symptoms (b = 0.09, SE = 0.02, p < 0.001) and anxiety (b = 0.13, SE = 0.02, p < 0.001), worse quality of life (b = 0.57, SE = 0.10, p < 0.001), and more breathlessness (b = 0.02, SE = 0.006, p < 0.001). Complexity did not have an independent effect on any outcome. Interactions between ambiguity and time since diagnosis were not statistically significant. Conclusions Ambiguity was prospectively associated with worse mood, quality of life, and breathlessness. Thus, ambiguity should be targeted in psychosocial interventions. Time since diagnosis did not affect the association between ambiguity and outcomes, suggesting that the impact of ambiguity is equally strong throughout the course of COPD. PMID:23772888

Impact of Fe(III)-OM complexes and Fe(III) polymerization on SOM pools reactivity under different land uses

NASA Astrophysics Data System (ADS)

Giannetta, B.; Plaza, C.; Zaccone, C.; Siebecker, M. G.; Rovira, P.; Vischetti, C.; Sparks, D. L.

2017-12-01

Soil organic matter (SOM) protection and long-term accumulation are controlled by adsorption to mineral surfaces in different ways, depending on its molecular structure and pedo-climatic conditions. Iron (Fe) oxides are known to be key regulators of the soil carbon (C) cycle, and Fe speciation in soils is highly dependent on environmental conditions and chemical interactions with SOM. However, the molecular structure and hydrolysis of Fe species formed in association with SOM is still poorly described. We hypothesize the existence of two pools of Fe which interact with SOM: mononuclear Fe(III)-SOM complexes and precipitated Fe(III) hydroxides. To verify our hypothesis, we investigated the interactions between Fe(III) and physically isolated soil fractions by means of batch experiments at pH 7. Specifically, we examined the fine silt plus clay (FSi+C) fraction, obtained by ultrasonic dispersion and wet sieving. The soil samples spanned several land uses, including coniferous forest (CFS), grassland (GS), technosols (TS) and agricultural (AS) soils. Solid phase products and supernatants were analyzed for C and Fe content. X-ray diffraction (XRD) and Brunauer-Emmett-Teller (BET) analysis were also performed. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was used to assess the main C functional groups involved in C complexation and desorption experiments. Preliminary linear combination fitting (LCF) of Fe K-edge extended X-ray absorption fine structure (EXAFS) spectra suggested the formation of ferrihydrite-like polymeric Fe(III) oxides in reacted CFS and GS samples, with higher C and Fe concentration. Conversely, mononuclear Fe(III) OM complexes dominated the speciation for TS and AS samples, characterized by lower C and Fe concentration, inhibiting the hydrolysis and polymerization of Fe (III). This approach will help revealing the mechanisms by which SOM pools can control Fe(III) speciation, and will elucidate how both Fe(III)-OM complexes and Fe(III) polymerization can affect SOM reactivity and, consequently, its mean residence time in different ecosystems.

Functional groups of ecosystem engineers: a proposed classification with comments on current issues.

PubMed

Berke, Sarah K

2010-08-01

Ecologists have long known that certain organisms fundamentally modify, create, or define habitats by altering the habitat's physical properties. In the past 15 years, these processes have been formally defined as "ecosystem engineering", reflecting a growing consensus that environmental structuring by organisms represents a fundamental class of ecological interactions occurring in most, if not all, ecosystems. Yet, the precise definition and scope of ecosystem engineering remains debated, as one should expect given the complexity, enormity, and variability of ecological systems. Here I briefly comment on a few specific current points of contention in the ecosystem engineering concept. I then suggest that ecosystem engineering can be profitably subdivided into four narrower functional categories reflecting four broad mechanisms by which ecosystem engineering occurs: structural engineers, bioturbators, chemical engineers, and light engineers. Finally, I suggest some conceptual model frameworks that could apply broadly within these functional groups.

Enhancing Trifocal Leadership Practices Using Simulation in a Pediatric Charge Nurse Orientation Program.

PubMed

Clark, Teresa J; Yoder-Wise, Patricia S

2015-07-01

A well-established charge nurse orientation program was enhanced with the addition of a simulation, addressing three primary populations (the trifocus) with whom charge nurses interact: patients, patients' parents, and other staff members. In this pilot quality improvement project, 20 staff nurses enrolled in the orientation program and were assigned a mentor. Only one participant used the mentorship opportunity; therefore, it is not discussed here. Twelve nurses completed all charge nurse classes and a simulation scenario of caring for a deteriorating infant. The nurses were given an opportunity to reflect on leadership practices after the simulation. Thematic analysis from qualitative, reflective data supported the enhanced understanding of managing complex patients, a code situation, and teams; guiding a team's novice nurse; leading as a charge nurse; and using clinical and critical thinking skills. All nurses reported that the simulation as experiential learning helped them to meet their leadership goals. Copyright 2015, SLACK Incorporated.

When high pressure, system constraints, and a social justice mission collide: A socio-structural analysis of emergency department social work services.

PubMed

Moore, Megan; Cristofalo, Margaret; Dotolo, Danae; Torres, Nicole; Lahdya, Alexandra; Ho, Leyna; Vogel, Mia; Forrester, Mollie; Conley, Bonnie; Fouts, Susan

2017-04-01

The emergency department (ED) can be a critical intervention point for many patients with multifaceted needs. Social workers have long been part of interdisciplinary ED teams. This study aimed to contribute to the limited understanding of social worker-patient interactions and factors influencing social work services in this setting. This paper reports a qualitative content analysis of social work medical record notes (N = 1509) of services provided to trauma patients in an urban, public, level 1 trauma center and an in-depth analysis of semi-structured interviews with ED social workers (N = 10). Eight major social work roles were identified: investigator, gatekeeper, resource broker, care coordinator, problem solver, crisis manager, advocate, discharge planner. Analyses revealed a complex interplay between ED social work services and multi-layered contexts. Using a social-ecological framework, we identified the interactions between micro or individual level factors, mezzo or local system level factors and macro environmental and systemic factors that play a role in ED interactions and patient services. Macro-level contextual influences were socio-structural forces including socioeconomic barriers to health, social hierarchies that reflected power differentials between providers and patients, and distrust or bias. Mezzo-level forces were limited resources, lack of healthcare system coordination, a challenging hierarchy within the medical model and the pressure to discharge patients quickly. Micro-level factors included characteristics of patients and social workers, complexity of patient stressors, empathic strain, lack of closure and compassion. All of these forces were at play in patient-social worker interactions and impacted service provision. Social workers were at times able to successfully navigate these forces, yet at other times these challenges were insurmountable. A conceptual model of ED social work and the influences on the patient-social worker interactions was developed to assist in guiding innovative research and practice models to improve services and outcomes in the complex, fast-paced ED. Copyright © 2017 Elsevier Ltd. All rights reserved.

When high pressure, system constraints, and a social justice mission collide: a socio-structural analysis of emergency department social work services

PubMed Central

Cristofalo, Margaret; Dotolo, Danae; Torres, Nicole; Lahdya, Alexandra; Ho, Leyna; Vogel, Mia; Forrester, Mollie; Conley, Bonnie; Fouts, Susan

2017-01-01

The emergency department (ED) can be a critical intervention point for many patients with multifaceted needs. Social workers have long been part of interdisciplinary ED teams. This study aimed to contribute to the limited understanding of social worker-patient interactions and factors influencing social work services in this setting. This paper reports a qualitative content analysis of social work medical record notes (N=1,509) of services provided to trauma patients in an urban, public, level 1 trauma center and an in-depth analysis of semi-structured interviews with ED social workers (N=10). Eight major social work roles were identified: investigator, gatekeeper, resource broker, care coordinator, problem solver, crisis manager, advocate, discharge planner. Analyses revealed a complex interplay between ED social work services and multi-layered contexts. Using a social-ecological framework, we identified the interactions between micro or individual level factors, mezzo or local system level factors and macro environmental and systemic factors that play a role in ED interactions and patient services. Macro-level contextual influences were socio-structural forces including socioeconomic barriers to health, social hierarchies that reflected power differentials between providers and patients, and distrust or bias. Mezzo-level forces were limited resources, lack of healthcare system coordination, a challenging hierarchy within the medical model and the pressure to discharge patients quickly. Micro-level factors included characteristics of patients and social workers, complexity of patient stressors, empathic strain, lack of closure and compassion. All of these forces were at play in patient-social worker interactions and impacted service provision. Social workers were at times able to successfully navigate these forces, yet at other times these challenges were insurmountable. A conceptual model of ED social work and the influences on the patient-social worker interactions was developed to assist in guiding innovative research and practice models to improve services and outcomes in the complex, fast-paced ED. PMID:28214722

Channel Model Optimization with Reflection Residual Component for Indoor MIMO-VLC System

NASA Astrophysics Data System (ADS)

Chen, Yong; Li, Tengfei; Liu, Huanlin; Li, Yichao

2017-12-01

A fast channel modeling method is studied to solve the problem of reflection channel gain for multiple input multiple output-visible light communications (MIMO-VLC) in the paper. For reducing the computational complexity when associating with the reflection times, no more than 3 reflections are taken into consideration in VLC. We think that higher order reflection link consists of corresponding many times line of sight link and firstly present reflection residual component to characterize higher reflection (more than 2 reflections). We perform computer simulation results for point-to-point channel impulse response, receiving optical power and receiving signal to noise ratio. Based on theoretical analysis and simulation results, the proposed method can effectively reduce the computational complexity of higher order reflection in channel modeling.

Storm and tide influenced depositional architecture of the Pliocene-Pleistocene Chad Formation, Chad Basin (Bornu Sub-basin) NE Nigeria: A mixed fluvial, deltaic, shoreface and lacustrine complex

NASA Astrophysics Data System (ADS)

Shettima, Bukar; Kyari, Aji Maina; Aji, Mallam Musa; Adams, Fatimoh Dupe

2018-07-01

Lithofacies analyses of the upper part of the Chad Formation (Bama Ridge Complex) in the Bornu Sub-basin of the Chad Basin indicated four facies associations; fluvial, deltaic, shoreface and lacustrine sequences. The fluvial sequences are composed of fining upward cycles with successive occurrence of planar crossbedded sandstone facies displaying unimodal paleocurrent system and rare mudstone facies typical of braided river system. The deltaic succession consists of both fining and coarsening upwards cycles with the former depicting fluvial setting of an upper delta plain while the later suggestive of mouth-bar sequences. The setting displays a polymodal current system of fluvial, waves, storms and tides that were primarily induced by complex interactions of seiches and lunar tides. Similar current systems devoid of fluvial patterns were reflected in the coarsening upward packages of the shoreface sequences. Lacustrine succession composed of thick bioturbated mudstone facies generally defines the base of these coarsening upward profiles, giving a fluvio-lacustrine geomorphic relief where complex interaction developed the deltaic and shoreface facies along its shorelines. Clay mineral fractions of the formation are dominantly kaolinitic, indicating a predominantly humid tropical-subtropical climatic condition during their deposition. This climatic regime falls within the African humid period of the early-mid Holocene that led to the third lacustrine transgression of the Lake Mega-Chad, whereas the subordinate smectite mineralization points to aridification that characterizes most of the post humid period to recent.

Reflection and Refraction of Light in Absorbing Media

NASA Astrophysics Data System (ADS)

Katsumata, Koichi; Sasaki, Shosuke

2018-05-01

The results of a rigorous calculation of optical phenomena in absorbing media based on Maxwell's equations are reported. In the case of an absorbing dielectric, we assume a complex dielectric constant. We find an expression for the angle of refraction as a function of the incident angle and the real and imaginary parts of the complex dielectric constant, all of which are real. The amplitudes of the reflected and transmitted waves are calculated on the same footing. These amplitudes are shown to be complex, from which we deduce the magnitude and phase change of the reflection and transmission coefficients. The same argument applies to an absorbing magnetic material if we replace the complex dielectric constant by a complex magnetic permeability.

Bioreactor engineering of stem cell environments.

PubMed

Tandon, Nina; Marolt, Darja; Cimetta, Elisa; Vunjak-Novakovic, Gordana

2013-11-15

Stem cells hold promise to revolutionize modern medicine by the development of new therapies, disease models and drug screening systems. Standard cell culture systems have limited biological relevance because they do not recapitulate the complex 3-dimensional interactions and biophysical cues that characterize the in vivo environment. In this review, we discuss the current advances in engineering stem cell environments using novel biomaterials and bioreactor technologies. We also reflect on the challenges the field is currently facing with regard to the translation of stem cell based therapies into the clinic. Copyright © 2013 Elsevier Inc. All rights reserved.

Evolution of the modern photon

NASA Astrophysics Data System (ADS)

Kidd, Richard; Ardini, James; Anton, Anatol

1989-01-01

The term ``photon'' represents at least four distinct models and carries different connotations for students and for practicing physicists. This reflects the long and complex historical evolution of the concept and its association with the largely misinterpreted principle of duality. The unsatisfactory nature of the corpuscular and wave packet models is discussed, and the pedagogical desirability urged of replacing them with a semiclassical approach in elementary presentations. Derivations of the photoelectric (PE) effect without photons are cited and a vector analysis is given, demonstrating that the PE effect cannot be considered as simply the interaction of a photon and electron.

Testing the Two-Layer Model for Correcting Clear Sky Reflectance near Clouds

NASA Technical Reports Server (NTRS)

Wen, Guoyong; Marshak, Alexander; Evans, Frank; Varnai, Tamas; Levy, Rob

2015-01-01

A two-layer model (2LM) was developed in our earlier studies to estimate the clear sky reflectance enhancement due to cloud-molecular radiative interaction at MODIS at 0.47 micrometers. Recently, we extended the model to include cloud-surface and cloud-aerosol radiative interactions. We use the LES/SHDOM simulated 3D true radiation fields to test the 2LM for reflectance enhancement at 0.47 micrometers. We find: The simple model captures the viewing angle dependence of the reflectance enhancement near cloud, suggesting the physics of this model is correct; the cloud-molecular interaction alone accounts for 70 percent of the enhancement; the cloud-surface interaction accounts for 16 percent of the enhancement; the cloud-aerosol interaction accounts for an additional 13 percent of the enhancement. We conclude that the 2LM is simple to apply and unbiased.

Acquiring Complex Focus-Marking: Finnish 4- to 5-Year-Olds Use Prosody and Word Order in Interaction

PubMed Central

Arnhold, Anja; Chen, Aoju; Järvikivi, Juhani

2016-01-01

Using a language game to elicit short sentences in various information structural conditions, we found that Finnish 4- to 5-year-olds already exhibit a characteristic interaction between prosody and word order in marking information structure. Providing insights into the acquisition of this complex system of interactions, the production data showed interesting parallels to adult speakers of Finnish on the one hand and to children acquiring other languages on the other hand. Analyzing a total of 571 sentences produced by 16 children, we found that children rarely adjusted input word order, but did systematically avoid marked OVS order in contrastive object focus condition. Focus condition also significantly affected four prosodic parameters, f0, duration, pauses and voice quality. Differing slightly from effects displayed in adult Finnish speech, the children produced larger f0 ranges for words in contrastive focus and smaller ones for unfocused words, varied only the duration of object constituents to be longer in focus and shorter in unfocused condition, inserted more pauses before and after focused constituents and systematically modified their use of non-modal voice quality only in utterances with narrow focus. Crucially, these effects were modulated by word order. In contrast to comparable data from children acquiring Germanic languages, the present findings reflect the more central role of word order and of interactions between word order and prosody in marking information structure in Finnish. Thus, the study highlights the role of the target language in determining linguistic development. PMID:27990130

Hydroxyl group as IR probe to detect the structure of ionic liquid-acetonitrile mixtures

NASA Astrophysics Data System (ADS)

Xu, Jing; Deng, Geng; Zhou, Yu; Ashraf, Hamad; Yu, Zhi-Wu

2018-06-01

Task-specific ionic liquids (ILs) are those with functional groups introduced in the cations or anions of ILs to bring about specific properties for various tasks. In this work, the hydrogen bonding interactions between a hydroxyl functionalized IL 1-(2-hydroxylethyl)-3-methylimidazolium tetrafluoroborate ([C2OHMIM][BF4]) and acetonitrile were investigated in detail by infrared spectroscopy, excess spectroscopy, two-dimensional correlation spectroscopy, combined with hydrogen nuclear magnetic resonance and density functional theory calculations (DFT). The hydroxyl group rather than C2sbnd H is found to be the main interaction site in the cation. And the ν(Osbnd H) is more sensitive than v(C-Hs) to the environment, which has been taken as an intrinsic probe to reflect the structural change of IL. Examining the region of ν(Osbnd H), by combining excess spectroscopy and DFT calculation, a number of species were identified in the mixtures. Other than the hydrogen bond between a cation and an anion, the hydroxyl group allows the formation of a hydrogen bond between two like-charged cations. The Osbnd H⋯O hydrogen bonding interactions in the hydroxyl-mediated cation-cation complexes are cooperative, while Osbnd H⋯F and C2sbnd H⋯F hydrogen bonding interactions in cation-anion complexes are anti-cooperative. These in-depth studies on the properties of the ionic liquid-acetonitrile mixtures may shed light on exploring their applications as mixed solvents and understanding the nature of doubly ionic hydrogen bonds.

Teleosts as Model Organisms To Understand Host-Microbe Interactions.

PubMed

Lescak, Emily A; Milligan-Myhre, Kathryn C

2017-08-01

Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis. Copyright © 2017 Lescak and Milligan-Myhre.

Teleosts as Model Organisms To Understand Host-Microbe Interactions

PubMed Central

2017-01-01

ABSTRACT Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis. PMID:28439034

Interdependence of the rad50 hook and globular domain functions.

PubMed

Hohl, Marcel; Kochańczyk, Tomasz; Tous, Cristina; Aguilera, Andrés; Krężel, Artur; Petrini, John H J

2015-02-05

Rad50 contains a conserved Zn(2+) coordination domain (the Rad50 hook) that functions as a homodimerization interface. Hook ablation phenocopies Rad50 deficiency in all respects. Here, we focused on rad50 mutations flanking the Zn(2+)-coordinating hook cysteines. These mutants impaired hook-mediated dimerization, but recombination between sister chromatids was largely unaffected. This may reflect that cohesin-mediated sister chromatid interactions are sufficient for double-strand break repair. However, Mre11 complex functions specified by the globular domain, including Tel1 (ATM) activation, nonhomologous end joining, and DNA double-strand break end resection were affected, suggesting that dimerization exerts a broad influence on Mre11 complex function. These phenotypes were suppressed by mutations within the coiled-coil and globular ATPase domains, suggesting a model in which conformational changes in the hook and globular domains are transmitted via the extended coils of Rad50. We propose that transmission of spatial information in this manner underlies the regulation of Mre11 complex functions. Copyright © 2015 Elsevier Inc. All rights reserved.

Triboluminescence and crystal structure of the complex [Eu(NО3 )3 (HMPA)3 ]: role of cleavage planes.

PubMed

Bukvetskii, B V; Mirochnik, A G; Zhikhareva, P A

2017-05-01

The atomic structure of crystals of the [Eu(NО 3 ) 3 (HMPA) 3 ] [hexamethylphosphotriamide (HMPA)] complex characterized by an intensive luminescence and triboluminescence was determined using X-ray structural analysis. Noncentrosymmetric crystals have a monoclinic syngony: a = 16.0686 (3), b = 11.0853 (2), c = 20.9655 Å (4), β = 93.232° (1), space group P2 1 , Z = 4, ρ calc  = 1.560 g/cm 3 . The crystal structure is represented by individual С 18 Н 54 EuN 12 O 12 P 3 complexes linked through van der Waals interactions with clearly expressed cleavage planes. The Eu(III) atom coordination polyhedron reflected the state of a distorted square antiprism. Structural aspects of the suggested model, including formation of triboluminescence properties, were considered and the role of the cleavage planes was discussed. Copyright © 2016 John Wiley & Sons, Ltd.

Expanding the Reach of Physics-Engaging Students in Interdisciplinary Research Involving complex, real-world situation

NASA Astrophysics Data System (ADS)

Bililign, Solomon

2014-03-01

Physics plays a very important role in most interdisciplinary efforts and can provide a solid foundation for students. Retention of students in STEM areas can be facilitated by enhanced interdisciplinary education and research since students are strongly attracted to research with societal relevance and show increasing enthusiasm about problems that have practical consequences. One such area of research is a collaborative Earth System Science. The Earth System is dynamic and complex. It is comprised of diverse components that interact. By providing students the opportunities to work in interdisciplinary groups on a problem that reflects a complex, real-world situation they can see the linkages between components of the Earth system that encompass climate and all its components (weather precipitation, temperature, etc.) and technology development and deployment of sensors and sensor networks and social impacts. By involving students in the creation of their own personalized professional development plan, students are more focused and engaged and are more likely to remain in the program.

Amplitude interpretation and visualization of three-dimensional reflection data

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

Enachescu, M.E.

1994-07-01

Digital recording and processing of modern three-dimensional surveys allow for relative good preservation and correct spatial positioning of seismic reflection amplitude. A four-dimensional seismic reflection field matrix R (x,y,t,A), which can be computer visualized (i.e., real-time interactively rendered, edited, and animated), is now available to the interpreter. The amplitude contains encoded geological information indirectly related to lithologies and reservoir properties. The magnitude of the amplitude depends not only on the acoustic impedance contrast across a boundary, but is also strongly affected by the shape of the reflective boundary. This allows the interpreter to image subtle tectonic and structural elements notmore » obvious on time-structure maps. The use of modern workstations allows for appropriate color coding of the total available amplitude range, routine on-screen time/amplitude extraction, and late display of horizon amplitude maps (horizon slices) or complex amplitude-structure spatial visualization. Stratigraphic, structural, tectonic, fluid distribution, and paleogeographic information are commonly obtained by displaying the amplitude variation A = A(x,y,t) associated with a particular reflective surface or seismic interval. As illustrated with several case histories, traditional structural and stratigraphic interpretation combined with a detailed amplitude study generally greatly enhance extraction of subsurface geological information from a reflection data volume. In the context of three-dimensional seismic surveys, the horizon amplitude map (horizon slice), amplitude attachment to structure and [open quotes]bright clouds[close quotes] displays are very powerful tools available to the interpreter.« less

Structure and interactions in biomaterials based on membrane-biopolymer self-assembly

NASA Astrophysics Data System (ADS)

Koltover, Ilya

Physical and chemical properties of artificial pure lipid membranes have been extensively studied during the last two decades and are relatively well understood. However, most real membrane systems of biological and biotechnological importance incorporate macromolecules either embedded into the membranes or absorbed onto their surfaces. We have investigated three classes of self-assembled membrane-biopolymer biomaterials: (i) Structure, interactions and stability of the two-dimensional crystals of the integral membrane protein bacteriorhodopsin (bR). We have conducted a synchrotron x-ray diffraction study of oriented bR multilayers. The important findings were as follows: (1) the protein 2D lattice exhibited diffraction patterns characteristic of a 2D solid with power-law decay of in-plane positional correlations, which allowed to measure the elastic constants of protein crystal; (2) The crystal melting temperature was a function of the multilayer hydration, reflecting the effect of inter-membrane repulsion on the stability of protein lattice; (3) Preparation of nearly perfect (mosaicity < 0.04° ) multilayers of fused bR membranes permitted, for the first time, application of powerful interface-sensitive x-ray scattering techniques to a membrane-protein system. (ii) Interactions between the particles chemically attached or absorbed onto the surfaces of flexible giant phospholipid vesicles. Using video-enhanced light microscopy we have observed a membrane-distortion induced attraction between the particles with the interaction range of the order of particle diameter. Fluid membranes decorated with many particles exhibited: (i) a finite-sized two-dimensional closed packed aggregates and (ii) a one-dimensional ring-like aggregates. (iii) Structure, stability and interactions in the cationic lipid-DNA complexes. Cationic liposomes complexed with DNA are among the most promising synthetic non-viral carriers of DNA vectors currently used in gene therapy applications. We have established that DNA complexes with cationic lipid (DOTAP) and a neutral lipid (DOPC) have a compact multilayer liquid crystalline structure ( L ca ) with DNA intercalated between the lipid bilayers in a periodic 2D smectic phase. Furthermore, a different 2D columnar phase of complexes was found in mixtures with a transfectionen-hancing lipid DOPE. This structure ( HcII ) derived from synchrotron x-ray diffraction consists of DNA coated by cationic lipid monolayers and arranged on a two-dimensional hexagonal lattice. Optical microscopy revealed that the L ca complexes bind stably to anionic vesicles (models of cellular membranes), whereas the more transfectant HcII complexes are unstable, rapidly fusing and releasing DNA upon adhering to anionic vesicles.

Fire in the west: It's no simple story

USGS Publications Warehouse

Betancourt, Julio L.; Swetnam, Thomas W.; Allen, Craig D.; Savage, Melissa

2003-01-01

As scientists who have long grappled with the complexities of fire history in the West, we take issue with Ray Ring’s overreaching storyline that the recent spate of stand-replacing forest fires reflects wholly natural processes operating across all Western landscapes (HCN, 5/26/03: A losing battle). Ring further asserts that the main driver of recent crown fires must be climatic change, and not the extraordinary fuel accumulations of the 20th century. If we want to cope with huge wildfires over the long term, Ring concludes, we should focus less on thinning our forests and more on cutting greenhouse gas emissions to curtail global warming. We appreciate that Ring’s simple storyline was meant to be provocative. We insist, however, that the circumstances driving Western wildfires are actually quite varied and complex, involving interactions between climate and fuels.

Children and adolescents' internal models of food-sharing behavior include complex evaluations of contextual factors.

PubMed

Markovits, Henry; Benenson, Joyce F; Kramer, Donald L

2003-01-01

This study examined internal representations of food sharing in 589 children and adolescents (8-19 years of age). Questionnaires, depicting a variety of contexts in which one person was asked to share a resource with another, were used to examine participants' expectations of food-sharing behavior. Factors that were varied included the value of the resource, the relation between the two depicted actors, the quality of this relation, and gender. Results indicate that internal models of food-sharing behavior showed systematic patterns of variation, demonstrating that individuals have complex contextually based internal models at all ages, including the youngest. Examination of developmental changes in use of individual patterns is consistent with the idea that internal models reflect age-specific patterns of interactions while undergoing a process of progressive consolidation.

Predicting Physical Interactions between Protein Complexes*

PubMed Central

Clancy, Trevor; Rødland, Einar Andreas; Nygard, Ståle; Hovig, Eivind

2013-01-01

Protein complexes enact most biochemical functions in the cell. Dynamic interactions between protein complexes are frequent in many cellular processes. As they are often of a transient nature, they may be difficult to detect using current genome-wide screens. Here, we describe a method to computationally predict physical interactions between protein complexes, applied to both humans and yeast. We integrated manually curated protein complexes and physical protein interaction networks, and we designed a statistical method to identify pairs of protein complexes where the number of protein interactions between a complex pair is due to an actual physical interaction between the complexes. An evaluation against manually curated physical complex-complex interactions in yeast revealed that 50% of these interactions could be predicted in this manner. A community network analysis of the highest scoring pairs revealed a biologically sensible organization of physical complex-complex interactions in the cell. Such analyses of proteomes may serve as a guide to the discovery of novel functional cellular relationships. PMID:23438732

Community and inquiry: journey of a science teacher

NASA Astrophysics Data System (ADS)

Goldberg, Jennifer; Welsh, Kate Muir

2009-09-01

In this case study, we examine a teacher's journey, including reflections on teaching science, everyday classroom interaction, and their intertwined relationship. The teacher's reflections include an awareness of being "a White middle-class born and raised teacher teaching other peoples' children." This awareness was enacted in the science classroom and emerges through approaches to inquiry . Our interest in Ms. Cook's journey grew out of discussions, including both informal and semi-structured interviews, in two research projects over a three-year period. Our interest was further piqued as we analyzed videotaped classroom interaction during science lessons and discovered connections between Ms. Cook's reflections and classroom interaction. In this article, we illustrate ways that her journey emerges as a conscientization. This, at least in part, shapes classroom interaction, which then again shapes her conscientization in a recursive, dynamic relationship. We examine her reflections on her "hegemonic (cultural and socio-economic) practices" and consider how these reflections help her reconsider such practices through analysis of classroom interaction. Analyses lead us to considering the importance of inquiry within this classroom community.

Binding Thermodynamics of Ferredoxin:NADP+ Reductase: Two Different Protein Substrates and One Energetics

PubMed Central

Martínez-Júlvez, Marta; Medina, Milagros; Velázquez-Campoy, Adrián

2009-01-01

Abstract The thermodynamics of the formation of binary and ternary complexes between Anabaena PCC 7119 FNR and its substrates, NADP+ and Fd, or Fld, has been studied by ITC. Despite structural dissimilarities, the main difference between Fd and Fld binding to FNR relates to hydrophobicity, reflected in different binding heat capacity and number of water molecules released from the interface. At pH 8, the formation of the binary complexes is both enthalpically and entropically driven, accompanied by the protonation of at least one ionizable group. His299 FNR has been identified as the main responsible for the proton exchange observed. However, at pH 10, where no protonation occurs and intrinsic binding parameters can be obtained, the formation of the binary complexes is entropically driven, with negligible enthalpic contribution. Absence of the FMN cofactor in Fld does not alter significantly the strength of the interaction, but considerably modifies the enthalpic and entropic contributions, suggesting a different binding mode. Ternary complexes show negative cooperativity (6-fold and 11-fold reduction in binding affinity, respectively), and an increase in the enthalpic contribution (more favorable) and a decrease in the entropic contribution (less favorable), with regard to the binary complexes energetics. PMID:19527656

Cationic Lipid-Nucleic Acid Complexes for Gene Delivery And Silencing: Pathways And Mechanisms for Plasmid Dna And Sirna

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

Ewert, K.K.; Zidovska, A.; Ahmad, A.

2012-07-17

Motivated by the promises of gene therapy, there is great interest in developing non-viral lipid-based vectors for therapeutic applications due to their low immunogenicity, low toxicity, ease of production, and the potential of transferring large pieces of DNA into cells. In fact, cationic liposome (CL) based vectors are among the prevalent synthetic carriers of nucleic acids (NAs) currently used in gene therapy clinical trials worldwide. These vectors are studied both for gene delivery with CL-DNA complexes and gene silencing with CL-siRNA (short interfering RNA) complexes. However, their transfection efficiencies and silencing efficiencies remain low compared to those of engineered viralmore » vectors. This reflects the currently poor understanding of transfection-related mechanisms at the molecular and self-assembled levels, including a lack of knowledge about interactions between membranes and double stranded NAs and between CL-NA complexes and cellular components. In this review we describe our recent efforts to improve the mechanistic understanding of transfection by CL-NA complexes, which will help to design optimal lipid-based carriers of DNA and siRNA for therapeutic gene delivery and gene silencing.« less

Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases

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

Bartocci, Alessio; Cappelletti, David; Pirani, Fernando

2015-05-14

The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl{sub 4} and CF{sub 4}. Their investigation was motivated by the widespread current interest for the intermolecular halogen bonding (XB), a structural motif recognized to play a role in fields ranging from elementary processes to biochemistry. The simulation of the static and dynamic behaviors of complex systems featuring XB requires the formulation of reliable and accurate model potentials, whose development relies on the detailed characterization of strength and nature of the interactions occurring in simple exemplary halogenated systems. We thus selected the prototypicalmore » Ng-CCl{sub 4} and Ng-CF{sub 4} and performed high-resolution molecular beam scattering experiments to measure the absolute scale of their intermolecular potentials, with high sensitivity. In general, we expected to probe typical van der Waals interactions, consisting of a combination of size (exchange) repulsion with dispersion/induction attraction. For the He/Ne-CF{sub 4}, the analysis of the glory quantum interference pattern, observable in the velocity dependence of the integral cross section, confirmed indeed this expectation. On the other hand, for the He/Ne/Ar-CCl{sub 4}, the scattering data unravelled much deeper potential wells, particularly for certain configurations of the interacting partners. The experimental data can be properly reproduced only including a shifting of the repulsive wall at shorter distances, accompanied by an increased role of the dispersion attraction, and an additional short-range stabilization component. To put these findings on a firmer ground, we performed, for selected geometries of the interacting complexes, accurate theoretical calculations aimed to evaluate the intermolecular interaction and the effects of the complex formation on the electron charge density of the constituting moieties. It was thus ascertained that the adjustments of the potential suggested by the analysis of the experiments actually reflect two chemically meaningful contributions, namely, a stabilizing interaction arising from the anisotropy of the charge distribution around the Cl atom in CCl{sub 4} and a stereospecific electron transfer that occurs at the intermolecular distances mainly probed by the experiments. Our model calculations suggest that the largest effect is for the vertex geometry of CCl{sub 4} while other geometries appear to play a minor to negligible role.« less

Interactions of multi-scale heterogeneity in the lithosphere: Australia

NASA Astrophysics Data System (ADS)

Kennett, B. L. N.; Yoshizawa, K.; Furumura, T.

2017-10-01

Understanding the complex heterogeneity of the continental lithosphere involves a wide variety of spatial scales and the synthesis of multiple classes of information. Seismic surface waves and multiply reflected body waves provide the main constraints on broad-scale structure, and bounds on the extent of the lithosphere-asthenosphere transition (LAT) can be found from the vertical gradients of S wavespeed. Information on finer-scale structures comes through body wave studies, including detailed seismic tomography and P-wave reflectivity extracted from stacked autocorrelograms of continuous component records. With the inclusion of deterministic large-scale structure and realistic medium-scale stochastic features fine-scale variations are subdued. The resulting multi-scale heterogeneity model for the Australian region gives a good representation of the character of observed seismograms and their geographic variations and matches the observations of P-wave reflectivity. P reflections in the 0.5-3.0 Hz band in the uppermost mantle suggest variations on vertical scales of a few hundred metres with amplitudes of the order of 1%. Interference of waves reflected or converted at sequences of such modest variations in physical properties produce relatively simple behaviour for lower frequencies, which can suggest simpler structures than are actually present. Vertical changes in the character of fine-scale heterogeneity can produce apparent discontinuities. In Central Australia a 'mid-lithospheric discontinuity' can be tracked via changes in frequency content of station reflectivity, with links to the broad-scale pattern of wavespeed gradients and, in particular, the gradients of radial anisotropy. Comparisons with xenolith results from southeastern Australia indicate a strong tie between geochemical stratification and P-wave reflectivity.

Revealing "The Space Between": Creating an Observation Scale to Understand Infant Mental Health Reflective Supervision

ERIC Educational Resources Information Center

Watson, Christopher L.; Harrison, Mary E.; Hennes, Jill E.; Harris, Maren M.

2016-01-01

The Reflective Interaction Observation Scale (RIOS) describes and operationalizes the nature of the interactions between a supervisor and supervisee(s) during reflective supervision. Developed in collaboration among researchers and clinicians from the University of Minnesota, the Minnesota Association for Infant and Early Childhood Mental Health,…

Static Modulation Wave of Arrays of Halogen Interactions Transduced to a Hierarchy of Nanoscale Change Stimuli of Crystalline Rotors Dynamics.

PubMed

Simonov, Sergey; Zorina, Leokadiya; Wzietek, Pawel; Rodríguez-Fortea, Antonio; Canadell, Enric; Mézière, Cécile; Bastien, Guillaume; Lemouchi, Cyprien; Garcia-Garibay, Miguel A; Batail, Patrick

2018-06-13

Here we present a study where what can be seen as a static modulation wave encompassing four successive arrays of interacting iodine atoms in crystalline 1,4-Bis((4'-(iodoethynyl)phenyl) ethynyl)bicyclo[2,2,2]octane rotors changes the structure from one-half molecule to three-and-a-half molecules in the asymmetric unit below a phase transition at 105 K. The remarkable finding is that the total 1 H spin-lattice relaxation rate, T 1 -1 , of unprecedented complexity to date in molecular rotors, is the weighted sum of the relaxation rates of the four contributing rotors relaxation rates, each with distinguishable exchange frequencies reflecting Arrhenius parameters with different activation barriers ( E a ) and attempt frequencies (τ o -1 ). This allows us to show in tandem with rotor-environment interaction energy calculations how the dynamics of molecular rotors are able to decode structural information from their surroundings with remarkable nanoscale precision.

Gender Effects in Classroom Interaction: Data Collection, Self-Analysis and Reflection.

ERIC Educational Resources Information Center

Drudy, Sheelagh; Chathain, Maire Ui

2002-01-01

Conducted an action research project among student teachers emphasizing teacher self-analysis and reflection and studied the patterns of classroom interactions with male and female students taught by these teachers in 136 classrooms in Irish secondary schools. Findings from the classroom interaction study motivated student teachers to take…

Fragments of the past activity of Sgr A* inferred from X-ray echoes in Sgr C

NASA Astrophysics Data System (ADS)

Chuard, D.; Terrier, R.; Goldwurm, A.; Soldi, S.; Clavel, M.; Morris, M.; Ponti, G.; Walls, M.; Chernyakova, M.

2017-10-01

Giant molecular clouds populating the central molecular zone have a high enough column density to reflect X-rays coming from strong compact sources in their neighbourhood, including possible powerful outbursts from the Galactic supermassive black hole Sgr A*. We study this reflected emission in observations of the molecular complex Sgr C made with the X-ray observatories XMM-Newton and Chandra between 2000 and 2014. We show that this complex exhibits clear variability in both space and time, which strongly favours the reflection scenario, the most likely illuminating source being Sgr A*. By comparing data to Monte-Carlo simulated reflection spectra, we are able to put the best constraints to date on the line-of-sight positions of the main bright clumps of the molecular complex. Ultimately, extending this approach by the inclusion of other molecular complexes allows us to partially reconstruct the past lightcurve of the Galactic supermassive black hole.

GLIMPCE Seismic reflection evidence of deep-crustal and upper-mantle intrusions and magmatic underplating associated with the Midcontinent Rift system of North America

USGS Publications Warehouse

Behrendt, John C.; Hutchinson, D.R.; Lee, M.; Thornber, C.R.; Tréhu, A.; Cannon, W.; Green, A.

1990-01-01

Deep-crustal and Moho reflections, recorded on vertical incidence and wide angle ocean bottom Seismometer (OBS) data in the 1986 GLIMPCE (Great Lakes International Multidisciplinary Program on Crustal Evolution) experiment, provide evidence for magmatic underplating and intrusions within the lower crust and upper mantle contemporaneous with crustal extension in the Midcontinent Rift system at 1100 Ma. The rift fill consists of 20-30 km (7-10 s) of basalt flows, secondary syn-rift volcaniclastic and post-basalt sedimentary rock. Moho reflections recorded in Lake Superior over the Midcontinent Rift system have times from 14-18 s (about 46 km to as great as 58 km) in contrast to times of about 11-13 s (about 36-42 km crustal thickness) beneath the surrounding Great Lakes. The Seismically complex deep-crust to mantle transition zone (30-60 km) in north-central Lake Superior, which is 100 km wider than the rift half-graben, reflects the complicated products of tectonic and magmatic interaction of lower-crustal and mantle components during evolution or shutdown of the aborted Midcontinent Rift. In effect, mantle was changed into crust by lowering Seismic velocity (through intrusion of lower density magmatic rocks) and increasing Moho (about 8.1 km s-1 depth. 

Reflective journals: unmasking student perceptions of anatomical education.

PubMed

Lazarus, L; Sookrajh, R; Satyapal, K S

2017-01-01

In medical education, reflection has been considered to be a core skill in professional competence. The anatomy laboratory is an ideal setting for faculty/ student interaction and provides invaluable opportunities for active learning and reflection on anatomical knowledge. This study was designed to record student attitudes regarding human cadaveric dissection, explore their experiences of anatomy through an analysis of their journal-reflective writings and determine whether this type of creative writing had a beneficial effect on those students who chose to complete them. A total of 75 journals from Medical and Allied Health Science students were collected and analysed. Results were categorised according to the following themes: (i) Dissecting room stressors (27.6%); (ii) Educational value of dissection (26.3%); (iii) Appreciation, Gratitude, Respect and Curiosity for the cadaver (18.9%); (iv) Positive and negative sentiments expressed in the dissecting room (25.8%); (v) Benefit of alternate teaching modalities (4.6%); (vi) Spirituality/Religious Beliefs (3.7%); (vii) Shared humanity and emotional bonds (3.69%); (viii) Acknowledgement of human anatomical variations (3.2%); (ix) Beauty and complexity of the human body (1.8%) and (x) Psychological detachment (0.9%). Students appreciated the opportunity to share their emotions and reflect on the humanistic dimension of anatomy as a subject. Student reflections illustrated clearly their thoughts and some of the difficult issues with which they wrestled. The anatomy laboratory is seen as the budding clinician's first encounter with a patient, albeit a cadaver. This was the first time that reflective journals were given to students in the discipline. Reflective journals allow students to express themselves in an open-ended and creative fashion. It also assists students to integrate anatomy and clinical medicine and assists in applying their basic anatomical knowledge in an authentic, yet safe environment.

Cancer risk and the complexity of the interactions between environmental and host factors: HENVINET interactive diagrams as simple tools for exploring and understanding the scientific evidence.

PubMed

Merlo, Domenico F; Filiberti, Rosangela; Kobernus, Michael; Bartonova, Alena; Gamulin, Marija; Ferencic, Zeljko; Dusinska, Maria; Fucic, Aleksandra

2012-06-28

Development of graphical/visual presentations of cancer etiology caused by environmental stressors is a process that requires combining the complex biological interactions between xenobiotics in living and occupational environment with genes (gene-environment interaction) and genomic and non-genomic based disease specific mechanisms in living organisms. Traditionally, presentation of causal relationships includes the statistical association between exposure to one xenobiotic and the disease corrected for the effect of potential confounders. Within the FP6 project HENVINET, we aimed at considering together all known agents and mechanisms involved in development of selected cancer types. Selection of cancer types for causal diagrams was based on the corpus of available data and reported relative risk (RR). In constructing causal diagrams the complexity of the interactions between xenobiotics was considered a priority in the interpretation of cancer risk. Additionally, gene-environment interactions were incorporated such as polymorphisms in genes for repair and for phase I and II enzymes involved in metabolism of xenobiotics and their elimination. Information on possible age or gender susceptibility is also included. Diagrams are user friendly thanks to multistep access to information packages and the possibility of referring to related literature and a glossary of terms. Diagrams cover both chemical and physical agents (ionizing and non-ionizing radiation) and provide basic information on the strength of the association between type of exposure and cancer risk reported by human studies and supported by mechanistic studies. Causal diagrams developed within HENVINET project represent a valuable source of information for professionals working in the field of environmental health and epidemiology, and as educational material for students. Cancer risk results from a complex interaction of environmental exposures with inherited gene polymorphisms, genetic burden collected during development and non genomic capacity of response to environmental insults. In order to adopt effective preventive measures and the associated regulatory actions, a comprehensive investigation of cancer etiology is crucial. Variations and fluctuations of cancer incidence in human populations do not necessarily reflect environmental pollution policies or population distribution of polymorphisms of genes known to be associated with increased cancer risk. Tools which may be used in such a comprehensive research, including molecular biology applied to field studies, require a methodological shift from the reductionism that has been used until recently as a basic axiom in interpretation of data. The complexity of the interactions between cells, genes and the environment, i.e. the resonance of the living matter with the environment, can be synthesized by systems biology. Within the HENVINET project such philosophy was followed in order to develop interactive causal diagrams for the investigation of cancers with possible etiology in environmental exposure. Causal diagrams represent integrated knowledge and seed tool for their future development and development of similar diagrams for other environmentally related diseases such as asthma or sterility. In this paper development and application of causal diagrams for cancer are presented and discussed.

Interactions Between Anandamide and Corticotropin-Releasing Factor Signaling Modulate Human Amygdala Function and Risk for Anxiety Disorders: An Imaging Genetics Strategy for Modeling Molecular Interactions.

PubMed

Demers, Catherine H; Drabant Conley, Emily; Bogdan, Ryan; Hariri, Ahmad R

2016-09-01

Preclinical models reveal that stress-induced amygdala activity and impairment in fear extinction reflect reductions in anandamide driven by corticotropin-releasing factor receptor type 1 (CRF1) potentiation of the anandamide catabolic enzyme fatty acid amide hydrolase. Here, we provide clinical translation for the importance of these molecular interactions using an imaging genetics strategy to examine whether interactions between genetic polymorphisms associated with differential anandamide (FAAH rs324420) and CRF1 (CRHR1 rs110402) signaling modulate amygdala function and anxiety disorder diagnosis. Analyses revealed that individuals with a genetic background predicting relatively high anandamide and CRF1 signaling exhibited blunted basolateral amygdala habituation, which further mediated increased risk for anxiety disorders among these same individuals. The convergence of preclinical and clinical data suggests that interactions between anandamide and CRF1 represent a fundamental molecular mechanism regulating amygdala function and anxiety. Our results further highlight the potential of imaging genetics to powerfully translate complex preclinical findings to clinically meaningful human phenotypes. Copyright © 2015 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Restoring fish ecological quality in estuaries: Implication of interactive and cumulative effects among anthropogenic stressors.

PubMed

Teichert, Nils; Borja, Angel; Chust, Guillem; Uriarte, Ainhize; Lepage, Mario

2016-01-15

Estuaries are subjected to multiple anthropogenic stressors, which have additive, antagonistic or synergistic effects. Current challenges include the use of large databases of biological monitoring surveys (e.g. the European Water Framework Directive) to help environmental managers prioritizing restoration measures. This study investigated the impact of nine stressor categories on the fish ecological status derived from 90 estuaries of the North East Atlantic countries. We used a random forest model to: 1) detect the dominant stressors and their non-linear effects; 2) evaluate the ecological benefits expected from reducing pressure from stressors; and 3) investigate the interactions among stressors. Results showed that largest restoration benefits were expected when mitigating water pollution and oxygen depletion. Non-additive effects represented half of pairwise interactions among stressors, and antagonisms were the most common. Dredged sediments, flow changes and oxygen depletion were predominantly implicated in non-additive interactions, whereas the remainder stressors often showed additive impacts. The prevalence of interactive impacts reflects a complex scenario for estuaries management; hence, we proposed a step-by-step restoration scheme focusing on the mitigation of stressors providing the maximum of restoration benefits under a multi-stress context. Copyright © 2015 Elsevier B.V. All rights reserved.

Secondary coordination sphere interactions within the biomimetic iron azadithiolate complexes related to Fe-only hydrogenase: dynamic measure of electron density about the Fe sites.

PubMed

Liu, Yu-Chiao; Tu, Ling-Kuang; Yen, Tao-Hung; Lee, Gene-Hsiang; Yang, Shu-Ting; Chiang, Ming-Hsi

2010-07-19

A series of iron azadithiolate complexes possessing an intramolecular secondary coordination sphere interaction and an ability to reduce HOAc at the potential near the first electron-transfer process are reported. A unique structural feature in which the aza nitrogen has its lone pair point toward the apical carbonyl carbon is observed in [Fe(2)(mu-S(CH(2))(2)NR(CH(2))(2)S)(CO)(6-x)L(x)](2) (R = (n)Pr, x = 0, 1a; R = (i)Pr, x = 0, 1b; R = (n)Pr, L = PPh(3), x = 1, 2; R = (n)Pr, L = P(n)Bu(3), x = 1, 3) as biomimetic models of the active site of Fe-only hydrogenase. The presence of this weak N...C(CO(ap)) interaction provides electronic perturbation at the Fe center. The distance of the N...C(CO(ap)) contact is 3.497 A in 1a. It increases by 0.455 A in 2 when electronic density of the Fe site is slightly enriched by a weak sigma-donating ligand, PPh(3). A longer distance (4.040 A) is observed for the P(n)Bu(3) derivative, 3. This N...C(CO(ap)) distance is thus a dynamic measure of electronic nature of the Fe(2) core. Variation of electronic richness within the Fe(2) moiety among the complexes reflects on their electrochemical response. Reduction of 2 is recorded at the potential of -2.17 V, which is 270 mV more negative than that of 1. Complex 3 requires additional 150 mV for the same reduction. Such cathodic shift results from CO substitution by phosphines. Electrocatalytic hydrogen production from HOAc by both kinds of complexes (all-CO and phosphine-substituted species) requires the potential close to that for reduction of the parent molecules in the absence of acids. The catalytic mechanism of 1a is proposed to involve proton uptake at the Fe(0)Fe(I) redox level instead of the Fe(0)Fe(0) level. This result is the first observation among the all-CO complexes with respect to electrocatalysis of HOAc.

Systems thinking and complexity: considerations for health promoting schools.

PubMed

Rosas, Scott R

2017-04-01

The health promoting schools concept reflects a comprehensive and integrated philosophy to improving student and personnel health and well-being. Conceptualized as a configuration of interacting, interdependent parts connected through a web of relationships that form a whole greater than the sum of its parts, school health promotion initiatives often target several levels (e.g. individual, professional, procedural and policy) simultaneously. Health promoting initiatives, such as those operationalized under the whole school approach, include several interconnected components that are coordinated to improve health outcomes in complex settings. These complex systems interventions are embedded in intricate arrangements of physical, biological, ecological, social, political and organizational relationships. Systems thinking and characteristics of complex adaptive systems are introduced in this article to provide a perspective that emphasizes the patterns of inter-relationships associated with the nonlinear, dynamic and adaptive nature of complex hierarchical systems. Four systems thinking areas: knowledge, networks, models and organizing are explored as a means to further manage the complex nature of the development and sustainability of health promoting schools. Applying systems thinking and insights about complex adaptive systems can illuminate how to address challenges found in settings with both complicated (i.e. multi-level and multisite) and complex aspects (i.e. synergistic processes and emergent outcomes). © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Lurasidone-β-cyclodextrin complexes: Physicochemical characterization and comparison of their antidepressant, antipsychotic activities against that of self microemulsifying formulation

NASA Astrophysics Data System (ADS)

Londhe, Vaishali Y.; Deshmane, Aishwarya B.; Singh, Sarita R.; Kulkarni, Yogesh A.

2018-04-01

Lurasidone hydrochloride (LHD) is an atypical antipsychotic drug has poor aqueous solubility and low bioavailability (9-19%). This study describes effect of different methods of complex formation with β-cyclodextrin (BCD) on enhancement of dissolution and on antidepressant, antipsychotic effects of LHD. Other purpose of this study is to compare pharmacodynamic effects of complexes with that of self microemulsifying drug delivery system of LHD (SMEDDS). Inclusion complexes (IC) of LHD and BCD were prepared by physical mixing (PM), kneading (KN) and spray drying (SD) in a 1:1 M ratio. These complexes were characterized by different techniques. KN and SD showing enhancement in dissolution, were compared with SMEDDS using Forced swim test (FST) and Tail suspension test (TST) for antidepressant action and Paw test for antipsychotic activity. Characterization of complexes confirmed interaction between LHD and BCD. Enhancement in dissolution is seen in following order SD > KN > PM > LHD. In all three animal models, SD, KN and SMEDDS showed statistically significant effect (p < .05) than drug alone showing enhancement in bioavailability. Complexation of LHD with BCD enhances dissolution which reflected in improvement of antidepressant and antipsychotic activity of drug. Solubility enhancement methods like complexation and self microemulsion improves pharmacodynamic activities of drug. Improvement of pharmacodynamic effect is seen in order, SD ≥ SMEDDS ≥ KN > LHD.

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.

PubMed

Van Leene, Jelle; Hollunder, Jens; Eeckhout, Dominique; Persiau, Geert; Van De Slijke, Eveline; Stals, Hilde; Van Isterdael, Gert; Verkest, Aurine; Neirynck, Sandy; Buffel, Yelle; De Bodt, Stefanie; Maere, Steven; Laukens, Kris; Pharazyn, Anne; Ferreira, Paulo C G; Eloy, Nubia; Renne, Charlotte; Meyer, Christian; Faure, Jean-Denis; Steinbrenner, Jens; Beynon, Jim; Larkin, John C; Van de Peer, Yves; Hilson, Pierre; Kuiper, Martin; De Veylder, Lieven; Van Onckelen, Harry; Inzé, Dirk; Witters, Erwin; De Jaeger, Geert

2010-08-10

Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)-cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK-cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants.

Manipulating transmission and reflection properties of a photonic crystal doped with quantum dot nanostructures

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

Solookinejad, G.; Panahi, M.; Sangachin, E. A.

The transmission and reflection properties of incident light in a defect dielectric structure is studied theoretically. The defect structure consists of donor and acceptor quantum dot nanostructures embedded in a photonic crystal. It is shown that the transmission and reflection properties of incident light can be controlled by adjusting the corresponding parameters of the system. The role of dipole–dipole interaction is considered as a new parameter in our calculations. It is noted that the features of transmission and reflection curves can be adjusted in the presence of dipole–dipole interaction. It is found that the absorption of weak probe light canmore » be converted to the probe amplification in the presence of dipole–dipole interaction. Moreover, the group velocity of transmitted and reflected probe light is discussed in detail in the absence and presence of dipole–dipole interaction. Our proposed model can be used as a new all-optical devices based on photonic materials doped with nanoparticles.« less

Does formal complexity reflect cognitive complexity? Investigating aspects of the Chomsky Hierarchy in an artificial language learning study.

PubMed

Öttl, Birgit; Jäger, Gerhard; Kaup, Barbara

2015-01-01

This study investigated whether formal complexity, as described by the Chomsky Hierarchy, corresponds to cognitive complexity during language learning. According to the Chomsky Hierarchy, nested dependencies (context-free) are less complex than cross-serial dependencies (mildly context-sensitive). In two artificial grammar learning (AGL) experiments participants were presented with a language containing either nested or cross-serial dependencies. A learning effect for both types of dependencies could be observed, but no difference between dependency types emerged. These behavioral findings do not seem to reflect complexity differences as described in the Chomsky Hierarchy. This study extends previous findings in demonstrating learning effects for nested and cross-serial dependencies with more natural stimulus materials in a classical AGL paradigm after only one hour of exposure. The current findings can be taken as a starting point for further exploring the degree to which the Chomsky Hierarchy reflects cognitive processes.

Does Formal Complexity Reflect Cognitive Complexity? Investigating Aspects of the Chomsky Hierarchy in an Artificial Language Learning Study

PubMed Central

Öttl, Birgit; Jäger, Gerhard; Kaup, Barbara

2015-01-01

This study investigated whether formal complexity, as described by the Chomsky Hierarchy, corresponds to cognitive complexity during language learning. According to the Chomsky Hierarchy, nested dependencies (context-free) are less complex than cross-serial dependencies (mildly context-sensitive). In two artificial grammar learning (AGL) experiments participants were presented with a language containing either nested or cross-serial dependencies. A learning effect for both types of dependencies could be observed, but no difference between dependency types emerged. These behavioral findings do not seem to reflect complexity differences as described in the Chomsky Hierarchy. This study extends previous findings in demonstrating learning effects for nested and cross-serial dependencies with more natural stimulus materials in a classical AGL paradigm after only one hour of exposure. The current findings can be taken as a starting point for further exploring the degree to which the Chomsky Hierarchy reflects cognitive processes. PMID:25885790

Measuring the complex optical conductivity of graphene by Fabry-Pérot reflectance spectroscopy [Determination of the optical index for few-layer graphene by reflectivity spectroscopy

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

Ghamsari, Behnood G.; Tosado, Jacob; Yamamoto, Mahito

Here, we have experimentally studied the optical refractive index of few-layer graphene through reflection spectroscopy at visible wavelengths. A laser scanning microscope (LSM) with a coherent supercontinuum laser source measured the reflectivity of an exfoliated graphene flake on a Si/SiO 2 substrate, containing monolayer, bilayer and trilayer areas, as the wavelength of the laser was varied from 545nm to 710nm. The complex refractive index of few-layer graphene, n-ik, was extracted from the reflectivity contrast to the bare substrate and the Fresnel reflection theory. Since the SiO 2 thickness enters to the modeling as a parameter, it was precisely measured atmore » the location of the sample. It was found that a common constant optical index cannot explain the wavelength-dependent reflectivity data for single-, double- and three-layer graphene simultaneously, but rather each individual few-layer graphene possesses a unique optical index whose complex values were precisely and accurately determined from the experimental data.« less

Measuring the complex optical conductivity of graphene by Fabry-Pérot reflectance spectroscopy [Determination of the optical index for few-layer graphene by reflectivity spectroscopy

DOE PAGES

Ghamsari, Behnood G.; Tosado, Jacob; Yamamoto, Mahito; ...

2016-09-29

Here, we have experimentally studied the optical refractive index of few-layer graphene through reflection spectroscopy at visible wavelengths. A laser scanning microscope (LSM) with a coherent supercontinuum laser source measured the reflectivity of an exfoliated graphene flake on a Si/SiO 2 substrate, containing monolayer, bilayer and trilayer areas, as the wavelength of the laser was varied from 545nm to 710nm. The complex refractive index of few-layer graphene, n-ik, was extracted from the reflectivity contrast to the bare substrate and the Fresnel reflection theory. Since the SiO 2 thickness enters to the modeling as a parameter, it was precisely measured atmore » the location of the sample. It was found that a common constant optical index cannot explain the wavelength-dependent reflectivity data for single-, double- and three-layer graphene simultaneously, but rather each individual few-layer graphene possesses a unique optical index whose complex values were precisely and accurately determined from the experimental data.« less

Engineering design of sub-micron topographies for simultaneously adherent and reflective metal-polymer interfaces

NASA Technical Reports Server (NTRS)

Brown, Christopher A.

1993-01-01

The approach of the project is to base the design of multi-function, reflective topographies on the theory that topographically dependent phenomena react with surfaces and interfaces at certain scales. The first phase of the project emphasizes the development of methods for understanding the sizes of topographic features which influence reflectivity. Subsequent phases, if necessary, will address the scales of interaction for adhesion and manufacturing processes. A simulation of the interaction of electromagnetic radiation, or light, with a reflective surface is performed using specialized software. Reflectivity of the surface as a function of scale is evaluated and the results from the simulation are compared with reflectivity measurements made on multi-function, reflective surfaces.

Insights into RNA polymerase catalysis and adaptive evolution gained from mutational analysis of a locus conferring rifampicin resistance

PubMed Central

Yurieva, Olga; Nikiforov, Vadim; O’Donnell, Michael

2017-01-01

Abstract S531 of Escherichia coli RNA polymerase (RNAP) β subunit is a part of RNA binding domain in transcription complex. While highly conserved, S531 is not involved in interactions within the transcription complex as suggested by X-ray analysis. To understand the basis for S531 conservation we performed systematic mutagenesis of this residue. We find that the most of the mutations significantly decreased initiation-to-elongation transition by RNAP. Surprisingly, some changes enhanced the production of full-size transcripts by suppressing abortive loss of short RNAs. S531-R increased transcript retention by establishing a salt bridge with RNA, thereby explaining the R substitution at the equivalent position in extremophilic organisms, in which short RNAs retention is likely to be an issue. Generally, the substitutions had the same effect on bacterial doubling time when measured at 20°. Raising growth temperature to 37° ablated the positive influence of some mutations on the growth rate in contrast to their in vitro action, reflecting secondary effects of cellular environment on transcription and complex involvement of 531 locus in the cell biology. The properties of generated RNAP variants revealed an RNA/protein interaction network that is crucial for transcription, thereby explaining the details of initiation-to-elongation transition on atomic level. PMID:29036608

Hydrogen/Deuterium Exchange Reflects Binding of Human Centrin 2 to Ca2+ and Xeroderma Pigmentosum Group C Peptide: An Example of EX1 Kinetics

PubMed Central

Sperry, Justin B.; Ryan, Zachary C.; Kumar, Rajiv; Gross, Michael L.

2012-01-01

Xeroderma pigmentosum (XP) is a genetic disease affecting 1 in 10,000-100,000 and predisposes people to early-age skin cancer, a disease that is increasing. Those with XP have decreased ability to repair UV-induced DNA damage, leading to increased susceptibility of cancerous non-melanomas and melanomas. A vital, heterotrimeric protein complex is linked to the nucleotide excision repair pathway for the damaged DNA. The complex consists of XPC protein, human centrin 2, and RAD23B. One of the members, human centrin 2, is a ubiquitous, acidic, Ca2+-binding protein belonging to the calmodulin superfamily. The XPC protein contains a sequence motif specific for binding to human centrin 2. We report here the Ca2+-binding properties of human centrin 2 and its interaction with the XPC peptide motif. We utilized a region-specific H/D exchange protocol to localize the interaction of the XPC peptide with the C-terminal domain of centrin, the binding of which is different than that of calmodulin complexes. The binding dynamics of human centrin 2 to the XPC peptide in the absence and presence of Ca2+ are revealed by the observation of EX1 H/D exchange regime, indicating that a locally unfolded population exists in solution and undergoes fast H/D exchange. PMID:23439742

Integrated Genomic and Network-Based Analyses of Complex Diseases and Human Disease Network.

PubMed

Al-Harazi, Olfat; Al Insaif, Sadiq; Al-Ajlan, Monirah A; Kaya, Namik; Dzimiri, Nduna; Colak, Dilek

2016-06-20

A disease phenotype generally reflects various pathobiological processes that interact in a complex network. The highly interconnected nature of the human protein interaction network (interactome) indicates that, at the molecular level, it is difficult to consider diseases as being independent of one another. Recently, genome-wide molecular measurements, data mining and bioinformatics approaches have provided the means to explore human diseases from a molecular basis. The exploration of diseases and a system of disease relationships based on the integration of genome-wide molecular data with the human interactome could offer a powerful perspective for understanding the molecular architecture of diseases. Recently, subnetwork markers have proven to be more robust and reliable than individual biomarker genes selected based on gene expression profiles alone, and achieve higher accuracy in disease classification. We have applied one of these methodologies to idiopathic dilated cardiomyopathy (IDCM) data that we have generated using a microarray and identified significant subnetworks associated with the disease. In this paper, we review the recent endeavours in this direction, and summarize the existing methodologies and computational tools for network-based analysis of complex diseases and molecular relationships among apparently different disorders and human disease network. We also discuss the future research trends and topics of this promising field. Copyright © 2015 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Ran-binding protein 5 (RanBP5) is related to the nuclear transport factor importin-beta but interacts differently with RanBP1.

PubMed Central

Deane, R; Schäfer, W; Zimmermann, H P; Mueller, L; Görlich, D; Prehn, S; Ponstingl, H; Bischoff, F R

1997-01-01

We report the identification and characterization of a novel 124-kDa Ran binding protein, RanBP5. This protein is related to importin-beta, the key mediator of nuclear localization signal (NLS)-dependent nuclear transport. RanBP5 was identified by two independent methods: it was isolated from HeLa cells by using its interaction with RanGTP in an overlay assay to monitor enrichment, and it was also found by the yeast two-hybrid selection method with RanBP1 as bait. RanBP5 binds to RanBP1 as part of a trimeric RanBP1-Ran-RanBP5 complex. Like importin-beta, RanBP5 strongly binds the GTP-bound form of Ran, stabilizing it against both intrinsic and RanGAP1-induced GTP hydrolysis and also against nucleotide exchange. The GAP resistance of the RanBP5-RanGTP complex can be relieved by RanBP1, which might reflect an in vivo role for RanBP1. RanBP5 is a predominantly cytoplasmic protein that can bind to nuclear pore complexes. We propose that RanBP5 is a mediator of a nucleocytoplasmic transport pathway that is distinct from the importin-alpha-dependent import of proteins with a classical NLS. PMID:9271386

Students' Engagement in Reflective Tasks: An Investigation of Interactive and Non-Interactive Discourse Corpora

ERIC Educational Resources Information Center

Farr, Fiona; Riordan, Elaine

2012-01-01

Reflective learning, a practice carrying relatively high educational value, has been with us for some time. Its popularity has grown to the extent that it is often adopted unquestioningly by educational practitioners. However, there are some important questions to be asked in relation to reflective practice. In reality, its impact on improved and…

Cannabis and Ecstasy/MDMA (3,4-methylenedioxymethamphetamine): an analysis of their neuropsychobiological interactions in recreational users.

PubMed

Parrott, A C; Milani, R M; Gouzoulis-Mayfrank, E; Daumann, J

2007-01-01

The majority of recreational Ecstasy/MDMA users (90-98%) also take cannabis. This co-drug usage is often viewed as a methodological confound, which needs to be removed statistically. Here we take a rather different approach, and debate the potential complexities of their psychobiological interactions. The ring-substituted amphetamine derivate MDMA (3,4-methylendioxymethamphetmaine, or 'Ecstasy') is a powerful CNS stimulant, whereas cannabis is a relaxant. Their co-usage may reflect opposing effects in three psychobiological areas: arousal, body temperature, and oxidative stress. Firstly MDMA is alerting whereas cannabis is sedating. Secondly MDMA is hyperthermic whereas cannabis is hypothermic. Thirdly MDMA increases oxidative stress whereas cannabinoids are antioxidant. Hence cannabis may modulate the acute and sub-acute reactions to MDMA, reduce the acute hyperthermia induced by MDMA, and ameliorate the oxidative stress caused by MDMA. The limited empirical evidence on each topic will be critically examined. In terms of chronic effects each drug is functionally damaging, so that polydrug users generally display cumulative neurobiological impairments. However in certain aspects their neuropsychobiological effects may interactive rather than additive. In particular, the combined use of cannabis and MDMA may have rather different neuropsychobiological implications, than their separate usage. In order to investigate these potential complexities, future research will need better empirical data on the exact patterns of co-drug usage.

Relationships between soil and leaf mineral composition are element-specific, environment-dependent and geographically structured in the emerging model Arabidopsis halleri.

PubMed

Stein, Ricardo J; Höreth, Stephan; de Melo, J Romário F; Syllwasschy, Lara; Lee, Gwonjin; Garbin, Mário L; Clemens, Stephan; Krämer, Ute

2017-02-01

Leaf mineral composition, the leaf ionome, reflects the complex interaction between a plant and its environment including local soil composition, an influential factor that can limit species distribution and plant productivity. Here we addressed within-species variation in plant-soil interactions and edaphic adaptation using Arabidopsis halleri, a well-suited model species as a facultative metallophyte and metal hyperaccumulator. We conducted multi-element analysis of 1972 paired leaf and soil samples from 165 European populations of A. halleri, at individual resolution to accommodate soil heterogeneity. Results were further confirmed under standardized conditions upon cultivation of 105 field-collected genotypes on an artificially metal-contaminated soil in growth chamber experiments. Soil-independent between- and within-population variation set apart leaf accumulation of zinc, cadmium and lead from all other nutrient and nonessential elements, concurring with differential hypothesized ecological roles in either biotic interaction or nutrition. For these metals, soil-leaf relationships were element-specific, differed between metalliferous and nonmetalliferous soils and were geographically structured both in the field and under standardized growth conditions, implicating complex scenarios of recent ecological adaptation. Our study provides an example and a reference for future related work and will serve as a basis for the molecular-genetic dissection and ecological analysis of the observed phenotypic variation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Anisotropic Coulomb Explosion of CO Ligands in Group 6 Metal Hexacarbonyls: Cr(CO)6, Mo(CO)6, W(CO)6.

PubMed

Tanaka, Hiroki; Nakashima, Nobuaki; Yatsuhashi, Tomoyuki

2016-09-08

Multiple ionization and subsequent Coulomb explosion have been studied for many organic molecules and their clusters; however, the metal complexes, particularly the large Coulombic interactions expected between a metal and its ligands, have not yet been explored. In this study, the angular distribution of CO(+), oxygen, and carbon ions ejected from metal hexacarbonyls (M(CO)6, M: Cr, Mo, W) having Oh symmetry by Coulomb explosion in femtosecond laser fields (>1 × 10(14) W cm(-2)) is investigated. The emissions of oxygen ions are well-explained in terms of the geometric alignment along a line inclined 45° relative to the CO-M-CO axis in a M(CO)4 plane. Unlike the explosion behavior of the oxygen ions located on the outer part of the molecule, the explosion behavior of the carbon ions was affected by the laser intensity, kinetic energy, and metal. This finding that the emission trends of carbon sandwiched between oxygen and metal atoms were the opposite of those for oxygen was explained by the obstruction by oxygen, the deformation of structure in bending coordinates, and the strong interaction with charged metal. The anisotropic Coulomb explosion of metal complexes reflecting their structural symmetry and central metal charge is a promising candidate for use in the investigation of large Coulombic interactions at the molecular level.

Run for your life, but bite for your rights? How interactions between natural and sexual selection shape functional morphology across habitats

NASA Astrophysics Data System (ADS)

Gomes, Verónica; Carretero, Miguel A.; Kaliontzopoulou, Antigoni

2018-02-01

A central issue in evolutionary biology is how morphology, performance, and habitat use coevolve. If morphological variation is tightly associated with habitat use, then differences in morphology should affect fitness through their effect on performance within specific habitats. In this study, we investigate how evolutionary forces mold morphological traits and performance differently given the surrounding environment, at the intraspecific level. For this purpose, we selected populations of the lizard Podarcis bocagei from two different habitat types, agricultural walls and dunes, which we expected to reflect saxicolous vs ground-dwelling habits. In the laboratory, we recorded morphological traits as well as performance traits by measuring sprint speed, climbing capacity, maneuverability, and bite force. Our results revealed fast-evolving ecomorphological variation among populations of P. bocagei, where a direct association existed between head morphology and bite performance. However, we could not establish links between limb morphology and locomotor performance at the individual level. Lizards from walls were better climbers than those from dunes, suggesting a very fast evolutionary response. Interestingly, a significant interaction between habitat and sex was detected in climbing performance. In addition, lizards from dunes bit harder than those from walls, although sexual differentiation was definitely the main factor driving variation in head functional morphology. Taking into account all the results, we found a complex interaction between natural and sexual selection on whole-organism performance, which are, in some cases, reflected in morphological variation.

Run for your life, but bite for your rights? How interactions between natural and sexual selection shape functional morphology across habitats.

PubMed

Gomes, Verónica; Carretero, Miguel A; Kaliontzopoulou, Antigoni

2018-01-02

A central issue in evolutionary biology is how morphology, performance, and habitat use coevolve. If morphological variation is tightly associated with habitat use, then differences in morphology should affect fitness through their effect on performance within specific habitats. In this study, we investigate how evolutionary forces mold morphological traits and performance differently given the surrounding environment, at the intraspecific level. For this purpose, we selected populations of the lizard Podarcis bocagei from two different habitat types, agricultural walls and dunes, which we expected to reflect saxicolous vs ground-dwelling habits. In the laboratory, we recorded morphological traits as well as performance traits by measuring sprint speed, climbing capacity, maneuverability, and bite force. Our results revealed fast-evolving ecomorphological variation among populations of P. bocagei, where a direct association existed between head morphology and bite performance. However, we could not establish links between limb morphology and locomotor performance at the individual level. Lizards from walls were better climbers than those from dunes, suggesting a very fast evolutionary response. Interestingly, a significant interaction between habitat and sex was detected in climbing performance. In addition, lizards from dunes bit harder than those from walls, although sexual differentiation was definitely the main factor driving variation in head functional morphology. Taking into account all the results, we found a complex interaction between natural and sexual selection on whole-organism performance, which are, in some cases, reflected in morphological variation.

The Structure of Borders in a Small World

PubMed Central

Thiemann, Christian; Theis, Fabian; Grady, Daniel; Brune, Rafael; Brockmann, Dirk

2010-01-01

Territorial subdivisions and geographic borders are essential for understanding phenomena in sociology, political science, history, and economics. They influence the interregional flow of information and cross-border trade and affect the diffusion of innovation and technology. However, it is unclear if existing administrative subdivisions that typically evolved decades ago still reflect the most plausible organizational structure of today. The complexity of modern human communication, the ease of long-distance movement, and increased interaction across political borders complicate the operational definition and assessment of geographic borders that optimally reflect the multi-scale nature of today's human connectivity patterns. What border structures emerge directly from the interplay of scales in human interactions is an open question. Based on a massive proxy dataset, we analyze a multi-scale human mobility network and compute effective geographic borders inherent to human mobility patterns in the United States. We propose two computational techniques for extracting these borders and for quantifying their strength. We find that effective borders only partially overlap with existing administrative borders, and show that some of the strongest mobility borders exist in unexpected regions. We show that the observed structures cannot be generated by gravity models for human traffic. Finally, we introduce the concept of link significance that clarifies the observed structure of effective borders. Our approach represents a novel type of quantitative, comparative analysis framework for spatially embedded multi-scale interaction networks in general and may yield important insight into a multitude of spatiotemporal phenomena generated by human activity. PMID:21124970

The structure of borders in a small world.

PubMed

Thiemann, Christian; Theis, Fabian; Grady, Daniel; Brune, Rafael; Brockmann, Dirk

2010-11-18

Territorial subdivisions and geographic borders are essential for understanding phenomena in sociology, political science, history, and economics. They influence the interregional flow of information and cross-border trade and affect the diffusion of innovation and technology. However, it is unclear if existing administrative subdivisions that typically evolved decades ago still reflect the most plausible organizational structure of today. The complexity of modern human communication, the ease of long-distance movement, and increased interaction across political borders complicate the operational definition and assessment of geographic borders that optimally reflect the multi-scale nature of today's human connectivity patterns. What border structures emerge directly from the interplay of scales in human interactions is an open question. Based on a massive proxy dataset, we analyze a multi-scale human mobility network and compute effective geographic borders inherent to human mobility patterns in the United States. We propose two computational techniques for extracting these borders and for quantifying their strength. We find that effective borders only partially overlap with existing administrative borders, and show that some of the strongest mobility borders exist in unexpected regions. We show that the observed structures cannot be generated by gravity models for human traffic. Finally, we introduce the concept of link significance that clarifies the observed structure of effective borders. Our approach represents a novel type of quantitative, comparative analysis framework for spatially embedded multi-scale interaction networks in general and may yield important insight into a multitude of spatiotemporal phenomena generated by human activity.

Nonlinear amplification of coherent waves in media with soliton-type refractive index pattern.

PubMed

Bugaychuk, S; Conte, R

2012-08-01

We derive the complex Ginzburg-Landau equation for the dynamical self-diffraction of optical waves in a nonlinear cavity. The case of the reflection geometry of wave interaction as well as a medium that possesses the cubic nonlinearity (including a local and a nonlocal nonlinear responses) and the relaxation is considered. A stable localized spatial structure in the form of a "dark" dissipative soliton is formed in the cavity in the steady state. The envelope of the intensity pattern, as well as of the dynamical grating amplitude, takes the shape of a tanh function. The obtained complex Ginzburg-Landau equation describes the dynamics of this envelope; at the same time, the evolution of this spatial structure changes the parameters of the output waves. New effects are predicted in this system due to the transformation of the dissipative soliton which takes place during the interaction of a pulse with a continuous wave, such as retention of the pulse shape during the transmission of impulses in a long nonlinear cavity, and giant amplification of a seed pulse, which takes energy due to redistribution of the pump continuous energy into the signal.

Inhibitory Network Interactions Shape the Auditory Processing of Natural Communication Signals in the Songbird Auditory Forebrain

PubMed Central

Pinaud, Raphael; Terleph, Thomas A.; Tremere, Liisa A.; Phan, Mimi L.; Dagostin, André A.; Leão, Ricardo M.; Mello, Claudio V.; Vicario, David S.

2008-01-01

The role of GABA in the central processing of complex auditory signals is not fully understood. We have studied the involvement of GABAA-mediated inhibition in the processing of birdsong, a learned vocal communication signal requiring intact hearing for its development and maintenance. We focused on caudomedial nidopallium (NCM), an area analogous to parts of the mammalian auditory cortex with selective responses to birdsong. We present evidence that GABAA-mediated inhibition plays a pronounced role in NCM's auditory processing of birdsong. Using immunocytochemistry, we show that approximately half of NCM's neurons are GABAergic. Whole cell patch-clamp recordings in a slice preparation demonstrate that, at rest, spontaneously active GABAergic synapses inhibit excitatory inputs onto NCM neurons via GABAA receptors. Multi-electrode electrophysiological recordings in awake birds show that local blockade of GABAA-mediated inhibition in NCM markedly affects the temporal pattern of song-evoked responses in NCM without modifications in frequency tuning. Surprisingly, this blockade increases the phasic and largely suppresses the tonic response component, reflecting dynamic relationships of inhibitory networks that could include disinhibition. Thus processing of learned natural communication sounds in songbirds, and possibly other vocal learners, may depend on complex interactions of inhibitory networks. PMID:18480371

Keeping Control: The Role of Senescence and Development in Plant Pathogenesis and Defense

PubMed Central

Häffner, Eva; Konietzki, Sandra; Diederichsen, Elke

2015-01-01

Many plant pathogens show interactions with host development. Pathogens may modify plant development according to their nutritional demands. Conversely, plant development influences pathogen growth. Biotrophic pathogens often delay senescence to keep host cells alive, and resistance is achieved by senescence-like processes in the host. Necrotrophic pathogens promote senescence in the host, and preventing early senescence is a resistance strategy of plants. For hemibiotrophic pathogens both patterns may apply. Most signaling pathways are involved in both developmental and defense reactions. Increasing knowledge about the molecular components allows to distinguish signaling branches, cross-talk and regulatory nodes that may influence the outcome of an infection. In this review, recent reports on major molecular players and their role in senescence and in pathogen response are reviewed. Examples of pathosystems with strong developmental implications illustrate the molecular basis of selected control strategies. A study of gene expression in the interaction between the hemibiotrophic vascular pathogen Verticillium longisporum and its cruciferous hosts shows processes that are fine-tuned to counteract early senescence and to achieve resistance. The complexity of the processes involved reflects the complex genetic control of quantitative disease resistance, and understanding the relationship between disease, development and resistance will support resistance breeding. PMID:27135337

Commentary: Fundamental problems with candidate gene-by-environment interaction studies - reflections on Moore and Thoemmes (2016).

PubMed

Border, Richard; Keller, Matthew C

2017-03-01

Moore and Thoemmes elaborate on one particular source of difficulty in the study of candidate gene-by-environment interactions (cG × E): how different biologically plausible configurations of gene-environment covariation can bias estimates of cG × E when not explicitly modeled. However, even if cG × E investigators were able to account for the sources of bias Moore and Thoemmes elaborate, it is unlikely that conventional approaches would yield reliable results. Published cG × E findings to date have generally employed inadequate analytic procedures, have relied on samples orders of magnitude too small to detect plausible effects, and have relied on a particular candidate gene approach that has been unfruitful and largely jettisoned in mainstream genetic analyses of complex traits. Analytic procedures for the study of gene-environment interplay must evolve to meet the challenges that the genetic architecture of complex traits presents, and investigators must collaborate on grander scales if we hope to begin to understand how specific genes and environments combine to affect behavior. © 2017 Association for Child and Adolescent Mental Health.

Functional ecology of soil microbial communities along a glacier forefield in Tierra del Fuego (Chile).

PubMed

Fernández-Martínez, Miguel A; Pointing, Stephen B; Pérez-Ortega, Sergio; Arróniz-Crespo, María; Green, T G Allan; Rozzi, Ricardo; Sancho, Leopoldo G; de Los Ríos, Asunción

2016-09-01

A previously established chronosequence from Pia Glacier forefield in Tierra del Fuego (Chile) containing soils of different ages (from bare soils to forest ones) is analyzed. We used this chronosequence as framework to postulate that microbial successional development would be accompanied by changes in functionality. To test this, the GeoChip functional microarray was used to identify diversity of genes involved in microbial carbon and nitrogen metabolism, as well as other genes related to microbial stress response and biotic interactions. Changes in putative functionality generally reflected succession-related taxonomic composition of soil microbiota. Major shifts in carbon fixation and catabolism were observed, as well as major changes in nitrogen metabolism. At initial microbial dominated succession stages, microorganisms could be mainly involved in pathways that help to increase nutrient availability, while more complex microbial transformations such as denitrification and methanogenesis, and later degradation of complex organic substrates, could be more prevalent at vegetated successional states. Shifts in virus populations broadly reflected changes in microbial diversity. Conversely, stress response pathways appeared relatively well conserved for communities along the entire chronosequence. We conclude that nutrient utilization is likely the major driver of microbial succession in these soils. [Int Microbiol 19(3):161-173 (2016)]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Climate sensitivity across marine domains of life: limits to evolutionary adaptation shape species interactions.

PubMed

Storch, Daniela; Menzel, Lena; Frickenhaus, Stephan; Pörtner, Hans-O

2014-10-01

Organisms in all domains, Archaea, Bacteria, and Eukarya will respond to climate change with differential vulnerabilities resulting in shifts in species distribution, coexistence, and interactions. The identification of unifying principles of organism functioning across all domains would facilitate a cause and effect understanding of such changes and their implications for ecosystem shifts. For example, the functional specialization of all organisms in limited temperature ranges leads us to ask for unifying functional reasons. Organisms also specialize in either anoxic or various oxygen ranges, with animals and plants depending on high oxygen levels. Here, we identify thermal ranges, heat limits of growth, and critically low (hypoxic) oxygen concentrations as proxies of tolerance in a meta-analysis of data available for marine organisms, with special reference to domain-specific limits. For an explanation of the patterns and differences observed, we define and quantify a proxy for organismic complexity across species from all domains. Rising complexity causes heat (and hypoxia) tolerances to decrease from Archaea to Bacteria to uni- and then multicellular Eukarya. Within and across domains, taxon-specific tolerance limits likely reflect ultimate evolutionary limits of its species to acclimatization and adaptation. We hypothesize that rising taxon-specific complexities in structure and function constrain organisms to narrower environmental ranges. Low complexity as in Archaea and some Bacteria provide life options in extreme environments. In the warmest oceans, temperature maxima reach and will surpass the permanent limits to the existence of multicellular animals, plants and unicellular phytoplankter. Smaller, less complex unicellular Eukarya, Bacteria, and Archaea will thus benefit and predominate even more in a future, warmer, and hypoxic ocean. © 2014 John Wiley & Sons Ltd.

Van der Waals Interactions Involving Proteins

NASA Technical Reports Server (NTRS)

Roth, Charles M.; Neal, Brian L.; Lenhoff, Abraham M.

1996-01-01

Van der Waals (dispersion) forces contribute to interactions of proteins with other molecules or with surfaces, but because of the structural complexity of protein molecules, the magnitude of these effects is usually estimated based on idealized models of the molecular geometry, e.g., spheres or spheroids. The calculations reported here seek to account for both the geometric irregularity of protein molecules and the material properties of the interacting media. Whereas the latter are found to fall in the generally accepted range, the molecular shape is shown to cause the magnitudes of the interactions to differ significantly from those calculated using idealized models. with important consequences. First, the roughness of the molecular surface leads to much lower average interaction energies for both protein-protein and protein-surface cases relative to calculations in which the protein molecule is approximated as a sphere. These results indicate that a form of steric stabilization may be an important effect in protein solutions. Underlying this behavior is appreciable orientational dependence, one reflection of which is that molecules of complementary shape are found to exhibit very strong attractive dispersion interactions. Although this has been widely discussed previously in the context of molecular recognition processes, the broader implications of these phenomena may also be important at larger molecular separations, e.g., in the dynamics of aggregation, precipitation, and crystal growth.

Educational Process Reflection (EPR): An Evaluation of a Model for Professional Development Concerning Social Interaction and Educational Climate in the Swedish Preschool

ERIC Educational Resources Information Center

Bygdeson-Larsson, Kerstin

2006-01-01

Educational process reflection (EPR) is a professional development model aimed at supporting preschool teachers reflecting on and changing their practice. A particular focus is on interaction between practitioners and children, and between the children themselves. In this article, I first describe the theoretical frameworks that helped shape EPR,…

Stable isotope evidence for hydrologic conditions during regional metamorphism in the Panamint Mountains, California

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

Bergfeld, D.; Nabelek, P.I.; Labotka, T.C.

1992-01-01

The Kingston Peak Formation forms part of the Panamint Mountains, California, metamorphic core-complex. Peak tremolite-grade metamorphism as exhibited in Wildrose Canyon occurred in the Jurassic; a retrograde thermal event may have occurred in the Cretaceous. The formation consists dominantly of interbedded siliceous limestones and graphitic calcareous schists. Stable isotopic analysis shows two distinct groups of data. delta O-18 values of calcite from the limestones range between 15.3 and 17.3[per thousand], probably reflecting their original Proterozoic depositional values. Likewise the delta C-13 values are also unshifted, ranging from +1% to +3.8%o. In contrast, delta O-18 values of calcite from the schistsmore » are for the most part > 20[per thousand]. These high values could reflect the original depostional conditions; however, they may be due to equilibration with silicate minerals which range from 14.9 to 17.9[per thousand]. Overall, the combined oxygen and carbon isotopic data indicate that most isotopic changes can be explained by closed-system equilibration. Only a limited amount of interaction with externally-derived fluids during metamorphism is evident in the isotopic data. The interaction may have been confined to vicinities of faults and fractures which are common in Wildrose Canyon.« less

Brightness-compensated 3-D optical flow algorithm for monitoring cochlear motion patterns

NASA Astrophysics Data System (ADS)

von Tiedemann, Miriam; Fridberger, Anders; Ulfendahl, Mats; de Monvel, Jacques Boutet

2010-09-01

A method for three-dimensional motion analysis designed for live cell imaging by fluorescence confocal microscopy is described. The approach is based on optical flow computation and takes into account brightness variations in the image scene that are not due to motion, such as photobleaching or fluorescence variations that may reflect changes in cellular physiology. The 3-D optical flow algorithm allowed almost perfect motion estimation on noise-free artificial sequences, and performed with a relative error of <10% on noisy images typical of real experiments. The method was applied to a series of 3-D confocal image stacks from an in vitro preparation of the guinea pig cochlea. The complex motions caused by slow pressure changes in the cochlear compartments were quantified. At the surface of the hearing organ, the largest motion component was the transverse one (normal to the surface), but significant radial and longitudinal displacements were also present. The outer hair cell displayed larger radial motion at their basolateral membrane than at their apical surface. These movements reflect mechanical interactions between different cellular structures, which may be important for communicating sound-evoked vibrations to the sensory cells. A better understanding of these interactions is important for testing realistic models of cochlear mechanics.

Brightness-compensated 3-D optical flow algorithm for monitoring cochlear motion patterns.

PubMed

von Tiedemann, Miriam; Fridberger, Anders; Ulfendahl, Mats; de Monvel, Jacques Boutet

2010-01-01

A method for three-dimensional motion analysis designed for live cell imaging by fluorescence confocal microscopy is described. The approach is based on optical flow computation and takes into account brightness variations in the image scene that are not due to motion, such as photobleaching or fluorescence variations that may reflect changes in cellular physiology. The 3-D optical flow algorithm allowed almost perfect motion estimation on noise-free artificial sequences, and performed with a relative error of <10% on noisy images typical of real experiments. The method was applied to a series of 3-D confocal image stacks from an in vitro preparation of the guinea pig cochlea. The complex motions caused by slow pressure changes in the cochlear compartments were quantified. At the surface of the hearing organ, the largest motion component was the transverse one (normal to the surface), but significant radial and longitudinal displacements were also present. The outer hair cell displayed larger radial motion at their basolateral membrane than at their apical surface. These movements reflect mechanical interactions between different cellular structures, which may be important for communicating sound-evoked vibrations to the sensory cells. A better understanding of these interactions is important for testing realistic models of cochlear mechanics.

Origin of attraction in p-benzoquinone complexes with benzene and p-hydroquinone.

PubMed

Tsuzuki, Seiji; Uchimaru, Tadafumi; Ono, Taizo

2017-08-30

The origin of the attraction in charge-transfer complexes (a p-hydroquinone-p-benzoquinone complex and benzene complexes with benzoquinone, tetracyanoethylene and Br 2 ) was analyzed using distributed multipole analysis and symmetry-adapted perturbation theory. Both methods show that the dispersion interactions are the primary source of the attraction in these charge-transfer complexes followed by the electrostatic interactions. The natures of the intermolecular interactions in these complexes are close to the π/π interactions of neutral aromatic molecules. The electrostatic interactions play important roles in determining the magnitude of the attraction. The contribution of charge-transfer interactions to the attraction is not large compared with the dispersion interactions in these complexes.

Selective attention determines emotional responses to novel visual stimuli.

PubMed

Raymond, Jane E; Fenske, Mark J; Tavassoli, Nader T

2003-11-01

Distinct complex brain systems support selective attention and emotion, but connections between them suggest that human behavior should reflect reciprocal interactions of these systems. Although there is ample evidence that emotional stimuli modulate attentional processes, it is not known whether attention influences emotional behavior. Here we show that evaluation of the emotional tone (cheery/dreary) of complex but meaningless visual patterns can be modulated by the prior attentional state (attending vs. ignoring) used to process each pattern in a visual selection task. Previously ignored patterns were evaluated more negatively than either previously attended or novel patterns. Furthermore, this emotional devaluation of distracting stimuli was robust across different emotional contexts and response scales. Finding that negative affective responses are specifically generated for ignored stimuli points to a new functional role for attention and elaborates the link between attention and emotion. This finding also casts doubt on the conventional marketing wisdom that any exposure is good exposure.

Reverse Ecology: from systems to environments and back.

PubMed

Levy, Roie; Borenstein, Elhanan

2012-01-01

The structure of complex biological systems reflects not only their function but also the environments in which they evolved and are adapted to. Reverse Ecology-an emerging new frontier in Evolutionary Systems Biology-aims to extract this information and to obtain novel insights into an organism's ecology. The Reverse Ecology framework facilitates the translation of high-throughput genomic data into large-scale ecological data, and has the potential to transform ecology into a high-throughput field. In this chapter, we describe some of the pioneering work in Reverse Ecology, demonstrating how system-level analysis of complex biological networks can be used to predict the natural habitats of poorly characterized microbial species, their interactions with other species, and universal patterns governing the adaptation of organisms to their environments. We further present several studies that applied Reverse Ecology to elucidate various aspects of microbial ecology, and lay out exciting future directions and potential future applications in biotechnology, biomedicine, and ecological engineering.

Polypeptide Translocation Through the Mitochondrial TOM Channel: Temperature-Dependent Rates at the Single-Molecule Level.

PubMed

Mahendran, Kozhinjampara R; Lamichhane, Usha; Romero-Ruiz, Mercedes; Nussberger, Stephan; Winterhalter, Mathias

2013-01-03

The TOM protein complex facilitates the transfer of nearly all mitochondrial preproteins across outer mitochondrial membranes. Here we characterized the effect of temperature on facilitated translocation of a mitochondrial presequence peptide pF1β. Ion current fluctuations analysis through single TOM channels revealed thermodynamic and kinetic parameters of substrate binding and allowed determining the energy profile of peptide translocation. The activation energy for the on-rate and off-rate of the presequence peptide into the TOM complex was symmetric with respect to the electric field and estimated to be about 15 and 22 kT per peptide. These values are above that expected for free diffusion of ions in water (6 kT) and reflect the stronger interaction in the channel. Both values are in the range for typical enzyme kinetics and suggest one process without involving large conformational changes within the channel protein.

Modeling hemoglobin at optical frequency using the unconditionally stable fundamental ADI-FDTD method.

PubMed

Heh, Ding Yu; Tan, Eng Leong

2011-04-12

This paper presents the modeling of hemoglobin at optical frequency (250 nm - 1000 nm) using the unconditionally stable fundamental alternating-direction-implicit finite-difference time-domain (FADI-FDTD) method. An accurate model based on complex conjugate pole-residue pairs is proposed to model the complex permittivity of hemoglobin at optical frequency. Two hemoglobin concentrations at 15 g/dL and 33 g/dL are considered. The model is then incorporated into the FADI-FDTD method for solving electromagnetic problems involving interaction of light with hemoglobin. The computation of transmission and reflection coefficients of a half space hemoglobin medium using the FADI-FDTD validates the accuracy of our model and method. The specific absorption rate (SAR) distribution of human capillary at optical frequency is also shown. While maintaining accuracy, the unconditionally stable FADI-FDTD method exhibits high efficiency in modeling hemoglobin.

Modeling hemoglobin at optical frequency using the unconditionally stable fundamental ADI-FDTD method

PubMed Central

Heh, Ding Yu; Tan, Eng Leong

2011-01-01

This paper presents the modeling of hemoglobin at optical frequency (250 nm – 1000 nm) using the unconditionally stable fundamental alternating-direction-implicit finite-difference time-domain (FADI-FDTD) method. An accurate model based on complex conjugate pole-residue pairs is proposed to model the complex permittivity of hemoglobin at optical frequency. Two hemoglobin concentrations at 15 g/dL and 33 g/dL are considered. The model is then incorporated into the FADI-FDTD method for solving electromagnetic problems involving interaction of light with hemoglobin. The computation of transmission and reflection coefficients of a half space hemoglobin medium using the FADI-FDTD validates the accuracy of our model and method. The specific absorption rate (SAR) distribution of human capillary at optical frequency is also shown. While maintaining accuracy, the unconditionally stable FADI-FDTD method exhibits high efficiency in modeling hemoglobin. PMID:21559129

[Interaction of trivaline with single-stranded polyribonucleotides].

PubMed

Strel'tsov, S A; Lysov, Iu P; Semenov, T E; Vengerov, Iu Iu; Khorlin, A A; Surovaia, A N; Gurskiĭ, G V

1991-01-01

Binding of tripeptide H-Val3-(NH)2-Dns (TVP) to polyribonucleotides was studied by fluorescence methods, circular and flow linear dichroism, equilibrium dialysis and electron microscopy. It was found that TVP binds to poly(U) in monomer, dimer and tetramer forms with binding constants of about 10(3), 40, 18.10(4) M, respectively. The cooperativity parameter for peptide dimer binding is 2000. The peptide forms tetramer complexes with poly(A), poly(C), poly(G) also. The formation of a complex between the peptide tetramer and nucleic acid is accompanied by a significant increase in the fluorescence intensity. The cooperative binding of TVP dimers to poly(U), poly(A), poly(C) is accompanied by a dramatic decrease in the flexibility of polynucleotide chains. However, it has a small effect (if any) on the flexibility of the poly(G) chain. The observed similarity of thermodynamic, optical and hydrodynamic++ properties of TVP complexes with single-stranded and double-stranded nucleic acids may reflect a similarity in the geometries of peptide complexes with nucleic acids. Electron microscopy studies show that peptide binding to poly(U) and dsDNA leads to compactization of the nucleic acids caused by interaction between the peptide tetramers bound to a nucleic acid. At the first stage of the compactization process the well-organized rod-like particles are formed, each consisting of one or more single-stranded polynucleotide fibers. Increasing the peptide concentration stimulates a side-by-side association and folding of the rods with the formation of macromolecular "leech-like" structures with the thickness of 20-50 nm.

A review of assertions about the processes and outcomes of social learning in natural resource management.

PubMed

Cundill, G; Rodela, R

2012-12-30

Social learning has become a central theme in natural resource management. This growing interest is underpinned by a number of assertions about the outcomes of social learning, and about the processes that support these outcomes. Yet researchers and practitioners who seek to engage with social learning through the natural resource management literature often become disorientated by the myriad processes and outcomes that are identified. We trace the roots of current assertions about the processes and outcomes of social learning in natural resource management, and assess the extent to which there is an emerging consensus on these assertions. Results suggest that, on the one hand, social learning is described as taking place through deliberative interactions amongst multiple stakeholders. During these interactions, it is argued that participants learn to work together and build relationships that allow for collective action. On the other hand, social learning is described as occurring through deliberate experimentation and reflective practice. During these iterative cycles of action, monitoring and reflection, participants learn how to cope with uncertainty when managing complex systems. Both of these processes, and their associated outcomes, are referred to as social learning. Where, therefore, should researchers and practitioners focus their attention? Results suggest that there is an emerging consensus that processes that support social learning involve sustained interaction between stakeholders, on-going deliberation and the sharing of knowledge in a trusting environment. There is also an emerging consensus that the key outcome of such learning is improved decision making underpinned by a growing awareness of human-environment interactions, better relationships and improved problem-solving capacities for participants. Copyright © 2012 Elsevier Ltd. All rights reserved.

Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions.

PubMed

Liu, Zhihai; Su, Minyi; Han, Li; Liu, Jie; Yang, Qifan; Li, Yan; Wang, Renxiao

2017-02-21

In structure-based drug design, scoring functions are widely used for fast evaluation of protein-ligand interactions. They are often applied in combination with molecular docking and de novo design methods. Since the early 1990s, a whole spectrum of protein-ligand interaction scoring functions have been developed. Regardless of their technical difference, scoring functions all need data sets combining protein-ligand complex structures and binding affinity data for parametrization and validation. However, data sets of this kind used to be rather limited in terms of size and quality. On the other hand, standard metrics for evaluating scoring function used to be ambiguous. Scoring functions are often tested in molecular docking or even virtual screening trials, which do not directly reflect the genuine quality of scoring functions. Collectively, these underlying obstacles have impeded the invention of more advanced scoring functions. In this Account, we describe our long-lasting efforts to overcome these obstacles, which involve two related projects. On the first project, we have created the PDBbind database. It is the first database that systematically annotates the protein-ligand complexes in the Protein Data Bank (PDB) with experimental binding data. This database has been updated annually since its first public release in 2004. The latest release (version 2016) provides binding data for 16 179 biomolecular complexes in PDB. Data sets provided by PDBbind have been applied to many computational and statistical studies on protein-ligand interaction and various subjects. In particular, it has become a major data resource for scoring function development. On the second project, we have established the Comparative Assessment of Scoring Functions (CASF) benchmark for scoring function evaluation. Our key idea is to decouple the "scoring" process from the "sampling" process, so scoring functions can be tested in a relatively pure context to reflect their quality. In our latest work on this track, i.e. CASF-2013, the performance of a scoring function was quantified in four aspects, including "scoring power", "ranking power", "docking power", and "screening power". All four performance tests were conducted on a test set containing 195 high-quality protein-ligand complexes selected from PDBbind. A panel of 20 standard scoring functions were tested as demonstration. Importantly, CASF is designed to be an open-access benchmark, with which scoring functions developed by different researchers can be compared on the same grounds. Indeed, it has become a popular choice for scoring function validation in recent years. Despite the considerable progress that has been made so far, the performance of today's scoring functions still does not meet people's expectations in many aspects. There is a constant demand for more advanced scoring functions. Our efforts have helped to overcome some obstacles underlying scoring function development so that the researchers in this field can move forward faster. We will continue to improve the PDBbind database and the CASF benchmark in the future to keep them as useful community resources.

Convergent functional architecture of the superior parietal lobule unraveled with multimodal neuroimaging approaches.

PubMed

Wang, Jiaojian; Yang, Yong; Fan, Lingzhong; Xu, Jinping; Li, Changhai; Liu, Yong; Fox, Peter T; Eickhoff, Simon B; Yu, Chunshui; Jiang, Tianzi

2015-01-01

The superior parietal lobule (SPL) plays a pivotal role in many cognitive, perceptive, and motor-related processes. This implies that a mosaic of distinct functional and structural subregions may exist in this area. Recent studies have demonstrated that the ongoing spontaneous fluctuations in the brain at rest are highly structured and, like coactivation patterns, reflect the integration of cortical locations into long-distance networks. This suggests that the internal differentiation of a complex brain region may be revealed by interaction patterns that are reflected in different neuroimaging modalities. On the basis of this perspective, we aimed to identify a convergent functional organization of the SPL using multimodal neuroimaging approaches. The SPL was first parcellated based on its structural connections as well as on its resting-state connectivity and coactivation patterns. Then, post hoc functional characterizations and connectivity analyses were performed for each subregion. The three types of connectivity-based parcellations consistently identified five subregions in the SPL of each hemisphere. The two anterior subregions were found to be primarily involved in action processes and in visually guided visuomotor functions, whereas the three posterior subregions were primarily associated with visual perception, spatial cognition, reasoning, working memory, and attention. This parcellation scheme for the SPL was further supported by revealing distinct connectivity patterns for each subregion in all the used modalities. These results thus indicate a convergent functional architecture of the SPL that can be revealed based on different types of connectivity and is reflected by different functions and interactions. © 2014 Wiley Periodicals, Inc.

Nonlinear viscous higher harmonics generation due to incident and reflecting internal wave beam collision

NASA Astrophysics Data System (ADS)

Aksu, Anil A.

2017-09-01

In this paper, we have considered the non-linear effects arising due to the collision of incident and reflected internal wave beams. It has already been shown analytically [Tabaei et al., "Nonlinear effects in reflecting and colliding internal wave beams," J. Fluid Mech. 526, 217-243 (2005)] and numerically [Rodenborn et al., "Harmonic generation by reflecting internal waves," Phys. Fluids 23, 026601 (2011)] that the internal wave beam collision generates the higher harmonics and mean flow in a linear stratification. In this paper, similar to previous analytical work, small amplitude wave theory is employed; however, it is formulated from energetics perspective which allows considering internal wave beams as the product of slowly varying amplitude and fast complex exponential. As a result, the mean energy propagation equation for the second harmonic wave is obtained. Finally, a similar dependence on the angle of incidence is obtained for the non-linear energy transfer to the second harmonic with previous analyses. A possible physical mechanism for this angle dependence on the second harmonic generation is also discussed here. In addition to previous studies, the viscous effects are also included in the mean energy propagation equation for the incident, the reflecting, and the second harmonic waves. Moreover, even though the mean flow obtained here is only confined to the interaction region, it is also affected by viscosity via the decay in the incident and the reflecting internal wave beams. Furthermore, a framework for the non-linear harmonic generation in non-linear stratification is also proposed here.

Quantifying Trading Behavior in Financial Markets Using Google Trends

NASA Astrophysics Data System (ADS)

Preis, Tobias; Moat, Helen Susannah; Stanley, H. Eugene

2013-04-01

Crises in financial markets affect humans worldwide. Detailed market data on trading decisions reflect some of the complex human behavior that has led to these crises. We suggest that massive new data sources resulting from human interaction with the Internet may offer a new perspective on the behavior of market participants in periods of large market movements. By analyzing changes in Google query volumes for search terms related to finance, we find patterns that may be interpreted as ``early warning signs'' of stock market moves. Our results illustrate the potential that combining extensive behavioral data sets offers for a better understanding of collective human behavior.

The "doctor-customer" relationship: Hippocrates in the modern marketplace.

PubMed

Mulhall, Kevin J; Ahmed, Aftab; Masterson, Eric

2002-01-01

We performed a consecutive survey of 100 people presenting to a hospital injury clinic to ascertain their attitude to terminology currently used to describe them in our own institution and in the international literature. The results of this demonstrated that the subjects significantly preferred the traditional assignation "patient" rather than terms such as client or customer. This finding reflects the need to remember peoples' attitudes and expectations from their consultation with their doctor. Although business models undoubtedly help in the provision of an efficient health care service, remaining at the centre of this encounter is a doctor-patient relationship that involves a more complex interaction than simply a market transaction.

Quantifying Trading Behavior in Financial Markets Using Google Trends

PubMed Central

Preis, Tobias; Moat, Helen Susannah; Stanley, H. Eugene

2013-01-01

Crises in financial markets affect humans worldwide. Detailed market data on trading decisions reflect some of the complex human behavior that has led to these crises. We suggest that massive new data sources resulting from human interaction with the Internet may offer a new perspective on the behavior of market participants in periods of large market movements. By analyzing changes in Google query volumes for search terms related to finance, we find patterns that may be interpreted as “early warning signs” of stock market moves. Our results illustrate the potential that combining extensive behavioral data sets offers for a better understanding of collective human behavior. PMID:23619126

Radical-lanthanide ferromagnetic interaction in a T bIII bis-phthalocyaninato complex

NASA Astrophysics Data System (ADS)

Komijani, Dorsa; Ghirri, Alberto; Bonizzoni, Claudio; Klyatskaya, Svetlana; Moreno-Pineda, Eufemio; Ruben, Mario; Soncini, Alessandro; Affronte, Marco; Hill, Stephen

2018-02-01

Recent studies have highlighted the importance of organic ligands in the field of molecular spintronics, via which delocalized electron-spin density can mediate magnetic coupling to otherwise localized 4 f moments of lanthanide ions, which show tremendous potential for single-molecule device applications. To this end, high-field/high-frequency electron paramagnetic resonance (EPR) spectroscopy is employed to study a neutral terbium bis-phthalocyaninato metalorganic complex, [TbPc2 ] 0, with the aim of understanding the magnetic interaction between the Ising-like moment of the lanthanide ion and the unpaired spin density on the coordinating organic radical ligand. The measurements were performed on a previously unknown [TbPc2 ] 0 structural phase crystallizing in the Pnma space group. EPR measurements on powder samples of [TbPc2 ] 0 reveal an anisotropic spectrum, which is attributed to the spin-1/2 radical coupled weakly to the EPR-silent T bIII ion. Extensive double-axis rotation studies on a single crystal reveal two independent spin-1/2 signals with differently oriented (albeit identical) uniaxial g -tensors, in complete agreement with x-ray structural studies that indicate two molecular orientations within the unit cell. The easy-axis nature of the radical EPR spectra thus reflects the coupling to the Ising-like T bIII moment. This is corroborated by studies of the isostructural [YPc2 ] 0 analog (where Y is nonmagnetic yttrium), which gives a completely isotropic radical EPR signal. The experimental results for the terbium complex are well explained on the basis of an effective model that introduces a weak ferromagnetic Heisenberg coupling between an isotropic spin-1/2 and an anisotropic spin-orbital moment, J =6 , that mimics the known, strong easy-axis Tb ⋯P c2 crystal-field interaction.

Harm reduction as a complex adaptive system: A dynamic framework for analyzing Tanzanian policies concerning heroin use

PubMed Central

Ratliff, Eric A.; Kaduri, Pamela; Masao, Frank; Mbwambo, Jessie K.K.; McCurdy, Sheryl A.

2016-01-01

Contrary to popular belief, policies on drug use are not always based on scientific evidence or composed in a rational manner. Rather, decisions concerning drug policies reflect the negotiation of actors’ ambitions, values, and facts as they organize in different ways around the perceived problems associated with illicit drug use. Drug policy is thus best represented as a complex adaptive system (CAS) that is dynamic, self-organizing, and coevolving. In this analysis, we use a CAS framework to examine how harm reduction emerged around heroin trafficking and use in Tanzania over the past thirty years (1985-present). This account is an organizational ethnography based on of the observant participation of the authors as actors within this system. We review the dynamic history and self-organizing nature of harm reduction, noting how interactions among system actors and components have coevolved with patterns of heroin us, policing, and treatment activities over time. Using a CAS framework, we describe harm reduction as a complex process where ambitions, values, facts, and technologies interact in the Tanzanian socio-political environment. We review the dynamic history and self-organizing nature of heroin policies, noting how the interactions within and between competing prohibitionist and harm reduction policies have changed with patterns of heroin use, policing, and treatment activities over time. Actors learn from their experiences to organize with other actors, align their values and facts, and implement new policies. Using a CAS approach provides researchers and policy actors a better understanding of patterns and intricacies in drug policy. This knowledge of how the system works can help improve the policy process through adaptive action to introduce new actors, different ideas, and avenues for communication into the system. PMID:26790689

Harm reduction as a complex adaptive system: A dynamic framework for analyzing Tanzanian policies concerning heroin use.

PubMed

Ratliff, Eric A; Kaduri, Pamela; Masao, Frank; Mbwambo, Jessie K K; McCurdy, Sheryl A

2016-04-01

Contrary to popular belief, policies on drug use are not always based on scientific evidence or composed in a rational manner. Rather, decisions concerning drug policies reflect the negotiation of actors' ambitions, values, and facts as they organize in different ways around the perceived problems associated with illicit drug use. Drug policy is thus best represented as a complex adaptive system (CAS) that is dynamic, self-organizing, and coevolving. In this analysis, we use a CAS framework to examine how harm reduction emerged around heroin trafficking and use in Tanzania over the past thirty years (1985-present). This account is an organizational ethnography based on of the observant participation of the authors as actors within this system. We review the dynamic history and self-organizing nature of harm reduction, noting how interactions among system actors and components have coevolved with patterns of heroin us, policing, and treatment activities over time. Using a CAS framework, we describe harm reduction as a complex process where ambitions, values, facts, and technologies interact in the Tanzanian sociopolitical environment. We review the dynamic history and self-organizing nature of heroin policies, noting how the interactions within and between competing prohibitionist and harm reduction policies have changed with patterns of heroin use, policing, and treatment activities over time. Actors learn from their experiences to organize with other actors, align their values and facts, and implement new policies. Using a CAS approach provides researchers and policy actors a better understanding of patterns and intricacies in drug policy. This knowledge of how the system works can help improve the policy process through adaptive action to introduce new actors, different ideas, and avenues for communication into the system. Copyright © 2015 Elsevier B.V. All rights reserved.

Genetically encoded photocross-linkers determine the biological binding site of exendin-4 peptide in the N-terminal domain of the intact human glucagon-like peptide-1 receptor (GLP-1R)

PubMed Central

Koole, Cassandra; Reynolds, Christopher A.; Mobarec, Juan C.; Hick, Caroline; Sexton, Patrick M.; Sakmar, Thomas P.

2017-01-01

The glucagon-like peptide-1 receptor (GLP-1R) is a key therapeutic target in the management of type II diabetes mellitus, with actions including regulation of insulin biosynthesis and secretion, promotion of satiety, and preservation of β-cell mass. Like most class B G protein-coupled receptors (GPCRs), there is limited knowledge linking biological activity of the GLP-1R with the molecular structure of an intact, full-length, and functional receptor·ligand complex. In this study, we have utilized genetic code expansion to site-specifically incorporate the photoactive amino acid p-azido-l-phenylalanine (azF) into N-terminal residues of a full-length functional human GLP-1R in mammalian cells. UV-mediated photolysis of azF was then carried out to induce targeted photocross-linking to determine the proximity of the azido group in the mutant receptor with the peptide exendin-4. Cross-linking data were compared directly with the crystal structure of the isolated N-terminal extracellular domain of the GLP-1R in complex with exendin(9–39), revealing both similarities as well as distinct differences in the mode of interaction. Generation of a molecular model to accommodate the photocross-linking constraints highlights the potential influence of environmental conditions on the conformation of the receptor·peptide complex, including folding dynamics of the peptide and formation of dimeric and higher order oligomeric receptor multimers. These data demonstrate that crystal structures of isolated receptor regions may not give a complete reflection of peptide/receptor interactions and should be combined with additional experimental constraints to reveal peptide/receptor interactions occurring in the dynamic, native, and full-length receptor state. PMID:28283573

In vitro DNA binding studies of therapeutic and prophylactic drug citral.

PubMed

Alam, Md Fazle; Varshney, Supriya; Khan, Masood Alam; Laskar, Amaj Ahmed; Younus, Hina

2018-07-01

The study of drug-DNA interactions is of great importance, as it paves the way towards the design of better therapeutic agents. Here, the interaction of DNA with a therapeutic and prophylactic drug citral has been studied. We have attempted to ascertain the mode of binding of citral with calf thymus DNA (Ct-DNA) through various biophysical techniques. Analysis of the UV-visible absorbance spectra and fluorescence spectra indicated the formation of a complex between citral and Ct-DNA. Competitive binding assays with ethidium bromide (EB), acridine orange (AO) and Hoechst 33258 reflected that citral possibly intercalates within the Ct-DNA. These observations were further confirmed by circular dichroism (CD) spectral analysis, viscosity measurements, DNA melting and molecular docking studies. This study is expected to contribute to a better understanding of molecular mechanisms of citral, and design of new drugs in the future. Copyright © 2018 Elsevier B.V. All rights reserved.

Fourier-transform infrared spectroscopy for rapid screening and live-cell monitoring: application to nanotoxicology.

PubMed

Sundaram, S K; Sacksteder, Colette A; Weber, Thomas J; Riley, Brian J; Addleman, R Shane; Harrer, Bruce J; Peterman, John W

2013-01-01

A significant challenge to realize the full potential of nanotechnology for therapeutic and diagnostic applications is to understand and evaluate how live cells interact with an external stimulus, such as a nanosized particle, and the toxicity and broad risk associated with these stimuli. It is difficult to capture the complexity and dynamics of these interactions by following omics-based approaches exclusively, which can be expensive and time-consuming. Attenuated total reflectance-Fourier transform infrared spectroscopy is well suited to provide noninvasive live-cell monitoring of cellular responses to potentially toxic nanosized particles or other stimuli. This alternative approach provides the ability to carry out rapid toxicity screenings and nondisruptive monitoring of live-cell cultures. We review the technical basis of the approach, the instrument configuration and interface with the biological media, the various effects that impact the data, subsequent data analysis and toxicity, and present some preliminary results on live-cell monitoring.

Science diplomacy: Investigating the perspective of scholars on politics-science collaboration in international affairs.

PubMed

Fähnrich, Birte

2017-08-01

Science diplomacy is a widely practiced area of international affairs, but academic research is rather sparse. The role of academia within this field of politics-science interaction has hardly been considered. This article analyzes this scholarly perspective: Based on a literature review, a case study of a German science diplomacy program is used to explore objectives, benefits, and constraints of science diplomacy for participating scholars. While political approaches suggest an ideal world where both sides profit from the collaboration, the findings of the case study point to another conclusion which shows that the interaction of scholars and officials in science diplomacy is far more complex. Thus, the contribution is regarded as both a useful starting point for further research and for a critical reflection of academics and politicians in science diplomacy practice to gauge what can be expected from the collaboration and what cannot.

Orientations to Reflective Practice.

ERIC Educational Resources Information Center

Wellington, Bud; Austin, Patricia

1996-01-01

Delineates five orientations to reflective practice: immediate, technical, deliberative, dialectic, and transpersonal, each reflecting different social science bases and beliefs and values about education. Views them as interactive, interdependent, noncompeting, aspects of reflective practice. (SK)

Complex Responses of Intertidal Molluscan Embryos to a Warming and Acidifying Ocean in the Presence of UV Radiation

PubMed Central

Davis, Andrew R.; Coleman, Daniel; Broad, Allison; Byrne, Maria; Dworjanyn, Symon A.; Przeslawski, Rachel

2013-01-01

Climate change and ocean acidification will expose marine organisms to synchronous multiple stressors, with early life stages being potentially most vulnerable to changing environmental conditions. We simultaneously exposed encapsulated molluscan embryos to three abiotic stressors—acidified conditions, elevated temperate, and solar UV radiation in large outdoor water tables in a multifactorial design. Solar UV radiation was modified with plastic filters, while levels of the other factors reflected IPCC predictions for near-future change. We quantified mortality and the rate of embryonic development for a mid-shore littorinid, Bembicium nanum, and low-shore opisthobranch, Dolabrifera brazieri. Outcomes were consistent for these model species with embryos faring significantly better at 26°C than 22°C. Mortality sharply increased at the lowest temperature (22°C) and lowest pH (7.6) examined, producing a significant interaction. Under these conditions mortality approached 100% for each species, representing a 2- to 4-fold increase in mortality relative to warm (26°C) non-acidified conditions. Predictably, development was more rapid at the highest temperature but this again interacted with acidified conditions. Development was slowed under acidified conditions at the lowest temperature. The presence of UV radiation had minimal impact on the outcomes, only slowing development for the littorinid and not interacting with the other factors. Our findings suggest that a warming ocean, at least to a threshold, may compensate for the effects of decreasing pH for some species. It also appears that stressors will interact in complex and unpredictable ways in a changing climate. PMID:23405238

Structural-conformational aspects of tRNA complexation with chloroethyl nitrosourea derivatives: A molecular modeling and spectroscopic investigation.

PubMed

Agarwal, Shweta; Tyagi, Gunjan; Chadha, Deepti; Mehrotra, Ranjana

2017-01-01

Chloroethyl nitrosourea derivatives (CENUs) represent an important family of anticancer chemotherapeutic agents, which are used in the treatment of different types of cancer such as brain tumors, resistant or relapsed Hodgkin's disease, small cell lung cancer and malignant melanoma. This work focuses towards understanding the interaction of chloroethyl nitrosourea derivatives; lomustine, nimustine and semustine with tRNA using spectroscopic approach in order to elucidate their auxiliary anticancer action mechanism inside the cell. Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR), Fourier transform infrared difference spectroscopy, circular dichroism spectroscopy and UV-visible spectroscopy were employed to investigate the binding parameters of tRNA-CENUs complexation. Results of present study demonstrate that all CENUs, studied here, interact with tRNA through guanine nitrogenous base residues and possibly further crosslink cytosine residues in paired region of tRNA. Moreover, spectral data collected for nimustine-tRNA and semustine-tRNA complex formation indicates towards the groove-directed-alkylation as their anti-malignant action, which involves the participation of uracil moiety located in major groove of tRNA. Besides this, tRNA-CENUs adduct formation did not alter the native conformation of biopolymer and tRNA remains in A-form after its interaction with all three nitrosourea derivatives studied. The binding constants (K a ) estimated for tRNA complexation with lomustine, nimustine and semustine are 2.55×10 2 M -1 , 4.923×10 2 M -1 and 4.223×10 2 M -1 respectively, which specify weak type of CENU's binding with tRNA. Moreover, molecular modeling simulations were also performed to predict preferential binding orientation of CENUs with tRNA that corroborates well with spectral outcomes. The findings, presented here, recognize tRNA binding properties of CENUs that can further help in rational designing of more specific and efficient RNA targeted chemotherapeutic agents. Copyright © 2016 Elsevier B.V. All rights reserved.

UV-vis spectroscopy and colorimetric models for detecting anthocyanin-metal complexes in plants: An overview of in vitro and in vivo techniques.

PubMed

Fedenko, Volodymyr S; Shemet, Sergiy A; Landi, Marco

2017-05-01

Although anthocyanin (ACN) biosynthesis is one of the best studied pathways of secondary metabolism in plants, the possible physiological and ecological role(s) of these pigments continue to intrigue scientists. Like other dihydroxy B-ring substituted flavonoids, ACNs have an ability to bind metal and metalloid ions, a property that has been exploited for a variety of purposes. For example, the metal binding ability may be used to stabilize ACNs from plant food sources, or to modify their colors for using them as food colorants. The complexation of metals with cyanidin derivatives can also be used as a simple, sensitive, cheap, and rapid method for determination concentrations of several metals in biological and environmental samples using UV-vis spectroscopy. Far less information is available on the ecological significance of ACN-metal complexes in plant-environment interactions. Metalloanthocyanins (protocyanin, nemophilin, commelinin, protodelphin, cyanosalvianin) are involved in the copigmentation phenomenon that leads to blue-pigmented petals, which may facilitate specific plant-pollinator interactions. ACN-metal formation and compartmentation into the vacuole has also been proposed to be part of an orchestrated detoxification mechanism in plants which experience metal/metalloid excess. However, investigations into ACN-metal interactions in plant biology may be limited because of the complexity of the analytical techniques required. To address this concern, here we describe simple methods for the detection of ACN-metal both in vitro and in vivo using UV-vis spectroscopy and colorimetric models. In particular, the use of UV-vis spectra, difference absorption spectra, and colorimetry techniques will be described for in vitro determination of ACN-metal features, whereas reflectance spectroscopy and colorimetric parameters related to CIE L * a * b * and CIE XYZ systems will be detailed for in vivo analyses. In this way, we hope to make this high-informative tool more accessible to plant physiologists and ecologists. Copyright © 2017 Elsevier GmbH. All rights reserved.

Using TLS to Improve Models of Volcano Conduit Processes (Invited)

NASA Astrophysics Data System (ADS)

Connor, C.; Connor, L.

2010-12-01

In volcanology, diverse numerical models of conduit flow have been developed to relate the properties of these flows to processes that occur at the surface during eruptions. Conduit models incorporate varying degrees of complexity and account for the transport properties of magmas, steady-state or transient behavior, and conduit geometry (e.g., 1- to 1.5 D, variable width and erodable conduit walls). Improvement of these models is important if we are to work toward deployment of eruption models at active volcanoes, link these models to geophysical observations (seismic, deformation, gravity) and eventually forecast eruption magnitude. One conclusion of a recent comparison of many conduit models is that next generation models need to better account for interaction of the erupting mixture with surrounding wall rocks (accounting for melting, solidification, and erosion) and better account for the effects of conduit shape on flows. We made progress toward accounting for this interaction by using TLS to map basaltic conduits in a deeply eroded volcanic field, the San Rafael volcanic field, Utah. TLS data were collected with UNAVCO support during a field campaign in summer 2010. A region of approximately 1 x 1 km was imaged from 9 TLS stations. TLS data reveal the exact geometries of several exposed conduits, their relationship to sills and dikes, and dramatic change in reflectivity of the Entrada sandstone country rock with alteration. The TLS data are particularly good for (a) quantifying rapid change in conduit shape and area as a function of height, (b) differentiating breccias zones (complex mixing zones along conduit margins) from areas of late stage intrusion, (c) imaging complexity of sill geometry near conduits, illustrating the mechanical and perhaps geochemical interaction between sills and conduits in volcanic fields. Overall, application of TLS in this volcanic field has resulted in substantial improvement in our models of volcanic conduit formation, growth, and interaction with shallow magma storage systems.

Toward a 3D model of human brain development for studying gene/environment interactions

PubMed Central

2013-01-01

This project aims to establish and characterize an in vitro model of the developing human brain for the purpose of testing drugs and chemicals. To accurately assess risk, a model needs to recapitulate the complex interactions between different types of glial cells and neurons in a three-dimensional platform. Moreover, human cells are preferred over cells from rodents to eliminate cross-species differences in sensitivity to chemicals. Previously, we established conditions to culture rat primary cells as three-dimensional aggregates, which will be humanized and evaluated here with induced pluripotent stem cells (iPSCs). The use of iPSCs allows us to address gene/environment interactions as well as the potential of chemicals to interfere with epigenetic mechanisms. Additionally, iPSCs afford us the opportunity to study the effect of chemicals during very early stages of brain development. It is well recognized that assays for testing toxicity in the developing brain must consider differences in sensitivity and susceptibility that arise depending on the time of exposure. This model will reflect critical developmental processes such as proliferation, differentiation, lineage specification, migration, axonal growth, dendritic arborization and synaptogenesis, which will probably display differences in sensitivity to different types of chemicals. Functional endpoints will evaluate the complex cell-to-cell interactions that are affected in neurodevelopment through chemical perturbation, and the efficacy of drug intervention to prevent or reverse phenotypes. The model described is designed to assess developmental neurotoxicity effects on unique processes occurring during human brain development by leveraging human iPSCs from diverse genetic backgrounds, which can be differentiated into different cell types of the central nervous system. Our goal is to demonstrate the feasibility of the personalized model using iPSCs derived from individuals with neurodevelopmental disorders caused by known mutations and chromosomal aberrations. Notably, such a human brain model will be a versatile tool for more complex testing platforms and strategies as well as research into central nervous system physiology and pathology. PMID:24564953

I-Hydrate training intervention for staff working in a care home setting: An observational study.

PubMed

Greene, Carolynn; Canning, Deebs; Wilson, Jennie; Bak, Aggie; Tingle, Alison; Tsiami, Amalia; Loveday, Heather

2018-05-23

Dehydration is a complex and well-recognised problem for older people residing in care homes. Within the social care sector support staff provide the majority of direct care for residents, and yet receive minimal training. To design, deliver and evaluate a hydration specific training session for care home staff to develop their knowledge and skills in supporting the hydration of care home residents. An observational study comprising a pre-test post-test survey of staff knowledge following a training intervention. Training of care home staff took place in two care homes in North West London. An interactive training session was developed and delivered, with content informed by observations of hydration care within the two homes and evaluated using CIRO model. Participant self-evaluation forms were used to collect data after the session regarding satisfaction and usefulness of the session, and pre and post levels of self-reported knowledge across six facets of hydration care. Training facilitators captured qualitative data in the form of field notes. Observations of hydration care explored the impact of training on practice. Eighteen training sessions were delivered. A total of 161 participant evaluation forms were returned. There was a significant increase in self-reported knowledge across all six facets of hydration care (p = 0.000). The majority of participants found the training enjoyable and useful, and expressed an expected change in their practice. Participants enjoyed the interactive components of the training. A lack of reflective practice skills meant participants were unable to reflect realistically about the hydration care provided in the home. Focused training on hydration in the care home environment benefits from being interactive and experiential. Although such training can be effective in increasing staff knowledge, inclusion of skills in reflective practice is required if this knowledge is to be translated into practice. Copyright © 2018 Elsevier Ltd. All rights reserved.

Advanced optical simulation of scintillation detectors in GATE V8.0: first implementation of a reflectance model based on measured data

NASA Astrophysics Data System (ADS)

Stockhoff, Mariele; Jan, Sebastien; Dubois, Albertine; Cherry, Simon R.; Roncali, Emilie

2017-06-01

Typical PET detectors are composed of a scintillator coupled to a photodetector that detects scintillation photons produced when high energy gamma photons interact with the crystal. A critical performance factor is the collection efficiency of these scintillation photons, which can be optimized through simulation. Accurate modelling of photon interactions with crystal surfaces is essential in optical simulations, but the existing UNIFIED model in GATE is often inaccurate, especially for rough surfaces. Previously a new approach for modelling surface reflections based on measured surfaces was validated using custom Monte Carlo code. In this work, the LUT Davis model is implemented and validated in GATE and GEANT4, and is made accessible for all users in the nuclear imaging research community. Look-up-tables (LUTs) from various crystal surfaces are calculated based on measured surfaces obtained by atomic force microscopy. The LUTs include photon reflection probabilities and directions depending on incidence angle. We provide LUTs for rough and polished surfaces with different reflectors and coupling media. Validation parameters include light output measured at different depths of interaction in the crystal and photon track lengths, as both parameters are strongly dependent on reflector characteristics and distinguish between models. Results from the GATE/GEANT4 beta version are compared to those from our custom code and experimental data, as well as the UNIFIED model. GATE simulations with the LUT Davis model show average variations in light output of  <2% from the custom code and excellent agreement for track lengths with R 2  >  0.99. Experimental data agree within 9% for relative light output. The new model also simplifies surface definition, as no complex input parameters are needed. The LUT Davis model makes optical simulations for nuclear imaging detectors much more precise, especially for studies with rough crystal surfaces. It will be available in GATE V8.0.

A trap potential model investigation of the optical activity induced in dye-DNA intercalation complexes

NASA Astrophysics Data System (ADS)

Kamiya, Mamoru

1988-02-01

The fundamental features of the optical activity induced in dye-DNA intercalation complexes are studied by application of the trap potential model which is useful to evaluate the induced rotational strength without reference to detailed geometrical information about the intercalation complexes. The specific effect of the potential depth upon the induced optical activity is explained in terms of the relative magnitudes of the wave-phase and helix-phase variations in the path of an electron moving on a restricted helical segment just like an exciton trapped around the dye intercalation site. The parallel and perpendicular components of the induced rotational strength well reflect basic properties of the helicity effects about the longitudinal and tangential axes of the DNA helical cylinder. The trap potential model is applied to optimize the potential parameters so as to reproduce the ionic strength effect upon the optical activity induced to proflavine-DNA intercalation complexes. From relationships between the optimized potential parameters and ionic strengths, it is inferred that increase in the ionic strength contributes to the optical activity induced by the nearest-neighbour interaction between intercalated proflavine and DNA base pairs.

An advanced application of the quantitative structure-activity relationship concept in electrokinetic chromatography of metal complexes.

PubMed

Oszwałdowski, Sławomir; Timerbaev, Andrei R

2008-02-01

The relevance of the quantitative structure-activity relationship (QSAR) principle in MEKC and microemulsion EKC (MEEKC) of metal-ligand complexes was evaluated for a better understanding of analyte migration mechanism. A series of gallium chelates were applied as test solutes with available experimental migration data in order to reveal the molecular properties that govern the separation. The QSAR models operating with n-octanol-water partition coefficients or van der Waals volumes were found to be valid for estimation of the retention factors (log k') of neutral compounds when using only an aqueous MEEKC electrolyte. On the other hand, consistent approximations of log k' for both uncharged and charged complexes in either EKC mode (and also with hydro-organic BGEs) were achievable with two-parametric QSARs in which the dipole moment is additionally incorporated as a structural descriptor, reflecting the electrostatic solute-pseudostationary phase interaction. The theoretical analysis of significant molecular parameters in MEKC systems, in which the micellar BGE is modified with an organic solvent, confirmed that concomitant consideration of hydrophobic, electrostatic, and solvation factors is essential for explaining the migration behavior of neutral metal complexes.

Correlations between Community Structure and Link Formation in Complex Networks

PubMed Central

Liu, Zhen; He, Jia-Lin; Kapoor, Komal; Srivastava, Jaideep

2013-01-01

Background Links in complex networks commonly represent specific ties between pairs of nodes, such as protein-protein interactions in biological networks or friendships in social networks. However, understanding the mechanism of link formation in complex networks is a long standing challenge for network analysis and data mining. Methodology/Principal Findings Links in complex networks have a tendency to cluster locally and form so-called communities. This widely existed phenomenon reflects some underlying mechanism of link formation. To study the correlations between community structure and link formation, we present a general computational framework including a theory for network partitioning and link probability estimation. Our approach enables us to accurately identify missing links in partially observed networks in an efficient way. The links having high connection likelihoods in the communities reveal that links are formed preferentially to create cliques and accordingly promote the clustering level of the communities. The experimental results verify that such a mechanism can be well captured by our approach. Conclusions/Significance Our findings provide a new insight into understanding how links are created in the communities. The computational framework opens a wide range of possibilities to develop new approaches and applications, such as community detection and missing link prediction. PMID:24039818

Synthesis, characterization, crystal structure, DNA/BSA binding ability and antibacterial activity of asymmetric europium complex based on 1,10- phenanthroline

NASA Astrophysics Data System (ADS)

Alfi, Nafiseh; Khorasani-Motlagh, Mozhgan; Rezvani, Ali Reza; Noroozifar, Meissam; Molčanov, Krešimir

2017-06-01

A heteroleptic europium coordination compound formulated as [Eu(phen)2(OH2)2(Cl)2](Cl)(H2O) (phen = 1,10-phenanthroline), has been synthesized and characterized by elemental analysis, FT-IR spectroscopy, and single-crystal X-ray diffractometer. Crystal structure analysis reveals the complex is crystallized in orthorhombic system with Pca21 space group. Electronic absorption and various emission methods for investigation of the binding system of europium(III) complex to Fish Salmon deoxyribonucleic acid (FS-DNA) and Bovamin Serum Albumin (BSA) have been explored. Furthermore, the binding constants, binding sites and the corresponding thermodynamic parameters of the interaction system based on the van't Hoff equation for FS-DNA and BSA were calculated. The thermodynamic parameters reflect the exothermic nature of emission process (ΔH°<0 and ΔS°<0). The experimental results seem to indicate that the [Eu(phen)2(OH2)2(Cl)2](Cl)(H2O) bound to FS-DNA by non-intercalative mode which the groove binding is preferable mode. Also, the complex exhibits a brilliant antimicrobial activity in vitro against standard bacterial strains.

Reflectivity and the Pedagogical Moment: The Normativity of Pedagogical Thinking and Acting.

ERIC Educational Resources Information Center

Van Manen, Max

1991-01-01

Discusses the relationship between reflection and action and its importance in teaching when time for reflection before decision making is rarely available. Describes anticipatory reflection, active or interactive reflection, recollective reflection, and mindfulness or tact. Emphasizes the importance of tact to teaching as the teacher develops…

Detecting higher-order interactions among the spiking events in a group of neurons.

PubMed

Martignon, L; Von Hasseln, H; Grün, S; Aertsen, A; Palm, G

1995-06-01

We propose a formal framework for the description of interactions among groups of neurons. This framework is not restricted to the common case of pair interactions, but also incorporates higher-order interactions, which cannot be reduced to lower-order ones. We derive quantitative measures to detect the presence of such interactions in experimental data, by statistical analysis of the frequency distribution of higher-order correlations in multiple neuron spike train data. Our first step is to represent a frequency distribution as a Markov field on the minimal graph it induces. We then show the invariance of this graph with regard to changes of state. Clearly, only linear Markov fields can be adequately represented by graphs. Higher-order interdependencies, which are reflected by the energy expansion of the distribution, require more complex graphical schemes, like constellations or assembly diagrams, which we introduce and discuss. The coefficients of the energy expansion not only point to the interactions among neurons but are also a measure of their strength. We investigate the statistical meaning of detected interactions in an information theoretic sense and propose minimum relative entropy approximations as null hypotheses for significance tests. We demonstrate the various steps of our method in the situation of an empirical frequency distribution on six neurons, extracted from data on simultaneous multineuron recordings from the frontal cortex of a behaving monkey and close with a brief outlook on future work.

Classroom learning and achievement: how the complexity of classroom interaction impacts students' learning

NASA Astrophysics Data System (ADS)

Podschuweit, Sören; Bernholt, Sascha; Brückmann, Maja

2016-05-01

Background: Complexity models have provided a suitable framework in various domains to assess students' educational achievement. Complexity is often used as the analytical focus when regarding learning outcomes, i.e. when analyzing written tests or problem-centered interviews. Numerous studies reveal negative correlations between the complexity of a task and the probability of a student solving it. Purpose: Thus far, few detailed investigations explore the importance of complexity in actual classroom lessons. Moreover, the few efforts made so far revealed inconsistencies. Hence, the present study sheds light on the influence the complexity of students' and teachers' class contributions have on students' learning outcomes. Sample: Videos of 10 German 8th grade physics courses covering three consecutive lessons on two topics each (electricity, mechanics) have been analyzed. The sample includes 10 teachers and 290 students. Design and methods: Students' and teachers' verbal contributions were coded manual-based according to the level of complexity. Additionally, pre-post testing of knowledge in electricity and mechanics was applied to assess the students' learning gain. ANOVA analysis was used to characterize the influence of the complexity on the learning gain. Results: Results indicate that the mean level of complexity in classroom contributions explains a large portion of variance in post-test results on class level. Despite this overarching trend, taking classroom activities into account as well reveals even more fine-grained patterns, leading to more specific relations between the complexity in the classroom and students' achievement. Conclusions: In conclusion, we argue for more reflected teaching approaches intended to gradually increase class complexity to foster students' level of competency.

Parasites Affect Food Web Structure Primarily through Increased Diversity and Complexity

PubMed Central

Dunne, Jennifer A.; Lafferty, Kevin D.; Dobson, Andrew P.; Hechinger, Ryan F.; Kuris, Armand M.; Martinez, Neo D.; McLaughlin, John P.; Mouritsen, Kim N.; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B.; Thieltges, David W.; Williams, Richard J.; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites “dominate” food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites' roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites' feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models. PMID:23776404

Parasites affect food web structure primarily through increased diversity and complexity

USGS Publications Warehouse

Dunne, Jennifer A.; Lafferty, Kevin D.; Dobson, Andrew P.; Hechinger, Ryan F.; Kuris, Armand M.; Martinez, Neo D.; McLaughlin, John P.; Mouritsen, Kim N.; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B.; Thieltges, David W.; Williams, Richard J.; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites ‘‘dominate’’ food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites’ roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites’ feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models.

Parasites affect food web structure primarily through increased diversity and complexity.

PubMed

Dunne, Jennifer A; Lafferty, Kevin D; Dobson, Andrew P; Hechinger, Ryan F; Kuris, Armand M; Martinez, Neo D; McLaughlin, John P; Mouritsen, Kim N; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B; Thieltges, David W; Williams, Richard J; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites "dominate" food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites' roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites' feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models.

Interpersonal Administration: Overcoming the Pygmalion Effect.

ERIC Educational Resources Information Center

Brown, Alan F.

1982-01-01

Researchers used a cognitive-reflective-interactive model for administrator development to help school administrators recognize their own personal constructs (implicit assumptions that affect decision-making). This recognition brings a clarification of self-understanding which, in conjunction with reflection and interaction with colleagues,…

Protochlorophyll complexes with similar steady-state fluorescence characteristics can differ in fluorescence lifetimes. A model study in Triton X-100.

PubMed

Myśliwa-Kurdziel, Beata; Solymosi, Katalin; Kruk, Jerzy; Böddi, Béla; Strzałka, Kazimierz

2007-03-01

The steady-state and time-resolved fluorescence characteristics of protochlorophyll (Pchl) dissolved in neat Triton X-100 and in Triton X-100 micelles were investigated, and the fluorescence lifetimes of different Pchl spectral forms were studied. Varying the concentration of Pchl or diluting the micellar solutions either with a buffer or with a micellar solution, 631-634, 645-655, 680-692 and above 700 nm emitting Pchl complexes were prepared, the ratios of which varied from one another. The fluorescence decay of the 631-634 nm emitting (monomeric) form had a mono-exponential character with a 5.4-ns fluorescence lifetime. The long-wavelength Pchl complexes (aggregates) had two fluorescence lifetime values within a range of 1.4-3.9 ns and 0.15-0.84 ns, which showed high variability in different environments. Depending on the conditions, either mono- or double-exponential fluorescence decay was found for a fluorescence band at 680-685 nm. These data show that despite their very similar steady-state fluorescence properties, Pchl complexes can differ in fluorescence lifetimes, which may reflect different molecular structures, intrinsic geometries or different molecular interactions. This underlines the importance of complex spectroscopic analysis for a precise description of native and artificial chlorophyllous pigment forms.

Crystal structures of palladium(II) ternary complexes of 5-x-2-aminobenzoic acid with 1,10-phenanthroline and their interaction with calf thymus DNA (where X=Cl, Br and I).

PubMed

Wang, Yue; Okabe, Nobuo; Odoko, Mamiko

2005-10-01

The crystal structures of a series of three palladium(II) ternary complexes of 5-halogeno-2-aminobenzoic acid (5-X-AB, where X=Cl, Br and I) with 1,10-phenanthroline [Pd(5-Cl-AB)(phen)] (1), [Pd(5-Br-AB)(phen)] (2) and [Pd(5-I-AB)(phen)] (3) have been determined, and their coordination geometries and the crystal architecture characterized. All of the complexes are an isostructure in which each Pd(II) atom has basically similar square planar coordination geometry. The substitute halogen group at 5-position of AB plays an important role in producing the coordination bonds of the carboxylate and amino groups in which the carboxylate O atom and the amino N atom act as the negative monodentate ligand atoms. The coordination bond distances of O-Pd increase in the order 1<2<3, while those of N-Pd decrease in the same order. The binding of the complexes to the calf thymus DNA has also been studied by the fluorescence method. Each of the complexes shows high binding propensity to DNA which can be reflected as the relative order 1<2<3.

Use of complex frequency plane to design broadband and sub-wavelength absorbers.

PubMed

Romero-García, V; Theocharis, G; Richoux, O; Pagneux, V

2016-06-01

The reflection of sound of frequency below 1 kHz, by a rigid-backed structure that contains sub-wavelength resonators is studied in this work. In particular, only single mode reflected waves are considered, an approximation which is accurate in this low frequency regime. A method of analysis of absorption that uses the structure of the reflection coefficient in the complex frequency plane is proposed. In the absence of losses, the reflection coefficient supports pairs of poles and zeros that are complex conjugate and which have imaginary parts linked to the energy leakage by radiation. When losses are introduced and balanced to the leakage, the critical coupling condition is satisfied and total absorption is obtained. Examples of a slot resonator and of multiple Helmholtz resonators are analyzed to obtain both narrow and broadband total absorption.

Large-scale investigation of Leishmania interaction networks with host extracellular matrix by surface plasmon resonance imaging.

PubMed

Fatoux-Ardore, Marie; Peysselon, Franck; Weiss, Anthony; Bastien, Patrick; Pratlong, Francine; Ricard-Blum, Sylvie

2014-02-01

We have set up an assay to study the interactions of live pathogens with their hosts by using protein and glycosaminoglycan arrays probed by surface plasmon resonance imaging. We have used this assay to characterize the interactions of Leishmania promastigotes with ~70 mammalian host biomolecules (extracellular proteins, glycosaminoglycans, growth factors, cell surface receptors). We have identified, in total, 27 new partners (23 proteins, 4 glycosaminoglycans) of procyclic promastigotes of six Leishmania species and 18 partners (15 proteins, 3 glycosaminoglycans) of three species of stationary-phase promastigotes for all the strains tested. The diversity of the interaction repertoires of Leishmania parasites reflects their dynamic and complex interplay with their mammalian hosts, which depends mostly on the species and strains of Leishmania. Stationary-phase Leishmania parasites target extracellular matrix proteins and glycosaminoglycans, which are highly connected in the extracellular interaction network. Heparin and heparan sulfate bind to most Leishmania strains tested, and 6-O-sulfate groups play a crucial role in these interactions. Numerous Leishmania strains bind to tropoelastin, and some strains are even able to degrade it. Several strains interact with collagen VI, which is expressed by macrophages. Most Leishmania promastigotes interact with several regulators of angiogenesis, including antiangiogenic factors (endostatin, anastellin) and proangiogenic factors (ECM-1, VEGF, and TEM8 [also known as anthrax toxin receptor 1]), which are regulated by hypoxia. Since hypoxia modulates the infection of macrophages by the parasites, these interactions might influence the infection of host cells by Leishmania.

Large-Scale Investigation of Leishmania Interaction Networks with Host Extracellular Matrix by Surface Plasmon Resonance Imaging

PubMed Central

Fatoux-Ardore, Marie; Peysselon, Franck; Weiss, Anthony; Bastien, Patrick; Pratlong, Francine

2014-01-01

We have set up an assay to study the interactions of live pathogens with their hosts by using protein and glycosaminoglycan arrays probed by surface plasmon resonance imaging. We have used this assay to characterize the interactions of Leishmania promastigotes with ∼70 mammalian host biomolecules (extracellular proteins, glycosaminoglycans, growth factors, cell surface receptors). We have identified, in total, 27 new partners (23 proteins, 4 glycosaminoglycans) of procyclic promastigotes of six Leishmania species and 18 partners (15 proteins, 3 glycosaminoglycans) of three species of stationary-phase promastigotes for all the strains tested. The diversity of the interaction repertoires of Leishmania parasites reflects their dynamic and complex interplay with their mammalian hosts, which depends mostly on the species and strains of Leishmania. Stationary-phase Leishmania parasites target extracellular matrix proteins and glycosaminoglycans, which are highly connected in the extracellular interaction network. Heparin and heparan sulfate bind to most Leishmania strains tested, and 6-O-sulfate groups play a crucial role in these interactions. Numerous Leishmania strains bind to tropoelastin, and some strains are even able to degrade it. Several strains interact with collagen VI, which is expressed by macrophages. Most Leishmania promastigotes interact with several regulators of angiogenesis, including antiangiogenic factors (endostatin, anastellin) and proangiogenic factors (ECM-1, VEGF, and TEM8 [also known as anthrax toxin receptor 1]), which are regulated by hypoxia. Since hypoxia modulates the infection of macrophages by the parasites, these interactions might influence the infection of host cells by Leishmania. PMID:24478075

Timing of magmatism following initial convergence at a passive margin, southwestern U.S. Cordillera, and ages of lower crustal magma sources

USGS Publications Warehouse

Barth, A.P.; Wooden, J.L.

2006-01-01

Initiation of the Cordilleran magmatic arc in the southwestern United States is marked by intrusion of granitic plutons, predominantly composed of alkali-calcic Fe- and Sr-enriched quartz monzodiorite and monzonite, that intruded Paleoproterozoic basement and its Paleozoic cratonal-miogeoclinal cover. Three intrusive suites, recognized on the basis of differences in high field strength element and large ion lithophile element abundances, contain texturally complex but chronologically distinctive zircons. These zircons record heterogeneous but geochemically discrete mafic crustal magma sources, discrete Permo-Triassic intrusion ages, and a prolonged postemplacement thermal history within the long-lived Cordilleran arc, leading to episodic loss of radiogenic Pb. Distinctive lower crustal magma sources reflect lateral heterogeneity within the composite lithosphere of the Proterozoic craton. Limited interaction between derived magmas and middle and upper crustal rocks probably reflects the relatively cool thermal structure of the nascent Cordilleran continental margin magmatic arc. ?? 2006 by The University of Chicago. All rights reserved.

Design and Construction of a Multi-wavelength, Micromirror Total Internal Reflectance Fluorescence Microscope

PubMed Central

Larson, Joshua; Kirk, Matt; Drier, Eric A.; O’Brien, William; MacKay, James F.; Friedman, Larry; Hoskins, Aaron

2015-01-01

Colocalization Single Molecule Spectroscopy (CoSMoS) has proven to be a useful method for studying the composition, kinetics, and mechanisms of complex cellular machines. Key to the technique is the ability to simultaneously monitor multiple proteins and/or nucleic acids as they interact with one another. Here we describe a protocol for constructing a CoSMoS micromirror Total Internal Reflection Fluorescence Microscope (mmTIRFM). Design and construction of a scientific microscope often requires a number of custom components and a significant time commitment. In our protocol, we have streamlined this process by implementation of a commercially available microscopy platform designed to accommodate the optical components necessary for a mmTIRFM. The mmTIRF system eliminates the need for machining custom parts by the end-user and facilitates optical alignment. Depending on the experience-level of the microscope builder, these time-savings and the following protocol can enable mmTIRF construction to be completed within two months. PMID:25188633

Design and construction of a multiwavelength, micromirror total internal reflectance fluorescence microscope.

PubMed

Larson, Joshua; Kirk, Matt; Drier, Eric A; O'Brien, William; MacKay, James F; Friedman, Larry J; Hoskins, Aaron A

2014-10-01

Colocalization single-molecule spectroscopy (CoSMoS) has proven to be a useful method for studying the composition, kinetics and mechanisms of complex cellular machines. Key to the technique is the ability to simultaneously monitor multiple proteins and/or nucleic acids as they interact with one another. Here we describe a protocol for constructing a CoSMoS micromirror total internal reflection fluorescence microscope (mmTIRFM). Design and construction of a scientific microscope often requires a number of custom components and a substantial time commitment. In our protocol, we have streamlined this process by implementation of a commercially available microscopy platform designed to accommodate the optical components necessary for an mmTIRFM. The mmTIRF system eliminates the need for machining custom parts by the end user and facilitates optical alignment. Depending on the experience level of the microscope builder, these time savings and the following protocol can enable mmTIRF construction to be completed within 2 months.

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

PubMed Central

Van Leene, Jelle; Hollunder, Jens; Eeckhout, Dominique; Persiau, Geert; Van De Slijke, Eveline; Stals, Hilde; Van Isterdael, Gert; Verkest, Aurine; Neirynck, Sandy; Buffel, Yelle; De Bodt, Stefanie; Maere, Steven; Laukens, Kris; Pharazyn, Anne; Ferreira, Paulo C G; Eloy, Nubia; Renne, Charlotte; Meyer, Christian; Faure, Jean-Denis; Steinbrenner, Jens; Beynon, Jim; Larkin, John C; Van de Peer, Yves; Hilson, Pierre; Kuiper, Martin; De Veylder, Lieven; Van Onckelen, Harry; Inzé, Dirk; Witters, Erwin; De Jaeger, Geert

2010-01-01

Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)–cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK–cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants. PMID:20706207

Unraveling spurious properties of interaction networks with tailored random networks.

PubMed

Bialonski, Stephan; Wendler, Martin; Lehnertz, Klaus

2011-01-01

We investigate interaction networks that we derive from multivariate time series with methods frequently employed in diverse scientific fields such as biology, quantitative finance, physics, earth and climate sciences, and the neurosciences. Mimicking experimental situations, we generate time series with finite length and varying frequency content but from independent stochastic processes. Using the correlation coefficient and the maximum cross-correlation, we estimate interdependencies between these time series. With clustering coefficient and average shortest path length, we observe unweighted interaction networks, derived via thresholding the values of interdependence, to possess non-trivial topologies as compared to Erdös-Rényi networks, which would indicate small-world characteristics. These topologies reflect the mostly unavoidable finiteness of the data, which limits the reliability of typically used estimators of signal interdependence. We propose random networks that are tailored to the way interaction networks are derived from empirical data. Through an exemplary investigation of multichannel electroencephalographic recordings of epileptic seizures--known for their complex spatial and temporal dynamics--we show that such random networks help to distinguish network properties of interdependence structures related to seizure dynamics from those spuriously induced by the applied methods of analysis.

Unraveling Spurious Properties of Interaction Networks with Tailored Random Networks

PubMed Central

Bialonski, Stephan; Wendler, Martin; Lehnertz, Klaus

2011-01-01

We investigate interaction networks that we derive from multivariate time series with methods frequently employed in diverse scientific fields such as biology, quantitative finance, physics, earth and climate sciences, and the neurosciences. Mimicking experimental situations, we generate time series with finite length and varying frequency content but from independent stochastic processes. Using the correlation coefficient and the maximum cross-correlation, we estimate interdependencies between these time series. With clustering coefficient and average shortest path length, we observe unweighted interaction networks, derived via thresholding the values of interdependence, to possess non-trivial topologies as compared to Erdös-Rényi networks, which would indicate small-world characteristics. These topologies reflect the mostly unavoidable finiteness of the data, which limits the reliability of typically used estimators of signal interdependence. We propose random networks that are tailored to the way interaction networks are derived from empirical data. Through an exemplary investigation of multichannel electroencephalographic recordings of epileptic seizures – known for their complex spatial and temporal dynamics – we show that such random networks help to distinguish network properties of interdependence structures related to seizure dynamics from those spuriously induced by the applied methods of analysis. PMID:21850239

Complex networks of functional connectivity in a wetland reconnected to its floodplain

USGS Publications Warehouse

Larsen, Laurel G.; Newman, Susan; Saunders, Colin; Harvey, Judson

2017-01-01

Disturbances such as fire or flood, in addition to changing the local magnitude of ecological, hydrological, or biogeochemical processes, can also change their functional connectivity—how those processes interact in space. Complex networks offer promise for quantifying functional connectivity in watersheds. The approach resolves connections between nodes in space based on statistical similarities in perturbation signals (derived from solute time series) and is sensitive to a wider range of timescales than traditional mass-balance modeling. We use this approach to test hypotheses about how fire and flood impact ecological and biogeochemical dynamics in a wetland (Everglades, FL, USA) that was reconnected to its floodplain. Reintroduction of flow pulses after decades of separation by levees fundamentally reconfigured functional connectivity networks. The most pronounced expansion was that of the calcium network, which reflects periphyton dynamics and may represent an indirect influence of elevated nutrients, despite the comparatively smaller observed expansion of phosphorus networks. With respect to several solutes, periphyton acted as a “biotic filter,” shifting perturbations in water-quality signals to different timescales through slow but persistent transformations of the biotic community. The complex-networks approach also revealed portions of the landscape that operate in fundamentally different regimes with respect to dissolved oxygen, separated by a threshold in flow velocity of 1.2 cm/s, and suggested that complete removal of canals may be needed to restore connectivity with respect to biogeochemical processes. Fire reconfigured functional connectivity networks in a manner that reflected localized burn severity, but had a larger effect on the magnitude of solute concentrations.

Complex networks of functional connectivity in a wetland reconnected to its floodplain

NASA Astrophysics Data System (ADS)

Larsen, Laurel G.; Newman, Susan; Saunders, Colin; Harvey, Judson W.

2017-07-01

Disturbances such as fire or flood, in addition to changing the local magnitude of ecological, hydrological, or biogeochemical processes, can also change their functional connectivity—how those processes interact in space. Complex networks offer promise for quantifying functional connectivity in watersheds. The approach resolves connections between nodes in space based on statistical similarities in perturbation signals (derived from solute time series) and is sensitive to a wider range of timescales than traditional mass-balance modeling. We use this approach to test hypotheses about how fire and flood impact ecological and biogeochemical dynamics in a wetland (Everglades, FL, USA) that was reconnected to its floodplain. Reintroduction of flow pulses after decades of separation by levees fundamentally reconfigured functional connectivity networks. The most pronounced expansion was that of the calcium network, which reflects periphyton dynamics and may represent an indirect influence of elevated nutrients, despite the comparatively smaller observed expansion of phosphorus networks. With respect to several solutes, periphyton acted as a "biotic filter," shifting perturbations in water-quality signals to different timescales through slow but persistent transformations of the biotic community. The complex-networks approach also revealed portions of the landscape that operate in fundamentally different regimes with respect to dissolved oxygen, separated by a threshold in flow velocity of 1.2 cm/s, and suggested that complete removal of canals may be needed to restore connectivity with respect to biogeochemical processes. Fire reconfigured functional connectivity networks in a manner that reflected localized burn severity, but had a larger effect on the magnitude of solute concentrations.

Obesity and diabetes in vulnerable populations: reflection on proximal and distal causes.

PubMed

Candib, Lucy M

2007-01-01

Around the world obesity and diabetes are climbing to epidemic proportion, even in countries previously characterized by scarcity. Likewise, people from low-income and minority communities, as well as immigrants from the developing world, increasingly visit physicians in North America with obesity, metabolic syndrome, or diabetes. Explanations limited to lifestyle factors such as diet and exercise are inadequate to explain the universality of what can be called a syndemic, a complex and widespread phenomenon in population health produced by multiple reinforcing conditions. Underlying the problem are complex factors-genetic, physiological, psychological, familial, social, economic, and political-coalescing to overdetermine these conditions. These interacting factors include events occurring during fetal life, maternal physiology and life context, the thrifty genotype, the nutritional transition, health impact of urbanization and immigration, social attributions and cultural perceptions of increased weight, and changes in food costs and availability resulting from globalization. Better appreciation of the complexity of causation underlying the worldwide epidemic of obesity and diabetes can refocus the work of clinicians and researchers to work at multiple levels to address prevention and treatment for these conditions among vulnerable populations.

Thorium–phosphorus triamidoamine complexes containing Th–P single- and multiple-bond interactions

PubMed Central

Wildman, Elizabeth P.; Balázs, Gábor; Wooles, Ashley J.; Scheer, Manfred; Liddle, Stephen T.

2016-01-01

Despite the burgeoning field of uranium-ligand multiple bonds, analogous complexes involving other actinides remain scarce. For thorium, under ambient conditions only a few multiple bonds to carbon, nitrogen, oxygen, sulfur, selenium and tellurium are reported, and no multiple bonds to phosphorus are known, reflecting a general paucity of synthetic methodologies and also problems associated with stabilising these linkages at the large thorium ion. Here we report structurally authenticated examples of a parent thorium(IV)–phosphanide (Th–PH2), a terminal thorium(IV)–phosphinidene (Th=PH), a parent dithorium(IV)–phosphinidiide (Th–P(H)-Th) and a discrete actinide–phosphido complex under ambient conditions (Th=P=Th). Although thorium is traditionally considered to have dominant 6d-orbital contributions to its bonding, contrasting to majority 5f-orbital character for uranium, computational analyses suggests that the bonding of thorium can be more nuanced, in terms of 5f- versus 6d-orbital composition and also significant involvement of the 7s-orbital and how this affects the balance of 5f- versus 6d-orbital bonding character. PMID:27682617

Thorium-phosphorus triamidoamine complexes containing Th-P single- and multiple-bond interactions.

PubMed

Wildman, Elizabeth P; Balázs, Gábor; Wooles, Ashley J; Scheer, Manfred; Liddle, Stephen T

2016-09-29

Despite the burgeoning field of uranium-ligand multiple bonds, analogous complexes involving other actinides remain scarce. For thorium, under ambient conditions only a few multiple bonds to carbon, nitrogen, oxygen, sulfur, selenium and tellurium are reported, and no multiple bonds to phosphorus are known, reflecting a general paucity of synthetic methodologies and also problems associated with stabilising these linkages at the large thorium ion. Here we report structurally authenticated examples of a parent thorium(IV)-phosphanide (Th-PH 2 ), a terminal thorium(IV)-phosphinidene (Th=PH), a parent dithorium(IV)-phosphinidiide (Th-P(H)-Th) and a discrete actinide-phosphido complex under ambient conditions (Th=P=Th). Although thorium is traditionally considered to have dominant 6d-orbital contributions to its bonding, contrasting to majority 5f-orbital character for uranium, computational analyses suggests that the bonding of thorium can be more nuanced, in terms of 5f- versus 6d-orbital composition and also significant involvement of the 7s-orbital and how this affects the balance of 5f- versus 6d-orbital bonding character.

Implementing the patient-centered medical home in complex adaptive systems: Becoming a relationship-centered patient-centered medical home.

PubMed

Flieger, Signe Peterson

This study explores the implementation experience of nine primary care practices becoming patient-centered medical homes (PCMH) as part of the New Hampshire Citizens Health Initiative Multi-Stakeholder Medical Home Pilot. The purpose of this study is to apply complex adaptive systems theory and relationship-centered organizations theory to explore how nine diverse primary care practices in New Hampshire implemented the PCMH model and to offer insights for how primary care practices can move from a structural PCMH to a relationship-centered PCMH. Eighty-three interviews were conducted with administrative and clinical staff at the nine pilot practices, payers, and conveners of the pilot between November and December 2011. The interviews were transcribed, coded, and analyzed using both a priori and emergent themes. Although there is value in the structural components of the PCMH (e.g., disease registries), these structures are not enough. Becoming a relationship-centered PCMH requires attention to reflection, sensemaking, learning, and collaboration. This can be facilitated by settings aside time for communication and relationship building through structured meetings about PCMH components as well as the implementation process itself. Moreover, team-based care offers a robust opportunity to move beyond the structures to focus on relationships and collaboration. (a) Recognize that PCMH implementation is not a linear process. (b) Implementing the PCMH from a structural perspective is not enough. Although the National Committee for Quality Assurance or other guidelines can offer guidance on the structural components of PCMH implementation, this should serve only as a starting point. (c) During implementation, set aside structured time for reflection and sensemaking. (d) Use team-based care as a cornerstone of transformation. Reflect on team structures and also interactions of the team members. Taking the time to reflect will facilitate greater sensemaking and learning and will ultimately help foster a relationship-centered PCMH.

Implementing the patient-centered medical home in complex adaptive systems: Becoming a relationship-centered patient-centered medical home

PubMed Central

Flieger, Signe Peterson

2017-01-01

Background This study explores the implementation experience of nine primary care practices becoming patient-centered medical homes (PCMH) as part of the New Hampshire Citizens Health Initiative Multi-Stakeholder Medical Home Pilot. Purpose The purpose of this study is to apply complex adaptive systems theory and relationship-centered organizations theory to explore how nine diverse primary care practices in New Hampshire implemented the PCMH model and to offer insights for how primary care practices can move from a structural PCMH to a relationship-centered PCMH. Methodology/Approach Eighty-three interviews were conducted with administrative and clinical staff at the nine pilot practices, payers, and conveners of the pilot between November and December 2011. The interviews were transcribed, coded, and analyzed using both a priori and emergent themes. Findings Although there is value in the structural components of the PCMH (e.g., disease registries), these structures are not enough. Becoming a relationship-centered PCMH requires attention to reflection, sensemaking, learning, and collaboration. This can be facilitated by settings aside time for communication and relationship building through structured meetings about PCMH components as well as the implementation process itself. Moreover, team-based care offers a robust opportunity to move beyond the structures to focus on relationships and collaboration. Practice Implications (a) Recognize that PCMH implementation is not a linear process. (b) Implementing the PCMH from a structural perspective is not enough. Although the National Committee for Quality Assurance or other guidelines can offer guidance on the structural components of PCMH implementation, this should serve only as a starting point. (c) During implementation, set aside structured time for reflection and sensemaking. (d) Use team-based care as a cornerstone of transformation. Reflect on team structures and also interactions of the team members. Taking the time to reflect will facilitate greater sensemaking and learning and will ultimately help foster a relationship-centered PCMH. PMID:26939031

Motivational interviewing interactions and the primary health care challenges presented by smokers with low motivation to stop smoking: a conversation analysis.

PubMed

Codern-Bové, Núria; Pujol-Ribera, Enriqueta; Pla, Margarida; González-Bonilla, Javier; Granollers, Silvia; Ballvé, José L; Fanlo, Gemma; Cabezas, Carmen

2014-11-26

Research indicates that one third of smokers have low motivation to stop smoking. The purpose of the study was to use Conversational Analysis to enhance understanding of the process in Motivational Interviewing sessions carried out by primary care doctors and nurses to motivate their patients to quit smoking. The present study is a substudy of the Systematic Intervention on Smoking Habits in Primary Health Care Project (Spanish acronym: ISTAPS). Motivational interviewing sessions with a subset of nine participants (two interview sessions were conducted with two of the nine) in the ISTAPS study who were current smokers and scored fewer than 5 points on the Richmond test that measures motivation to quit smoking were videotaped and transcribed. A total of 11 interviews conducted by five primary health care professionals in Barcelona, Spain, were analysed. Qualitative Content Analysis was used to develop an analytical guide for coding transcriptions. Conversation Analysis allowed detailed study of the exchange of words during the interaction. Motivational Interviewing sessions had three phases: assessment, reflection on readiness to change, and summary. The interaction was constructed during an office visit, where interactional dilemmas arise and can be resolved in various ways. Some actions by professionals (use of reiterations, declarations, open-ended questions) helped to construct a framework of shared relationship; others inhibited this relationship (focusing on risks of smoking, clinging to the protocol, and prematurely emphasizing change). Some professionals tended to resolve interactional dilemmas (e.g., resistance) through a confrontational or directive style. Interactions that did not follow Motivational Interviewing principles predominated in seven of the interviews analysed. Conversational analysis showed that the complexity of the intervention increases when a health professional encounters individuals with low motivation for change, and interactional dilemmas may occur that make it difficult to follow Motivational Interview principles. Incorporating different forms of expression during the Motivational Interviewing could help to build patient-centred health care relationships and, for patients with low motivation to stop smoking, offer an opportunity to reflect on tobacco use during the office visit. The study findings could be included in professional training to improve the quality of motivational interviewing.

Formation of Ordered Arrays of Proteins on Surfaces

NASA Technical Reports Server (NTRS)

Lenhoff, A. M.

1996-01-01

Van der Waals (dispersion) forces contribute to interactions of proteins with other molecules or with surfaces, but because of the structural complexity of protein molecules, the magnitude of these effects is usually estimated based on idealized models of the molecular geometry, e.g., spheres or spheroids. The calculations reported here seek to account for both the geometric irregularity of protein molecules and the material properties of the interacting media. While the latter are found to fall in the generally accepted range, the molecular shape is shown to cause the magnitudes of the interactions to differ significantly from those calculated using idealized models, with important consequences. First, the roughness of the molecular surface leads to much lower average interaction energies for both protein-protein and protein-surface cases relative to calculations in which the protein molecule is approximated as a sphere. These results indicate that a form of steric stabilization may be an important effect in protein solutions. Underlying this behavior is appreciable orientational dependence, one reflection of which is that molecules of complementary shape are found to exhibit very strong attractive dispersion interactions. Although this has been widely discussed previously in the context of molecular recognition processes, the broader implications of these phenomena may also be important at larger molecular separations, e.g., in the dynamics of aggregation, precipitation and crystal growth.

Deficits of long-term memory in ecstasy users are related to cognitive complexity of the task.

PubMed

Brown, John; McKone, Elinor; Ward, Jeff

2010-03-01

Despite animal evidence that methylenedioxymethamphetamine (ecstasy) causes lasting damage in brain regions related to long-term memory, results regarding human memory performance have been variable. This variability may reflect the cognitive complexity of the memory tasks. However, previous studies have tested only a limited range of cognitive complexity. Furthermore, comparisons across different studies are made difficult by regional variations in ecstasy composition and patterns of use. The objective of this study is to evaluate ecstasy-related deficits in human verbal memory over a wide range of cognitive complexity using subjects drawn from a single geographical population. Ecstasy users were compared to non-drug using controls on verbal tasks with low cognitive complexity (stem completion), moderate cognitive complexity (stem-cued recall and word list learning) and high cognitive complexity (California Verbal Learning Test, Verbal Paired Associates and a novel Verbal Triplet Associates test). Where significant differences were found, both groups were also compared to cannabis users. More cognitively complex memory tasks were associated with clearer ecstasy-related deficits than low complexity tasks. In the most cognitively demanding task, ecstasy-related deficits remained even after multiple learning opportunities, whereas the performance of cannabis users approached that of non-drug using controls. Ecstasy users also had weaker deliberate strategy use than both non-drug and cannabis controls. Results were consistent with the proposal that ecstasy-related memory deficits are more reliable on tasks with greater cognitive complexity. This could arise either because such tasks require a greater contribution from the frontal lobe or because they require greater interaction between multiple brain regions.

Processing complex pseudo-words in mild cognitive impairment: The interaction of preserved morphological rule knowledge with compromised cognitive ability.

PubMed

Manouilidou, Christina; Dolenc, Barbara; Marvin, Tatjana; Pirtošek, Zvezdan

2016-01-01

Mild cognitive impairment (MCI) affects the cognitive performance of elderly adults. However, the level of severity is not high enough to be diagnosed with dementia. Previous research reports subtle language impairments in individuals with MCI specifically in domains related to lexical meaning. The present study used both off-line (grammaticality judgment) and on-line (lexical decision) tasks to examine aspects of lexical processing and how they are affected by MCI. 21 healthy older adults and 23 individuals with MCI saw complex pseudo-words that violated various principles of word formation in Slovenian and decided if each letter string was an actual word of their language. The pseudo-words ranged in their degree of violability. A task effect was found, with MCI performance to be similar to that of healthy controls in the off-line task but different in the on-line task. Overall, the MCI group responded slower than the elderly controls. No significant differences were observed in the off-line task, while the on-line task revealed a main effect of Violation type, a main effect of Group and a significant Violation × Group interaction reflecting a difficulty for the MCI group to process pseudo-words in real time. That is, while individuals with MCI seem to preserve morphological rule knowledge, they experience additional difficulties while processing complex pseudo-words. This was attributed to an executive dysfunction associated with MCI that delays the recognition of ungrammatical formations.

Speciation of aqueous Ni(II)-carboxylate and Ni(II)-fulvic acid solutions: Combined ATR-FTIR and XAFS analysis

NASA Astrophysics Data System (ADS)

Strathmann, Timothy J.; Myneni, Satish C. B.

2004-09-01

Aqueous solutions containing Ni(II) and a series of structurally related carboxylic acids were analyzed using attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and Ni K-edge X-ray absorption fine structure spectroscopy (XAFS). XAFS spectra were also collected for solutions containing Ni 2+ and chelating ligands (ethylenediaminetetraacetic acid, nitrilotriacetic acid (NTA)) as well as soil fulvic acid. Limited spectral changes are observed for aqueous Ni(II) complexes with monocarboxylates (formate, acetate) and long-chain polycarboxylates (succinate, tricarballylate), where individual donor groups are separated by multiple bridging methylene groups. These spectral changes indicate weak interactions between Ni(II) and carboxylates, and the trends are similar to some earlier reports for crystalline Ni(II)-acetate solids, for which X-ray crystallography studies have indicated monodentate Ni(II)-carboxylate coordination. Nonetheless, electrostatic or outer-sphere coordination cannot be ruled out for these complexes. However, spectral changes observed for short-chain dicarboxylates (oxalate, malonate) and carboxylates that contain an alcohol donor group adjacent to one of the carboxylate groups (lactate, malate, citrate) demonstrate inner-sphere metal coordination by multiple donor groups. XAFS spectral fits of Ni(II) solutions containing soil fulvic acid are consistent with inner-sphere Ni(II) coordination by one or more carboxylate groups, but spectra are noisy and outer-sphere modes of coordination cannot be ruled out. These molecular studies refine our understanding of the interactions between carboxylates and weakly complexing divalent transition metals, such as Ni(II).

Sharing the responsibility for driver distraction across road transport systems: a systems approach to the management of distracted driving.

PubMed

Young, Kristie L; Salmon, Paul M

2015-01-01

Distracted driving is acknowledged universally as a large and growing road safety problem. Compounding the problem is that distracted driving is a complex, multifaceted issue influenced by a multitude of factors, organisations and individuals. As such, management of the problem is not straightforward. Numerous countermeasures have been developed and implemented across the globe. The vast majority of these measures have derived from the traditional reductionist, driver-centric approach to distraction and have failed to fully reflect the complex mix of actors and components that give rise to drivers becoming distracted. An alternative approach that is gaining momentum in road safety is the systems approach, which considers all components of the system and their interactions as an integrated whole. In this paper, we review the current knowledge base on driver distraction and argue that the systems approach is not currently being realised in practice. Adopting a more holistic, systems approach to distracted driving will not only improve existing knowledge and interventions from the traditional approach, but will enhance our understanding and management of distraction by considering the complex relationships and interactions of the multiple actors and the myriad sources, enablers and interventions that make up the distracted driving system. It is only by recognising and understanding how all of the system components work together to enable distraction to occur, that we can start to work on solutions to help mitigate the occurrence and consequences of distracted driving. Copyright © 2014 Elsevier Ltd. All rights reserved.

Using diel movement behavior to infer foraging strategies related to ecological and social factors in elephants.

PubMed

Polansky, Leo; Douglas-Hamilton, Iain; Wittemyer, George

2013-01-01

Adaptive movement behaviors allow individuals to respond to fluctuations in resource quality and distribution in order to maintain fitness. Classically, studies of the interaction between ecological conditions and movement behavior have focused on such metrics as travel distance, velocity, home range size or patch occupancy time as the salient metrics of behavior. Driven by the emergence of very regular high frequency data, more recently the importance of interpreting the autocorrelation structure of movement as a behavioral metric has become apparent. Studying movement of a free ranging African savannah elephant population, we evaluated how two movement metrics, diel displacement (DD) and movement predictability (MP - the degree of autocorrelated movement activity at diel time scales), changed in response to variation in resource availability as measured by the Normalized Difference Vegetation Index. We were able to capitalize on long term (multi-year) yet high resolution (hourly) global positioning system tracking datasets, the sample size of which allows robust analysis of complex models. We use optimal foraging theory predictions as a framework to interpret our results, in particular contrasting the behaviors across changes in social rank and resource availability to infer which movement behaviors at diel time scales may be optimal in this highly social species. Both DD and MP increased with increasing forage availability, irrespective of rank, reflecting increased energy expenditure and movement predictability during time periods of overall high resource availability. However, significant interactions between forage availability and social rank indicated a stronger response in DD, and a weaker response in MP, with increasing social status. Relative to high ranking individuals, low ranking individuals expended more energy and exhibited less behavioral movement autocorrelation during lower forage availability conditions, likely reflecting sub-optimal movement behavior. Beyond situations of contest competition, rank status appears to influence the extent to which individuals can modify their movement strategies across periods with differing forage availability. Large-scale spatiotemporal resource complexity not only impacts fine scale movement and optimal foraging strategies directly, but likely impacts rates of inter- and intra-specific interactions and competition resulting in socially based movement responses to ecological dynamics.

Reflection as a Means of Developing Expertise in Problem Solving, Decision Making, and Complex Thinking of Designers.

ERIC Educational Resources Information Center

Moallem, Mahnaz

This paper focuses on reflection and reflective thinking as a means of developing expertise in instructional designers. The need for the reflective instructional designer is discussed, and reflective thinking is examined from several perspectives, i.e., controlled thinking, tacit knowledge, epistemic assumption, abductive reasoning, willingness to…

Assessing oral literacy demand in genetic counseling dialogue: preliminary test of a conceptual framework.

PubMed

Roter, Debra L; Erby, Lori H; Larson, Susan; Ellington, Lee

2007-10-01

Health literacy deficits affect half the American patient population and are linked to poor health, ineffective disease management and high rates of hospitalization. Restricted literacy has also been linked with less satisfying medical visits and communication difficulties, particularly in terms of the interpersonal and informational aspects of care. Despite growing attention to these issues by researchers and policy makers, few studies have attempted to conceptualize and assess those aspects of dialogue that challenge persons with low literacy skills, i.e., the oral literacy demand within medical encounters. The current study uses videotapes and transcripts of 152 prenatal and cancer pretest genetic counseling sessions recorded with simulated clients to develop a conceptual framework to explore oral literacy demand and its consequences for medical interaction and related outcomes. Ninety-six prenatal and 81 cancer genetic counselors-broadly representative of the US National Society of Genetic Counselors-participated in the study. Key elements of the conceptual framework used to define oral literacy demand include: (1) use of unfamiliar technical terms; (2) general language complexity, reflected in the application of Microsoft Word grammar summary statistics to session transcripts; and, (3) structural characteristics of dialogue, including pacing, density, and interactivity. Genetic counselor outcomes include self-ratings of session satisfaction, informativeness, and development of rapport. The simulated clients rated their satisfaction with session communication, the counselor's effective use of nonverbal skills, and the counselor's affective demeanor during the session. Sessions with greater overall technical term use were longer and used more complex language reflected in readability indices and multi-syllabic vocabulary (measures averaging p<.05). Sessions with a high proportionate use of technical terms were characterized by shorter visits, high readability demand, slow speech speed, fewer and more dense counselor speaking turns and low interactivity (p<.05). The higher the use of technical terms, and the more dense and less interactive the dialogue, the less satisfied the simulated clients were and the lower their ratings were of counselors' nonverbal effectiveness and affective demeanor (all relationships p<.05). Counselors' self-ratings of informativeness were also inversely related to use of technical terms (p<.05). Just as print material can be made more reader-friendly and effective following established guidelines, the medical dialogue may also be made more patient-centered and meaningful by having providers monitor their vocabulary and language, as well as the structural characteristics of interaction, thereby lowering the literacy demand of routine medical dialogue. These consequences are important for all patients but may be even more so for patients with restricted literacy.

New approaches to quantifying aerosol influence on the cloud radiative effect

DOE PAGES

Feingold, Graham; McComiskey, Allison; Yamaguchi, Takanobu; ...

2016-02-01

The topic of cloud radiative forcing associated with the atmospheric aerosol has been the focus of intense scrutiny for decades. The enormity of the problem is reflected in the need to understand aspects such as aerosol composition, optical properties, cloud condensation, and ice nucleation potential, along with the global distribution of these properties, controlled by emissions, transport, transformation, and sinks. Equally daunting is that clouds themselves are complex, turbulent, microphysical entities and, by their very nature, ephemeral and hard to predict. Atmospheric general circulation models represent aerosol–cloud interactions at ever-increasing levels of detail, but these models lack the resolution tomore » represent clouds and aerosol–cloud interactions adequately. There is a dearth of observational constraints on aerosol–cloud interactions. In this paper, we develop a conceptual approach to systematically constrain the aerosol–cloud radiative effect in shallow clouds through a combination of routine process modeling and satellite and surface-based shortwave radiation measurements. Finally, we heed the call to merge Darwinian and Newtonian strategies by balancing microphysical detail with scaling and emergent properties of the aerosol–cloud radiation system.« less

Compensated Sex and Sexual Risk: Sexual, Social and Economic Interactions between Homosexually- and Heterosexually-Identified Men of Low Income in Two Cities of Peru

PubMed Central

Fernández-Dávila, Percy; Salazar, Ximena; Cáceres, Carlos F.; Maiorana, Andre; Kegeles, Susan; Coates, Thomas J.; Martinez, Josefa

2009-01-01

This study describes the complex dynamics of the sexual, economic and social interactions between a group of feminized homosexual men and men who have sex with men and self-identify as heterosexual (‘mostaceros’), in lower-income peripheral urban areas of Lima and Trujillo, Peru. The study examined sexual risk between these two groups of men, and the significance of the economic exchanges involved in their sexual interactions. Using a Grounded Theory approach, 23 individual interviews and 7 focus groups were analyzed. The results reveal that cultural, economic and gender factors mold sexual and social relations among a group of men who have sex with men in Peru. Compensated sex is part of the behaviors of these men, reflecting a complicated construction of sexuality based on traditional conceptions of gender roles, sexual identity and masculinity. Several factors (e.g. difficulty in negotiating condom use, low self-esteem, low risk perception, alcohol and drug consumption), in the context of compensated sex, play a role in risk-taking for HIV infection. PMID:19890491

New approaches to quantifying aerosol influence on the cloud radiative effect

PubMed Central

Feingold, Graham; McComiskey, Allison; Yamaguchi, Takanobu; Johnson, Jill S.; Carslaw, Kenneth S.; Schmidt, K. Sebastian

2016-01-01

The topic of cloud radiative forcing associated with the atmospheric aerosol has been the focus of intense scrutiny for decades. The enormity of the problem is reflected in the need to understand aspects such as aerosol composition, optical properties, cloud condensation, and ice nucleation potential, along with the global distribution of these properties, controlled by emissions, transport, transformation, and sinks. Equally daunting is that clouds themselves are complex, turbulent, microphysical entities and, by their very nature, ephemeral and hard to predict. Atmospheric general circulation models represent aerosol−cloud interactions at ever-increasing levels of detail, but these models lack the resolution to represent clouds and aerosol−cloud interactions adequately. There is a dearth of observational constraints on aerosol−cloud interactions. We develop a conceptual approach to systematically constrain the aerosol−cloud radiative effect in shallow clouds through a combination of routine process modeling and satellite and surface-based shortwave radiation measurements. We heed the call to merge Darwinian and Newtonian strategies by balancing microphysical detail with scaling and emergent properties of the aerosol−cloud radiation system. PMID:26831092

Novel use of UV broad-band excitation and stretched exponential function in the analysis of fluorescent dissolved organic matter: study of interaction between protein and humic-like components

NASA Astrophysics Data System (ADS)

Panigrahi, Suraj Kumar; Mishra, Ashok Kumar

2017-09-01

A combination of broad-band UV radiation (UV A and UV B; 250-400 nm) and a stretched exponential function (StrEF) has been utilised in efforts towards convenient and sensitive detection of fluorescent dissolved organic matter (FDOM). This approach enables accessing the gross fluorescence spectral signature of both protein-like and humic-like components in a single measurement. Commercial FDOM components are excited with the broad-band UV excitation; the variation of spectral profile as a function of varying component ratio is analysed. The underlying fluorescence dynamics and non-linear quenching of amino acid moieties are studied with the StrEF (exp(-V[Q] β )). The complex quenching pattern reflects the inner filter effect (IFE) as well as inter-component interactions. The inter-component interactions are essentially captured through the ‘sphere of action’ and ‘dark complex’ models. The broad-band UV excitation ascertains increased excitation energy, resulting in increased population density in the excited state and thereby resulting in enhanced sensitivity.

Study of calixarenes thin films as chemical sensors for the detection of explosives

NASA Astrophysics Data System (ADS)

Montmeat, P.; Veignal, F.; Methivier, C.; Pradier, C. M.; Hairault, L.

2014-02-01

Calix(n)arenes (n = 4, 6, 8) are used as sensitive coatings for Quartz Crystal Microbalance (QCM)-based chemical sensors, and specially for the detection of dinitrotoluene as a model explosive molecule. Calix(n)arenes complex organic architectures were deposited by spray on gold-coated wafer surfaces, and DNT detection tests were performed by measuring both frequency changes and IR spectra during exposure to DNT vapours. The adsorption of DNT on calixarenes surface is proved by Polarisation Modulation Infrared Reflection-Absorption Spectroscopy (PM-IRRAS) experiments, which brings a chemical characterisation of the sensing surfaces. Kinetics of interaction of DNT with the surface was measured by QCM. When deposited onto QCM, calixarenes showed an excellent sensitivity to DNT vapours; no significant effect of the size of the cage was observed. The main drawback is the poor reversibility of these sensors, possibly due to a too strong interaction of dinitrotoluene inside the cage of the calixarenes, or to a loss of the ternary structure of these molecules, which in turn induces a loss of interaction strength with host molecules.

Changes in the interaction of resting-state neural networks from adolescence to adulthood.

PubMed

Stevens, Michael C; Pearlson, Godfrey D; Calhoun, Vince D

2009-08-01

This study examined how the mutual interactions of functionally integrated neural networks during resting-state fMRI differed between adolescence and adulthood. Independent component analysis (ICA) was used to identify functionally connected neural networks in 100 healthy participants aged 12-30 years. Hemodynamic timecourses that represented integrated neural network activity were analyzed with tools that quantified system "causal density" estimates, which indexed the proportion of significant Granger causality relationships among system nodes. Mutual influences among networks decreased with age, likely reflecting stronger within-network connectivity and more efficient between-network influences with greater development. Supplemental tests showed that this normative age-related reduction in causal density was accompanied by fewer significant connections to and from each network, regional increases in the strength of functional integration within networks, and age-related reductions in the strength of numerous specific system interactions. The latter included paths between lateral prefrontal-parietal circuits and "default mode" networks. These results contribute to an emerging understanding that activity in widely distributed networks thought to underlie complex cognition influences activity in other networks. (c) 2009 Wiley-Liss, Inc.

New approaches to quantifying aerosol influence on the cloud radiative effect.

PubMed

Feingold, Graham; McComiskey, Allison; Yamaguchi, Takanobu; Johnson, Jill S; Carslaw, Kenneth S; Schmidt, K Sebastian

2016-05-24

The topic of cloud radiative forcing associated with the atmospheric aerosol has been the focus of intense scrutiny for decades. The enormity of the problem is reflected in the need to understand aspects such as aerosol composition, optical properties, cloud condensation, and ice nucleation potential, along with the global distribution of these properties, controlled by emissions, transport, transformation, and sinks. Equally daunting is that clouds themselves are complex, turbulent, microphysical entities and, by their very nature, ephemeral and hard to predict. Atmospheric general circulation models represent aerosol-cloud interactions at ever-increasing levels of detail, but these models lack the resolution to represent clouds and aerosol-cloud interactions adequately. There is a dearth of observational constraints on aerosol-cloud interactions. We develop a conceptual approach to systematically constrain the aerosol-cloud radiative effect in shallow clouds through a combination of routine process modeling and satellite and surface-based shortwave radiation measurements. We heed the call to merge Darwinian and Newtonian strategies by balancing microphysical detail with scaling and emergent properties of the aerosol-cloud radiation system.

Strong Shock Propagating Over A Random Bed of Spherical Particles

NASA Astrophysics Data System (ADS)

Mehta, Yash; Salari, Kambiz; Jackson, Thomas L.; Balachandar, S.; Thakur, Siddharth

2017-11-01

The study of shock interaction with particles has been largely motivated because of its wide-ranging applications. The complex interaction between the compressible flow features, such as shock wave and expansion fan, and the dispersed phase makes this multi-phase flow very difficult to predict and control. In this talk we will be presenting results on fully resolved inviscid simulations of shock interaction with random bed of particles. One of the fascinating observations from these simulations are the flow field fluctuations due to the presence of randomly distributed particles. Rigorous averaging (Favre averaging) of the governing equations results in Reynolds stress like term, which can be classified as pseudo turbulence in this case. We have computed this ``Reynolds stress'' term along with individual fluctuations and the turbulent kinetic energy. Average pressure was also computed to characterize the strength of the transmitted and the reflected waves. This work was supported by the U.S. Department of Energy, National Nuclear Security Administration, Advanced Simulation and Computing Program, as a Cooperative Agreement under the Predictive Science Academic Alliance Program.

Nurturing Cultural Change in Care for Older People: Seeing the Cherry Tree Blossom.

PubMed

Snoeren, Miranda M W C; Janssen, Bienke M; Niessen, Theo J H; Abma, Tineke A

2016-12-01

There is a need for person-centred approaches and empowerment of staff within the residential care for older people; a movement called 'culture change'. There is however no single path for achieving culture change. With the aim of increasing understandings about cultural change processes and the promotion of cultural values and norms associated with person-centred practices, this article presents an action research project set on a unit in the Netherlands providing care for older people with dementia. The project is presented as a case study. This study examines what has contributed to the improvement of participation of older people with dementia in daily occupational and leisure activities according to practitioners. Data was collected by participant observation, interviews and focus groups. The results show that simultaneous to the improvement of the older people's involvement in daily activities a cultural transformation took place and that the care became more person-centred. Spontaneous interactions and responses rather than planned interventions, analysis and reflection contributed to this. Furthermore, it proved to be beneficial that the process of change and the facilitation of that process reflected the same values as those underlying the cultural change. It is concluded that changes arise from dynamic, interactive and non-linear processes which are complex in nature and difficult to predict and to control. Nevertheless, managers and facilitators can facilitate such change by generating movement through the introduction of small focused projects that meet the stakeholders' needs, by creating conditions for interaction and sense making, and by promoting the new desired cultural values.

Neural responses in songbird forebrain reflect learning rates, acquired salience, and stimulus novelty after auditory discrimination training.

PubMed

Bell, Brittany A; Phan, Mimi L; Vicario, David S

2015-03-01

How do social interactions form and modulate the neural representations of specific complex signals? This question can be addressed in the songbird auditory system. Like humans, songbirds learn to vocalize by imitating tutors heard during development. These learned vocalizations are important in reproductive and social interactions and in individual recognition. As a model for the social reinforcement of particular songs, male zebra finches were trained to peck for a food reward in response to one song stimulus (GO) and to withhold responding for another (NoGO). After performance reached criterion, single and multiunit neural responses to both trained and novel stimuli were obtained from multiple electrodes inserted bilaterally into two songbird auditory processing areas [caudomedial mesopallium (CMM) and caudomedial nidopallium (NCM)] of awake, restrained birds. Neurons in these areas undergo stimulus-specific adaptation to repeated song stimuli, and responses to familiar stimuli adapt more slowly than to novel stimuli. The results show that auditory responses differed in NCM and CMM for trained (GO and NoGO) stimuli vs. novel song stimuli. When subjects were grouped by the number of training days required to reach criterion, fast learners showed larger neural responses and faster stimulus-specific adaptation to all stimuli than slow learners in both areas. Furthermore, responses in NCM of fast learners were more strongly left-lateralized than in slow learners. Thus auditory responses in these sensory areas not only encode stimulus familiarity, but also reflect behavioral reinforcement in our paradigm, and can potentially be modulated by social interactions. Copyright © 2015 the American Physiological Society.

Core–shell interaction and its impact on the optical absorption of pure and doped core-shell CdSe/ZnSe nanoclusters

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

Wang, Xinqin; Cui, Yingqi; Zeng, Qun

The structural, electronic, and optical properties of core-shell nanoclusters, (CdSe){sub x}@(CdSe){sub y} and their Zn-substituted complexes of x = 2–4 and y = 16–28, were studied with density functional theory calculations. The substitution was applied in the cores, the shells, and/or the whole clusters. All these clusters are characterized by their core-shell structures in which the core-shell interaction was found different from those in core or in shell, as reflected by their bondlengths, volumes, and binding energies. Moreover, the core and shell combine together to compose a new cluster with electronic and optical properties different from those of separated individuals,more » as reflected by their HOMO-LUMO gaps and optical absorptions. With the substitution of Cd by Zn, the structural, electronic, and optical properties of clusters change regularly. The binding energy increases with Zn content, attributed to the strong Zn–Se bonding. For the same core/shell, the structure with a CdSe shell/core has a narrower gap than that with a ZnSe shell/core. The optical absorption spectra also change accordingly with Zn substitution. The peaks blueshift with increasing Zn concentration, accompanying with shape variations in case large number of Cd atoms are substituted. Our calculations reveal the core-shell interaction and its influence on the electronic and optical properties of the core-shell clusters, suggesting a composition–structure–property relationship for the design of core-shell CdSe and ZnSe nanoclusters.« less

Neuroimaging predictors of AED resistance in new-onset epilepsies.

PubMed

Cendes, Fernando

2011-07-01

The best prognostic factors in early-onset epilepsies are the response to the first antiepileptic drug (AED) trial, age at seizure onset, number of seizures prior to treatment, and the presence of a lesion or abnormal neurologic examination. However, early and adequate response to AED is most likely an epiphenomenon reflecting the nature of underlying epileptogenicity, which may be defined as a complex interaction of underlying pathology, genetics, and environment. Patients with the same type of epileptogenic lesion, for example, hippocampal sclerosis, may have a varying response to AED. Modern neuroimaging, in particular quantitative magnetic resonance imaging (MRI) techniques may be helpful to better understand this complex interaction of factors leading to refractoriness. Patients who respond well to AEDs have no or minor MRI abnormalities, and among those with underlying lesions there is an inverse correlation between outcome and the extent of MRI-defined neuronal damage outside the main lesion, which may be undetectable by visual analyses of routine MRI. The extent of neuronal damage appears to be related to the severity of initial precipitating injuries, probably interacts with genetic factors, and may progress over time when seizures are uncontrolled. The presence and extent of abnormalities detected by quantitative MRI may also be helpful to guide AED withdrawal in those patients who are seizure free for >2 years. Combined MRI measures may have potential clinical value for predicting AED response in near future. Wiley Periodicals, Inc. © 2011 International League Against Epilepsy.

RNAi High-Throughput Screening of Single- and Multi-Cell-Type Tumor Spheroids: A Comprehensive Analysis in Two and Three Dimensions.

PubMed

Fu, Jiaqi; Fernandez, Daniel; Ferrer, Marc; Titus, Steven A; Buehler, Eugen; Lal-Nag, Madhu A

2017-06-01

The widespread use of two-dimensional (2D) monolayer cultures for high-throughput screening (HTS) to identify targets in drug discovery has led to attrition in the number of drug targets being validated. Solid tumors are complex, aberrantly growing microenvironments that harness structural components from stroma, nutrients fed through vasculature, and immunosuppressive factors. Increasing evidence of stromally-derived signaling broadens the complexity of our understanding of the tumor microenvironment while stressing the importance of developing better models that reflect these interactions. Three-dimensional (3D) models may be more sensitive to certain gene-silencing events than 2D models because of their components of hypoxia, nutrient gradients, and increased dependence on cell-cell interactions and therefore are more representative of in vivo interactions. Colorectal cancer (CRC) and breast cancer (BC) models composed of epithelial cells only, deemed single-cell-type tumor spheroids (SCTS) and multi-cell-type tumor spheroids (MCTS), containing fibroblasts were developed for RNAi HTS in 384-well microplates with flat-bottom wells for 2D screening and round-bottom, ultra-low-attachment wells for 3D screening. We describe the development of a high-throughput assay platform that can assess physiologically relevant phenotypic differences between screening 2D versus 3D SCTS, 3D SCTS, and MCTS in the context of different cancer subtypes. This assay platform represents a paradigm shift in how we approach drug discovery that can reduce the attrition rate of drugs that enter the clinic.

Reflective Silvered Polyimide Films Via In Situ Thermal Reduction Silver (I) Complexes

NASA Technical Reports Server (NTRS)

Southward, Robin E. (Inventor); Thompson, David W. (Inventor); St.Clair, Anne K. (Inventor); Stoakley, Diane M. (Inventor)

2000-01-01

Self-metallizing. flexible polyimide films with highly reflective surfaces are prepared by an in situ self-metallization procedure involving thermally initiated reduction of polymer-soluble silver(I) complexes. Polyamic acid solutions are doped with silver(I) acetate and solubilizing agents. Thermally curing the silver(I) doped resins leads to flexible. metallized films which have reflectivities as high as 100%. abrasion-resistant surfaces. thermal stability and, in some cases, electrical conductivity, rendering them useful for space applications.

First and Higher Order Effects on Zero Order Radiative Transfer Model

NASA Astrophysics Data System (ADS)

Neelam, M.; Mohanty, B.

2014-12-01

Microwave radiative transfer model are valuable tool in understanding the complex land surface interactions. Past literature has largely focused on local sensitivity analysis for factor priotization and ignoring the interactions between the variables and uncertainties around them. Since land surface interactions are largely nonlinear, there always exist uncertainties, heterogeneities and interactions thus it is important to quantify them to draw accurate conclusions. In this effort, we used global sensitivity analysis to address the issues of variable uncertainty, higher order interactions, factor priotization and factor fixing for zero-order radiative transfer (ZRT) model. With the to-be-launched Soil Moisture Active Passive (SMAP) mission of NASA, it is very important to have a complete understanding of ZRT for soil moisture retrieval to direct future research and cal/val field campaigns. This is a first attempt to use GSA technique to quantify first order and higher order effects on brightness temperature from ZRT model. Our analyses reflect conditions observed during the growing agricultural season for corn and soybeans in two different regions in - Iowa, U.S.A and Winnipeg, Canada. We found that for corn fields in Iowa, there exist significant second order interactions between soil moisture, surface roughness parameters (RMS height and correlation length) and vegetation parameters (vegetation water content, structure and scattering albedo), whereas in Winnipeg, second order interactions are mainly due to soil moisture and vegetation parameters. But for soybean fields in both Iowa and Winnipeg, we found significant interactions only to exist between soil moisture and surface roughness parameters.

Ethylene-responsive element-binding factor 5, ERF5, is involved in chitin-induced innate immunity response.

PubMed

Son, Geon Hui; Wan, Jinrong; Kim, Hye Jin; Nguyen, Xuan Canh; Chung, Woo Sik; Hong, Jong Chan; Stacey, Gary

2012-01-01

Our recent work demonstrated that chitin treatment modulated the expression of 118 transcription factor (TF) genes in Arabidopsis. To investigate the potential roles of these TF in chitin signaling and plant defense, we initiated an interaction study among these TF proteins, as well as two chitin-activated mitogen-activated protein kinases (MPK3 and MPK6), using a yeast two-hybrid system. This study revealed interactions among the following proteins: three ethylene-responsive element-binding factors (ERF), five WRKY transcription factors, one scarecrow-like (SCL), and the two MPK, in addition to many other interactions, reflecting a complex TF interaction network. Most of these interactions were subsequently validated by other methods, such as pull-down and in planta bimolecular fluorescence complementation assays. The key node ERF5 was shown to interact with multiple proteins in the network, such as ERF6, ERF8, and SCL13, as well as MPK3 and MPK6. Interestingly, ERF5 appeared to negatively regulate chitin signaling and plant defense against the fungal pathogen Alternaria brassicicola and positively regulate salicylic acid signaling and plant defense against the bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Therefore, ERF5 may play an important role in plant innate immunity, likely through coordinating chitin and other defense pathways in plants in response to different pathogens.

Optical magnetic mirrors without metals

DOE PAGES

Liu, Sheng; Sinclair, Michael B.; Mahony, Thomas S.; ...

2014-01-01

The reflection of an optical wave from metal, arising from strong interactions between the optical electric field and the free carriers of the metal, is accompanied by a phase reversal of the reflected electric field. A far less common route to achieving high reflectivity exploits strong interactions between the material and the optical magnetic field to produce a “magnetic mirror” that does not reverse the phase of the reflected electric field. At optical frequencies, the magnetic properties required for strong interaction can be achieved only by using artificially tailored materials. Here, we experimentally demonstrate, for the first time to themore » best of our knowledge, the magnetic mirror behavior of a low-loss all-dielectric metasurface at infrared optical frequencies through direct measurements of the phase and amplitude of the reflected optical wave. The enhanced absorption and emission of transverse-electric dipoles placed close to magnetic mirrors can lead to exciting new advances in sensors, photodetectors, and light sources.« less

Human interaction with robotic systems: performance and workload evaluations.

PubMed

Reinerman-Jones, L; Barber, D J; Szalma, J L; Hancock, P A

2017-10-01

We first tested the effect of differing tactile informational forms (i.e. directional cues vs. static cues vs. dynamic cues) on objective performance and perceived workload in a collaborative human-robot task. A second experiment evaluated the influence of task load and informational message type (i.e. single words vs. grouped phrases) on that same collaborative task. In both experiments, the relationship of personal characteristics (attentional control and spatial ability) to performance and workload was also measured. In addition to objective performance and self-report of cognitive load, we evaluated different physiological responses in each experiment. Results showed a performance-workload association for directional cues, message type and task load. EEG measures however, proved generally insensitive to such task load manipulations. Where significant EEG effects were observed, right hemisphere amplitude differences predominated, although unexpectedly these latter relationships were negative. Although EEG measures were partially associated with performance, they appear to possess limited utility as measures of workload in association with tactile displays. Practitioner Summary: As practitioners look to take advantage of innovative tactile displays in complex operational realms like human-robotic interaction, associated performance effects are mediated by cognitive workload. Despite some patterns of association, reliable reflections of operator state can be difficult to discern and employ as the number, complexity and sophistication of these respective measures themselves increase.

Pharmacogenomic Approaches for Automated Medication Risk Assessment in People with Polypharmacy

PubMed Central

Liu, Jiazhen; Friedman, Carol; Finkelstein, Joseph

2018-01-01

Abstract Medication regimen may be optimized based on individual drug efficacy identified by pharmacogenomic testing. However, majority of current pharmacogenomic decision support tools provide assessment only of single drug-gene interactions without taking into account complex drug-drug and drug-drug-gene interactions which are prevalent in people with polypharmacy and can result in adverse drug events or insufficient drug efficacy. The main objective of this project was to develop comprehensive pharmacogenomic decision support for medication risk assessment in people with polypharmacy that simultaneously accounts for multiple drug and gene effects. To achieve this goal, the project addressed two aims: (1) development of comprehensive knowledge repository of actionable pharmacogenes; (2) introduction of scoring approaches reflecting potential adverse effect risk levels of complex medication regimens accounting for pharmacogenomic polymorphisms and multiple drug metabolizing pathways. After pharmacogenomic knowledge repository was introduced, a scoring algorithm has been built and pilot-tested using a limited data set. The resulting total risk score for frequently hospitalized older adults with polypharmacy (72.04±17.84) was statistically significantly different (p<0.05) from the total risk score for older adults with polypharmacy with low hospitalization rate (8.98±2.37). An initial prototype assessment demonstrated feasibility of our approach and identified steps for improving risk scoring algorithms.

Spatial diversity of rocky midlittoral macro-invertebrates associated with the endangered species Patella ferruginea (Mollusca: Gastropoda) of Tunisian coastline

NASA Astrophysics Data System (ADS)

Tlig-Zouari, Sabiha; Rabaoui, Lotfi; Fguiri, Hosni; Diawara, Moctar; Ben Hassine, Oum Kalthoum

2010-04-01

The present study focuses on horizontal spatial variability of benthic macrofauna associated with Patella ferruginea. Thirty-six samples collected at 12 transects belonging to 4 midlittoral sites along the rocky Tunisian coastline, were examined. A total of 44 species belonging to 5 taxa were found. Multivariate analysis applied on gathered data did not show a horizontal spatial variability at small scale (between transects), but at large scale, between sites as well as sectors. Thus, three groups of communities were identified (GI: Korbous and El Haouaria; GIIa: Zembra Island and GIIb: Kelibia). The distribution of species abundance within these groups revealed that crustaceans were the most abundant taxon, due to the overwhelming dominance of Chthamalus stellatus. This substratum appeared to create favourable micro-habitats for the installation of molluscs including gastropods. Regarding the low diversity index ( H') and evenness ( J), they seemed to reflect a disturbance and a demographic unbalance within these communities. The heterogeneity of substrate surface, created by C. stellatus specimens appeared to be caused by various complex interactions established between the key components of these communities in particular suspension feeders, predators, herbivorous molluscs and macroalgae. Thus, the dynamic status of each of these communities is the result of these complex interactions.

Phage or foe: an insight into the impact of viral predation on microbial communities.

PubMed

Fernández, Lucía; Rodríguez, Ana; García, Pilar

2018-05-01

Since their discovery, bacteriophages have been traditionally regarded as the natural enemies of bacteria. However, recent advances in molecular biology techniques, especially data from "omics" analyses, have revealed that the interplay between bacterial viruses and their hosts is far more intricate than initially thought. On the one hand, we have become more aware of the impact of viral predation on the composition and genetic makeup of microbial communities thanks to genomic and metagenomic approaches. Moreover, data obtained from transcriptomic, proteomic, and metabolomic studies have shown that responses to phage predation are complex and diverse, varying greatly depending on the bacterial host, phage, and multiplicity of infection. Interestingly, phage exposure may alter different phenotypes, including virulence and biofilm formation. The complexity of the interactions between microbes and their viral predators is also evidenced by the link between quorum-sensing signaling pathways and bacteriophage resistance. Overall, new data increasingly suggests that both temperate and virulent phages have a positive effect on the evolution and adaptation of microbial populations. From this perspective, further research is still necessary to fully understand the interactions between phage and host under conditions that allow co-existence of both populations, reflecting more accurately the dynamics in natural microbial communities.

Interactional dynamics of same-sex marriage legislation in the United States

PubMed Central

2017-01-01

Understanding how people form opinions and make decisions is a complex phenomenon that depends on both personal practices and interactions. Recent availability of real-world data has enabled quantitative analysis of opinion formation, which illuminates phenomena that impact physical and social sciences. Public policies exemplify complex opinion formation spanning individual and population scales, and a timely example is the legalization of same-sex marriage in the United States. Here, we seek to understand how this issue captures the relationship between state-laws and Senate representatives subject to geographical and ideological factors. Using distance-based correlations, we study how physical proximity and state-government ideology may be used to extract patterns in state-law adoption and senatorial support of same-sex marriage. Results demonstrate that proximal states have similar opinion dynamics in both state-laws and senators’ opinions, and states with similar state-government ideology have analogous senators’ opinions. Moreover, senators’ opinions drive state-laws with a time lag. Thus, change in opinion not only results from negotiations among individuals, but also reflects inherent spatial and political similarities and temporal delays. We build a social impact model of state-law adoption in light of these results, which predicts the evolution of state-laws legalizing same-sex marriage over the last three decades. PMID:28680669

Challenges in devising economic spray thresholds for a major pest of Australian canola, the redlegged earth mite (Halotydeus destructor).

PubMed

Arthur, Aston L; Hoffmann, Ary A; Umina, Paul A

2015-10-01

A key component for spray decision-making in IPM programmes is the establishment of economic injury levels (EILs) and economic thresholds (ETs). We aimed to establish an EIL for the redlegged earth mite (Halotydeus destructor Tucker) on canola. Complex interactions between mite numbers, feeding damage and plant recovery were found, highlighting the challenges in linking H. destructor numbers to yield. A guide of 10 mites plant(-1) was established at the first-true-leaf stage; however, simple relationships were not evident at other crop development stages, making it difficult to establish reliable EILs based on mite number. Yield was, however, strongly associated with plant damage and plant densities, reflecting the impact of mite feeding damage and indicating a plant-based alternative for establishing thresholds for H. destructor. Drawing on data from multiple field trials, we show that plant densities below 30-40 plants m(-2) could be used as a proxy for mite damage when reliable estimates of mite densities are not possible. This plant-based threshold provides a practical tool that avoids the difficulties of accurately estimating mite densities. The approach may be applicable to other situations where production conditions are unpredictable and interactions between pests and plant hosts are complex. © 2015 Society of Chemical Industry.

Interactional dynamics of same-sex marriage legislation in the United States.

PubMed

Roy, Subhradeep; Abaid, Nicole

2017-06-01

Understanding how people form opinions and make decisions is a complex phenomenon that depends on both personal practices and interactions. Recent availability of real-world data has enabled quantitative analysis of opinion formation, which illuminates phenomena that impact physical and social sciences. Public policies exemplify complex opinion formation spanning individual and population scales, and a timely example is the legalization of same-sex marriage in the United States. Here, we seek to understand how this issue captures the relationship between state-laws and Senate representatives subject to geographical and ideological factors. Using distance-based correlations, we study how physical proximity and state-government ideology may be used to extract patterns in state-law adoption and senatorial support of same-sex marriage. Results demonstrate that proximal states have similar opinion dynamics in both state-laws and senators' opinions, and states with similar state-government ideology have analogous senators' opinions. Moreover, senators' opinions drive state-laws with a time lag. Thus, change in opinion not only results from negotiations among individuals, but also reflects inherent spatial and political similarities and temporal delays. We build a social impact model of state-law adoption in light of these results, which predicts the evolution of state-laws legalizing same-sex marriage over the last three decades.

Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets.

PubMed

Formanowicz, Dorota; Kozak, Adam; Głowacki, Tomasz; Radom, Marcin; Formanowicz, Piotr

2013-12-01

Systems biology approach to investigate biological phenomena seems to be very promising because it is capable to capture one of the fundamental properties of living organisms, i.e. their inherent complexity. It allows for analysis biological entities as complex systems of interacting objects. The first and necessary step of such an analysis is building a precise model of the studied biological system. This model is expressed in the language of some branch of mathematics, as for example, differential equations. During the last two decades the theory of Petri nets has appeared to be very well suited for building models of biological systems. The structure of these nets reflects the structure of interacting biological molecules and processes. Moreover, on one hand, Petri nets have intuitive graphical representation being very helpful in understanding the structure of the system and on the other hand, there is a lot of mathematical methods and software tools supporting an analysis of the properties of the nets. In this paper a Petri net based model of the hemojuvelin-hepcidin axis involved in the maintenance of the human body iron homeostasis is presented. The analysis based mainly on T-invariants of the model properties has been made and some biological conclusions have been drawn. Copyright © 2013 Elsevier Inc. All rights reserved.

Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.

PubMed

Yang, Ming; Ge, Yan; Wu, Jiayan; Xiao, Jingfa; Yu, Jun

2011-05-20

Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. Copyright © 2011. Published by Elsevier Ltd.

Attosecond electromagnetic pulse generation due to the interaction of a relativistic soliton with a breaking-wake plasma wave.

PubMed

Isanin, A V; Bulanov, S S; Kamenets, F F; Pegoraro, F

2005-03-01

During the interaction of a low-frequency relativistic soliton with the electron density modulations of a wake plasma wave, part of the electromagnetic energy of the soliton is reflected in the form of an extremely short and ultraintense electromagnetic pulse. We calculate the spectra of the reflected and of the transmitted electromagnetic pulses analytically. The reflected wave has the form of a single cycle attosecond pulse.

Enrichment of trace elements in garnet amphibolites from a paleo-subduction zone: Catalina Schist, southern California

USGS Publications Warehouse

Sorensen, Sorena S.; Grossman, J.N.

1989-01-01

The abundance, P-T stability, solubility, and element-partitioning behavior of minerals such as rutile, garnet, sphene, apatite, zircon, zoisite, and allanite are critical variables in models for mass transfer from the slab to the mantle wedge in deep regions of subduction zones. The influence of these minerals on the composition of subduction-related magmas has been inferred (and disputed) from inverse modelling of the geochemistry of island-arc basalt, or by experiment. Although direct samples of the dehydration + partial-melting region of a mature subduction zone have not been reported from subduction complexes, garnet amphibolites from melanges of circumpacific and Caribbean blueschist terranes reflect high T (>600??C) conditions in shallower regions. Such rocks record geochemical processes that affected deep-seated, high-T portions of paleo-subduction zones. In the Catalina Schist, a subduction-zone metamorphic terrane of southern California, metasomatized and migmatitic garnet amphibolites occur as blocks in a matrix of meta-ultramafic rocks. This mafic and ultramafic complex may represent either slab-derived material accreted to the mantle wedge of a nascent subduction zone or a portion of a shear zone closely related to the slab-mantle wedge contact, or both. The trace-element geochemistry of the complex and the distribution of trace elements among the minerals of garnet amphibolites were studied by INAA, XRF, electron microprobe, and SEM. In order of increasing alteration from a probable metabasalt protolith, three common types of garnet amphibolite blocks in the Catalina Schist are: (1) non-migmatitic, clinopyroxene-bearing blocks, which are compositionally similar to MORB that has lost an albite component; (2) garnet-amphibolite blocks, which have rinds that reflect local interaction between metabasite, metaperidotite, and fluid; and (3) migmatites that are extremely enriched in Th, HFSE, LREE, and other trace elements. These trace-element enrichments are mineralogically controlled by rutile, garnet, sphene, apatite, zircon, zoisite, and allanite. Alkali and alkaline earth elements are much less enriched in the solid assemblage, and thus appear to be decoupled from the other elements in the inferred metasomatic process(es). The compositions of migmatitic garnet amphibolite blocks seem to complement that of "average" island-arc tholeiite. Trace-element metasomatism reflects fluid-solid, rather than melt-solid, interaction. The metasomatic effects indicate that H2O-rich fluid, perhaps with a significant component of Na-Al silicate and alkalis, carried Th, U, Sr, REE, and HFSE. Fractionations of LREE in migmatites resemble those of migmatitic metasedimentary rocks underlying the mafic and ultramafic complex. "Exotic" LREE deposited in allanite in migmatites could have been derived from fluids in equilibrium with subducted sediment. If the paleo-subduction zone represented by the mafic and ultramafic complex of the Catalina Schist had continued its thermal and fluid evolution, a selvage of similarly enriched rocks might have been generated along the slab-mantle wedge contact between ~30 and 85 km depth. Rocks affected by "subduction-zone metasomatism," although rarely recognized at the surface, could be volumetrically significant products of the initiation of subduction and may prove to be geochemical probes of convergent margins that approach the significance of xenoliths in the study of other magmatic environments. ?? 1989.

FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility.

PubMed

Marcu, Orly; Dodson, Emma-Joy; Alam, Nawsad; Sperber, Michal; Kozakov, Dima; Lensink, Marc F; Schueler-Furman, Ora

2017-03-01

CAPRI rounds 28 and 29 included, for the first time, peptide-receptor targets of three different systems, reflecting increased appreciation of the importance of peptide-protein interactions. The CAPRI rounds allowed us to objectively assess the performance of Rosetta FlexPepDock, one of the first protocols to explicitly include peptide flexibility in docking, accounting for peptide conformational changes upon binding. We discuss here successes and challenges in modeling these targets: we obtain top-performing, high-resolution models of the peptide motif for cases with known binding sites but there is a need for better modeling of flanking regions, as well as better selection criteria, in particular for unknown binding sites. These rounds have also provided us the opportunity to reassess the success criteria, to better reflect the quality of a peptide-protein complex model. Using all models submitted to CAPRI, we analyze the correlation between current classification criteria and the ability to retrieve critical interface features, such as hydrogen bonds and hotspots. We find that loosening the backbone (and ligand) RMSD threshold, together with a restriction on the side chain RMSD measure, allows us to improve the selection of high-accuracy models. We also suggest a new measure to assess interface hydrogen bond recovery, which is not assessed by the current CAPRI criteria. Finally, we find that surprisingly much can be learned from rather inaccurate models about binding hotspots, suggesting that the current status of peptide-protein docking methods, as reflected by the submitted CAPRI models, can already have a significant impact on our understanding of protein interactions. Proteins 2017; 85:445-462. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Contraction and Expansion of the Upper Zambezi Wetlands in Response to Precipitation Regime Changes and Impacts on Carbon, Energy and Water Fluxes

NASA Astrophysics Data System (ADS)

Lowman, L.; Barros, A. P.

2017-12-01

The Upper Zambezi River Basin (UZRB) serves as the headwater catchment of the fourth-largest river in Africa, provides essential freshwater resources to arid and semi-arid regions within its boundaries, and recharges the Northern Kalahari Aquifer. Shallow and clayey soils give way to seasonal waterlogging, especially along drainage lines, favoring the establishment of wetlands. Woodland savanna, grasslands and miombo dominate the UZRB's diverse ecosystem, marking a complex transition zone between the Congo tropical rainforest and the Kalahari Desert that reflects spatial rainfall gradients. Satellite imagery shows that permanent wetlands are located in low-lying convergence zones in the northeast and northwest corners of UZRB where surface-groundwater interactions are most vigorous. However, orographic precipitation gradients cannot fully explain interannual changes in wetland area and vegetation density. We hypothesize that changes in vegetation density result from nonlinear interactions and feedbacks among precipitation, canopy biophysical properties, soil moisture and groundwater processes modulated by topography and regional hydrogeology. This work aims to understand how changes in vegetation density, particularly in and around permanent and intermittent wetlands, impact carbon, energy and water fluxes. Using the MODIS Nadir BRDF-Adjusted Reflectance product, a seasonally-varying wetland class is derived that reflects inter-annual precipitation and groundwater variability. The Duke Coupled Hydrology Model with Prognostic Vegetation is adapted to include C4 photosynthesis for the UZRB grasslands and used to simulate changes in canopy density and impacts on gross primary productivity, evapotranspiration, and soil moisture at high spatial and temporal resolution. Initial results using the column-wise model provide a baseline for understanding surface fluxes before incorporating groundwater and subsurface flows crucial to investigating the implicit nonlinearities of the region.

An improved approach to the analysis of drug-protein binding by distance geometry

NASA Technical Reports Server (NTRS)

Goldblum, A.; Kieber-Emmons, T.; Rein, R.

1986-01-01

The calculation of side chain centers of coordinates and the subsequent generation of side chain-side chain and side chain-backbone distance matrices is suggested as an improved method for viewing interactions inside proteins and for the comparison of protein structures. The use of side chain distance matrices is demonstrated with free PTI, and the use of difference distance matrices for side chains is shown for free and trypsin-bound PTI as well as for the X-ray structures of trypsin complexes with PTI and with benzamidine. It is found that conformational variations are reflected in the side chain distance matrices much more than in the standard C-C distance representations.

Skin Color in the Development of Identity: A Biopsychosocial Model

PubMed Central

Fullilove, Mindy Thompson; Reynolds, Tyrone

1984-01-01

The role of skin color in the development of identity has been studied by a variety of paradigms. This paper applies the biopsychosocial model to this problem, with the hope that systems hierarchies offer a way to understand how many variables have an impact on a single point. This model postulates that complex social interactions are the life setting for the individual whose development also reflects biological endowment, including the contributions of heredity and nurturance. The final personal integration of an adult understanding of skin color requires an active assertion by the individual. This model is explored through the writings of Jessie Fauset, a leading participant in the literary movement known as the Harlem Renaissance. PMID:6748102

Interrogating ultrafast dynamics of a salicylideneaniline derivative within faujasite zeolites

NASA Astrophysics Data System (ADS)

Alarcos, Noemí; Sánchez, Félix; Douhal, Abderrazzak

2017-09-01

We report on femtosecond (fs) studies of (E)-2-(2-hydroxybenzyliden) amino-4-nitrophenol (HBA-4NP) in dichloromethane (DCM) and triacetin (TAC) solutions, and within NaX and NaY zeolites. In solution, an ultrafast (≤80 fs) excited-state intramolecular proton-transfer (ESIPT) reaction produces a keto (K) tautomer, which undergoes a rotational process in ∼4 (DCM) and ∼7 ps (TAC) toward the formation of non-emitting structures. Within NaX and NaY, where monomers and aggregates are formed, host-guest and guest-guest interactions play an important role in the ultrafast behaviour of these complexes. These results clearly reflect how nanoconfinement and zeolite composition affect the encapsulated dye photodynamics.

A combined case of macroprolactinoma, growth hormone excess and Graves' disease.

PubMed

Hussein, Z; Tress, B; Colman, P G

2005-06-01

Thyrotoxicosis due to Graves disease is a relatively common endocrine disorder. The occurrence of a prolactinoma with co-secretion of growth hormone (GH) is on the other hand, rare. We report the rare co-existence of Graves' disease in a patient with macroprolactinoma and GH hypersecretion and describe the successful response to medical therapy with dopamine agonist and antithyroid therapy. We hypothesize that hyperprolactinaemia played a role in promoting autoimmune thyroid disease in our patient and that treatment of hyperprolactinaemia may have been important in suppressing autoimmune disease activity in Graves' disease. This case also reflects on the close and complex interactions between thyroid hormones, prolactin (PRL), GH and testosterone (T).

Cognitive and Learning Impairments

NASA Astrophysics Data System (ADS)

Lewis, Clayton

People with cognitive disabilities are gaining in a long struggle for recognition of their right to control their lives. In the information society access to the Web is essential to this control. Cognitive barriers to this access are diverse, reflecting the complexity of human cognitive faculties. These barriers are not well managed in current accessibility practice and policy, in part because cognitive accessibility, like usability, cannot be reduced to a checklist of simple attributes. Advances in representing the meaning as well as the form of information, and in supporting configurable presentation and interaction methods, will yield progress. Increased inclusion of people with cognitive disabilities in the processes of technology development and policy making will also pay off.

Embodied Space: a Sensorial Approach to Spatial Experience

NASA Astrophysics Data System (ADS)

Durão, Maria João

2009-03-01

A reflection is presented on the significance of the role of the body in the interpretation and future creation of spatial living structures. The paper draws on the body as cartography of sensorial meaning that includes vision, touch, smell, hearing, orientation and movement to discuss possible relationships with psychological and sociological parameters of 'sensorial space'. The complex dynamics of body-space is further explored from the standpoint of perceptual variables such as color, light, materialities, texture and their connections with design, technology, culture and symbology. Finally, the paper discusses the integration of knowledge and experimentation in the design of future habitats where body-sensitive frameworks encompass flexibility, communication, interaction and cognitive-driven solutions.

What their terms of living and dying might be: hospice social workers discuss Oregon's Death with Dignity Act.

PubMed

Norton, Elizabeth M; Miller, Pamela J

2012-01-01

This article presents data from a qualitative study of nine social work hospice practitioners and experts as they discuss Oregon's Death with Dignity Act. Three themes emerged from the analysis: (a) values regarding physician-assisted death; (b) agency policies about the option; and (c) the role of hospice social workers with physician-assisted death. Three states now allow terminally ill persons to obtain a lethal prescription if criteria are met. Two other states are actively considering and may pass similar legislation over time. Hospice social work practitioners work with patients and families as they consider this option and their voices reflect the complexities and nuances of these interactions.

Transforming Violent Selves through Reflection in Critical Communicative Research

ERIC Educational Resources Information Center

Flecha, Ainhoa; Pulido, Cristina; Christou, Miranda

2011-01-01

Currently, teenagers are being socialized into a world of violent realities, not only through social interaction but also through interaction via the media, especially via the Internet. Research conducted using the critical communicative methodology has shown that this methodology helps young people to reflect critically about their violent…

Interaction of a finite-length ion beam with a background plasma - Reflected ions at the quasi-parallel bow shock

NASA Technical Reports Server (NTRS)

Onsager, T. G.; Winske, D.; Thomsen, M. F.

1991-01-01

The coupling of a finite-length, field-aligned, ion beam with a uniform background plasma is investigated using one-dimensional hybrid computer simulations. The finite-length beam is used to study the interaction between the incident solar wind and ions reflected from the earth's quasi-parallel bow shock, where the reflection process may vary with time. The coupling between the reflected ions and the solar wind is relevant to ion heating at the bow shock and possibly to the formation of hot, flow anomalies and re-formation of the shock itself. Consistent with linear theory, the waves which dominate the interaction are the electromagnetic right-hand polarized resonant and nonresonant modes. However, in addition to the instability growth rates, the length of time that the waves are in contact with the beam is also an important factor in determining which wave mode will dominate the interaction. It is found that interaction will result in strong coupling, where a significant fraction of the available free energy is converted into thermal energy in a short time, provided the beam is sufficiently dense or sufficiently long.

Primary progressive aphasia and the evolving neurology of the language network

PubMed Central

Mesulam, M.-Marsel; Rogalski, Emily J.; Wieneke, Christina; Hurley, Robert S.; Geula, Changiz; Bigio, Eileen H.; Thompson, Cynthia K.; Weintraub, Sandra

2014-01-01

Primary progressive aphasia (PPA) is caused by selective neurodegeneration of the language-dominant cerebral hemisphere; a language deficit initially arises as the only consequential impairment and remains predominant throughout most of the course of the disease. Agrammatic, logopenic and semantic subtypes, each reflecting a characteristic pattern of language impairment and corresponding anatomical distribution of cortical atrophy, represent the most frequent presentations of PPA. Such associations between clinical features and the sites of atrophy have provided new insights into the neurology of fluency, grammar, word retrieval, and word comprehension, and have necessitated modification of concepts related to the functions of the anterior temporal lobe and Wernicke’s area. The underlying neuropathology of PPA is, most commonly, frontotemporal lobar degeneration in the agrammatic and semantic forms, and Alzheimer disease (AD) pathology in the logopenic form; the AD pathology often displays atypical and asymmetrical anatomical features consistent with the aphasic phenotype. The PPA syndrome reflects complex interactions between disease-specific neuropathological features and patient-specific vulnerability. A better understanding of these interactions might help us to elucidate the biology of the language network and the principles of selective vulnerability in neurodegenerative diseases. We review these aspects of PPA, focusing on advances in our understanding of the clinical features and neuropathology of PPA and what they have taught us about the neural substrates of the language network. PMID:25179257

Primary progressive aphasia and the evolving neurology of the language network.

PubMed

Mesulam, M-Marsel; Rogalski, Emily J; Wieneke, Christina; Hurley, Robert S; Geula, Changiz; Bigio, Eileen H; Thompson, Cynthia K; Weintraub, Sandra

2014-10-01

Primary progressive aphasia (PPA) is caused by selective neurodegeneration of the language-dominant cerebral hemisphere; a language deficit initially arises as the only consequential impairment and remains predominant throughout most of the course of the disease. Agrammatic, logopenic and semantic subtypes, each reflecting a characteristic pattern of language impairment and corresponding anatomical distribution of cortical atrophy, represent the most frequent presentations of PPA. Such associations between clinical features and the sites of atrophy have provided new insights into the neurology of fluency, grammar, word retrieval, and word comprehension, and have necessitated modification of concepts related to the functions of the anterior temporal lobe and Wernicke's area. The underlying neuropathology of PPA is, most commonly, frontotemporal lobar degeneration in the agrammatic and semantic forms, and Alzheimer disease (AD) pathology in the logopenic form; the AD pathology often displays atypical and asymmetrical anatomical features consistent with the aphasic phenotype. The PPA syndrome reflects complex interactions between disease-specific neuropathological features and patient-specific vulnerability. A better understanding of these interactions might help us to elucidate the biology of the language network and the principles of selective vulnerability in neurodegenerative diseases. We review these aspects of PPA, focusing on advances in our understanding of the clinical features and neuropathology of PPA and what they have taught us about the neural substrates of the language network.

Architecture of an Antagonistic Tree/Fungus Network: The Asymmetric Influence of Past Evolutionary History

PubMed Central

Vacher, Corinne; Piou, Dominique; Desprez-Loustau, Marie-Laure

2008-01-01

Background Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions. Methology/Principal Findings Based on a long-term (1972–2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns. Conclusion/Significance Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependant on recent ecological processes. PMID:18320058

Insights on the mechanism of action of immunostimulants in relation to their pharmacological potency. The effects of imidazoquinolines on TLR8.

PubMed

Kubli-Garfias, Carlos; Vázquez-Ramírez, Ricardo; Trejo-Muñoz, Cynthia; Berber, Arturo

2017-01-01

Imidazoquinolines are powerful immunostimulants (IMMS) that function through Toll-like receptors, particularly TLR7 and TLR8. In addition to enhancing the immune response, IMMS also function as antineoplastic drugs and vaccine adjuvants. These small compounds display almost the same molecular structure, except in some cases in which atom in position 1 varies and changes the imidazole characteristics. A variable acyclic side chain is also always attached at atom in position 2, while another chain may be attached at atom in position 1. These structural differences alter immune responses, such as the production of interferon regulatory factor and nuclear factor-κB (IRF-NFκB). In this work, quantum mechanics theory and computational chemistry methods were applied to study the physicochemical properties of the crystal binding site of TLR8 complexed with the following six IMMS molecules: Hybrid-2, XG1-236, DS802, CL075, CL097 and R848 (resiquimod). The PDB IDs of the crystals were: 4R6A, 4QC0, 4QBZ, 3W3K, 3W3J, and 3W3N respectively. Thus, were calculated, the total energy, solvation energy, interaction energy (instead of free energy) of the system and interaction energy of the polar region of the IMMS. Additionally, the dipole moment, electrostatic potential, polar surface, atomic charges, hydrogen bonds, and polar and hydrophobic interactions, among others, were assessed. Together, these properties revealed important differences among the six TLR8-immunostimulant complexes, reflected as different interaction energies and therefore different electrostatic environments and binding energies. Remarkably, the interaction energy of a defined polar region composed of the highly polarized N3, N5 atoms and the N11 amino group, acted as a polar pharmacophore that correlates directly with the reported immunopharmacological potency of the six complexed molecules. Based on these results, it was concluded that accurate physicochemical analysis of the crystal binding site could reveal the binding energy (measured as interaction energy) and associated molecular mechanism of action between IMMS and TLR8. These findings may facilitate the development and design of improved small molecules with IMMS properties that are targeted to the TLR system and have enhanced pharmacological effectiveness and reduced toxicity.

Insights on the mechanism of action of immunostimulants in relation to their pharmacological potency. The effects of imidazoquinolines on TLR8

PubMed Central

Kubli-Garfias, Carlos; Vázquez-Ramírez, Ricardo; Trejo-Muñoz, Cynthia; Berber, Arturo

2017-01-01

Imidazoquinolines are powerful immunostimulants (IMMS) that function through Toll-like receptors, particularly TLR7 and TLR8. In addition to enhancing the immune response, IMMS also function as antineoplastic drugs and vaccine adjuvants. These small compounds display almost the same molecular structure, except in some cases in which atom in position 1 varies and changes the imidazole characteristics. A variable acyclic side chain is also always attached at atom in position 2, while another chain may be attached at atom in position 1. These structural differences alter immune responses, such as the production of interferon regulatory factor and nuclear factor-κB (IRF-NFκB). In this work, quantum mechanics theory and computational chemistry methods were applied to study the physicochemical properties of the crystal binding site of TLR8 complexed with the following six IMMS molecules: Hybrid-2, XG1-236, DS802, CL075, CL097 and R848 (resiquimod). The PDB IDs of the crystals were: 4R6A, 4QC0, 4QBZ, 3W3K, 3W3J, and 3W3N respectively. Thus, were calculated, the total energy, solvation energy, interaction energy (instead of free energy) of the system and interaction energy of the polar region of the IMMS. Additionally, the dipole moment, electrostatic potential, polar surface, atomic charges, hydrogen bonds, and polar and hydrophobic interactions, among others, were assessed. Together, these properties revealed important differences among the six TLR8-immunostimulant complexes, reflected as different interaction energies and therefore different electrostatic environments and binding energies. Remarkably, the interaction energy of a defined polar region composed of the highly polarized N3, N5 atoms and the N11 amino group, acted as a polar pharmacophore that correlates directly with the reported immunopharmacological potency of the six complexed molecules. Based on these results, it was concluded that accurate physicochemical analysis of the crystal binding site could reveal the binding energy (measured as interaction energy) and associated molecular mechanism of action between IMMS and TLR8. These findings may facilitate the development and design of improved small molecules with IMMS properties that are targeted to the TLR system and have enhanced pharmacological effectiveness and reduced toxicity. PMID:28582454

The Dual Role of Vegetation as a Constraint on Mass and Energy Flux into the Critical Zone and as an Emergent Property of Geophysical Critical Zone Structure

NASA Astrophysics Data System (ADS)

Brooks, P. D.; Swetnam, T. L.; Barnard, H. R.; Singha, K.; Harpold, A.; Litvak, M. E.

2017-12-01

Spatial patterns in vegetation long have been used to scale both landsurface-atmosphere exchanges of water and carbon as well as to infer subsurface structure. These pursuits typical proceed in isolation and rarely do inferences gained from one community propagate to related efforts in another. Perhaps more importantly, vegetation often is treated as an emergent property of landscape-climate interactions rather than an active modifier of both critical zone structure and energy fluxes. We posit that vegetation structure and activity are under utilized as a tool towards understanding landscape evolution and present examples that begin to disentangle the role of vegetation as both an emergent property and an active control on critical zone structure and function. As climate change, population growth, and land use changes threaten water resources worldwide, the need for the new insights vegetation can provide becomes not just a basic science priority, but a pressing applied science question with clear societal importance. This presentation will provide an overview of recent efforts to address the dual role of vegetation in both modifying and reflecting critical zone structure in the western North American forests. For example, interactions between topography and stand scale vegetation structure influence both solar radiation and turbulence altering landscape scale partitioning of evaporation vs transpiration with major impacts of surface water supply. Similarly, interactions between topographic shading, lateral redistribution of plant available water, and subsurface storage create a mosaic of drought resistance and resilience across complex terrain. These complex interactions between geophysical and vegetation components of critical zone structure result in predictable patterns in catchment scale hydrologic partitioning within individual watersheds while simultaneously suggesting testable hypotheses for why catchments under similar climate regimes respond so differently to drought stress.

Pyridine Nucleotide Complexes with Bacillus anthracis Coenzyme A-Disulfide Reductase: A Structural Analysis of Dual NAD(P)H Specificity

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

Wallen,J.; Paige, C.; Mallett, T.

2008-01-01

We have recently reported that CoASH is the major low-molecular weight thiol in Bacillus anthracis, and we have now characterized the kinetic and redox properties of the B. anthracis coenzyme A-disulfide reductase (CoADR, BACoADR) and determined the crystal structure at 2.30 Angstroms resolution. While the Staphylococcus aureus and Borrelia burgdorferi CoADRs exhibit strong preferences for NADPH and NADH, respectively, B. anthracis CoADR can use either pyridine nucleotide equally well. Sequence elements within the respective NAD(P)H-binding motifs correctly reflect the preferences for S. aureus and Bo. burgdorferi CoADRs, but leave questions as to how BACoADR can interact with both pyridine nucleotides.more » The structures of the NADH and NADPH complexes at ca. 2.3 Angstroms resolution reveal that a loop consisting of residues Glu180-Thr187 becomes ordered and changes conformation on NAD(P)H binding. NADH and NADPH interact with nearly identical conformations of this loop; the latter interaction, however, involves a novel binding mode in which the 2'-phosphate of NADPH points out toward solvent. In addition, the NAD(P)H-reduced BACoADR structures provide the first view of the reduced form (Cys42-SH/CoASH) of the Cys42-SSCoA redox center. The Cys42-SH side chain adopts a new conformation in which the conserved Tyr367'-OH and Tyr425'-OH interact with the nascent thiol(ate) on the flavin si-face. Kinetic data with Y367F, Y425F, and Y367, 425F BACoADR mutants indicate that Tyr425' is the primary proton donor in catalysis, with Tyr367' functioning as a cryptic alternate donor in the absence of Tyr425'.« less

Modulation of Cytochrome P450 Metabolism and Transport across Intestinal Epithelial Barrier by Ginger Biophenolics

PubMed Central

Yang, Chunhua; Donthamsetty, Shashikiran; Cantuaria, Guilherme; Jadhav, Gajanan R.; Vangala, Subrahmanyam; Reid, Michelle D.; Aneja, Ritu

2014-01-01

Natural and complementary therapies in conjunction with mainstream cancer care are steadily gaining popularity. Ginger extract (GE) confers significant health-promoting benefits owing to complex additive and/or synergistic interactions between its bioactive constituents. Recently, we showed that preservation of natural “milieu” confers superior anticancer activity on GE over its constituent phytochemicals, 6-gingerol (6G), 8-gingerol (8G), 10-gingerol (10G) and 6-shogaol (6S), through enterohepatic recirculation. Here we further evaluate and compare the effects of GE and its major bioactive constituents on cytochrome P450 (CYP) enzyme activity in human liver microsomes by monitoring metabolites of CYP-specific substrates using LC/MS/MS detection methods. Our data demonstrate that individual gingerols are potent inhibitors of CYP isozymes, whereas GE exhibits a much higher half-maximal inhibition value, indicating no possible herb-drug interactions. However, GE's inhibition of CYP1A2 and CYP2C8 reflects additive interactions among the constituents. In addition, studies performed to evaluate transporter-mediated intestinal efflux using Caco-2 cells revealed that GE and its phenolics are not substrates of P-glycoprotein (Pgp). Intriguingly, however, 10G and 6S were not detected in the receiver compartment, indicating possible biotransformation across the Caco-2 monolayer. These data strengthen the notion that an interplay of complex interactions among ginger phytochemicals when fed as whole extract dictates its bioactivity highlighting the importance of consuming whole foods over single agents. Our study substantiates the need for an in-depth analysis of hepatic biotransformation events and distribution profiles of GE and its active phenolics for the design of safe regimens. PMID:25251219

Modelling and Order of Acoustic Transfer Functions Due to Reflections from Augmented Objects

NASA Astrophysics Data System (ADS)

Kuster, Martin; de Vries, Diemer

2006-12-01

It is commonly accepted that the sound reflections from real physical objects are much more complicated than what usually is and can be modelled by room acoustics modelling software. The main reason for this limitation is the level of detail inherent in the physical object in terms of its geometrical and acoustic properties. In the present paper, the complexity of the sound reflections from a corridor wall is investigated by modelling the corresponding acoustic transfer functions at several receiver positions in front of the wall. The complexity for different wall configurations has been examined and the changes have been achieved by altering its acoustic image. The results show that for a homogenous flat wall, the complexity is significant and for a wall including various smaller objects, the complexity is highly dependent on the position of the receiver with respect to the objects.

Particle-Surface Interaction Model and Method of Determining Particle-Surface Interactions

NASA Technical Reports Server (NTRS)

Hughes, David W. (Inventor)

2012-01-01

A method and model of predicting particle-surface interactions with a surface, such as the surface of a spacecraft. The method includes the steps of: determining a trajectory path of a plurality of moving particles; predicting whether any of the moving particles will intersect a surface; predicting whether any of the particles will be captured by the surface and/or; predicting a reflected trajectory and velocity of particles reflected from the surface.

Magnitude and nature of carbohydrate-aromatic interactions in fucose-phenol and fucose-indole complexes: CCSD(T) level interaction energy calculations.

PubMed

Tsuzuki, Seiji; Uchimaru, Tadafumi; Mikami, Masuhiro

2011-10-20

The CH/π contact structures of the fucose-phenol and fucose-indole complexes and the stabilization energies by formation of the complexes (E(form)) were studied by ab initio molecular orbital calculations. The three types of interactions (CH/π and OH/π interactions and OH/O hydrogen bonds) were compared and evaluated in a single molecular system and at the same level of theory. The E(form) calculated for the most stable CH/π contact structure of the fucose-phenol complex at the CCSD(T) level (-4.9 kcal/mol) is close to that for the most stable CH/π contact structure of the fucose-benzene complex (-4.5 kcal/mol). On the other hand the most stable CH/π contact structure of the fucose-indole complex has substantially larger E(form) (-6.5 kcal/mol). The dispersion interaction is the major source of the attraction in the CH/π contact structures of the fucose-phenol and fucose-indole complexes as in the case of the fucose-benzene complex. The electrostatic interactions in the CH/π contact structures are small (less than 1.5 kcal/mol). The nature of the interactions between the nonpolar surface of the carbohydrate and aromatic rings is completely different from that of the conventional hydrogen bonds where the electrostatic interaction is the major source of the attraction. The distributed multipole analysis and DFT-SATP analysis show that the dispersion interactions in the CH/π contact structure of fucose-indole complex are substantially larger than those in the CH/π contact structures of fucose-benzene and fucose-phenol complexes. The large dispersion interactions are responsible for the large E(form) for the fucose-indole complex.

Scaling in cognitive performance reflects multiplicative multifractal cascade dynamics

PubMed Central

Stephen, Damian G.; Anastas, Jason R.; Dixon, James A.

2012-01-01

Self-organized criticality purports to build multi-scaled structures out of local interactions. Evidence of scaling in various domains of biology may be more generally understood to reflect multiplicative interactions weaving together many disparate scales. The self-similarity of power-law scaling entails homogeneity: fluctuations distribute themselves similarly across many spatial and temporal scales. However, this apparent homogeneity can be misleading, especially as it spans more scales. Reducing biological processes to one power-law relationship neglects rich cascade dynamics. We review recent research into multifractality in executive-function cognitive tasks and propose that scaling reflects not criticality but instead interactions across multiple scales and among fluctuations of multiple sizes. PMID:22529819

Adsorption of Nucleic Acid/Protein Supramolecular Complexes on Goethite: The Influence of Solution Interactions on Behavior at the Solution-Mineral Interface

NASA Astrophysics Data System (ADS)

Schmidt, M.; Martinez, C. E.

2017-12-01

Adsorption of biomolecule rich supramolecular complexes onto mineral surfaces plays an important role in the development of organo-mineral associations in soils. In this study, a series of supramolecular complexes of a model nucleic acid (deoxyribonucleic acid (DNA)) and protein (bovine serum albumin (BSA)) are synthesized, characterized and exposed to goethite to probe their adsorption behavior. To synthesize DNA/BSA complexes, a fixed DNA concentration (0.1 mg/mL) was mixed with a range of BSA concentrations (0.025-0.5 mg/mL) in 5 mM KCl at pH=5.0. Circular dichroism spectroscopy demonstrates strong, cooperative, Hill-type binding between DNA and BSA (Ka= 4.74 x 105 M-1) with DNA saturation achieved when BSA concentration reaches 0.4 mg/mL. Dynamic light scattering measurements of DNA/BSA complexes suggest binding accompanies disruption of DNA-DNA intermolecular electrostatic repulsion, resulting in a decrease of the DNA slow relaxation mode with increasing amount of BSA. Zeta potential measurements show increasing amounts of BSA lead to a reduction of negative charge on DNA/BSA complexes, in line with light scattering results. In situ attenuated total reflectance Fourier transform infrared spectroscopic studies of adsorption of DNA/BSA complexes onto goethite show that complexation of BSA with DNA appears to hinder direct coordination of DNA backbone phosphodiester groups with goethite, relative to DNA by itself. Furthermore, increasing amount of BSA (up to 0.4 mg/mL) in DNA/BSA complexes enhances DNA adsorption, possibly as a result of reduced repulsion between adsorbed DNA helices. When BSA concentration exceeds 0.4 mg/mL, a decrease in adsorbed DNA is observed. We hypothesize that this discrepancy in behavior between systems with BSA concentrations below and above saturation of DNA is caused by initial fast adsorption of loosely associated BSA on goethite, restricting access to goethite surface sites. Overall, these results highlight the impact of solution interaction between biomolecules on subsequent behavior at mineral surfaces. This work represents a bridge between model experiments with individual biomolecules and more complex natural systems, yielding a fundamental viewpoint of the formation of organo-mineral associations in soils.

Developing and evaluating the implementation of a complex intervention: using mixed methods to inform the design of a randomised controlled trial of an oral healthcare intervention after stroke

PubMed Central

2011-01-01

Background Many interventions delivered within the stroke rehabilitation setting could be considered complex, though some are more complex than others. The degree of complexity might be based on the number of and interactions between levels, components and actions targeted within the intervention. The number of (and variation within) participant groups and the contexts in which it is delivered might also reflect the extent of complexity. Similarly, designing the evaluation of a complex intervention can be challenging. Considerations include the necessity for intervention standardisation, the multiplicity of outcome measures employed to capture the impact of a multifaceted intervention and the delivery of the intervention across different clinical settings operating within varying healthcare contexts. Our aim was to develop and evaluate the implementation of a complex, multidimensional oral health care (OHC) intervention for people in stroke rehabilitation settings which would inform the development of a randomised controlled trial. Methods After reviewing the evidence for the provision of OHC following stroke, multi-disciplinary experts informed the development of our intervention. Using both quantitative and qualitative methods we evaluated the implementation of the complex OHC intervention across patients, staff and service levels of care. We also adopted a pragmatic approach to patient recruitment, the completion of assessment tools and delivery of OHC, alongside an attention to the context in which it was delivered. Results We demonstrated the feasibility of implementing a complex OHC intervention across three levels of care. The complementary nature of the mixed methods approach to data gathering provided a complete picture of the implementation of the intervention and a detailed understanding of the variations within and interactions between the components of the intervention. Information on the feasibility of the outcome measures used to capture impact across a range of components was also collected, though some process orientated uncertainties including eligibility and recruitment rates remain to be further explored within a Phase II exploratory trial. Conclusions Complex interventions can be captured and described in a manner which facilitates evaluation in the form of exploratory and subsequently definitive clinical trials. If effective, the evidence captured relating to the intervention context will facilitate translation into clinical practice. PMID:21729277

Effect of end reflections on conversion efficiency of coaxial relativistic backward wave oscillator

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

Teng, Yan; Chen, Changhua; Sun, Jun

2015-11-07

This paper theoretically investigates the effect of end reflections on the operation of the coaxial relativistic backward wave oscillator (CRBWO). It is found that the considerable enhancement of the end reflection at one end increases the conversion efficiency, but excessively large end reflections at both ends weaken the asynchronous wave-beam interaction and thus reduce the conversion efficiency. Perfect reflection at the post end significantly improves the interaction between the electron beam and the asynchronous harmonic so that the conversion efficiency is notably increased. Based on the theoretical research, the diffraction-CRBWO with the generated microwave diffracted and output through the frontmore » end of the coaxial slow wave structure cavity is proposed. The post end is conductively closed to provide the perfect reflection. This promotes the amplitude and uniformity of the longitudinal electric field on the beam transmission line and improves the asynchronous wave-beam interaction. In numerical simulations under the diode voltage and current of 450 kV and 5.84 kA, microwave generation with the power of 1.45 GW and the conversion efficiency of 55% are obtained at the frequency of 7.45 GHz.« less

Do Low Income Youth of Color See "The Bigger Picture" When Discussing Type 2 Diabetes: A Qualitative Evaluation of a Public Health Literacy Campaign.

PubMed

Schillinger, Dean; Tran, Jessica; Fine, Sarah

2018-04-24

As Type 2 diabetes spikes among minority and low-income youth, there is an urgent need to tackle the drivers of this preventable disease. The Bigger Picture (TBP) is a counter-marketing campaign using youth-created, spoken-word public service announcements (PSAs) to reframe the epidemic as a socio-environmental phenomenon requiring communal action, civic engagement and norm change. We examined whether and how TBP PSAs advance health literacy among low-income, minority youth. We showed nine PSAs, asking individuals open-ended questions via questionnaire, then facilitating a focus group to reflect upon the PSAs. Questionnaire responses revealed a balance between individual vs. public health literacy. Some focused on individual responsibility and behaviors, while others described socio-environmental forces underlying risk. The focus group generated a preponderance of public health literacy responses, emphasizing future action. Striking sociopolitical themes emerged, reflecting tensions minority and low-income youth experience, such as entrapment vs. liberation. Our findings speak to the structural barriers and complexities underlying diabetes risk, and the ability of spoken word medium to make these challenges visible and motivate action. Delivering TBP content to promote interactive reflection has potential to change behavioral norms and build capacity to confront the social, economic and structural factors that influence behaviors.

Long-term practice effects on a new skilled motor learning: an electrophysiological study.

PubMed

Fattapposta, F; Amabile, G; Cordischi, M V; Di Venanzio, D; Foti, A; Pierelli, F; D'Alessio, C; Pigozzi, F; Parisi, A; Morrocutti, C

1996-12-01

Cortical functions concerned with the execution of skilled movements can be studied through complex interactive tasks. Skilled performance task (SPT) offers the greatest deal of information about the electrophysiological components reflecting pre-programming, execution of the movement and control of the results. Overall, these components are indicated as "movement-related brain macropotentials' (MRBMs). Among them, Bereitschaftspotential (BP) reflects cerebral processes related to the preparation of movement and skilled performance positivity (SPP) reflects control processes on the result of performance. There is some evidence supporting a training effect on MRBMs, but less clear is whether long-term practice of a skilled activity could modify learning strategies of a new skilled task. We recorded MRBMs in subjects trained for a long time to perform a highly skillful athletic activity, i.e. gun shooting, and in a group of control subjects without any former experience in skilled motor activities. Our findings demonstrated the existence of a relationship between pre-programming and performance control, as suggested by decrease of BP amplitude and increase of SPP amplitude in presence of high levels of performance. Long-term practice seems to develop better control models on performance, that reduce the need of a high mental effort in pre-programming a skilled action.

Cooperative interactions in dense thermal Rb vapour confined in nm-scale cells

NASA Astrophysics Data System (ADS)

Keaveney, James

Gravitational wave detectors are a new class of observatories aiming to detect gravitational waves from cosmic sources. All-reflective interferometer configurations have been proposed for future detectors, replacing transmissive optics with diffractive elements, thereby reducing thermal issues associated with power absorption. However, diffraction gratings introduce additional phase noise, creating more stringent conditions for alignment stability, and further investigations are required into all-reflective interferometers. A suitable mathematical framework using Gaussian modes is required for analysing the alignment stability using diffraction gratings. Such a framework was created, whereby small beam displacements are modelled using a modal technique. It was confirmed that the original modal-based model does not contain the phase changes associated with grating displacements. Experimental tests verified that the phase of a diffracted Gaussian beam is independent of the beam shape. Phase effects were further examined using a rigorous time-domain simulation tool. These findings show that the perceived phase difference is based on an intrinsic change of coordinate system within the modal-based model, and that the extra phase can be added manually to the modal expansion. This thesis provides a well-tested and detailed mathematical framework that can be used to develop simulation codes to model more complex layouts of all-reflective interferometers.

Structural complexity and molecular heterogeneity of a butterfly ejaculate reflect a complex history of selection

PubMed Central

Cherwin, Tamara S.; Plakke, Melissa S.; Hill, Jason; Small, Brandon S.; Goetz, Breanna J.; Wheat, Christopher W.; Morehouse, Nathan I.

2017-01-01

Male ejaculates are often structurally complex, and this complexity is likely to influence key reproductive interactions between males and females. However, despite its potential evolutionary significance, the molecular underpinnings of ejaculate structural complexity have received little empirical attention. To address this knowledge gap, we sought to understand the biochemical and functional properties of the structurally complex ejaculates of Pieris rapae butterflies. Males in this species produce large ejaculates called spermatophores composed of an outer envelope, an inner matrix, and a bolus of sperm. Females are thought to benefit from the nutrition contained in the soluble inner matrix through increases in longevity and fecundity. However, the indigestible outer envelope of the spermatophore delays female remating, allowing males to monopolize paternity for longer. Here, we show that these two nonsperm-containing spermatophore regions, the inner matrix and the outer envelope, differ in their protein composition and functional properties. We also reveal how these divergent protein mixtures are separately stored in the male reproductive tract and sequentially transferred to the female reproductive tract during spermatophore assembly. Intriguingly, we discovered large quantities of female-derived proteases in both spermatophore regions shortly after mating, which may contribute to spermatophore digestion and hence, female control over remating rate. Finally, we report evidence of past selection on these spermatophore proteins and female proteases, indicating a complex evolutionary history. Our findings illustrate how structural complexity of ejaculates may allow functionally and/or spatially associated suites of proteins to respond rapidly to divergent selective pressures, such as sexual conflict or reproductive cooperation. PMID:28630352

Fostering Reflective Writing and Interactive Exchange through Blogging in an Advanced Language Course

ERIC Educational Resources Information Center

Lee, Lina

2010-01-01

Blog technology is a potential medium for encouraging reflective writing through self-expression and interactive exchange through social networking. This paper reports on a study using blogs as out-of-class assignments for the development of learners' language competence. The study involved seventeen university students at advanced level who kept…

Reflections on Online Learning Designs and Cross-Institutional Research Collaborations: Revisiting "Classrooms without Walls" in Two Australian Universities

ERIC Educational Resources Information Center

Rossi, Dolene; van Rensburg, Henriette; Clark, Damien; Harreveld, R. E.; Beer, Colin; Danaher, P. A.

2015-01-01

The article on which this paper reflects ["Exploring a Cross-Institutional Research Collaboration and Innovation: Deploying Social Software and Web 2.0 Technologies to Investigate Online Learning Designs and Interactions in Two Australian Universities"] presented elements of a research project investigating learning interactions in…

Validation of the Two-Layer Model for Correcting Clear Sky Reflectance Near Clouds

NASA Technical Reports Server (NTRS)

Wen, Guoyong; Marshak, Alexander; Evans, K. Frank; Vamal, Tamas

2014-01-01

A two-layer model was developed in our earlier studies to estimate the clear sky reflectance enhancement near clouds. This simple model accounts for the radiative interaction between boundary layer clouds and molecular layer above, the major contribution to the reflectance enhancement near clouds for short wavelengths. We use LES/SHDOM simulated 3D radiation fields to valid the two-layer model for reflectance enhancement at 0.47 micrometer. We find: (a) The simple model captures the viewing angle dependence of the reflectance enhancement near cloud, suggesting the physics of this model is correct; and (b) The magnitude of the 2-layer modeled enhancement agree reasonably well with the "truth" with some expected underestimation. We further extend our model to include cloud-surface interaction using the Poisson model for broken clouds. We found that including cloud-surface interaction improves the correction, though it can introduced some over corrections for large cloud albedo, large cloud optical depth, large cloud fraction, large cloud aspect ratio. This over correction can be reduced by excluding scenes (10 km x 10km) with large cloud fraction for which the Poisson model is not designed for. Further research is underway to account for the contribution of cloud-aerosol radiative interaction to the enhancement.

Analysis of function-related interactions of ATP, sodium and potassium ions with Na+- and K+-transporting ATPase studied with a thiol reagent as tool.

PubMed

Grosse, R; Eckert, K; Malur, J; Repke, K R

1978-01-01

The paper describes the interaction of ATP, Na+ and K+ with (NaK)-ATPase exploiting the inactivation by reaction with NBD-chloride as an analytical tool for the evaluation of enzyme ligandation with the various effectors. 1. The inactivation of (NaK)-ATPase by reaction with NBD-chloride showing under all conditions studied a pseudo first-order rate rests on the alkylation of thiol groups in or near catalytic centre. ATP bound to catalytic centre prevents from enzyme inactivation by NDD-chloride through protection of these thiol groups from alkylation. Na+ and K+ affect the reactivity of the thiol groups towards NBD-chloride either indirectly via influencing ATP binding or more directly via changing the conformation of catalytic centre. Proceeding from these interrelations, the interaction of the various effectors with the enzyme was analyzed. 2. The K'D-values of various nucleotides determined by our approach correspond to the values obtained by independent methods. As shown for the first time, two catalytic centres per enzyme molecule exist. They exhibit high or low affinity to both ATP and ADP apparently caused by anticooperative interaction of the half-units of the enzyme through intersubunit communication ("half-of-the-sites reactivity"). 3. In the absence of ATP, Na+ or K+ ligandation of (NaK)-ATPase produce opposite effects on the reactivity of the thiol groups of catalytic centres reflecting different changes of their conformation. This corresponds to the well-known antagonistic effect of Na+ and K+ on some partial reactions of (NaK)-ATPase. The Na+ and K+ concentrations required to change thiol reactivity are rather high, i.e. the ionophoric centres for both Na+ and K+ are not readily accessible for cation complexation in the absence of enzyme complexation with ATP. 4. Na+ being without effect on ATP binding to the enzyme also does not influence the inactivating reaction with NBD-chloride while K+ by decreasing ATP binding dramatically decreases the protective effect of ATP. The K+ affinity of the enzyme-ATP complex is by more than two orders of magnitude higher than that of free enzyme. Na+ ligandation of the K+-liganded enzyme-ATP complex reverses the effect of K+ ligandation and produces a protective effect which distinctly surpasses that of the complexation of free enzyme with ATP. Hence, the enzyme molecule carries simultaneously ionophoric centres for both Na+ and K+. 5. The findings that per enzyme molecule ionophoric centres for Na+ and K+, and two catalytic centres with anticooperative interaction coexist corroborate the corresponding basic predictions of the flip-flop concept of (NaK)-ATPase pump mechanism, and explain some peculiar kinetic features of transport and enzyme activities of (NaK)-ATPase.

What Kind of Reflection Do We Need in Public Management?

ERIC Educational Resources Information Center

Knassmüller, Monika; Meyer, Renate E.

2013-01-01

In a rapidly changing and increasingly complex environment, the importance of reflection for public managers has been acknowledged almost unanimously by academics as well as practitioners. In this article we highlight the necessity to look at reflection in a more nuanced way. Reflection is a broad and multifaceted concept and public sector work…

Heterotroph Interactions Alter Prochlorococcus Transcriptome Dynamics during Extended Periods of Darkness

PubMed Central

Coe, Allison; Roggensack, Sara E.

2018-01-01

ABSTRACT Microbes evolve within complex ecological communities where biotic interactions impact both individual cells and the environment as a whole. Here we examine how cellular regulation in the marine cyanobacterium Prochlorococcus is influenced by a heterotrophic bacterium, Alteromonas macleodii, under different light conditions. We monitored the transcriptome of Prochlorococcus, grown either alone or in coculture, across a diel light:dark cycle and under the stress of extended darkness—a condition that cells would experience when mixed below the ocean’s euphotic zone. More Prochlorococcus transcripts exhibited 24-h periodic oscillations in coculture than in pure culture, both over the normal diel cycle and after the shift to extended darkness. This demonstrates that biotic interactions, and not just light, can affect timing mechanisms in Prochlorococcus, which lacks a self-sustaining circadian oscillator. The transcriptomes of replicate pure cultures of Prochlorococcus lost their synchrony within 5 h of extended darkness and reflected changes in stress responses and metabolic functions consistent with growth cessation. In contrast, when grown with Alteromonas, replicate Prochlorococcus transcriptomes tracked each other for at least 13 h in the dark and showed signs of continued biosynthetic and metabolic activity. The transcriptome patterns suggest that the heterotroph may be providing energy or essential biosynthetic substrates to Prochlorococcus in the form of organic compounds, sustaining this autotroph when it is deprived of solar energy. Our findings reveal conditions where mixotrophic metabolism may benefit marine cyanobacteria and highlight new impacts of community interactions on basic Prochlorococcus cellular processes. IMPORTANCE Prochlorococcus is the most abundant photosynthetic organism on the planet. These cells play a central role in the physiology of surrounding heterotrophs by supplying them with fixed organic carbon. It is becoming increasingly clear, however, that interactions with heterotrophs can affect autotrophs as well. Here we show that such interactions have a marked impact on the response of Prochlorococcus to the stress of extended periods of darkness, as reflected in transcriptional dynamics. These data suggest that diel transcriptional rhythms within Prochlorococcus, which are generally considered to be strictly under the control of light quantity, quality, and timing, can also be influenced by biotic interactions. Together, these findings provide new insights into the importance of microbial interactions on Prochlorococcus physiology and reveal conditions where heterotroph-derived compounds may support autotrophs—contrary to the canonical autotroph-to-heterotroph trophic paradigm. PMID:29854954

Consequences of inducing intrinsic disorder in a high-affinity protein-protein interaction.

PubMed

Papadakos, Grigorios; Sharma, Amit; Lancaster, Lorna E; Bowen, Rebecca; Kaminska, Renata; Leech, Andrew P; Walker, Daniel; Redfield, Christina; Kleanthous, Colin

2015-04-29

The kinetic and thermodynamic consequences of intrinsic disorder in protein-protein recognition are controversial. We address this by inducing one partner of the high-affinity colicin E3 rRNase domain-Im3 complex (K(d) ≈ 10(-12) M) to become an intrinsically disordered protein (IDP). Through a variety of biophysical measurements, we show that a single alanine mutation at Tyr507 within the hydrophobic core of the isolated colicin E3 rRNase domain causes the enzyme to become an IDP (E3 rRNase(IDP)). E3 rRNase(IDP) binds stoichiometrically to Im3 and forms a structure that is essentially identical to the wild-type complex. However, binding of E3 rRNase(IDP) to Im3 is 4 orders of magnitude weaker than that of the folded rRNase, with thermodynamic parameters reflecting the disorder-to-order transition on forming the complex. Critically, pre-steady-state kinetic analysis of the E3 rRNase(IDP)-Im3 complex demonstrates that the decrease in affinity is mostly accounted for by a drop in the electrostatically steered association rate. Our study shows that, notwithstanding the advantages intrinsic disorder brings to biological systems, this can come at severe kinetic and thermodynamic cost.

The structure of the Caenorhabditis elegans manganese superoxide dismutase MnSOD-3-azide complex

DOE PAGES

Hunter, Gary J.; Trinh, Chi H.; Bonetta, Rosalin; ...

2015-08-27

C. elegans MnSOD-3 has been implicated in the longevity pathway and its mechanism of catalysis is relevant to the aging process and carcinogenesis. The structures of MnSOD-3 provide unique crystallographic evidence of a dynamic region of the tetrameric interface (residues 41–54). We have determined the structure of the MnSOD-3-azide complex to 1.77-Å resolution. The analysis of this complex shows that the substrate analog, azide, binds end-on to the manganese center as a sixth ligand and that it ligates directly to a third and new solvent molecule also positioned within interacting distance to the His30 and Tyr34 residues of the substratemore » access funnel. This is the first structure of a eukaryotic MnSOD-azide complex that demonstrates the extended, uninterrupted hydrogen-bonded network that forms a proton relay incorporating three outer sphere solvent molecules, the substrate analog, the gateway residues, Gln142, and the solvent ligand. This configuration supports the formation and release of the hydrogen peroxide product in agreement with the 5-6-5 catalytic mechanism for MnSOD. The high product dissociation constant k₄ of MnSOD-3 reflects low product inhibition making this enzyme efficient even at high levels of superoxide.« less

Sound-structure interaction analysis of an infinite-long cylindrical shell submerged in a quarter water domain and subject to a line-distributed harmonic excitation

NASA Astrophysics Data System (ADS)

Guo, Wenjie; Li, Tianyun; Zhu, Xiang; Miao, Yuyue

2018-05-01

The sound-structure coupling problem of a cylindrical shell submerged in a quarter water domain is studied. A semi-analytical method based on the double wave reflection method and the Graf's addition theorem is proposed to solve the vibration and acoustic radiation of an infinite cylindrical shell excited by an axially uniform harmonic line force, in which the acoustic boundary conditions consist of a free surface and a vertical rigid surface. The influences of the complex acoustic boundary conditions on the vibration and acoustic radiation of the cylindrical shell are discussed. It is found that the complex acoustic boundary has crucial influence on the vibration of the cylindrical shell when the cylindrical shell approaches the boundary, and the influence tends to vanish when the distances between the cylindrical shell and the boundaries exceed certain values. However, the influence of the complex acoustic boundary on the far-field sound pressure of the cylindrical shell cannot be ignored. The far-field acoustic directivity of the cylindrical shell varies with the distances between the cylindrical shell and the boundaries, besides the driving frequency. The work provides more understanding on the vibration and acoustic radiation behaviors of cylindrical shells with complex acoustic boundary conditions.

[Concept analysis of reflective thinking].

PubMed

Van Vuuren, M; Botes, A

1999-09-01

The nursing practice is described as a scientific practice, but also as a practice where caring is important. The purpose of nursing education is to provide competent nursing practitioners. This implies that future practitioners must have both critical analytical thinking abilities, as well as empathy and moral values. Reflective thinking could probably accommodate these thinking skills. It seems that the facilitation of reflective thinking skills is essential in nursing education. The research question that is relevant in this context is: "What is reflective thinking?" The purpose of this article is to report on the concept analysis of reflective thinking and in particular on the connotative meaning (critical attributes) thereof. The method used to perform the concept analysis is based on the original method of Wilson (1987) as described by Walker & Avant (1995). As part of the concept analysis the connotations (critical attributes) are identified, reduced and organized into three categories, namely pre-requisites, processes and outcomes. A model case is described which confirms the essential critical attributes of reflective thinking. Finally a theoretical definition of reflective thinking is derived and reads as follows: Reflective thinking is a cyclic, hierarchical and interactive construction process. It is initiated, extended and continued because of personal cognitive-affective interaction (individual dimension) as well as interaction with the social environment (social dimension). to realize reflective thinking, a level of internalization on the cognitive and affective domain is required. The result of reflective thinking is a integrated framework of knowledge (meaningful learning) and a internalized value system providing a new perspective on and better understanding of a problem. Reflective thinking further leads to more effective decision making- and problem solving skills.

Ethical analysis in HTA of complex health interventions.

PubMed

Lysdahl, Kristin Bakke; Oortwijn, Wija; van der Wilt, Gert Jan; Refolo, Pietro; Sacchini, Dario; Mozygemba, Kati; Gerhardus, Ansgar; Brereton, Louise; Hofmann, Bjørn

2016-03-22

In the field of health technology assessment (HTA), there are several approaches that can be used for ethical analysis. However, there is a scarcity of literature that critically evaluates and compares the strength and weaknesses of these approaches when they are applied in practice. In this paper, we analyse the applicability of some selected approaches for addressing ethical issues in HTA in the field of complex health interventions. Complex health interventions have been the focus of methodological attention in HTA. However, the potential methodological challenges for ethical analysis are as yet unknown. Six of the most frequently described and applied ethical approaches in HTA were critically assessed against a set of five characteristics of complex health interventions: multiple and changing perspectives, indeterminate phenomena, uncertain causality, unpredictable outcomes, and ethical complexity. The assessments are based on literature and the authors' experiences of developing, applying and assessing the approaches. The Interactive, participatory HTA approach is by its nature and flexibility, applicable across most complexity characteristics. Wide Reflective Equilibrium is also flexible and its openness to different perspectives makes it better suited for complex health interventions than more rigid conventional approaches, such as Principlism and Casuistry. Approaches developed for HTA purposes are fairly applicable for complex health interventions, which one could expect because they include various ethical perspectives, such as the HTA Core Model® and the Socratic approach. This study shows how the applicability for addressing ethical issues in HTA of complex health interventions differs between the selected ethical approaches. Knowledge about these differences may be helpful when choosing and applying an approach for ethical analyses in HTA. We believe that the study contributes to increasing awareness and interest of the ethical aspects of complex health interventions in general.

Life in unexpected places: Employing visual thinking strategies in global health training.

PubMed

Allison, Jill; Mulay, Shree; Kidd, Monica

2017-01-01

The desire to make meaning out of images, metaphor, and other representations indicates higher-order cognitive skills that can be difficult to teach, especially in the complex and unfamiliar environments like those encountered in many global health experiences. Because reflecting on art can help develop medical students' imaginative and interpretive skills, we used visual thinking strategies (VTS) during an immersive 4-week global health elective for medical students to help them construct new understanding of the social determinants of health in a low-resource setting. We were aware of no previous formal efforts to use art in global health training. We assembled a group of eight medical students in front of a street mural in Kathmandu and used VTS methods to interpret the scene with respect to the social determinants of health. We recorded and transcribed the conversation and conducted a thematic analysis of student responses. Students shared observations about the mural in a supportive, nonjudgmental fashion. Two main themes emerged from their observations: those of human-environment interactions (specifically community dynamics, subsistence land use, resources, and health) and entrapment/control, particularly relating to expectations of, and demands on, women in traditional farming communities. They used the images as well as their experience in Nepali communities to consolidate complex community health concepts. VTS helped students articulate their deepening understanding of the social determinants of health in Nepal, suggesting that reflection on visual art can help learners apply, analyze, and evaluate complex concepts in global health. We demonstrate the relevance of drawing upon many aspects of cultural learning, regarding art as a kind of text that holds valuable information. These findings may help provide innovative opportunities for teaching and evaluating global health training in the future.

The Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex.

PubMed

Brites, Daniela; Gagneux, Sebastien

2017-01-01

The Mycobacterium tuberculosis Complex (MTBC) consists of a clonal group of several mycobacterial lineages pathogenic to a range of different mammalian hosts. In this chapter, we discuss the origins and the evolutionary forces shaping the genomic diversity of the human-adapted MTBC. Advances in whole-genome sequencing have brought invaluable insights into the macro-evolution of the MTBC, and the biogeographical distribution of the different MTBC lineages, the phylogenetic relationships between these lineages. Moreover, micro-evolutionary processes start to be better understood, including those influencing bacterial mutation rates and those governing the fate of new mutations emerging within patients during treatment. Current genomic and epidemiological evidence reflect the fact that, through ecological specialization, the MTBC affecting humans became an obligate and extremely well-adapted human pathogen. Identifying the adaptive traits of human-adapted MTBC and unraveling the bacterial loci that interact with human genomic variation might help identify new targets for developing better vaccines and designing more effective treatments.

What is psychiatry? Co-producing complexity in mental health

PubMed Central

Pickersgill, Martyn

2012-01-01

What is psychiatry? Such a question is increasingly important to engage with in light of the development of new diagnostic frameworks that have wide-ranging and international clinical and societal implications. I suggest in this reflective essay that ‘psychiatry' is not a singular entity that enjoins consistent forms of critique along familiar axes; rather, it is a heterogeneous assemblage of interacting material and symbolic elements (some of which endure, and some of which are subject to innovation). In underscoring the diversity of psychiatry, I seek to move towards further sociological purchase on what remains a contested and influential set of discourses and practices. This approach foregrounds the relationships between scientific knowledge, biomedical institutions, social action and subjective experience; these articulations co-produce both psychiatry and each other. One corollary of this emphasis on multiplicity and incoherence within psychiatric theory, research and practice, is that critiques which elide this complexity are rendered problematic. Engagements with psychiatry are, I argue, best furthered by recognising its multifaceted nature. PMID:23226975

Mammalian HspB1 (Hsp27) is a molecular sensor linked to the physiology and environment of the cell.

PubMed

Arrigo, André-Patrick

2017-07-01

Constitutively expressed small heat shock protein HspB1 regulates many fundamental cellular processes and plays major roles in many human pathological diseases. In that regard, this chaperone has a huge number of apparently unrelated functions that appear linked to its ability to recognize many client polypeptides that are subsequently modified in their activity and/or half-life. A major parameter to understand how HspB1 is dedicated to interact with particular clients in defined cellular conditions relates to its complex oligomerization and phosphorylation properties. Indeed, HspB1 structural organization displays dynamic and complex rearrangements in response to changes in the cellular environment or when the cell physiology is modified. These structural modifications probably reflect the formation of structural platforms aimed at recognizing specific client polypeptides. Here, I have reviewed data from the literature and re-analyzed my own studies to describe and discuss these fascinating changes in HspB1 structural organization.

Simulations for designing and interpreting intervention trials in infectious diseases.

PubMed

Halloran, M Elizabeth; Auranen, Kari; Baird, Sarah; Basta, Nicole E; Bellan, Steven E; Brookmeyer, Ron; Cooper, Ben S; DeGruttola, Victor; Hughes, James P; Lessler, Justin; Lofgren, Eric T; Longini, Ira M; Onnela, Jukka-Pekka; Özler, Berk; Seage, George R; Smith, Thomas A; Vespignani, Alessandro; Vynnycky, Emilia; Lipsitch, Marc

2017-12-29

Interventions in infectious diseases can have both direct effects on individuals who receive the intervention as well as indirect effects in the population. In addition, intervention combinations can have complex interactions at the population level, which are often difficult to adequately assess with standard study designs and analytical methods. Herein, we urge the adoption of a new paradigm for the design and interpretation of intervention trials in infectious diseases, particularly with regard to emerging infectious diseases, one that more accurately reflects the dynamics of the transmission process. In an increasingly complex world, simulations can explicitly represent transmission dynamics, which are critical for proper trial design and interpretation. Certain ethical aspects of a trial can also be quantified using simulations. Further, after a trial has been conducted, simulations can be used to explore the possible explanations for the observed effects. Much is to be gained through a multidisciplinary approach that builds collaborations among experts in infectious disease dynamics, epidemiology, statistical science, economics, simulation methods, and the conduct of clinical trials.

Social cognitive theory, metacognition, and simulation learning in nursing education.

PubMed

Burke, Helen; Mancuso, Lorraine

2012-10-01

Simulation learning encompasses simple, introductory scenarios requiring response to patients' needs during basic hygienic care and during situations demanding complex decision making. Simulation integrates principles of social cognitive theory (SCT) into an interactive approach to learning that encompasses the core principles of intentionality, forethought, self-reactiveness, and self-reflectiveness. Effective simulation requires an environment conducive to learning and introduces activities that foster symbolic coding operations and mastery of new skills; debriefing builds self-efficacy and supports self-regulation of behavior. Tailoring the level of difficulty to students' mastery level supports successful outcomes and motivation to set higher standards. Mindful selection of simulation complexity and structure matches course learning objectives and supports progressive development of metacognition. Theory-based facilitation of simulated learning optimizes efficacy of this learning method to foster maturation of cognitive processes of SCT, metacognition, and self-directedness. Examples of metacognition that are supported through mindful, theory-based implementation of simulation learning are provided. Copyright 2012, SLACK Incorporated.

A general method for computing the total solar radiation force on complex spacecraft structures

NASA Technical Reports Server (NTRS)

Chan, F. K.

1981-01-01

The method circumvents many of the existing difficulties in computational logic presently encountered in the direct analytical or numerical evaluation of the appropriate surface integral. It may be applied to complex spacecraft structures for computing the total force arising from either specular or diffuse reflection or even from non-Lambertian reflection and re-radiation.

Reflection Matrix Method for Controlling Light After Reflection From a Diffuse Scattering Surface

DTIC Science & Technology

2016-12-22

reflective inverse diffusion, which was a proof-of-concept experiment that used phase modulation to shape the wavefront of a laser causing it to refocus...after reflection from a rough surface. By refocusing the light, reflective inverse diffusion has the potential to eliminate the complex radiometric model...photography. However, the initial reflective inverse diffusion experiments provided no mathematical background and were conducted under the premise that the

Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.

PubMed

Krystek, S; Stouch, T; Novotny, J

1993-12-05

An empirical function was used to calculate free energy change (delta G) of complex formation between the following inhibitors and enzymes: Kunitz inhibitor (BPTI) with trypsin, trypsinogen and kallikrein; turkey ovomucoid 3rd domain (OMTKY3) with alpha-chymotrypsin and the Streptomyces griseus protease B; the potato chymotrypsin inhibitor with the protease B; and the barely chymotrypsin inhibitor and eglin-c with subtilisin and thermitase. Using X-ray coordinates of the nine complexes, we estimated the contributions that hydrophobic effect, electrostatic interactions and side-chain conformational entropy make towards the stability of the complexes. The calculated delta G values showed good agreement with the experimentally measured ones, the only exception being the kallikrein/BPTI complex whose X-ray structure was solved at an exceptionally low pH. In complexes with different enzymes, the same inhibitor residues contributed identically towards complex formation (delta G(residue) Spearman rank correlation coefficient 0.7 to 1.0). The most productive enzyme-contacting residues in OMTKY3, eglin-c, and the chymotrypsin inhibitors were found in analogous positions on their respective binding loops; thus, our calculations identified a functional (energetic) motif that parallels the well-known structural similarity of the binding loops. The delta G values calculated for BPTI complexed with trypsin (-21.7 kcal) and trypsinogen (-23.4 kcal) were similar and close to the experimental delta G value of the trypsin/BPTI complex (-18.1 kcal), lending support to the suggestion that the 10(7) difference in the observed stabilities (KA) of these two complexes reflects the energetic cost of conformational changes induced in trypsinogen during the pre-equilibrium stages of complex formation. In almost all of the complexes studied, the stabilization free energy contributed by the inhibitors was larger than that donated by the enzymes. In the trypsin-BPTI complex, the calculated delta G contribution of the amino group from the BPTI residue Lys15 (9.7 kcal) was somewhat higher than that arrived at in experiments with semisynthetic inhibitor analogs (7.5 kcal). In OMTKY3, different binding loop residues are known to affect differently the binding (delta delta G) to alpha-chymotrypsin and protease B; a good qualitative agreement was found between the calculated delta G(residue) estimates and the experimental delta delta G data (correlation coefficient 0.7). Large variations were observed in local surface complementarity and related interfacial volume in the two OMTKY3 complexes (by 20 to 60% for some side-chains).(ABSTRACT TRUNCATED AT 400 WORDS)

Use of high-speed visualization for the study of shock-wave interactions with deformable porous materials

NASA Astrophysics Data System (ADS)

Skews, Beric W.; Glick, Gavin; Doyle, Graham K.; Lamond, Paul W.

1997-05-01

This paper describes the use of high-speed photography, and videography, in the study of material distortion and movement when a shock wave traverses a highly deformable porous structure, such as a blob of foam or a porous bed of particles. The effects of surface porosity can be significant in determining the nature of reflection of shock waves from surfaces. Not only are wave geometries substantially modified but the resulting wall pressures are also strongly affected. It, in addition, the surface is highly deformable by being made up of an elastic matrix or a collection of discrete particles, then the reflection geometry and loading can be even more complex. It is known, for example, that shock wave impact on open-cell polyurethane foam attached to a wall can cause a significant increase in pressure on the wall compared to reflection off a plane rigid wall without covering. The motion of the interface is an essential consideration in understanding the dynamics of these interactions. These studies could have application to the effects of blast wave propagation over complex surfaces such as forests, grasslands, and snow; as well as in establishing the efficacy of safety padding and attenuation materials under shock and impact loading conditions. Studies on an assortment of materials are presented, using a variety of visualization techniques. Recording methods used range from short duration flash photography (both shadow and schlieren), through multi-frame videography; to single frame, multi-exposure video capture with a camera capable of rates up to 1 million pictures per second. In the case of shock wave impact on specimens of polyurethane foam, the results clearly show the expulsion and reingestion of shock heated gas from within the foam body as the material collapses and then recovers, coupled with longitudinal and transverse oscillations of the body of the foam material. For blast wave propagation over porous beds, occurrence of particle lift off, bed fluidization, and the generation of surface dunes are evident. The recordings allow the calculation of the velocities and accelerations of the various interfaces and particles to be made, using suitable image processing techniques. Thus, estimates may be made of the unsteady drag forces acting on the individual particles.

Lessons from Philippines MPA Management: Social Ecological Interactions, Participation, and MPA Performance

NASA Astrophysics Data System (ADS)

Twichell, Julia; Pollnac, Richard; Christie, Patrick

2018-06-01

International interest in increasing marine protected area (MPA) coverage reflects broad recognition of the MPA as a key tool for marine ecosystems and fisheries management. Nevertheless, effective management remains a significant challenge. The present study contributes to enriching an understanding of best practices for MPA management through analysis of archived community survey data collected in the Philippines by the Learning Project (LP), a collaboration with United States Coral Triangle Initiative (USCTI), United States Agency for International Development (USAID), and partners. We evaluate stakeholder participation and social ecological interactions among resource users in MPA programs in the Palawan, Occidental Mindoro, and Batangas provinces in the Philippines. Analysis indicates that a complex suite of social ecological factors, including demographics, conservation beliefs, and scientifically correct knowledge influence participation, which in turn is related to perceived MPA performance. Findings indicate positive feedbacks within the system that have potential to strengthen perceptions of MPA success. The results of this evaluation provide empirical reinforcement to current inquiries concerning the role of participation in influencing MPA performance.

Specific interactions study in complexes of poly(mono-n-alkyl itaconates) with tertiary polyamides.

PubMed

Katime, Issa; Meaurio, Emilio; Cesteros, Luis C; Mendizábal, Eduardo

2003-07-01

This paper reports an FT-IR study of blends of poly(mono-n-alkyl itaconates) with poly(N,N-dimethylacrylamide) (PDMA) and poly(ethyloxazoline) (PEOX). Strong hydrogen bonding has been found, and both polybases have shown similar acceptor strengths. Derivative techniques show asymmetric profiles for the free carbonyl band of the polybases, resulting in shifted band locations. The extent of the interassociation has been estimated by spectral curve fitting of the polybase carbonyl band. The results show that the interaction degree in blends with PEOX does not depend on the length of the poly(monoalkyl itaconate) side group, while an inter-associating ability loss is observed in blends with PDMA as the side-group size of the polyacid increases. This different behavior is attributed to the greater interspacing between vicinal carbonyl groups in PEOX. This band shows conformational sensitivity and reflects the conformational changes that occur as the steric hindrances present in the medium (due to the bulky side groups of the polyacids) increase.

Optical properties of azobenzene-functionalized self-assembled monolayers: Intermolecular coupling and many-body interactions

NASA Astrophysics Data System (ADS)

Cocchi, Caterina; Moldt, Thomas; Gahl, Cornelius; Weinelt, Martin; Draxl, Claudia

2016-12-01

In a joint theoretical and experimental work, the optical properties of azobenzene-functionalized self-assembled monolayers (SAMs) are studied at different molecular packing densities. Our results, based on density-functional and many-body perturbation theory, as well as on differential reflectance (DR) spectroscopy, shed light on the microscopic mechanisms ruling photo-absorption in these systems. While the optical excitations are intrinsically excitonic in nature, regardless of the molecular concentration, in densely packed SAMs intermolecular coupling and local-field effects are responsible for a sizable weakening of the exciton binding strength. Through a detailed analysis of the character of the electron-hole pairs, we show that distinct excitations involved in the photo-isomerization at low molecular concentrations are dramatically broadened by intermolecular interactions. Spectral shifts in the calculated DR spectra are in good agreement with the experimental results. Our findings represent an important step forward to rationalize the excited-state properties of these complex materials.

Bridging the gap between supernovae and their remnants through multi-dimensional hydrodynamic modeling

NASA Astrophysics Data System (ADS)

Orlando, S.; Miceli, M.; Petruk, O.

2017-02-01

Supernova remnants (SNRs) are diffuse extended sources characterized by a complex morphology and a non-uniform distribution of ejecta. Such a morphology reflects pristine structures and features of the progenitor supernova (SN) and the early interaction of the SN blast wave with the inhomogeneous circumstellar medium (CSM). Deciphering the observations of SNRs might open the possibility to investigate the physical properties of both the interacting ejecta and the shocked CSM. This requires accurate numerical models which describe the evolution from the SN explosion to the remnant development and which connect the emission properties of the remnants to the progenitor SNe. Here we show how multi-dimensional SN-SNR hydrodynamic models have been very effective in deciphering observations of SNR Cassiopeia A and SN 1987A, thus unveiling the structure of ejecta in the immediate aftermath of the SN explosion and constraining the 3D pre-supernova structure and geometry of the environment surrounding the progenitor SN.

The crystal structure of two macrolide glycosyltransferases provides a blueprint for host cell antibiotic immunity

PubMed Central

Bolam, David N.; Roberts, Shirley; Proctor, Mark R.; Turkenburg, Johan P.; Dodson, Eleanor J.; Martinez-Fleites, Carlos; Yang, Min; Davis, Benjamin G.; Davies, Gideon J.; Gilbert, Harry J.

2007-01-01

Glycosylation of macrolide antibiotics confers host cell immunity from endogenous and exogenous agents. The Streptomyces antibioticus glycosyltransferases, OleI and OleD, glycosylate and inactivate oleandomycin and diverse macrolides including erythromycin, respectively. The structure of these enzyme–ligand complexes, in tandem with kinetic analysis of site-directed variants, provide insight into the interaction of macrolides with their synthetic apparatus. Erythromycin binds to OleD and the 23S RNA of its target ribosome in the same conformation and, although the antibiotic contains a large number of polar groups, its interaction with these macromolecules is primarily through hydrophobic contacts. Erythromycin and oleandomycin, when bound to OleD and OleI, respectively, adopt different conformations, reflecting a subtle effect on sugar positioning by virtue of a single change in the macrolide backbone. The data reported here provide structural insight into the mechanism of resistance to both endogenous and exogenous antibiotics, and will provide a platform for the future redesign of these catalysts for antibiotic remodelling. PMID:17376874

p47phox Molecular Activation for Assembly of the Neutrophil NADPH Oxidase Complex*

PubMed Central

Marcoux, Julien; Man, Petr; Petit-Haertlein, Isabelle; Vivès, Corinne; Forest, Eric; Fieschi, Franck

2010-01-01

The p47phox cytosolic factor from neutrophilic NADPH oxidase has always been resistant to crystallogenesis trials due to its modular organization leading to relative flexibility. Hydrogen/deuterium exchange coupled to mass spectrometry was used to obtain structural information on the conformational mechanism that underlies p47phox activation. We confirmed a relative opening of the protein with exposure of the SH3 Src loops that are known to bind p22phox upon activation. A new surface was shown to be unmasked after activation, representing a potential autoinhibitory surface that may block the interaction of the PX domain with the membrane in the resting state. Within this surface, we identified 2 residues involved in the interaction with the PX domain. The double mutant R162A/D166A showed a higher affinity for specific phospholipids but none for the C-terminal part of p22phox, reflecting an intermediate conformation between the autoinhibited and activated forms. PMID:20592030

The design and implementation of the immune epitope database and analysis resource

PubMed Central

Peters, Bjoern; Sidney, John; Bourne, Phil; Bui, Huynh-Hoa; Buus, Soeren; Doh, Grace; Fleri, Ward; Kronenberg, Mitch; Kubo, Ralph; Lund, Ole; Nemazee, David; Ponomarenko, Julia V.; Sathiamurthy, Muthu; Schoenberger, Stephen P.; Stewart, Scott; Surko, Pamela; Way, Scott; Wilson, Steve; Sette, Alessandro

2016-01-01

Epitopes are defined as parts of antigens interacting with receptors of the immune system. Knowledge about their intrinsic structure and how they affect the immune response is required to continue development of techniques that detect, monitor, and fight diseases. Their scientific importance is reflected in the vast amount of epitope-related information gathered, ranging from interactions between epitopes and major histocompatibility complex molecules determined by X-ray crystallography to clinical studies analyzing correlates of protection for epitope based vaccines. Our goal is to provide a central resource capable of capturing this information, allowing users to access and connect realms of knowledge that are currently separated and difficult to access. Here, we portray a new initiative, “The Immune Epitope Database and Analysis Resource.” We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide. PMID:15895191

Relative importance of evolutionary dynamics depends on the composition of microbial predator-prey community.

PubMed

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-06-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities.

Relative importance of evolutionary dynamics depends on the composition of microbial predator–prey community

PubMed Central

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-01-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities. PMID:26684728

Mast cell: an emerging partner in immune interaction.

PubMed

Gri, Giorgia; Frossi, Barbara; D'Inca, Federica; Danelli, Luca; Betto, Elena; Mion, Francesca; Sibilano, Riccardo; Pucillo, Carlo

2012-01-01

Mast cells (MCs) are currently recognized as effector cells in many settings of the immune response, including host defense, immune regulation, allergy, chronic inflammation, and autoimmune diseases. MC pleiotropic functions reflect their ability to secrete a wide spectrum of preformed or newly synthesized biologically active products with pro-inflammatory, anti-inflammatory and/or immunosuppressive properties, in response to multiple signals. Moreover, the modulation of MC effector phenotypes relies on the interaction of a wide variety of membrane molecules involved in cell-cell or cell-extracellular-matrix interaction. The delivery of co-stimulatory signals allows MC to specifically communicate with immune cells belonging to both innate and acquired immunity, as well as with non-immune tissue-specific cell types. This article reviews and discusses the evidence that MC membrane-expressed molecules play a central role in regulating MC priming and activation and in the modulation of innate and adaptive immune response not only against host injury, but also in peripheral tolerance and tumor-surveillance or -escape. The complex expression of MC surface molecules may be regarded as a measure of connectivity, with altered patterns of cell-cell interaction representing functionally distinct MC states. We will focalize our attention on roles and functions of recently discovered molecules involved in the cross-talk of MCs with other immune partners.

Mast Cell: An Emerging Partner in Immune Interaction

PubMed Central

Gri, Giorgia; Frossi, Barbara; D’Inca, Federica; Danelli, Luca; Betto, Elena; Mion, Francesca; Sibilano, Riccardo; Pucillo, Carlo

2012-01-01

Mast cells (MCs) are currently recognized as effector cells in many settings of the immune response, including host defense, immune regulation, allergy, chronic inflammation, and autoimmune diseases. MC pleiotropic functions reflect their ability to secrete a wide spectrum of preformed or newly synthesized biologically active products with pro-inflammatory, anti-inflammatory and/or immunosuppressive properties, in response to multiple signals. Moreover, the modulation of MC effector phenotypes relies on the interaction of a wide variety of membrane molecules involved in cell–cell or cell-extracellular-matrix interaction. The delivery of co-stimulatory signals allows MC to specifically communicate with immune cells belonging to both innate and acquired immunity, as well as with non-immune tissue-specific cell types. This article reviews and discusses the evidence that MC membrane-expressed molecules play a central role in regulating MC priming and activation and in the modulation of innate and adaptive immune response not only against host injury, but also in peripheral tolerance and tumor-surveillance or -escape. The complex expression of MC surface molecules may be regarded as a measure of connectivity, with altered patterns of cell–cell interaction representing functionally distinct MC states. We will focalize our attention on roles and functions of recently discovered molecules involved in the cross-talk of MCs with other immune partners. PMID:22654879

Genetic Correlation and Gene–Environment Interaction Between Alcohol Problems and Educational Level in Young Adulthood*

PubMed Central

Latvala, Antti; Dick, Danielle M.; Tuulio-Henriksson, Annamari; Suvisaari, Jaana; Viken, Richard J.; Rose, Richard J.; Kaprio, Jaakko

2011-01-01

Objective: A lower level of education often co-occurs with alcohol problems, but factors underlying this co-occurrence are not well understood. Specifically, whether these outcomes share part of their underlying genetic influences has not been widely studied. Educational level also reflects various environmental influences that may moderate the genetic etiology of alcohol problems, but gene–environment interactions between educational attainment and alcohol problems are unknown. Method: We studied the two nonmutually exclusive possibilities of common genetic influences and gene–environment interaction between alcohol problems and low education using a population-based sample (n = 4,858) of Finnish young adult twins (Mage = 24.5 years, range: 22.8–28.6 years). Alcohol problems were assessed with the Rutgers Alcohol Problem Index and self-reported maximum number of drinks consumed in a 24-hour period. Years of education, based on completed and ongo-ing studies, represented educational level. Results: Educational level was inversely associated with alcohol problems in young adulthood, and this association was most parsimoniously explained by overlapping genetic influences. Independent of this co-occurrence, higher education was associated with increased relative importance of genetic influences on alcohol problems, whereas environmental factors had a greater effect among twins with lower education. Conclusions: Our findings suggest a complex relationship between educational level and alcohol problems in young adulthood. Lower education is related to higher levels of alcohol problems, and this co-occurrence is influenced by genetic factors affecting both phenotypes. In addition, educational level moderates the importance of genetic and environmental influences on alcohol problems, possibly reflecting differences in social-control mechanisms related to educational level. PMID:21388594

Distinct structural features of the peroxide response regulator from group A Streptococcus drive DNA binding.

PubMed

Lin, Chang Sheng-Huei; Chao, Shi-Yu; Hammel, Michal; Nix, Jay C; Tseng, Hsiao-Ling; Tsou, Chih-Cheng; Fei, Chun-Hsien; Chiou, Huo-Sheng; Jeng, U-Ser; Lin, Yee-Shin; Chuang, Woei-Jer; Wu, Jiunn-Jong; Wang, Shuying

2014-01-01

Group A streptococcus (GAS, Streptococcus pyogenes) is a strict human pathogen that causes severe, invasive diseases. GAS does not produce catalase, but has an ability to resist killing by reactive oxygen species (ROS) through novel mechanisms. The peroxide response regulator (PerR), a member of ferric uptake regulator (Fur) family, plays a key role for GAS to cope with oxidative stress by regulating the expression of multiple genes. Our previous studies have found that expression of an iron-binding protein, Dpr, is under the direct control of PerR. To elucidate the molecular interactions of PerR with its cognate promoter, we have carried out structural studies on PerR and PerR-DNA complex. By combining crystallography and small-angle X-ray scattering (SAXS), we confirmed that the determined PerR crystal structure reflects its conformation in solution. Through mutagenesis and biochemical analysis, we have identified DNA-binding residues suggesting that PerR binds to the dpr promoter at the per box through a winged-helix motif. Furthermore, we have performed SAXS analysis and resolved the molecular architecture of PerR-DNA complex, in which two 30 bp DNA fragments wrap around two PerR homodimers by interacting with the adjacent positively-charged winged-helix motifs. Overall, we provide structural insights into molecular recognition of DNA by PerR and define the hollow structural arrangement of PerR-30bpDNA complex, which displays a unique topology distinct from currently proposed DNA-binding models for Fur family regulators.

Small-world bias of correlation networks: From brain to climate

NASA Astrophysics Data System (ADS)

Hlinka, Jaroslav; Hartman, David; Jajcay, Nikola; Tomeček, David; Tintěra, Jaroslav; Paluš, Milan

2017-03-01

Complex systems are commonly characterized by the properties of their graph representation. Dynamical complex systems are then typically represented by a graph of temporal dependencies between time series of state variables of their subunits. It has been shown recently that graphs constructed in this way tend to have relatively clustered structure, potentially leading to spurious detection of small-world properties even in the case of systems with no or randomly distributed true interactions. However, the strength of this bias depends heavily on a range of parameters and its relevance for real-world data has not yet been established. In this work, we assess the relevance of the bias using two examples of multivariate time series recorded in natural complex systems. The first is the time series of local brain activity as measured by functional magnetic resonance imaging in resting healthy human subjects, and the second is the time series of average monthly surface air temperature coming from a large reanalysis of climatological data over the period 1948-2012. In both cases, the clustering in the thresholded correlation graph is substantially higher compared with a realization of a density-matched random graph, while the shortest paths are relatively short, showing thus distinguishing features of small-world structure. However, comparable or even stronger small-world properties were reproduced in correlation graphs of model processes with randomly scrambled interconnections. This suggests that the small-world properties of the correlation matrices of these real-world systems indeed do not reflect genuinely the properties of the underlying interaction structure, but rather result from the inherent properties of correlation matrix.

Small-world bias of correlation networks: From brain to climate.

PubMed

Hlinka, Jaroslav; Hartman, David; Jajcay, Nikola; Tomeček, David; Tintěra, Jaroslav; Paluš, Milan

2017-03-01

Complex systems are commonly characterized by the properties of their graph representation. Dynamical complex systems are then typically represented by a graph of temporal dependencies between time series of state variables of their subunits. It has been shown recently that graphs constructed in this way tend to have relatively clustered structure, potentially leading to spurious detection of small-world properties even in the case of systems with no or randomly distributed true interactions. However, the strength of this bias depends heavily on a range of parameters and its relevance for real-world data has not yet been established. In this work, we assess the relevance of the bias using two examples of multivariate time series recorded in natural complex systems. The first is the time series of local brain activity as measured by functional magnetic resonance imaging in resting healthy human subjects, and the second is the time series of average monthly surface air temperature coming from a large reanalysis of climatological data over the period 1948-2012. In both cases, the clustering in the thresholded correlation graph is substantially higher compared with a realization of a density-matched random graph, while the shortest paths are relatively short, showing thus distinguishing features of small-world structure. However, comparable or even stronger small-world properties were reproduced in correlation graphs of model processes with randomly scrambled interconnections. This suggests that the small-world properties of the correlation matrices of these real-world systems indeed do not reflect genuinely the properties of the underlying interaction structure, but rather result from the inherent properties of correlation matrix.

Synergistic foaming and surface properties of a weakly interacting mixture of soy glycinin and biosurfactant stevioside.

PubMed

Wan, Zhi-Li; Wang, Li-Ying; Wang, Jin-Mei; Yuan, Yang; Yang, Xiao-Quan

2014-07-16

The adsorption of the mixtures of soy glycinin (11S) with a biosurfactant stevioside (STE) at the air-water interface was studied to understand its relation with foaming properties. A combination of several techniques such as dynamic surface tension, dilatational rheology, fluorescence spectroscopy, and isothermal titration calorimetry (ITC) was used. In the presence of intermediate STE concentrations (0.25-0.5%), the weak binding of STE with 11S in bulk occurred by hydrophobic interactions, which could induce conformational changes of 11S, as evidenced by fluorescence and ITC. Accordingly, the strong synergy in reducing surface tension and the plateau in surface elasticity for mixed 11S-STE layers formed from the weakly interacting mixtures were clearly observed. This effect could be explained by the complexation with STE, which might facilitate the partial dissociation and further unfolding of 11S upon adsorption, thus enhancing the protein-protein and protein-STE interfacial interactions. These surface properties were positively reflected in foams produced by the weakly interacting system, which exhibited good foaming capacity and considerable stability probably due to better response to external stresses. However, at high STE concentrations (1-2%), as a consequence of the interface dominated by STE due to the preferential adsorption of STE molecules, the surface elasticity of layers dramatically decreased, and the resultant foams became less stable.

Visual sensory networks and effective information transfer in animal groups.

PubMed

Strandburg-Peshkin, Ariana; Twomey, Colin R; Bode, Nikolai W F; Kao, Albert B; Katz, Yael; Ioannou, Christos C; Rosenthal, Sara B; Torney, Colin J; Wu, Hai Shan; Levin, Simon A; Couzin, Iain D

2013-09-09

Social transmission of information is vital for many group-living animals, allowing coordination of motion and effective response to complex environments. Revealing the interaction networks underlying information flow within these groups is a central challenge. Previous work has modeled interactions between individuals based directly on their relative spatial positions: each individual is considered to interact with all neighbors within a fixed distance (metric range), a fixed number of nearest neighbors (topological range), a 'shell' of near neighbors (Voronoi range), or some combination (Figure 1A). However, conclusive evidence to support these assumptions is lacking. Here, we employ a novel approach that considers individual movement decisions to be based explicitly on the sensory information available to the organism. In other words, we consider that while spatial relations do inform interactions between individuals, they do so indirectly, through individuals' detection of sensory cues. We reconstruct computationally the visual field of each individual throughout experiments designed to investigate information propagation within fish schools (golden shiners, Notemigonus crysoleucas). Explicitly considering visual sensing allows us to more accurately predict the propagation of behavioral change in these groups during leadership events. Furthermore, we find that structural properties of visual interaction networks differ markedly from those of metric and topological counterparts, suggesting that previous assumptions may not appropriately reflect information flow in animal groups. Copyright © 2013 Elsevier Ltd. All rights reserved.

Protein-lipid interactions at the air/water interface.

PubMed

Lad, Mitaben D; Birembaut, Fabrice; Frazier, Richard A; Green, Rebecca J

2005-10-07

Surface pressure measurements and external reflection FTIR spectroscopy have been used to probe protein-lipid interactions at the air/water interface. Spread monomolecular layers of stearic acid and phosphocholine were prepared and held at different compressed phase states prior to the introduction of protein to the buffered subphase. Contrasting interfacial behaviour of the proteins, albumin and lysozyme, was observed and revealed the role of both electrostatic and hydrophobic interactions in protein adsorption. The rate of adsorption of lysozyme to the air/water interface increased dramatically in the presence of stearic acid, due to strong electrostatic interactions between the negatively charged stearic acid head group and lysozyme, whose net charge at pH 7 is positive. Introduction of albumin to the subphase resulted in solubilisation of the stearic acid via the formation of an albumin-stearic acid complex and subsequent adsorption of albumin. This observation held for both human and bovine serum albumin. Protein adsorption to a PC layer held at low surface pressure revealed adsorption rates similar to adsorption to the bare air/water interface and suggested very little interaction between the protein and the lipid. For PC layers in their compressed phase state some adsorption of protein occurred after long adsorption times. Structural changes of both lysozyme and albumin were observed during adsorption, but these were dramatically reduced in the presence of a lipid layer compared to that of adsorption to the pure air/water interface.

Applying systems theory to the evaluation of a whole school approach to violence prevention.

PubMed

Kearney, Sarah; Leung, Loksee; Joyce, Andrew; Ollis, Debbie; Green, Celia

2016-02-01

Issue addressed Our Watch led a complex 12-month evaluation of a whole school approach to Respectful Relationships Education (RRE) implemented in 19 schools. RRE is an emerging field aimed at preventing gender-based violence. This paper will illustrate how from an implementation science perspective, the evaluation was a critical element in the change process at both a school and policy level. Methods Using several conceptual approaches from systems science, the evaluation sought to examine how the multiple systems layers - student, teacher, school, community and government - interacted and influenced each other. A distinguishing feature of the evaluation included 'feedback loops'; that is, evaluation data was provided to participants as it became available. Evaluation tools included a combination of standardised surveys (with pre- and post-intervention data provided to schools via individualised reports), reflection tools, regular reflection interviews and summative focus groups. Results Data was shared during implementation with project staff, department staff and schools to support continuous improvement at these multiple systems levels. In complex settings, implementation can vary according to context; and the impact of evaluation processes, tools and findings differed across the schools. Interviews and focus groups conducted at the end of the project illustrated which of these methods were instrumental in motivating change and engaging stakeholders at both a school and departmental level and why. Conclusion The evaluation methods were a critical component of the pilot's approach, helping to shape implementation through data feedback loops and reflective practice for ongoing, responsive and continuous improvement. Future health promotion research on complex interventions needs to examine how the evaluation itself is influencing implementation. So what? The pilot has demonstrated that the evaluation, including feedback loops to inform project activity, were an asset to implementation. This has implications for other health promotion activities, where evaluation tools could be utilised to enhance, rather than simply measure, an intervention. The findings are relevant to a range of health promotion research activities because they demonstrate the importance of meta-evaluation techniques that seek to understand how the evaluation itself was influencing implementation and outcomes.

Reflective Practice in Group Co-Leadership

ERIC Educational Resources Information Center

Okech, Jane E. Atieno

2008-01-01

Group literature on co-leaders' experiences and perceptions while leading groups illuminate reflective practice as highly influential to co-leader relationships and performances. Using practical examples grounded by interdisciplinary literature on reflective practice, this article explores and expands dialogue on the complex interplay between…

Goal-Setting and Self-Reflection to Enhance Learners' Interaction in an ESP Context

ERIC Educational Resources Information Center

Lozano Velandia, Sergio Andrés

2015-01-01

This qualitative action research study explored the interactions of young-adult learners carrying out self-reflection on their learning processes in an ESP (English for special purposes) course at an airline training-center in Bogotá, Colombia. Needs analysis revealed that learners had poor knowledge of technical English, and lacked strong…

Intermolecular interaction in nucleobases and dimethyl sulfoxide/water molecules: A DFT, NBO, AIM and NCI analysis.

PubMed

Venkataramanan, Natarajan Sathiyamoorthy; Suvitha, Ambigapathy; Kawazoe, Yoshiyuki

2017-11-01

This study aims to cast light on the physico-chemical nature and energetics of interactions between the nucleobases and water/DMSO molecules which occurs through the non-conventional CH⋯O/N-H bonds using a comprehensive quantum-chemical approach. The computed interaction energies do not show any appreciable change for all the nucleobase-solvent complexes, conforming the experimental findings on the hydration enthalpies. Compared to water, DMSO form complexes with high interaction energies. The quantitative molecular electrostatic potentials display a charge transfer during the complexation. NBO analysis shows the nucleobase-DMSO complexes, have higher stabilization energy values than the nucleobase-water complexes. AIM analysis illustrates that the in the nucleobase-DMSO complexes, SO⋯H-N type interaction have strongest hydrogen bond strength with high E HB values. Furthermore, the Laplacian of electron density and total electron density were negative indicating the partial covalent nature of bonding in these systems, while the other bonds are classified as noncovalent interactions. EDA analysis indicates, the electrostatic interaction is more pronounced in the case of nucleobase-water complexes, while the dispersion contribution is more dominant in nucleobase-DMSO complexes. NCI-RDG analysis proves the existence of strong hydrogen bonding in nucleobase-DMSO complex, which supports the AIM results. Copyright © 2017 Elsevier Inc. All rights reserved.

Describing the complexity of systems: multivariable "set complexity" and the information basis of systems biology.

PubMed

Galas, David J; Sakhanenko, Nikita A; Skupin, Alexander; Ignac, Tomasz

2014-02-01

Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity," we use an information theory approach to formulate general measures of systems complexity. We examine the properties of multivariable dependency starting with the concept of interaction information. We then present a new measure for unbiased detection of multivariable dependency, "differential interaction information." This quantity for two variables reduces to the pairwise "set complexity" previously proposed as a context-dependent measure of information in biological systems. We generalize it here to an arbitrary number of variables. Critical limiting properties of the "differential interaction information" are key to the generalization. This measure extends previous ideas about biological information and provides a more sophisticated basis for the study of complexity. The properties of "differential interaction information" also suggest new approaches to data analysis. Given a data set of system measurements, differential interaction information can provide a measure of collective dependence, which can be represented in hypergraphs describing complex system interaction patterns. We investigate this kind of analysis using simulated data sets. The conjoining of a generalized set complexity measure, multivariable dependency analysis, and hypergraphs is our central result. While our focus is on complex biological systems, our results are applicable to any complex system.

Reflections around Artefacts: Using a Deliberative Approach to Teaching Reflective Practices in Fashion Studies

ERIC Educational Resources Information Center

Ryan, Michael; Brough, Dean

2012-01-01

While requiring students to think reflectively is a desirable teaching goal, it is often fraught with complexity and is sometimes poorly implemented in higher education. In this paper, we describe an approach to academic reflective practices that fitted a design subject in fashion education and was perceived as effective in enhancing student…

Extreme Mesozoic crustal thinning in the Eastern Iberia margin: The example of the Columbrets Basin (Valencia Trough)

NASA Astrophysics Data System (ADS)

Mohn, G.; Etheve, N.; Frizon de Lamotte, D.; Roca, E.; Tugend, J.; Gómez-Romeu, J.

2017-12-01

Eastern Iberia preserves a complex succession of Mesozoic rifts partly or completely inverted during the Late Cretaceous and Cenozoic in relation with Africa-Eurasia convergence. Notably, the Valencia Trough, classically viewed as part of the Cenozoic West Mediterranean basins, preserves in its southwestern part a thick Mesozoic succession (locally »10km thick) over a highly thinned continental basement (locally only »3,5km thick). This sub-basin referred to as the Columbrets Basin, represents a Late Jurassic-Early Cretaceous hyper-extended rift basin weakly overprinted by subsequent events. Its initial configuration is well preserved allowing us to unravel its 3D architecture and tectono-stratigraphic evolution in the frame of the Mesozoic evolution of eastern Iberia. The Columbrets Basin benefits from an extensive dataset combining high resolution reflection seismic profiles, drill holes, refraction seismic data and Expanding Spread Profiles. Its Mesozoic architecture is controlled by interactions between extensional deformation and halokinesis involving the Upper Triassic salt. The thick uppermost Triassic to Cretaceous succession describes a general synclinal shape, progressively stretched and dismembered towards the basin borders. The SE-border of the basin is characterized by a large extensional detachment fault acting at crustal scale and interacting locally with the Upper Triassic décollement. This extensional structure accommodates the exhumation of the continental basement and part of the crustal thinning. Eventually our results highlight the complex interaction between extreme crustal thinning and occurrence of a pre-rift salt level for the deformation style and tectono-stratigraphic evolution of hyper-extended rift basins.

Virtual Neurorobotics (VNR) to Accelerate Development of Plausible Neuromorphic Brain Architectures.

PubMed

Goodman, Philip H; Buntha, Sermsak; Zou, Quan; Dascalu, Sergiu-Mihai

2007-01-01

Traditional research in artificial intelligence and machine learning has viewed the brain as a specially adapted information-processing system. More recently the field of social robotics has been advanced to capture the important dynamics of human cognition and interaction. An overarching societal goal of this research is to incorporate the resultant knowledge about intelligence into technology for prosthetic, assistive, security, and decision support applications. However, despite many decades of investment in learning and classification systems, this paradigm has yet to yield truly "intelligent" systems. For this reason, many investigators are now attempting to incorporate more realistic neuromorphic properties into machine learning systems, encouraged by over two decades of neuroscience research that has provided parameters that characterize the brain's interdependent genomic, proteomic, metabolomic, anatomic, and electrophysiological networks. Given the complexity of neural systems, developing tenable models to capture the essence of natural intelligence for real-time application requires that we discriminate features underlying information processing and intrinsic motivation from those reflecting biological constraints (such as maintaining structural integrity and transporting metabolic products). We propose herein a conceptual framework and an iterative method of virtual neurorobotics (VNR) intended to rapidly forward-engineer and test progressively more complex putative neuromorphic brain prototypes for their ability to support intrinsically intelligent, intentional interaction with humans. The VNR system is based on the viewpoint that a truly intelligent system must be driven by emotion rather than programmed tasking, incorporating intrinsic motivation and intentionality. We report pilot results of a closed-loop, real-time interactive VNR system with a spiking neural brain, and provide a video demonstration as online supplemental material.

Predictability decomposition detects the impairment of brain-heart dynamical networks during sleep disorders and their recovery with treatment

NASA Astrophysics Data System (ADS)

Faes, Luca; Marinazzo, Daniele; Stramaglia, Sebastiano; Jurysta, Fabrice; Porta, Alberto; Giandomenico, Nollo

2016-05-01

This work introduces a framework to study the network formed by the autonomic component of heart rate variability (cardiac process η) and the amplitude of the different electroencephalographic waves (brain processes δ, θ, α, σ, β) during sleep. The framework exploits multivariate linear models to decompose the predictability of any given target process into measures of self-, causal and interaction predictability reflecting respectively the information retained in the process and related to its physiological complexity, the information transferred from the other source processes, and the information modified during the transfer according to redundant or synergistic interaction between the sources. The framework is here applied to the η, δ, θ, α, σ, β time series measured from the sleep recordings of eight severe sleep apnoea-hypopnoea syndrome (SAHS) patients studied before and after long-term treatment with continuous positive airway pressure (CPAP) therapy, and 14 healthy controls. Results show that the full and self-predictability of η, δ and θ decreased significantly in SAHS compared with controls, and were restored with CPAP for δ and θ but not for η. The causal predictability of η and δ occurred through significantly redundant source interaction during healthy sleep, which was lost in SAHS and recovered after CPAP. These results indicate that predictability analysis is a viable tool to assess the modifications of complexity and causality of the cerebral and cardiac processes induced by sleep disorders, and to monitor the restoration of the neuroautonomic control of these processes during long-term treatment.

Fire, flow and dynamic equilibrium in stream macroinvertebrate communities

USGS Publications Warehouse

Arkle, R.S.; Pilliod, D.S.; Strickler, K.

2010-01-01

The complex effects of disturbances on ecological communities can be further complicated by subsequent perturbations within an ecosystem. We investigated how wildfire interacts with annual variations in peak streamflow to affect the stability of stream macroinvertebrate communities in a central Idaho wilderness, USA. We conducted a 4-year retrospective analysis of unburned (n = 7) and burned (n = 6) catchments, using changes in reflectance values (??NBR) from satellite imagery to quantify the percentage of each catchment's riparian and upland vegetation that burned at high and low severity. For this wildland fire complex, increasing riparian burn severity and extent were associated with greater year-to-year variation, rather than a perennial increase, in sediment loads, organic debris, large woody debris (LWD) and undercut bank structure. Temporal changes in these variables were correlated with yearly peak flow in burned catchments but not in unburned reference catchments, indicating that an interaction between fire and flow can result in decreased habitat stability in burned catchments. Streams in more severely burned catchments exhibited increasingly dynamic macroinvertebrate communities and did not show increased similarity to reference streams over time. Annual variability in macroinvertebrates was attributed, predominantly, to the changing influence of sediment, LWD, riparian cover and organic debris, as quantities of these habitat components fluctuated annually depending on burn severity and annual peak streamflows. These analyses suggest that interactions among fire, flow and stream habitat may increase inter-annual habitat variability and macroinvertebrate community dynamics for a duration approaching the length of the historic fire return interval of the study area. ?? 2009 Blackwell Publishing Ltd.

Multiple-stressor effects of sediment, phosphorus and nitrogen on stream macroinvertebrate communities.

PubMed

Davis, Stephen J; Ó hUallacháin, Daire; Mellander, Per-Erik; Kelly, Ann-Marie; Matthaei, Christoph D; Piggott, Jeremy J; Kelly-Quinn, Mary

2018-05-10

Multiple stressors affect stream ecosystems worldwide and their interactions are of particular concern, with gaps existing in understanding stressor impacts on stream communities. Addressing these knowledge gaps will aid in targeting and designing of appropriate mitigation measures. In this study, the agricultural stressors fine sediment (ambient, low, medium, high), phosphorus (ambient, enriched) and nitrogen (ambient, enriched) were manipulated simultaneously in 64 streamside mesocosms to determine their individual and combined effects on the macroinvertebrate community (benthos and drift). Stressor levels were chosen to reflect those typically observed in European agricultural streams. A 21-day colonisation period was followed by a 14-day manipulative period. Results indicate that added sediment had the most pervasive effects, significantly reducing total macroinvertebrate abundance, total EPT abundance and abundances of three common EPT taxa. The greatest effect was at high sediment cover (90%), with decreasing negative impacts at medium (50%) and low (30%) covers. Added sediment also led to higher drift propensities for nine of the twelve drift variables. The effects of nitrogen and phosphorus were relatively weak compared to sediment. Several complex and unpredictable 2-way or 3-way interactions among stressors were observed. While sediment addition generally reduced total abundance at high levels, this decrease was amplified by P enrichment at low sediment, whereas the opposite effect occurred at medium sediment and little effect at high sediment. These results have direct implications for water management as they highlight the importance of managing sediment inputs while also considering the complex interactions which can occur between sediment and nutrient stressors. Copyright © 2018 Elsevier B.V. All rights reserved.

Spatial complexity reduces interaction strengths in the meta-food web of a river floodplain mosaic

USGS Publications Warehouse

Bellmore, James Ryan; Baxter, Colden Vance; Connolly, Patrick J.

2015-01-01

Theory states that both the spatial complexity of landscapes and the strength of interactions between consumers and their resources are important for maintaining biodiversity and the 'balance of nature.' Spatial complexity is hypothesized to promote biodiversity by reducing potential for competitive exclusion; whereas, models show weak trophic interactions can enhance stability and maintain biodiversity by dampening destabilizing oscillations associated with strong interactions. Here we show that spatial complexity can reduce the strength of consumer-resource interactions in natural food webs. By sequentially aggregating food webs of individual aquatic habitat patches across a floodplain mosaic, we found that increasing spatial complexity resulted in decreases in the strength of interactions between predators and prey, owing to a greater proportion of weak interactions and a reduced proportion of strong interactions in the meta-food web. The main mechanism behind this pattern was that some patches provided predation refugia for species which were often strongly preyed upon in other patches. If weak trophic interactions do indeed promote stability, then our findings may signal an additional mechanism by which complexity and stability are linked in nature. In turn, this may have implications for how the values of landscape complexity, and the costs of biophysical homogenization, are assessed.

Setting performance standards for medical practice: a theoretical framework.

PubMed

Southgate, L; Hays, R B; Norcini, J; Mulholland, H; Ayers, B; Woolliscroft, J; Cusimano, M; McAvoy, P; Ainsworth, M; Haist, S; Campbell, M

2001-05-01

The assessment of performance in the real world of medical practice is now widely accepted as the goal of assessment at the postgraduate level. This is largely a validity issue, as it is recognised that tests of knowledge and in clinical simulations cannot on their own really measure how medical practitioners function in the broader health care system. However, the development of standards for performance-based assessment is not as well understood as in competency assessment, where simulations can more readily reflect narrower issues of knowledge and skills. This paper proposes a theoretical framework for the development of standards that reflect the more complex world in which experienced medical practitioners work. The paper reflects the combined experiences of a group of education researchers and the results of literature searches that included identifying current health system data sources that might contribute information to the measurement of standards. Standards that reflect the complexity of medical practice may best be developed through an "expert systems" analysis of clinical conditions for which desired health care outcomes reflect the contribution of several health professionals within a complex, three-dimensional, contextual model. Examples of the model are provided, but further work is needed to test validity and measurability.

Synthesis and X-ray Crystallography of [Mg(H2O)6][AnO2(C2H5COO)3]2 (An = U, Np, or Pu).

PubMed

Serezhkin, Viktor N; Grigoriev, Mikhail S; Abdulmyanov, Aleksey R; Fedoseev, Aleksandr M; Savchenkov, Anton V; Serezhkina, Larisa B

2016-08-01

Synthesis and X-ray crystallography of single crystals of [Mg(H2O)6][AnO2(C2H5COO)3]2, where An = U (I), Np (II), or Pu (III), are reported. Compounds I-III are isostructural and crystallize in the trigonal crystal system. The structures of I-III are built of hydrated magnesium cations [Mg(H2O)6](2+) and mononuclear [AnO2(C2H5COO)3](-) complexes, which belong to the AB(01)3 crystallochemical group of uranyl complexes (A = AnO2(2+), B(01) = C2H5COO(-)). Peculiarities of intermolecular interactions in the structures of [Mg(H2O)6][UO2(L)3]2 complexes depending on the carboxylate ion L (acetate, propionate, or n-butyrate) are investigated using the method of molecular Voronoi-Dirichlet polyhedra. Actinide contraction in the series of U(VI)-Np(VI)-Pu(VI) in compounds I-III is reflected in a decrease in the mean An═O bond lengths and in the volume and sphericity degree of Voronoi-Dirichlet polyhedra of An atoms.

A Climate Information Platform for Copernicus (CLIPC): managing the data flood

NASA Astrophysics Data System (ADS)

Juckes, Martin; Swart, Rob; Bärring, Lars; Groot, Annemarie; Thysse, Peter; Som de Cerff, Wim; Costa, Luis; Lückenkötter, Johannes; Callaghan, Sarah; Bennett, Victoria

2016-04-01

The FP7 project "Climate Information Platform for Copernicus" (CLIPC) is developing a demonstration portal for the Copernicus Climate Change Service (C3S). The project confronts many problems associated with the huge diversity of underlying data, complex multi-layered uncertainties and extremely complex and evolving user requirements. The infrastructure is founded on a comprehensive approach to managing data and documentation, using global domain independent standards where possible. An extensive thesaurus of terms provides both a robust and flexible foundation for data discovery services and accessible definitions to support users. It is, of course, essential to provide information to users through an interface which reflects their expectations rather than the intricacies of abstract data models. CLIPC has reviewed user engagement activities from other collaborative European projects, conducted user polls, interviews and meetings and is now entering an evaluation phase in which users discuss new features and options in the portal design. The CLIPC portal will provide access to raw climate science data and climate impact indicators derived from that data. The portal needs the flexibility to support access to extremely large datasets as well as providing means to manipulate data and explore complex products interactively.

Intrathymic lymphopoiesis: stromal cell-associated proliferation of T cells is independent of lymphocyte genotype.

PubMed

Kyewski, B A; Travis, M; Kaplan, H S

1984-09-01

We analyzed the genetic restriction of direct cell-cell interactions between thymocytes and a) cortical epithelial cells, b) macrophages, and c) medullary dendritic cells in the mouse thymus. Thymectomized (C3H X C57BL/Ka)F1 hybrid mice were doubly grafted with P1 and P2 neonatal thymus grafts, were lethally irradiated, and were reconstituted with a mixture of P1 and P2 bone marrow cells which differed in the Thy-1 locus. The contributions of both parental inocula to the composition of the free and stromal cell-associated T cell compartments were analyzed separately in thymic grafts of each parental strain. The lymphoid composition in both compartments essentially reflected the peripheral T cell-chimerism in the host. The development of lymphostromal complexes was not restricted by the genotype of the partner cells. Statistical analysis of the distributions of P1 and P2 T cells among free thymocytes and within individual lymphostromal complexes, however, suggests that the T cells of an individual complex are the progeny of oligoclonal proliferation. Thus, both epithelial cells and bone marrow-derived stromal cells seem to be involved in different stages of intrathymic lymphopoiesis.

Flexible Stoichiometry and Asymmetry of the PIDDosome Core Complex by Heteronuclear NMR Spectroscopy and Mass Spectrometry

PubMed Central

Nematollahi, Lily A.; Garza-Garcia, Acely; Bechara, Chérine; Esposito, Diego; Morgner, Nina; Robinson, Carol V.; Driscoll, Paul C.

2015-01-01

Homotypic death domain (DD)–DD interactions are important in the assembly of oligomeric signaling complexes such as the PIDDosome that acts as a platform for activation of caspase-2-dependent apoptotic signaling. The structure of the PIDDosome core complex exhibits an asymmetric three-layered arrangement containing five PIDD-DDs in one layer, five RAIDD-DDs in a second layer and an additional two RAIDD-DDs. We addressed complex formation between PIDD-DD and RAIDD-DD in solution using heteronuclear nuclear magnetic resonance (NMR) spectroscopy, nanoflow electrospray ionization mass spectrometry and size-exclusion chromatography with multi-angle light scattering. The DDs assemble into complexes displaying molecular masses in the range 130–158 kDa and RAIDD-DD:PIDD-DD stoichiometries of 5:5, 6:5 and 7:5. These data suggest that the crystal structure is representative of only the heaviest species in solution and that two RAIDD-DDs are loosely attached to the 5:5 core. Two-dimensional 1H,15N-NMR experiments exhibited signal loss upon complexation consistent with the formation of high-molecular-weight species. 13C-Methyl-transverse relaxation optimized spectroscopy measurements of the PIDDosome core exhibit signs of differential line broadening, cross-peak splitting and chemical shift heterogeneity that reflect the presence of non-equivalent sites at interfaces within an asymmetric complex. Experiments using a mutant RAIDD-DD that forms a monodisperse 5:5 complex with PIDD-DD show that the spectroscopic signature derives from the quasi- but non-exact equivalent environments of each DD. Since this characteristic was previously demonstrated for the complex between the DDs of CD95 and FADD, the NMR data for this system are consistent with the formation of a structure homologous to the PIDDosome core. PMID:25528640

What do we gain from simplicity versus complexity in species distribution models?

USGS Publications Warehouse

Merow, Cory; Smith, Matthew J.; Edwards, Thomas C.; Guisan, Antoine; McMahon, Sean M.; Normand, Signe; Thuiller, Wilfried; Wuest, Rafael O.; Zimmermann, Niklaus E.; Elith, Jane

2014-01-01

Species distribution models (SDMs) are widely used to explain and predict species ranges and environmental niches. They are most commonly constructed by inferring species' occurrence–environment relationships using statistical and machine-learning methods. The variety of methods that can be used to construct SDMs (e.g. generalized linear/additive models, tree-based models, maximum entropy, etc.), and the variety of ways that such models can be implemented, permits substantial flexibility in SDM complexity. Building models with an appropriate amount of complexity for the study objectives is critical for robust inference. We characterize complexity as the shape of the inferred occurrence–environment relationships and the number of parameters used to describe them, and search for insights into whether additional complexity is informative or superfluous. By building ‘under fit’ models, having insufficient flexibility to describe observed occurrence–environment relationships, we risk misunderstanding the factors shaping species distributions. By building ‘over fit’ models, with excessive flexibility, we risk inadvertently ascribing pattern to noise or building opaque models. However, model selection can be challenging, especially when comparing models constructed under different modeling approaches. Here we argue for a more pragmatic approach: researchers should constrain the complexity of their models based on study objective, attributes of the data, and an understanding of how these interact with the underlying biological processes. We discuss guidelines for balancing under fitting with over fitting and consequently how complexity affects decisions made during model building. Although some generalities are possible, our discussion reflects differences in opinions that favor simpler versus more complex models. We conclude that combining insights from both simple and complex SDM building approaches best advances our knowledge of current and future species ranges.

Vortex loops and Majoranas

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

Chesi, Stefano; CEMS, RIKEN, Wako, Saitama 351-0198; Jaffe, Arthur

2013-11-15

We investigate the role that vortex loops play in characterizing eigenstates of interacting Majoranas. We give some general results and then focus on ladder Hamiltonian examples as a test of further ideas. Two methods yield exact results: (i) A mapping of certain spin Hamiltonians to quartic interactions of Majoranas shows that the spectra of these two examples coincide. (ii) In cases with reflection-symmetric Hamiltonians, we use reflection positivity for Majoranas to characterize vortices in the ground states. Two additional methods suggest wider applicability of these results: (iii) Numerical evidence suggests similar behavior for certain systems without reflection symmetry. (iv) Amore » perturbative analysis also suggests similar behavior without the assumption of reflection symmetry.« less

New nonlinear optical effect: self-reflection phenomenon due to exciton-biexciton-light interaction in semiconductors

NASA Astrophysics Data System (ADS)

Khadzhi, P. I.; Lyakhomskaya, K. D.; Nadkin, L. Y.; Markov, D. A.

2002-05-01

The characteristic peculiarities of the self-reflection of a strong electromagnetic wave in a system of coherent excitons and biexcitons due to the exciton-photon interaction and optical exciton-biexciton conversion in semiconductors were investigated as one of the manifestations of nonlinear optical Stark-effect. It was found that a monotonously decreasing standing wave with an exponential decreasing spatial tail is formed in the semiconductor. Under the action of the field of a strong pulse, an optically homogeneous medium is converted, into the medium with distributed feedback. The appearance of the spatially separated narrow pears of the reflective index, extinction and reflection coefficients is predicted.

A Type-2 fuzzy data fusion approach for building reliable weighted protein interaction networks with application in protein complex detection.

PubMed

Mehranfar, Adele; Ghadiri, Nasser; Kouhsar, Morteza; Golshani, Ashkan

2017-09-01

Detecting the protein complexes is an important task in analyzing the protein interaction networks. Although many algorithms predict protein complexes in different ways, surveys on the interaction networks indicate that about 50% of detected interactions are false positives. Consequently, the accuracy of existing methods needs to be improved. In this paper we propose a novel algorithm to detect the protein complexes in 'noisy' protein interaction data. First, we integrate several biological data sources to determine the reliability of each interaction and determine more accurate weights for the interactions. A data fusion component is used for this step, based on the interval type-2 fuzzy voter that provides an efficient combination of the information sources. This fusion component detects the errors and diminishes their effect on the detection protein complexes. So in the first step, the reliability scores have been assigned for every interaction in the network. In the second step, we have proposed a general protein complex detection algorithm by exploiting and adopting the strong points of other algorithms and existing hypotheses regarding real complexes. Finally, the proposed method has been applied for the yeast interaction datasets for predicting the interactions. The results show that our framework has a better performance regarding precision and F-measure than the existing approaches. Copyright © 2017 Elsevier Ltd. All rights reserved.

The effect of aerosols on the earth-atmosphere albedo

NASA Technical Reports Server (NTRS)

Herman, B. M.; Browning, S. R.

1975-01-01

The paper presents calculations of the change in reflected flux by the earth-atmosphere system in response to increases in the atmospheric aerosol loading for a range of complex indices of refraction, solar elevation angle and ground albedo. Results show that, for small values of ground albedo, the reflected solar flux may either increase or decrease with increasing aerosol loadings, depending upon the complex part of the index of refraction of the aerosols. For high ground albedos, an increase in aerosol levels always results in a decrease of reflected flux (i.e., a warming of the earth-atmosphere system).

Reflection and interference of electromagnetic waves in inhomogeneous media

NASA Technical Reports Server (NTRS)

Geiger, F. E.; Kyle, H. L.

1973-01-01

Solutions were obtained of the wave equation for a plane horizontally polarized electro-magnetic wave incident on a semi infinite two dimensional inhomogeneous medium. Two problems were considered: An inhomogeneous half space, and an inhomogeneous layer of arbitrary thickness. Solutions of the wave equation were obtained in terms of Hankel functions with complex arguments. Numerical calculations were made of the reflection coefficient R at the interface of the homogeneous medium. The startling results show that the reflection coefficient for a complex dielectric constant with gradient, can be less than that of the same medium with zero gradient.

Sequence co-evolution gives 3D contacts and structures of protein complexes

PubMed Central

Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

2014-01-01

Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution. DOI: http://dx.doi.org/10.7554/eLife.03430.001 PMID:25255213

Structural study of surfactant-dependent interaction with protein

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

Mehan, Sumit; Aswal, Vinod K., E-mail: vkaswal@barc.gov.in; Kohlbrecher, Joachim

2015-06-24

Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

Structural study of surfactant-dependent interaction with protein

NASA Astrophysics Data System (ADS)

Mehan, Sumit; Aswal, Vinod K.; Kohlbrecher, Joachim

2015-06-01

Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

Filtering Gene Ontology semantic similarity for identifying protein complexes in large protein interaction networks.

PubMed

Wang, Jian; Xie, Dong; Lin, Hongfei; Yang, Zhihao; Zhang, Yijia

2012-06-21

Many biological processes recognize in particular the importance of protein complexes, and various computational approaches have been developed to identify complexes from protein-protein interaction (PPI) networks. However, high false-positive rate of PPIs leads to challenging identification. A protein semantic similarity measure is proposed in this study, based on the ontology structure of Gene Ontology (GO) terms and GO annotations to estimate the reliability of interactions in PPI networks. Interaction pairs with low GO semantic similarity are removed from the network as unreliable interactions. Then, a cluster-expanding algorithm is used to detect complexes with core-attachment structure on filtered network. Our method is applied to three different yeast PPI networks. The effectiveness of our method is examined on two benchmark complex datasets. Experimental results show that our method performed better than other state-of-the-art approaches in most evaluation metrics. The method detects protein complexes from large scale PPI networks by filtering GO semantic similarity. Removing interactions with low GO similarity significantly improves the performance of complex identification. The expanding strategy is also effective to identify attachment proteins of complexes.

Luminescent Rhenium(I) and Iridium(III) Polypyridine Complexes as Biological Probes, Imaging Reagents, and Photocytotoxic Agents.

PubMed

Lo, Kenneth Kam-Wing

2015-12-15

Although the interactions of transition metal complexes with biological molecules have been extensively studied, the use of luminescent transition metal complexes as intracellular sensors and bioimaging reagents has not been a focus of research until recently. The main advantages of luminescent transition metal complexes are their high photostability, long-lived phosphorescence that allows time-resolved detection, and large Stokes shifts that can minimize the possible self-quenching effect. Also, by the use of transition metal complexes, the degree of cellular uptake can be readily determined using inductively coupled plasma mass spectrometry. For more than a decade, we have been interested in the development of luminescent transition metal complexes as covalent labels and noncovalent probes for biological molecules. We argue that many transition metal polypyridine complexes display triplet charge transfer ((3)CT) emission that is highly sensitive to the local environment of the complexes. Hence, the biological labeling and binding interactions can be readily reflected by changes in the photophysical properties of the complexes. In this laboratory, we have modified luminescent tricarbonylrhenium(I) and bis-cyclometalated iridium(III) polypyridine complexes of general formula [Re(bpy-R(1))(CO)3(py-R(2))](+) and [Ir(ppy-R(3))2(bpy-R(4))](+), respectively, with reactive functional groups and used them to label the amine and sulfhydryl groups of biomolecules such as oligonucleotides, amino acids, peptides, and proteins. Additionally, using a range of biological substrates such as biotin, estradiol, and indole, we have designed luminescent rhenium(I) and iridium(III) polypyridine complexes as noncovalent probes for biological receptors. The interesting results generated from these studies have prompted us to investigate the possible applications of luminescent transition metal complexes in intracellular systems. Thus, in the past few years, we have developed an interest in the cytotoxic activity, cellular uptake, and bioimaging applications of these complexes. Additionally, we and other research groups have demonstrated that many transition metal complexes have facile cellular uptake and organelle-localization properties and that their cytotoxic activity can be readily controlled. For example, complexes that can target the nucleus, nucleolus, mitochondria, lysosomes, endoplasmic reticulum, and Golgi apparatus have been identified. We anticipate that this selective localization property can be utilized in the development of intracellular sensors and bioimaging reagents. Thus, we have functionalized luminescent rhenium(I) and iridium(III) polypyridine complexes with various pendants, including molecule-binding moieties, sugar molecules, bioorthogonal functional groups, and polymeric chains such as poly(ethylene glycol) and polyethylenimine, and examined their potentials as biological reagents. This Account describes our design of luminescent rhenium(I) and iridium(III) polypyridine complexes and explains how they can serve as a new generation of biological reagents for diagnostic and therapeutic applications.

Key competencies of the psychodynamic psychotherapist and how to teach them in supervision.

PubMed

Sarnat, Joan

2010-03-01

Four of Rodolfa et al.'s (2005) competencies in professional psychology-relationship, self-reflection, assessment-case conceptualization, and intervention-are key for the psychodynamic psychotherapist. Relationship lies at the heart of what is understood to be curative about psychodynamic psychotherapy. Self-reflection implies a complex and highly developed process that includes but goes beyond Rodolfa et al.'s and Kaslow, Dunn, and Smith's (2008) definitions. Competent assessment, diagnosis, and case conceptualization entails making inferences about unconscious processes by observing the client and also one's own experience, and integrating these inferences with theory. Effective psychodynamic intervention is derived from what the psychotherapist has experienced, processed, and conceptualized about the relationship with the client and about the client's internal object world. An extended vignette shows these competencies emerging in a psychotherapist-in-training, facilitated by an intense interaction with a supervisor. Although the supervisory and clinical tasks are different, the supervisor provides a relationship experience that models these same competencies for the supervisee and catalyzes their development in the supervisee. PsycINFO Database Record (c) 2010 APA, all rights reserved

Classification of M1/M2-polarized human macrophages by label-free hyperspectral reflectance confocal microscopy and multivariate analysis.

PubMed

Bertani, Francesca R; Mozetic, Pamela; Fioramonti, Marco; Iuliani, Michele; Ribelli, Giulia; Pantano, Francesco; Santini, Daniele; Tonini, Giuseppe; Trombetta, Marcella; Businaro, Luca; Selci, Stefano; Rainer, Alberto

2017-08-21

The possibility of detecting and classifying living cells in a label-free and non-invasive manner holds significant theranostic potential. In this work, Hyperspectral Imaging (HSI) has been successfully applied to the analysis of macrophagic polarization, given its central role in several pathological settings, including the regulation of tumour microenvironment. Human monocyte derived macrophages have been investigated using hyperspectral reflectance confocal microscopy, and hyperspectral datasets have been analysed in terms of M1 vs. M2 polarization by Principal Components Analysis (PCA). Following PCA, Linear Discriminant Analysis has been implemented for semi-automatic classification of macrophagic polarization from HSI data. Our results confirm the possibility to perform single-cell-level in vitro classification of M1 vs. M2 macrophages in a non-invasive and label-free manner with a high accuracy (above 98% for cells deriving from the same donor), supporting the idea of applying the technique to the study of complex interacting cellular systems, such in the case of tumour-immunity in vitro models.

Crustal structure in the Falcón Basin area, northwestern Venezuela, from seismic and gravimetric evidence

NASA Astrophysics Data System (ADS)

Bezada, Maximiliano J.; Schmitz, Michael; Jácome, María Inés; Rodríguez, Josmat; Audemard, Franck; Izarra, Carlos; The Bolivar Active Seismic Working Group

2008-05-01

The Falcón Basin in northwestern Venezuela has a complex geological history driven by the interactions between the South American and Caribbean plates. Igneous intrusive bodies that outcrop along the axis of the basin have been associated with crustal thinning, and gravity modeling has shown evidence for a significantly thinned crust beneath the basin. In this study, crustal scale seismic refraction/wide-angle reflection data derived from onshore/offshore active seismic experiments are interpreted and forward-modeled to generate a P-wave velocity model for a ˜450 km long profile. The final model shows thinning of the crust beneath the Falcón Basin where depth to Moho decreases to 27 km from a value of 40 km about 100 km to the south. A deeper reflected phase on the offshore section is interpreted to be derived from the downgoing Caribbean slab. Velocity values were converted to density and the resulting gravimetric response was shown to be consistent with the regional gravity anomaly. The crustal thinning proposed here supports a rift origin for the Falcón Basin.

Modelling the optical response of human retinal photoreceptors to plane wave illumination with the finite integration technique

NASA Astrophysics Data System (ADS)

Akhlagh Moayed, Alireza; Dang, Shannon; Ramahi, Omar M.; Bizheva, Kostadinka K.

2009-02-01

The early stages of ocular diseases such as Diabetic Retinopathy are manifested by morphological changes in retinal tissue occurring on cellular level. Therefore, a number of ophthalmic diseases can be diagnosed at an early stage by detecting spatial and temporal variations in the scattering profile of retinal tissue. It was recently demonstrated that, OCT can be used to probe the functional response of retinal photoreceptors to external light stimulation [1]-[3]. fUHROCT measures localized differential changes in the retina reflectivity over time resulting from external light stimulation of the retina. Currently the origins of the observed reflectivity changes are not well understood. However, due to the complex nature of retinal physiology using purely experimental approaches in this case is problematic. For example fUHROCT is sensitive to small changes in the refractive index of biological tissue which as demonstrated previously, can result from a number of processes such as membrane hyperpolarization, osmotic swelling, metabolic changes, etc. In this paper, we present a computational model of interaction between photoreceptor cells and optical plane wave based on the Finite Integration Technique (FIT).

The role of electrolyte and polyelectrolyte on the adsorption of the anionic surfactant, sodium dodecylbenzenesulfonate, at the air-water interface.

PubMed

Zhang, X L; Taylor, D J F; Thomas, R K; Penfold, J

2011-04-15

The role of the polyelectrolyte, poly(ethyleneimine), PEI, and the electrolytes NaCl and CaCl(2), on the adsorption of the anionic surfactant, sodium dodecylbenzenesulfonate, LAS, at the air-water interface have been investigated by neutron reflectivity and surface tension. The surface tension data for the PEI/LAS mixtures are substantially affected by pH and the addition of electrolyte, and are consistent with a strong adsorption of surface polymer/surfactant complexes down to relatively low surfactant concentrations. The effects are most pronounced at high pH, and this is confirmed by the adsorption data obtained directly from neutron reflectivity. However, the effects of the addition of PEI and electrolyte on the LAS adsorption are not as pronounced as previously reported for PEI/SDS mixtures. This is attributed primarily to the steric hindrance of the LAS phenyl group resulting in a reduction in the ion-dipole attraction between the LAS sulfonate and amine groups that dominates the interaction at high pH. Copyright © 2011 Elsevier Inc. All rights reserved.

Aerodynamic Design and Numerical Analysis of Supersonic Turbine for Turbo Pump

NASA Astrophysics Data System (ADS)

Fu, Chao; Zou, Zhengping; Kong, Qingguo; Cheng, Honggui; Zhang, Weihao

2016-09-01

Supersonic turbine is widely used in the turbo pump of modern rocket. A preliminary design method for supersonic turbine has been developed considering the coupling effects of turbine and nozzle. Numerical simulation has been proceeded to validate the feasibility of the design method. As the strong shockwave reflected on the mixing plane, additional numerical simulated error would be produced by the mixing plane model in the steady CFD. So unsteady CFD is employed to investigate the aerodynamic performance of the turbine and flow field in passage. Results showed that the preliminary design method developed in this paper is suitable for designing supersonic turbine. This periodical variation of complex shockwave system influences the development of secondary flow, wake and shock-boundary layer interaction, which obviously affect the secondary loss in vane passage. The periodical variation also influences the strength of reflecting shockwave, which affects the profile loss in vane passage. Besides, high circumferential velocity at vane outlet and short blade lead to high radial pressure gradient, which makes the low kinetic energy fluid moves towards hub region and produces additional loss.

dsRNA binding properties of RDE-4 and TRBP reflect their distinct roles in RNAi.

PubMed

Parker, Greg S; Maity, Tuhin Subhra; Bass, Brenda L

2008-12-26

Double-stranded RNA (dsRNA)-binding proteins facilitate Dicer functions in RNA interference. Caenorhabditis elegans RDE-4 facilitates cleavage of long dsRNA to small interfering RNA (siRNA), while human trans-activation response RNA-binding protein (TRBP) functions downstream to pass siRNA to the RNA-induced silencing complex. We show that these distinct in vivo roles are reflected in in vitro binding properties. RDE-4 preferentially binds long dsRNA, while TRBP binds siRNA with an affinity that is independent of dsRNA length. These properties are mechanistically based on the fact that RDE-4 binds cooperatively, via contributions from multiple domains, while TRBP binds noncooperatively. Our studies offer a paradigm for how dsRNA-binding proteins, which are not sequence specific, discern dsRNA length. Additionally, analyses of the ability of RDE-4 deletion constructs and RDE-4/TRBP chimeras to reconstitute Dicer activity suggest RDE-4 promotes activity using its dsRNA-binding motif 2 to bind dsRNA, its linker region to interact with Dicer, and its C-terminus for Dicer activation.

Validating spatial structure in canopy water content using geostatistics

NASA Technical Reports Server (NTRS)

Sanderson, E. W.; Zhang, M. H.; Ustin, S. L.; Rejmankova, E.; Haxo, R. S.

1995-01-01

Heterogeneity in ecological phenomena are scale dependent and affect the hierarchical structure of image data. AVIRIS pixels average reflectance produced by complex absorption and scattering interactions between biogeochemical composition, canopy architecture, view and illumination angles, species distributions, and plant cover as well as other factors. These scales affect validation of pixel reflectance, typically performed by relating pixel spectra to ground measurements acquired at scales of 1m(exp 2) or less (e.g., field spectra, foilage and soil samples, etc.). As image analysis becomes more sophisticated, such as those for detection of canopy chemistry, better validation becomes a critical problem. This paper presents a methodology for bridging between point measurements and pixels using geostatistics. Geostatistics have been extensively used in geological or hydrogeolocial studies but have received little application in ecological studies. The key criteria for kriging estimation is that the phenomena varies in space and that an underlying controlling process produces spatial correlation between the measured data points. Ecological variation meets this requirement because communities vary along environmental gradients like soil moisture, nutrient availability, or topography.

A mathematical model of the structure and evolution of small scale discrete auroral arcs

NASA Technical Reports Server (NTRS)

Seyler, C. E.

1990-01-01

A three dimensional fluid model which includes the dispersive effect of electron inertia is used to study the nonlinear macroscopic plasma dynamics of small scale discrete auroral arcs within the auroral acceleration zone and ionosphere. The motion of the Alfven wave source relative to the magnetospheric and ionospheric plasma forms an oblique Alfven wave which is reflected from the topside ionosphere by the negative density gradient. The superposition of the incident and reflected wave can be described by a steady state analytical solution of the model equations with the appropriate boundary conditions. This two dimensional discrete auroral arc equilibrium provides a simple explanation of auroral acceleration associated with the parallel electric field. Three dimensional fully nonlinear numerical simulations indicate that the equilibrium arc configuration evolves three dimensionally through collisionless tearing and reconnection of the current layer. The interaction of the perturbed flow and the transverse magnetic field produces complex transverse structure that may be the origin of the folds and curls observed to be associated with small scale discrete arcs.