The commerce and crossover of resources: resource conservation in the service of resilience.

PubMed

Chen, Shoshi; Westman, Mina; Hobfoll, Stevan E

2015-04-01

Conservation of resources (COR) theory was originally introduced as a framework for understanding and predicting the consequences of major and traumatic stress, but following the work of Hobfoll and Shirom (1993), COR theory has been adopted to understanding and predicting work-related stress and both the stress and resilience that occur within work settings and work culture. COR theory underscores the critical role of resource possession, lack, loss and gain and depicts personal, social and material resources co-travelling in resource caravans, rather than piecemeal. We briefly review the principles of COR theory and integrate it in the crossover model, which provides a key mechanism for multi-person exchange of emotions, experiences and resources. Understanding the impact of resource reservoirs, resource passageways and crossover provides a framework for research and intervention promoting resilience to employees as well as to organizations. It emphasizes that the creation and maintenance of resource caravan passageways promote resource gain climates through resource crossover processes. Copyright © 2014 John Wiley & Sons, Ltd.

Reasons Why Training and Development Fails...and What You Can Do about It.

ERIC Educational Resources Information Center

Phillips, Jack L.; Phillips, Patricia P.

2002-01-01

Among the reasons why training and development fail are lack of alignment with needs, failure to recognize nontraining solutions, lack of objectives, expensive solutions, lack of accountability for results, failure to prepare for transfer, lack of management support, failure to isolate the effects of training, lack of executive commitment and…

Starting from the Classroom: How an Inter-Segmental Faculty Group Works toward Increased K-16 Alignment

ERIC Educational Resources Information Center

De Roy, Tessa Carmen

2011-01-01

There is a lack of alignment between K-12 and higher education about the expectations for student skill and content knowledge. Too often, students leave the K-12 system ill prepared for success in higher education. One approach to increasing alignment has been supported by the California Partnership for Achieving Student Success (Cal-PASS), which…

Mastering School Reform.

ERIC Educational Resources Information Center

Goens, George A.; Clover, Sharon I. R.

School organizations must become responsive and flexible to address rapidly changing social, economic, and demographic conditions. Reform attempts to date have not worked because they were layered on old structures and perceptions in a fragmented, piecemeal fashion. The fundamental transformation of education that is required demands a paradigm…

BCG Approaches for Improved Management of Estuaries

EPA Science Inventory

Estuaries and other complex aquatic systems are exposed to a variety of stressors that act at several scales, but are managed piecemeal - - often resulting in a “death by 1000 cuts” caused by cumulative impacts to these valued resources. To address this, managers need tools that...

Developmental Differences in Holistic Interference of Facial Part Recognition

PubMed Central

Nakabayashi, Kazuyo; Liu, Chang Hong

2013-01-01

Research has shown that adults’ recognition of a facial part can be disrupted if the part is learnt without a face context but tested in a whole face. This has been interpreted as the holistic interference effect. The present study investigated whether children of 6- and 9–10-year-olds would show a similar effect. Participants were asked to judge whether a probe part was the same as or different from a test part whereby the part was presented either in isolation or in a whole face. The results showed that while all the groups were susceptible to a holistic interference, the youngest group was most severely affected. Contrary to the view that piecemeal processing precedes holistic processing in the cognitive development, our findings demonstrate that holistic processing is already present at 6 years of age. It is the ability to inhibit the influence of holistic information on piecemeal processing that seems to require a longer period of development into at an older and adult age. PMID:24204847

Why Quality Is within Our Grasp ... If We Reach.

ERIC Educational Resources Information Center

Rhodes, Lewis A.

1990-01-01

Today's calls for school restructuring demand a greater response than piecemeal tinkering. The impetus for total organizational change started over 30 years ago in Japan as industrial leaders adapted W. Edwards Deming's beliefs and strategies concerning psychology, systems, perceptual theoretical frameworks, and causes of variation. Quality…

A Unified Approach to the Study of Chemical Reactions in Freshman Chemistry.

ERIC Educational Resources Information Center

Cassen, T.; DuBois, Thomas D.

1982-01-01

Provides rationale and objectives for presenting chemical reactions in a unified, logical six-stage approach rather than a piecemeal approach. Stages discussed include: introduction, stable electronic configurations and stable oxidation states, reactions between two free elements, ion transfer/proton transfer reactions, double displacement…

The Potential of the Portfolio Approach

ERIC Educational Resources Information Center

Cavanna, Anthony; Olchefske, Joseph; Fleischman, Steve

2006-01-01

Despite some encouraging signs that education reform efforts are raising achievement in one school here and another there, such piecemeal approaches have not yet yielded positive systemic results. To achieve districtwide improvement, a growing number of school systems are adopting a "portfolio approach" to district governance by replacing the…

Federal Policy and Adolescent AIDS.

ERIC Educational Resources Information Center

Wilcox, Brian L.

1990-01-01

Maintains that federal policy on adolescent Acquired Immune Deficiency Syndrome health care and research is nonexistent or piecemeal. Despite the work of the Centers for Disease Control, efforts at preventive education are uncoordinated, resulting from the decentralized nature of the public health and education systems, and are hampered by social…

Early School Adjustment and Educational Attainment

ERIC Educational Resources Information Center

Magnuson, Katherine; Duncan, Greg J.; Lee, Kenneth T. H.; Metzger, Molly W.

2016-01-01

Although school attainment is a cumulative process combining mastery of both academic and behavioral skills, most studies have offered only a piecemeal view of the associations between middle-childhood capacities and subsequent schooling outcomes. Using a 20-year longitudinal data set, this study estimates the association between children's…

Numerical and Probabilistic Analysis of Asteroid and Comet Impact Hazard Mitigation

DTIC Science & Technology

2010-09-01

object on Jupiter are reminders and warning signals that we should take seriously. The extinction of the dinosaurs has been attributed to the impact of a...experimentally determined absorption patterns. These energy deposition processes are independent, so a piecemeal approach is physically reasonable . We

How to Teach Verbal Problems

ERIC Educational Resources Information Center

Dahmus, Maurice E.

1970-01-01

Presents a technique for teaching the lower ninety percent in mathematics. Concentrates on converting English statements, both expressed and implied, into one or many mathematical statements. Emphasis on translating in a direct, piecemeal, pure, and complete manner (DPPC). This method differs from others in that it is concrete rather than…

Belittled: The State of Play on Bullying

ERIC Educational Resources Information Center

Cox, Eva; Goodman, James

2005-01-01

Abused, ignored, sidelined, belittled. It's the human face of a systemic problem. Eva Cox and James Goodman report on a recent study of workplace bullying that highlights its effects on those being bullied, and the rather piecemeal administrative efforts to deal with it so far. (Contains 7 tables.)

Myopic Loss Aversion: Demystifying the Key Factors Influencing Decision Problem Framing

ERIC Educational Resources Information Center

Hardin, Andrew M.; Looney, Clayton Arlen

2012-01-01

Advancement of myopic loss aversion theory has been hamstrung by conflicting results, methodological inconsistencies, and a piecemeal approach toward understanding the key factors influencing decision problem framing. A series of controlled experiments provides a more holistic view of the variables promoting myopia. Extending the information…

The Large-Scale Structure of Scientific Method

ERIC Educational Resources Information Center

Kosso, Peter

2009-01-01

The standard textbook description of the nature of science describes the proposal, testing, and acceptance of a theoretical idea almost entirely in isolation from other theories. The resulting model of science is a kind of piecemeal empiricism that misses the important network structure of scientific knowledge. Only the large-scale description of…

Educational Neuroscience: Motivations, Methodology, and Implications

ERIC Educational Resources Information Center

Campbell, Stephen R.

2011-01-01

"What does the brain have to do with learning?" "Prima facie", this may seem like a strange thing for anyone to say, especially educational scholars, researchers, practitioners, and policy makers. There are, however, valid objections to injecting various and sundry neuroscientific considerations piecemeal into the vast field of education. These…

ICIS and the Reduction of Paperback.

ERIC Educational Resources Information Center

Alvir, Howard P.

Methods by which campuses with similar information needs for similar decisions can set up a common data base are identified and discussed. Advantages and disadvantages of achieving the common data base by bulk paperwork, functional objectives, and piecemeal empiricism are considered. Practical suggestions for instituting each method are given. Use…

Pre-Service Teachers' Maturing Perceptions of a TPACK-Framed Signature Pedagogy in Science Education

ERIC Educational Resources Information Center

Hechter, Richard P.

2012-01-01

Teacher education programs across North America are transforming. What were once piecemeal programs consisting of often unrelated courses are now becoming coherent and intertwined trajectories toward teacher certification. Part of this transformation can be attributed to the weaving of "signature pedagogies" throughout overarching…

First Things First! Creating the New American Primary School

ERIC Educational Resources Information Center

Takanishi, Ruby

2016-01-01

Challenging policymakers, educators, reformers, and citizens to replace piecemeal reforms with fundamental redesign, "First Things First!" calls for a different way of organizing the American primary school. Ruby Takanishi outlines a new framework for integrating early education with primary education (pre-K-5), including both short- and…

Provision for Community College Faculty Development in Collective Bargaining Agreements

ERIC Educational Resources Information Center

Wallace, Terry H. Smith

1976-01-01

Trends of collective negotiations were examined as they affect inservice education, through an examination of collective bargaining agreements. Conclusion: the trend is presently one of negotiation of provisions in a piecemeal fashion rather than one with the goal of establishing comprehensive professional improvement programs. (Editor/JT)

Analysis of Learning Conceptions Based on Three Modules.

ERIC Educational Resources Information Center

Haygood, E. Langston; Iran-Nejad, Asghar

Three learning modules are described and investigated as they reflect different students' conceptions of and approaches to learning. The Schoolwork Module (SWM) focuses on task performance and involves a passive, incremental, piecemeal, and rote memory method of learning, parallel to what might be implied by the Information Processing model of…

Design of practical alignment device in KSTAR Thomson diagnostic

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

Lee, J. H., E-mail: jhlee@nfri.re.kr; University of Science and Technology; Lee, S. H.

2016-11-15

The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak’s Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broadmore » wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR’s Thomson scattering diagnostics.« less

Design of practical alignment device in KSTAR Thomson diagnostic.

PubMed

Lee, J H; Lee, S H; Yamada, I

2016-11-01

The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak's Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broad wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR's Thomson scattering diagnostics.

The Curriculum Gap

ERIC Educational Resources Information Center

Carroll, Kathleen

2015-01-01

The challenge of updating curriculum to align with Common Core State Standards is a national one felt by states, districts, and teachers alike. Teachers generally express enthusiasm for the Common Core, but consistently cite a lack of high-quality curricula as an impediment to teaching them. The demand for core-aligned quality materials has far…

Natural language processing, pragmatics, and verbal behavior

PubMed Central

Cherpas, Chris

1992-01-01

Natural Language Processing (NLP) is that part of Artificial Intelligence (AI) concerned with endowing computers with verbal and listener repertoires, so that people can interact with them more easily. Most attention has been given to accurately parsing and generating syntactic structures, although NLP researchers are finding ways of handling the semantic content of language as well. It is increasingly apparent that understanding the pragmatic (contextual and consequential) dimension of natural language is critical for producing effective NLP systems. While there are some techniques for applying pragmatics in computer systems, they are piecemeal, crude, and lack an integrated theoretical foundation. Unfortunately, there is little awareness that Skinner's (1957) Verbal Behavior provides an extensive, principled pragmatic analysis of language. The implications of Skinner's functional analysis for NLP and for verbal aspects of epistemology lead to a proposal for a “user expert”—a computer system whose area of expertise is the long-term computer user. The evolutionary nature of behavior suggests an AI technology known as genetic algorithms/programming for implementing such a system. ImagesFig. 1 PMID:22477052

Why we need multi-level health workforce governance: Case studies from nursing and medicine in Germany.

PubMed

Kuhlmann, Ellen; Larsen, Christa

2015-12-01

Health workforce needs have moved up on the reform agendas, but policymaking often remains 'piece-meal work' and does not respond to the complexity of health workforce challenges. This article argues for innovation in healthcare governance as a key to greater sustainability of health human resources. The aim is to develop a multi-level approach that helps to identify gaps in governance and improve policy interventions. Pilot research into nursing and medicine in Germany, carried out between 2013 and 2015 using a qualitative methodology, serves to illustrate systems-based governance weaknesses. Three explorative cases address major responses to health workforce shortages, comprising migration/mobility of nurses, reform of nursing education, and gender-sensitive work management of hospital doctors. The findings illustrate a lack of connections between transnational/EU and organizational governance, between national and local levels, occupational and sector governance, and organizations/hospital management and professional development. Consequently, innovations in the health workforce need a multi-level governance approach to get transformative potential and help closing the existing gaps in governance. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A Method for Assessing Required Course-Related Skills and Prerequisite Structure

ERIC Educational Resources Information Center

Johnson, Michael D.; Wang, Jyhwen

2015-01-01

Engineering curricula should be dynamic with a goal of constant improvement and refinement. Unfortunately, this is often not the case; courses are developed, altered, and expanded in a piecemeal manner. Namely, as time progresses many programmes end up with courses that are developed and not a developed curriculum. To remedy this shortcoming…

On Conflict: A Curriculum Unit with Comments.

ERIC Educational Resources Information Center

Kirkland, Olin

This experimental eight week unit is designed to give students a more detailed understanding of the concepts and realities of conflict, violence, war, and international behavior than is usually done with the ordinary piecemeal textbook approach to human interaction. After trial classroom use, it was determined that the activity may be used in…

Joint Space Doctrine: Catapulting into the Future

DTIC Science & Technology

1994-01-01

Information dominance will provide the stimulus for the military space program in the near term. Maximizing the capabilities of the information weapon, however, requires formulating joint space doctrine that has broad support and applicability. This doctrine will provide a significant advantage for the United States over those nations which employ space assets in a piecemeal

An Introductory Idea for Teaching Two-Component Phase Diagrams

ERIC Educational Resources Information Center

Peckham, Gavin D.; McNaught, Ian J.

2011-01-01

The teaching of two-component phase diagrams has attracted little attention in this "Journal," and it is hoped that this article will make a useful contribution. Current physical chemistry textbooks describe two-component phase diagrams adequately, but do so in a piecemeal fashion one section at a time; first solid-liquid equilibria, then…

Case Marking Uniformity in Developmental Pronoun Errors

ERIC Educational Resources Information Center

Fitzgerald, Colleen E.; Rispoli, Matthew; Hadley, Pamela A.

2017-01-01

The purpose of this study was to determine if children acquire grammatical case as a unified system or in a piecemeal fashion. In English language acquisition, many children make developmental errors in marking case on subject position pronouns (e.g., "Me" do it, "Him" like it). It is unknown whether children who produce…

Choosing Music: Exploratory Studies into the Low Uptake of Music GCSE

ERIC Educational Resources Information Center

Lamont, Alexandra; Maton, Karl

2008-01-01

School music has a comparatively low take-up rate as a qualification among English secondary school pupils. Existing research on the issue has proffered possible reasons for this phenomenon but has generally been piecemeal and undertheorised. This paper sets out a fresh theoretical perspective capable of providing a basis for systematic empirical…

An Intersubjective Analysis of Engineering Leadership across Organizational Locations: Implications for Higher Education

ERIC Educational Resources Information Center

Rottmann, Cindy; Reeve, Douglas W.; Sacks, Robin; Klassen, Mike

2016-01-01

Engineering leadership education has become increasingly popular over the past decade in response to national calls for educational change. Despite the growing popularity of the movement, however, reform efforts continue to be piecemeal in their delivery, driven largely by the priorities of program leaders who established them (Graham, 2012). If…

Hospital CRM: unexplored frontier of revenue growth?

PubMed

Young, Thomas

2007-10-01

Customer relationship management (CRM) has a less-than-stellar reputation, in large part because efforts to implement it have been piecemeal and not well funded. The technologies now exist to make CRM much more effective than it has been in the past. Many hospitals today are demonstrating a substantial ROI from implementing a comprehensive CRM program.

Changing Minds with the Story of Adaptation: Strategies for Teaching Young Children about Natural Selection

ERIC Educational Resources Information Center

Emmons, Natalie; Smith, Hayley; Kelemen, Deborah

2016-01-01

Research Findings: Educational guidelines recommend a delayed, piecemeal approach to instruction on adaptation by natural selection. This approach is questionable given suggestions that older students' pervasive misunderstandings about adaptation are rooted in cognitive biases that develop early. In response to this, Kelemen et al. (2014) recently…

Promoting the Persistence of Indigenous Students through Teaching at the Cultural Interface

ERIC Educational Resources Information Center

Martin, Gregory; Nakata, Vicky; Nakata, Martin; Day, Andrew

2017-01-01

The promise of higher education remains elusive for many Indigenous students in Australia. To date, institutional efforts to improve the persistence and retention of Indigenous students have been largely piecemeal, poorly integrated and designed to remediate skill deficits. Yet, market-led expansion of Australian higher education is driving…

Finding Connections: Using Accounting Concepts in a Career Planning Class

ERIC Educational Resources Information Center

Wang, Michelle

2013-01-01

In higher education, the most common challenge for students is the ability to find a connection between one subject that they have learned and another subject. Thus, students' learning becomes compartmentalized and piecemeal. For instance, accounting students may find attending a drawing class boring and a waste of time. Science students may…

The Continued Influence of Implied and Explicitly Stated Misinformation in News Reports

ERIC Educational Resources Information Center

Rich, Patrick R.; Zaragoza, Maria S.

2016-01-01

The piecemeal reporting of unfolding news events can lead to the reporting of mistaken information (or misinformation) about the cause of the newsworthy event, which later needs to be corrected. Studies of the "continued influence effect" have shown, however, that corrections are not entirely effective in reversing the effects of initial…

Technology meets ergonomics in the dental clinic: new toys for old games?

PubMed

Rucker, L M

2000-01-01

Although there have been considerable advances in dental equipment, the introduction of such technology has often been piecemeal and "rushed to market." As a result there has been insufficient attention paid to ergonomic considerations and a systematic approach to, and theory of, dental ergonomics have not yet emerged.

Constructing the Components of a Lab Report Using Peer Review

ERIC Educational Resources Information Center

Berry, David E.; Fawkes, Kelli L.

2010-01-01

A protocol that emphasizes lab report writing using a piecemeal approach coupled with peer review is described. As the lab course progresses, the focus of the report writing changes sequentially through the abstract and introduction, the discussion, and the procedure. Two styles of lab programs are presented. One style rotates the students through…

Earth's future in the Anthropocene: Technological interventions between piecemeal and utopian social engineering

NASA Astrophysics Data System (ADS)

Schäfer, Stefan; Stelzer, Harald; Maas, Achim; Lawrence, Mark G.

2014-04-01

An extensive discussion in the academic and policy communities is developing around the possibility of climate engineering through stratospheric aerosol injection (SAI). In this contribution, we develop a perspective on this issue in the context of the wider setting of societal development in the Anthropocene. We draw on Karl Popper's concepts of piecemeal and utopian social engineering to examine how different visions of societal development relate to SAI. Based on this reflection, we argue that the debate on SAI is fueled not only by the inequitable distribution of its effects and potential atmospheric and climatic side effects, as disconcerting as some of these effects and side effects may be, but also, and perhaps primarily, by its apparent privileging of the status quo and incremental change over a more immediate and radical change in societal organization. Although differing ideological orientations might thus help explain the intensity of parts of the debate, the understanding from which they follow, in which societal development is deduced from postulated technological characteristics and assumptions about a technology's use, hides from view a more subtle understanding of the relationship between technology and politics.

Towards a team-based, collaborative approach to embedding e-learning within undergraduate nursing programmes.

PubMed

Kiteley, Robin J; Ormrod, Graham

2009-08-01

E-learning approaches are incorporated in many undergraduate nursing programmes but there is evidence to suggest that these are often piecemeal and have little impact on the wider, nurse education curriculum. This is consistent with a broader view of e-learning within the higher education (HE) sector, which suggests that higher education institutions (HEIs) are struggling to make e-learning a part of their mainstream delivery [HEFCE, 2005. HEFCE Strategy for E-Learning 2005/12. Bristol, UK, Higher Education Funding Council for England (HEFCE). [online] Available at: Accessed: 30 May 07]. This article discusses some of the challenges that face contemporary nurse education and seeks to account for reasons as to why e-learning may not be fully embedded within the undergraduate curriculum. These issues are considered within a wider debate about the need to align e-learning approaches with a shift towards a more student focused learning and teaching paradigm. The article goes on to consider broader issues in the literature on the adoption, embedding and diffusion of innovations, particularly in relation to the value of collaboration. A collaborative, team-based approach to e-learning development is considered as a way of facilitating sustainable, responsive and multidisciplinary developments within a field which is constantly changing and evolving.

Alcohol policy in South Africa: a review of policy development processes between 1994 and 2009.

PubMed

Parry, Charles D H

2010-08-01

Implementation of effective policies to reduce harmful alcohol consumption requires both a good understanding of the policy development process and which strategies are likely to work. To contribute to this understanding by reviewing four specific policy development initiatives that have taken place in South Africa between 1994 and 2009: restrictions on alcohol advertising and counter-advertising, regulation of retail sales of alcohol, alcohol taxation and controls on alcohol packaging. Material was drawn from a record of meetings and conferences held between 1994 and 2009 and a database of reports, newspaper clippings and policy documentation. When the policy process resulted in a concrete outcome there was always a clear recognition of the problem and policy alternatives, but success was more likely if there was an alignment of 'political' forces and/or when there was a determined bureaucracy. The impact of the other factors such as the media, community mobilization, non-governmental organizations (NGOs), the liquor industry and research are also discussed. Future avenues for policy research are identified, including the need for more systematic studies that give greater consideration to economic factors. Alcohol policy development in South Africa takes place in a piecemeal fashion and is the product of various competing influences. Having a comprehensive national alcohol strategy cutting across different sectors may be a better way for other developing countries to proceed.

Understanding the Value of Enterprise Architecture for Organizations: A Grounded Theory Approach

ERIC Educational Resources Information Center

Nassiff, Edwin

2012-01-01

There is a high rate of information system implementation failures attributed to the lack of alignment between business and information technology strategy. Although enterprise architecture (EA) is a means to correct alignment problems and executives highly rate the importance of EA, it is still not used in most organizations today. Current…

The Description and Indexing of Editorial Cartoons: An Exploratory Study

ERIC Educational Resources Information Center

Landbeck, Christopher Ryan

2013-01-01

While access to images in general has improved in the last 20 years, due to both advances in electronic storage and dissemination and to improvements in the intellectual provisions of them, access to editorial cartoons lags behind access to other types of images. While there have been piecemeal or ad hoc efforts to organize large cartoon…

Comparing the Role of Education in Serving Socioeconomic and Political Development in Tanzania and Cuba.

ERIC Educational Resources Information Center

Mtonga, Harry L.

1993-01-01

Compares Tanzania and Cuba to show how, in each case, the state has used education in political and socioeconomic development as a means of achieving socialism. In Cuba, the school system has contributed to creation of the new society, whereas Tanzania continues with piecemeal reconstruction of the educational system. (SLD)

Transformational Dialogue for Public Education: Moving from Tweaking to Transforming at the State Level

ERIC Educational Resources Information Center

Kim, Daniel H.

2014-01-01

The importance of public education has never been greater as we enter the dawn of a new millennium. Innumerable efforts have been focused on improving public education, but the unfortunate result has been an array of fractured, piecemeal efforts. What is needed is a systemic approach to go from "tweaking" to "transforming"…

State Civic Education Policy: Framework and Gap Analysis Tool. Special Report

ERIC Educational Resources Information Center

Baumann, Paul; Brennan, Jan

2017-01-01

The civic education policy framework and gap analysis tool are intended to guide state leaders as they address the complexities of preparing students for college, career and civic life. They allow for adaptation to state- and site-specific circumstances and may be adopted in whole or in piecemeal fashion, according to states' individual…

Nurses' Satisfaction With Using Nursing Information Systems From Technology Acceptance Model and Information Systems Success Model Perspectives: A Reductionist Approach.

PubMed

Lin, Hsien-Cheng

2017-02-01

Nursing information systems can enhance nursing practice and the efficiency and quality of administrative affairs within the nursing department and thus have been widely considered for implementation. Close alignment of human-computer interaction can advance optimal clinical performance with the use of information systems. However, a lack of introduction of the concept of alignment between users' perceptions and technological functionality has caused dissatisfaction, as shown in the existing literature. This study provides insight into the alignment between nurses' perceptions and how technological functionality affects their satisfaction with Nursing Information System use through a reductionist perspective of alignment. This cross-sectional study collected data from 531 registered nurses in Taiwan. The results indicated that "perceived usefulness in system quality alignment," "perceived usefulness in information quality alignment," "perceived ease of use in system quality alignment," "perceived ease of use in information quality alignment," and "perceived ease of use in service quality alignment" have significantly affected nurses' satisfaction with Nursing Information System use. However, "perceived usefulness in service quality alignment" had no significant effect on nurses' satisfaction. This study also provides some meaningful implications for theoretical and practical aspects of design.

"No Child Left Behind," the "Individuals with Disabilities Education Act" and Functional Curricula: A Conflict of Interest?

ERIC Educational Resources Information Center

Bouck, Emily C.

2009-01-01

Is a functional curriculum aligned with the federal education policies of No Child Left Behind (2002) and the Individuals with Disabilities Education Act (IDEA, 2004)? This article analyzes the alignment, or lack thereof, between this approach to educating secondary students with mild mental impairment and the two main federal education laws…

Operational Initiative in Theory and Doctrine

DTIC Science & Technology

2015-05-21

1984 Paret translation of On War uses the term initiative with far more frequency than the original German text ; given that Paret contextually...logical evolution of thought throughout doctrine, from core texts and dominant military theory prior to 1905 through the current catalogued system...Unfortunately, no such cohesive map currently exists; rather, military theorists have charted the terrain of initiative piecemeal. This section seeks to

Induction of Teachers into 21st Century Learning Communities: Creating the Next Generation of Educational Practice

ERIC Educational Resources Information Center

Carroll, Thomas G.

2005-01-01

Every child deserves a quality education. Providing competent, caring, qualified teachers in schools organized for success is the way to get there, but the devil is in the details. By tinkering on the edges, adopting piecemeal approaches to attracting, supporting, and retaining highly qualified teachers for the students who need them most, the…

New Jersey Land-Use Planning Techniques and Legislation. Agricultural Experiment Station Bulletin AE-338.

ERIC Educational Resources Information Center

Schneider, Lee D.

In response to recent urban to rural migration trends and the development of rather piecemeal land use policies and practices by local, state, and Federal decision makers, the U.S. Department of Agriculture has established a regional project (NE-78) and this report reflects the first of three major project objectives (to describe and appraise…

Coming to Grips with Change: The Initial Training of Geography Teachers in Hong Kong

ERIC Educational Resources Information Center

Stimpson, Philip

2004-01-01

Hong Kong styles itself as "the city that never sleeps", "the ever changing city". The dynamism and pace of change in teacher education, however, has to be seen as laggardly in comparison. This is not to say there has been no experiment but changes have been piecemeal and "add-ons". Teacher education in Hong Kong has…

An Unfinished Jigsaw: The 16+ Curriculum in the 1990s.

ERIC Educational Resources Information Center

Kershaw, Noel

Education reform in Great Britain during the last 15 years has been piecemeal, and all the pieces are not yet in place for broad and balanced post-16 education. The last 10 years of debate have achieved much common ground among the goals perceived by government, industry, and education. Three major ways of looking at the post-16 curriculum have…

Autistic trait interactions underlie sex-dependent facial recognition abilities in the normal population.

PubMed

Valla, Jeffrey M; Maendel, Jeffrey W; Ganzel, Barbara L; Barsky, Andrew R; Belmonte, Matthew K

2013-01-01

Autistic face processing difficulties are either uniquely social or due to a piecemeal cognitive "style." Co-morbidity of social deficits and piecemeal cognition in autism makes teasing apart these accounts difficult. These traits vary normally, and are more separable in the general population, suggesting another way to compare accounts. Participants completed the Autism Quotient survey of autistic traits, and one of three face recognition tests: full-face, eyes-only, or mouth-only. Social traits predicted performance in the full-face condition in both sexes. Eyes-only males' performance was predicted by a social × cognitive trait interaction: attention to detail boosted face recognition in males with few social traits, but hindered performance in those reporting many social traits. This suggests social/non-social Autism Spectrum Conditions (ASC) trait interactions at the behavioral level. In the presence of few ASC-like difficulties in social reciprocity, an ASC-like attention to detail may confer advantages on typical males' face recognition skills. On the other hand, when attention to detail co-occurs with difficulties in social reciprocity, a detailed focus may exacerbate such already present social difficulties, as is thought to occur in autism.

Generativity and imagination in autism spectrum disorder: evidence from individual differences in children's impossible entity drawings.

PubMed

Low, Jason; Goddard, Elizabeth; Melser, Joseph

2009-06-01

This study examined the cognitive underpinnings of spontaneous imagination in autism spectrum disorder (ASD) by way of individual differences. Children with ASD (N = 27) and matched typically developing (TD) children were administered Karmiloff-Smith's (1990) imaginative drawing task, along with measures that tapped specific executive functions (generativity, visuospatial planning, and central coherence processing style) and false belief theory of mind (ToM) understanding. The ASD group drawings displayed deficits in imaginative content and a piecemeal pictorial style. ASD participants also showed group deficits in generativity, planning and ToM, and exhibited weak coherence. Individual differences in generativity were related to imaginative drawing content in the ASD group, and the association was mediated through planning ability. Variations in weak coherence were separately related to a piecemeal drawing style in the ASD group. Variations in generativity were also linked with imaginative drawing content in the TD group; the connection unfolded when it received pooled variance from receptive language ability, and thereupon mediated through false belief reasoning to cue imaginative content. Results are discussed in terms of how generativity plays a broad and important role for imagination in ASD and typical development, albeit in different ways.

Globalization and health: a framework for analysis and action.

PubMed Central

Woodward, D.; Drager, N.; Beaglehole, R.; Lipson, D.

2001-01-01

Globalization is a key challenge to public health, especially in developing countries, but the linkages between globalization and health are complex. Although a growing amount of literature has appeared on the subject, it is piecemeal, and suffers from a lack of an agreed framework for assessing the direct and indirect health effects of different aspects of globalization. This paper presents a conceptual framework for the linkages between economic globalization and health, with the intention that it will serve as a basis for synthesizing existing relevant literature, identifying gaps in knowledge, and ultimately developing national and international policies more favourable to health. The framework encompasses both the indirect effects on health, operating through the national economy, household economies and health-related sectors such as water, sanitation and education, as well as more direct effects on population-level and individual risk factors for health and on the health care system. Proposed also is a set of broad objectives for a programme of action to optimize the health effects of economic globalization. The paper concludes by identifying priorities for research corresponding with the five linkages identified as critical to the effects of globalization on health. PMID:11584737

Development by Design in Colombia: Making Mitigation Decisions Consistent with Conservation Outcomes

PubMed Central

Saenz, Shirley; Walschburger, Tomas; González, Juan Carlos; León, Jorge; McKenney, Bruce; Kiesecker, Joseph

2013-01-01

Mitigation policy and regulatory frameworks are consistent in their strong support for the mitigation hierarchy of: (1) avoiding impacts, (2) minimizing impacts, and then (3) offsetting/compensating for residual impacts. While mitigation frameworks require developers to avoid, minimize and restore biodiversity on-site before considering an offset for residual impacts, there is a lack of quantitative guidance for this decision-making process. What are the criteria for requiring impacts be avoided altogether? Here we examine how conservation planning can guide the application of the mitigation hierarchy to address this issue. In support of the Colombian government's aim to improve siting and mitigation practices for planned development, we examined five pilot projects in landscapes expected to experience significant increases in mining, petroleum and/or infrastructure development. By blending landscape-level conservation planning with application of the mitigation hierarchy, we can proactively identify where proposed development and conservation priorities would be in conflict and where impacts should be avoided. The approach we outline here has been adopted by the Colombian Ministry of Environment and Sustainable Development to guide licensing decisions, avoid piecemeal licensing, and promote mitigation decisions that maintain landscape condition. PMID:24339972

Development by design in Colombia: making mitigation decisions consistent with conservation outcomes.

PubMed

Saenz, Shirley; Walschburger, Tomas; González, Juan Carlos; León, Jorge; McKenney, Bruce; Kiesecker, Joseph

2013-01-01

Mitigation policy and regulatory frameworks are consistent in their strong support for the mitigation hierarchy of: (1) avoiding impacts, (2) minimizing impacts, and then (3) offsetting/compensating for residual impacts. While mitigation frameworks require developers to avoid, minimize and restore biodiversity on-site before considering an offset for residual impacts, there is a lack of quantitative guidance for this decision-making process. What are the criteria for requiring impacts be avoided altogether? Here we examine how conservation planning can guide the application of the mitigation hierarchy to address this issue. In support of the Colombian government's aim to improve siting and mitigation practices for planned development, we examined five pilot projects in landscapes expected to experience significant increases in mining, petroleum and/or infrastructure development. By blending landscape-level conservation planning with application of the mitigation hierarchy, we can proactively identify where proposed development and conservation priorities would be in conflict and where impacts should be avoided. The approach we outline here has been adopted by the Colombian Ministry of Environment and Sustainable Development to guide licensing decisions, avoid piecemeal licensing, and promote mitigation decisions that maintain landscape condition.

Understanding suicide among indigenous adolescents: a review using the PRECEDE model.

PubMed Central

Clarke, V. A.; Frankish, C. J.; Green, L. W.

1997-01-01

AIM: To use the available literature to identify the causes of suicide among indigenous adolescents. METHOD: The PRECEDE model provided a framework to organize the material and identify the areas where relatively little research had been reported. RESULTS: The epidemiological diagnosis showed that suicide was greater in indigenous than non-indigenous populations and particularly high among adolescent males. Environments of native persons are characterized by remoteness, poverty, cultural displacement, and family disintegration. The educational and organizational diagnosis identified predisposing factors reflecting the social environments previously identified, the enabling factors of televised suicides, and firearm and alcohol availability, in conjunction with an absence of positive expectations. Finally the administrative and policy diagnosis identified a piecemeal, short term perspective, often lacking cultural sensitivity. Although there was more literature from the United States than from Canada, Australia or New Zealand, the pictures emerging were consistent, with problems being identified across continents. Literature was more abundant in relation to the epidemiological, environmental, and educational/ organizational diagnoses than in relation to policy and administration. CONCLUSION: The increased suicide rates among indigenous adolescents were not a product of their native origins, but of the social milieu in which these people generally found themselves. PMID:9213160

Understanding suicide among indigenous adolescents: a review using the PRECEDE model.

PubMed

Clarke, V A; Frankish, C J; Green, L W

1997-06-01

To use the available literature to identify the causes of suicide among indigenous adolescents. The PRECEDE model provided a framework to organize the material and identify the areas where relatively little research had been reported. The epidemiological diagnosis showed that suicide was greater in indigenous than non-indigenous populations and particularly high among adolescent males. Environments of native persons are characterized by remoteness, poverty, cultural displacement, and family disintegration. The educational and organizational diagnosis identified predisposing factors reflecting the social environments previously identified, the enabling factors of televised suicides, and firearm and alcohol availability, in conjunction with an absence of positive expectations. Finally the administrative and policy diagnosis identified a piecemeal, short term perspective, often lacking cultural sensitivity. Although there was more literature from the United States than from Canada, Australia or New Zealand, the pictures emerging were consistent, with problems being identified across continents. Literature was more abundant in relation to the epidemiological, environmental, and educational/ organizational diagnoses than in relation to policy and administration. The increased suicide rates among indigenous adolescents were not a product of their native origins, but of the social milieu in which these people generally found themselves.

A Meta-Analysis of Urban Climate Change Adaptation ...

EPA Pesticide Factsheets

The concentration of people, infrastructure, and ecosystem services in urban areas make them prime sites for climate change adaptation. While advances have been made in developing frameworks for adaptation planning and identifying both real and potential barriers to action, empirical work evaluating urban adaptation planning processes has been relatively piecemeal. Existing assessments of current experience with urban adaptation provide necessarily broad generalizations based on the available peer-reviewed literature. This paper uses a meta-analysis of U.S. cities’ current experience with urban adaptation planning drawing from 54 sources that include peer-reviewed literature, government reports, white papers, and reports published by non-governmental organizations. The analysis specifically evaluates the institutional support structures being developed for urban climate change adaptation. The results demonstrate that adaptation planning is driven by a desire to reduce vulnerability and often catalyzes new collaborations and coordination mechanisms in urban governance. As a result, building capacity for urban climate change adaptation planning requires a focus not only on city governments themselves but also on the complex horizontal and vertical networks that have arisen around such efforts. Existing adaptation planning often lacks attention to equity issues, social vulnerability, and the influence of non-climatic factors on vulnerability. Engaging city govern

Biological intuition in alignment-free methods: response to Posada.

PubMed

Ragan, Mark A; Chan, Cheong Xin

2013-08-01

A recent editorial in Journal of Molecular Evolution highlights opportunities and challenges facing molecular evolution in the era of next-generation sequencing. Abundant sequence data should allow more-complex models to be fit at higher confidence, making phylogenetic inference more reliable and improving our understanding of evolution at the molecular level. However, concern that approaches based on multiple sequence alignment may be computationally infeasible for large datasets is driving the development of so-called alignment-free methods for sequence comparison and phylogenetic inference. The recent editorial characterized these approaches as model-free, not based on the concept of homology, and lacking in biological intuition. We argue here that alignment-free methods have not abandoned models or homology, and can be biologically intuitive.

Alignment methods: strategies, challenges, benchmarking, and comparative overview.

PubMed

Löytynoja, Ari

2012-01-01

Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters. Errors in this homology statement, that is errors in the alignment of the sequences, are likely to lead to errors in the downstream analyses. Sequence alignment and phylogenetic inference are tightly connected and many popular alignment programs use the phylogeny to divide the alignment problem into smaller tasks. They then neglect the phylogenetic tree, however, and produce alignments that are not evolutionarily meaningful. The use of phylogeny-aware methods reduces the error but the resulting alignments, with evolutionarily correct representation of homology, can challenge the existing practices and methods for viewing and visualising the sequences. The inter-dependency of alignment and phylogeny can be resolved by joint estimation of the two; methods based on statistical models allow for inferring the alignment parameters from the data and correctly take into account the uncertainty of the solution but remain computationally challenging. Widely used alignment methods are based on heuristic algorithms and unlikely to find globally optimal solutions. The whole concept of one correct alignment for the sequences is questionable, however, as there typically exist vast numbers of alternative, roughly equally good alignments that should also be considered. This uncertainty is hidden by many popular alignment programs and is rarely correctly taken into account in the downstream analyses. The quest for finding and improving the alignment solution is complicated by the lack of suitable measures of alignment goodness. The difficulty of comparing alternative solutions also affects benchmarks of alignment methods and the results strongly depend on the measure used. As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended.

The Modern Synthesis in the Light of Microbial Genomics.

PubMed

Booth, Austin; Mariscal, Carlos; Doolittle, W Ford

2016-09-08

We review the theoretical implications of findings in genomics for evolutionary biology since the Modern Synthesis. We examine the ways in which microbial genomics has influenced our understanding of the last universal common ancestor, the tree of life, species, lineages, and evolutionary transitions. We conclude by advocating a piecemeal toolkit approach to evolutionary biology, in lieu of any grand unified theory updated to include microbial genomics.

Do the Duration and Frequency of Physical Education Predict Academic Achievement, Self-Concept, Social Skills, Food Consumption, and Body Mass Index?

ERIC Educational Resources Information Center

Simms, Kathryn; Bock, Sara; Hackett, Lewis

2014-01-01

Objective: Prior research on the efficacy of physical education has been conducted in a piecemeal fashion. More specifically, studies typically test a single benefit hypothesized to be associated with physical education (e.g. body mass index [BMI]) while excluding others (e.g. social skills) and not controlling for important confounds (e.g. diet).…

The Potential for Collaborative Agri-Environment Schemes in England: Can a Well-Designed Collaborative Approach Address Farmers' Concerns with Current Schemes?

ERIC Educational Resources Information Center

Emery, Steven B.; Franks, Jeremy R.

2012-01-01

There is increasing recognition that whilst agri-environment schemes in England have had discernable benefits, their success in relation to certain species and resources has been inhibited by the piecemeal implementation of Environmental Stewardship (ES) on the basis of single farm agreements. In this paper we examine the receptivity of farmers to…

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

PubMed

Zheng, Qi; Grice, Elizabeth A

2016-10-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

Using confidence intervals to evaluate the focus alignment of spectrograph detector arrays.

PubMed

Sawyer, Travis W; Hawkins, Kyle S; Damento, Michael

2017-06-20

High-resolution spectrographs extract detailed spectral information of a sample and are frequently used in astronomy, laser-induced breakdown spectroscopy, and Raman spectroscopy. These instruments employ dispersive elements such as prisms and diffraction gratings to spatially separate different wavelengths of light, which are then detected by a charge-coupled device (CCD) or complementary metal-oxide-semiconductor (CMOS) detector array. Precise alignment along the optical axis (focus position) of the detector array is critical to maximize the instrumental resolution; however, traditional approaches of scanning the detector through focus lack a quantitative measure of precision, limiting the repeatability and relying on one's experience. Here we propose a method to evaluate the focus alignment of spectrograph detector arrays by establishing confidence intervals to measure the alignment precision. We show that propagation of uncertainty can be used to estimate the variance in an alignment, thus providing a quantitative and repeatable means to evaluate the precision and confidence of an alignment. We test the approach by aligning the detector array of a prototype miniature echelle spectrograph. The results indicate that the procedure effectively quantifies alignment precision, enabling one to objectively determine when an alignment has reached an acceptable level. This quantitative approach also provides a foundation for further optimization, including automated alignment. Furthermore, the procedure introduced here can be extended to other alignment techniques that rely on numerically fitting data to a model, providing a general framework for evaluating the precision of alignment methods.

"Don't Be Too Polite, Girls!" Women, Work, and Vocational Education and Training: A Critical Review of the Literature.

ERIC Educational Resources Information Center

Butler, Elaine; Ferrier, Fran

Most of the research on women and vocational education and training (VET) in Australia and elsewhere that was published in 1987-1998 may be characterized as follows: (1) it was undertaken to inform or support policy decisions and is therefore framed by political and ideological agendas; (2) it is piecemeal; (3) it tends to consider women as…

Aligning the unalignable: bacteriophage whole genome alignments.

PubMed

Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

2016-01-13

In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework

PubMed Central

Zheng, Qi; Grice, Elizabeth A.

2016-01-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost’s algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost. PMID:27706155

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies.

PubMed

Kim, Jiwoong; Kim, Min Soo; Koh, Andrew Y; Xie, Yang; Zhan, Xiaowei

2016-10-10

Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipelines lack several key features: (i) an integrated alignment tool, (ii) operon-level analysis, and (iii) the ability to process large datasets. Here we introduce our open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data, FMAP (Functional Mapping and Analysis Pipeline). FMAP performs alignment, gene family abundance calculations, and statistical analysis (three levels of analyses are provided: differentially-abundant genes, operons and pathways). The resulting output can be easily visualized with heatmaps and functional pathway diagrams. FMAP functional predictions are consistent with currently available functional analysis pipelines. FMAP is a comprehensive tool for providing functional analysis of metagenomic/metatranscriptomic sequencing data. With the added features of integrated alignment, operon-level analysis, and the ability to process large datasets, FMAP will be a valuable addition to the currently available functional analysis toolbox. We believe that this software will be of great value to the wider biology and bioinformatics communities.

The identification of complete domains within protein sequences using accurate E-values for semi-global alignment

PubMed Central

Kann, Maricel G.; Sheetlin, Sergey L.; Park, Yonil; Bryant, Stephen H.; Spouge, John L.

2007-01-01

The sequencing of complete genomes has created a pressing need for automated annotation of gene function. Because domains are the basic units of protein function and evolution, a gene can be annotated from a domain database by aligning domains to the corresponding protein sequence. Ideally, complete domains are aligned to protein subsequences, in a ‘semi-global alignment’. Local alignment, which aligns pieces of domains to subsequences, is common in high-throughput annotation applications, however. It is a mature technique, with the heuristics and accurate E-values required for screening large databases and evaluating the screening results. Hidden Markov models (HMMs) provide an alternative theoretical framework for semi-global alignment, but their use is limited because they lack heuristic acceleration and accurate E-values. Our new tool, GLOBAL, overcomes some limitations of previous semi-global HMMs: it has accurate E-values and the possibility of the heuristic acceleration required for high-throughput applications. Moreover, according to a standard of truth based on protein structure, two semi-global HMM alignment tools (GLOBAL and HMMer) had comparable performance in identifying complete domains, but distinctly outperformed two tools based on local alignment. When searching for complete protein domains, therefore, GLOBAL avoids disadvantages commonly associated with HMMs, yet maintains their superior retrieval performance. PMID:17596268

Validation of Splicing Events in Transcriptome Sequencing Data

PubMed Central

Kaisers, Wolfgang; Ptok, Johannes; Schwender, Holger; Schaal, Heiner

2017-01-01

Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence. FASTQ files obtained from 54 human dermal fibroblast samples were aligned against the human genome (GRCh38) using TopHat and STAR aligner. Statistical properties of gap-sites validated by gqs and wgis were evaluated by their sequence similarity to known exon-intron borders. Within the 54 samples, TopHat identifies 1,000,380 and STAR reports 6,487,577 gap-sites. Due to the lack of strand information, however, the percentage of identified GT-AG gap-sites is rather low. While gap-sites from TopHat contain ≈89% GT-AG, gap-sites from STAR only contain ≈42% GT-AG dinucleotide pairs in merged data from 54 fibroblast samples. Validation with gqs yields 156,251 gap-sites from TopHat alignments and 166,294 from STAR alignments. Validation with wgis yields 770,327 gap-sites from TopHat alignments and 1,065,596 from STAR alignments. Both alignment algorithms, TopHat and STAR, report gap-sites with considerable false discovery rate, which can drastically be reduced by validation with gqs and wgis. PMID:28545234

Boresight alignment method for mobile laser scanning systems

NASA Astrophysics Data System (ADS)

Rieger, P.; Studnicka, N.; Pfennigbauer, M.; Zach, G.

2010-06-01

Mobile laser scanning (MLS) is the latest approach towards fast and cost-efficient acquisition of 3-dimensional spatial data. Accurately evaluating the boresight alignment in MLS systems is an obvious necessity. However, recent systems available on the market may lack of suitable and efficient practical workflows on how to perform this calibration. This paper discusses an innovative method for accurately determining the boresight alignment of MLS systems by employing 3D laser scanners. Scanning objects using a 3D laser scanner operating in a 2D line-scan mode from various different runs and scan directions provides valuable scan data for determining the angular alignment between inertial measurement unit and laser scanner. Field data is presented demonstrating the final accuracy of the calibration and the high quality of the point cloud acquired during an MLS campaign.

Extreme Magneto-transport of Bulk Carbon Nanotubes in Sorted Electronic Concentrations and Aligned High Performance Fiber

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

Bulmer, John S.; Lekawa-Raus, Agnieszka; Rickel, Dwight G.

We explored high-field (60 T) magneto-resistance (MR) with two carbon nanotube (CNT) material classes: (1) unaligned single-wall CNTs (SWCNT) films with controlled metallic SWCNT concentrations and doping degree and (2) CNT fiber with aligned, long-length microstructure. All unaligned SWCNT films showed localized hopping transport where high-field MR saturation definitively supports spin polarization instead of a more prevalent wave function shrinking mechanism. Nitric acid exposure induced an insulator to metal transition and reduced the positive MR component. Aligned CNT fiber, already on the metal side of the insulator to metal transition, had positive MR without saturation and was assigned to classicalmore » MR involving electronic mobility. Subtracting high-field fits from the aligned fiber’s MR yielded an unconfounded negative MR, which was assigned to weak localization. It is concluded that fluctuation induced tunnelling, an extrinsic transport model accounting for most of the aligned fiber’s room temperature resistance, appears to lack MR field dependence.« less

Extreme Magneto-transport of Bulk Carbon Nanotubes in Sorted Electronic Concentrations and Aligned High Performance Fiber.

PubMed

Bulmer, John S; Lekawa-Raus, Agnieszka; Rickel, Dwight G; Balakirev, Fedor F; Koziol, Krzysztof K

2017-09-22

We explored high-field (60 T) magneto-resistance (MR) with two carbon nanotube (CNT) material classes: (1) unaligned single-wall CNTs (SWCNT) films with controlled metallic SWCNT concentrations and doping degree and (2) CNT fiber with aligned, long-length microstructure. All unaligned SWCNT films showed localized hopping transport where high-field MR saturation definitively supports spin polarization instead of a more prevalent wave function shrinking mechanism. Nitric acid exposure induced an insulator to metal transition and reduced the positive MR component. Aligned CNT fiber, already on the metal side of the insulator to metal transition, had positive MR without saturation and was assigned to classical MR involving electronic mobility. Subtracting high-field fits from the aligned fiber's MR yielded an unconfounded negative MR, which was assigned to weak localization. It is concluded that fluctuation induced tunnelling, an extrinsic transport model accounting for most of the aligned fiber's room temperature resistance, appears to lack MR field dependence.

Extreme Magneto-transport of Bulk Carbon Nanotubes in Sorted Electronic Concentrations and Aligned High Performance Fiber

DOE PAGES

Bulmer, John S.; Lekawa-Raus, Agnieszka; Rickel, Dwight G.; ...

2017-09-22

We explored high-field (60 T) magneto-resistance (MR) with two carbon nanotube (CNT) material classes: (1) unaligned single-wall CNTs (SWCNT) films with controlled metallic SWCNT concentrations and doping degree and (2) CNT fiber with aligned, long-length microstructure. All unaligned SWCNT films showed localized hopping transport where high-field MR saturation definitively supports spin polarization instead of a more prevalent wave function shrinking mechanism. Nitric acid exposure induced an insulator to metal transition and reduced the positive MR component. Aligned CNT fiber, already on the metal side of the insulator to metal transition, had positive MR without saturation and was assigned to classicalmore » MR involving electronic mobility. Subtracting high-field fits from the aligned fiber’s MR yielded an unconfounded negative MR, which was assigned to weak localization. It is concluded that fluctuation induced tunnelling, an extrinsic transport model accounting for most of the aligned fiber’s room temperature resistance, appears to lack MR field dependence.« less

Philosophy, policies, and procedures - The three P's of flight-deck operations

NASA Technical Reports Server (NTRS)

Degani, Asaf; Wiener, Earl L.

1991-01-01

Standard operating procedures are drafted and provided to flightcrews to dictate the manner in which tasks are carried out. Failure to conform to Standard Operating Procedures (SOP) is frequently listed as the cause of violations, incidents, and accidents. However, procedures are often designed piecemeal, rather than being based on a sound philosophy of operations and policies that follow from such a philosophy. A framework of philosophy, policies, and procedures is proposed.

The Tactical Center of Gravity: How Useful is the Concept?

DTIC Science & Technology

1990-01-06

through the Huertgen Forest, across the Kall River, capture the town of Kommerscheidt, and then capture Schmidt. The regiment also was required to protect...south through the woods, cross country to the Kall River, to take Kommerscheidt. The 3rd Battalion was to follow the 1st Battalion and take Schmidt on...desperate struggle. The lead battalions were destroyed piecemeal by the Germans in Kommerscheidt and Schmidt and along the Kall Trail. Poor

A new statistical framework to assess structural alignment quality using information compression

PubMed Central

Collier, James H.; Allison, Lloyd; Lesk, Arthur M.; Garcia de la Banda, Maria; Konagurthu, Arun S.

2014-01-01

Motivation: Progress in protein biology depends on the reliability of results from a handful of computational techniques, structural alignments being one. Recent reviews have highlighted substantial inconsistencies and differences between alignment results generated by the ever-growing stock of structural alignment programs. The lack of consensus on how the quality of structural alignments must be assessed has been identified as the main cause for the observed differences. Current methods assess structural alignment quality by constructing a scoring function that attempts to balance conflicting criteria, mainly alignment coverage and fidelity of structures under superposition. This traditional approach to measuring alignment quality, the subject of considerable literature, has failed to solve the problem. Further development along the same lines is unlikely to rectify the current deficiencies in the field. Results: This paper proposes a new statistical framework to assess structural alignment quality and significance based on lossless information compression. This is a radical departure from the traditional approach of formulating scoring functions. It links the structural alignment problem to the general class of statistical inductive inference problems, solved using the information-theoretic criterion of minimum message length. Based on this, we developed an efficient and reliable measure of structural alignment quality, I-value. The performance of I-value is demonstrated in comparison with a number of popular scoring functions, on a large collection of competing alignments. Our analysis shows that I-value provides a rigorous and reliable quantification of structural alignment quality, addressing a major gap in the field. Availability: http://lcb.infotech.monash.edu.au/I-value Contact: arun.konagurthu@monash.edu Supplementary information: Online supplementary data are available at http://lcb.infotech.monash.edu.au/I-value/suppl.html PMID:25161241

Segmentation of Dilated Hemorrhoidal Veins in Hemorrhoidal Disease.

PubMed

Díaz-Flores, Lucio; Gutiérrez, Ricardo; González-Gómez, Miriam; García, Pino; Sáez, Francisco J; Díaz-Flores, Lucio; Carrasco, José Luis; Madrid, Juan F

2018-06-18

Vein segmentation is a vascular remodeling process mainly studied in experimental conditions and linked to hemodynamic factors, with clinical implications. The aim of this work is to assess the morphologic characteristics, associated findings, and mechanisms that participate in vein segmentation in humans. To this end, we examined 156 surgically obtained cases of hemorrhoidal disease. Segmentation occurred in 65 and was most prominent in 15, which were selected for serial sections, immunohistochemistry, and immunofluorescence procedures. The dilated veins showed differently sized spaces, separated by thin septa. Findings associated with vein segmentation were: (a) vascular channels formed from the vein intima endothelial cells (ECs) and located in the vein wall and/or intraluminal fibrin, (b) vascular loops formed by interconnected vascular channels (venous-venous connections), which encircled vein wall components or fibrin and formed folds/pillars/papillae (FPPs; the encircling ECs formed the FPP cover and the encircled components formed the core), and (c) FPP splitting, remodeling, alignment, and fusion, originating septa. Thrombosis was observed in some nonsegmented veins, while the segmented veins only occasionally contained thrombi. Dense microvasculature was also present in the interstitium and around veins. In conclusion, the findings suggest that hemorrhoidal vein segmentation is an adaptive process in which a piecemeal angiogenic mechanism participates, predominantly by intussusception, giving rise to intravascular FPPs, followed by linear rearrangement, remodeling and fusion of FPPs, and septa formation. Identification of other markers, as well as the molecular bases, hemodynamic relevance, and possible therapeutic implications of vein segmentation in dilated hemorrhoidal veins require further studies. © 2018 S. Karger AG, Basel.

Exploring Faculty Integration of Moodle Resources: Effects of Theory-Based Training on Performance Objectives, Moodle Resource Integration, and Their Alignment

ERIC Educational Resources Information Center

Agamba, Joachim Jack

2012-01-01

Higher education institutions have been noted to be lacking in increasing the utilization of technology for student achievement. The lack of motivation by individual faculty members to optimize their use of technology has been identified as one of the main problems affecting appropriate technology use. The purpose of this research was to determine…

In the Multiagency Operating Environment of the 21st Century, Are Joint Qualified Officers Enough?

DTIC Science & Technology

2008-10-24

field; militaries that lack U.S. capabilities are no less useful if we have leaders educated to find the advantages brought by other countries’ forces...Gates, “Landon Lecture” (lecture, Manhattan: Kansas State University, 26 November 2007). 33 Henrietta Holsman Fore, “Aligning ‘Soft’ Power with ‘Hard...National Strategic Studies. Gates, Robert M. “Langdon Lecture.” Manhattan, KS, 26 November 2007 Holsman Fore, Henrietta . “Aligning ‘Soft’ with ‘Hard

Efficacy of laparoscopically assisted high ligation of patent processus vaginalis in children.

PubMed

Ahmed, H; Youssef, M K; Salem, E A; Fawzi, A M; Desoky, E A E; Eliwa, A M; Sakr, A M N; Shahin, A M S

2016-02-01

Laparoscopic hernia repairs have been proven to be efficient and safe for children, despite the slightly higher recurrence rate compared with the classic surgical repair. They have the advantage of easy and precise identification of the type of defect and its correction, both in ipsilateral and contralateral sides. The objectives of this study were to evaluate the efficacy, safety and outcome of the laparoscopically assisted piecemeal high ligation of a patent processus vaginalis (PPV) in children. A total of 40 children were enrolled into this prospective study; they were aged ≥ 6 months and had an inguinal hernia. The peritoneal cavity, including the contralateral side, was inspected for the possibility of bilateral hernias using a 3-mm 30° telescope. Another 3-mm port was introduced through the same infra-umbilical incision. The hernia was manually reduced or with the aid of a working infra-umbilical grasper. A prolene or vicryl 2/0 or 3/0 suture on a curved semicircle round-bodied taper-ended 25-30 mm needle was introduced through a very small inguinal skin-crease incision. It was passed through the abdominal wall layers to the peritoneum and was manipulated by the laparoscopic grasper to pick up the peritoneum in piecemeal all around the internal ring. The needle was then pushed to the outside near to the entrance site, thus forming a semicircle around the internal ring. The suture was then tied and the knot was subcutaneously buried. The primary outcome of the procedure was the incidence of intraoperative diagnosis and surgical repair of contralateral hernias in pre-operatively diagnosed unilateral cases. The secondary outcomes were defined as the incidence of complications and hernia recurrence. The exploratory laparoscopy found contralateral patent processus vaginalis (CPPV) with a detection rate of 28.1%. Chan et al., Esposito et al., Toufique et al. and Niyogi et al. reported similar figures for laparoscopic contralateral hernia detection rates of 28%, 39%, 39.7% and 29.2%, respectively. The limitations of this study were the small sample size, plus the risk factors and clinical significance for CPPV. Laparascopically assisted piecemeal closure of the internal inguinal ring in children is a safe and effective procedure. It helps in detecting a contralateral hernia without prolonging the operative time. Copyright © 2015 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.

GATA: A graphic alignment tool for comparative sequenceanalysis

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

Nix, David A.; Eisen, Michael B.

2005-01-01

Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dotplot analysis is often used to estimate non-coding sequence relatedness. Yet dotmore » plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.« less

Prosody and alignment: a sequential perspective

NASA Astrophysics Data System (ADS)

Szczepek Reed, Beatrice

2010-12-01

In their analysis of a corpus of classroom interactions in an inner city high school, Roth and Tobin describe how teachers and students accomplish interactional alignment by prosodically matching each other's turns. Prosodic matching, and specific prosodic patterns are interpreted as signs of, and contributions to successful interactional outcomes and positive emotions. Lack of prosodic matching, and other specific prosodic patterns are interpreted as features of unsuccessful interactions, and negative emotions. This forum focuses on the article's analysis of the relation between interpersonal alignment, emotion and prosody. It argues that prosodic matching, and other prosodic linking practices, play a primarily sequential role, i.e. one that displays the way in which participants place and design their turns in relation to other participants' turns. Prosodic matching, rather than being a conversational action in itself, is argued to be an interactional practice (Schegloff 1997), which is not always employed for the accomplishment of `positive', or aligning actions.

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees.

PubMed

Kück, Patrick; Meusemann, Karen; Dambach, Johannes; Thormann, Birthe; von Reumont, Björn M; Wägele, Johann W; Misof, Bernhard

2010-03-31

Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment profiling, alignment masking should routinely be used to improve tree reconstructions. Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements.

Get your science used—Six guidelines to improve your products

USGS Publications Warehouse

Perry, Suzanne C.; Blanpied, Michael L.; Burkett, Erin R.; Campbell, Nnenia M.; Carlson, Anders; Cox, Dale A.; Driedger, Carolyn L.; Eisenman, David P.; Fox-Glassman, Katherine T.; Hoffman, Sherry; Hoffman, Susanna M.; Jaiswal, Kishor S.; Jones, Lucile M.; Luco, Nicolas; Marx, Sabine M.; McGowan, Sean M.; Mileti, Dennis S.; Moschetti, Morgan P.; Ozman, David; Pastor, Elizabeth; Petersen, Mark D.; Porter, Keith A.; Ramsey, David W.; Ritchie, Liesel A.; Fitzpatrick, Jessica K.; Rukstales, Kenneth S.; Sellnow, Timothy L.; Vaughon, Wendy L.; Wald, David J.; Wald, Lisa A.; Wein, Anne; Zarcadoolas, Christina

2016-03-03

On the basis of research and practice into how people think, use tools, make decisions, and understand scientific/technical information, the social and behavioral scientists, marketers, and social-impact designers at the NSHM workshop provided remarkably consistent guidelines to develop successful science products, such as text, maps, and other products. In this report the guidelines are numbered for clarity, but they can be applied repeatedly, piecemeal, or out of order to fit each project and your resources.

Railroad Redevelopment Planning.

DTIC Science & Technology

1981-01-01

TEST CHART4A IONAL BUREAU’ Of STANDARDS- 1963-A -- m-ma REDQEVELcOPMENT PLANNIING *p W44 it -- 8 UNVRSITY OF C@O RAOO AT GENVER Tis docmr bpf Cr)o~d...officials began work on a set of guidelines in order to have some form of planned development u versus a piecemeal approach. According to a city...place. The city worked closely with various developers and their architects on the guidelines and the resulting ordinance was generally acceptable to

Videofluoroscopic Predictors of Penetration-Aspiration in Parkinson's Disease Patients.

PubMed

Argolo, Natalie; Sampaio, Marília; Pinho, Patrícia; Melo, Ailton; Nóbrega, Ana Caline

2015-12-01

Parkinson's disease (PD) patients show a high prevalence of swallowing disorders and tracheal aspiration of food. The videofluoroscopic study of swallowing (VFSS) allows clinicians to visualize the visuoperceptual and temporal parameters associated with swallowing disorders in an attempt to predict aspiration risk. However, this subject remains understudied in PD populations. Our aim was to identify the predictors of penetration-aspiration in PD patients using the VFSS. Consecutive patients were evaluated using VFSS with different consistencies and volumes of food. A speech-language pathologist measured the type of intra-oral bolus organization, loss of bolus control, bolus location at the initiation of the pharyngeal swallow, the presence of multiple swallows, piecemeal deglutition, bolus residue in the pharyngeal recesses and temporal measures. Scores ≥3 on the penetration-aspiration scale (PAS) indicated the occurrence of penetration-aspiration. Using logistic marginal regression, we found that residue in the vallecula, residue in the upper esophageal sphincter and piecemeal deglutition were associated with penetration-aspiration (odds ratio (OR) = 4.09, 2.87 and 3.83; P = 0.0040, 0.0071 and 0.0009, respectively). Penetration/aspiration occurred only with fluids (both of thin and thick consistency), and no significant differences were observed between fluid types or food volumes. The mechanisms underlying dysphagia and penetration/aspiration in PD patients and indications for further studies are discussed.

Science Lab Report Writing in Postsecondary Education: Mediating Teaching and Learning Strategies between Students and Instructors

NASA Astrophysics Data System (ADS)

Kalaskas, Anthony Bacaoat

The lab report is a genre commonly assigned by lab instructors and written by science majors in undergraduate science programs. The teaching and learning of the lab report, however, is a complicated and complex process that both instructors and students regularly contend with. This thesis is a qualitative study that aims to mediate the mismatch between students and instructors by ascertaining their attitudes, beliefs, and values regarding lab report writing. In this way, this thesis may suggest changes to teaching and learning strategies that lead to an improvement of lab report writing done by students. Given that little research has been conducted in this area thus far, this thesis also serves as a pilot study. A literature review is first conducted on the history of the lab report to delineate its development since its inception into American postsecondary education in the late 19th century. Genre theory and Vygotsky's zone of proximal development (ZPD) serve as the theoretical lenses for this thesis. Surveys and interviews are conducted with biology majors and instructors in the Department of Biology at George Mason University. Univariate analysis and coding are applied to elucidate responses from participants. The findings suggest that students may lack the epistemological background to understand lab reports as a process of doing science. This thesis also finds that both instructors and students consider the lab report primarily as a pedagogical genre as opposed to an apprenticeship genre. Additionally, although instructors were found to have utilized an effective piecemeal teaching strategy, there remains a lack of empathy among instructors for students. Collectively, these findings suggest that instructors should modify teaching strategies to determine and address student weaknesses more directly.

The National Shipbuilding Research Program. 1997 Ship Production Symposium. Implementation of Integrated CAD/CAM Systems in Small and Medium Sized Shipyards: A Case Study

DTIC Science & Technology

1997-04-01

implied, with respect to the accuracy, completeness or usefulness of the information contained in this report/ manual , or that the use of any information...shipyards throughout the world have introduced various aspects of CAD/CAM piecemeal as substitutes for manual processes, the greatest improvement in...possibility of multiple models of the molded geometry being developed, which would cause the loss of geometry control. Numerous AutoLisp routines were used

Coil tubing fishing operations utilize a first time technique to strip over and recover 9500 feet of stuck slickline wire

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

Forgenie, V.H.; Heiberger, E.M.; Kelso, L.K.

1995-12-31

Coil tubing was utilized to perform a modified strip over operation and recover 9500 ft. of stuck slickline (0.108 in.) wire. The technique, thought to be an industry first, eliminated the risky option of recovering the wire piecemeal via conventional wireline fishing operations. This paper documents the background that lead to the development of the technique. An operational summary details its implementation and illustrations are included of the special tools and techniques employed.

Comparing Product Category Rules from Different Programs: Learned Outcomes Towards Global Alignment

EPA Science Inventory

Purpose Product category rules (PCRs) provide category-specific guidance for estimating and reporting product life cycle environmental impacts, typically in the form of environmental product declarations and product carbon footprints. Lack of global harmonization between PCRs or ...

Accuracy of the volume-viscosity swallow test for clinical screening of oropharyngeal dysphagia and aspiration.

PubMed

Clavé, Pere; Arreola, Viridiana; Romea, Maise; Medina, Lucía; Palomera, Elisabet; Serra-Prat, Mateu

2008-12-01

To determine the accuracy of the bedside volume-viscosity swallow test (V-VST) for clinical screening of impaired safety and efficacy of deglutition. We studied 85 patients with dysphagia and 12 healthy subjects. Series of 5-20 mL nectar (295.02 mPa.s), liquid (21.61 mPa.s) and pudding (3682.21 mPa.s) bolus were administered during the V-VST and videofluoroscopy. Cough, fall in oxygen saturation > or =3%, and voice changes were considered signs of impaired safety, and piecemeal deglutition and oropharyngeal residue, signs of impaired efficacy. Videofluoroscopy showed patients had prolonged swallow response (> or =1064 ms); 52.1% had safe swallow at nectar, 32.9%, at liquid (p<0.05), and 80.6% at pudding viscosity (p<0.05); 29.4% had aspirations, and 45.8% oropharyngeal residue. The V-VST showed 83.7% sensitivity and 64.7% specificity for bolus penetration into the larynx and 100% sensitivity and 28.8% specificity for aspiration. Sensitivity of V-VST was 69.2% for residue, 88.4% for piecemeal deglutition, and 84.6% for identifying patients whose deglutition improved by enhancing bolus viscosity. Specificity was 80.6%, 87.5%, and 73.7%, respectively. The V-VST is a sensitive clinical method to identify patients with dysphagia at risk for respiratory and nutritional complications, and patients whose deglutition could be improved by enhancing bolus viscosity. Patients with a positive test should undergo videofluoroscopy.

Move to learn: Integrating spatial information from multiple viewpoints.

PubMed

Holmes, Corinne A; Newcombe, Nora S; Shipley, Thomas F

2018-05-11

Recalling a spatial layout from multiple orientations - spatial flexibility - is challenging, even when the global configuration can be viewed from a single vantage point, but more so when it must be viewed piecemeal. In the current study, we examined whether experiencing the transition between multiple viewpoints enhances spatial memory and flexible recall for a spatial configuration viewed simultaneously (Exp. 1) and sequentially (Exp. 2), whether the type of transition matters, and whether action provides an additional advantage over passive experience. In Experiment 1, participants viewed an array of dollhouse furniture from four viewpoints, but with all furniture simultaneously visible. In Experiment 2, participants viewed the same array piecemeal, from four partitioned viewpoints that allowed for viewing only a segment at a time. The transition between viewpoints involved rotation of the array or participant movement around it. Rotation and participant movement were passively experienced or actively generated. The control condition presented the dollhouse as a series of static views. Across both experiments, participant movement significantly enhanced spatial memory relative to array rotation or static views. However, in Exp. 2, there was a further advantage for actively walking around the array compared to being passively pushed. These findings suggest that movement around a stable environment is key to spatial memory and flexible recall, with action providing an additional boost to the integration of temporally segmented spatial events. Thus, spatial memory may be more flexible than prior data indicate, when studied under more natural acquisition conditions. Copyright © 2018 Elsevier B.V. All rights reserved.

Intergovernmental Organizations in Sub-Saharan Africa: Partners for Security and Capacity Building

DTIC Science & Technology

2009-05-11

realistic, long-term goals taking into account the current capacities of our partners. Any lack of balance increases the risk of delay or even failure in...ungoverned territories are potential terrorist sanctuaries due to lack of an effective state presence and the conduciveness of these territories to the...variables that will combine to form a daunting set of strategic challenges for the Obama Administration.”). 32 Henrietta Holsman Fore, “Aligning ‘Soft

Alfven Wave Reflection Model of Field-Aligned Currents at Mercury

NASA Technical Reports Server (NTRS)

Lyatsky, Wladislaw; Khazanov, George V.; Slavin, James

2010-01-01

An Alfven Wave Reflection (AWR) model is proposed that provides closure for strong field-aligned currents (FACs) driven by the magnetopause reconnection in the magnetospheres of planets having no significant ionospheric and surface electrical conductance. The model is based on properties of the Alfven waves, generated at high altitudes and reflected from the low-conductivity surface of the planet. When magnetospheric convection is very slow, the incident and reflected Alfven waves propagate along approximately the same path. In this case, the net field-aligned currents will be small. However, as the convection speed increases. the reflected wave is displaced relatively to the incident wave so that the incident and reflected waves no longer compensate each other. In this case, the net field-aligned current may be large despite the lack of significant ionospheric and surface conductivity. Our estimate shows that for typical solar wind conditions at Mercury, the magnitude of Region 1-type FACs in Mercury's magnetosphere may reach hundreds of kilo-Amperes. This AWR model of field-aligned currents may provide a solution to the long-standing problem of the closure of FACs in the Mercury's magnetosphere. c2009 Elsevier Inc. All rights reserved.

Early functional outcome after lateral UKA is sensitive to postoperative lower limb alignment.

PubMed

van der List, J P; Chawla, H; Villa, J C; Zuiderbaan, H A; Pearle, A D

2017-03-01

The predictive role of patient-specific characteristics and radiographic parameters on medial unicompartmental knee arthroplasty (UKA) outcomes is well known, but knowledge of these predictors is lacking in lateral UKA. Therefore, purpose of this study was to assess the predictive role of these parameters on short-term functional outcomes of lateral UKA. In this retrospective cohort study, Western Ontario and McMaster Universities Arthritis Index scores were collected at 2-year follow-up (median 2.2 years, range 2.0-4.0 years) in 39 patients who underwent lateral UKA. Patient-specific characteristics included age, BMI and gender, while radiographic parameters included osteoarthritis severity of all three compartments and both preoperative and postoperative hip-knee-ankle alignment. BMI, gender, age and preoperative valgus alignment were not correlated with functional outcomes, while postoperative valgus alignment was correlated with functional outcomes (0.561; p = 0.001). Postoperative valgus of 3°-7° was correlated with better outcomes than more neutral (-2° to 3° valgus) alignment (96.7 vs. 85.6; p = 0.011). Postoperative alignment was a predictor when corrected for patient-specific characteristics (regression coefficient 4.1; p < 0.001) and radiological parameters (regression coefficient 3.8; p = 0.002). Postoperative valgus alignment of 3°-7° was correlated with the best short-term functional outcomes in lateral UKA surgery, while patient-specific parameters and preoperative alignment were not correlated with functional outcomes. Based on these findings, a surgeon should aim for valgus alignment of 3°-7° when performing lateral UKA surgery for optimal functional outcomes. Prognostic study, Level II.

Comparing Product Category Rules from Different Programs: Learned Outcomes Towards Global Alignment (Presentation)

EPA Science Inventory

Purpose Product category rules (PCRs) provide category-specific guidance for estimating and reporting product life cycle environmental impacts, typically in the form of environmental product declarations and product carbon footprints. Lack of global harmonization between PCRs or ...

Authentic Classroom Leaders: The Student Perspective

ERIC Educational Resources Information Center

Downing, Megan S.

2016-01-01

In a qualitative study assessing students' perceptions of faculty-student interaction in the online learning environment, findings demonstrated that students make meaning of faculty-student interaction in ways that align with authentic leadership behaviors. Faculty interaction, or lack thereof, shaped students' perceptions of faculty authenticity…

The Rigors of Aligning Performance

DTIC Science & Technology

2015-06-01

organization merged 6 its field activities into regional facilities engineering commands (FECs). Today, FECs provide one-stop shopping for NAVFAC clients...many are old and antiquated , sometimes the systems mesh together other times they do not. Training is lacking on the various systems.  Communication

On the contributions of astroparticle physics to cosmology

NASA Astrophysics Data System (ADS)

Falkenburg, Brigitte

2014-05-01

Studying astroparticle physics sheds new light on scientific explanation and on the ways in which cosmology is empirically underdetermined or not. Astroparticle physics extends the empirical domain of cosmology from purely astronomical data to "multi-messenger astrophysics", i.e., measurements of all kinds of cosmic rays including very high energetic gamma rays, neutrinos, and charged particles. My paper investigates the ways in which these measurements contribute to cosmology and compares them with philosophical views about scientific explanation, the relation between theory and data, and scientific realism. The "standard models" of cosmology and particle physics lack of unified foundations. Both are "piecemeal physics" in Cartwright's sense, but contrary to her metaphysics of a "dappled world" the work in both fields of research aims at unification. Cosmology proceeds "top-down", from models to data and from large scale to small-scale structures of the universe. Astroparticle physics proceeds "bottom-up", from data taking to models and from subatomic particles to large-scale structures of the universe. In order to reconstruct the causal stories of cosmic rays and the nature of their sources, several pragmatic unifying strategies are employed. Standard views about scientific explanation and scientific realism do not cope with these "bottom-up" strategies and the way in which they contribute to cosmology. In addition it has to be noted that the shift to "multi-messenger astrophysics" transforms the relation between cosmological theory and astrophysical data in a mutually holistic way.

OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.

PubMed

Verzotto, Davide; M Teo, Audrey S; Hillmer, Axel M; Nagarajan, Niranjan

2016-01-01

Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies (for example, optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences. We introduce a novel seed-and-extend glocal (short for global-local) alignment method, OPTIMA (and a sliding-window extension for overlap alignment, OPTIMA-Overlap), which is the first to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel statistical model, agnostic with respect to technology-dependent error rates, for conservatively evaluating the significance of alignments without relying on expensive permutation-based tests. We show that OPTIMA and OPTIMA-Overlap outperform other state-of-the-art approaches (1.6-2 times more sensitive) and are more efficient (170-200 %) and precise in their alignments (nearly 99 % precision). These advantages are independent of the quality of the data, suggesting that our indexing approach and statistical evaluation are robust, provide improved sensitivity and guarantee high precision.

Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle

USDA-ARS?s Scientific Manuscript database

Water buffalo (Bubalus bubalis L.) represent a significant livestock species with high economic importance and promising characteristics for production; however, like many other livestock species, they lack a highly polished and contiguous reference genome assembly for use in high-resolution compara...

Report: EPA Prepared to Implement Strategic Human Capital Management Activities But Challenges Remain

EPA Pesticide Factsheets

Report #2004-P-00024, September 20, 2004. EPA’s headquarters and regional offices are prepared to implement strategic human capital management activities, but an alignment of office-level activities to the Agency’s Strategy for Human Capital is lacking.

76 FR 24089 - Credit Risk Retention

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-29

... Resecuritization Transactions D. Additional Exemptions E. Safe Harbor for Certain Foreign-Related Transactions VII..., when incentives are not properly aligned and there is a lack of discipline in the origination process... incentive problems among various parties involved in the process.\\8\\ \\7\\ Securitization may reduce the cost...

Winning Teams: Mobilization -- Related Correlates of Success in American World War II Infantry Divisions.

DTIC Science & Technology

1985-05-10

piecemeal to form an overall impression of a division first battle. 4 5 The 92nd Infantry Division, consisting of black 4 enlisted men and black and white...The conventional wisdom was that the 92nd’s failure reflected a complex of problems at the time 47associated with black divisions. There were, as we...attacked after Ii. having been hurriedly rushed forward to plug holes in the line.9 8 None of the divisions unsuccessful in their first major battles

Mental health services conceptualised as complex adaptive systems: what can be learned?

PubMed

Ellis, Louise A; Churruca, Kate; Braithwaite, Jeffrey

2017-01-01

Despite many attempts at promoting systems integration, seamless care, and partnerships among service providers and users, mental health services internationally continue to be fragmented and piecemeal. We exploit recent ideas from complexity science to conceptualise mental health services as complex adaptive systems (CASs). The core features of CASs are described and Australia's headspace initiative is used as an example of the kinds of problems currently being faced. We argue that adopting a CAS lens can transform services, creating more connected care for service users with mental health conditions.

Digital Video Over Space Systems and Networks

NASA Technical Reports Server (NTRS)

Grubbs, Rodney

2010-01-01

This slide presentation reviews the use of digital video with space systems and networks. The earliest use of video was the use of film precluding live viewing, which gave way to live television from space. This has given way to digital video using internet protocol for transmission. This has provided for many improvements with new challenges. Some of these ehallenges are reviewed. The change to digital video transmitted over space systems can provide incredible imagery, however the process must be viewed as an entire system, rather than piece-meal.

Science, Technology, and Warfare. Proceedings of the Military History Symposium (3rd) Held at the United States Air Force Academy (Colorado Springs, Colorado) on 8-9 May 1969

DTIC Science & Technology

1970-09-01

between science-technology and warfare. The stereotyped theory of a linear relationship between science, technology, and warfare satisfies the facts...therefore discarded piecemeal. Only with Mahan’s theory did this condition change. Morison then considers the opposite problem today: one in which the...1938), 1:531. = A s is now very well known, the impetus theory expounded with variations by all the most important writers on philosophy of motion

Oesophageal food impaction in achalasia treated with Coca-Cola and nifedipine.

PubMed

Koumi, Andriani; Panos, Marios Zenon

2010-01-01

Achalasia is characterised by the loss of peristaltic movement in the distal oesophagus and failure of the lower oesophageal sphincter relaxation, which results in impaired oesophageal emptying. We report a case of a 92-year-old frail woman with a history of achalasia, who presented with acute oesophageal obstruction due to impaction of a large amount of food material. She was treated successfully with nifedipine, in combination with Coca-Cola (original product, not sugar free), so avoiding the risks associated with repeated endoscopic intubation and piecemeal removal of the oesophageal content.

Magnetic field alignment of coil-coil diblock copolymers and blends via intrinsic chain anisotropy

NASA Astrophysics Data System (ADS)

Rokhlenko, Yekaterina; Majewski, Pawel; Larson, Steven; Yager, Kevin; Gopalan, Padma; Avgeropoulos, Apostolos; Chan, Edwin; Osuji, Chinedum

Magnetic fields can control alignment of self-assembled soft materials such as block copolymers provided there is a suitably large magnetic susceptibility anisotropy present in the system. Recent results have highlighted the existence of a non-trivial intrinsic anisotropy in coil-coil diblock copolymers, specifically in lamellar-forming PS-b-P4VP, which enables alignment at field strengths of a few tesla in systems lacking mesogenic components. Alignment is predicated on correlation in the orientation of end-end vectors implied by the localization of block junctions at the microdomain interface and is observed on cooling across the order-disorder transition in the presence of the field. For appropriate combinations of field strength and grain size, we can leverage intrinsic chain anisotropy to magnetically direct self-assembly of many non-mesogenic systems, including other coil-coil BCPs like PS-b-PDMS and PS-b-PMMA, blends of BCPs of disparate morphologies and MWs, and blends of BCPs with homopolymers. This is noteworthy as blends of PS-b-P4VP with PEO provide a route to form functional materials such as nanoporous films by dissolution of PEO, or aligned ion conduction materials. We survey these various systems using TEM and in-situ X-ray scattering to study the phase behavior and temperature-, time- and field- dependent dynamics of alignment.

Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks

PubMed Central

Wadhwab, Gulshan; Upadhyayaa, K. C.

2016-01-01

The amount of data on molecular interactions is growing at an enormous pace, whereas the progress of methods for analysing this data is still lacking behind. Particularly, in the area of comparative analysis of biological networks, where one wishes to explore the similarity between two biological networks, this holds a potential problem. In consideration that the functionality primarily runs at the network level, it advocates the need for robust comparison methods. In this paper, we describe Net2Align, an algorithm for pairwise global alignment that can perform node-to-node correspondences as well as edge-to-edge correspondences into consideration. The uniqueness of our algorithm is in the fact that it is also able to detect the type of interaction, which is essential in case of directed graphs. The existing algorithm is only able to identify the common nodes but not the common edges. Another striking feature of the algorithm is that it is able to remove duplicate entries in case of variable datasets being aligned. This is achieved through creation of a local database which helps exclude duplicate links. In a pervasive computational study on gene regulatory network, we establish that our algorithm surpasses its counterparts in its results. Net2Align has been implemented in Java 7 and the source code is available as supplementary files. PMID:28356678

Postsecondary Transition Programs for Underprepared Writers

ERIC Educational Resources Information Center

Antonetti, Christine M.

2017-01-01

There is a large population of students who enter postsecondary institutions underprepared in the area of writing, which can negatively affect their academic success in various disciplines. Lack of alignment between secondary and postsecondary education writing curricula is a common cause of why students are underprepared in writing. Identifying…

Sequence Similarity Presenter: a tool for the graphic display of similarities of long sequences for use in presentations.

PubMed

Fröhlich, K U

1994-04-01

A new method for the presentation of alignments of long sequences is described. The degree of identity for the aligned sequences is averaged for sections of a fixed number of residues. The resulting values are converted to shades of gray, with white corresponding to lack of identity and black corresponding to perfect identity. A sequence alignment is represented as a bar filled with varying shades of gray. The display is compact and allows for a fast and intuitive recognition of the distribution of regions with a high similarity. It is well suited for the presentation of alignments of long sequences, e.g. of protein superfamilies, in plenary lectures. The method is implemented as a HyperCard stack for Apple Macintosh computers. Several options for the modification of the output are available (e.g. background reduction, size of the summation window, consideration of amino acid similarity, inclusion of graphic markers to indicate specific domains). The output is a PostScript file which can be printed, imported as EPS or processed further with Adobe Illustrator.

Log-odds sequence logos

PubMed Central

Yu, Yi-Kuo; Capra, John A.; Stojmirović, Aleksandar; Landsman, David; Altschul, Stephen F.

2015-01-01

Motivation: DNA and protein patterns are usefully represented by sequence logos. However, the methods for logo generation in common use lack a proper statistical basis, and are non-optimal for recognizing functionally relevant alignment columns. Results: We redefine the information at a logo position as a per-observation multiple alignment log-odds score. Such scores are positive or negative, depending on whether a column’s observations are better explained as arising from relatedness or chance. Within this framework, we propose distinct normalized maximum likelihood and Bayesian measures of column information. We illustrate these measures on High Mobility Group B (HMGB) box proteins and a dataset of enzyme alignments. Particularly in the context of protein alignments, our measures improve the discrimination of biologically relevant positions. Availability and implementation: Our new measures are implemented in an open-source Web-based logo generation program, which is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/logoddslogo/index.html. A stand-alone version of the program is also available from this site. Contact: altschul@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25294922

Brain Stem Cavernous Malformations: Operative Nuances of a Less-Invasive Resection Technique.

PubMed

Singh, Harminder; Elarjani, Turki; da Silva, Harley Brito; Shetty, Rakshith; Kim, Louis; Sekhar, Laligam N

2017-12-08

Different operative techniques are reported for the resection of brainstem cavernous malformations (BSCMs). The senior author has previously reported on a less-invasive technique of entering the brain stem with piecemeal removal of BSCMs, especially the deep-seated ones. To present a larger series of these lesions, emphasizing the approach to the brain stem via case selection. We discuss the nuances of the less-invasive operative technique through case illustrations and intraoperative videos. A retrospective review of 46 consecutive cases of BSCMs, with their clinical and radiographic data, was performed. Nine cases were selected to illustrate 7 different operative approaches, and discuss surgical nuances of the less-invasive technique unique to each. Postoperative morbidity, defined as an increase in modified Rankin Scale, was observed in 5 patients (10.9%). A residual BSCM was present in 2 patients (4.3%); both underwent reoperation to remove the remainder. At follow-up of 31.1 ± 27.8 mo, 3 patients experienced recurrence (6.5%). Overall, 65% of our patients improved, 20% stayed the same, and 11% worsened postsurgery. Two patients died, yielding a mortality of 4.3%. Using the less-invasive resection technique for piecemeal BSCM removal, in appropriately selected patients, has yielded comparable to improved patient outcomes over existing large series. In our experience, lateral, anterolateral, and posterolateral approaches are favorable over direct midline (dorsal or ventral) approaches. A thorough understanding of brain-stem safe-entry zones, in conjunction with appropriate approach selection, is key to a good outcome in challenging cases. Copyright © 2017 by the Congress of Neurological Surgeons

Recurrence Factors in Giant Cell Tumors of the Spine.

PubMed

Ouyang, Han-Qiang; Jiang, Liang; Liu, Xiao-Guang; Wei, Feng; Yang, Shao-Min; Meng, Na; Jiang, Ping; Yu, Miao; Wu, Feng-Liang; Dang, Lei; Zhou, Hua; Zhang, Hua; Liu, Zhong-Jun

2017-07-05

Giant cell tumors (GCTs) are benign, locally aggressive tumors. We examined the rate of local recurrence of spinal GCTs and sought to identify recurrence factors in patients who underwent surgery. Between 1995 and 2014, 94 mobile spine GCT patients were treated at our hospital, comprising 43 male and 51 female patients with an average age of 33.4 years. Piecemeal intralesional spondylectomy and total en bloc spondylectomy (TES) were performed. Radiotherapy was suggested for recurrent or residual GCT cases. Since denosumab was not available before 2014 in our country, only interferon and/or zoledronic acid was suggested. Of the 94 patients, four underwent conservative treatment and 90 underwent operations. Seventy-five patients (79.8%) were followed up for a minimum of 24 months or until death. The median follow-up duration was 75.3 months. The overall recurrence rate was 37.3%. Ten patients (13.3%) died before the last follow-up (median: 18.5 months). Two patients (2.6%) developed osteogenic sarcoma. The local recurrence rate was 80.0% (24/30) in patients who underwent intralesional curettage, 8.8% (3/34) in patients who underwent extracapsular piecemeal spondylectomy, and 0 (0/9) in patients who underwent TES. The risk factors for local recurrence were lesions located in the cervical spine (P = 0.049), intralesional curettage (P < 0.001), repeated surgeries (P = 0.014), and malignancy (P < 0.001). Malignant transformation was a significant risk factor for death (P < 0.001). Cervical spinal tumors, curettage, and nonintact tumors were risk factors for local recurrence. Intralesional curettage and malignancy were the most important significant factors for local recurrence and death, respectively.

Comparing subjective contours for Kanizsa squares and linear edge alignments ('New York Titanic' figures).

PubMed

Gillam, Barbara; Marlow, Phillip J

2014-01-01

One current view is that subjective contours may involve high-level detection of a salient shape with back propagation to early visual areas where small receptive fields allow for scrutiny of relevant details. This idea applies to Kanizsa-type figures. However, Gillam and Chan (2002 Psychological Science, 13, 279-282) using figures based on Gillam's graphic 'New York Titanic' (Gillam, 1997 Thresholds: Limits of perception. New York: Arts Magazine) showed that strong subjective contours can be seen along the linearly aligned edges of a set of shapes if occlusion cues of 'extrinsic edge' and 'entropy contrast' are strong. Here we compared ratings of the strength of subjective contours along linear alignments with those seen in Kanizsa figures. The strongest subjective contour for a single set of linearly aligned shapes was similar in strength to the edges of a Kanizsa square (controlling for support ratio) despite the lack of a salient region. The addition of a second set of linearly aligned inducers consistent with a common surface increased subjective-contour strength, as did having four rather than two 'pacmen' in the Kanizsa figure, indicating a role for surface support. We argue that linear subjective contours allow for the investigation of certain occlusion cues and the interactions between them that are not easily explored with Kanizsa figures.

Teachers' Basic Knowledge of Reading Instruction: Insights from a Teacher Preparation Program

ERIC Educational Resources Information Center

Berkeley, Sheri; Regan, Kelley; Dimitrov, Dimiter; Guckert, Mary; Ray, Sharon

2016-01-01

Effective reading instruction is essential for all students, and especially students with disabilities; however, studies have indicated that both pre-service and in-service teachers lack an adequate knowledge of reading. To ensure adequate teacher knowledge, teacher preparation reform advocates suggest purposeful alignment of teacher preparation…

Achieving Success: Perceptions of Students from Migrant Farmwork Families

ERIC Educational Resources Information Center

McHatton, Patricia Alvarez; Zalaquett, Carlos P.; Cranson-Gingras, Ann

2006-01-01

In their pursuit of an education, students from migrant farmworker families experience multiple challenges such as high mobility rates and a lack of curriculum alignment and credit transfer across local, state, and national boundaries. Despite these challenges, many of these students graduate from high school and successfully transition into…

Teaching on Purpose: A Collegium Community Model for Supporting Intentional Teaching

ERIC Educational Resources Information Center

Robinson, Jennifer Meta; Kearns, Katherine Dowell; Gresalfi, Melissa; Sievert, April K.; Christensen, Tyler Booth

2015-01-01

The "collegium" learning community teaches mid-career graduate students intentionally to prepare for and create learning opportunities for their undergraduate students, what the authors call "teaching on purpose." The design addresses the lack of alignment between research on learning and preparation of faculty for teaching,…

Evaluation and Management: Continuous Professional Growth. [Federal Policy Platform Series. Brief 4

ERIC Educational Resources Information Center

New Leaders, 2014

2014-01-01

Despite the recent push to design and adopt educator evaluation systems, many states and local educational agencies (LEAs) have focused primarily on teacher evaluations and lack the appropriate attention to design and implementation of school leader evaluations and aligned professional development. And, since principals are responsible for…

Aligning Digital Video Technology with Game Pedagogy in Physical Education

ERIC Educational Resources Information Center

Koekoek, Jeroen; van der Mars, Hans; van der Kamp, John; Walinga, Wytse; van Hilvoorde, Ivo

2018-01-01

The rapid development of digital technology has expanded the prospects and promises for its application in physical education programs. Physical educators are becoming increasingly interested in technology but often remain inadequately equipped to effectively integrate these technological resources in their daily practice, and/or lack the…

Alignment between Informal Educator Perceptions and Audience Expectations of Climate Change Education

ERIC Educational Resources Information Center

Stylinski, Cathlyn; Heimlich, Joe; Palmquist, Sasha; Wasserman, Deborah; Youngs, Renae

2017-01-01

To understand the complexities of climate change on educator-visitor relationships, we compared educators' perceptions with audiences' expectations for informal science education institutions. Our findings suggest two disconnects: (a) a professional recognition that climate change education is related to institutional mission but a lack of…

Classification systems for causes of stillbirth and neonatal death, 2009-2014: an assessment of alignment with characteristics for an effective global system.

PubMed

Leisher, Susannah Hopkins; Teoh, Zheyi; Reinebrant, Hanna; Allanson, Emma; Blencowe, Hannah; Erwich, Jan Jaap; Frøen, J Frederik; Gardosi, Jason; Gordijn, Sanne; Gülmezoglu, A Metin; Heazell, Alexander E P; Korteweg, Fleurisca; Lawn, Joy; McClure, Elizabeth M; Pattinson, Robert; Smith, Gordon C S; Tunçalp, Ӧzge; Wojcieszek, Aleena M; Flenady, Vicki

2016-09-15

To reduce the burden of 5.3 million stillbirths and neonatal deaths annually, an understanding of causes of deaths is critical. A systematic review identified 81 systems for classification of causes of stillbirth (SB) and neonatal death (NND) between 2009 and 2014. The large number of systems hampers efforts to understand and prevent these deaths. This study aimed to assess the alignment of current classification systems with expert-identified characteristics for a globally effective classification system. Eighty-one classification systems were assessed for alignment with 17 characteristics previously identified through expert consensus as necessary for an effective global system. Data were extracted independently by two authors. Systems were assessed against each characteristic and weighted and unweighted scores assigned to each. Subgroup analyses were undertaken by system use, setting, type of death included and type of characteristic. None of the 81 systems were aligned with more than 9 of the 17 characteristics; most (82 %) were aligned with four or fewer. On average, systems were aligned with 19 % of characteristics. The most aligned system (Frøen 2009-Codac) still had an unweighted score of only 9/17. Alignment with individual characteristics ranged from 0 to 49 %. Alignment was somewhat higher for widely used as compared to less used systems (22 % v 17 %), systems used only in high income countries as compared to only in low and middle income countries (20 % vs 16 %), and systems including both SB and NND (23 %) as compared to NND-only (15 %) and SB-only systems (13 %). Alignment was higher with characteristics assessing structure (23 %) than function (15 %). There is an unmet need for a system exhibiting all the characteristics of a globally effective system as defined by experts in the use of systems, as none of the 81 contemporary classification systems assessed was highly aligned with these characteristics. A particular concern in terms of global effectiveness is the lack of alignment with "ease of use" among all systems, including even the most-aligned. A system which meets the needs of users would have the potential to become the first truly globally effective classification system.

Removing the Taboo on the Surgical Violation (Cut-Through) of Cancer.

PubMed

Robbins, K Thomas; Bradford, Carol R; Rodrigo, Juan P; Suárez, Carlos; de Bree, Remco; Kowalski, Luiz P; Rinaldo, Alessandra; Silver, Carl E; Lund, Valerie J; Nibu, Ken-Ichi; Ferlito, Alfio

2016-10-01

The surgical dictum of en bloc resection without violating cancer tissue has been challenged by novel treatments in head and neck cancer. An analysis of treatment outcomes involving piecemeal removal of sinonasal, laryngeal, oropharyngeal, and hypopharyngeal cancer shows that it did not compromise tumor control. The rationale for the evolution toward use of this technique is outlined. While complete resection with clear margins remains a key end point in surgical oncology, we believe it is time to acknowledge that this time-honored dictum of avoiding tumor violation is no longer valid in selected situations.

A life threatening uterine inversion and massive post partum hemorrhage caused by placenta accrete during Caesarean section in a primigravida: a case report.

PubMed

Tsivos, Dimitris; Malik, Fozia; Arambage, Kirana; Hagan, Philip; Lee, Cheng

2009-02-12

A 32-year-old Caucasian primigravida was admitted for elective Caesarean Section at 36 weeks and 6 days with the diagnosis of preeclampsia. Traction of the umbilical cord after delivery of a healthy baby resulted in uterine inversion. The placenta was found to be densely adherent to the posterior uterine wall. Piecemeal excision of the placenta as close as possible to the uterine lining was then performed. In this way we were able to control a massive post partum hemorrhage and preserve the fertility of the patient.

Oesophageal food impaction in achalasia treated with Coca-Cola and nifedipine

PubMed Central

Koumi, Andriani; Panos, Marios Zenon

2010-01-01

Achalasia is characterised by the loss of peristaltic movement in the distal oesophagus and failure of the lower oesophageal sphincter relaxation, which results in impaired oesophageal emptying. We report a case of a 92-year-old frail woman with a history of achalasia, who presented with acute oesophageal obstruction due to impaction of a large amount of food material. She was treated successfully with nifedipine, in combination with Coca-Cola (original product, not sugar free), so avoiding the risks associated with repeated endoscopic intubation and piecemeal removal of the oesophageal content. PMID:22242073

Instructional Alignment of Workplace Readiness Skills in Career and Technical Education

ERIC Educational Resources Information Center

Martin, Sarah Jane

2009-01-01

The United States faces a skills shortage that goes beyond academic and technical skills. Employers report entry-level workers lack the necessary "soft" skills, also referred to as workplace readiness skills, needed for success in the workforce; thus, calling on educational institutions to make improvements in high school curriculum in…

Achieving Alignment of Perspectival Framings in Problem-Solving Discourse

ERIC Educational Resources Information Center

van de Sande, Carla C.; Greeno, James G.

2012-01-01

We use a concept of framing to explain 3 cases in which participants initially lacked mutual understanding but then achieved significant mutual understanding. The cases were all consistent with a pattern of "positional framing" that includes a human participant who is inquiring, which we call a "listener", and a "source", which may be another…

Historical Understanding and Media Literacy: A Dispositional Alignment

ERIC Educational Resources Information Center

Bellino, Michelle

2008-01-01

Media literacy has been posited as a cross-curricular necessity for twenty-first century students, but one of the challenges of infusing media literacy into any discipline is the lack of a consistent definition. This article argues that media literacy is best conceptualized as a thinking disposition that evaluates the construction of media form,…

Working towards the Assurance of Graduate Attributes for Indigenous Cultural Competency: The Case for Alignment between Policy, Professional Development and Curriculum Processes

ERIC Educational Resources Information Center

Goerke, Veronica; Kickett, Marion

2013-01-01

In the Australian higher education environment, often preoccupied with internationalisation of education and associated issues around intercultural competencies, there is an uncomfortable awareness of the commensurate lack of attention on 'Indigenisation of the curriculum" and the interconnected 'Indigenous cultural competencies". This…

A Study of Power and Individualism in Virtual Teams: Trends, Challenges, and Solutions

ERIC Educational Resources Information Center

Jablonski, Deirdre

2013-01-01

This study investigated the relationship between cultural values and effectiveness of virtual team processes. In order to render an acceptable degree of comparison, four specific team outcomes of virtual team effectiveness were aligned on Hofstede's cultural dimensions of power distance and individualism. The lack of awareness of how power and…

Genome-Wide Prediction of Intrinsic Disorder; Sequence Alignment of Intrinsically Disordered Proteins

ERIC Educational Resources Information Center

Midic, Uros

2012-01-01

Intrinsic disorder (ID) is defined as a lack of stable tertiary and/or secondary structure under physiological conditions in vitro. Intrinsically disordered proteins (IDPs) are highly abundant in nature. IDPs possess a number of crucial biological functions, being involved in regulation, recognition, signaling and control, e.g. their functional…

Impact of RFID Information-Sharing Coordination over a Supply Chain with Reverse Logistics

ERIC Educational Resources Information Center

Nativi Nicolau, Juan Jose

2016-01-01

Companies have adopted environmental practices such as reverse logistics over the past few decades. However, studies show that aligning partners inside the green supply chain can be a substantial problem. This lack of coordination can increase overall supply chain cost. Information technology such as Radio Frequency Identification (RFID) has the…

A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

PubMed

Han, Renmin; Wang, Liansan; Liu, Zhiyong; Sun, Fei; Zhang, Fa

2015-12-01

Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction. Copyright © 2015 Elsevier Inc. All rights reserved.

Single-cell dynamics of mast cell-CD4+ CD25+ regulatory T cell interactions.

PubMed

Frossi, Barbara; D'Incà, Federica; Crivellato, Enrico; Sibilano, Riccardo; Gri, Giorgia; Mongillo, Marco; Danelli, Luca; Maggi, Laura; Pucillo, Carlo E

2011-07-01

The biological behavior of immune cells is determined by their intrinsic properties and interactions with other cell populations within their microenvironment. Several studies have confirmed the existence of tight spatial interactions between mast cells (MCs) and Tregs in different settings. For instance, we have recently identified the functional cross-talk between MCs and Tregs, through the OX40L-OX40 axis, as a new mechanism of reciprocal influence. However, there is scant information regarding the single-cell dynamics of this process. In this study, time-lapse video microscopy revealed direct interactions between Tregs and MCs in both murine and human cell co-cultures, resulting in the inhibition of the MC degranulation response. MCs incubated with WT, but not OX40-deficient, Tregs mediated numerous and long-lasting interactions and displayed different morphological features lacking the classical signs of exocytosis. MC degranulation and Ca2+ mobilization upon activation were inhibited by Tregs on a single-cell basis, without affecting overall cytokine secretion. Transmission electron microscopy showed ultrastructural evidence of vesicle-mediated secretion reconcilable with the morphological pattern of piecemeal degranulation. Our results suggest that MC morphological and functional changes following MC-Treg interactions can be ascribed to cell-cell contact and represent a transversal, non-species-specific mechanism of immune response regulation. Further research, looking at the molecular composition of this interaction will broaden our understanding of its contribution to immunity. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Autoimmune hepatitis in children and adolescents: clinical study, diagnosis and therapeutic response].

PubMed

Ferreira, Alexandre R; Roquete, Mariza L V; Penna, Francisco J; Toppa, Nivaldo H

2002-01-01

The aim of this study was to evaluate the clinical, laboratory and histopathological characteristics and the response to immunosuppression in children and adolescents with autoimmune hepatitis (AIH). The present research is a descriptive study consisting of 39 children and adolescents with AIH who receive care at the Department of Pediatric Gastroenterology of Hospital das Clínicas (UFMG) from 1986 to 1998. Children's age ranged from 1.6 to 17 years (mean 8.7 +/- 3.49), most of them were females (87.2%). There were three types of clinical presentations: chronic (53.9%), acute (41%), and serious hepatic failure (5.1%). The most relevant laboratory parameters were the aminotransferases and gamma-globulin increase. Antinuclear antibodies were positive in 66.7% of the patients, while smooth muscle antibodies were positive in 52.8% and anti-LKM1 in 3% of the patients. In the histopathology the most important findings were the piecemeal necrosis (93.7%), moderate to severe portal inflammation (78.1%), definitive or incomplete cirrhosis (76.9%), absence of lesion of biliary ducts (93.7%) and presence of rosettes (90.6%). During the treatment, 77.8% obtained complete resolution, associated to side effects in 27.8% of them. Seven patients died (17.9%). During the treatment there was significant z score reduction (p<0.05) for height/age. After carrying out this study, we observed that the typical characteristics of AIH were: female sex, several clinical presentations, increased aminotransferase, and hypergammaglobulinemia. Histopathology showed a predominance of incipient and/or definitive cirrhosis associated with moderate to severe portal inflammation and piecemeal necrosis. Treatment using corticosteroids and azathioprine, turned out to be effective. However, the reduction in the height/age z score probably represents an adverse effect of corticoid treatment.

Wide-field piecemeal cold snare polypectomy of large sessile serrated polyps without a submucosal injection is safe.

PubMed

Tate, David J; Awadie, Halim; Bahin, Farzan F; Desomer, Lobke; Lee, Ralph; Heitman, Steven J; Goodrick, Kathleen; Bourke, Michael J

2018-03-01

BACKGROUND AND STUDY AIMS : Large series suggest endoscopic mucosal resection is safe and effective for the removal of large (≥ 10 mm) sessile serrated polyps (SSPs), but it exposes the patient to the risks of electrocautery, including delayed bleeding. We examined the feasibility and safety of piecemeal cold snare polypectomy (pCSP) for the resection of large SSPs.  Sequential large SSPs (10 - 35 mm) without endoscopic evidence of dysplasia referred over 12 months to a tertiary endoscopy center were considered for pCSP. A thin-wire snare was used in all cases. Submucosal injection was not performed. High definition imaging of the defect margin was used to ensure the absence of residual serrated tissue. Adverse events were assessed at 2 weeks and surveillance was planned for between 6 and 12 months.  41 SSPs were completely removed by pCSP in 34 patients. The median SSP size was 15 mm (interquartile range [IQR] 14.5 - 20 mm; range 10 - 35 mm). The median procedure duration was 4.5 minutes (IQR 1.4 - 6.3 minutes). There was no evidence of perforation or significant intraprocedural bleeding. At 2-week follow-up, there were no significant adverse events, including delayed bleeding and post polypectomy syndrome. First follow-up has been undertaken for 15 /41 lesions at a median of 6 months with no evidence of recurrence.  There is potential for pCSP to become the standard of care for non-dysplastic large SSPs. This could reduce the burden of removing SSPs on patients and healthcare systems, particularly by avoidance of delayed bleeding. © Georg Thieme Verlag KG Stuttgart · New York.

Oropharyngeal Dysphagia in patients with obstructive sleep apnea syndrome.

PubMed

Schindler, Antonio; Mozzanica, Francesco; Sonzini, Giulia; Plebani, Daniela; Urbani, Emanuele; Pecis, Marica; Montano, Nicola

2014-02-01

Although previous studies demonstrated that patients with obstructive sleep apnea syndrome (OSAS) may present subclinical manifestations of dysphagia, in not one were different textures and volumes systematically studied. The aim of this study was to analyze the signs and symptoms of oropharyngeal dysphagia using fiberoptic endoscopic evaluation of swallowing (FEES) with boluses of different textures and volumes in a large cohort of patients with OSAS. A total of 72 OSAS patients without symptoms of dysphagia were enrolled. The cohort was divided in two groups: 30 patients with moderate OSAS and 42 patients with severe OSAS. Each patient underwent a FEES examination using 5, 10 and 20 ml of liquids and semisolids, and solids. Spillage, penetration, aspiration, retention, and piecemeal deglutition were considered. The penetration-aspiration scale (PAS), pooling score (PS), and dysphagia outcome and severity scale (DOSS) were used for quantitative analysis. Each patient completed the SWAL-QOL questionnaire. Forty-six patients (64 %) presented spillage, 20 (28 %) piecemeal deglutition, 26 (36 %) penetration, and 30 (44 %) retention. No differences were found in the PAS, PS, and DOSS scores between patients with moderate and severe OSAS. Patients with severe OSAS scored higher General Burden and Food selection subscales of the SWAL-QOL. Depending on the DOSS score, the cohort of patients was divided into those with and those without signs of dysphagia. Patients with signs of dysphagia scored lower in the General Burden and Symptoms subscales of the SWAL-QOL. OSAS patients show signs of swallowing impairment in about half of the population; clinicians involved in the management of these patients should include questions on swallowing when taking the medical history.

Submucosal Tunneling Endoscopic Resection vs Thoracoscopic Enucleation for Large Submucosal Tumors in the Esophagus and the Esophagogastric Junction.

PubMed

Chen, Tao; Lin, Zong-Wu; Zhang, Yi-Qun; Chen, Wei-Feng; Zhong, Yun-Shi; Wang, Qun; Yao, Li-Qing; Zhou, Ping-Hong; Xu, Mei-Dong

2017-12-01

Submucosal tunneling endoscopic resection (STER) is regarded as a promising method for resection of submucosal tumors (SMTs); however, little is known about a comprehensive comparison of STER and thoracoscopic enucleation (TE). The aim of this study was to compare the clinical outcomes of STER and TE for large symptomatic SMTs in the esophagus and esophagogastric junction, as well as to analyze the factors that affect the feasibility and safety of STER. We enrolled 166 patients with large symptomatic SMTs in the esophagus and esophagogastric junction from September 2011 to March 2016 in this retrospective study. The clinicopathologic features and treatment results were collected and analyzed. En bloc resection was achieved in 84.6% of the patients in the STER group and 86.7% of the patients in the TE group (p = 0.708). Notably, the procedure time and hospital stay in the STER group were considerably shorter than those in the TE group. Tumor transverse diameter is a significant risk factor for piecemeal resection, adverse events, and technical difficulties. No recurrence or metastasis was found during a mean follow-up period of more than 2 years. Submucosal tunneling endoscopic resection is effective and safe for large SMTs in the esophagus and esophagogastric junction. This procedure has the advantage of being more minimally invasive with a shorter procedure time and hospital stay compared with TE. Submucosal tunneling endoscopic resection for tumors with a transverse diameter ≥3.5 cm and an irregular shape is associated with relatively high risk for piecemeal resection, adverse events, and technical difficulties. Copyright © 2017 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Increasing ocean sciences in K and 1st grade classrooms through ocean sciences curriculum aligned to A Framework for K-12 Science Education, and implementation support.

NASA Astrophysics Data System (ADS)

Pedemonte, S.; Weiss, E. L.

2016-02-01

Ocean and climate sciences are rarely introduced at the early elementary levels. Reasons for this vary, but include little direct attention at the national and state levels; lack of quality instructional materials; and, lack of teacher content knowledge. Recent recommendations by the National Research Council, "revise the Earth and Space sciences core ideas and grade band endpoints to include more attention to the ocean whenever possible" (NRC, 2012, p. 336) adopted in the Next Generation Science Standards (NGSS), may increase the call for ocean and climate sciences to be addressed. In response to these recommendations' and the recognition that an understanding of some of the Disciplinary Core Ideas (DCIs) would be incomplete without an understanding of processes or phenomena unique to the ocean and ocean organisms; the ocean Literacy community have created documents that show the alignment of NGSS with the Ocean Literacy Principles and Fundamental Concepts (Ocean Literacy, 2013) as well as the Ocean Literacy Scope and Sequence for Grades K-12 (Ocean Literacy, 2010), providing a solid argument for how and to what degree ocean sciences should be part of the curriculum. However, the percentage of science education curricula focused on the ocean remains very low. This session will describe a new project, that draws on the expertise of curriculum developers, ocean literacy advocates, and researchers to meet the challenges of aligning ocean sciences curriculum to NGSS, and supporting its implementation. The desired outcomes of the proposed project are to provide a rigorous standards aligned curricula that addresses all of the Life Sciences, and some Earth and Space Sciences and Engineering Design Core Ideas for Grades K and 1; and provides teachers with the support they need to understand the content and begin implementation. The process and lessons learned will be shared.

Using a Brand Revitalization Project to Develop Students' Analytical and Creativity Skills

ERIC Educational Resources Information Center

Geissler, Gary L.

2015-01-01

The skillset that students acquire during college is not always well-aligned and/or well-developed relative to the skills needed to be successful in the business world. Employers have complained for many years that graduating students often lack adequate critical thinking and communication skills, in particular. In the marketing field (and other…

Interactive-GIS-Tutor (IGIST) Integration: Creating a Digital Space Gateway within a Textbook-Bound South African Geography Class

ERIC Educational Resources Information Center

Fleischmann, E. M-L.; van der Westhuizen, C. P.; Cilliers, D.

2015-01-01

Currently there is a global drive among political and educational institutions to implement geographic information system (GIS) practice in secondary schools. However, Geography teachers worldwide, including in South Africa, face significant practical challenges in this regard. Lack of curriculum aligned GIS resources, funds and teacher GIS…

Aligning Demographics and Resources: A Call to Support Spiritual-but-Not-Religious College Students

ERIC Educational Resources Information Center

Mendizabal, Juan Cruz

2018-01-01

This article discusses the rapidly growing population of spiritual-but-not-religious (SBNR) college students and describes the disparity in SBNR-dedicated resources for student support. This disparity is embedded in various tensions that cause low SBNR visibility in universities, including a lack of SBNR programming models in broader higher…

Isn't It Time We Did Something about the Lack of Teaching Preparation in Business Doctoral Programs?

ERIC Educational Resources Information Center

Marx, Robert D.; Garcia, Joseph E.; Butterfield, D. Anthony; Kappen, Jeffrey A.; Baldwin, Timothy T.

2016-01-01

In this essay, we explore "why" there has traditionally been so little emphasis on teaching preparation in business doctoral programs. Program administrators and faculty typically espouse support for teaching development; yet the existing reward systems are powerfully aligned in favor of a focus on research competency. Indeed, through…

A life threatening uterine inversion and massive post partum hemorrhage caused by placenta accrete during Caesarean section in a primigravida: a case report

PubMed Central

2009-01-01

Background A 32-year-old Caucasian primigravida was admitted for elective Caesarean Section at 36 weeks and 6 days with the diagnosis of preeclampsia. Case presentation Traction of the umbilical cord after delivery of a healthy baby resulted in uterine inversion. The placenta was found to be densely adherent to the posterior uterine wall. Piecemeal excision of the placenta as close as possible to the uterine lining was then performed. Conclusion In this way we were able to control a massive post partum hemorrhage and preserve the fertility of the patient. PMID:19210798

Emerging geomorphic approaches to guide river management practices

NASA Astrophysics Data System (ADS)

Brierley, Gary; Hooke, Janet

2015-12-01

Humans have been modifying river systems across much of the world for many thousands of years. Initially, piecemeal impacts inadvertently affected particular parts of landscapes. Subsequently, many rivers have been subjected to multiple layers of human disturbance, and changes have become widespread and systematic. Increasingly, human impacts reflect deliberative actions as part of river management programmes. These activities entail significant choices in determining the desirable (or acceptable) state and behavioural regime of a river. Typically, contemporary decision-making reflects negotiations among multiple stakeholders, seeking to provide balanced approaches to the management of socio-economic, cultural, and environmental values (e.g. Jähnig et al., 2011).

Deciding Termination for Ancestor Match- Bounded String Rewriting Systems

NASA Technical Reports Server (NTRS)

Geser, Alfons; Hofbauer, Dieter; Waldmann, Johannes

2005-01-01

Termination of a string rewriting system can be characterized by termination on suitable recursively defined languages. This kind of termination criteria has been criticized for its lack of automation. In an earlier paper we have shown how to construct an automated termination criterion if the recursion is aligned with the rewrite relation. We have demonstrated the technique with Dershowitz's forward closure criterion. In this paper we show that a different approach is suitable when the recursion is aligned with the inverse of the rewrite relation. We apply this idea to Kurth's ancestor graphs and obtain ancestor match-bounded string rewriting systems. Termination is shown to be decidable for this class. The resulting method improves upon those based on match-boundedness or inverse match-boundedness.

Band alignment and interfacial chemical structure of the HfLaO/InGaZnO4 heterojunction investigated by x-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Qian, Ling-Xuan; Wu, Ze-Han; Zhang, Yi-Yu; Liu, Yuan; Song, Jia-Qi; Liu, Xing-Zhao; Li, Yan-Rong

2017-04-01

Amorphous InGaZnO4 thin film transistors (a-IGZO TFTs) with HfLaO gate dielectrics have been widely demonstrated to possess extremely excellent electrical characteristics, and thus show great potential for applications in various next-generation electronic products. Nevertheless, the in-depth understanding of HfLaO/IGZO interfacial features is still lacking, which makes further device optimization lack clear guidance. In this work, the band alignment and interfacial chemical structure of a sputtering-prepared HfLaO/IGZO heterojunction was investigated through x-ray photoelectron spectroscopy. The valence and conduction band offsets (ΔE v and ΔE c) at the interface were determined to be 0.57 eV and 1.48 eV, respectively. The relatively large ΔE v is mainly attributed to the formation of the interfacial layer (IL) and thus the upward band bending from IGZO to the surface of HfLaO. Furthermore, it was found that the oxygen vacancies on the surface of IGZO were significantly suppressed upon the deposition of HfLaO, which not only explained the previously reported ultrahigh performance of a-IGZO/HfLaO TFTs to some extent, but also additionally validated the formation of the IL. Our findings have successfully revealed the importance of ILs in modifying the band alignment and interfacial trap states of HfLaO/IGZO heterojunctions, thus suggesting a potential route to further optimizing a-IGZO/HfLaO TFTs so as to satisfy the requirements of next-generation technologies.

A novel automated method for doing registration and 3D reconstruction from multi-modal RGB/IR image sequences

NASA Astrophysics Data System (ADS)

Kirby, Richard; Whitaker, Ross

2016-09-01

In recent years, the use of multi-modal camera rigs consisting of an RGB sensor and an infrared (IR) sensor have become increasingly popular for use in surveillance and robotics applications. The advantages of using multi-modal camera rigs include improved foreground/background segmentation, wider range of lighting conditions under which the system works, and richer information (e.g. visible light and heat signature) for target identification. However, the traditional computer vision method of mapping pairs of images using pixel intensities or image features is often not possible with an RGB/IR image pair. We introduce a novel method to overcome the lack of common features in RGB/IR image pairs by using a variational methods optimization algorithm to map the optical flow fields computed from different wavelength images. This results in the alignment of the flow fields, which in turn produce correspondences similar to those found in a stereo RGB/RGB camera rig using pixel intensities or image features. In addition to aligning the different wavelength images, these correspondences are used to generate dense disparity and depth maps. We obtain accuracies similar to other multi-modal image alignment methodologies as long as the scene contains sufficient depth variations, although a direct comparison is not possible because of the lack of standard image sets from moving multi-modal camera rigs. We test our method on synthetic optical flow fields and on real image sequences that we created with a multi-modal binocular stereo RGB/IR camera rig. We determine our method's accuracy by comparing against a ground truth.

Community and Institutional Adaptation to Riverbank Erosion along the Jamuna River, Bangladesh

NASA Astrophysics Data System (ADS)

Ali, F. M. M.

2009-04-01

The paper examines adaptation to the river erosion hazard in Bangladesh through its most exacting river, the braided Jamuna. The Jamuna River has destroyed and continues to threaten significant areas of settlements, farmed land and infrastructure. Local communities experience a social disintegration and pauperisation which lasts for generations. Although advanced for several decades, the public engineering effort to mitigate the erosion is piecemeal and has had limited success to date. The research takes an interdisciplinary approach to the hazard, in both content and method. Using Remote Sensing data to distinguish regions of dormant, explosive, minimal and constant erosion, the physical morphology of the river is linked to the community adaptation through the creation of PPGIS mapping depicting historical institutional displacement. This spatial information is linked to the qualitative investigation focusing on the expression of values in adaptation by examining social structures and investigating technological development. Drawing on Bourdieu's ideas of fields, capital and habitus, interview data is gathered from: displacees; local elites; the engineering-science community; and the political-administrative structure. The analysis is conducted along four themes; the spatial history of community displacement; social values; institutional operation; and learning in practice. Findings show the marked persistence of displaced local institutions. Dormant erosion zones host the most displaced institutions, acting as refuges once the risk is lowered through engineering or serendipity. The non-material values deeply impacted by the hazard underpin the strong local aspiration for engineering intervention. However, political discontinuity, associated institutional instability and spatial biasing of construction hinders the success of erosion mitigation and the development of appropriate national technological expertise. The small national economic resource base, shortsighted negotiations with international lenders and reduced public confidence in water sector engineering are also confounding factors. Evidence suggests that social and technological progress occurs when values, institutional results and political commitment align.

Large system change challenges: addressing complex critical issues in linked physical and social domains

NASA Astrophysics Data System (ADS)

Waddell, Steve; Cornell, Sarah; Hsueh, Joe; Ozer, Ceren; McLachlan, Milla; Birney, Anna

2015-04-01

Most action to address contemporary complex challenges, including the urgent issues of global sustainability, occurs piecemeal and without meaningful guidance from leading complex change knowledge and methods. The potential benefit of using such knowledge is greater efficacy of effort and investment. However, this knowledge and its associated tools and methods are under-utilized because understanding about them is low, fragmented between diverse knowledge traditions, and often requires shifts in mindsets and skills from expert-led to participant-based action. We have been engaged in diverse action-oriented research efforts in Large System Change for sustainability. For us, "large" systems can be characterized as large-scale systems - up to global - with many components, of many kinds (physical, biological, institutional, cultural/conceptual), operating at multiple levels, driven by multiple forces, and presenting major challenges for people involved. We see change of such systems as complex challenges, in contrast with simple or complicated problems, or chaotic situations. In other words, issues and sub-systems have unclear boundaries, interact with each other, and are often contradictory; dynamics are non-linear; issues are not "controllable", and "solutions" are "emergent" and often paradoxical. Since choices are opportunity-, power- and value-driven, these social, institutional and cultural factors need to be made explicit in any actionable theory of change. Our emerging network is sharing and building a knowledge base of experience, heuristics, and theories of change from multiple disciplines and practice domains. We will present our views on focal issues for the development of the field of large system change, which include processes of goal-setting and alignment; leverage of systemic transitions and transformation; and the role of choice in influencing critical change processes, when only some sub-systems or levels of the system behave in purposeful ways, while others are undeniably and unavoidably deterministic.

The culture of academic medicine: faculty perceptions of the lack of alignment between individual and institutional values.

PubMed

Pololi, Linda; Kern, David E; Carr, Phyllis; Conrad, Peter; Knight, Sharon

2009-12-01

Energized, talented faculty are essential to achieving the missions of academic medical centers (AMCs) in education, research and health care. The alignment of individuals' values with workplace experiences are linked to meaningfulness of work and productivity. To determine faculty values and their alignment with institutional values. A qualitative hypothesis-generating interview study to understand the professional experiences of faculty and organizational approach in five AMCs that were nationally representative in regional and organizational characteristics. Analysis was inductive and data driven. Using stratified, purposeful sampling, we interviewed 96 male and female faculty at different career stages (early career, plateaued, senior faculty and those who had left academic medicine) and diverse specialties (generalists, medical and surgical subspecialists, and research scientists). Dominant themes that emerged from the data. Faculty described values relating to excellence in clinical care, community service (including care for the underserved and disadvantaged), teaching, intellectual rigor/freedom and discovery, all values that mirror the stated missions of AMCs. However, many faculty also described behaviors that led them to conclude that their AMCs, in practice, undervalued excellence in clinical care, and their social and educational missions. Themes were seen across gender, career stage, race and discipline, except that female leaders appeared more likely than male leaders to identify incongruence of individual values and organizational practices. In this study of five diverse medical schools, faculty values were well aligned with stated institutional missions; however, many perceived that institutional behaviors were not always aligned with individual faculty values.

Customisation of the exome data analysis pipeline using a combinatorial approach.

PubMed

Pattnaik, Swetansu; Vaidyanathan, Srividya; Pooja, Durgad G; Deepak, Sa; Panda, Binay

2012-01-01

The advent of next generation sequencing (NGS) technologies have revolutionised the way biologists produce, analyse and interpret data. Although NGS platforms provide a cost-effective way to discover genome-wide variants from a single experiment, variants discovered by NGS need follow up validation due to the high error rates associated with various sequencing chemistries. Recently, whole exome sequencing has been proposed as an affordable option compared to whole genome runs but it still requires follow up validation of all the novel exomic variants. Customarily, a consensus approach is used to overcome the systematic errors inherent to the sequencing technology, alignment and post alignment variant detection algorithms. However, the aforementioned approach warrants the use of multiple sequencing chemistry, multiple alignment tools, multiple variant callers which may not be viable in terms of time and money for individual investigators with limited informatics know-how. Biologists often lack the requisite training to deal with the huge amount of data produced by NGS runs and face difficulty in choosing from the list of freely available analytical tools for NGS data analysis. Hence, there is a need to customise the NGS data analysis pipeline to preferentially retain true variants by minimising the incidence of false positives and make the choice of right analytical tools easier. To this end, we have sampled different freely available tools used at the alignment and post alignment stage suggesting the use of the most suitable combination determined by a simple framework of pre-existing metrics to create significant datasets.

Tough and flexible CNT-polymeric hybrid scaffolds for engineering cardiac constructs.

PubMed

Kharaziha, Mahshid; Shin, Su Ryon; Nikkhah, Mehdi; Topkaya, Seda Nur; Masoumi, Nafiseh; Annabi, Nasim; Dokmeci, Mehmet R; Khademhosseini, Ali

2014-08-01

In the past few years, a considerable amount of effort has been devoted toward the development of biomimetic scaffolds for cardiac tissue engineering. However, most of the previous scaffolds have been electrically insulating or lacked the structural and mechanical robustness to engineer cardiac tissue constructs with suitable electrophysiological functions. Here, we developed tough and flexible hybrid scaffolds with enhanced electrical properties composed of carbon nanotubes (CNTs) embedded aligned poly(glycerol sebacate):gelatin (PG) electrospun nanofibers. Incorporation of varying concentrations of CNTs from 0 to 1.5% within the PG nanofibrous scaffolds (CNT-PG scaffolds) notably enhanced fiber alignment and improved the electrical conductivity and toughness of the scaffolds while maintaining the viability, retention, alignment, and contractile activities of cardiomyocytes (CMs) seeded on the scaffolds. The resulting CNT-PG scaffolds resulted in stronger spontaneous and synchronous beating behavior (3.5-fold lower excitation threshold and 2.8-fold higher maximum capture rate) compared to those cultured on PG scaffold. Overall, our findings demonstrated that aligned CNT-PG scaffold exhibited superior mechanical properties with enhanced CM beating properties. It is envisioned that the proposed hybrid scaffolds can be useful for generating cardiac tissue constructs with improved organization and maturation. Copyright © 2014 Elsevier Ltd. All rights reserved.

FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.

PubMed

Gatto, Alberto; Torroja-Fungairiño, Carlos; Mazzarotto, Francesco; Cook, Stuart A; Barton, Paul J R; Sánchez-Cabo, Fátima; Lara-Pezzi, Enrique

2014-04-01

Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in the analysis of alternative splicing. This is particularly important for the identification of exon-exon junctions, which is a critical step in any analysis workflow. Here we performed a systematic benchmarking of alignment tools to dissect the impact of design and method on the mapping, detection and quantification of splice junctions from multi-exon reads. Accordingly, we devised a novel pipeline based on TopHat2 combined with a splice junction detection algorithm, which we have named FineSplice. FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F1 scores under most tested conditions. The proposed strategy conjugates an efficient mapping solution with a semi-supervised anomaly detection scheme to filter out false positives and allows reliable estimation of expressed junctions from the alignment output. Ultimately this provides more accurate information to identify meaningful splicing patterns. FineSplice is freely available at https://sourceforge.net/p/finesplice/.

Value Based Care and Patient-Centered Care: Divergent or Complementary?

PubMed

Tseng, Eric K; Hicks, Lisa K

2016-08-01

Two distinct but overlapping care philosophies have emerged in cancer care: patient-centered care (PCC) and value-based care (VBC). Value in healthcare has been defined as the quality of care (measured typically by healthcare outcomes) modified by cost. In this conception of value, patient-centeredness is one important but not necessarily dominant quality measure. In contrast, PCC includes multiple domains of patient-centeredness and places the patient and family central to all decisions and evaluations of quality. The alignment of PCC and VBC is complicated by several tensions, including a relative lack of patient experience and preference measures, and conceptions of cost that are payer-focused instead of patient-focused. Several strategies may help to align these two philosophies, including the use of patient-reported outcomes in clinical trials and value determinations, and the purposeful integration of patient preference in clinical decisions and guidelines. Innovative models of care, including accountable care organizations and oncology patient-centered medical homes, may also facilitate alignment through improved care coordination and quality-based payment incentives. Ultimately, VBC and PCC will only be aligned if patient-centered outcomes, perspectives, and preferences are explicitly incorporated into the definitions and metrics of quality, cost, and value that will increasingly influence the delivery of cancer care.

Writing the Learning Organization: A Framework for Teaching and Research

ERIC Educational Resources Information Center

Amidon, Stevens R.

2005-01-01

The marginalization of business writing as a discipline has been traced to a lack of research and to the fact that many in the field teach in business departments that do not value the work of scholars in English studies. One way out of this position may be an act of disciplinary border crossing--aligning the field of business writing with…

Reducing School Factors That Lead to Student Dropout at Sussex Central High School

ERIC Educational Resources Information Center

Jerns, Pamela Renee

2012-01-01

The focus of this Executive Position Paper (EPP) is to address the dropout rate at Sussex Central High School (SCHS) in the Indian River School District (IRSD). Studies conducted for this EPP align with current research--student dropout is a result of culminating school-based factors that include poor attendance and lack of exposure to rigorous…

Blended Learning in Chemistry Laboratory Courses: Enhancing Learning Outcomes and Aligning Student Needs with Available Resources

ERIC Educational Resources Information Center

Burchett, Shayna Brianne

2016-01-01

Freshman science courses are intended to prepare students for the rigor and expectations of subsequent college science. While secondary education aims to prepare students for the college curriculum, many incoming freshman lack the sense of responsibility for their own learning that is essential for success in a college-level course. The freshman…

"I'm Not a Natural Mathematician": Inquiry-Based Learning, Constructive Alignment and Introductory Quantitative Social Science

ERIC Educational Resources Information Center

Clark, Tom; Foster, Liam

2017-01-01

There is continuing concern about the paucity of social science graduates who have the quantitative skills required by academia and industry. Not only do students often lack the confidence to explore, and use, statistical techniques, the dominance of qualitative research in many disciplines has also often constrained programme-level integration of…

A Microworld-Based Role-Playing Game Development Approach to Engaging Students in Interactive, Enjoyable, and Effective Mathematics Learning

ERIC Educational Resources Information Center

Wang, Sheng-Yuan; Chang, Shao-Chen; Hwang, Gwo-Jen; Chen, Pei-Ying

2018-01-01

In traditional teacher-centered mathematics instruction, students might show low learning motivation owing to the lack of applied contexts. Game-based learning has been recognized as a potential approach to addressing this issue; however, without proper alignment between the gaming and math-applied contexts, the benefits of game-based learning…

Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks*

PubMed Central

Bandeira, Nuno

2016-01-01

Peptide and protein identification remains challenging in organisms with poorly annotated or rapidly evolving genomes, as are commonly encountered in environmental or biofuels research. Such limitations render tandem mass spectrometry (MS/MS) database search algorithms ineffective as they lack corresponding sequences required for peptide-spectrum matching. We address this challenge with the spectral networks approach to (1) match spectra of orthologous peptides across multiple related species and then (2) propagate peptide annotations from identified to unidentified spectra. We here present algorithms to assess the statistical significance of spectral alignments (Align-GF), reduce the impurity in spectral networks, and accurately estimate the error rate in propagated identifications. Analyzing three related Cyanothece species, a model organism for biohydrogen production, spectral networks identified peptides from highly divergent sequences from networks with dozens of variant peptides, including thousands of peptides in species lacking a sequenced genome. Our analysis further detected the presence of many novel putative peptides even in genomically characterized species, thus suggesting the possibility of gaps in our understanding of their proteomic and genomic expression. A web-based pipeline for spectral networks analysis is available at http://proteomics.ucsd.edu/software. PMID:27609420

The structural and optical properties of type III human collagen biosynthetic corneal substitutes

PubMed Central

Hayes, Sally; Lewis, Phillip; Islam, M. Mirazul; Doutch, James; Sorensen, Thomas; White, Tomas; Griffith, May; Meek, Keith M.

2015-01-01

The structural and optical properties of clinically biocompatible, cell-free hydrogels comprised of synthetically cross-linked and moulded recombinant human collagen type III (RHCIII) with and without the incorporation of 2-methacryloyloxyethyl phosphorylcholine (MPC) were assessed using transmission electron microscopy (TEM), X-ray scattering, spectroscopy and refractometry. These findings were examined alongside similarly obtained data from 21 human donor corneas. TEM demonstrated the presence of loosely bundled aggregates of fine collagen filaments within both RHCIII and RHCIII-MPC implants, which X-ray scattering showed to lack D-banding and be preferentially aligned in a uniaxial orientation throughout. This arrangement differs from the predominantly biaxial alignment of collagen fibrils that exists in the human cornea. By virtue of their high water content (90%), very fine collagen filaments (2–9 nm) and lack of cells, the collagen hydrogels were found to transmit almost all incident light in the visible spectrum. They also transmitted a large proportion of UV light compared to the cornea which acts as an effective UV filter. Patients implanted with these hydrogels should be cautious about UV exposure prior to regrowth of the epithelium and in-growth of corneal cells into the implants. PMID:26159106

Exopolysaccharide microchannels direct bacterial motility and organize multicellular behavior

DOE PAGES

Berleman, James E.; Zemla, Marcin; Remis, Jonathan P.; ...

2016-05-06

The myxobacteria are a family of soil bacteria that form biofilms of complex architecture, aligned multilayered swarms or fruiting body structures that are simple or branched aggregates containing myxospores. Here, we examined the structural role of matrix exopolysaccharide (EPS) in the organization of these surface-dwelling bacterial cells. Using time-lapse light and fluorescence microscopy, as well as transmission electron microscopy and focused ion beam/scanning electron microscopy (FIB/SEM) electron microscopy, we found that Myxococcus xanthus cell organization in biofilms is dependent on the formation of EPS microchannels. Cells are highly organized within the three-dimensional structure of EPS microchannels that are required formore » cell alignment and advancement on surfaces. Mutants lacking EPS showed a lack of cell orientation and poor colony migration. Purified, cell-free EPS retains a channel-like structure, and can complement EPS - mutant motility defects. In addition, EPS provides the cooperative structure for fruiting body formation in both the simple mounds of M. xanthus and the complex, tree-like structures of Chondromyces crocatus. We furthermore investigated the possibility that EPS impacts community structure as a shared resource facilitating cooperative migration among closely related isolates of M. xanthus.« less

Oxygen-promoted catalyst sintering influences number density, alignment, and wall number of vertically aligned carbon nanotubes

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

Shi, Wenbo; Li, Jinjing; Polsen, Erik S.

A lack of synthetic control and reproducibility during vertically aligned carbon nanotube (CNT) synthesis has stifled many promising applications of organic nanomaterials. Oxygen-containing species are particularly precarious in that they have both beneficial and deleterious effects and are notoriously difficult to control. In this paper, we demonstrated diatomic oxygen's ability, independent of water, to tune oxide-supported catalyst thin film dewetting and influence nanoscale (diameter and wall number) and macro-scale (alignment and density) properties for as-grown vertically aligned CNTs. In particular, single- or few-walled CNT forests were achieved at very low oxygen loading, with single-to-multi-walled CNT diameters ranging from 4.8 ±more » 1.3 nm to 6.4 ± 1.1 nm over 0–800 ppm O 2, and an expected variation in alignment, where both were related to the annealed catalyst morphology. Morphological differences were not the result of subsurface diffusion, but instead occurred via Ostwald ripening under several hundred ppm O 2, and this effect was mitigated by high H 2 concentrations and not due to water vapor (as confirmed in O 2-free water addition experiments), supporting the importance of O 2 specifically. Further characterization of the interface between the Fe catalyst and Al 2O 3 support revealed that either oxygen-deficit metal oxide or oxygen-adsorption on metals could be functional mechanisms for the observed catalyst nanoparticle evolution. Finally, taken as a whole, our results suggest that the impacts of O 2 and H 2 on the catalyst evolution have been underappreciated and underleveraged in CNT synthesis, and these could present a route toward facile manipulation of CNT forest morphology through control of the reactive gaseous atmosphere alone.« less

Oxygen-promoted catalyst sintering influences number density, alignment, and wall number of vertically aligned carbon nanotubes.

PubMed

Shi, Wenbo; Li, Jinjing; Polsen, Erik S; Oliver, C Ryan; Zhao, Yikun; Meshot, Eric R; Barclay, Michael; Fairbrother, D Howard; Hart, A John; Plata, Desiree L

2017-04-20

A lack of synthetic control and reproducibility during vertically aligned carbon nanotube (CNT) synthesis has stifled many promising applications of organic nanomaterials. Oxygen-containing species are particularly precarious in that they have both beneficial and deleterious effects and are notoriously difficult to control. Here, we demonstrated diatomic oxygen's ability, independent of water, to tune oxide-supported catalyst thin film dewetting and influence nanoscale (diameter and wall number) and macro-scale (alignment and density) properties for as-grown vertically aligned CNTs. In particular, single- or few-walled CNT forests were achieved at very low oxygen loading, with single-to-multi-walled CNT diameters ranging from 4.8 ± 1.3 nm to 6.4 ± 1.1 nm over 0-800 ppm O 2 , and an expected variation in alignment, where both were related to the annealed catalyst morphology. Morphological differences were not the result of subsurface diffusion, but instead occurred via Ostwald ripening under several hundred ppm O 2 , and this effect was mitigated by high H 2 concentrations and not due to water vapor (as confirmed in O 2 -free water addition experiments), supporting the importance of O 2 specifically. Further characterization of the interface between the Fe catalyst and Al 2 O 3 support revealed that either oxygen-deficit metal oxide or oxygen-adsorption on metals could be functional mechanisms for the observed catalyst nanoparticle evolution. Taken as a whole, our results suggest that the impacts of O 2 and H 2 on the catalyst evolution have been underappreciated and underleveraged in CNT synthesis, and these could present a route toward facile manipulation of CNT forest morphology through control of the reactive gaseous atmosphere alone.

Oxygen-promoted catalyst sintering influences number density, alignment, and wall number of vertically aligned carbon nanotubes

DOE PAGES

Shi, Wenbo; Li, Jinjing; Polsen, Erik S.; ...

2017-04-11

A lack of synthetic control and reproducibility during vertically aligned carbon nanotube (CNT) synthesis has stifled many promising applications of organic nanomaterials. Oxygen-containing species are particularly precarious in that they have both beneficial and deleterious effects and are notoriously difficult to control. In this paper, we demonstrated diatomic oxygen's ability, independent of water, to tune oxide-supported catalyst thin film dewetting and influence nanoscale (diameter and wall number) and macro-scale (alignment and density) properties for as-grown vertically aligned CNTs. In particular, single- or few-walled CNT forests were achieved at very low oxygen loading, with single-to-multi-walled CNT diameters ranging from 4.8 ±more » 1.3 nm to 6.4 ± 1.1 nm over 0–800 ppm O 2, and an expected variation in alignment, where both were related to the annealed catalyst morphology. Morphological differences were not the result of subsurface diffusion, but instead occurred via Ostwald ripening under several hundred ppm O 2, and this effect was mitigated by high H 2 concentrations and not due to water vapor (as confirmed in O 2-free water addition experiments), supporting the importance of O 2 specifically. Further characterization of the interface between the Fe catalyst and Al 2O 3 support revealed that either oxygen-deficit metal oxide or oxygen-adsorption on metals could be functional mechanisms for the observed catalyst nanoparticle evolution. Finally, taken as a whole, our results suggest that the impacts of O 2 and H 2 on the catalyst evolution have been underappreciated and underleveraged in CNT synthesis, and these could present a route toward facile manipulation of CNT forest morphology through control of the reactive gaseous atmosphere alone.« less

Co-effects of matrix low elasticity and aligned topography on stem cell neurogenic differentiation and rapid neurite outgrowth

NASA Astrophysics Data System (ADS)

Yao, Shenglian; Liu, Xi; Yu, Shukui; Wang, Xiumei; Zhang, Shuming; Wu, Qiong; Sun, Xiaodan; Mao, Haiquan

2016-05-01

The development of novel biomaterials that deliver precise regulatory signals to direct stem cell fate for nerve regeneration is the focus of current intensive research efforts. In this study, a hierarchically aligned fibrillar fibrin hydrogel (AFG) that was fabricated through electrospinning and the concurrent molecular self-assembly process mimics both the soft and oriented features of nerve tissue, thus providing hybrid biophysical cues to instruct cell behavior in vitro and in vivo. The electrospun hydrogels were examined by scanning electron microscopy (SEM), polarized light microscopy, small angle X-ray scattering assay and atomic force microscopy (AFM), showing a hierarchically linear-ordered structure from the nanoscale to the macroscale with a soft elastic character (elasticity ~1 kPa). We found that this low elasticity and aligned topography of AFG exhibit co-effects on promoting the neurogenic differentiation of human umbilical cord mesenchymal stem cells (hUMSCs) in comparison to random fibrin hydrogel (RFG) and tissue culture plate (TCP) control after two week cell culture in growth medium lacking supplementation with soluble neurogenic induction factors. In addition, AFG also induces dorsal root ganglion (DRG) neurons to rapidly project numerous long neurite outgrowths longitudinally along the AFG fibers for a total neurite extension distance of 1.96 mm in three days in the absence of neurotrophic factor supplementation. Moreover, the AFG implanted in a rat T9 dorsal hemisection spinal cord injury model was found to promote endogenous neural cell fast migration and axonal invasion along AFG fibers, resulting in aligned tissue cables in vivo. Our results suggest that matrix stiffness and aligned topography may instruct stem cell neurogenic differentiation and rapid neurite outgrowth, providing great promise for biomaterial design for applications in nerve regeneration.The development of novel biomaterials that deliver precise regulatory signals to direct stem cell fate for nerve regeneration is the focus of current intensive research efforts. In this study, a hierarchically aligned fibrillar fibrin hydrogel (AFG) that was fabricated through electrospinning and the concurrent molecular self-assembly process mimics both the soft and oriented features of nerve tissue, thus providing hybrid biophysical cues to instruct cell behavior in vitro and in vivo. The electrospun hydrogels were examined by scanning electron microscopy (SEM), polarized light microscopy, small angle X-ray scattering assay and atomic force microscopy (AFM), showing a hierarchically linear-ordered structure from the nanoscale to the macroscale with a soft elastic character (elasticity ~1 kPa). We found that this low elasticity and aligned topography of AFG exhibit co-effects on promoting the neurogenic differentiation of human umbilical cord mesenchymal stem cells (hUMSCs) in comparison to random fibrin hydrogel (RFG) and tissue culture plate (TCP) control after two week cell culture in growth medium lacking supplementation with soluble neurogenic induction factors. In addition, AFG also induces dorsal root ganglion (DRG) neurons to rapidly project numerous long neurite outgrowths longitudinally along the AFG fibers for a total neurite extension distance of 1.96 mm in three days in the absence of neurotrophic factor supplementation. Moreover, the AFG implanted in a rat T9 dorsal hemisection spinal cord injury model was found to promote endogenous neural cell fast migration and axonal invasion along AFG fibers, resulting in aligned tissue cables in vivo. Our results suggest that matrix stiffness and aligned topography may instruct stem cell neurogenic differentiation and rapid neurite outgrowth, providing great promise for biomaterial design for applications in nerve regeneration. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01169a

A critical look at persistent problems in the diagnosis, staging and treatment of temporal bone carcinoma.

PubMed

Zanoletti, Elisabetta; Lovato, Andrea; Stritoni, Paola; Martini, Alessandro; Mazzoni, Antonio; Marioni, Gino

2015-12-01

Temporal bone squamous cell carcinoma (TBSCC) is an uncommon malignancy with a distinctly poor prognosis in advanced cases. There is still much controversy surrounding the rational diagnostic/therapeutic approach to TBSCC. Diagnostic differences are due mainly to: the small number of cases reported (even in the largest available series); the inappropriate histological heterogeneity of several case series; the lack of an internationally-accepted staging system for TBSCC; the frequent absence of adequate radiological imaging to enable a malignancy's local, regional and distant extension to be studied in detail; and a non-standardized approach to final histological assessment of the surgical margins. As for the therapeutic approaches, several issues are still debated, including the choice between en bloc and piecemeal primary surgery for the tumor's removal, and the role of elective neck dissection. Although radiotherapy seems to be an effective adjuvant therapy in advanced cases, its role in low-stage tumors or as a primary treatment has yet to be established. The value of chemotherapy is also still unclear. The treatment strategy for TBSCC is often based on the combined experience of a given surgeon and institution, bearing the results reportedly achieved by other oncology centers in mind. To date, the optimal management of TBSCC is still elusive. We aimed to critically review the ongoing crucial issues concerning the management of TBSCC, analyzing how it is diagnosed, staged and treated, the management of recurrences, rational follow-up schedules, and prognostic factors for this disease. Copyright © 2015 Elsevier Ltd. All rights reserved.

The precariousness of the franchise state: Voluntary sector health services and international NGOs in Tanzania, 1960s - mid-1980s.

PubMed

Jennings, Michael

2015-09-01

This paper challenges conventional narratives on the role of international non-governmental organisations (INGOs) in the delivery of health services in Tanzania. Adopting an historical gaze which focuses on the 1960s to mid-1980s the paper argues that the 'franchise state' in the Tanzanian health system was not created by collusion between international donors and INGOs, underpinned by a set of health sector reforms that advocated the use of non-state actors; but was rather the legacy of the colonial health system bequeathed to the post-independence state. It was a system in which voluntary non-state actors (but, importantly, not INGOs) were already entrenched as key providers; and in which many of the features of the franchise state - fragmentation, structural weaknesses, lack of accountability to users - were already long established. But if INGOs did not create these features, as their critics attest, they did contribute to the maintenance and extension of these features. The short-term perspectives of NGOs, their small-scale piecemeal engagement, and the extra demands they placed upon their voluntary actor partners, left little scope for the development of sustainable, national and accountable solutions to the health needs of the country. In exploring these ideas, the paper contributes to a more nuanced understanding of the path dependency that created Tanzania's health system. The analysis also contributes to a deepening of the understanding of the make-up of the voluntary sector beyond a narrow gaze on the institution of the INGO. Copyright © 2015 Elsevier Ltd. All rights reserved.

The state of the psychology health service provider workforce.

PubMed

Michalski, Daniel S; Kohout, Jessica L

2011-12-01

Numerous efforts to describe the health service provider or clinical workforce in psychology have been conducted during the past 30 years. The American Psychological Association (APA) has studied trends in the doctoral education pathway and the resultant effects on the broader psychology workforce. During this period, the creation and growth of the PsyD degree and the formalization of the predoctoral internship placement system (the APPIC Match) have been well noted, but efforts to gain a complete understanding of professional practice are lacking. Specifically, piecemeal research on the provider workforce has led to the study of specific subpopulations using varying approaches and definitions of those providing direct clinical service. Consequently, estimates of the supply and need for health service providers are distinctly divergent and generate protracted debate in organized psychology. The APA membership directory and the APA Doctorate Employment Surveys have traditionally been relied on for workforce analyses. Yet, these data have become characterized by limited generalizability in recent years because of declining survey response rates and the fact that APA member data may not be as representative of the entire psychology health service provider population as they were previously. The 2008 APA Survey of Psychology Health Service Providers targeted these limitations by including nonmember psychologists in the sampling frame. Results revealed emerging themes in the demographics, work settings, and delivery of health services of the psychology health service provider workforce. Future areas of research for APA and organized psychology to undertake in addressing need and demand are suggested. (PsycINFO Database Record (c) 2011 APA, all rights reserved).

GTSE1 tunes microtubule stability for chromosome alignment and segregation by inhibiting the microtubule depolymerase MCAK

PubMed Central

Bendre, Shweta; Hall, Conrad; Lin, Yu-Chih

2016-01-01

The dynamic regulation of microtubules (MTs) during mitosis is critical for accurate chromosome segregation and genome stability. Cancer cell lines with hyperstabilized kinetochore MTs have increased segregation errors and elevated chromosomal instability (CIN), but the genetic defects responsible remain largely unknown. The MT depolymerase MCAK (mitotic centromere-associated kinesin) can influence CIN through its impact on MT stability, but how its potent activity is controlled in cells remains unclear. In this study, we show that GTSE1, a protein found overexpressed in aneuploid cancer cell lines and tumors, regulates MT stability during mitosis by inhibiting MCAK MT depolymerase activity. Cells lacking GTSE1 have defects in chromosome alignment and spindle positioning as a result of MT instability caused by excess MCAK activity. Reducing GTSE1 levels in CIN cancer cell lines reduces chromosome missegregation defects, whereas artificially inducing GTSE1 levels in chromosomally stable cells elevates chromosome missegregation and CIN. Thus, GTSE1 inhibition of MCAK activity regulates the balance of MT stability that determines the fidelity of chromosome alignment, segregation, and chromosomal stability. PMID:27881713

Using hidden Markov models to align multiple sequences.

PubMed

Mount, David W

2009-07-01

A hidden Markov model (HMM) is a probabilistic model of a multiple sequence alignment (msa) of proteins. In the model, each column of symbols in the alignment is represented by a frequency distribution of the symbols (called a "state"), and insertions and deletions are represented by other states. One moves through the model along a particular path from state to state in a Markov chain (i.e., random choice of next move), trying to match a given sequence. The next matching symbol is chosen from each state, recording its probability (frequency) and also the probability of going to that state from a previous one (the transition probability). State and transition probabilities are multiplied to obtain a probability of the given sequence. The hidden nature of the HMM is due to the lack of information about the value of a specific state, which is instead represented by a probability distribution over all possible values. This article discusses the advantages and disadvantages of HMMs in msa and presents algorithms for calculating an HMM and the conditions for producing the best HMM.

Effects of dialysate to serum sodium (Na+) alignment in chronic hemodialysis (HD) patients: retrospective cohort study from a quality improvement project.

PubMed

Raimann, Jochen G; Ficociello, Linda H; Usvyat, Len A; Zhang, Hanjie; Pacelli, Lisa; Moore, Sandi; Sheppard, Penny; Xiao, Qingqing; Wang, Yuedong; Mullon, Claudy; Balter, Paul; Sullivan, Terry; Kotanko, Peter

2018-04-02

Evidence indicates favorable effects of dialysate (DNa + ) to serum sodium concentration (SNa + ) alignment, however, results from larger sample populations are needed. For this reason, we conducted a retrospective propensity score-matched cohort study from a quality improvement project to investigate the effects of alignment on population of maintenance hemodialysis patients. At 4 participating hemodialysis (HD) clinics, patients with SNa + lower than the standard DNa + of 137 mEq/L who received HD with DNa + aligned to the average of the last 4 SNa + measurements were evaluated (clinicaltrials.gov # NCT01825590 ). In this retrospective data analysis, an intention-to-treat (primary) and an as-treated "intervention" (secondary) cohort were created. "Aligned" patients from both cohorts (N = 163 for the primary and N = 137 for the secondary) were then propensity-score matched in a 1:1 fashion to "unaligned" patients from the Renal Research Institute database. The propensity score was generated based on age, gender, white race, Hispanic ethnicity, absence or presence of diabetes, hemodialysis vintage, interdialytic weight gain (IDWG; as a percentage of postdialysis body weight), catheter as primary dialysis access, predialysis systolic blood pressure, serum sodium concentration, hospitalization count during baseline. T-Test was employed for group comparisons of changes to the primary (volume-related and hemodynamic parameters) and tertiary outcomes. All-cause and fluid overload-related hospitalization admission rates were compared using Wilcoxon Rank Sum test and Cox regression analysis for repeated events. In the primary analysis, aligned and unaligned subjects showed comparable demographics at baseline. Treatment effects were significant for IDWG [-0.12 (95% CI -0.24 to 0) L] and showed decreasing non-significant trends for pre-dialysis hemodynamic parameters. Count comparison and Cox regression analysis showed no clear advantage of alignment in terms of all-cause and fluid overload-related hospitalization. Results from the largest sodium alignment program to date suggest positive treatment effects on volume-related and hemodynamic parameters, but no clear effect on risk of hospitalization. Well-matched control patients minimized confounding effects. Small effects and lack of significant differences may be explained by a low baseline DNa + limiting the interventional change.

STEM: How a Poorly Defined Acronym Is Shaping Education and Workforce Development Policy in the United States. WCER Working Paper No. 2014-2

ERIC Educational Resources Information Center

Oleson, Amanda K.; Hora, Matthew T.; Benbow, Ross J.

2014-01-01

The fields of science, technology, engineering, and mathematics, more ubiquitously known by the acronym "STEM," have received a substantial amount of attention in recent years. As part of a research study investigating the alignment (or lack thereof) between the goals and priorities of educators and employers, we found it difficult to…

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.

PubMed

Padial, José M; Grant, Taran; Frost, Darrel R

2014-06-26

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates that insertions and deletions occurred in twice as many aligned positions as implied by the optimal similarity-alignment, confirming previous findings that sequence turnover through insertion and deletion events plays a greater role in molecular evolution than indicated by similarity-alignments. Our results also provide a clear empirical demonstration of the different effects of wildcard taxa produced by missing data in parsimony and maximum likelihood analyses. Specifically, maximum likelihood analyses consistently (81% bootstrap frequency) provided spurious resolution despite a lack of evidence, whereas parsimony correctly depicted the ambiguity due to missing data by collapsing unsupported nodes. We provide a new taxonomy for the group that retains previously recognized Linnaean taxa except for Ceuthomantidae, Strabomantidae, and Strabomantinae. A phenotypically diagnosable superfamily is recognized formally as Brachycephaloidea, with the informal, unranked name terrarana retained as the standard common name for these frogs. We recognize three families within Brachycephaloidea that are currently diagnosable solely on molecular grounds (Brachycephalidae, Craugastoridae, and Eleutherodactylidae), as well as five subfamilies (Craugastorinae, Eleutherodactylinae, Holoadeninae, Phyzelaphryninae, and Pristimantinae) corresponding in large part to previous families and subfamilies. Our analyses upheld the monophyly of all tested genera, but we found numerous subgeneric taxa to be non-monophyletic and modified the taxonomy accordingly.

Exploring cultural tensions in cross-cultural social work practice.

PubMed

Yan, Miu Chung

2008-10-01

Discussion of cultural tension in the social work literature is piecemeal. As part of a grounded theory study, this article reports some major findings on cultural tensions experienced by 30 frontline social workers. Cultural tensions caused by cultural similarities and differences among social workers, clients, organizations, and society are multifaceted. Social workers, however, are always at the center of the tensions. Findings indicate that the social work profession may need to consider the neutrality claim of the profession, the different experience of ethnic minority social workers, and the need of critical reflexivity for reflective practitioners. Implications for social work practice, social work education for ethnic minority social workers, and social work research are discussed.

Hydropedology: Synergistic integration of soil science and hydrology in the Critical Zone

USGS Publications Warehouse

Lin, H.S.; McDonnell, J.J.; Nimmo, John R.; Pachepsky, Y. A.

2016-01-01

Soil and water are the two critical components of theEarth’s Critical Zone (Figure 1): Soil modulates the connection between bedrock and the atmospheric boundary layer and water is a major driving force and transport agent between these two zones. The interactions between soil and water are so intimate and complex that they cannot be effectively studied in a piecemeal manner; they require a systems approach. In this spirit, hydropedology has emerged in recent years as a synergistic integration of soil science and hydrology that offers a renewed perspective and an integrated approach to understanding interactive pedologic and hydrologic processes and their properties in the Critical Zone.

Conservation success as a function of good alignment of social and ecological structures and processes.

PubMed

Bodin, Orjan; Crona, Beatrice; Thyresson, Matilda; Golz, Anna-Lea; Tengö, Maria

2014-10-01

How to create and adjust governing institutions so that they align (fit) with complex ecosystem processes and structures across scales is an issue of increasing concern in conservation. It is argued that lack of such social-ecological fit makes governance and conservation difficult, yet progress in explicitly defining and rigorously testing what constitutes a good fit has been limited. We used a novel modeling approach and data from case studies of fishery and forest conservation to empirically test presumed relationships between conservation outcomes and certain patterns of alignment of social-ecological interdependences. Our approach made it possible to analyze conservation outcome on a systems level while also providing information on how individual actors are positioned in the complex web of social-ecological interdependencies. We found that when actors who shared resources were also socially linked, conservation at the level of the whole social-ecological system was positively affected. When the scales at which individual actors used resources and the scale at which ecological resources were interconnected to other ecological resources were aligned through tightened feedback loops, conservation outcome was better than when they were not aligned. The analysis of individual actors' positions in the web of social-ecological interdependencies was helpful in understanding why a system has a certain level of social-ecological fit. Results of analysis of positions showed that different actors contributed in very different ways to achieve a certain fit and revealed some underlying difference between the actors, for example in terms of actors' varying rights to access and use different ecological resources. © 2014 Society for Conservation Biology.

SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.

PubMed

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA.

Optical Alignment of the Global Precipitation Measurement (GPM) Star Trackers

NASA Technical Reports Server (NTRS)

Hetherington, Samuel; Osgood, Dean; McMann, Joe; Roberts, Viki; Gill, James; Mclean, Kyle

2013-01-01

The optical alignment of the star trackers on the Global Precipitation Measurement (GPM) core spacecraft at NASA Goddard Space Flight Center (GSFC) was challenging due to the layout and structural design of the GPM Lower Bus Structure (LBS) in which the star trackers are mounted as well as the presence of the star tracker shades that blocked line-of-sight to the primary star tracker optical references. The initial solution was to negotiate minor changes in the original LBS design to allow for the installation of a removable item of ground support equipment (GSE) that could be installed whenever measurements of the star tracker optical references were needed. However, this GSE could only be used to measure secondary optical reference cube faces not used by the star tracker vendor to obtain the relationship information and matrix transformations necessary to determine star tracker alignment. Unfortunately, due to unexpectedly large orthogonality errors between the measured secondary adjacent cube faces and the lack of cube calibration data, we required a method that could be used to measure the same reference cube faces as originally measured by the vendor. We describe an alternative technique to theodolite auto-collimation for measurement of an optical reference mirror pointing direction when normal incidence measurements are not possible. This technique was used to successfully align the GPM star trackers and has been used on a number of other NASA flight projects. We also discuss alignment theory as well as a GSFC-developed theodolite data analysis package used to analyze angular metrology data.

SWPhylo – A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees

PubMed Central

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA. PMID:29511354

Using College Placement Exams as Early Signals of College Readiness: An Examination of California's Early Assessment Program and New York's At Home in College Program

ERIC Educational Resources Information Center

Venezia, Andrea; Voloch, Daniel

2012-01-01

A promising strategy for promoting successful college transition and increasing college completion rates is to help students avoid developmental coursework by preparing them for placement exams before they enroll in college. A lack of content alignment between high school exit exams and college entrance exams is one of many troubling disconnects…

Department of Defense Mobile Device Strategy. Version 2.0

DTIC Science & Technology

2012-05-01

pilots and initiatives across DoD under common objectives, ensuring that the war:fighter benefits from such activities and aligns with efforts...regularly travel from place to place; and a growing number of teleworkers are beginning to operate from locations other than their primary offices...workforce with the benefits of mobile technology. Although achieving pockets of success, this unconstrained piloting has also resulted in the lack of

Beyond the Skills Gap: How the Lack of Systemic Supports for Teaching and Learning Undermines Employer, Student, and Societal Interests. WCER Working Paper No. 2016-9

ERIC Educational Resources Information Center

Hora, Matthew T.; Benbow, Ross J.; Oleson, Amanda K.

2016-01-01

The idea of a skills gap suggests that employers have jobs available but cannot find skilled applicants because higher education is poorly aligned with workforce needs. This idea is shaping higher education and workforce development policy at the national and state levels, yet limited research exists on the experiences of employers and educators…

The Six-Legged Subject: A Survey of Secondary Science Teachers’ Incorporation of Insects into U.S. Life Science Instruction

PubMed Central

Ingram, Erin

2018-01-01

To improve students’ understanding and appreciation of insects, entomology education efforts have supported insect incorporation in formal education settings. While several studies have explored student ideas about insects and the incorporation of insects in elementary and middle school classrooms, the topic of how and why insects are incorporated in secondary science classrooms remains relatively unexplored. Using survey research methods, this study addresses the gap in the literature by (1) describing in-service secondary science teachers’ incorporation of insects in science classrooms; (2) identifying factors that support or deter insect incorporation and (3) identifying teachers’ preferred resources to support future entomology education efforts. Findings indicate that our sample of U.S. secondary science teachers commonly incorporate various insects in their classrooms, but that incorporation is infrequent throughout the academic year. Insect-related lesson plans are commonly used and often self-created to meet teachers’ need for standards-aligned curriculum materials. Obstacles to insect incorporation include a perceived lack of alignment of insect education materials to state or national science standards and a lack of time and professional training to teach about insects. Recommendations are provided for entomology and science education organizations to support teachers in overcoming these obstacles. PMID:29538297

The Six-Legged Subject: A Survey of Secondary Science Teachers' Incorporation of Insects into U.S. Life Science Instruction.

PubMed

Ingram, Erin; Golick, Douglas

2018-03-14

To improve students' understanding and appreciation of insects, entomology education efforts have supported insect incorporation in formal education settings. While several studies have explored student ideas about insects and the incorporation of insects in elementary and middle school classrooms, the topic of how and why insects are incorporated in secondary science classrooms remains relatively unexplored. Using survey research methods, this study addresses the gap in the literature by (1) describing in-service secondary science teachers' incorporation of insects in science classrooms; (2) identifying factors that support or deter insect incorporation and (3) identifying teachers' preferred resources to support future entomology education efforts. Findings indicate that our sample of U.S. secondary science teachers commonly incorporate various insects in their classrooms, but that incorporation is infrequent throughout the academic year. Insect-related lesson plans are commonly used and often self-created to meet teachers' need for standards-aligned curriculum materials. Obstacles to insect incorporation include a perceived lack of alignment of insect education materials to state or national science standards and a lack of time and professional training to teach about insects. Recommendations are provided for entomology and science education organizations to support teachers in overcoming these obstacles.

Non-rigid registration for fusion of carotid vascular ultrasound and MRI volumetric datasets

NASA Astrophysics Data System (ADS)

Chan, R. C.; Sokka, S.; Hinton, D.; Houser, S.; Manzke, R.; Hanekamp, A.; Reddy, V. Y.; Kaazempur-Mofrad, M. R.; Rasche, V.

2006-03-01

In carotid plaque imaging, MRI provides exquisite soft-tissue characterization, but lacks the temporal resolution for tissue strain imaging that real-time 3D ultrasound (3DUS) can provide. On the other hand, real-time 3DUS currently lacks the spatial resolution of carotid MRI. Non-rigid alignment of ultrasound and MRI data is essential for integrating complementary morphology and biomechanical information for carotid vascular assessment. We assessed non-rigid registration for fusion of 3DUS and MRI carotid data based on deformable models which are warped to maximize voxel similarity. We performed validation in vitro using isolated carotid artery imaging. These samples were subjected to soft-tissue deformations during 3DUS and were imaged in a static configuration with standard MR carotid pulse sequences. Registration of the source ultrasound sequences to the target MR volume was performed and the mean absolute distance between fiducials within the ultrasound and MR datasets was measured to determine inter-modality alignment quality. Our results indicate that registration errors on the order of 1mm are possible in vitro despite the low-resolution of current generation 3DUS transducers. Registration performance should be further improved with the use of higher frequency 3DUS prototypes and efforts are underway to test those probes for in vivo 3DUS carotid imaging.

A multicenter cohort study of spinal osteoid osteomas: results of surgical treatment and analysis of local recurrence.

PubMed

Quraishi, Nasir A; Boriani, Stefano; Sabou, Silviu; Varga, Peter P; Luzzati, Alessandro; Gokaslan, Ziya L; Fehlings, Michael G; Fisher, Charles G; Dekutoski, Mark B; Rhines, Laurence D; Reynolds, Jeremy J; Germscheid, Niccole M; Bettegowda, Chetan; Williams, Richard P

2017-03-01

Spinal osteoid osteomas are benign primary tumors arising predominantly from the posterior column of the spine. These "osteoblastic" lesions have traditionally been treated with intralesional excision. The purpose of the present study was to review the treatment and local recurrence rates for symptomatic spinal osteoid osteomas. Multicenter ambispective cross-sectional observational cohort study. During the study period, a total of 84 patients (65 males, 19 females) were diagnosed with a spinal osteoid osteoma and received surgical treatment. The mean age at surgery was 21.8 ± 9.0 years (range: 6.7-52.4 years) and the mean follow-up was 2.7 years (13 days-14.5 years). Local recurrence, perioperative morbidity, and cross-sectional survival. Using the AOSpine Knowledge Forum Tumor multicenter ambispective database, surgically treated osteoid osteoma cases were identified. Patient demographic, clinical and diagnostic, treatment, local recurrence, perioperative morbidity, and cross-sectional survival data were collected and retrieved. Descriptive statistics were summarized using mean/standard deviation or frequency/percentage. In our study, most of the tumors were localized in the mobile spine (81 of 84 [96%]); all patients reported pain as a symptom. According to the postoperative assessment, 10 (12%) patients received an en bloc resection with marginal or wide margins, whereas two (2%) patients received en bloc resections with intralesional margins, 69 (82%) patients were treated by piecemeal "intralesional" resection, and three (4%) patients were not assessed. A total of six patients (7%) experienced a local recurrence, all of which occurred in patients who had received an intralesional resection. Benign bone-forming tumors of the spine are uncommon. Most patients in our series underwent a piecemeal resection with intralesional margins. This remains safe with a low local recurrence rate. En bloc excision may provide more chance of complete excision of the nidus but is not mandatory. The importance of complete excision of the nidus cannot be overemphasized. Copyright © 2016 Elsevier Inc. All rights reserved.

Suggestive evidence of a vesicle-mediated mode of cell degranulation in chromaffin cells. A high-resolution scanning electron microscopy investigation

PubMed Central

Crivellato, Enrico; Solinas, Paola; Isola, Raffaella; Ribatti, Domenico; Riva, Alessandro

2010-01-01

In this study we used a modified osmium maceration method for high-resolution scanning electron microscopy to study some ultrastructural details fitting the schema of piecemeal degranulation in chromaffin cells. Piecemeal degranulation refers to a particulate pattern of cell secretion that is accomplished by vesicle-mediated extracellular transport of granule-stored material. We investigated adrenal samples from control and angiotensin II-treated rats, and identified a variable proportion of smooth, 30–60-nm-diameter vesicles in the cytoplasm of chromaffin cells. A percentage of these vesicles were interspersed in the cytosol among chromaffin granules but the majority appeared to be attached to granules. Remarkably, the number of unattached cytoplasmic vesicles was greatly increased in chromaffin cells from angiotensin II-treated animals. Vesicles of the same structure and dimension were detected close to or attached to the cytoplasmic face of the plasma membrane; these, too, were increased in number in chromaffin cells from rats stimulated with angiotensin II. In specimens shaken with a rotating agitator during maceration, the cytoplasmic organelles could be partially removed and the fine structure of the vesicular interaction with the inner side of the plasma membrane emerged most clearly. A proportion of chromaffin granules showed protrusions that we interpreted as vesicular structures budding from the granular envelope. In some instances, the transection plane intersected granules with putative vesicles emerging from the surfaces. In these cases, the protrusions of budding vesicles could be observed from the internal side. This study provides high-resolution scanning electron microscopy images compatible with a vesicle-mediated degranulation mode of cell secretion in adrenal chromaffin cells. The data indicating an increase in the number of vesicles observed in chromaffin cells after stimulation with the chromaffin cell secretagogue angiotensin II suggests that this secretory process may be susceptible to fine regulation. PMID:20136671

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.

Impact of Growing Business on Software Processes

NASA Astrophysics Data System (ADS)

Nikitina, Natalja; Kajko-Mattsson, Mira

When growing their businesses, software organizations should not only put effort into developing and executing their business strategies, but also into managing and improving their internal software development processes and aligning them with business growth strategies. It is only in this way they may confirm that their businesses grow in a healthy and sustainable way. In this paper, we map out one software company's business growth on the course of its historical events and identify its impact on the company's software production processes and capabilities. The impact concerns benefits, challenges, problems and lessons learned. The most important lesson learned is that although business growth has become a stimulus for starting thinking and improving software processes, the organization lacked guidelines aiding it in and aligning it to business growth. Finally, the paper generates research questions providing a platform for future research.

Aligning physical learning spaces with the curriculum: AMEE Guide No. 107.

PubMed

Nordquist, Jonas; Sundberg, Kristina; Laing, Andrew

2016-08-01

This Guide explores emerging issues on the alignment of learning spaces with the changing curriculum in medical education. As technology and new teaching methods have altered the nature of learning in medical education, it is necessary to re-think how physical learning spaces are aligned with the curriculum. The better alignment of learning spaces with the curriculum depends on more directly engaged leadership from faculty and the community of medical education for briefing the requirements for the design of all kinds of learning spaces. However, there is a lack of precedent and well-established processes as to how new kinds of learning spaces should be programmed. Such programmes are essential aspects of optimizing the intended experience of the curriculum. Faculty and the learning community need better tools and instruments to support their leadership role in briefing and programming. A Guide to critical concepts for exploring the alignment of curriculum and learning spaces is provided. The idea of a networked learning landscape is introduced as a way of assessing and evaluating the alignment of physical spaces to the emerging curriculum. The concept is used to explore how technology has widened the range of spaces and places in which learning happens as well as enabling new styles of learning. The networked learning landscaped is explored through four different scales within which learning is accommodated: the classroom, the building, the campus, and the city. High-level guidance on the process of briefing for the networked learning landscape is provided, to take into account the wider scale of learning spaces and the impact of technology. Key to a successful measurement process is argued to be the involvement of relevant academic stakeholders who can identify the strategic direction and purpose for the design of the learning environments in relation to the emerging demands of the curriculum.

Co-effects of matrix low elasticity and aligned topography on stem cell neurogenic differentiation and rapid neurite outgrowth.

PubMed

Yao, Shenglian; Liu, Xi; Yu, Shukui; Wang, Xiumei; Zhang, Shuming; Wu, Qiong; Sun, Xiaodan; Mao, Haiquan

2016-05-21

The development of novel biomaterials that deliver precise regulatory signals to direct stem cell fate for nerve regeneration is the focus of current intensive research efforts. In this study, a hierarchically aligned fibrillar fibrin hydrogel (AFG) that was fabricated through electrospinning and the concurrent molecular self-assembly process mimics both the soft and oriented features of nerve tissue, thus providing hybrid biophysical cues to instruct cell behavior in vitro and in vivo. The electrospun hydrogels were examined by scanning electron microscopy (SEM), polarized light microscopy, small angle X-ray scattering assay and atomic force microscopy (AFM), showing a hierarchically linear-ordered structure from the nanoscale to the macroscale with a soft elastic character (elasticity ∼1 kPa). We found that this low elasticity and aligned topography of AFG exhibit co-effects on promoting the neurogenic differentiation of human umbilical cord mesenchymal stem cells (hUMSCs) in comparison to random fibrin hydrogel (RFG) and tissue culture plate (TCP) control after two week cell culture in growth medium lacking supplementation with soluble neurogenic induction factors. In addition, AFG also induces dorsal root ganglion (DRG) neurons to rapidly project numerous long neurite outgrowths longitudinally along the AFG fibers for a total neurite extension distance of 1.96 mm in three days in the absence of neurotrophic factor supplementation. Moreover, the AFG implanted in a rat T9 dorsal hemisection spinal cord injury model was found to promote endogenous neural cell fast migration and axonal invasion along AFG fibers, resulting in aligned tissue cables in vivo. Our results suggest that matrix stiffness and aligned topography may instruct stem cell neurogenic differentiation and rapid neurite outgrowth, providing great promise for biomaterial design for applications in nerve regeneration.

Molecular engineering of lanthanide ion chelating phospholipids generating assemblies with a switched magnetic susceptibility.

PubMed

Isabettini, Stéphane; Massabni, Sarah; Hodzic, Arnel; Durovic, Dzana; Kohlbrecher, Joachim; Ishikawa, Takashi; Fischer, Peter; Windhab, Erich J; Walde, Peter; Kuster, Simon

2017-08-09

Lanthanide ion (Ln 3+ ) chelating amphiphiles are powerful molecules for tailoring the magnetic response of polymolecular assemblies. Mixtures of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dimyristoyl-sn-glycero-3-phospho-ethanolamine-diethylene triaminepentaacetate (DMPE-DTPA) complexed to Ln 3+ deliver highly magnetically responsive bicelles. Their magnetic properties are readily tuned by changing the bicellar size or the magnetic susceptibility Δχ of the bilayer lipids. The former technique is intrinsically bound to the region of the phase diagram guarantying the formation of bicelles. Methods aiming towards manipulating the Δχ of the bilayer are comparatively more robust, flexible and lacking. Herein, we synthesized a new Ln 3+ chelating phospholipid using glutamic acid as a backbone: DMPE-Glu-DTPA. The chelate polyhedron was specifically engineered to alter the Δχ, whilst remaining geometrically similar to DMPE-DTPA. Planar asymmetric assemblies hundreds of nanometers in size were achieved presenting unprecedented magnetic alignments. The DMPE-Glu-DTPA/Ln 3+ complex switched the Δχ, achieving perpendicular alignment of assemblies containing Dy 3+ and parallel alignment of those containing Tm 3+ . Moreover, samples with chelated Yb 3+ were more alignable than the Tm 3+ chelating counterparts. Such a possibility has never been demonstrated for planar Ln 3+ chelating polymolecular assemblies. The physico-chemical properties of these novel assemblies were further studied by monitoring the alignment behavior at different temperatures and by including 16 mol% of cholesterol (Chol-OH) in the phospholipid bilayer. The DMPE-Glu-DTPA/Ln 3+ complex and the resulting assemblies are promising candidates for applications in numerous fields including pharmaceutical technologies, structural characterization of membrane biomolecules by NMR spectroscopy, as contrasting agents for magnetic resonance imaging, and for the development of smart optical gels.

Mesenchymal Stem Cells in Oriented PLGA/ACECM Composite Scaffolds Enhance Structure-Specific Regeneration of Hyaline Cartilage in a Rabbit Model

PubMed Central

Guo, Weimin; Zheng, Xifu; Zhang, Weiguo; Chen, Mingxue; Wang, Zhenyong; Hao, Chunxiang; Huang, Jingxiang; Yuan, Zhiguo; Zhang, Yu; Wang, Mingjie; Peng, Jiang; Wang, Aiyuan; Wang, Yu; Sui, Xiang; Xu, Wenjing

2018-01-01

Articular cartilage lacks a blood supply and nerves. Hence, articular cartilage regeneration remains a major challenge in orthopedics. Decellularized extracellular matrix- (ECM-) based strategies have recently received particular attention. The structure of native cartilage exhibits complex zonal heterogeneity. Specifically, the development of a tissue-engineered scaffold mimicking the aligned structure of native cartilage would be of great utility in terms of cartilage regeneration. Previously, we fabricated oriented PLGA/ACECM (natural, nanofibrous, articular cartilage ECM) composite scaffolds. In vitro, we found that the scaffolds not only guided seeded cells to proliferate in an aligned manner but also exhibited high biomechanical strength. To detect whether oriented cartilage regeneration was possible in vivo, we used mesenchymal stem cell (MSC)/scaffold constructs to repair cartilage defects. The results showed that cartilage defects could be completely regenerated. Histologically, these became filled with hyaline cartilage and subchondral bone. Moreover, the aligned structure of cartilage was regenerated and was similar to that of native tissue. In conclusion, the MSC/scaffold constructs enhanced the structure-specific regeneration of hyaline cartilage in a rabbit model and may be a promising treatment strategy for the repair of human cartilage defects. PMID:29666653

Conductive micropatterned polyurethane films as tissue engineering scaffolds for Schwann cells and PC12 cells.

PubMed

Wu, Yaobin; Wang, Ling; Hu, Tianli; Ma, Peter X; Guo, Baolin

2018-05-15

Controlling cellular alignment and elongation has been demonstrated as an important parameter for developing nerve tissue engineering scaffolds. Many approaches have been developed to guide cellular orientation for nerve regeneration such as micropatterning techniques. However, most of materials used for developing micropatterning scaffolds lack of bioactivity and biofunctionability. Here we present a functional conductive micropatterned scaffold based on bioactive conductive biodegradable polyurethane prepared using a micro-molding technique. These conductive micropatterned scaffolds are able to not only induce the Schwann cells (SCs) alignment and elongation by the micropatterned surface but also enhance the nerve growth factor (NGF) gene expression of SCs by the bioactivity of these materials. Additionally, the combined effect of the bioactivity of such conductive materials and the micropatterned structure also dramatically promotes the neurite extension and elongation of PC12 cells in a highly aligned direction. These data suggest that these conductive micropatterned scaffolds that easily control cellular orientation and organization, and dramatically enhance NGF gene expression and significantly induce the neurite extension of PC12 cells, have a great potential for nerve regeneration applications. Copyright © 2018 Elsevier Inc. All rights reserved.

The chromokinesin Kid is required for maintenance of proper metaphase spindle size.

PubMed

Tokai-Nishizumi, Noriko; Ohsugi, Miho; Suzuki, Emiko; Yamamoto, Tadashi

2005-11-01

The human chromokinesin Kid/kinesin-10, a plus end-directed microtubule (MT)-based motor with both microtubule- and DNA-binding domains, is required for proper chromosome alignment at the metaphase plate. Here, we performed RNA interference experiments to deplete endogenous Kid from HeLa cells and confirmed defects in metaphase chromosome arm alignment in Kid-depleted cells. In addition, we noted a shortening of the spindle length, resulting in a pole-to-pole distance only 80% of wild type. The spindle microtubule-bundles with which Kid normally colocalize became less robust. Rescue of the two Kid deficiency phenotypes-imprecise chromosome alignment at metaphase and shortened spindles- exhibited distinct requirements. Mutants lacking either the DNA-binding domain or the MT motor ATPase failed to rescue the former defect, whereas rescue of the shortened spindle phenotype required neither activity. Kid also exhibits microtubule bundling activity in vitro, and rescue of the shortened spindle phenotype and the bundling activity displayed similar domain requirements, except that rescue required a coiled-coil domain not needed for bundling. These results suggest that distinct from its role in chromosome movement, Kid contributes to spindle morphogenesis by mediating spindle microtubules stabilization.

The Chromokinesin Kid Is Required for Maintenance of Proper Metaphase Spindle SizeD⃞

PubMed Central

Tokai-Nishizumi, Noriko; Ohsugi, Miho; Suzuki, Emiko; Yamamoto, Tadashi

2005-01-01

The human chromokinesin Kid/kinesin-10, a plus end-directed microtubule (MT)-based motor with both microtubule- and DNA-binding domains, is required for proper chromosome alignment at the metaphase plate. Here, we performed RNA interference experiments to deplete endogenous Kid from HeLa cells and confirmed defects in metaphase chromosome arm alignment in Kid-depleted cells. In addition, we noted a shortening of the spindle length, resulting in a pole-to-pole distance only 80% of wild type. The spindle microtubule-bundles with which Kid normally colocalize became less robust. Rescue of the two Kid deficiency phenotypes—imprecise chromosome alignment at metaphase and shortened spindles— exhibited distinct requirements. Mutants lacking either the DNA-binding domain or the MT motor ATPase failed to rescue the former defect, whereas rescue of the shortened spindle phenotype required neither activity. Kid also exhibits microtubule bundling activity in vitro, and rescue of the shortened spindle phenotype and the bundling activity displayed similar domain requirements, except that rescue required a coiled-coil domain not needed for bundling. These results suggest that distinct from its role in chromosome movement, Kid contributes to spindle morphogenesis by mediating spindle microtubules stabilization. PMID:16176979

One member, two leaders: extending leader-member exchange theory to a dual leadership context.

PubMed

Vidyarthi, Prajya R; Erdogan, Berrin; Anand, Smriti; Liden, Robert C; Chaudhry, Anjali

2014-05-01

In this study, we develop and test a model that extends leader-member exchange (LMX) theory to a dual leadership context. Drawing upon relative deprivation theory, we assert that when employees work for 2 leaders, each relationship exists within the context of the other relationship. Thus, the level of alignment or misalignment between the 2 relationships has implications for employees' job satisfaction and voluntary turnover. Employing polynomial regression on time-lagged data gathered from 159 information technology consultants nested in 26 client projects, we found that employee outcomes are affected by the quality of the relationship with both agency and client leaders, such that the degree of alignment between the 2 LMXs explained variance in outcomes beyond that explained by both LMXs. Results also revealed that a lack of alignment in the 2 LMXs led to asymmetric effects on outcomes, such that the relationship with agency leader mattered more than the relationship with one's client leader. Finally, frequency of communication with the agency leader determined the degree to which agency LMX affected job satisfaction in the low client LMX condition. (c) 2014 APA, all rights reserved.

Assessment and pedagogy: a case study of two oral hygiene lecturers in South Africa.

PubMed

Vergotine, G

2012-08-01

There is evidence that most South African oral hygiene lecturers lack appropriate qualifications in the field of education. Their teaching skills are based mainly on clinical and practical experience, and this may impact on their understanding of the educational foundations of teaching, learning and assessment. To explore oral hygiene lecturers' knowledge and use of pedagogy and assessment and its alignment. A qualitative descriptive study design was used and case studies of two oral hygiene lecturers, each with qualifications in Education, were analyzed according to three themes: curriculum, pedagogy and assessment. The results showed that both participants had a good understanding of formative assessment (FA) and summative assessment (SA). They made use of FA but in neither case was the application ideal. Both used a range of teaching and assessment strategies but felt accountable to external demands of meeting outcomes. They linked their understanding of pedagogy and assessment to assist in the development of their courses and reported that this alignment had improved the quality of their programmes. This alignment by oral hygiene lecturers can influence curricular and pedagogic strategies. The professional educational development of lecturers in oral hygiene could be influential in improving the profession within the country.

Mesenchymal Stem Cells in Oriented PLGA/ACECM Composite Scaffolds Enhance Structure-Specific Regeneration of Hyaline Cartilage in a Rabbit Model.

PubMed

Guo, Weimin; Zheng, Xifu; Zhang, Weiguo; Chen, Mingxue; Wang, Zhenyong; Hao, Chunxiang; Huang, Jingxiang; Yuan, Zhiguo; Zhang, Yu; Wang, Mingjie; Peng, Jiang; Wang, Aiyuan; Wang, Yu; Sui, Xiang; Xu, Wenjing; Liu, Shuyun; Lu, Shibi; Guo, Quanyi

2018-01-01

Articular cartilage lacks a blood supply and nerves. Hence, articular cartilage regeneration remains a major challenge in orthopedics. Decellularized extracellular matrix- (ECM-) based strategies have recently received particular attention. The structure of native cartilage exhibits complex zonal heterogeneity. Specifically, the development of a tissue-engineered scaffold mimicking the aligned structure of native cartilage would be of great utility in terms of cartilage regeneration. Previously, we fabricated oriented PLGA/ACECM (natural, nanofibrous, articular cartilage ECM) composite scaffolds. In vitro, we found that the scaffolds not only guided seeded cells to proliferate in an aligned manner but also exhibited high biomechanical strength. To detect whether oriented cartilage regeneration was possible in vivo, we used mesenchymal stem cell (MSC)/scaffold constructs to repair cartilage defects. The results showed that cartilage defects could be completely regenerated. Histologically, these became filled with hyaline cartilage and subchondral bone. Moreover, the aligned structure of cartilage was regenerated and was similar to that of native tissue. In conclusion, the MSC/scaffold constructs enhanced the structure-specific regeneration of hyaline cartilage in a rabbit model and may be a promising treatment strategy for the repair of human cartilage defects.

Template-Based Modeling of Protein-RNA Interactions.

PubMed

Zheng, Jinfang; Kundrotas, Petras J; Vakser, Ilya A; Liu, Shiyong

2016-09-01

Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.

Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

PubMed Central

Montplaisir, Lisa

2014-01-01

Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students’ perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students’ perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (posttest) of the course. Alignment between student perception and determined knowledge was significantly more accurate on the posttest compared with the pretest. Students whose determined knowledge was in the upper quartile had significantly better alignment between their perception and determined knowledge on the pre- and posttest than students in the lower quartile. No difference exists between how students perceived their knowledge between upper- and lower-quartile students. There was a significant difference in alignment of perception and determined knowledge between males and females on the posttest, with females being more accurate in their perception of knowledge. This study provides evidence of discrepancies that exist between what students perceive they know and what they actually know. PMID:26086662

The Status of Legal Authority for Injury Prevention Practice in State Health Departments

PubMed Central

Thombley, Melisa L.; Kohn, Melvin A.; Jesada, Rebecca A.

2012-01-01

Despite the potential for public health strategies to decrease the substantial burden of injuries, injury prevention infrastructure in state health departments is underdeveloped. We sought to describe the legal support for injury prevention activities at state health departments. We searched the Lexis database for state laws providing authority for those activities, and categorized the scope of those laws. Only 10 states have authority that covers the full scope of injury prevention practice; in the others, legal authority is piecemeal, nonspecific, or nonexistent. More comprehensive legal authority could help health departments access data for surveillance, work with partners, address sensitive issues, and garner funding. Efforts should be undertaken to enhance legal support for injury prevention activities across the country. PMID:22515850

Scientists at play in a field of the Lord

NASA Astrophysics Data System (ADS)

Long, David E.

2010-03-01

The Answers in Genesis Creation Museum opened in May of 2007. During the opening day, a loosely affiliated group of scientists joined in a Rally for Reason as they termed it to protest the museum's potential effect on science in the United States. This paper discusses ethnographic data collected before and during the rally. Scientist narratives disclose the rationale for their participation at the rally, unpacking their hopes, fears and social ideals vis-à-vis their perception of the Museum's impact. With these ideals, I discuss the lacking discourse between the values of ideal of science literacy, the contested authority of museums and their publics, and a lacking conception of how a valuerationality aligned towards the Museum's message continues to be culturally produced.

Federal research, development, and demonstration priorities for carbon dioxide removal in the United States

NASA Astrophysics Data System (ADS)

Sanchez, Daniel L.; Amador, Giana; Funk, Jason; Mach, Katharine J.

2018-01-01

Atmospheric carbon dioxide removal (CDR) technologies may be critical to achieving deep decarbonization. Yet a lack of technical and commercial maturity of CDR technologies hinders potential deployment. Needs for commercialization span research, development, and demonstration (RD&D) activities, including development of new materials, reactors, and processes, and rigorous monitoring of a portfolio of demonstration projects. As a world leader in supporting science and engineering, the United States (US) can play an important role in reducing costs and clarifying the sustainable scale of CDR. To date, federal agencies have focused on voluntary or piecemeal CDR programs. Here, we present a synthesis of research and developement needs, relevant agency authority, barriers to coordination, and interventions to enhance RD&D across the federal government of the US. On the basis of agency authority and expertise, the Department of Energy, Department of Agriculture, Department of the Interior, National Oceanic and Atmospheric Administration, and National Science Foundation are most central to conducting research, funding projects, monitoring effects, and promulgating regulations. Key enablers for successful programs include embracing technological diversity and administrative efficiency, fostering agency buy-in, and achieving commercial deployment. Based on these criteria, the executive branch could effectively coordinate RD&D strategy through two complementary pathways: (1) renewing intra-agency commitment to CDR in five primary agencies, including both research and demonstration, and (2) coordinating research prioritization and outcomes across agencies, led by the Office of Science and Technology Policy and loosely based on the National Nanotechnology Initiative. Both pathways can be stimulated by executive order or Congressional mandate. Executive branch implementation can begin at any time; future Farm and Energy Bills provide legislative vehicles for enhancing programs.

Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers.

PubMed

Mote, Kaustubh R; Gopinath, T; Traaseth, Nathaniel J; Kitchen, Jason; Gor'kov, Peter L; Brey, William W; Veglia, Gianluigi

2011-11-01

Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring (1)H-(15)N dipolar couplings (DC) and (15)N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal (rotational) angles of the protein domains can be directly derived from analytical expression of DC and CSA values, or, alternatively, obtained by refining protein structures using these values as harmonic restraints in simulated annealing calculations. The Achilles' heel of this approach is the lack of suitable experiments for sequential assignment of the amide resonances. In this Article, we present a new pulse sequence that integrates proton driven spin diffusion (PDSD) with sensitivity-enhanced PISEMA in a 3D experiment ([(1)H,(15)N]-SE-PISEMA-PDSD). The incorporation of 2D (15)N/(15)N spin diffusion experiments into this new 3D experiment leads to the complete and unambiguous assignment of the (15)N resonances. The feasibility of this approach is demonstrated for the membrane protein sarcolipin reconstituted in magnetically aligned lipid bicelles. Taken with low electric field probe technology, this approach will propel the determination of sequential assignment as well as structure and topology of larger integral membrane proteins in aligned lipid bilayers. © Springer Science+Business Media B.V. 2011

Automatic construction of patient-specific finite-element mesh of the spine from IVDs and vertebra segmentations

NASA Astrophysics Data System (ADS)

Castro-Mateos, Isaac; Pozo, Jose M.; Lazary, Aron; Frangi, Alejandro F.

2016-03-01

Computational medicine aims at developing patient-specific models to help physicians in the diagnosis and treatment selection for patients. The spine, and other skeletal structures, is an articulated object, composed of rigid bones (vertebrae) and non-rigid parts (intervertebral discs (IVD), ligaments and muscles). These components are usually extracted from different image modalities, involving patient repositioning. In the case of the spine, these models require the segmentation of IVDs from MR and vertebrae from CT. In the literature, there exists a vast selection of segmentations methods, but there is a lack of approaches to align the vertebrae and IVDs. This paper presents a method to create patient-specific finite element meshes for biomechanical simulations, integrating rigid and non-rigid parts of articulated objects. First, the different parts are aligned in a complete surface model. Vertebrae extracted from CT are rigidly repositioned in between the IVDs, initially using the IVDs location and then refining the alignment using the MR image with a rigid active shape model algorithm. Finally, a mesh morphing algorithm, based on B-splines, is employed to map a template finite-element (volumetric) mesh to the patient-specific surface mesh. This morphing reduces possible misalignments and guarantees the convexity of the model elements. Results show that the accuracy of the method to align vertebrae into MR, together with IVDs, is similar to that of the human observers. Thus, this method is a step forward towards the automation of patient-specific finite element models for biomechanical simulations.

Standardized Representation of Clinical Study Data Dictionaries with CIMI Archetypes

PubMed Central

Sharma, Deepak K.; Solbrig, Harold R.; Prud’hommeaux, Eric; Pathak, Jyotishman; Jiang, Guoqian

2016-01-01

Researchers commonly use a tabular format to describe and represent clinical study data. The lack of standardization of data dictionary’s metadata elements presents challenges for their harmonization for similar studies and impedes interoperability outside the local context. We propose that representing data dictionaries in the form of standardized archetypes can help to overcome this problem. The Archetype Modeling Language (AML) as developed by the Clinical Information Modeling Initiative (CIMI) can serve as a common format for the representation of data dictionary models. We mapped three different data dictionaries (identified from dbGAP, PheKB and TCGA) onto AML archetypes by aligning dictionary variable definitions with the AML archetype elements. The near complete alignment of data dictionaries helped map them into valid AML models that captured all data dictionary model metadata. The outcome of the work would help subject matter experts harmonize data models for quality, semantic interoperability and better downstream data integration. PMID:28269909

Standardized Representation of Clinical Study Data Dictionaries with CIMI Archetypes.

PubMed

Sharma, Deepak K; Solbrig, Harold R; Prud'hommeaux, Eric; Pathak, Jyotishman; Jiang, Guoqian

2016-01-01

Researchers commonly use a tabular format to describe and represent clinical study data. The lack of standardization of data dictionary's metadata elements presents challenges for their harmonization for similar studies and impedes interoperability outside the local context. We propose that representing data dictionaries in the form of standardized archetypes can help to overcome this problem. The Archetype Modeling Language (AML) as developed by the Clinical Information Modeling Initiative (CIMI) can serve as a common format for the representation of data dictionary models. We mapped three different data dictionaries (identified from dbGAP, PheKB and TCGA) onto AML archetypes by aligning dictionary variable definitions with the AML archetype elements. The near complete alignment of data dictionaries helped map them into valid AML models that captured all data dictionary model metadata. The outcome of the work would help subject matter experts harmonize data models for quality, semantic interoperability and better downstream data integration.

Atomic layer deposition of ruthenium on plasma-treated vertically aligned carbon nanotubes for high-performance ultracapacitors.

PubMed

Kim, Jun Woo; Kim, Byungwoo; Park, Suk Won; Kim, Woong; Shim, Joon Hyung

2014-10-31

It is challenging to realize a conformal metal coating by atomic layer deposition (ALD) because of the high surface energy of metals. In this study, ALD of ruthenium (Ru) on vertically aligned carbon nanotubes (CNTs) was carried out. To activate the surface of CNTs that lack surface functional groups essential for ALD, oxygen plasma was applied ex situ before ALD. X-ray photoelectron spectroscopy and Raman spectroscopy confirmed surface activation of CNTs by the plasma pretreatment. Transmission electron microscopy analysis with energy-dispersive x-ray spectroscopy composition mapping showed that ALD Ru grew conformally along CNTs walls. ALD Ru/CNTs were electrochemically oxidized to ruthenium oxide (RuOx) that can be a potentially useful candidate for use in the electrodes of ultracapacitors. Electrode performance of RuOx/CNTs was evaluated using cyclic voltammetry and galvanostatic charge-discharge measurements.

Teflon/SiO₂ Bilayer Passivation for Improving the Electrical Reliability of Oxide TFTs Fabricated Using a New Two-Photomask Self-Alignment Process.

PubMed

Fan, Ching-Lin; Shang, Ming-Chi; Li, Bo-Jyun; Lin, Yu-Zuo; Wang, Shea-Jue; Lee, Win-Der; Hung, Bohr-Ran

2015-04-13

This study proposes a two-photomask process for fabricating amorphous indium-gallium-zinc oxide (a-IGZO) thin-film transistors (TFTs) that exhibit a self-aligned structure. The fabricated TFTs, which lack etching-stop (ES) layers, have undamaged a-IGZO active layers that facilitate superior performance. In addition, we demonstrate a bilayer passivation method that uses a polytetrafluoroethylene (Teflon) and SiO₂ combination layer for improving the electrical reliability of the fabricated TFTs. Teflon was deposited as a buffer layer through thermal evaporation. The Teflon layer exhibited favorable compatibility with the underlying IGZO channel layer and effectively protected the a-IGZO TFTs from plasma damage during SiO₂ deposition, resulting in a negligible initial performance drop in the a-IGZO TFTs. Compared with passivation-free a-IGZO TFTs, passivated TFTs exhibited superior stability even after 168 h of aging under ambient air at 95% relative humidity.

Evaluation of ERTS imagery for spectral geological mapping in diverse terranes of New York State

NASA Technical Reports Server (NTRS)

Isachsen, Y. W.; Fakundiny, R. H.; Forster, S. W.

1974-01-01

Linear anomalies dominate the new geological information derived from ERTS-1 imagery, total lengths now exceeding 6000 km. Experimentation with a variety of viewing techniques suggests that conventional photogeologic analyses of band 7 results in the location of more than 97 percent of all linears found. The maxima on rose diagrams for ERTS-1 anomalies correspond well with those for mapped faults and topographic lineaments, despite a difference in relative magnitudes of maxima thought due to solar illumination direction. A multiscale analysis of linears showed that single topographic linears at 1:2,500,000 became segmented at 1:1,000,000, aligned zones of shorter parallel, en echelon, or conjugate linears at 1:500,000, and still shorter linears lacking obvious alignment at 1:250,000. Visible glacial features include individual drumlins, best seen in winter imagery, drumlinoids, eskers, ice-marginal drainage channels, glacial lake shorelines and sand plains, and end moraines.

Global dynamics of selective attention and its lapses in primary auditory cortex.

PubMed

Lakatos, Peter; Barczak, Annamaria; Neymotin, Samuel A; McGinnis, Tammy; Ross, Deborah; Javitt, Daniel C; O'Connell, Monica Noelle

2016-12-01

Previous research demonstrated that while selectively attending to relevant aspects of the external world, the brain extracts pertinent information by aligning its neuronal oscillations to key time points of stimuli or their sampling by sensory organs. This alignment mechanism is termed oscillatory entrainment. We investigated the global, long-timescale dynamics of this mechanism in the primary auditory cortex of nonhuman primates, and hypothesized that lapses of entrainment would correspond to lapses of attention. By examining electrophysiological and behavioral measures, we observed that besides the lack of entrainment by external stimuli, attentional lapses were also characterized by high-amplitude alpha oscillations, with alpha frequency structuring of neuronal ensemble and single-unit operations. Entrainment and alpha-oscillation-dominated periods were strongly anticorrelated and fluctuated rhythmically at an ultra-slow rate. Our results indicate that these two distinct brain states represent externally versus internally oriented computational resources engaged by large-scale task-positive and task-negative functional networks.

Microbially assisted recording of the Earth's magnetic field in sediment.

PubMed

Zhao, Xiangyu; Egli, Ramon; Gilder, Stuart A; Müller, Sebastian

2016-02-11

Sediments continuously record variations of the Earth's magnetic field and thus provide an important archive for studying the geodynamo. The recording process occurs as magnetic grains partially align with the geomagnetic field during and after sediment deposition, generating a depositional remanent magnetization (DRM) or post-DRM (PDRM). (P)DRM acquisition mechanisms have been investigated for over 50 years, yet many aspects remain unclear. A key issue concerns the controversial role of bioturbation, that is, the mechanical disturbance of sediment by benthic organisms, during PDRM acquisition. A recent theory on bioturbation-driven PDRM appears to solve many inconsistencies between laboratory experiments and palaeomagnetic records, yet it lacks experimental proof. Here we fill this gap by documenting the important role of bioturbation-induced rotational diffusion for (P)DRM acquisition, including the control exerted on the recorded inclination and intensity, as determined by the equilibrium between aligning and perturbing torques acting on magnetic particles.

Nerve Cells Decide to Orient inside an Injectable Hydrogel with Minimal Structural Guidance.

PubMed

Rose, Jonas C; Cámara-Torres, María; Rahimi, Khosrow; Köhler, Jens; Möller, Martin; De Laporte, Laura

2017-06-14

Injectable biomaterials provide the advantage of a minimally invasive application but mostly lack the required structural complexity to regenerate aligned tissues. Here, we report a new class of tissue regenerative materials that can be injected and form an anisotropic matrix with controlled dimensions using rod-shaped, magnetoceptive microgel objects. Microgels are doped with small quantities of superparamagnetic iron oxide nanoparticles (0.0046 vol %), allowing alignment by external magnetic fields in the millitesla order. The microgels are dispersed in a biocompatible gel precursor and after injection and orientation are fixed inside the matrix hydrogel. Regardless of the low volume concentration of the microgels below 3%, at which the geometrical constrain for orientation is still minimum, the generated macroscopic unidirectional orientation is strongly sensed by the cells resulting in parallel nerve extension. This finding opens a new, minimal invasive route for therapy after spinal cord injury.

Introduction to the fathead minnow genome browser and ...

EPA Pesticide Factsheets

Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minnow genomic sequence. This work is meant to extend the utility of fathead minnow genome as a resource and enable the continued development of this species as a model organism. The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporti

Negotiation From a Near and Distant Time Perspective

PubMed Central

Henderson, Marlone D.; Trope, Yaacov; Carnevale, Peter J.

2011-01-01

Across 3 experiments, the authors examined the effects of temporal distance on negotiation behavior. They found that greater temporal distance from negotiation decreased preference for piecemeal, single-issue consideration over integrative, multi-issue consideration (Experiment 1). They also found that greater temporal distance from an event being negotiated increased interest in conceding on the lowest priority issue and decreased interest in conceding on the highest priority issue (Experiment 2). Lastly, they found increased temporal distance from an event being negotiated produced a greater proportion of multi-issue offers, a greater likelihood of conceding on the lowest priority issue in exchange for a concession on the highest priority issue, and greater individual and joint outcomes (Experiment 3). Implications for conflict resolution and construal level theory are discussed. PMID:17014295

Teaching Engineering Practices

NASA Astrophysics Data System (ADS)

Cunningham, Christine M.; Carlsen, William S.

2014-03-01

Engineering is featured prominently in the Next Generation Science Standards (NGSS) and related reform documents, but how its nature and methods are described is problematic. This paper is a systematic review and critique of that representation, and proposes that the disciplinary core ideas of engineering (as described in the NGSS) can be disregarded safely if the practices of engineering are better articulated and modeled through student engagement in engineering projects. A clearer distinction between science and engineering practices is outlined, and prior research is described that suggests that precollege engineering design can strengthen children's understandings about scientific concepts. However, a piecemeal approach to teaching engineering practices is unlikely to result in students understanding engineering as a discipline. The implications for science teacher education are supplemented with lessons learned from a number of engineering education professional development projects.

The challenges of educating the public about astrobiology via the mass media

NASA Astrophysics Data System (ADS)

Race, Margaret

Scientific information in astrobiology is being generated at a pace that traditional textbooks cannot easily match. For the most part, students, teachers and the general public will continue to learn piecemeal about the latest advances in the field through headlines and mass media coverage centered around discoveries and new interpretations as they occur. Yet journalists and reporters are themselves unschooled in this emerging interdisciplinary field. While it is important to continue developing astrobiological curricular materials for future use by students in formal settings, it is equally important to find novel ways for educating the mass media in the interim. Current planning in anticipation of a Mars sample return mission has focused on a variety of ways to enlist the mass media in an educational as well as informational role.

Cogestion and recreation site demand: a model of demand-induced quality effects

USGS Publications Warehouse

Douglas, Aaron J.; Johnson, Richard L.

1993-01-01

This analysis focuses on problems of estimating site-specific dollar benefits conferred by outdoor recreation sites in the face of congestion costs. Encounters, crowding effects and congestion costs have often been treated by natural resource economists in a piecemeal fashion. In the current paper, encounters and crowding effects are treated systematically. We emphasize the quantitative impact of congestion costs on site-specific estimates of benefits conferred by improvements in outdoor recreation sites. The principal analytic conclusion is that techniques that streamline on data requirements produce biased estimates of benefits conferred by site improvements at facilities with significant crowding effects. The principal policy recommendation is that the Federal and state agencies should collect and store information on visitation rates, encounter levels and congestion costs at various outdoor recreation sites.

The doubling of stellar black hole nuclei

NASA Astrophysics Data System (ADS)

Kazandjian, Mher V.; Touma, J. R.

2013-04-01

It is strongly believed that Andromeda's double nucleus signals a disc of stars revolving around its central supermassive black hole on eccentric Keplerian orbits with nearly aligned apsides. A self-consistent stellar dynamical origin for such apparently long-lived alignment has so far been lacking, with indications that cluster self-gravity is capable of sustaining such lopsided configurations if and when stimulated by external perturbations. Here, we present results of N-body simulations which show unstable counter-rotating stellar clusters around supermassive black holes saturating into uniformly precessing lopsided nuclei. The double nucleus in our featured experiment decomposes naturally into a thick eccentric disc of apo-apse aligned stars which is embedded in a lighter triaxial cluster. The eccentric disc reproduces key features of Keplerian disc models of Andromeda's double nucleus; the triaxial cluster has a distinctive kinematic signature which is evident in Hubble Space Telescope observations of Andromeda's double nucleus, and has been difficult to reproduce with Keplerian discs alone. Our simulations demonstrate how the combination of an eccentric disc and a triaxial cluster arises naturally when a star cluster accreted over a preexisting and counter-rotating disc of stars drives disc and cluster into a mutually destabilizing dance. Such accretion events are inherent to standard galaxy formation scenarios. They are here shown to double stellar black hole nuclei as they feed them.

Vertically Aligned and Interconnected SiC Nanowire Networks Leading to Significantly Enhanced Thermal Conductivity of Polymer Composites.

PubMed

Yao, Yimin; Zhu, Xiaodong; Zeng, Xiaoliang; Sun, Rong; Xu, Jian-Bin; Wong, Ching-Ping

2018-03-21

Efficient heat removal via thermal management materials has become one of the most critical challenges in the development of modern microelectronic devices. However, previously reported polymer composites exhibit limited enhancement of thermal conductivity, even when highly loaded with thermally conductive fillers, because of the lack of efficient heat transfer pathways. Herein, we report vertically aligned and interconnected SiC nanowire (SiCNW) networks as efficient fillers for polymer composites, achieving significantly enhanced thermal conductivity. The SiCNW networks are produced by freeze-casting nanowire aqueous suspensions followed by thermal sintering to consolidate the nanowire junctions, exhibiting a hierarchical architecture in which honeycomb-like SiCNW layers are aligned. The composite obtained by infiltrating SiCNW networks with epoxy resin, at a relatively low SiCNW loading of 2.17 vol %, represents a high through-plane thermal conductivity (1.67 W m -1 K -1 ) compared to the pure matrix, which is equivalent to a significant enhancement of 406.6% per 1 vol % loading. The orderly SiCNW network which can act as a macroscopic expressway for phonon transport is believed to be the main contributor for the excellent thermal performance. This strategy provides insights for the design of high-performance composites with potential to be used in advanced thermal management materials.

Template-Based Modeling of Protein-RNA Interactions

PubMed Central

Zheng, Jinfang; Kundrotas, Petras J.; Vakser, Ilya A.

2016-01-01

Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes. PMID:27662342

How To Build an Integrated Neighborhood Approach to Support Community-Dwelling Older People?

PubMed Central

Cramm, Jane Murray; Nieboer, Anna Petra

2016-01-01

Background: Although the need for integrated neighborhood approaches (INAs) is widely recognized, we lack insight into strategies like INA. We describe diverse Dutch INA partners’ experiences to provide integrated person- and population-centered support to community-dwelling older people using an adapted version of Valentijn and colleagues’ integrated care model. Our main objective was to explore the experiences with INA participation. We sought to increase our understanding of the challenges facing these partners and identify factors facilitating and inhibiting integration within and among multiple levels. Methods: Twenty-one interviews with INA partners (including local health and social care organizations, older people, municipal officers, and a health insurer) were conducted and subjected to latent content analysis. Results: This study showed that integrated care and support provision through an INA is a complex, dynamic process requiring multilevel alignment of activities. The INA achieved integration at the personal, service, and professional levels only occasionally. Micro-level bottom-up initiatives were not aligned with top-down incentives, forcing community workers to establish integration despite rather than because of meso- and macro-level contexts. Conclusions: Top-down incentives should be better aligned with bottom-up initiatives. This study further demonstrated the importance of community-level engagement in integrated care and support provision. PMID:27616960

Global analysis of sagittal spinal alignment in major deformities: correlation between lack of lumbar lordosis and flexion of the knee.

PubMed

Obeid, Ibrahim; Hauger, Olivier; Aunoble, Stéphane; Bourghli, Anouar; Pellet, Nicolas; Vital, Jean-Marc

2011-09-01

It has become well recognised that sagittal balance of the spine is the result of an interaction between the spine and the pelvis. Knee flexion is considered to be the last compensatory mechanism in case of sagittal imbalance, but only few studies have insisted on the relationship between spino-pelvic parameters and lower extremity parameters. Correlation between the lack of lumbar lordosis and knee flexion has not yet been established. A retrospective study was carried out on 28 patients with major spinal deformities. The EOS system was used to measure spinal and pelvic parameters and the knee flexion angle; the lack of lumbar lordosis was calculated after prediction of lumbar lordosis with two different formulas. Correlation analysis between the different measured parameters was performed. Lumbar lordosis correlated with sacral slope (r = -0.71) and moderately with knee flexion angle (r = 0.42). Pelvic tilt correlated moderately with knee flexion angle (r = 0.55). Lack of lumbar lordosis correlated best with knee flexion angle (r = 0.72 and r = 0.63 using the two formulas, respectively). Knee flexion as a compensatory mechanism to sagittal imbalance was well correlated to the lack of lordosis and, depending on the importance of the former parameter, the best procedure to correct sagittal imbalance could be chosen.

Multiple Frequency Audio Signal Communication as a Mechanism for Neurophysiology and Video Data Synchronization

PubMed Central

Topper, Nicholas C.; Burke, S.N.; Maurer, A.P.

2014-01-01

BACKGROUND Current methods for aligning neurophysiology and video data are either prepackaged, requiring the additional purchase of a software suite, or use a blinking LED with a stationary pulse-width and frequency. These methods lack significant user interface for adaptation, are expensive, or risk a misalignment of the two data streams. NEW METHOD A cost-effective means to obtain high-precision alignment of behavioral and neurophysiological data is obtained by generating an audio-pulse embedded with two domains of information, a low-frequency binary-counting signal and a high, randomly changing frequency. This enabled the derivation of temporal information while maintaining enough entropy in the system for algorithmic alignment. RESULTS The sample to frame index constructed using the audio input correlation method described in this paper enables video and data acquisition to be aligned at a sub-frame level of precision. COMPARISONS WITH EXISTING METHOD Traditionally, a synchrony pulse is recorded on-screen via a flashing diode. The higher sampling rate of the audio input of the camcorder enables the timing of an event to be detected with greater precision. CONCLUSIONS While On-line analysis and synchronization using specialized equipment may be the ideal situation in some cases, the method presented in the current paper presents a viable, low cost alternative, and gives the flexibility to interface with custom off-line analysis tools. Moreover, the ease of constructing and implements this set-up presented in the current paper makes it applicable to a wide variety of applications that require video recording. PMID:25256648

Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure.

PubMed

Lakshmi, Balasubramanian; Sinduja, Chandrasekaran; Archunan, Govind; Srinivasan, Narayanaswamy

2014-06-01

High conservation of glycyl residues in homologous proteins is fairly frequent. It is commonly understood that glycine tends to be highly conserved either because of its unique Ramachandran angles or to avoid steric clash that would arise with a larger side chain. Using a database of aligned 3D structures of homologous proteins we identified conserved Gly in 288 alignment positions from 85 families. Ninety-six of these alignment positions correspond to conserved Gly residue with (φ, ψ) values allowed for non-glycyl residues. Reasons for this observation were investigated by in-silico mutation of these glycyl residues to Ala. We found in 94% of the cases a short contact exists between the C(β) atom of the introduced Ala with the atoms which are often distant in the primary structure. This suggests the lack of space even for a short side chain thereby explaining high conservation of glycyl residues even when they adopt (φ, ψ) values allowed for Ala. In 189 alignment positions, the conserved glycyl residues adopt (φ, ψ) values which are disallowed for Ala. In-silico mutation of these Gly residues to Ala almost always results in steric hindrance involving C(β) atom of Ala as one would expect by comparing Ramachandran maps for Ala and Gly. Rare occurrence of the disallowed glycyl conformations even in ultrahigh resolution protein structures are accompanied by short contacts in the crystal structures and such disallowed conformations are not conserved in the homologues. These observations raise the doubt on the accuracy of such glycyl conformations in proteins. © 2014 The Protein Society.

Mechanical regulation of fibroblast migration and collagen remodelling in healing myocardial infarcts

PubMed Central

Rouillard, Andrew D; Holmes, Jeffrey W

2012-01-01

Effective management of healing and remodelling after myocardial infarction is an important problem in modern cardiology practice. We have recently shown that the level of infarct anisotropy is a critical determinant of heart function following a large anterior infarction, which suggests that therapeutic gains may be realized by controlling infarct anisotropy. However, factors regulating infarct anisotropy are not well understood. Mechanical, structural and chemical guidance cues have all been shown to regulate alignment of fibroblasts and collagen in vitro, and prior studies have proposed that each of these cues could regulate anisotropy of infarct scar tissue, but understanding of fibroblast behaviour in the complex environment of a healing infarct is lacking. We developed an agent-based model of infarct healing that accounted for the combined influence of these cues on fibroblast alignment, collagen deposition and collagen remodelling. We pooled published experimental data from several sources in order to determine parameter values, then used the model to test the importance of each cue for predicting collagen alignment measurements from a set of recent cryoinfarction experiments. We found that although chemokine gradients and pre-existing matrix structures had important effects on collagen organization, a response of fibroblasts to mechanical cues was critical for correctly predicting collagen alignment in infarct scar. Many proposed therapies for myocardial infarction, such as injection of cells or polymers, alter the mechanics of the infarct region. Our modelling results suggest that such therapies could change the anisotropy of the healing infarct, which could have important functional consequences. This model is therefore a potentially important tool for predicting how such interventions change healing outcomes. PMID:22495588

Multiple frequency audio signal communication as a mechanism for neurophysiology and video data synchronization.

PubMed

Topper, Nicholas C; Burke, Sara N; Maurer, Andrew Porter

2014-12-30

Current methods for aligning neurophysiology and video data are either prepackaged, requiring the additional purchase of a software suite, or use a blinking LED with a stationary pulse-width and frequency. These methods lack significant user interface for adaptation, are expensive, or risk a misalignment of the two data streams. A cost-effective means to obtain high-precision alignment of behavioral and neurophysiological data is obtained by generating an audio-pulse embedded with two domains of information, a low-frequency binary-counting signal and a high, randomly changing frequency. This enabled the derivation of temporal information while maintaining enough entropy in the system for algorithmic alignment. The sample to frame index constructed using the audio input correlation method described in this paper enables video and data acquisition to be aligned at a sub-frame level of precision. Traditionally, a synchrony pulse is recorded on-screen via a flashing diode. The higher sampling rate of the audio input of the camcorder enables the timing of an event to be detected with greater precision. While on-line analysis and synchronization using specialized equipment may be the ideal situation in some cases, the method presented in the current paper presents a viable, low cost alternative, and gives the flexibility to interface with custom off-line analysis tools. Moreover, the ease of constructing and implements this set-up presented in the current paper makes it applicable to a wide variety of applications that require video recording. Copyright © 2014 Elsevier B.V. All rights reserved.

PRODUCTION OF HIGHLY-ALIGNED COLLAGEN LAMELLAE BY COMBINING SHEAR FORCE AND THIN-FILM CONFINEMENT

PubMed Central

Saeidi, Nima; Sander, Edward A.; Zareian, Ramin

2012-01-01

Load-bearing tissues owe their mechanical strength to their highly-anisotropic collagenous structure. To date, attempts to engineer mechanically strong connective tissue have failed mainly due to the lack of the ability to reproduce native collagen organization in constructs synthesized by cultured cells in vitro. The ability to influence the direction of the self-assembling collagen molecules and produce highly anisotropic structures has applications ranging from de novo engineering of complex tissues to the production of organized scaffolds for cell culture contact guidance. In this investigation we have used the simple technique of spin coating to produce highly-aligned arrays of collagen fibrils. By a simple modification of the method we have also successfully produced orthogonal collagen lamellae. Alternating collagen lamellae are frequently seen in load-bearing tissues such as cornea, annulus fibrosus, and cortical bone. Culturing of corneal fibroblasts onto aligned collagen shows that the cells adopt the organization of the fibrils. In this investigation, we observed the reversal of fibrillar growth direction or “hook” formation similar to those seen previously in a microfluidic shear-flow chamber. Although the results of this investigation clearly show that it is possible to produce small areas (O) 1 cm2 of collagen fibrils with enough alignment to guide fibroblasts, there is evidence that thin film instabilities are likely to be a significant barrier to producing organized collagen fibrils over larger areas. Successful application of this method to produce highly-controlled and organized collagenous structures will require the development of techniques to control thin film instability and will be the subject of the future work. PMID:21362500

Lazy, not biased: Susceptibility to partisan fake news is better explained by lack of reasoning than by motivated reasoning.

PubMed

Pennycook, Gordon; Rand, David G

2018-06-20

Why do people believe blatantly inaccurate news headlines ("fake news")? Do we use our reasoning abilities to convince ourselves that statements that align with our ideology are true, or does reasoning allow us to effectively differentiate fake from real regardless of political ideology? Here we test these competing accounts in two studies (total N = 3446 Mechanical Turk workers) by using the Cognitive Reflection Test (CRT) as a measure of the propensity to engage in analytical reasoning. We find that CRT performance is negatively correlated with the perceived accuracy of fake news, and positively correlated with the ability to discern fake news from real news - even for headlines that align with individuals' political ideology. Moreover, overall discernment was actually better for ideologically aligned headlines than for misaligned headlines. Finally, a headline-level analysis finds that CRT is negatively correlated with perceived accuracy of relatively implausible (primarily fake) headlines, and positively correlated with perceived accuracy of relatively plausible (primarily real) headlines. In contrast, the correlation between CRT and perceived accuracy is unrelated to how closely the headline aligns with the participant's ideology. Thus, we conclude that analytic thinking is used to assess the plausibility of headlines, regardless of whether the stories are consistent or inconsistent with one's political ideology. Our findings therefore suggest that susceptibility to fake news is driven more by lazy thinking than it is by partisan bias per se - a finding that opens potential avenues for fighting fake news. Copyright © 2018 Elsevier B.V. All rights reserved.

Aligning the Mountain and the Molehill: How the Combatant Commander Coordinates his Theater Security Cooperation Plan with the State Department

DTIC Science & Technology

2005-02-14

hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed , and...the national level, the National Security Act of 1947 (NSA 47) mandates the need for interagency cooperation.6 In this regard, the National Security...within DoD, it lacks a central body or mechanism to provide the overarching, truly ’global’ oversight and guidance needed to ensure adequate interagency

Calibration Transfer in LIBS and Raman Spectroscopy for Planetary Applications

NASA Astrophysics Data System (ADS)

Dyar, M. D.; Thomas, B. F.; Parente, M.; Gemp, I.; Mullen, T. H.

2017-12-01

Planetary scientists rely on spectral libraries and instrument reproducibility to interpret results from missions. Major investments have been made into assembling libraries, but they often naively assume that spectra of single crystals versus powders and from varying instruments will be the same. Calibration transfer (CT) seeks to algorithmically resolve discrepancies among datasets from different instruments or conditions. It offers the ability to align suites of spectra with a small number of common samples, allowing better models to be built with combined data sets. LIBS and Raman data present different challenges for CT. Quantitative geochemical analyses by LIBS spectroscopy are limited by lack of consistency among repeated laser shots and across instruments. Many different factors affect the presence/absence of emission lines and their intensities, such as laser power/plasma temperature, angle of incidence, detector sensitivity/resolution. To overcome these, models in which disparate datasets are projected into a joint low-dimensional subspace where all data can be aligned before quantitative analysis, such as Correlation Analysis for Domain Adaptation (CADA), have proven very effective. They require some overlap between the populations of spectra to be aligned. For example, prediction of SiO2 on 80 samples from two different LIBS labs show errors of ±16-29 wt.% when the training and test sets have no overlap, and ±4.94 wt% SiO2 when CADA is used. Uncorrected Earth-Mars spectral differences are likely to cause errors with the same order of magnitude. As with other types of reflectance spectroscopy, Raman data are plagued by differences among single crystal/powder samples and laser wavelength that affect peak intensities, and by spectral offsets from instruments with varying resolution and wavenumber alignment schemes. These problems persist even within the archetypal RRUFF database. Pre-processing transformation functions such as optimized baseline removal, normalization, squashing, and smoothing improve mineral matching accuracy. Alignment methods can record shifts between corresponding peaks from the same mineral from pairs of instruments. By considering many pairs of minerals, corrections at each energy increment can be determined, creating a transfer function to align the data.

INDUCED EEG GAMMA OSCILLATION ALIGNMENT IMPROVES DIFFERENTIATION BETWEEN AUTISM AND ADHD GROUP RESPONSES IN A FACIAL CATEGORIZATION TASK

PubMed Central

Gross, Eric; El-Baz, Ayman S.; Sokhadze, Guela E.; Sears, Lonnie; Casanova, Manuel F.; Sokhadze, Estate M.

2012-01-01

Introduction Children diagnosed with an autism spectrum disorder (ASD) often lack the ability to recognize and properly respond to emotional stimuli. Emotional deficits also characterize children with attention deficit/hyperactivity disorder (ADHD), in addition to exhibiting limited attention span. These abnormalities may effect a difference in the induced EEG gamma wave burst (35–45 Hz) peaked approximately 300–400 milliseconds following an emotional stimulus. Because induced gamma oscillations are not fixed at a definite point in time post-stimulus, analysis of averaged EEG data with traditional methods may result in an attenuated gamma burst power. Methods We used a data alignment technique to improve the averaged data, making it a better representation of the individual induced EEG gamma oscillations. A study was designed to test the response of a subject to emotional stimuli, presented in the form of emotional facial expression images. In a four part experiment, the subjects were instructed to identify gender in the first two blocks of the test, followed by differentiating between basic emotions in the final two blocks (i.e. anger vs. disgust). EEG data was collected from ASD (n=10), ADHD (n=9), and control (n=11) subjects via a 128 channel EGI system, and processed through a continuous wavelet transform and bandpass filter to isolate the gamma frequencies. A custom MATLAB code was used to align the data from individual trials between 200–600 ms post-stimulus, EEG site, and condition by maximizing the Pearson product-moment correlation coefficient between trials. The gamma power for the 400 ms window of maximum induced gamma burst was then calculated and compared between subject groups. Results and Conclusion Condition (anger/disgust recognition, gender recognition) × Alignment × Group (ADHD, ASD, Controls) interaction was significant at most of parietal topographies (e.g., P3–P4, P7–P8). These interactions were better manifested in the aligned data set. Our results show that alignment of the induced gamma oscillations improves sensitivity of this measure in differentiation of EEG responses to emotional facial stimuli in ADHD and ASD. PMID:22754277

INDUCED EEG GAMMA OSCILLATION ALIGNMENT IMPROVES DIFFERENTIATION BETWEEN AUTISM AND ADHD GROUP RESPONSES IN A FACIAL CATEGORIZATION TASK.

PubMed

Gross, Eric; El-Baz, Ayman S; Sokhadze, Guela E; Sears, Lonnie; Casanova, Manuel F; Sokhadze, Estate M

2012-01-01

INTRODUCTION: Children diagnosed with an autism spectrum disorder (ASD) often lack the ability to recognize and properly respond to emotional stimuli. Emotional deficits also characterize children with attention deficit/hyperactivity disorder (ADHD), in addition to exhibiting limited attention span. These abnormalities may effect a difference in the induced EEG gamma wave burst (35-45 Hz) peaked approximately 300-400 milliseconds following an emotional stimulus. Because induced gamma oscillations are not fixed at a definite point in time post-stimulus, analysis of averaged EEG data with traditional methods may result in an attenuated gamma burst power. METHODS: We used a data alignment technique to improve the averaged data, making it a better representation of the individual induced EEG gamma oscillations. A study was designed to test the response of a subject to emotional stimuli, presented in the form of emotional facial expression images. In a four part experiment, the subjects were instructed to identify gender in the first two blocks of the test, followed by differentiating between basic emotions in the final two blocks (i.e. anger vs. disgust). EEG data was collected from ASD (n=10), ADHD (n=9), and control (n=11) subjects via a 128 channel EGI system, and processed through a continuous wavelet transform and bandpass filter to isolate the gamma frequencies. A custom MATLAB code was used to align the data from individual trials between 200-600 ms post-stimulus, EEG site, and condition by maximizing the Pearson product-moment correlation coefficient between trials. The gamma power for the 400 ms window of maximum induced gamma burst was then calculated and compared between subject groups. RESULTS AND CONCLUSION: Condition (anger/disgust recognition, gender recognition) × Alignment × Group (ADHD, ASD, Controls) interaction was significant at most of parietal topographies (e.g., P3-P4, P7-P8). These interactions were better manifested in the aligned data set. Our results show that alignment of the induced gamma oscillations improves sensitivity of this measure in differentiation of EEG responses to emotional facial stimuli in ADHD and ASD.

Improvement of the insertion axis for cochlear implantation with a robot-based system.

PubMed

Torres, Renato; Kazmitcheff, Guillaume; De Seta, Daniele; Ferrary, Evelyne; Sterkers, Olivier; Nguyen, Yann

2017-02-01

It has previously reported that alignment of the insertion axis along the basal turn of the cochlea was depending on surgeon' experience. In this experimental study, we assessed technological assistances, such as navigation or a robot-based system, to improve the insertion axis during cochlear implantation. A preoperative cone beam CT and a mastoidectomy with a posterior tympanotomy were performed on four temporal bones. The optimal insertion axis was defined as the closest axis to the scala tympani centerline avoiding the facial nerve. A neuronavigation system, a robot assistance prototype, and software allowing a semi-automated alignment of the robot were used to align an insertion tool with an optimal insertion axis. Four procedures were performed and repeated three times in each temporal bone: manual, manual navigation-assisted, robot-based navigation-assisted, and robot-based semi-automated. The angle between the optimal and the insertion tool axis was measured in the four procedures. The error was 8.3° ± 2.82° for the manual procedure (n = 24), 8.6° ± 2.83° for the manual navigation-assisted procedure (n = 24), 5.4° ± 3.91° for the robot-based navigation-assisted procedure (n = 24), and 3.4° ± 1.56° for the robot-based semi-automated procedure (n = 12). A higher accuracy was observed with the semi-automated robot-based technique than manual and manual navigation-assisted (p < 0.01). Combination of a navigation system and a manual insertion does not improve the alignment accuracy due to the lack of friendly user interface. On the contrary, a semi-automated robot-based system reduces both the error and the variability of the alignment with a defined optimal axis.

Eco-efficiency analysis of an agricultural research complex.

PubMed

Reith, Charles C; Guidry, Michael J

2003-07-01

The Model Sustainable Agricultural Complex (MSAC) is a 600-acre experimental farm in south-central Louisiana, in the very southern reaches of the United States, approximately 40 km north of the Gulf of Mexico. The MSAC consists of many land uses and facilities, including a dairy, crawfish center, beef herd, sugarcane crop, and equestrian center, as well as numerous features and programs for research, education, and residence. The mission of the MSAC, which is operated by the Department of Renewable Resources at the University of Louisiana at Lafayette, has been to accommodate research and education in production agriculture, while generating revenues through the delivery of food products into the local economy. In recent years, environmental conservation has been increasingly important at the MSAC. Best management practices (BMPs) were implemented to reduce soil loss and mitigate nonpoint source pollution. Research was initiated to quantify the effectiveness of these BMPs, and workshops were conducted to explain preliminary results to local farmers. However, environmental improvements at the MSAC had until 2000 been piecemeal, which may be said as well for agriculture overall. What is needed is a comprehensive integrated approach to analyzing and improving environmental performance, as is possible when implementing an environmental management system (EMS). This manuscript describes our efforts to integrate piecemeal environmental improvements into a farm-wide program of systematic improvement. This process began with a qualitative ranking of the MSAC's inputs and outputs, followed by a quantification of certain key parameters related to the consumption of resources and provision of services at the Complex. Certain measures related to the Complex's eco-efficiency were combined into a ratio that provides a useful target for management and continuous improvement. Eco-efficiency, which is defined as 'the efficiency with which receivables are converted into deliverables', is a good way to apply the lessons of industry to the agricultural sector, for instance, by monitoring and managing resource efficiency as an aspect in an EMS such as prescribed by ISO 14000. This will require disciplined recordkeeping and managed conservation, and will promote long-term environmental improvement.

Neuropeptide AF Induces Piecemeal Degranulation in Murine Mucosal Mast Cells: A New Mediator in Neuro-Immune Communication in the Intestinal Lamina Propria?

PubMed

Abdellah, Nada; van Remoortel, Samuel; Mohey-Elsaeed, Omnia; Mustafa, Mohamed-Nabil; Ahmed, Yasser A; Timmermans, Jean-Pierre; Buckinx, Roeland

2018-06-01

Neuropeptides AF (NPAF), FF (NPFF) and SF (NPSF) are RFamide neuropeptides known to be widely expressed in the mammalian central nervous system, where they fulfill a wide range of functions with pain modulation being the most prominent one. Recent evidence indicates that RFamides act as mediators in mast cell-sensory nerve communications related to allergic disease. Previous work by our group has shown that the expression levels of some members of the Mas-related gene receptor (Mrgpr) family in both enteric neurons and mucosal mast cells change during intestinal inflammation. The Mrgpr subtypes C11 and A4 can be activated by NPAF, while A1 and C11 are triggered by NPFF. The aim of the present study was to investigate whether RFamides of the NPFF group are expressed in the gastrointestinal tract and to identify possible targets and receptors that might be involved in RFamide-associated mast cell modulation. To this end, the expression and distribution patterns of NPFF/AF receptors and the NPFF precursor protein were determined in bone marrow-derived mucosal mast cells (BMMCs) by immunocytochemistry and (RT-) PCR. BMMCs were found to express MrgprA4 and A1, and functional analysis of the effects of NPAF by means of a β-hexosaminidase assay, mMCP-1 ELISA, electron microscopy and live cell calcium imaging revealed a piecemeal degranulation induced by NPAF. However, knock-out of MrgprA4 and A1 did not reduce the effect of NPAF, indicating that the BMMC response to NPAF was receptor independent. ProNPFF was expressed in neurons and BMMCs, suggesting that both cell types are potential sources of NPAF in situ. Our results show that the RFamide NPAF can be considered as a novel modulator of BMMC activity in the neuro-immune communication in the gastrointestinal tract, although the exact signaling pathway remains to be elucidated. Anat Rec, 00:000-000, 2018. © 2018 Wiley Periodicals, Inc. Anat Rec, 301:1103-1114, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Enhancing student performance: Linking the geography curriculum, instruction, and assessment in the English-speaking Caribbean

NASA Astrophysics Data System (ADS)

Collymore, Jennifer C.

In a 21st century knowledge society individuals are expected to use their knowledge and skills to think critically, problem solve, make decisions, comprehend new ideas, communicate, and collaborate effectively with others. Helping students achieve this level of performance is no easy task and it brings into focus the fact that the effectiveness of any education system rests on the systemic coordination or alignment of three crucial components: curriculum, instruction and assessment (referred to as the CIA). These components must work in concert to facilitate and enhance student performance. However, educational reform typically targets these components in isolation, often treating only one component, rather than the system as a whole. The misalignment of these components can adversely affect student performance in any discipline. When the CIA components are out of alignment, it is difficult to evaluate student and system performance and achieve improvement in an educational system. Therefore, using geography education in Trinidad & Tobago as a case study, this study examined the nature of the alignment among the CIA components in the advanced geography system in the English- Speaking Caribbean and the extent to which the alignment may be affecting student performance. The study sought to determine the possible sources and causes of misalignment, the challenges to achieving alignment, and ways of achieving greater coordination among the CIA components of the system. The methodology employed in the study involved the use of classroom observations, interviews, and the Surveys of Enacted Curriculum Alignment Model which uses content analyses and surveys. The results showed that there were varying degrees of alignment among the components. There was acceptable alignment (Alignment Index ≥ 0.25) between the curriculum and assessment. However, the alignment between curriculum and instruction or assessment and instruction was poor (Alignment Index ≤ 0.12). The baseline threshold for acceptable alignment was 0.25. The misalignment between the curriculum and assessment stemmed from the fact that there were items tested in the assessment that were not identified in the examination syllabus. In terms of the misalignment between the curriculum/assessment and instruction, teachers were misallocating their teaching time and efforts; spending too much time teaching the skills and practices of the discipline rather than the core content areas and they were spending too much time teaching the content at the lower order cognitive level of recall. In addition, while research promotes student-centered approaches, cooperative learning, dialogic discourse, open informal questioning and discursive forms of writing, teachers still primarily use teacher-centered approaches, individualize instruction, monologic discourse and closed recall questions. The teachers' instructional practices are not affording students the opportunity to acquire and display their knowledge at the higher levels of cognition. The cause of the misalignment was attributed to a vague, overloaded syllabus and limited teaching time; vague evaluative criteria and feedback from the Examination Council; inadequate and insufficient teacher training and professional development; a lack of administrative support and mentorship for inexperienced teachers; and teacher frustration. Subsequently, the study offers a number of evidence based recommendations that range from the modification and refinement of the geography CIA triad to professional development programs and the design of interventions that can advance the teaching and learning of the discipline. Though the study is undertaken in a specific context, the educational issues addressed in the study transcend time, scale, and geographic boundaries and the results can inform the decision-making and practices of educators and education policy-makers everywhere.

History of Science in the Physics Curriculum: A Directed Content Analysis of Historical Sources

NASA Astrophysics Data System (ADS)

Seker, Hayati; Guney, Burcu G.

2012-05-01

Although history of science is a potential resource for instructional materials, teachers do not have a tendency to use historical materials in their lessons. Studies showed that instructional materials should be adaptable and consistent with curriculum. This study purports to examine the alignment between history of science and the curriculum in the light of the facilitator model on the use of history of science in science teaching, and to expose possible difficulties in preparing historical materials. For this purpose, qualitative content analysis method was employed. Codes and themes were defined beforehand, with respect to levels and their sublevels of the model. The analysis revealed several problems with the alignment of historical sources for the physics curriculum: limited information about scientists' personal lives, the difficulty of linking with content knowledge, the lack of emphasis on scientific process in the physics curriculum, differences between chronology and sequence of topics, the lack of information about scientists' reasoning. Based on the findings of the analysis, it would be difficult to use original historical sources; educators were needed to simplify historical knowledge within a pedagogical perspective. There is a need for historical sources, like Harvard Case Histories in Experimental Science, since appropriate historical information to the curriculum objectives can only be obtained by simplifying complex information at the origin. The curriculum should leave opportunities for educators interested in history of science, even historical sources provides legitimate amount of information for every concepts in the curriculum.

Mutational analysis of the MS2 lysis protein L

PubMed Central

Chamakura, Karthik R.; Edwards, Garrett B.

2017-01-01

Small single-stranded nucleic acid phages effect lysis by expressing a single protein, the amurin, lacking muralytic enzymatic activity. Three amurins have been shown to act like ‘protein antibiotics’ by inhibiting cell-wall biosynthesis. However, the L lysis protein of the canonical ssRNA phage MS2, a 75 aa polypeptide, causes lysis by an unknown mechanism without affecting net peptidoglycan synthesis. To identify residues important for lytic function, randomly mutagenized alleles of L were generated, cloned into an inducible plasmid and the transformants were selected on agar containing the inducer. From a total of 396 clones, 67 were unique single base-pair changes that rendered L non-functional, of which 44 were missense mutants and 23 were nonsense mutants. Most of the non-functional missense alleles that accumulated in levels comparable to the wild-type allele are localized in the C-terminal half of L, clustered in and around an LS dipeptide sequence. The LS motif was used to align L genes from ssRNA phages lacking any sequence similarity to MS2 or to each other. This alignment revealed a conserved domain structure, in terms of charge, hydrophobic character and predicted helical content. None of the missense mutants affected membrane-association of L. Several of the L mutations in the central domains were highly conservative and recessive, suggesting a defect in a heterotypic protein–protein interaction, rather than in direct disruption of the bilayer structure, as had been previously proposed for L. PMID:28691656

Reexamination of the immature hominid maxilla from Tangier, Morocco.

PubMed

Minugh-Purvis, N

1993-12-01

Reexamination of the immature Upper Pleistocene hominid maxilla from Mugharet el-'Aliya (Tangier), Morocco is undertaken in light of new evidence on the growth and development of Upper Pleistocene hominids. Metric and qualitative comparisons were made with 17 immature Upper Pleistocene maxillae, and with a recent Homo sapiens sapiens sample. No unambiguous criteria for aligning the maxilla with Neandertals were found, although one character, the degree of maxillary flexion on the zygoma, strongly suggests that this child could be a representative of H.s. sapiens. The probable lack of a canine fossa in Mugharet el-'Aliya 1, the primary criterion used previously to align it with Neandertals, cannot be accurately extrapolated to its adult form from this juvenile. The present evidence suggests that it is inappropriate to refer to this fossil as "Neandertal-like" or as a North African "neandertaloid." Thus, the Tangier maxilla should not be cited as evidence for the presence of Neandertal facial features in North Africa during the Upper Pleistocene.

Teflon/SiO2 Bilayer Passivation for Improving the Electrical Reliability of Oxide TFTs Fabricated Using a New Two-Photomask Self-Alignment Process

PubMed Central

Fan, Ching-Lin; Shang, Ming-Chi; Li, Bo-Jyun; Lin, Yu-Zuo; Wang, Shea-Jue; Lee, Win-Der; Hung, Bohr-Ran

2015-01-01

This study proposes a two-photomask process for fabricating amorphous indium–gallium–zinc oxide (a-IGZO) thin-film transistors (TFTs) that exhibit a self-aligned structure. The fabricated TFTs, which lack etching-stop (ES) layers, have undamaged a-IGZO active layers that facilitate superior performance. In addition, we demonstrate a bilayer passivation method that uses a polytetrafluoroethylene (Teflon) and SiO2 combination layer for improving the electrical reliability of the fabricated TFTs. Teflon was deposited as a buffer layer through thermal evaporation. The Teflon layer exhibited favorable compatibility with the underlying IGZO channel layer and effectively protected the a-IGZO TFTs from plasma damage during SiO2 deposition, resulting in a negligible initial performance drop in the a-IGZO TFTs. Compared with passivation-free a-IGZO TFTs, passivated TFTs exhibited superior stability even after 168 h of aging under ambient air at 95% relative humidity. PMID:28788026

Effect of growth pressure on the synthesis of vertically aligned carbon nanotubes and their growth termination.

PubMed

Park, Sangeun; Song, Wooseok; Kim, Yooseok; Song, Inkyung; Kim, Sung Hwan; Lee, Su Il; Jang, Sung Won; Parkl, Chong-Yun

2014-07-01

When vertically aligned carbon nanotubes (VACNTs) are synthesized by thermal chemical vapor deposition (TCVD), their structural features such as height and density can be determined by TCVD growth conditions. In this study we investigated the effect of growth pressure on the structural features of VACNTs. Changes in growth pressure significantly affected the height, density, and crystalinity of synthesized VACNTs. In addition, we suggest that the growth termination of VACNTs could be due to the lack of carbon feedstock supply to the center of the VACNT film induced by the pressure-dependent adsorption of amorphous carbon at the edge of the VACNT film. In addition, the field emission characteristics of the VACNT film were carried out. The turn-on voltage of the VACNT film was 1.62 V/microm and the field enhancement factor (beta) was 2478. These results provide useful information for practical applications of VACNTs, such as field emission display and X-ray source.

Medical and Transmission Vector Vocabulary Alignment with Schema.org

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

Smith, William P.; Chappell, Alan R.; Corley, Courtney D.

Available biomedical ontologies and knowledge bases currently lack formal and standards-based interconnections between disease, disease vector, and drug treatment vocabularies. The PNNL Medical Linked Dataset (PNNL-MLD) addresses this gap. This paper describes the PNNL-MLD, which provides a unified vocabulary and dataset of drug, disease, side effect, and vector transmission background information. Currently, the PNNL-MLD combines and curates data from the following research projects: DrugBank, DailyMed, Diseasome, DisGeNet, Wikipedia Infobox, Sider, and PharmGKB. The main outcomes of this effort are a dataset aligned to Schema.org, including a parsing framework, and extensible hooks ready for integration with selected medical ontologies. The PNNL-MLDmore » enables researchers more quickly and easily to query distinct datasets. Future extensions to the PNNL-MLD will include Traditional Chinese Medicine, broader interlinks across genetic structures, a larger thesaurus of synonyms and hypernyms, explicit coding of diseases and drugs across research systems, and incorporating vector-borne transmission vocabularies.« less

Correlation of molecular expression with diel rhythm of oviposition in Calliphora vicina (Robineau-Desvoidy) (Diptera: Calliphoridae) and implications for forensic entomology.

PubMed

George, Kelly A; Archer, Melanie S; Toop, Tes

2015-01-01

This study explored the molecular mechanisms potentially underlying blow fly nocturnal oviposition. A behavioral study revealed that Calliphora vicina (Robineau-Desvoidy) (Diptera: Calliphoridae) possesses a diel rhythm of oviposition in light under 12:12 light/dark conditions. Reversal to 12:12 dark/light resulted in oviposition behavior changing to align with the adjusted regime in most females, but four of 59 experimental females lacked a diel rhythm of oviposition (were arrhythmic). Real-time PCR was used to monitor the molecular expression levels of known circadian genes per and tim in C. vicina to determine whether gene expression and behavior correlated. As with behavior, reversing light/dark conditions changed rhythmic gene expression to align with an adjusted light regime. This suggests that although it is unlikely that C. vicina will colonize dead bodies at night, arrhythmic females and oviposition in the dark was demonstrated. © 2014 American Academy of Forensic Sciences.

Talking about sex in the gender identity clinic: implications for training and practice.

PubMed

Speer, Susan A

2013-11-01

This article provides the first systematic examination of the ways 'talk about sex' is occasioned and managed by doctors and patients in real-life interactions in a National Health Service Gender Identity Clinic. Drawing on a corpus of 194 recordings of psychiatric assessment sessions, the article examines how parties initiate and develop talk about sex, and which strategies appear to work best for doctor-patient alignment. The analyses revealed that the most aligning methods were for clinicians to make transitions from asking questions about relationships in general to talk about sex, or to build opportunistically on patients' relationship talk. However, talk about sex that lacked specificity or which made inaccurate presumptions about patients' sex lives, generated misalignment between clinician and patient. I suggest that such misalignment is not intrinsically bad. Rather, it provides evidence for the virtues of a more nuanced understanding of patient-centred communication. The article concludes with a discussion of the importance of grounding communication skills training and clinical practice in recordings of actual consultations.

Factors Influencing Registered Nurses' Perceptions of Their Professional Identity: An Integrative Literature Review.

PubMed

Rasmussen, Philippa; Henderson, Ann; Andrew, Nicky; Conroy, Tiffany

2018-05-01

This review synthesizes contemporary research investigating the factors influencing RNs' perceptions of their professional identity. The method used was an integrative literature review. Factors influencing RNs' perceptions of their professional identity were synthesized into three categories: the self, the role, and the context. The self is the nurse who enacts the role in practice, and the context is the practice setting. Poor alignment of these categories leads to stress, tension, and uncertainty affecting work-force retention. Strong alignment leads to satisfaction with the nursing role, increased staff retention, and improved quality of care and patient outcomes. These three categories should be considered when planning nursing professional development activities. This integrative review identified a lack of research addressing how nurses' perceptions of their professional identity change over time. A deeper understanding of their perspective is needed to establish whether career longevity and continued professional development are influences. J Contin Educ Nurs. 2018;49(5):225-232. Copyright 2018, SLACK Incorporated.

Rotating states of self-propelling particles in two dimensions.

PubMed

Chen, Hsuan-Yi; Leung, Kwan-Tai

2006-05-01

We present particle-based simulations and a continuum theory for steady rotating flocks formed by self-propelling particles (SPPs) in two-dimensional space. Our models include realistic but simple rules for the self-propelling, drag, and interparticle interactions. Among other coherent structures, in particle-based simulations we find steady rotating flocks when the velocity of the particles lacks long-range alignment. Physical characteristics of the rotating flock are measured and discussed. We construct a phenomenological continuum model and seek steady-state solutions for a rotating flock. We show that the velocity and density profiles become simple in two limits. In the limit of weak alignment, we find that all particles move with the same speed and the density of particles vanishes near the center of the flock due to the divergence of centripetal force. In the limit of strong body force, the density of particles within the flock is uniform and the velocity of the particles close to the center of the flock becomes small.

European health policy challenges.

PubMed

Maynard, Alan

2005-09-01

Few countries are immune to the international health care 'virus' of reform, with many countries regularly re-cycling changes that shift costs and benefits in ways that are arbitrary, inefficient and offer short term political palliation. Much of this activity has little evidence base and reveals lack of clarity in defining public policy goals, establishing trade-offs and aligning incentive structures with these objectives. Well established failures in health care delivery systems such as variations in medical practice and continuing absence of systematic outcome measurement, have persisted for decades as nations grapple inefficiently with recurring problems of expenditure inflation and waiting times. The lack of emphasis on evidence to inform the efficient management of chronic disease and the reduction of health inequalities is a product of perverse incentives and managerial inertia that maintains the incomes of powerful interest groups. Copyright (c) 2005 John Wiley & Sons, Ltd.

University teachers' perspectives on the role of the Laplace transform in engineering education

NASA Astrophysics Data System (ADS)

Holmberg née González Sampayo, Margarita; Bernhard, Jonte

2017-07-01

The Laplace transform is an important tool in many branches of engineering, for example, electric and control engineering, but is also regarded as a difficult topic for students to master. We have interviewed 22 university teachers from five universities in three countries (Mexico, Spain and Sweden) about their views on relationships among mathematics, physics and technology/application aspects in the process of learning the Laplace transform in engineering education. Strikingly, the teachers held a spectrum of qualitatively differing views, ranging from seeing virtually no connection (e.g. some thought the Laplace transform has no relevance in engineering), through to regarding the aspects as intimately, almost inseparably linked. The lack of awareness of the widely differing views among teachers might lead to a lack of constructive alignment among different courses that is detrimental to the quality of engineering education.

When staff is underpaid: dealing with the individual coping strategies of health personnel.

PubMed Central

Van Lerberghe, Wim; Conceicao, Claudia; Van Damme, Wim; Ferrinho, Paulo

2002-01-01

Health sector workers respond to inadequate salaries and working conditions by developing various individual "coping strategies"--some, but not all, of which are of a predatory nature. The paper reviews what is known about these practices and their potential consequences (competition for time, brain drain and conflicts of interest). By and large, governments have rarely been proactive in dealing with such problems, mainly because of their reluctance to address the issue openly. The effectiveness of many of these piecemeal reactions, particularly attempts to prohibit personnel from developing individual coping strategies, has been disappointing. The paper argues that a more proactive approach is required. Governments will need to recognize the dimension of the phenomenon and systematically assess the consequences of policy initiatives on the situation and behaviour of the individuals that make up their workforce. PMID:12163923

Articular nodular fasciitis of the right shoulder joint: report of an unusual case with focus on immunohistochemical differential diagnosis.

PubMed

Tajima, Shogo; Zuki, Tomoyukisu; Koda, Kenji

2015-01-01

The mesenchymal lesion nodular fasciitis (NF) can affect various sites of the body but usually arises in subcutaneous tissue or occasionally skeletal muscle. NF is not commonly known to arise in joints, and articular NF is extremely rare. Herein, we present a case of a 54-year-old woman with articular NF. No sign of recurrence was observed after surgical piecemeal removal with a suspected positive surgical margin. In our case, a differential diagnosis of NF, desmoid-type fibromatosis, and low-grade myofibroblastic sarcoma was considered. Stromal hyalinization, a characteristic of articular NF, made the diagnosis somewhat difficult, although typical NF morphology was present. Immunohistochemical analysis of α-smooth muscle actin, desmin, β-catenin, and protein gene product 9.5 expression along with close morphological examination provided a reliable distinction.

Remembering preservation in hippocampal amnesia

PubMed Central

Clark, Ian A.; Maguire, Eleanor A.

2017-01-01

The lesion-deficit model dominates neuropsychology. This is unsurprising given powerful demonstrations that focal brain lesions can affect specific aspects of cognition. Nowhere is this more evident than in patients with bilateral hippocampal damage. In the last sixty years the amnesia and other impairments exhibited by these patients have helped to delineate the functions of the hippocampus and shape the field of memory. We do not question the value of this approach. However, less prominent are the cognitive processes that remain intact following hippocampal lesions. Here, we collate the piecemeal reports of preservation of function following focal bilateral hippocampal damage, highlighting a wealth of information often veiled by the field’s focus on deficits. We consider how a systematic understanding of what is preserved as well as what is lost could add an important layer of precision to models of memory and the hippocampus. PMID:26361051

A world unglued: simultanagnosia as a spatial restriction of attention

PubMed Central

Dalrymple, Kirsten A.; Barton, Jason J. S.; Kingstone, Alan

2013-01-01

Simultanagnosia is a disorder of visual attention that leaves a patient's world unglued: scenes and objects are perceived in a piecemeal manner. It is generally agreed that simultanagnosia is related to an impairment of attention, but it is unclear whether this impairment is object- or space-based in nature. We first consider the findings that support a concept of simultanagnosia as deficit of object-based attention. We then examine the evidence suggesting that simultanagnosia results from damage to a space-based attentional system, and in particular a model of simultanagnosia as a narrowed spatial window of attention. We ask whether seemingly object-based deficits can be explained by space-based mechanisms, and consider the evidence that object processing influences spatial deficits in this condition. Finally, we discuss limitations of a space-based attentional explanation. PMID:23616758

Myths and realities: Defining re-engineering for a large organization

NASA Technical Reports Server (NTRS)

Yin, Sandra; Mccreary, Julia

1992-01-01

This paper describes the background and results of three studies concerning software reverse engineering, re-engineering, and reuse (R3) hosted by the Internal Revenue Service in 1991 and 1992. The situation at the Internal Revenue--aging, piecemeal computer systems and outdated technology maintained by a large staff--is familiar to many institutions, especially among management information systems. The IRS is distinctive for the sheer magnitude and diversity of its problems; the country's tax records are processed using assembly language and COBOL and spread across tape and network DBMS files. How do we proceed with replacing legacy systems? The three software re-engineering studies looked at methods, CASE tool support, and performed a prototype project using re-engineering methods and tools. During the course of these projects, we discovered critical issues broader than the mechanical definitions of methods and tool technology.

Lunar and terrestrial crust formation

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

Walker, D.

1983-11-15

Planetary crusts may be accreted, produced in primordial differentiation, or built up piecemeal by serial magmatism. The existence of old, polygenetic, laterally heterogeneous, partial melt rocks in the lunar highlands suggests that the moon produced its early crust by serial magmatism. This view can be reconciled with lunar Eu anomalies, previously thought to support the magma ocean model of crust formation, if complications in the fractionation of mare basalts are reconized. Phase equilibrium and magmatic density information for mare basalts suggest a model in which plagioclase fractionation can occur even though plagioclase is not a near-liquidus phase. The crytic fractionationmore » of clinopryoxene in MORB provides a precedent for this model. The necessity for a lunar magma ocean is questioned, but a role for a terrestrial magma ocean of sorts at depth is suggested.« less

The Health Care System Under French National Health Insurance: Lessons for Health Reform in the United States

PubMed Central

Rodwin, Victor G.

2003-01-01

The French health system combines universal coverage with a public–private mix of hospital and ambulatory care and a higher volume of service provision than in the United States. Although the system is far from perfect, its indicators of health status and consumer satisfaction are high; its expenditures, as a share of gross domestic product, are far lower than in the United States; and patients have an extraordinary degree of choice among providers. Lessons for the United States include the importance of government’s role in providing a statutory framework for universal health insurance; recognition that piecemeal reform can broaden a partial program (like Medicare) to cover, eventually, the entire population; and understanding that universal coverage can be achieved without excluding private insurers from the supplementary insurance market. PMID:12511380

The case against one-shot testing for initial dental licensure.

PubMed

Chambers, David W; Dugoni, Arthur A; Paisley, Ian

2004-03-01

High-stakes testing are expected to meet standards for cost-effectiveness, fairness, transparency, high reliability, and high validity. It is questionable whether initial licensure examinations in dentistry meet such standards. Decades of piecemeal adjustments in the system have resulted in limited improvement. The essential flaw in the system is reliance on a one-shot sample of a small segment of the skills, understanding, and supporting values needed for today's professional practice of dentistry. The "snapshot" approach to testing produces inherently substandard levels of reliability and validity. A three-step alternative is proposed: boards should (1) define the competencies required of beginning practitioners, (2) establish the psychometric standards needed to make defensible judgments about candidates, and (3) base licensure decisions only on portfolios of evidence that test for defined competencies at established levels of quality.

Angle and Base of Gait Long Leg Axial and Intraoperative Simulated Weightbearing Long Leg Axial Imaging to Capture True Frontal Plane Tibia to Calcaneus Alignment in Valgus and Varus Deformities of the Rearfoot and Ankle.

PubMed

Boffeli, Troy J; Waverly, Brett J

2016-01-01

The long leg axial view is primarily used to evaluate the frontal plane alignment of the calcaneus in relation to the long axis of the tibia when standing. This view allows both angular measurement and assessment for the apex of varus and valgus deformity of the rearfoot and ankle with clinical utility in the preoperative, intraoperative, and postoperative settings. The frontal plane alignment of the calcaneus to the long axis of the tibia is rarely fixed in the varus or valgus position because of the inherent flexibility of the foot and ankle, which makes patient positioning critical to obtain accurate and reproducible images. Inconsistent patient positioning and imaging techniques are commonly encountered with the long leg axial view for a variety of reasons, including the lack of a standardized or validated protocol. This angle and base of gait imaging protocol involves positioning the patient to align the tibia with the long axis of the foot, which is represented by the second metatarsal. Non-weightbearing long leg axial imaging is commonly performed intraoperatively, which requires a modified patient positioning technique to capture simulated weightbearing long leg axial images. A case series is presented to demonstrate our angle and base of gait long leg axial and intraoperative simulated weightbearing long leg axial imaging protocols that can be applied throughout all phases of patient care for various foot and ankle conditions. Copyright © 2015 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Mediated Electron Transfer at Vertically Aligned Single-Walled Carbon Nanotube Electrodes During Detection of DNA Hybridization.

PubMed

Wallen, Rachel; Gokarn, Nirmal; Bercea, Priscila; Grzincic, Elissa; Bandyopadhyay, Krisanu

2015-12-01

Vertically aligned single-walled carbon nanotube (VASWCNT) assemblies are generated on cysteamine and 2-mercaptoethanol (2-ME)-functionalized gold surfaces through amide bond formation between carboxylic groups generated at the end of acid-shortened single-walled carbon nanotubes (SWCNTs) and amine groups present on the gold surfaces. Atomic force microscopy (AFM) imaging confirms the vertical alignment mode of SWCNT attachment through significant changes in surface roughness compared to bare gold surfaces and the lack of any horizontally aligned SWCNTs present. These SWCNT assemblies are further modified with an amine-terminated single-stranded probe-DNA. Subsequent hybridization of the surface-bound probe-DNA in the presence of complementary strands in solution is followed using impedance measurements in the presence of Fe(CN)6 (3-/4-) as the redox probe in solution, which show changes in the interfacial electrochemical properties, specifically the charge-transfer resistance, due to hybridization. In addition, hybridization of the probe-DNA is also compared when it is attached directly to the gold surfaces without any intermediary SWCNTs. Contrary to our expectations, impedance measurements show a decrease in charge-transfer resistance with time due to hybridization with 300 nM complementary DNA in solution with the probe-DNA attached to SWCNTs. In contrast, an increase in charge-transfer resistance is observed with time during hybridization when the probe-DNA is attached directly to the gold surfaces. The decrease in charge-transfer resistance during hybridization in the presence of VASWCNTs indicates an enhancement in the electron transfer process of the redox probe at the VASWCNT-modified electrode. The results suggest that VASWCNTs are acting as mediators of electron transfer, which facilitate the charge transfer of the redox probe at the electrode-solution interface.

Mediated Electron Transfer at Vertically Aligned Single-Walled Carbon Nanotube Electrodes During Detection of DNA Hybridization

NASA Astrophysics Data System (ADS)

Wallen, Rachel; Gokarn, Nirmal; Bercea, Priscila; Grzincic, Elissa; Bandyopadhyay, Krisanu

2015-06-01

Vertically aligned single-walled carbon nanotube (VASWCNT) assemblies are generated on cysteamine and 2-mercaptoethanol (2-ME)-functionalized gold surfaces through amide bond formation between carboxylic groups generated at the end of acid-shortened single-walled carbon nanotubes (SWCNTs) and amine groups present on the gold surfaces. Atomic force microscopy (AFM) imaging confirms the vertical alignment mode of SWCNT attachment through significant changes in surface roughness compared to bare gold surfaces and the lack of any horizontally aligned SWCNTs present. These SWCNT assemblies are further modified with an amine-terminated single-stranded probe-DNA. Subsequent hybridization of the surface-bound probe-DNA in the presence of complementary strands in solution is followed using impedance measurements in the presence of Fe(CN)6 3-/4- as the redox probe in solution, which show changes in the interfacial electrochemical properties, specifically the charge-transfer resistance, due to hybridization. In addition, hybridization of the probe-DNA is also compared when it is attached directly to the gold surfaces without any intermediary SWCNTs. Contrary to our expectations, impedance measurements show a decrease in charge-transfer resistance with time due to hybridization with 300 nM complementary DNA in solution with the probe-DNA attached to SWCNTs. In contrast, an increase in charge-transfer resistance is observed with time during hybridization when the probe-DNA is attached directly to the gold surfaces. The decrease in charge-transfer resistance during hybridization in the presence of VASWCNTs indicates an enhancement in the electron transfer process of the redox probe at the VASWCNT-modified electrode. The results suggest that VASWCNTs are acting as mediators of electron transfer, which facilitate the charge transfer of the redox probe at the electrode-solution interface.

Multivariate curve resolution based chromatographic peak alignment combined with parallel factor analysis to exploit second-order advantage in complex chromatographic measurements.

PubMed

Parastar, Hadi; Akvan, Nadia

2014-03-13

In the present contribution, a new combination of multivariate curve resolution-correlation optimized warping (MCR-COW) with trilinear parallel factor analysis (PARAFAC) is developed to exploit second-order advantage in complex chromatographic measurements. In MCR-COW, the complexity of the chromatographic data is reduced by arranging the data in a column-wise augmented matrix, analyzing using MCR bilinear model and aligning the resolved elution profiles using COW in a component-wise manner. The aligned chromatographic data is then decomposed using trilinear model of PARAFAC in order to exploit pure chromatographic and spectroscopic information. The performance of this strategy is evaluated using simulated and real high-performance liquid chromatography-diode array detection (HPLC-DAD) datasets. The obtained results showed that the MCR-COW can efficiently correct elution time shifts of target compounds that are completely overlapped by coeluted interferences in complex chromatographic data. In addition, the PARAFAC analysis of aligned chromatographic data has the advantage of unique decomposition of overlapped chromatographic peaks to identify and quantify the target compounds in the presence of interferences. Finally, to confirm the reliability of the proposed strategy, the performance of the MCR-COW-PARAFAC is compared with the frequently used methods of PARAFAC, COW-PARAFAC, multivariate curve resolution-alternating least squares (MCR-ALS), and MCR-COW-MCR. In general, in most of the cases the MCR-COW-PARAFAC showed an improvement in terms of lack of fit (LOF), relative error (RE) and spectral correlation coefficients in comparison to the PARAFAC, COW-PARAFAC, MCR-ALS and MCR-COW-MCR results. Copyright © 2014 Elsevier B.V. All rights reserved.

Ahp2 (Hop2) function in Arabidopsis thaliana (Ler) is required for stabilization of close alignment and synaptonemal complex formation except for the two short arms that contain nucleolus organizer regions.

PubMed

Stronghill, P; Pathan, N; Ha, H; Supijono, E; Hasenkampf, C

2010-08-01

A cytological comparative analysis of male meiocytes was performed for Arabidopsis wild type and the ahp2 (hop2) mutant with emphasis on ahp2's largely uncharacterized prophase I. Leptotene progression appeared normal in ahp2 meiocytes; chromosomes exhibited regular axis formation and assumed a typical polarized nuclear organization. In contrast, 4',6'-diamidino-2-phenylindole-stained ahp2 pachytene chromosome spreads demonstrated a severe reduction in stabilized pairing. However, transmission electron microscopy (TEM) analysis of sections from meiocytes revealed that ahp2 chromosome axes underwent significant amounts of close alignment (44% of total axis). This apparent paradox strongly suggests that the Ahp2 protein is involved in the stabilization of homologous chromosome close alignment. Fluorescent in situ hybridization in combination with Zyp1 immunostaining revealed that ahp2 mutants undergo homologous synapsis of the nucleolus-organizer-region-bearing short arms of chromosomes 2 and 4, despite the otherwise "nucleus-wide" lack of stabilized pairing. The duration of ahp2 zygotene was significantly prolonged and is most likely due to difficulties in chromosome alignment stabilization and subsequent synaptonemal complex formation. Ahp2 and Mnd1 proteins have previously been shown, "in vitro," to form a heterodimer. Here we show, "in situ," that the Ahp2 and Mnd1 proteins are synchronous in their appearance and disappearance from meiotic chromosomes. Both the Ahp2 and Mnd1 proteins localize along the chromosomal axis. However, localization of the Ahp2 protein was entirely foci-based whereas Mnd1 protein exhibited an immunostaining pattern with some foci along the axis and a diffuse staining for the rest of the chromosome.

Characterizing synaptic protein development in human visual cortex enables alignment of synaptic age with rat visual cortex

PubMed Central

Pinto, Joshua G. A.; Jones, David G.; Williams, C. Kate; Murphy, Kathryn M.

2015-01-01

Although many potential neuroplasticity based therapies have been developed in the lab, few have translated into established clinical treatments for human neurologic or neuropsychiatric diseases. Animal models, especially of the visual system, have shaped our understanding of neuroplasticity by characterizing the mechanisms that promote neural changes and defining timing of the sensitive period. The lack of knowledge about development of synaptic plasticity mechanisms in human cortex, and about alignment of synaptic age between animals and humans, has limited translation of neuroplasticity therapies. In this study, we quantified expression of a set of highly conserved pre- and post-synaptic proteins (Synapsin, Synaptophysin, PSD-95, Gephyrin) and found that synaptic development in human primary visual cortex (V1) continues into late childhood. Indeed, this is many years longer than suggested by neuroanatomical studies and points to a prolonged sensitive period for plasticity in human sensory cortex. In addition, during childhood we found waves of inter-individual variability that are different for the four proteins and include a stage during early development (<1 year) when only Gephyrin has high inter-individual variability. We also found that pre- and post-synaptic protein balances develop quickly, suggesting that maturation of certain synaptic functions happens within the 1 year or 2 of life. A multidimensional analysis (principle component analysis) showed that most of the variance was captured by the sum of the four synaptic proteins. We used that sum to compare development of human and rat visual cortex and identified a simple linear equation that provides robust alignment of synaptic age between humans and rats. Alignment of synaptic ages is important for age-appropriate targeting and effective translation of neuroplasticity therapies from the lab to the clinic. PMID:25729353

An appraisal of policies and institutional frameworks impacting on smallholder agricultural water management in Zimbabwe

NASA Astrophysics Data System (ADS)

Nyagumbo, I.; Rurinda, J.

Policies and institutional frameworks associated with and / or impacting on agricultural water management (AWM) in smallholder farming systems in Zimbabwe were analyzed through literature reviews, feedback from stakeholder workshops, key informant interviews and evaluation of policy impacts on implemented case study projects/programmes. The study showed that Zimbabwe has gone a long way towards developing a water management policy addressing both equity and access, through the Water and ZINWA of 1998. However, lack of incentives for improving efficient management and utilization of water resources once water has reached the farm gate was apparent, apart from punitive economic instruments levied on usage of increased volumes of water. For example, the new water reforms of 1998 penalized water savers through loss of any unused water in their permits to other users. In addition, the ability of smallholder farmers to access water for irrigation or other purposes was influenced by macro and micro-economic policies such as Economic Structural and Adjustment Programme (ESAP), Zimbabwe Programme for Economic and Social Transformation (ZIMPREST), prevailing monetary and fiscal policies, as well as the Land and Agrarian Reform policies. For instance, the implementation of ESAP from 1991 to 95 resulted in a decline in government support to management of communal irrigation schemes, and as a result only gravity-fed schemes survived. Also AWM projects/programmes that were in progress were prematurely terminated. While considerable emphasis was placed on rehabilitation of irrigation infrastructure since the fast track land reform in 1998, the policies remained rather silent on strategies for water management in rainfed systems. The piecemeal nature and fragmentation of policies and institutional frameworks scattered across government ministries and sectors were complex and created difficulties for smallholder farmers to access water resources. Poor policy implementation strategies and lack of funding were some of the major weaknesses in Zimbabwe’s AWM policies. It was apparent that the prevailing institutional frameworks that underwent restructuring exercises since 2000, failed to effectively deliver services to smallholder farmers due to lack of human and financial capital. Nevertheless, the study showed that policies that can improve efficient utilization of agricultural water in rainfed systems need to target timely provision of the prime movers, i.e. credit, input markets and viable output markets, among other factors, so as to fully utilize good rainfall seasons. It was recommended that a forum led by ZINWA be set up to harmonize AWM issues across sectors and monitor their implementation. Such a forum would be mandated mainly to run periodic water management workshops in which relevant and interested stakeholders participate. ZINWA stands for Zimbabwe National Water Authority.

Training in Compensatory Strategies Enhances Rapport in Interactions Involving People with Möbius Syndrome

PubMed Central

Michael, John; Bogart, Kathleen; Tylén, Kristian; Krueger, Joel; Bech, Morten; Østergaard, John Rosendahl; Fusaroli, Riccardo

2015-01-01

In the exploratory study reported here, we tested the efficacy of an intervention designed to train teenagers with Möbius syndrome (MS) to increase the use of alternative communication strategies (e.g., gestures) to compensate for their lack of facial expressivity. Specifically, we expected the intervention to increase the level of rapport experienced in social interactions by our participants. In addition, we aimed to identify the mechanisms responsible for any such increase in rapport. In the study, five teenagers with MS interacted with three naïve participants without MS before the intervention, and with three different naïve participants without MS after the intervention. Rapport was assessed by self-report and by behavioral coders who rated videos of the interactions. Individual non-verbal behavior was assessed via behavioral coders, whereas verbal behavior was automatically extracted from the sound files. Alignment was assessed using cross recurrence quantification analysis and mixed-effects models. The results showed that observer-coded rapport was greater after the intervention, whereas self-reported rapport did not change significantly. Observer-coded gesture and expressivity increased in participants with and without MS, whereas overall linguistic alignment decreased. Fidgeting and repetitiveness of verbal behavior also decreased in both groups. In sum, the intervention may impact non-verbal and verbal behavior in participants with and without MS, increasing rapport as well as overall gesturing, while decreasing alignment. PMID:26500605

Size-tunable band alignment and optoelectronic properties of transition metal dichalcogenide van der Waals heterostructures

NASA Astrophysics Data System (ADS)

Zhao, Yipeng; Yu, Wangbing; Ouyang, Gang

2018-01-01

2D transition metal dichalcogenide (TMDC)-based heterostructures exhibit several fascinating properties that can address the emerging market of energy conversion and storage devices. Current achievements show that the vertical stacked TMDC heterostructures can form type II band alignment and possess significant optoelectronic properties. However, a detailed analytical understanding of how to quantify the band alignment and band offset as well as the optimized power conversion efficiency (PCE) is still lacking. Herein, we propose an analytical model to exhibit the PCEs of TMDC van der Waals (vdW) heterostructures and explore the intrinsic mechanism of photovoltaic conversion based on the detailed balance principle and atomic-bond-relaxation correlation mechanism. We find that the PCE of monolayer MoS2/WSe2 can be up to 1.70%, and that of the MoS2/WSe2 vdW heterostructures increases with thickness, owing to increasing optical absorption. Moreover, the results are validated by comparing them with the available evidence, providing realistic efficiency targets and design principles. Highlights • Both electronic and optoelectronic models are developed for vertical stacked MoS2/WSe2 heterostructures. • The underlying mechanism on size effect of electronic and optoelectronic properties for vertical stacked MoS2/WSe2 heterostructures is clarified. • The macroscopically measurable quantities and the microscopical bond identities are connected.

Multiview echocardiography fusion using an electromagnetic tracking system.

PubMed

Punithakumar, Kumaradevan; Hareendranathan, Abhilash R; Paakkanen, Riitta; Khan, Nehan; Noga, Michelle; Boulanger, Pierre; Becher, Harald

2016-08-01

Three-dimensional ultrasound is an emerging modality for the assessment of complex cardiac anatomy and function. The advantages of this modality include lack of ionizing radiation, portability, low cost, and high temporal resolution. Major limitations include limited field-of-view, reliance on frequently limited acoustic windows, and poor signal to noise ratio. This study proposes a novel approach to combine multiple views into a single image using an electromagnetic tracking system in order to improve the field-of-view. The novel method has several advantages: 1) it does not rely on image information for alignment, and therefore, the method does not require image overlap; 2) the alignment accuracy of the proposed approach is not affected by any poor image quality as in the case of image registration based approaches; 3) in contrast to previous optical tracking based system, the proposed approach does not suffer from line-of-sight limitation; and 4) it does not require any initial calibration. In this pilot project, we were able to show that using a heart phantom, our method can fuse multiple echocardiographic images and improve the field-of view. Quantitative evaluations showed that the proposed method yielded a nearly optimal alignment of image data sets in three-dimensional space. The proposed method demonstrates the electromagnetic system can be used for the fusion of multiple echocardiography images with a seamless integration of sensors to the transducer.

Creating a meaningful infection control program: one home healthcare agency's lessons.

PubMed

Poff, Renee McCoy; Browning, Sarah Via

2014-03-01

Creating a meaningful infection control program in the home care setting proved to be challenging for agency leaders of one hospital-based home healthcare agency. Challenges arose when agency leaders provided infection control (IC) data to the hospital's IC Committee. The IC Section Chief asked for national benchmark comparisons to align home healthcare reporting to that of the hospital level. At that point, it was evident that the home healthcare IC program lacked definition and structure. The purpose of this article is to share how one agency built a meaningful IC program.

3D patterned substrates for bioartificial blood vessels - The effect of hydrogels on aligned cells on a biomaterial surface.

PubMed

Zhao, Xinxin; Irvine, Scott Alexander; Agrawal, Animesh; Cao, Ye; Lim, Pei Qi; Tan, Si Ying; Venkatraman, Subbu S

2015-10-01

The optimal bio-artificial blood vessel construct is one that has a compliant tubular core with circumferentially aligned smooth muscle cells (SMCs). Obtaining this well-aligned pattern of SMCs on a scaffold is highly beneficial as this cellular orientation preserves the SMC contractile phenotype. We used 3D patterning to create channels on a polycaprolactone (PCL) scaffold; SMCs were then found to be aligned within the microchannels. To preserve this alignment, and to provide a protective coating that could further incorporate cells, we evaluated the use of two hydrogels, one based on poly(ethylene glycol) diacrylate (PEGDA) and the other based on gelatin. Hydrogels were either physically coated on the PCL surfaces or covalently linked via suitable surface modification of PCL. For covalent immobilization of PEGDA hydrogel, alkene groups were introduced on PCL, while for gelatin covalent linkage, serum proteins were introduced. It is, however, crucial that the hydrogel coating does not disrupt the cellular patterning and distribution. We show in this work that both the process of coating as well as the nature of the coating are critical to preservation of the aligned SMCs. The covalent coating methods involving the crosslinking of hydrogels with the surface of PCL films promoted hydrogel retention time on the film as compared with physical deposition. Furthermore, subsequent hydrogel degradation is affected by the components of the cell culture medium, hinting at a possible route to in vivo biodegradation. Surface features control cellular orientation and subsequently influence their functionality, a useful effect for cellularized biomedical devices. Such devices also can benefit from protective and cell friendly hydrogel coatings. However, literature is lacking on the fate of cells that have endured hydrogel coating whilst orientated on a biomaterial surface. In particular, elucidation of the cells ability to remain adherent and orientated post hydrogel addition. Coating requires two procedures that may be deleterious to the orientated cells: the surface pretreatment for gel binding and the hydrogel crosslinking reaction. We compare transglutaminase gelatin crosslinking and UV initiated PEGDA crosslinking, coated onto smooth muscle cells orientated on patterned PCL surfaces. This original study will be of considerable use to the wider biomaterials community. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Strain activation of bovine aortic smooth muscle cell proliferation and alignment: study of strain dependency and the role of protein kinase A and C signaling pathways

NASA Technical Reports Server (NTRS)

Mills, I.; Cohen, C. R.; Kamal, K.; Li, G.; Shin, T.; Du, W.; Sumpio, B. E.

1997-01-01

Smooth muscle cell (SMC) phenotype can be altered by physical forces as demonstrated by cyclic strain-induced changes in proliferation, orientation, and secretion of macromolecules. However, the magnitude of strain required and the intracellular coupling pathways remain ill defined. To examine the strain requirements for SMC proliferation, we selectively seeded bovine aortic SMC either on the center or periphery of silastic membranes which were deformed with 150 mm Hg vacuum (0-7% center; 7-24% periphery). SMC located in either the center or peripheral regions showed enhanced proliferation compared to cells grown under the absence of cyclic strain. Moreover, SMC located in the center region demonstrated significantly (P < 0.005) greater proliferation as compared to those in the periphery. In contrast, SMC exposed to high strain (7-24%) demonstrated alignment perpendicular to the strain gradient, whereas SMC in the center (0-7%) remained aligned randomly. To determine the mechanisms of these phenomena, we examined the effect of cyclic strain on bovine aortic SMC signaling pathways. We observed strain-induced stimulation of the cyclic AMP pathway including adenylate cyclase activity and cyclic AMP accumulation. In addition, exposure of SMC to cyclic strain caused a significant increase in protein kinase C (PKC) activity and enzyme translocation from the cytosol to a particulate fraction. Further study was conducted to examine the effect of strain magnitude on signaling, particularly protein kinase A (PKA) activity as well as cAMP response element (CRE) binding protein levels. We observed significantly (P < 0.05) greater PKA activity and CRE binding protein levels in SMC located in the center as compared to the peripheral region. However, inhibition of PKA (with 10 microM Rp-cAMP) or PKC (with 5-20 ng/ml staurosporine) failed to alter either the strain-induced increase in SMC proliferation or alignment. These data characterize the strain determinants for activation of SMC proliferation and alignment. Although strain activated both the AC/cAMP/PKA and the PKC pathways in SMC, singular inhibition of PKA and PKC failed to prevent strain-induced alignment and proliferation, suggesting either their lack of involvement or the multifactorial nature of these responses.

Determinants of change in Medicaid pharmaceutical cost sharing: does evidence affect policy?

PubMed

Soumerai, S B; Ross-Degnan, D; Fortess, E E; Walser, B L

1997-01-01

Since 1980, many Medicaid programs have instituted, adjusted, or abolished pharmaceutical copayments or limitations on the number of prescriptions per patient (caps). Studies indicate that prescription caps can harm patients and increase Medicaid costs. However, because there is little information on how state policy makers select and evaluate such policies, in-depth telephone interviews were conducted with key informants in Medicaid programs that had recently made changes in cost-sharing policies. Among the barriers to evidence-based policy making were lack of political power, skills, and infrastructure; crisis-oriented decisions; compartmentalized budgeting; lack of advocates for disadvantaged patients; and the absence of timely research. Research was applied successfully when the interests of patient advocates and the drug industry were aligned and when Medicaid analysis were able to identify and communicate relevant research to policy makers at the time, or "teachable moment," that policy was being changed.

Medical education in India: current challenges and the way forward.

PubMed

Solanki, Anjali; Kashyap, Surender

2014-12-01

Medical education in India is suffering from various shortcomings at conceptual as well as implementation level. With the expansion in medical education, the doctor to patient ratio has increased but these numbers do not align well with the overall quality of medical care in the country. To address this issue, a comprehensive analysis of various associated factors is essential. Indian medical education is suffering from a maldistribution of resources, unregulated growth in the private sector, lack of uniform admission procedures and traditional curricula lacking innovative approaches. To achieve higher standards of medical education, our goal should be to re-evaluate each and every aspect; create an efficient accreditation system; promote an equal distribution of resources, redesign curricula with stricter implementation and improved assessment methodologies; all of which will generate efficient medical graduates and consequently better health care delivery, and resulting in desired change within the system.

The Value of History, Physical Examination, and Radiographic Findings in the Diagnosis of Symptomatic Meniscal Tear among Middle-Age Subjects with Knee Pain

PubMed Central

Katz, Jeffrey N.; Smith, Savannah R.; Yang, Heidi Y.; Martin, Scott D.; Wright, John; Donnell-Fink, Laurel A.; Losina, Elena

2016-01-01

Objective To evaluate the utility of clinical history, radiographic and physical exam findings in the diagnosis of symptomatic meniscal tear (SMT) in patients over age 45, in whom concomitant osteoarthritis is prevalent. Methods In a cross-sectional study of patients from two orthopedic surgeons’ clinics we assessed clinical history, physical examination and radiographic findings in patients over 45 with knee pain. The orthopedic surgeons rated their confidence that subjects’ symptoms were due to MT; we defined the diagnosis of SMT as at least 70% confidence. We used logistic regression to identify factors independently associated with diagnosis of SMT and we used the regression results to construct an index of the likelihood of SMT. Results In 174 participants, six findings were associated independently with the expert clinician having ≥70% confidence that symptoms were due to MT: localized pain, ability to fully bend the knee, pain duration <1 year, lack of varus alignment, lack of pes planus, and absence of joint space narrowing on radiographs. The index identified a low risk group with 3% likelihood of SMT. Conclusion While clinicians traditionally rely upon mechanical symptoms in this diagnostic setting, our findings did not support the conclusion that mechanical symptoms were associated with the expert’s confidence that symptoms were due to MT. An index that includes history of localized pain, full flexion, duration <1 year, pes planus, varus alignment, and joint space narrowing can be used to stratify patients according to their risk of SMT and it identifies a subgroup with very low risk. PMID:27390312

A Phenomenological Examination of Perceived Skills and Concepts Necessary for Teaching Scientific Thinking

NASA Astrophysics Data System (ADS)

Kapetanis, Ana Cristina

The use of high stakes testing to improve educational outcomes falls short in many settings. Proposals for improvement include providing more opportunities for students to extend their thinking, gaining experience in the social nature of science, and learning how to interpret, explain, and justify results. This phenomenological qualitative project study took place in a small independent school in the southeastern United States that lacked a cohesive elementary science program and was looking to create a vertically aligned science curriculum based on constructivism. The research question asked what skills and concepts teachers believed should be included in an elementary science program in order for students to learn scientific inquiry to be better prepared for middle and upper school science subjects. Using focus groups, observations, and interviews of a small sample of 4 teachers, data were collected, transcribed, and categorized through open coding. Inductive analysis was employed to look for patterns and emerging themes that painted a picture of how teachers viewed the current science program and what attributes they felt were important in the creation of a new curriculum. The findings revealed that teachers felt there was lack of a vertically aligned science curriculum, availability of resources throughout the school, and consistent support to provide an effective science program. The recommendations called for developing an elementary science program that includes all strands proposed by the National Science Education Standards and would provide students with opportunities to engage in scientific inquiry, conduct detailed observations, and learn to support conclusions using data. The implications for positive social change include development of programs that result in integrated science learning.

Weathering the empire: meteorological research in the early British Straits Settlements.

PubMed

Williamson, Fiona

2015-09-01

This article explores meteorological interest and experimentation in the early history of the Straits Settlements. It centres on the establishment of an observatory in 1840s Singapore and examines the channels that linked the observatory to a global community of scientists, colonial officers and a reading public. It will argue that, although the value of overseas meteorological investigation was recognized by the British government, investment was piecemeal and progress in the field often relied on the commitment and enthusiasm of individuals. In the Straits Settlements, as elsewhere, these individuals were drawn from military or medical backgrounds, rather than trained as dedicated scientists. Despite this, meteorology was increasingly recognized as of fundamental importance to imperial interests. Thus this article connects meteorology with the history of science and empire more fully and examines how research undertaken in British dependencies is revealing of the operation of transnational networks in the exchange of scientific knowledge.

Autoimmune hepatitis in a teenage boy: 'overlap' or 'outlier' syndrome--dilemma for internists.

PubMed

Talukdar, Arunansu; Khanra, Dibbendhu; Mukherjee, Kabita; Saha, Manjari

2013-02-08

An 18-year-old boy presented with upper gastrointestinal bleeding and jaundice. Investigations revealed coarse hepatomegaly, splenomegaly and advanced oesophageal varices. Blood reports showed marked rise of alkaline phosphatase and more than twofold rise of transaminases and IgG. Liver histology was suggestive of piecemeal necrosis, interphase hepatitis and bile duct proliferation. Antinuclear antibody was positive in high titre along with positive antismooth muscle antibody and antimitochondrial antibody. The patient was positive for human leukocyte antigen DR3 type. Although an 'overlap' syndrome exists between autoimmune hepatitis (AIH) and primary biliary cirrhosis (PBC), a cholestatic variant of AIH, a rare 'outlier' syndrome could not be excluded in our case. Moreover, 'the chicken or the egg', AIH or PBC, the dilemma for the internists continued. The patient was put on steroid and ursodeoxycholic acid with unsatisfactory response. The existing international criteria for diagnosis of AIH are not generous enough to accommodate its variant forms.

An Interpolation Method for Obtaining Thermodynamic Properties Near Saturated Liquid and Saturated Vapor Lines

NASA Technical Reports Server (NTRS)

Nguyen, Huy H.; Martin, Michael A.

2004-01-01

The two most common approaches used to formulate thermodynamic properties of pure substances are fundamental (or characteristic) equations of state (Helmholtz and Gibbs functions) and a piecemeal approach that is described in Adebiyi and Russell (1992). This paper neither presents a different method to formulate thermodynamic properties of pure substances nor validates the aforementioned approaches. Rather its purpose is to present a method to generate property tables from existing property packages and a method to facilitate the accurate interpretation of fluid thermodynamic property data from those tables. There are two parts to this paper. The first part of the paper shows how efficient and usable property tables were generated, with the minimum number of data points, using an aerospace industry standard property package. The second part describes an innovative interpolation technique that has been developed to properly obtain thermodynamic properties near the saturated liquid and saturated vapor lines.

Integrating Multiple Approaches to Solving Solar Wind Turbulence Problems (Invited)

NASA Astrophysics Data System (ADS)

Karimabadi, H.; Roytershteyn, V.

2013-12-01

The ultimate understanding of the solar wind turbulence must explain the physical process and their connection at all scales ranging from the largest down to electron kinetic scales. This is a daunting task and as a result a more piecemeal approach to the problem has been followed. For example, the role of each wave has been explored in isolation and in simulations with scales limited to those of the underlying waves. In this talk, we present several issues with this approach and offer an alternative with an eye towards more realistic simulations of solar wind turbulence. The main simulation techniques used have been MHD, Hall MHD, hybrid, fully kinetic, and gyrokinetic. We examine the limitations of each approach and their viability for studies of solar wind turbulence. Finally, the effect of initial conditions on the resulting turbulence and their comparison with solar wind are demonstrated through several kinetic simulations.

Reforming Management of Behavior Symptoms and Psychiatric Conditions in Long-Term Care Facilities: A Different Perspective.

PubMed

Levenson, Steven A; Desai, Abhilash K

2017-04-01

Despite much attention including national initiatives, concerns remain about the approaches to managing behavior symptoms and psychiatric conditions across all settings, including in long-term care settings such as nursing homes and assisted living facilities. One key reason why problems persist is because most efforts to "reform" and "correct" the situation have failed to explore or address root causes and instead have promoted inadequate piecemeal "solutions." Further improvement requires jumping off the bandwagon and rethinking the entire issue, including recognizing and applying key concepts of clinical reasoning and the care delivery process to every situation. The huge negative impact of cognitive biases and rote approaches on related clinical problem solving and decision making and patient outcomes also must be addressed. Copyright © 2017 AMDA – The Society for Post-Acute and Long-Term Care Medicine. Published by Elsevier Inc. All rights reserved.

The reform of home care services in Ontario: opportunity lost or lesson learned?

PubMed

Randall, Glen

2007-06-01

With the release of the Romanow Commission report, Canadian governments are poised to consider the creation of a national home care program. If occupational and physical therapists are to have input in shaping such a program, they will need to learn from lost opportunities of the past. This paper provides an overview of recent reforms to home care in Ontario with an emphasis on rehabilitation services. Data were collected from documents and 28 key informant interviews with rehabilitation professionals. Home care in Ontario has evolved in a piecemeal manner without rehabilitation professionals playing a prominent role in program design. Rehabilitation services play a critical role in facilitating hospital discharges, minimizing readmissions, and improving the quality of peoples' lives. Canadians will benefit if occupational and physical therapists seize the unique opportunity before them to provide meaningful input into creating a national home care program.

Darfur refugees in Cairo: mental health and interpersonal conflict in the aftermath of genocide.

PubMed

Meffert, Susan M; Marmar, Charles R

2009-11-01

Hundreds of thousands of Darfur people affected by the Sudanese genocide have fled to Cairo, Egypt, in search of assistance. Collaborating with Africa and Middle East Refugee Assistance (AMERA), the authors conducted a mental health care needs assessment among Darfur refugees in Cairo. Information was collected using individual and focus group interviews to identify gaps in mental health care and develop understandings of emotional and relationship problems. The refugee mental health care system has a piecemeal structure with gaps in outpatient services. There is moderate to severe emotional distress among many Darfur refugees, including symptoms of depression and trauma, and interpersonal conflict, both domestic violence and broader community conflict, elevated relative to pregenocide levels. Given the established relationships between symptoms of depression/traumatic stress and interpersonal violence, improving mental health is important for both preventing mental health decompensation and stemming future cycles of intra- and intergroup conflict.

Heat, Human Performance, and Occupational Health: A Key Issue for the Assessment of Global Climate Change Impacts.

PubMed

Kjellstrom, Tord; Briggs, David; Freyberg, Chris; Lemke, Bruno; Otto, Matthias; Hyatt, Olivia

2016-01-01

Ambient heat exposure is a well-known health hazard, which reduces human performance and work capacity at heat levels already common in tropical and subtropical areas. Various health problems have been reported. Increasing heat exposure during the hottest seasons of each year is a key feature of global climate change. Heat exhaustion and reduced human performance are often overlooked in climate change health impact analysis. Later this century, many among the four billion people who live in hot areas worldwide will experience significantly reduced work capacity owing to climate change. In some areas, 30-40% of annual daylight hours will become too hot for work to be carried out. The social and economic impacts will be considerable, with global gross domestic product (GDP) losses greater than 20% by 2100. The analysis to date is piecemeal. More analysis of climate change-related occupational health impact assessments is greatly needed.

Lessons from America? US magnet hospitals and their implications for UK nursing.

PubMed

Buchan, J

1994-02-01

This paper examines possible implications of the US 'magnet hospital' concept for the UK nursing labour market. Magnet hospitals have been researched in the US and have been demonstrated to exhibit lower nurse turnover and higher levels of reported job satisfaction than other hospitals. Key characteristics include a decentralized organizational structure, a commitment to flexible working hours, an emphasis on professional autonomy and development, and systematic communication between management and staff. The paper examines the labour market characteristics of UK nurses and US nurses and finds many similarities. Detailed case studies of employment practice in 10 US hospitals and 10 Scottish hospitals are reported, with specific attention to remuneration practice, methods of organizing nursing care, establishment-setting and flexible hours. The paper concludes that there are features of the magnet hospital concept which are of relevance and applicable to the UK nursing labour market, but that piecemeal importation of ideas is unlikely to be beneficial.

Outcomes in Treatment for Intradural Spinal Cord Ependymomas

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

Volpp, P. Brian; Han, Khanh; Kagan, A. Robert

2007-11-15

Purpose: Spinal cord ependymomas are rare tumors, accounting for <2% of all primary central nervous system tumors. This study assessed the treatment outcomes for patients diagnosed with spinal cord ependymomas within the Southern California Kaiser Permanente system. Methods and Materials: We studied 23 patients treated with surgery with or without external beam radiotherapy (EBRT). The local and distant control rates and overall survival rates were determined. Results: The overall local control, overall recurrence, and 9-year overall survival rate was 96%, 17.4%, and 63.9%, respectively. Conclusions: The results of our study indicate that en bloc gross total resection should be themore » initial treatment, with radiotherapy reserved primarily for postoperative cases with unfavorable characteristics such as residual tumor, anaplastic histologic features, or piecemeal resection. Excellent local control and overall survival rates can be achieved using modern microsurgical techniques, with or without local radiotherapy.« less

Using the mass media to inform and educate the public about planetary protection and exploration risks

NASA Astrophysics Data System (ADS)

Race, M.

For the foreseeable future, the public will continue to learn piecemeal about the latest advances in Astrobiology through headlines and mass media coverage of missions, discoveries or controversies. Journalists and reporters are themselves unschooled in this emerging interdisciplinary field, yet play a critical role in explaining details to the public. While it is important to develop curricular materials for future use in formal educational settings, it is equally important to find novel ways for educating and updating journalists in this fast paced field. Risk communication plans for Mars exploration and other solar system missions should include special efforts aimed at assisting mass media professionals in both their informational and educational roles. If journalists and reporters have a deeper and more comprehensive understanding of the science and societal issues associated with missions, the result may well be more accurate explanations, improved public understanding, and continued support for exploration.

Toward a United States Arctic research policy

NASA Astrophysics Data System (ADS)

Roederer, Juan G.

Of all countries bordering on the Arctic, the United States is the only one without a national institute, laboratory, or any other organization devoted to the sustained planning and support of Arctic research. Up to now, the responsibility for planning, implementing, and funding Arctic research has been divided between several federal agencies, the state of Alaska, and private groups whose mandates or objectives are often unconnected.The result of this pluralistic approach to U.S. science in the Arctic is that basic research has been conducted in piecemeal fashion. Individual studies are proposed and supported separately, and their costly logistic requirements must be funded in competition with research carried out under less-demanding environmental conditions in the rest of the country. Fundamental data-gathering and interpretation of information has been the responsibility of public agencies whose missions are separate and whose budgets may not reflect the priorities of Arctic issues.

Psychological Perspectives on Pathways Linking Socioeconomic Status and Physical Health

PubMed Central

Matthews, Karen A.; Gallo, Linda C.

2011-01-01

Low socioeconomic status (SES) is a reliable correlate of poor physical health. Rather than treat SES as a covariate, health psychology has increasingly focused on the psychobiological pathways that inform understanding why SES is related to physical health. This review assesses the status of research that has examined stress and its associated distress, and social and personal resources as pathways. It highlights work on biomarkers and biological pathways related to SES that can serve as intermediate outcomes in future studies. Recent emphasis on the accumulation of psychobiological risks across the life course is summarized and represents an important direction for future research. Studies that test pathways from SES to candidate psychosocial pathways to health outcomes are few in number but promising. Future research should test integrated models rather than taking piecemeal approaches to evidence. Much work remains to be done, but the questions are of great health significance. PMID:20636127

Tissue alignment enhances remodeling potential of tendon-derived cells - Lessons from a novel microtissue model of tendon scarring.

PubMed

Foolen, Jasper; Wunderli, Stefania L; Loerakker, Sandra; Snedeker, Jess G

2018-01-01

Tendinopathy is a widespread and unresolved clinical challenge, in which associated pain and hampered mobility present a major cause for work-related disability. Tendinopathy associates with a change from a healthy tissue with aligned extracellular matrix (ECM) and highly polarized cells that are connected head-to-tail, towards a diseased tissue with a disorganized ECM and randomly distributed cells, scar-like features that are commonly attributed to poor innate regenerative capacity of the tissue. A fundamental clinical dilemma with this scarring process is whether treatment strategies should focus on healing the affected (disorganized) tissue or strengthen the remaining healthy (anisotropic) tissue. The question was thus asked whether the intrinsic remodeling capacity of tendon-derived cells depends on the organization of the 3D extracellular matrix (isotropic vs anisotropic). Progress in this field is hampered by the lack of suitable in vitro tissue platforms. We aimed at filling this critical gap by creating and exploiting a next generation tissue platform that mimics aspects of the tendon scarring process; cellular response to a gradient in tissue organization from isotropic (scarred/non-aligned) to highly anisotropic (unscarred/aligned) was studied, as was a transient change from isotropic towards highly anisotropic. Strikingly, cells residing in an 'unscarred' anisotropic tissue indicated superior remodeling capacity (increased gene expression levels of collagen, matrix metalloproteinases MMPs, tissue inhibitors of MMPs), when compared to their 'scarred' isotropic counterparts. A numerical model then supported the hypothesis that cellular remodeling capacity may correlate to cellular alignment strength. This in turn may have improved cellular communication, and could thus relate to the more pronounced connexin43 gap junctions observed in anisotropic tissues. In conclusion, increased tissue anisotropy was observed to enhance the cellular potential for functional remodeling of the matrix. This may explain the poor regenerative capacity of tenocytes in chronic tendinopathy, where the pathological process has resulted in ECM disorganization. Additionally, it lends support to treatment strategies that focus on strengthening the remaining healthy tissue, rather than regenerating scarred tissue. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Assessment practices of third- and fifth-grade science teachers: A comparison to the style/format, process, and content of Ohio's proficiency tests

NASA Astrophysics Data System (ADS)

Janson, David C.

This descriptive study is addressed to policy-makers, textbook publisher, teachers, principals, and curriculum directors. It compares the assessment practices of ten elementary teachers over a period of 11 weeks with Ohio's fourth and sixth grade science Proficiency Tests. Results show that the teachers' assessment practices were not aligned with Ohio's Proficiency Test. The tests used in the participants' classroom contained a disproportionate number of items characterized as low-level in terms of their cognitive function. Classroom test items generally fell into three categories---true/false, completion, and matching. The remaining items were predominantly low-level multiple-choice items requiring simple recall of information. The teachers in this study showed a heavy reliance on the packaged assessments that accompanied their adopted textbook series with little use of teacher-designed instruments. This differs from the findings of previous researchers who reported that most teacher assessments were done with teacher-made tests. The lack of alignment between classroom tests and Ohio's Proficiency Test is a concern because previous researchers and the teachers in this study believe that aligning classroom tests with high-stakes assessment improves student performance. Other research shows teachers teach what they test suggesting that the curriculum would be better aligned with State expectations if classroom tests were more in line with the proficiency tests. This study found that textbooks and their assessment packages are not aligned to most state standards and that teachers need help developing better assessments. The results of this study suggest directions school administrators might take to facilitate inservice training for current teachers and could be helpful to textbook publishers as well as educators serving on adoption committees. Since high-stakes testing of students in the nation's public schools and school accountability seem destined to remain a part of the American educational system, educators at all levels---teachers and administrators at the local level, consultants and administrators at the state level, and policymakers at the state and national levels---may want to consider the implications of these findings.

KinView: A visual comparative sequence analysis tool for integrated kinome research

PubMed Central

McSkimming, Daniel Ian; Dastgheib, Shima; Baffi, Timothy R.; Byrne, Dominic P.; Ferries, Samantha; Scott, Steven Thomas; Newton, Alexandra C.; Eyers, Claire E.; Kochut, Krzysztof J.; Eyers, Patrick A.

2017-01-01

Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats. Here, we present the Multiple Sequence Alignment Ontology (MSAOnt), which represents a profile or consensus alignment in an ontological format. Subsets of the alignment are easily selected through the SPARQL Protocol and RDF Query Language for downstream statistical analysis or visualization. We have also created the Kinome Viewer (KinView), an interactive integrative visualization that places eukaryotic protein kinase cancer variants in the context of natural sequence variation and experimentally determined post-translational modifications, which play central roles in the regulation of cellular signaling pathways. Using KinView, we identified differential phosphorylation patterns between tyrosine and serine/threonine kinases in the activation segment, a major kinase regulatory region that is often mutated in proliferative diseases. We discuss cancer variants that disrupt phosphorylation sites in the activation segment, and show how KinView can be used as a comparative tool to identify differences and similarities in natural variation, cancer variants and post-translational modifications between kinase groups, families and subfamilies. Based on KinView comparisons, we identify and experimentally characterize a regulatory tyrosine (Y177PLK4) in the PLK4 C-terminal activation segment region termed the P+1 loop. To further demonstrate the application of KinView in hypothesis generation and testing, we formulate and validate a hypothesis explaining a novel predicted loss-of-function variant (D523NPKCβ) in the regulatory spine of PKCβ, a recently identified tumor suppressor kinase. KinView provides a novel, extensible interface for performing comparative analyses between subsets of kinases and for integrating multiple types of residue specific annotations in user friendly formats. PMID:27731453

Histology of the heterostracan dermal skeleton: Insight into the origin of the vertebrate mineralised skeleton.

PubMed

Keating, Joseph N; Marquart, Chloe L; Donoghue, Philip C J

2015-06-01

Living vertebrates are divided into those that possess a fully formed and fully mineralised skeleton (gnathostomes) versus those that possess only unmineralised cartilaginous rudiments (cyclostomes). As such, extinct phylogenetic intermediates of these living lineages afford unique insights into the evolutionary assembly of the vertebrate mineralised skeleton and its canonical tissue types. Extinct jawless and jawed fishes assigned to the gnathostome stem evidence the piecemeal assembly of skeletal systems, revealing that the dermal skeleton is the earliest manifestation of a homologous mineralised skeleton. Yet the nature of the primitive dermal skeleton, itself, is poorly understood. This is principally because previous histological studies of early vertebrates lacked a phylogenetic framework required to derive evolutionary hypotheses. Nowhere is this more apparent than within Heterostraci, a diverse clade of primitive jawless vertebrates. To this end, we surveyed the dermal skeletal histology of heterostracans, inferred the plesiomorphic heterostracan skeleton and, through histological comparison to other skeletonising vertebrate clades, deduced the ancestral nature of the vertebrate dermal skeleton. Heterostracans primitively possess a four-layered skeleton, comprising a superficial layer of odontodes composed of dentine and enameloid; a compact layer of acellular parallel-fibred bone containing a network of vascular canals that supply the pulp canals (L1); a trabecular layer consisting of intersecting radial walls composed of acellular parallel-fibred bone, showing osteon-like development (L2); and a basal layer of isopedin (L3). A three layered skeleton, equivalent to the superficial layer L2 and L3 and composed of enameloid, dentine and acellular bone, is possessed by the ancestor of heterostracans + jawed vertebrates. We conclude that an osteogenic component is plesiomorphic with respect to the vertebrate dermal skeleton. Consequently, we interpret the dermal skeleton of denticles in chondrichthyans and jawless thelodonts as independently and secondarily simplified. J. Morphol. 276:657-680, 2015. © 2015 The Authors Journal of Morphology Published by Wiley Periodicals, Inc. © 2015 The Authors Journal of Morphology Published by Wiley Periodicals, Inc.

Large-Scale Patterns in a Minimal Cognitive Flocking Model: Incidental Leaders, Nematic Patterns, and Aggregates

NASA Astrophysics Data System (ADS)

Barberis, Lucas; Peruani, Fernando

2016-12-01

We study a minimal cognitive flocking model, which assumes that the moving entities navigate using the available instantaneous visual information exclusively. The model consists of active particles, with no memory, that interact by a short-ranged, position-based, attractive force, which acts inside a vision cone (VC), and lack velocity-velocity alignment. We show that this active system can exhibit—due to the VC that breaks Newton's third law—various complex, large-scale, self-organized patterns. Depending on parameter values, we observe the emergence of aggregates or millinglike patterns, the formation of moving—locally polar—files with particles at the front of these structures acting as effective leaders, and the self-organization of particles into macroscopic nematic structures leading to long-ranged nematic order. Combining simulations and nonlinear field equations, we show that position-based active models, as the one analyzed here, represent a new class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems. The reported results are of prime importance in the study, interpretation, and modeling of collective motion patterns in living and nonliving active systems.

Assessment of ERTS-1 imagery as a tool for regional geological analysis in New York State. [Lake Ontario

NASA Technical Reports Server (NTRS)

Isachsen, Y. W. (Principal Investigator); Fakundiny, R. H.; Forster, S. W.

1974-01-01

The author has identified the following significant results. Linear anomalies dominate the new geological information derived from ERTS-1 imagery, total lengths now exceeding 26,500 km. Maxima on rose diagrams for ERTS-1 anomalies correspond well with those for mapped faults and topographic lineaments. Multi-scale analysis of linears shows that single topographic linears at 1:2,500,000 may become dashed linears at 1:1,000,000 aligned zones of shorter parallel, en echelon, or conjugate linears at 1:5000,000, and shorter linears lacking any conspicuous zonal alignment at 1:250,000. Field work in the Catskills suggests that the prominent new NNE lineaments may be surface manifestations of dip slip faulting in the basement, and that it may become possible to map major joint sets over extensive plateau regions directly on the imagery. Most circular features found were explained away by U-2 airfoto analysis but several remain as anomalies. Visible glacial features include individual drumlins, drumlinoids, eskers, ice-marginal drainage channels, glacial lake shorelines, sand plains, and end moraines.

Location memory biases reveal the challenges of coordinating visual and kinesthetic reference frames

PubMed Central

Simmering, Vanessa R.; Peterson, Clayton; Darling, Warren; Spencer, John P.

2008-01-01

Five experiments explored the influence of visual and kinesthetic/proprioceptive reference frames on location memory. Experiments 1 and 2 compared visual and kinesthetic reference frames in a memory task using visually-specified locations and a visually-guided response. When the environment was visible, results replicated previous findings of biases away from the midline symmetry axis of the task space, with stability for targets aligned with this axis. When the environment was not visible, results showed some evidence of bias away from a kinesthetically-specified midline (trunk anterior–posterior [a–p] axis), but there was little evidence of stability when targets were aligned with body midline. This lack of stability may reflect the challenges of coordinating visual and kinesthetic information in the absence of an environmental reference frame. Thus, Experiments 3–5 examined kinesthetic guidance of hand movement to kinesthetically-defined targets. Performance in these experiments was generally accurate with no evidence of consistent biases away from the trunk a–p axis. We discuss these results in the context of the challenges of coordinating reference frames within versus between multiple sensori-motor systems. PMID:17703284

Large-Scale Patterns in a Minimal Cognitive Flocking Model: Incidental Leaders, Nematic Patterns, and Aggregates.

PubMed

Barberis, Lucas; Peruani, Fernando

2016-12-09

We study a minimal cognitive flocking model, which assumes that the moving entities navigate using the available instantaneous visual information exclusively. The model consists of active particles, with no memory, that interact by a short-ranged, position-based, attractive force, which acts inside a vision cone (VC), and lack velocity-velocity alignment. We show that this active system can exhibit-due to the VC that breaks Newton's third law-various complex, large-scale, self-organized patterns. Depending on parameter values, we observe the emergence of aggregates or millinglike patterns, the formation of moving-locally polar-files with particles at the front of these structures acting as effective leaders, and the self-organization of particles into macroscopic nematic structures leading to long-ranged nematic order. Combining simulations and nonlinear field equations, we show that position-based active models, as the one analyzed here, represent a new class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems. The reported results are of prime importance in the study, interpretation, and modeling of collective motion patterns in living and nonliving active systems.

What can we learn from a two-brain approach to verbal interaction?

PubMed

Schoot, Lotte; Hagoort, Peter; Segaert, Katrien

2016-09-01

Verbal interaction is one of the most frequent social interactions humans encounter on a daily basis. In the current paper, we zoom in on what the multi-brain approach has contributed, and can contribute in the future, to our understanding of the neural mechanisms supporting verbal interaction. Indeed, since verbal interaction can only exist between individuals, it seems intuitive to focus analyses on inter-individual neural markers, i.e. between-brain neural coupling. To date, however, there is a severe lack of theoretically-driven, testable hypotheses about what between-brain neural coupling actually reflects. In this paper, we develop a testable hypothesis in which between-pair variation in between-brain neural coupling is of key importance. Based on theoretical frameworks and empirical data, we argue that the level of between-brain neural coupling reflects speaker-listener alignment at different levels of linguistic and extra-linguistic representation. We discuss the possibility that between-brain neural coupling could inform us about the highest level of inter-speaker alignment: mutual understanding. Copyright © 2016 Elsevier Ltd. All rights reserved.

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

PubMed Central

Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang

2011-01-01

I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and FG-MD, were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of beta-proteins are still needed to further improve the I-TASSER pipeline. PMID:22069036

Let's be professional about this: ideology and the psychological contracts of registered nurses.

PubMed

O'Donohue, Wayne; Nelson, Lindsay

2007-07-01

This study explores whether there is evidence of an ideological component in the psychological contracts of professional employees, as well as evidence of credible supporting commitments by their employer. Fundamental changes in the employment context have prompted many individuals to seek a closer alignment between themselves and their work, as well as with the organizational and broader societal contexts. For many professional employees identification with their professional ideology is a significant factor in producing such an alignment. The study uses an exploratory qualitative approach to analyse interview data collected from a sample of registered nurses employed in an Australian public hospital. The analysis identifies psychological contract terms best understood by reference to an ideological currency. It also suggests that the organization is perceived as obligated to provide credible support for that professional contribution, and the perceived lack of such support has significant impacts. The findings raise doubts about the utility of the concept of a psychological contract that recognizes only economic and socio-emotional exchanges for understanding the psychological contracts of professional employees.

Accurate and exact CNV identification from targeted high-throughput sequence data.

PubMed

Nord, Alex S; Lee, Ming; King, Mary-Claire; Walsh, Tom

2011-04-12

Massively parallel sequencing of barcoded DNA samples significantly increases screening efficiency for clinically important genes. Short read aligners are well suited to single nucleotide and indel detection. However, methods for CNV detection from targeted enrichment are lacking. We present a method combining coverage with map information for the identification of deletions and duplications in targeted sequence data. Sequencing data is first scanned for gains and losses using a comparison of normalized coverage data between samples. CNV calls are confirmed by testing for a signature of sequences that span the CNV breakpoint. With our method, CNVs can be identified regardless of whether breakpoints are within regions targeted for sequencing. For CNVs where at least one breakpoint is within targeted sequence, exact CNV breakpoints can be identified. In a test data set of 96 subjects sequenced across ~1 Mb genomic sequence using multiplexing technology, our method detected mutations as small as 31 bp, predicted quantitative copy count, and had a low false-positive rate. Application of this method allows for identification of gains and losses in targeted sequence data, providing comprehensive mutation screening when combined with a short read aligner.

Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration.

PubMed

Deelen, Patrick; Bonder, Marc Jan; van der Velde, K Joeri; Westra, Harm-Jan; Winder, Erwin; Hendriksen, Dennis; Franke, Lude; Swertz, Morris A

2014-12-11

To gain statistical power or to allow fine mapping, researchers typically want to pool data before meta-analyses or genotype imputation. However, the necessary harmonization of genetic datasets is currently error-prone because of many different file formats and lack of clarity about which genomic strand is used as reference. Genotype Harmonizer (GH) is a command-line tool to harmonize genetic datasets by automatically solving issues concerning genomic strand and file format. GH solves the unknown strand issue by aligning ambiguous A/T and G/C SNPs to a specified reference, using linkage disequilibrium patterns without prior knowledge of the used strands. GH supports many common GWAS/NGS genotype formats including PLINK, binary PLINK, VCF, SHAPEIT2 & Oxford GEN. GH is implemented in Java and a large part of the functionality can also be used as Java 'Genotype-IO' API. All software is open source under license LGPLv3 and available from http://www.molgenis.org/systemsgenetics. GH can be used to harmonize genetic datasets across different file formats and can be easily integrated as a step in routine meta-analysis and imputation pipelines.

Field-Aligned Current Systems at Mercury

NASA Astrophysics Data System (ADS)

Heyner, Daniel; Exner, Willi

2017-04-01

Mercury exhibits a very dynamic magnetosphere, which is partially due to strong dayside reconnection and fast magnetospheric convection. It has been shown that dayside reconnection occurs even on low magnetic shear angles across the magnetopause. This drives quasi-steady region 1 field-aligned currents (FAC) that are observable in in-situ MESSENGER data. Here, the structure of the Hermean FAC-system is discussed and compared to the terrestrial counterpart. Due to the lack of a significant ionosphere at Mercury, it has to be examined how much of the poloidal FAC is reflected back to the magnetosphere, closed via toroidal currents in the planetary interior or via Pedersen currents in the tenuous exosphere. This investigation gives insights into the planetary conductivity structure as well as the exospheric plasma densities. Furthermore, it will be examined how much the only partially developed ring current at Mercury produces possible region 2 FAC signatures. We conclude with requirements to simulations that are needed to forecast the FAC structure on the southern hemisphere that will be closely studied with the upcoming BepiColombo mission.

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome.

PubMed

Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

2010-11-27

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs.

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome

PubMed Central

Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

2010-01-01

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs. PMID:21364831

Describing sequencing results of structural chromosome rearrangements with a suggested next-generation cytogenetic nomenclature.

PubMed

Ordulu, Zehra; Wong, Kristen E; Currall, Benjamin B; Ivanov, Andrew R; Pereira, Shahrin; Althari, Sara; Gusella, James F; Talkowski, Michael E; Morton, Cynthia C

2014-05-01

With recent rapid advances in genomic technologies, precise delineation of structural chromosome rearrangements at the nucleotide level is becoming increasingly feasible. In this era of "next-generation cytogenetics" (i.e., an integration of traditional cytogenetic techniques and next-generation sequencing), a consensus nomenclature is essential for accurate communication and data sharing. Currently, nomenclature for describing the sequencing data of these aberrations is lacking. Herein, we present a system called Next-Gen Cytogenetic Nomenclature, which is concordant with the International System for Human Cytogenetic Nomenclature (2013). This system starts with the alignment of rearrangement sequences by BLAT or BLAST (alignment tools) and arrives at a concise and detailed description of chromosomal changes. To facilitate usage and implementation of this nomenclature, we are developing a program designated BLA(S)T Output Sequence Tool of Nomenclature (BOSToN), a demonstrative version of which is accessible online. A standardized characterization of structural chromosomal rearrangements is essential both for research analyses and for application in the clinical setting. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Accountable care organizations may have difficulty avoiding the failures of integrated delivery networks of the 1990s.

PubMed

Burns, Lawton R; Pauly, Mark V

2012-11-01

Accountable care organizations are intended to improve the quality and lower the cost of health care through several mechanisms, such as disease management programs, care coordination, and aligning financial incentives for hospitals and physicians. Providers employed several of these mechanisms in forming the integrated delivery networks of the 1990s. The networks failed, however, because of heavy financial losses stemming from hospitals' purchase of physician practices and their inability to align incentives, garner capitated contracts, and develop the infrastructure to manage risk. Although the current mechanisms underlying accountable care organizations continue to evolve, whether and how they will have an impact on quality and costs remains open to question. Care coordination and information technology are proving more complicated and expensive to implement than anticipated, providers may lack the ability to implement these mechanisms, and primary care providers are in short supply. As in the 1990s, success depends on targeting specific populations, such as people with multiple chronic conditions who need and may benefit from coordinated care.

[Communication prostheses and behavioral alignment in hospital leaflets].

PubMed

Vasconcellos-Silva, Paulo Roberto; Rivera, Francisco Javier Uribe; Rozemberg, Brani

2003-08-01

Review was made of publications that describe experience with printed material distributed to the lay public in hospital institutions. From the 146 leaflets examined, those aimed at professionals or disabled people, thus leaving 75 papers that illustrate the present pattern for the rationality behind the production, use and evaluation of this type of resource. In a general manner, such leaflets invest in the power of "ideal printed information" to align behavior with the hospital's biomedical agenda. The underlying rationality that permeates them perceives the "perfect information package" as one that efficiently describes its technical content for the purpose of unidirectional persuasion, is up-to-date in relation to readability scales and embellished by graphic design, and emphasizes the priorities defined by the professionals. Such "communication prostheses" should be capable of electronic validation by means of software suitable for proportioning the "doses" to the subject matter. Information as a drug, cognitivism, the lack of research on message reception and the need for communicative action for the deconstruction of systems of closed thinking within the hospital environment have been discussed.

Failure of Anisotropic Unstructured Mesh Adaption Based on Multidimensional Residual Minimization

NASA Technical Reports Server (NTRS)

Wood, William A.; Kleb, William L.

2003-01-01

An automated anisotropic unstructured mesh adaptation strategy is proposed, implemented, and assessed for the discretization of viscous flows. The adaption criteria is based upon the minimization of the residual fluctuations of a multidimensional upwind viscous flow solver. For scalar advection, this adaption strategy has been shown to use fewer grid points than gradient based adaption, naturally aligning mesh edges with discontinuities and characteristic lines. The adaption utilizes a compact stencil and is local in scope, with four fundamental operations: point insertion, point deletion, edge swapping, and nodal displacement. Evaluation of the solution-adaptive strategy is performed for a two-dimensional blunt body laminar wind tunnel case at Mach 10. The results demonstrate that the strategy suffers from a lack of robustness, particularly with regard to alignment of the bow shock in the vicinity of the stagnation streamline. In general, constraining the adaption to such a degree as to maintain robustness results in negligible improvement to the solution. Because the present method fails to consistently or significantly improve the flow solution, it is rejected in favor of simple uniform mesh refinement.

Coherent clusters of inertial particles in homogeneous turbulence

NASA Astrophysics Data System (ADS)

Baker, Lucia; Frankel, Ari; Mani, Ali; Coletti, Filippo

2016-11-01

Clustering of heavy particles in turbulent flows manifests itself in a broad spectrum of physical phenomena, including sediment transport, cloud formation, and spray combustion. However, a clear topological definition of particle cluster has been lacking, limiting our ability to describe their features and dynamics. Here we introduce a definition of coherent cluster based on self-similarity, and apply it to the distribution of heavy particles in direct numerical simulations of homogeneous isotropic turbulence. We consider a range of particle Stokes numbers, with and without the effect of gravity. Clusters show self-similarity at length scales larger than twice the Kolmogorov length, with a specific fractal dimension. In the absence of gravity, clusters demonstrate a tendency to sample regions of the flow where strain is dominant over vorticity, and to align themselves with the local vorticity vector; when gravity is present, the clusters tend to align themselves with gravity, and their fall speed is different from the average settling velocity. This approach yields observations which are consistent with findings obtained from previous studies while opening new avenues for analysis of the topology and evolution of particle clusters in a wealth of applications.

Large eddy simulation of orientation and rotation of ellipsoidal particles in isotropic turbulent flows

NASA Astrophysics Data System (ADS)

Chen, Jincai; Jin, Guodong; Zhang, Jian

2016-03-01

The rotational motion and orientational distribution of ellipsoidal particles in turbulent flows are of significance in environmental and engineering applications. Whereas the translational motion of an ellipsoidal particle is controlled by the turbulent motions at large scales, its rotational motion is determined by the fluid velocity gradient tensor at small scales, which raises a challenge when predicting the rotational dispersion of ellipsoidal particles using large eddy simulation (LES) method due to the lack of subgrid scale (SGS) fluid motions. We report the effects of the SGS fluid motions on the orientational and rotational statistics, such as the alignment between the long axis of ellipsoidal particles and the vorticity, the mean rotational energy at various aspect ratios against those obtained with direct numerical simulation (DNS) and filtered DNS. The performances of a stochastic differential equation (SDE) model for the SGS velocity gradient seen by the particles and the approximate deconvolution method (ADM) for LES are investigated. It is found that the missing SGS fluid motions in LES flow fields have significant effects on the rotational statistics of ellipsoidal particles. Alignment between the particles and the vorticity is weakened; and the rotational energy of the particles is reduced in LES. The SGS-SDE model leads to a large error in predicting the alignment between the particles and the vorticity and over-predicts the rotational energy of rod-like particles. The ADM significantly improves the rotational energy prediction of particles in LES.

Lessons for major system change: centralization of stroke services in two metropolitan areas of England

PubMed Central

Ramsay, Angus; Perry, Catherine; Boaden, Ruth; McKevitt, Christopher; Morris, Stephen; Pursani, Nanik; Rudd, Anthony; Tyrrell, Pippa; Wolfe, Charles; Fulop, Naomi

2016-01-01

Objectives Our aim was to identify the factors influencing the selection of a model of acute stroke service centralization to create fewer high-volume specialist units in two metropolitan areas of England (London and Greater Manchester). It considers the reasons why services were more fully centralized in London than in Greater Manchester. Methods In both areas, we analysed 316 documents and conducted 45 interviews with people leading transformation, service user organizations, providers and commissioners. Inductive and deductive analyses were used to compare the processes underpinning change in each area, with reference to propositions for achieving major system change taken from a realist review of the existing literature (the Best framework), which we critique and develop further. Results In London, system leadership was used to overcome resistance to centralization and align stakeholders to implement a centralized service model. In Greater Manchester, programme leaders relied on achieving change by consensus and, lacking decision-making authority over providers, accommodated rather than challenged resistance by implementing a less radical transformation of services. Conclusions A combination of system (top-down) and distributed (bottom-up) leadership is important in enabling change. System leadership provides the political authority required to coordinate stakeholders and to capitalize on clinical leadership by aligning it with transformation goals. Policy makers should examine how the structures of system authority, with performance management and financial levers, can be employed to coordinate transformation by aligning the disparate interests of providers and commissioners. PMID:26811375

Lessons for major system change: centralization of stroke services in two metropolitan areas of England.

PubMed

Turner, Simon; Ramsay, Angus; Perry, Catherine; Boaden, Ruth; McKevitt, Christopher; Morris, Stephen; Pursani, Nanik; Rudd, Anthony; Tyrrell, Pippa; Wolfe, Charles; Fulop, Naomi

2016-07-01

Our aim was to identify the factors influencing the selection of a model of acute stroke service centralization to create fewer high-volume specialist units in two metropolitan areas of England (London and Greater Manchester). It considers the reasons why services were more fully centralized in London than in Greater Manchester. In both areas, we analysed 316 documents and conducted 45 interviews with people leading transformation, service user organizations, providers and commissioners. Inductive and deductive analyses were used to compare the processes underpinning change in each area, with reference to propositions for achieving major system change taken from a realist review of the existing literature (the Best framework), which we critique and develop further. In London, system leadership was used to overcome resistance to centralization and align stakeholders to implement a centralized service model. In Greater Manchester, programme leaders relied on achieving change by consensus and, lacking decision-making authority over providers, accommodated rather than challenged resistance by implementing a less radical transformation of services. A combination of system (top-down) and distributed (bottom-up) leadership is important in enabling change. System leadership provides the political authority required to coordinate stakeholders and to capitalize on clinical leadership by aligning it with transformation goals. Policy makers should examine how the structures of system authority, with performance management and financial levers, can be employed to coordinate transformation by aligning the disparate interests of providers and commissioners. © The Author(s) 2016.

Alignment-free protein interaction network comparison

PubMed Central

Ali, Waqar; Rito, Tiago; Reinert, Gesine; Sun, Fengzhu; Deane, Charlotte M.

2014-01-01

Motivation: Biological network comparison software largely relies on the concept of alignment where close matches between the nodes of two or more networks are sought. These node matches are based on sequence similarity and/or interaction patterns. However, because of the incomplete and error-prone datasets currently available, such methods have had limited success. Moreover, the results of network alignment are in general not amenable for distance-based evolutionary analysis of sets of networks. In this article, we describe Netdis, a topology-based distance measure between networks, which offers the possibility of network phylogeny reconstruction. Results: We first demonstrate that Netdis is able to correctly separate different random graph model types independent of network size and density. The biological applicability of the method is then shown by its ability to build the correct phylogenetic tree of species based solely on the topology of current protein interaction networks. Our results provide new evidence that the topology of protein interaction networks contains information about evolutionary processes, despite the lack of conservation of individual interactions. As Netdis is applicable to all networks because of its speed and simplicity, we apply it to a large collection of biological and non-biological networks where it clusters diverse networks by type. Availability and implementation: The source code of the program is freely available at http://www.stats.ox.ac.uk/research/proteins/resources. Contact: w.ali@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161230

Chimpanzee ‘folk physics’: bringing failures into focus

PubMed Central

Seed, Amanda; Seddon, Eleanor; Greene, Bláthnaid; Call, Josep

2012-01-01

Differences between individuals are the raw material from which theories of the evolution and ontogeny of cognition are built. For example, when 4-year-old children pass a test requiring them to communicate the content of another's falsely held belief, while 3-year-olds fail, we know that something must change over the course of the third year of life. In the search for what develops or evolves, the typical route is to probe the extents and limits of successful individuals' ability. Another is to focus on those that failed, and find out what difference or lack prevented them from passing the task. Recent research in developmental psychology has harnessed individual differences to illuminate the cognitive mechanisms that emerge to enable success. We apply this approach to explaining some of the failures made by chimpanzees when using tools to solve problems. Twelve of 16 chimpanzees failed to discriminate between a complete and a broken tool when, after being set down, the ends of the broken one were aligned in front of them. There was a correlation between performance on this aligned task and another in which after being set down, the centre of both tools was covered, suggesting that the limiting factor was not the representation of connection, but memory or attention. Some chimpanzees that passed the aligned task passed a task in which the location of the broken tool was never visible but had to be inferred. PMID:22927573

Alignment of human cardiomyocytes on laser patterned biphasic core/shell nanowire assemblies

NASA Astrophysics Data System (ADS)

Kiefer, Karin; Lee, Juseok; Haidar, Ayman; Martinez Miró, Marina; Akkan, Cagri Kaan; Veith, Michael; Cenk Aktas, Oral; Abdul-Khaliq, Hashim

2014-12-01

The management of end stage heart failure patients is only possible by heart transplantation or by the implantation of artificial hearts as a bridge for later transplantation. However, these therapeutic strategies are limited by a lack of donor hearts and by the associated complications, such as coagulation and infection, due to the used artificial mechanical circulatory assist devices. Therefore, new strategies for myocardial regenerative approaches are under extensive research to produce contractile myocardial tissue in the future to replace non-contractile myocardial ischemic and scarred tissue. Different approaches, such as cell transplantation, have been studied intensively. Although successful approaches have been observed, there are still limitations to the application. It is envisaged that myocardial tissue engineering can be used to help replace infarcted non-contractile tissue. The developed tissue should later mimic the aligned fibrillar structure of the extracellular matrix and provide important guidance cues for the survival, function and the needed orientation of cardiomyocytes. Nanostructured surfaces have been tested to provide a guided direction that cells can follow. In the present study, the cellular adhesion/alignment of human cardiomyocytes and the biocompatibility have been investigated after cultivation on different laser-patterned nanowires compared with unmodified nanowires. As a result, the nanostructured surfaces possessed good biocompatibility before and after laser modification. The laser-induced scalability of the pattern enabled the growth and orientation of the adhered myocardial tissue. Such approaches may be used to modify the surface of potential scaffolds to develop myocardial contractile tissue in the future.

Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course.

PubMed

Ziegler, Brittany; Montplaisir, Lisa

2014-01-01

Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students' perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students' perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (posttest) of the course. Alignment between student perception and determined knowledge was significantly more accurate on the posttest compared with the pretest. Students whose determined knowledge was in the upper quartile had significantly better alignment between their perception and determined knowledge on the pre- and posttest than students in the lower quartile. No difference exists between how students perceived their knowledge between upper- and lower-quartile students. There was a significant difference in alignment of perception and determined knowledge between males and females on the posttest, with females being more accurate in their perception of knowledge. This study provides evidence of discrepancies that exist between what students perceive they know and what they actually know. © 2014 B. Ziegler and L. Montplaisir. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Priorities for Evaluating Palliative Care Outcomes in Intensive Care Units.

PubMed

Bakitas, Marie; Dionne-Odom, J Nicholas; Kamal, Arif; Maguire, Jennifer M

2015-09-01

Defining the quality of intensive care unit (ICU) care when patients are dying is challenging. Palliative care has been recommended to improve outcomes of dying ICU patients; however, traditional ICU quality indicators do not always align with palliative care. Evidence suggests that some aspects of ICU care improve when palliative care is integrated; however, consensus is lacking concerning the outcomes that should be measured. Overcoming challenges to measuring palliative care will require consensus development and rigorous research on the best way to evaluate ICU palliative care services. Copyright © 2015 Elsevier Inc. All rights reserved.

Novel generation of liquid crystalline photo-actuators based on stretched porous polyethylene films.

PubMed

Ryabchun, Alexander; Bobrovsky, Alexey; Stumpe, Joachim; Shibaev, Valery

2012-06-14

The preparation of photo-actuators based on stretched porous polyethylene and an azobenzene-containing liquid crystalline polymer network is reported for the first time. It is revealed that this kind of photo-actuator possesses the following advantages: the lack of a need for using aligning coatings and cells preparation, high deformation of the actuator and its complete reversibility, good mechanical properties, and relatively low cost of fabrication. In addition some kinetic and thermodynamic features of the bending and unbending processes have been studied. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Non-polypoid colorectal neoplasms: Classification, therapy and follow-up.

PubMed

Facciorusso, Antonio; Antonino, Matteo; Di Maso, Marianna; Barone, Michele; Muscatiello, Nicola

2015-05-07

In the last years, an increasing interest has been raised on non-polypoid colorectal tumors (NPT) and in particular on large flat neoplastic lesions beyond 10 mm tending to grow laterally, called laterally spreading tumors (LST). LSTs and large sessile polyps have a greater frequency of high-grade dysplasia and local invasiveness as compared to pedunculated lesions of the same size and usually represent a technical challenge for the endoscopist in terms of either diagnosis and resection. According to the Paris classification, NPTs are distinguished in slightly elevated (0-IIa, less than 2.5 mm), flat (0-IIb) or slightly depressed (0-IIc). NPTs are usually flat or slightly elevated and tend to spread laterally while in case of depressed lesions, cell proliferation growth progresses in depth in the colonic wall, thus leading to an increased risk of submucosal invasion (SMI) even for smaller neoplasms. NPTs may be frequently missed by inexperienced endoscopists, thus a careful training and precise assessment of all suspected mucosal areas should be performed. Chromoendoscopy or, if possible, narrow-band imaging technique should be considered for the estimation of SMI risk of NPTs, and the characterization of pit pattern and vascular pattern may be useful to predict the risk of SMI and, therefore, to guide the therapeutic decision. Lesions suitable to endoscopic resection are those confined to the mucosa (or superficial layer of submucosa in selected cases) whereas deeper invasion makes endoscopic therapy infeasible. Endoscopic mucosal resection (EMR, piecemeal for LSTs > 20 mm, en bloc for smaller neoplasms) remains the first-line therapy for NPTs, whereas endoscopic submucosal dissection in high-volume centers or surgery should be considered for large LSTs for which en bloc resection is mandatory and cannot be achieved by means of EMR. After piecemeal EMR, follow-up colonoscopy should be performed at 3 mo to assess resection completeness. In case of en bloc resection, surveillance colonoscopy should be scheduled at 3 years for adenomatous lesions ≥ 1 cm, or in presence of villous features or high-grade dysplasia patients (regardless of the size), while less intensive surveillance (colonoscopy at 5-10 years) is needed in case of single (or two) NPT < 1 cm presenting tubular features or low-grade dysplasia at histology.

Non-polypoid colorectal neoplasms: Classification, therapy and follow-up

PubMed Central

Facciorusso, Antonio; Antonino, Matteo; Di Maso, Marianna; Barone, Michele; Muscatiello, Nicola

2015-01-01

In the last years, an increasing interest has been raised on non-polypoid colorectal tumors (NPT) and in particular on large flat neoplastic lesions beyond 10 mm tending to grow laterally, called laterally spreading tumors (LST). LSTs and large sessile polyps have a greater frequency of high-grade dysplasia and local invasiveness as compared to pedunculated lesions of the same size and usually represent a technical challenge for the endoscopist in terms of either diagnosis and resection. According to the Paris classification, NPTs are distinguished in slightly elevated (0-IIa, less than 2.5 mm), flat (0-IIb) or slightly depressed (0-IIc). NPTs are usually flat or slightly elevated and tend to spread laterally while in case of depressed lesions, cell proliferation growth progresses in depth in the colonic wall, thus leading to an increased risk of submucosal invasion (SMI) even for smaller neoplasms. NPTs may be frequently missed by inexperienced endoscopists, thus a careful training and precise assessment of all suspected mucosal areas should be performed. Chromoendoscopy or, if possible, narrow-band imaging technique should be considered for the estimation of SMI risk of NPTs, and the characterization of pit pattern and vascular pattern may be useful to predict the risk of SMI and, therefore, to guide the therapeutic decision. Lesions suitable to endoscopic resection are those confined to the mucosa (or superficial layer of submucosa in selected cases) whereas deeper invasion makes endoscopic therapy infeasible. Endoscopic mucosal resection (EMR, piecemeal for LSTs > 20 mm, en bloc for smaller neoplasms) remains the first-line therapy for NPTs, whereas endoscopic submucosal dissection in high-volume centers or surgery should be considered for large LSTs for which en bloc resection is mandatory and cannot be achieved by means of EMR. After piecemeal EMR, follow-up colonoscopy should be performed at 3 mo to assess resection completeness. In case of en bloc resection, surveillance colonoscopy should be scheduled at 3 years for adenomatous lesions ≥ 1 cm, or in presence of villous features or high-grade dysplasia patients (regardless of the size), while less intensive surveillance (colonoscopy at 5-10 years) is needed in case of single (or two) NPT < 1 cm presenting tubular features or low-grade dysplasia at histology. PMID:25954088

Striving for transparent and credible research: practical guidelines for behavioral ecologists

PubMed Central

Winney, Isabel S.; Krystalli, Anna; Croucher, Michael

2017-01-01

Abstract Science is meant to be the systematic and objective study of the world but evidence suggests that scientific practices are sometimes falling short of this expectation. In this invited idea, we argue that any failure to conduct research according to a documented plan (lack of reliability) and/or any failure to ensure that reconducting the same project would provide the same finding (lack of reproducibility), will result in a low probability of independent studies reaching the same outcome (lack of replicability). After outlining the challenges facing behavioral ecology and science more broadly and incorporating advice from international organizations such as the Center for Open Science (COS), we present clear guidelines and tutorials on what we think open practices represent for behavioral ecologists. In addition, we indicate some of the currently most appropriate and freely available tools for adopting these practices. Finally, we suggest that all journals in our field, such as Behavioral Ecology, give additional weight to transparent studies and therefore provide greater incentives to align our scientific practices to our scientific values. Overall, we argue that producing demonstrably credible science is now fully achievable for the benefit of each researcher individually and for our community as a whole. PMID:29622916

Roles of N-glycans in the polymerization-dependent aggregation of mutant Ig-μ chains in the early secretory pathway.

PubMed

Giannone, Chiara; Fagioli, Claudio; Valetti, Caterina; Sitia, Roberto; Anelli, Tiziana

2017-02-03

The polymeric structure of secretory IgM allows efficient antigen binding and complement fixation. The available structural models place the N-glycans bound to asparagines 402 and 563 of Ig-μ chains within a densely packed core of native IgM. These glycans are found in the high mannose state also in secreted IgM, suggesting that polymerization hinders them to Golgi processing enzymes. Their absence alters polymerization. Here we investigate their role following the fate of aggregation-prone mutant μ chains lacking the Cμ1 domain (μ∆). Our data reveal that μ∆ lacking 563 glycans (μ∆5) form larger intracellular aggregates than μ∆ and are not secreted. Like μ∆, they sequester ERGIC-53, a lectin previously shown to promote polymerization. In contrast, μ∆ lacking 402 glycans (μ∆4) remain detergent soluble and accumulate in the ER, as does a double mutant devoid of both (μ∆4-5). These results suggest that the two C-terminal Ig-μ glycans shape the polymerization-dependent aggregation by engaging lectins and acting as spacers in the alignment of individual IgM subunits in native polymers.

Roles of N-glycans in the polymerization-dependent aggregation of mutant Ig-μ chains in the early secretory pathway

PubMed Central

Giannone, Chiara; Fagioli, Claudio; Valetti, Caterina; Sitia, Roberto; Anelli, Tiziana

2017-01-01

The polymeric structure of secretory IgM allows efficient antigen binding and complement fixation. The available structural models place the N-glycans bound to asparagines 402 and 563 of Ig-μ chains within a densely packed core of native IgM. These glycans are found in the high mannose state also in secreted IgM, suggesting that polymerization hinders them to Golgi processing enzymes. Their absence alters polymerization. Here we investigate their role following the fate of aggregation-prone mutant μ chains lacking the Cμ1 domain (μ∆). Our data reveal that μ∆ lacking 563 glycans (μ∆5) form larger intracellular aggregates than μ∆ and are not secreted. Like μ∆, they sequester ERGIC-53, a lectin previously shown to promote polymerization. In contrast, μ∆ lacking 402 glycans (μ∆4) remain detergent soluble and accumulate in the ER, as does a double mutant devoid of both (μ∆4–5). These results suggest that the two C-terminal Ig-μ glycans shape the polymerization-dependent aggregation by engaging lectins and acting as spacers in the alignment of individual IgM subunits in native polymers. PMID:28157181

Gastroenterology Curriculum in the Canadian Medical School System.

PubMed

Dang, ThucNhi Tran; Wong, Clarence; Bistritz, Lana

2017-01-01

Background and Purpose. Gastroenterology is a diverse subspecialty that covers a wide array of topics. The preclinical gastroenterology curriculum is often the only formal training that medical students receive prior to becoming residents. There is no Canadian consensus on learning objectives or instructional methods and a general lack of awareness of curriculum at other institutions. This results in variable background knowledge for residents and lack of guidance for course development. Objectives. (1) Elucidate gastroenterology topics being taught at the preclinical level. (2) Determine instructional methods employed to teach gastroenterology content. Results . A curriculum map of gastroenterology topics was constructed from 10 of the medical schools that responded. Topics often not taught included pediatric GI diseases, surgery and trauma, food allergies/intolerances, and obesity. Gastroenterology was taught primarily by gastroenterologists and surgeons. Didactic and small group teaching was the most employed teaching method. Conclusion. This study is the first step in examining the Canadian gastroenterology curriculum at a preclinical level. The data can be used to inform curriculum development so that topics generally lacking are better incorporated in the curriculum. The study can also be used as a guide for further curriculum design and alignment across the country.

Micrometer scale guidance of mesenchymal stem cells to form structurally oriented large-scale tissue engineered cartilage.

PubMed

Chou, Chih-Ling; Rivera, Alexander L; Williams, Valencia; Welter, Jean F; Mansour, Joseph M; Drazba, Judith A; Sakai, Takao; Baskaran, Harihara

2017-09-15

Current clinical methods to treat articular cartilage lesions provide temporary relief of the symptoms but fail to permanently restore the damaged tissue. Tissue engineering, using mesenchymal stem cells (MSCs) combined with scaffolds and bioactive factors, is viewed as a promising method for repairing cartilage injuries. However, current tissue engineered constructs display inferior mechanical properties compared to native articular cartilage, which could be attributed to the lack of structural organization of the extracellular matrix (ECM) of these engineered constructs in comparison to the highly oriented structure of articular cartilage ECM. We previously showed that we can guide MSCs undergoing chondrogenesis to align using microscale guidance channels on the surface of a two-dimensional (2-D) collagen scaffold, which resulted in the deposition of aligned ECM within the channels and enhanced mechanical properties of the constructs. In this study, we developed a technique to roll 2-D collagen scaffolds containing MSCs within guidance channels in order to produce a large-scale, three-dimensional (3-D) tissue engineered cartilage constructs with enhanced mechanical properties compared to current constructs. After rolling the MSC-scaffold constructs into a 3-D cylindrical structure, the constructs were cultured for 21days under chondrogenic culture conditions. The microstructure architecture and mechanical properties of the constructs were evaluated using imaging and compressive testing. Histology and immunohistochemistry of the constructs showed extensive glycosaminoglycan (GAG) and collagen type II deposition. Second harmonic generation imaging and Picrosirius red staining indicated alignment of neo-collagen fibers within the guidance channels of the constructs. Mechanical testing indicated that constructs containing the guidance channels displayed enhanced compressive properties compared to control constructs without these channels. In conclusion, using a novel roll-up method, we have developed large scale MSC based tissue-engineered cartilage that shows microscale structural organization and enhanced compressive properties compared to current tissue engineered constructs. Tissue engineered cartilage constructs made with human mesenchymal stem cells (hMSCs), scaffolds and bioactive factors are a promising solution to treat cartilage defects. A major disadvantage of these constructs is their inferior mechanical properties compared to the native tissue, which is likely due to the lack of structural organization of the extracellular matrix of the engineered constructs. In this study, we developed three-dimensional (3-D) cartilage constructs from rectangular scaffold sheets containing hMSCs in micro-guidance channels and characterized their mechanical properties and metabolic requirements. The work led to a novel roll-up method to embed 2-D microscale structures in 3-D constructs. Further, micro-guidance channels incorporated within the 3-D cartilage constructs led to the production of aligned cell-produced matrix and enhanced mechanical function. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A novel technique for reference point generation to aid in intraoral scan alignment.

PubMed

Renne, Walter G; Evans, Zachary P; Mennito, Anthony; Ludlow, Mark

2017-11-12

When using a completely digital workflow on larger prosthetic cases it is often difficult to communicate to the laboratory or chairside Computer Aided Design and Computer Aided Manufacturing system the provisional prosthetic information. The problem arises when common hard tissue data points are limited or non-existent such as in complete arch cases in which the 3D model of the complete arch provisional restorations must be aligned perfectly with the 3D model of the complete arch preparations. In these instances, soft tissue is not enough to ensure an accurate automatic or manual alignment due to a lack of well-defined reference points. A new technique is proposed for the proper digital alignment of the 3D virtual model of the provisional prosthetic to the 3D virtual model of the prepared teeth in cases where common and coincident hard tissue data points are limited. Clinical considerations: A technique is described in which fiducial composite resin dots are temporarily placed on the intraoral keratinized tissue in strategic locations prior to final impressions. These fiducial dots provide coincident and clear 3D data points that when scanned into a digital impression allow superimposition of the 3D models. Composite resin dots on keratinized tissue were successful at allowing accurate merging of provisional restoration and post-preparation 3D models for the purpose of using the provisional restorations as a guide for final CLINICAL SIGNIFICANCE: Composite resin dots placed temporarily on attached tissue were successful at allowing accurate merging of the provisional restoration 3D models to the preparation 3D models for the purposes of using the provisional restorations as a guide for final restoration design and manufacturing. In this case, they allowed precise superimposition of the 3D models made in the absence of any other hard tissue reference points, resulting in the fabrication of ideal final restorations. © 2017 Wiley Periodicals, Inc.

Instrumentation Strategies to Reduce the Risks of Proximal Junctional Kyphosis in Adult Scoliosis: A Detailed Biomechanical Analysis.

PubMed

Aubin, Carl-Eric; Cammarata, Marco; Wang, Xiaoyu; Mac-Thiong, Jean-Marc

2015-05-01

Biomechanical analysis of proximal junctional kyphosis (PJK) through numerical simulations. Assessment of the effect of sagittal alignment, the upper instrumented vertebral level (UIV), and 4 other surgical variables on biomechanical indices related to the PJK risks. Despite retrospective clinical studies, biomechanical analysis of individual parameters associated with PJK is lacking to support instrumentation strategies to reduce the PJK risks. Instrumentations of 6 adult scoliosis cases with different operative strategies were simulated (1,152 simulations). Proximal junctional (PJ) angle and flexion loads were evaluated against the sagittal alignment and the proximal instrumentation level. Instrumenting 1 more proximal vertebra allowed the PJ angle, proximal moment, and force to be reduced by 18%, 25%, and 16%, respectively. Shifting sagittal alignment by 20 mm posteriorly increased the PJ angle and proximal moment by 16% and 22%, and increased the equivalent posterior extensor force by 37%. Bilateral complete facetectomy, posterior ligaments resection, and the combination of the 2 resulted in an increase of the PJ angle (by 10%, 28%, and 53%, respectively), flexion forces (by 4%, 12%, and 22%, respectively), and proximal moments (by 16%, 44%, and 83%, respectively). Transverse process hooks at UIV compared with pedicle screws allowed 26% lower PJ angle and flexion loads. The use of proximal transition rods with proximal diameter reduced from 5.5 to 4 mm slightly reduced PJ angle, flexion force, and moment (less than 8%). The increase in sagittal rod curvature from 10° to 40° increased the PJ angle (from 6% to 19%), flexion force (from 3% to 10%), and moment (from 9% to 27%). Simulated posteriorly shifted sagittal alignment was associated with higher PJK risks, whereas extending instrumentation proximally allowed a lower mechanical risk of PJK. Preserving PJ intervertebral elements and using a more flexible anchorage at UIV help reduce the biomechanical risks of PJK. Copyright © 2015 Scoliosis Research Society. Published by Elsevier Inc. All rights reserved.

Value of History, Physical Examination, and Radiographic Findings in the Diagnosis of Symptomatic Meniscal Tear Among Middle-Aged Subjects With Knee Pain.

PubMed

Katz, Jeffrey N; Smith, Savannah R; Yang, Heidi Y; Martin, Scott D; Wright, John; Donnell-Fink, Laurel A; Losina, Elena

2017-04-01

To evaluate the utility of clinical history, radiographic findings, and physical examination findings in the diagnosis of symptomatic meniscal tear (SMT) in patients over age 45 years, in whom concomitant osteoarthritis is prevalent. In a cross-sectional study of patients from 2 orthopedic surgeons' clinics, we assessed clinical history, physical examination findings, and radiographic findings in patients age >45 years with knee pain. The orthopedic surgeons rated their confidence that subjects' symptoms were due to meniscal tear; we defined the diagnosis of SMT as at least 70% confidence. We used logistic regression to identify factors independently associated with diagnosis of SMT, and we used the regression results to construct an index of the likelihood of SMT. In 174 participants, 6 findings were associated independently with the expert clinician having ≥70% confidence that symptoms were due to meniscal tear: localized pain, ability to fully bend the knee, pain duration <1 year, lack of varus alignment, lack of pes planus, and absence of joint space narrowing on radiographs. The index identified a low-risk group with 3% likelihood of SMT. While clinicians traditionally rely upon mechanical symptoms in this diagnostic setting, our findings did not support the conclusion that mechanical symptoms were associated with the expert's confidence that symptoms were due to meniscal tear. An index that includes history of localized pain, full flexion, duration <1 year, pes planus, varus alignment, and joint space narrowing can be used to stratify patients according to their risk of SMT, and it identifies a subgroup with very low risk. © 2016, American College of Rheumatology.

Safety risks associated with the lack of integration and interfacing of hospital health information technologies: a qualitative study of hospital electronic prescribing systems in England.

PubMed

Cresswell, Kathrin M; Mozaffar, Hajar; Lee, Lisa; Williams, Robin; Sheikh, Aziz

2017-07-01

Substantial sums of money are being invested worldwide in health information technology. Realising benefits and mitigating safety risks is however highly dependent on effective integration of information within systems and/or interfacing to allow information exchange across systems. As part of an English programme of research, we explored the social and technical challenges relating to integration and interfacing experienced by early adopter hospitals of standalone and hospital-wide multimodular integrated electronic prescribing (ePrescribing) systems. We collected longitudinal qualitative data from six hospitals, which we conceptualised as case studies. We conducted 173 interviews with users, implementers and software suppliers (at up to three different times), 24 observations of system use and strategic meetings, 17 documents relating to implementation plans, and 2 whole-day expert round-table discussions. Data were thematically analysed initially within and then across cases, drawing on perspectives surrounding information infrastructures. We observed that integration and interfacing problems obstructed effective information transfer in both standalone and multimodular systems, resulting in threats to patient safety emerging from the lack of availability of timely information and duplicate data entry. Interfacing problems were immediately evident in some standalone systems where users had to cope with multiple log-ins, and this did not attenuate over time. Multimodular systems appeared at first sight to obviate such problems. However, with these systems, there was a perceived lack of data coherence across modules resulting in challenges in presenting a comprehensive overview of the patient record, this possibly resulting from the piecemeal implementation of modules with different functionalities. Although it was possible to access data from some primary care systems, we found poor two-way transfer of data between hospitals and primary care necessitating workarounds, which in turn led to the opportunity for new errors associated with duplicate and manual information transfer. Extending ePrescribing to include modules with other clinically important information needed to support care was still an aspiration in most sites, although some advanced multimodular systems had begun implementing this functionality. Multimodular systems were, however, seen as being difficult to interface with external systems. The decision to pursue a strategy of purchasing standalone systems and then interfacing these, or one of buying hospital-wide multimodular systems, is a pivotal one for hospitals in realising the vision of achieving a fully integrated digital record, and this should be predicated on a clear appreciation of the relative trade-offs between these choices. While multimodular systems offered somewhat better usability, standalone systems provided greater flexibility and opportunity for innovation, particularly in relation to interoperability with external systems and in relation to customisability to the needs of different user groups. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Role of Australian primary healthcare organisations (PHCOs) in primary healthcare (PHC) workforce planning: lessons from abroad.

PubMed

Naccarella, Lucio; Buchan, James; Newton, Bill; Brooks, Peter

2011-08-01

To review international experience in order to inform Australian PHC workforce policy on the role of primary healthcare organisations (PHCOs/Medicare Locals) in PHC workforce planning. A NZ and UK study tour was conducted by the lead author, involving 29 key informant interviews with regard to PHCOs roles and the effect on PHC workforce planning. Interviews were audio-taped with consent, transcribed and analysed thematically. Emerging themes included: workforce planning is a complex, dynamic, iterative process and key criteria exist for doing workforce planning well; PHCOs lacked a PHC workforce policy framework to do workforce planning; PHCOs lacked authority, power and appropriate funding to do workforce planning; there is a need to align workforce planning with service planning; and a PHC Workforce Planning and Development Benchmarking Database is essential for local planning and evaluating workforce reforms. With the Australian government promoting the role of PHCOs in health system reform, reflections from abroad highlight the key action within PHC and PHCOs required to optimise PHC workforce planning.

Radiology operations: what you don't know could be costing you millions.

PubMed

Joffe, Sam; Drew, Donna; Bansal, Manju; Hase, Michael

2007-01-01

Rapid growth in advanced imaging procedures has left hospital radiology departments struggling to keep up with demand, resulting in loss of patients to facilities that can offer service more quickly. While the departments appear to be working at full capacity, an operational analysis of over 400 hospital radiology departments in the US by GE Healthcare has determined that, paradoxically, many departments are in fact underutilized and operating for below their potential capacity. While CT cycle time in hospitals that were studied averaged 35 minutes, top performing hospitals operated the same equipment at a cycle time of 15 minutes, yielding approximately double the throughput volume. Factors leading to suboptimal performance include accounting metrics that mask true performance, leadership focus on capital investment rather than operations, under staffing, under scheduling, poorly aligned incentives, a fragmented view of operations, lack of awareness of latent opportunities, and lack of sufficient skills and processes to implement improvements. The study showed how modest investments in radiology operations can dramatically improve access to services and profitability.

ProvenCare-Psoriasis: A disease management model to optimize care.

PubMed

Gionfriddo, Michael R; Pulk, Rebecca A; Sahni, Dev R; Vijayanagar, Sonal G; Chronowski, Joseph J; Jones, Laney K; Evans, Michael A; Feldman, Steven R; Pride, Howard

2018-03-15

There are a variety of evidence-based treatments available for psoriasis. The transition of this evidence into practice is challenging. In this article, we describe the design of our disease management approach for Psoriasis (ProvenCare®) and present preliminary evidence of the effect of its implementation. In designing our approach, we identified three barriers to optimal care: 1) lack of a standardized and discrete disease activity measure within the electronic health record, 2) lack of a system-wide, standardized approach to care, and 3) non-uniform financial access to appropriate non-pharmacologic treatments. We implemented several solutions, which collectively form our approach. We standardized the documentation of clinical data such as body surface area (BSA), created a disease management algorithm for psoriasis, and aligned incentives to facilitate the implementation of the algorithm. This approach provides more coordinated, cost effective care for psoriasis, while being acceptable to key stakeholders. Future work will examine the effect of the implementation of our approach on important clinical and patient outcomes.

Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography.

PubMed

Galaz-Montoya, Jesús G; Hecksel, Corey W; Baldwin, Philip R; Wang, Eryu; Weaver, Scott C; Schmid, Michael F; Ludtke, Steven J; Chiu, Wah

2016-06-01

Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen, the cryo-electron microscopy (cryoEM) grid and/or the carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions. Copyright © 2016 Elsevier Inc. All rights reserved.

Health sector operational planning and budgeting processes in Kenya—“never the twain shall meet”

PubMed Central

Molyneux, Sassy; Goodman, Catherine

2015-01-01

Summary Operational planning is considered an important tool for translating government policies and strategic objectives into day‐to‐day management activities. However, developing countries suffer from persistent misalignment between policy, planning and budgeting. The Medium Term Expenditure Framework (MTEF) was introduced to address this misalignment. Kenya adopted the MTEF in the early 2000s, and in 2005, the Ministry of Health adopted the Annual Operational Plan process to adapt the MTEF to the health sector. This study assessed the degree to which the health sector Annual Operational Plan process in Kenya has achieved alignment between planning and budgeting at the national level, using document reviews, participant observation and key informant interviews. We found that the Kenyan health sector was far from achieving planning and budgeting alignment. Several factors contributed to this problem including weak Ministry of Health stewardship and institutionalized separation between planning and budgeting processes; a rapidly changing planning and budgeting environment; lack of reliable data to inform target setting and poor participation by key stakeholders in the process including a top‐down approach to target setting. We conclude that alignment is unlikely to be achieved without consideration of the specific institutional contexts and the power relationships between stakeholders. In particular, there is a need for institutional integration of the planning and budgeting processes into a common cycle and framework with common reporting lines and for improved data and local‐level input to inform appropriate and realistic target setting. © 2015 The Authors. International Journal of Health Planning and Management published by John Wiley & Sons, Ltd. PMID:25783862

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

PubMed

Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

2005-01-01

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

Alignment Algorithms and Per-Particle CTF Correction for Single Particle Cryo-Electron Tomography

PubMed Central

Galaz-Montoya, Jesús G.; Hecksel, Corey W.; Baldwin, Philip R.; Wang, Eryu; Weaver, Scott C.; Schmid, Michael F.; Ludtke, Steven J.; Chiu, Wah

2016-01-01

Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen grid and carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions. PMID:27016284

[Leaders as intermediates between economic incentive models and professional motivation].

PubMed

Korlén, Sara; Essén, Anna; Lindgren, Peter; Amer-Wåhlin, Isis; von Thiele Schwarz, Ulrica

2018-05-24

The application of economic incentives to providers in health care governance is debated. Advocates argue that it drives efficiency and improvement, opponents claim that it leads to unintended consequences for patients and professionals. Research shows that incentives can increase well-defined activities and targets, but there is a lack of substantial evidence that applications in health care lead to desired outcomes. The motivational literature acknowledges internal sources of motivation as important determinants of behavior, and the literature about professions suggests that professional values of serving patient needs is a key motivator. The management literature identifies the important role of leaders in aligning external demands and rewards to staff preferences, using their own management and leadership skills. Findings in health services research confirm the vital role of leaders for successful implementation and improvement work. In sum, internal motivators and the role of leaders are important to acknowledge also when understanding how economic governance models are put into practice.Our recently published qualitative case study provides empirical examples of how clinical leaders function as intermediaries between a local care choice model, including financial incentives, and the motivation of staff. The strategies deployed by the leaders aimed to align the economic logics of the model to the professional focus on increasing patient value. The main conclusion from these empirical examples, as well as previous research, is that health care managers play a key role in aligning economic incentive models with professional values and in translating such models in to feasible tasks related to the provision of high quality care.

Is the sagittal postural alignment different in normal and dysphonic adult speakers?

PubMed

Franco, Débora; Martins, Fernando; Andrea, Mário; Fragoso, Isabel; Carrão, Luís; Teles, Júlia

2014-07-01

Clinical research in the field of voice disorders, in particular functional dysphonia, has suggested abnormal laryngeal posture due to muscle adaptive changes, although specific evidence regarding body posture has been lacking. The aim of our study was to verify if there were significant differences in sagittal spine alignment between normal (41 subjects) and dysphonic speakers (33 subjects). Cross-sectional study. Seventy-four adults, 35 males and 39 females, were submitted to sagittal plane photographs so that spine alignment could be analyzed through the Digimizer-MedCalc Software Ltd program. Perceptual and acoustic evaluation and nasoendoscopy were used for dysphonic judgments: normal and dysphonic speakers. For thoracic length curvature (TL) and for the kyphosis index (KI), a significant effect of dysphonia was observed with mean TL and KI significantly higher for the dysphonic speakers than for the normal speakers. Concerning the TL variable, a significant effect of sex was found, in which the mean of the TL was higher for males than females. The interaction between dysphonia and sex did not have a significant effect on TL and KI variables. For the lumbar length curvature variable, a significant main effect of sex was demonstrated; there was no significant main effect of dysphonia or significant sex×dysphonia interaction. Findings indicated significant differences in some sagittal spine posture measures between normal and dysphonic speakers. Postural measures can add useful information to voice assessment protocols and should be taken into account when considering particular treatment strategies. Copyright © 2014 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

Kinematic evaluation of the classical ballet step "plié".

PubMed

Gontijo, Kaanda Nabilla Souza; Candotti, Cláudia Tarragô; Feijó, Grace Dos Santos; Ribeiro, Lais Paixão; Loss, Jefferson Fagundes

2015-06-01

Lack of alignment between the lowerlimb structures, such as the hips, knees, and longitudinal arches of the feet, has been described as an important predisposing factor in musculoskeletal injury among classical ballet dancers. However, no studies were found that analyzed basic ballet movements with quantification of objective criteria of the movements. The purposes of this study were: 1. to establish a methodology to quantify, using kinematic evaluation, the technical criteria that guide the correct execution of all phases of the plié (simultaneous flexion of the hips, knees, and ankle joints); and 2. to explore whether experienced ballet dancers respect those criteria when performing the plié. The technical criteria considered were the following: 1. midfoot stability; 2. pelvic positioning in a neutral alignment; 3. pelvic stability, represented by pelvic angle variation; and 4. vertical alignment of the knee joint with the second toe of the ipsilateral foot. Twenty dancers from Porto Alegre, Brazil, with 18 years of uninterrupted ballet training, were filmed while performing plié using four synchronized cameras. The descriptive statistical analysis involved calculating the median, minimum, and maximum of each of the technical criteria. Results showed that for criterion 1, the 20 dancers showed great stabilization of the midfoot; for criteria 2 and 3, 18 dancers displayed pelvic instability tending toward retroversion throughout execution of the plié; and for criterion 4, 13 dancers presented with medial misalignment of the knees at all phases of the plié. Using these criteria, it was possible to characterize the plié from a kinematic point of view.

A case report of historical trauma among American Indians on a rural Northern Plains reservation.

PubMed

Heckert, Wende; Eisenhauer, Christine

2014-01-01

This case report describes historical trauma on a rural American Indian reservation and outlines participatory action approaches for nurses. The prevalence of historical trauma often goes unnoticed by healthcare professionals because of its multifaceted nature and subsequent lack of provider understanding. Nurses accustomed to looking only for physical and psychosocial signs of trauma may not specifically understand how to align significant historical trauma events with prevention, education, and healthcare delivery. Nursing interventions developed through participatory action and directed at individual, family, and community levels of care are most effective in treating and preventing cumulative effects of historical trauma.

The case for transforming governmental public health.

PubMed

Salinsky, Eileen; Gursky, Elin A

2006-01-01

Changing threats to the public's health necessitate a profound transformation of the public health enterprise. Despite recent attention to the biodefense role of public health, policymakers have not developed a clear, realistic vision for the structure and functionality of the governmental public health system. Lack of leadership and organizational disconnects across levels of government have prevented strategic alignment of resources and undermined momentum for meaningful change. A transformed public health system is needed to address the demands of emergency preparedness and health protection. Such transformation should include focused, risk-based resource allocation; regional planning; technological upgrades; workforce restructuring; improved integration of private-sector assets; and better performance monitoring.

Image RPI Reawakens Plasmaspheric Refilling Research

NASA Technical Reports Server (NTRS)

Gallagher, D. L.; Smith, Z. B.

2007-01-01

The plasmasphere is a toroidal region of cold plasma surrounding the Earth that results from ionospheric outflow and accumulation. The physics of refilling and the dynamics of this region have been studied for nearly 50-years. During that time many models have been proposed, but little has been done to test these models due to a lack of observational information. With the launch of the IMAGE Mission in March 2000 the Radio Plasma Imager has provided true field aligned density measurements that uniquely enable the testing of these models and a final determination of the physical processes important for the plasmasphere's recovery from storm-time conditions.

Graph edit distance from spectral seriation.

PubMed

Robles-Kelly, Antonio; Hancock, Edwin R

2005-03-01

This paper is concerned with computing graph edit distance. One of the criticisms that can be leveled at existing methods for computing graph edit distance is that they lack some of the formality and rigor of the computation of string edit distance. Hence, our aim is to convert graphs to string sequences so that string matching techniques can be used. To do this, we use a graph spectral seriation method to convert the adjacency matrix into a string or sequence order. We show how the serial ordering can be established using the leading eigenvector of the graph adjacency matrix. We pose the problem of graph-matching as a maximum a posteriori probability (MAP) alignment of the seriation sequences for pairs of graphs. This treatment leads to an expression in which the edit cost is the negative logarithm of the a posteriori sequence alignment probability. We compute the edit distance by finding the sequence of string edit operations which minimizes the cost of the path traversing the edit lattice. The edit costs are determined by the components of the leading eigenvectors of the adjacency matrix and by the edge densities of the graphs being matched. We demonstrate the utility of the edit distance on a number of graph clustering problems.

ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.

PubMed

Otto, Thomas Dan; Catanho, Marcos; Tristão, Cristian; Bezerra, Márcia; Fernandes, Renan Mathias; Elias, Guilherme Steinberger; Scaglia, Alexandre Capeletto; Bovermann, Bill; Berstis, Viktors; Lifschitz, Sergio; de Miranda, Antonio Basílio; Degrave, Wim

2010-03-01

Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith-Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach. The database can be accessed through http://proteinworlddb.org

Mycofier: a new machine learning-based classifier for fungal ITS sequences.

PubMed

Delgado-Serrano, Luisa; Restrepo, Silvia; Bustos, Jose Ricardo; Zambrano, Maria Mercedes; Anzola, Juan Manuel

2016-08-11

The taxonomic and phylogenetic classification based on sequence analysis of the ITS1 genomic region has become a crucial component of fungal ecology and diversity studies. Nowadays, there is no accurate alignment-free classification tool for fungal ITS1 sequences for large environmental surveys. This study describes the development of a machine learning-based classifier for the taxonomical assignment of fungal ITS1 sequences at the genus level. A fungal ITS1 sequence database was built using curated data. Training and test sets were generated from it. A Naïve Bayesian classifier was built using features from the primary sequence with an accuracy of 87 % in the classification at the genus level. The final model was based on a Naïve Bayes algorithm using ITS1 sequences from 510 fungal genera. This classifier, denoted as Mycofier, provides similar classification accuracy compared to BLASTN, but the database used for the classification contains curated data and the tool, independent of alignment, is more efficient and contributes to the field, given the lack of an accurate classification tool for large data from fungal ITS1 sequences. The software and source code for Mycofier are freely available at https://github.com/ldelgado-serrano/mycofier.git .

SYNCHRONIZATION OF HETEROGENEOUS OSCILLATORS UNDER NETWORK MODIFICATIONS: PERTURBATION AND OPTIMIZATION OF THE SYNCHRONY ALIGNMENT FUNCTION

PubMed Central

Taylor, Dane; Skardal, Per Sebastian; Sun, Jie

2016-01-01

Synchronization is central to many complex systems in engineering physics (e.g., the power-grid, Josephson junction circuits, and electro-chemical oscillators) and biology (e.g., neuronal, circadian, and cardiac rhythms). Despite these widespread applications—for which proper functionality depends sensitively on the extent of synchronization—there remains a lack of understanding for how systems can best evolve and adapt to enhance or inhibit synchronization. We study how network modifications affect the synchronization properties of network-coupled dynamical systems that have heterogeneous node dynamics (e.g., phase oscillators with non-identical frequencies), which is often the case for real-world systems. Our approach relies on a synchrony alignment function (SAF) that quantifies the interplay between heterogeneity of the network and of the oscillators and provides an objective measure for a system’s ability to synchronize. We conduct a spectral perturbation analysis of the SAF for structural network modifications including the addition and removal of edges, which subsequently ranks the edges according to their importance to synchronization. Based on this analysis, we develop gradient-descent algorithms to efficiently solve optimization problems that aim to maximize phase synchronization via network modifications. We support these and other results with numerical experiments. PMID:27872501

Circadian clocks of both plants and pollinators influence flower seeking behavior of the pollinator hawkmoth Manduca sexta.

PubMed

Fenske, Myles P; Nguyen, LeAnn P; Horn, Erin K; Riffell, Jeffrey A; Imaizumi, Takato

2018-02-12

Most plant-pollinator interactions occur during specific periods during the day. To facilitate these interactions, many flowers are known to display their attractive qualities, such as scent emission and petal opening, in a daily rhythmic fashion. However, less is known about how the internal timing mechanisms (the circadian clocks) of plants and animals influence their daily interactions. We examine the role of the circadian clock in modulating the interaction between Petunia and one of its pollinators, the hawkmoth Manduca sexta. We find that desynchronization of the Petunia circadian clock affects moth visitation preference for Petunia flowers. Similarly, moths with circadian time aligned to plants show stronger flower-foraging activities than moths that lack this alignment. Moth locomotor activity is circadian clock-regulated, although it is also strongly repressed by light. Moths show a time-dependent burst increase in flight activity during subjective night. In addition, moth antennal responsiveness to the floral scent compounds exhibits a 24-hour rhythm in both continuous light and dark conditions. This study highlights the importance of the circadian clocks in both plants and animals as a crucial factor in initiating specialized plant-pollinator relationships.

Depth map occlusion filling and scene reconstruction using modified exemplar-based inpainting

NASA Astrophysics Data System (ADS)

Voronin, V. V.; Marchuk, V. I.; Fisunov, A. V.; Tokareva, S. V.; Egiazarian, K. O.

2015-03-01

RGB-D sensors are relatively inexpensive and are commercially available off-the-shelf. However, owing to their low complexity, there are several artifacts that one encounters in the depth map like holes, mis-alignment between the depth and color image and lack of sharp object boundaries in the depth map. Depth map generated by Kinect cameras also contain a significant amount of missing pixels and strong noise, limiting their usability in many computer vision applications. In this paper, we present an efficient hole filling and damaged region restoration method that improves the quality of the depth maps obtained with the Microsoft Kinect device. The proposed approach is based on a modified exemplar-based inpainting and LPA-ICI filtering by exploiting the correlation between color and depth values in local image neighborhoods. As a result, edges of the objects are sharpened and aligned with the objects in the color image. Several examples considered in this paper show the effectiveness of the proposed approach for large holes removal as well as recovery of small regions on several test images of depth maps. We perform a comparative study and show that statistically, the proposed algorithm delivers superior quality results compared to existing algorithms.

Modular microfluidic systems using reversibly attached PDMS fluid control modules

NASA Astrophysics Data System (ADS)

Skafte-Pedersen, Peder; Sip, Christopher G.; Folch, Albert; Dufva, Martin

2013-05-01

The use of soft lithography-based poly(dimethylsiloxane) (PDMS) valve systems is the dominating approach for high-density microscale fluidic control. Integrated systems enable complex flow control and large-scale integration, but lack modularity. In contrast, modular systems are attractive alternatives to integration because they can be tailored for different applications piecewise and without redesigning every element of the system. We present a method for reversibly coupling hard materials to soft lithography defined systems through self-aligning O-ring features thereby enabling easy interfacing of complex-valve-based systems with simpler detachable units. Using this scheme, we demonstrate the seamless interfacing of a PDMS-based fluid control module with hard polymer chips. In our system, 32 self-aligning O-ring features protruding from the PDMS fluid control module form chip-to-control module interconnections which are sealed by tightening four screws. The interconnection method is robust and supports complex fluidic operations in the reversibly attached passive chip. In addition, we developed a double-sided molding method for fabricating PDMS devices with integrated through-holes. The versatile system facilitates a wide range of applications due to the modular approach, where application specific passive chips can be readily attached to the flow control module.

Design of Urban Public Spaces: Intent vs. Reality

PubMed Central

Martin, W. Mike; Stewart, Tom; Troelsen, Jens

2018-01-01

This study investigated how two public spaces for sport and recreation were utilized by different user groups, and how this aligned with the initial design objectives for these spaces. Two newly built urban spaces situated in Copenhagen, Denmark, provided the context for this investigation. The System for Observing Play and Recreation in Communities (SOPARC) was used to examine the physical activity of users in these two urban spaces. The architects responsible for designing each space were interviewed to ascertain the intended target group of each space and to unravel the reasons behind the design decisions. The SOPARC observations revealed that males were more vigorously active than females when using the recreation facilities, and the observed users did not align with the intended target groups. The interviews suggested that design decisions were based on minimal interdisciplinary knowledge, and that expert knowledge was chosen randomly. These findings point to a systematic lack of evidence-based practice when designing sport and recreational facilities. This article has implications for landscape architects and urban planners; a new method must be developed to embed interdisciplinary knowledge in the planning process of future sport and recreation projects. This must be done in a systematic way to make the design process transparent. PMID:29690509

Direct observation of the alignment of ferromagnetic spins by antiferromagnetic spins

NASA Astrophysics Data System (ADS)

Nolting, F.; Scholl, A.; Stöhr, J.; Seo, J. W.; Fompeyrine, J.; Siegwart, H.; Locquet, J.-P.; Anders, S.; Lüning, J.; Fullerton, E. E.; Toney, M. F.; Scheinfein, M. R.; Padmore, H. A.

2000-06-01

The arrangement of spins at interfaces in a layered magnetic material often has an important effect on the properties of the material. One example of this is the directional coupling between the spins in an antiferromagnet and those in an adjacent ferromagnet, an effect first discovered in 1956 and referred to as exchange bias. Because of its technological importance for the development of advanced devices such as magnetic read heads and magnetic memory cells, this phenomenon has received much attention. Despite extensive studies, however, exchange bias is still poorly understood, largely due to the lack of techniques capable of providing detailed information about the arrangement of magnetic moments near interfaces. Here we present polarization-dependent X-ray magnetic dichroism spectro-microscopy that reveals the micromagnetic structure on both sides of a ferromagnetic-antiferromagnetic interface. Images of thin ferromagnetic Co films grown on antiferromagnetic LaFeO3 show a direct link between the arrangement of spins in each material. Remanent hysteresis loops, recorded for individual ferromagnetic domains, show a local exchange bias. Our results imply that the alignment of the ferromagnetic spins is determined, domain by domain, by the spin directions in the underlying antiferromagnetic layer.

The phylogeny and evolutionary history of tyrannosauroid dinosaurs.

PubMed

Brusatte, Stephen L; Carr, Thomas D

2016-02-02

Tyrannosauroids--the group of carnivores including Tyrannosaurs rex--are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography, and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent, and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued, and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work.

The phylogeny and evolutionary history of tyrannosauroid dinosaurs

PubMed Central

Brusatte, Stephen L.; Carr, Thomas D.

2016-01-01

Tyrannosauroids—the group of carnivores including Tyrannosaurs rex—are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography, and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent, and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued, and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work. PMID:26830019

Some aspects of the reform of the health care systems in Austria, Germany and Switzerland.

PubMed

Theurl, E

1999-01-01

The health care systems in Austria, Germany and Switzerland owe their institutional structure to different historical developments. While Austria and Germany voted for the Bismarck-Model of social health insurance, Switzerland adopted a voluntary system of health insurance. In all three countries, until very recently, the different challenges which the health care sector faced were met by piecemeal approaches and by stop and go policies, which, in the long run were not very successful either in containing costs or in improving efficacy and efficiency. During the 1990 more fundamental reforms in the health care systems of all three countries took place. Germany and Switzerland chose the path of deregulation of the health insurance system, which consequently strengthened the competition between the insurance companies, and, to some extent between the suppliers of medical services. While this can be seen as an essential part of the reform process for these two countries. Austria favors a state-oriented and interventionist approach in order to meet the challenges.

Serotonin dynamics in and around the central nervous system: is autism solvable without fundamental insights?

PubMed

Janušonis, Skirmantas

2014-12-01

Altered serotonin (5-hydroxytryptamine, 5-HT) signaling has been implicated in some developmental abnormalities of autism spectrum disorder (ASD). However, the presumed role of 5-HT in ASD raises new questions in fundamental neuroscience. Specifically, it is not clear if the current piecemeal approach to 5-HT signaling in the mammalian body is effective and whether new conceptual approaches may be required. This review briefly discusses 5-HT production and circulation in the central nervous system and outside of it, especially with regard to ASD, and proposes a more encompassing approach that questions the utility of the "neurotransmitter" concept. It then introduces the idea of a generalized 5-HT packet that may offer insights into possible links between serotonergic varicosities and blood platelets. These approaches have theoretical significance, but they are also well positioned to advance our understanding of some long-standing problems in autism research. Copyright © 2014 ISDN. Published by Elsevier Ltd. All rights reserved.

Our Cannibalistic Galaxy

NASA Astrophysics Data System (ADS)

Majewski, S. R.

2004-12-01

It is now evident that our Milky Way has cannibalistic tendencies. Recently found examples of satellite star systems being digested by our galaxy demonstrate that Milky Way-like spiral galaxies continue to grow through the piecemeal accumulation of mass from smaller neighbors, as predicted by Cold Dark Matter (CDM) models of structure formation. Cross-sections of the Milky Way halo reveal it to be networked with long-lived, coherent debris streams of stars and star clusters that attest to its accretive formation. These dynamically cold streams, created from the tidal disruption of satellite star systems, in turn provide useful tools to explore both the nature of Galactic dwarf satellites as well as the the dark matter distribution of the Milky Way; the results of such work, however, yield some unexpected results compared to current CDM models. (Research described has been supported by NASA/JPL, the National Science Foundation, The David and Lucile Packard Foundation, the Research Corporation, and the F.H. Levinson Fund of the Peninsula Community Foundation.)

Enhancements Needed in GE Crop and Food Regulation in the U.S.

PubMed Central

Benbrook, Charles

2016-01-01

Genetically engineered (GE) crops, multi-ingredient foods derived from one or more GE ingredients, and GE agricultural inputs are regulated in the United States under a “Coordinated Framework” that was literally cobbled together in the early 1990s. Via this Framework, responsibility is spread across three federal agencies for the assessment and management of potential risks arising from the planting of GE crops, the raising of GE animals, or uses of GE inputs. The Framework was incomplete and conceptually flawed from the beginning. Despite multiple, piecemeal efforts to update aspects of GE risk assessment and regulatory policy, the Coordinated Framework survives to this day largely unchanged. Its shortcomings are recognized in both the scientific and legal communities, but meaningful reforms thus far remain out of reach, blocked by the intense controversy now surrounding all things biotech. Five generic reforms and another five specific initiatives are described to create a more robust, science-driven GE regulatory infrastructure in the U.S. PMID:27066473

The phylogeny and evolutionary history of tyrannosauroid dinosaurs

NASA Astrophysics Data System (ADS)

Brusatte, Stephen L.; Carr, Thomas D.

2016-02-01

Tyrannosauroids—the group of carnivores including Tyrannosaurs rex—are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography, and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent, and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued, and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work.

Unified-theory-of-reinforcement neural networks do not simulate the blocking effect.

PubMed

Calvin, Nicholas T; J McDowell, J

2015-11-01

For the last 20 years the unified theory of reinforcement (Donahoe et al., 1993) has been used to develop computer simulations to evaluate its plausibility as an account for behavior. The unified theory of reinforcement states that operant and respondent learning occurs via the same neural mechanisms. As part of a larger project to evaluate the operant behavior predicted by the theory, this project was the first replication of neural network models based on the unified theory of reinforcement. In the process of replicating these neural network models it became apparent that a previously published finding, namely, that the networks simulate the blocking phenomenon (Donahoe et al., 1993), was a misinterpretation of the data. We show that the apparent blocking produced by these networks is an artifact of the inability of these networks to generate the same conditioned response to multiple stimuli. The piecemeal approach to evaluate the unified theory of reinforcement via simulation is critiqued and alternatives are discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Implications of intelligent, integrated microsystems for product design and development

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

MYERS,DAVID R.; MCWHORTER,PAUL J.

2000-04-19

Intelligent, integrated microsystems combine some or all of the functions of sensing, processing information, actuation, and communication within a single integrated package, and preferably upon a single silicon chip. As the elements of these highly integrated solutions interact strongly with each other, the microsystem can be neither designed nor fabricated piecemeal, in contrast to the more familiar assembled products. Driven by technological imperatives, microsystems will best be developed by multi-disciplinary teams, most likely within the flatter, less hierarchical organizations. Standardization of design and process tools around a single, dominant technology will expedite economically viable operation under a common production infrastructure.more » The production base for intelligent, integrated microsystems has elements in common with the mathematical theory of chaos. Similar to chaos theory, the development of microsystems technology will be strongly dependent on, and optimized to, the initial product requirements that will drive standardization--thereby further rewarding early entrants to integrated microsystem technology.« less

Caldera collapse: Perspectives from comparing Galápagos volcanoes, nuclear-test sinks, sandbox models, and volcanoes on Mars

USGS Publications Warehouse

Howard, K.A.

2010-01-01

The 1968 trapdoor collapse (1.5 km3) of Fernandina caldera in the Galapágos Islands developed the same kinds of structures as found in small sandbox-collapse models and in concentrically zoned sinks formed in desert alluvium by fault subsidence into underground nuclear-explosion cavities. Fernandina’s collapse developed through shear failure in which the roof above the evacuating chamber was lowered mostly intact. This coherent subsidence contrasts to chaotic piecemeal collapse at small, rocky pit craters, underscoring the role of rock strength relative to subsidence size. The zoning at Fernandina implies that the deflated magma chamber underlay a central basin and a bordering inward-dipping monocline, which separates a blind inner reverse fault from an outer zone of normal faulting. Similar concentric zoning patterns can be recognized in coherent subsidence structures ranging over 16 orders of magnitude in size, from sandbox experiments to the giant Olympus Mons caldera on Mars.

Charon Toolkit for Parallel, Implicit Structured-Grid Computations: Functional Design

NASA Technical Reports Server (NTRS)

VanderWijngaart, Rob F.; Kutler, Paul (Technical Monitor)

1997-01-01

In a previous report the design concepts of Charon were presented. Charon is a toolkit that aids engineers in developing scientific programs for structured-grid applications to be run on MIMD parallel computers. It constitutes an augmentation of the general-purpose MPI-based message-passing layer, and provides the user with a hierarchy of tools for rapid prototyping and validation of parallel programs, and subsequent piecemeal performance tuning. Here we describe the implementation of the domain decomposition tools used for creating data distributions across sets of processors. We also present the hierarchy of parallelization tools that allows smooth translation of legacy code (or a serial design) into a parallel program. Along with the actual tool descriptions, we will present the considerations that led to the particular design choices. Many of these are motivated by the requirement that Charon must be useful within the traditional computational environments of Fortran 77 and C. Only the Fortran 77 syntax will be presented in this report.

Science, policy and the management of sewage materials. The New York City experience.

PubMed

Swanson, R Lawrence; Bortman, Marci L; O'Connor, Thomas P; Stanford, Harold M

2004-11-01

Development of national policy on sewage sludge management is a classic example of incremental policy formulation [Fiorino, D.J. 1995. Making Environmental Policy. University of California Press. Berkeley, CA. p. 269]. Consequently, policy has developed piecemeal, and results are, in some ways, different than intended. Land application of sewage sludge has not been a panacea. Many of the same types of policy are now being raised about it. We demonstrate this by examining the management of sewage materials by New York City from near the turn of the 20th century, when ocean dumping was viewed as a means to alleviate some of the gross pollution in New York Harbor, to when ocean dumping was banned, and thence to the present when sludge is applied to land as "biosolids." Lessons learned during this long, sometimes contentious history can be applied to present situations--specifically not understanding the long-term consequences of land-based reuse and disposal technologies.

Self-organization of meaning and the reflexive communication of information

PubMed Central

Leydesdorff, Loet; Petersen, Alexander M.; Ivanova, Inga

2017-01-01

Following a suggestion from Warren Weaver, we extend the Shannon model of communication piecemeal into a complex systems model in which communication is differentiated both vertically and horizontally. This model enables us to bridge the divide between Niklas Luhmann’s theory of the self-organization of meaning in communications and empirical research using information theory. First, we distinguish between communication relations and correlations among patterns of relations. The correlations span a vector space in which relations are positioned and can be provided with meaning. Second, positions provide reflexive perspectives. Whereas the different meanings are integrated locally, each instantiation opens global perspectives – ‘horizons of meaning’ – along eigenvectors of the communication matrix. These next-order codifications of meaning can be expected to generate redundancies when interacting in instantiations. Increases in redundancy indicate new options and can be measured as local reduction of prevailing uncertainty (in bits). The systemic generation of new options can be considered as a hallmark of the knowledge-based economy. PMID:28232771

Groundwater sustainability and urban development - a major challenge for the 21st century

NASA Astrophysics Data System (ADS)

Foster, Stephen

2016-04-01

Groundwater is a critical, but often under appreciated, resource for urban water supply, a serious and costly hazard to urban infrastructure, and the 'invisible link' between various facets of the urbanisation process. An overview is presented of the benefits of urban groundwater use, together with some insidious and persistent problems that groundwater can present (especially those related to groundwater pollution from inadequate sanitation) for urban development. Spontaneous piecemeal approaches invariably mean that 'one person's solution becomes another person's problem' - and there is a strong argument for groundwater considerations to be part of a more holistic approach to urban infrastructure planning and management. However this is not a simple task because of the widespread vacuum of institutional responsibility and accountability for groundwater in urban areas. The current state of urban groundwater management will be reviewed, and pragmatic solutions to strengthening various facets of urban groundwater governance and management presented, using examples from Latin America and South Asia.

Marine legislation--the ultimate 'horrendogram': international law, European directives & national implementation.

PubMed

Boyes, Suzanne J; Elliott, Michael

2014-09-15

The EU is a pre-eminent player in sustainable development, adopting more than 200 pieces of legislation that have direct repercussions for marine environmental policy and management. Over five decades, measures have aimed to protect the marine environment by tackling the impact of human activities, but maritime affairs have been dealt with by separate sectoral policies without fully integrating all relevant sectors. Such compartmentalisation has resulted in a patchwork of EU legislation and resultant national legislation leading to a piecemeal approach to marine protection. These are superimposed on international obligations emanating from UN and other bodies and are presented here as complex 'horrendograms' showing the complexity across vertical governance. These horrendograms have surprised marine experts despite them acknowledging the many uses and users of the marine environment. Encouragingly since 2000, the evolution in EU policy has progressed to more holistic directives and here we give an overview of this change. Copyright © 2014 Elsevier Ltd. All rights reserved.

Uncertainties in the Management of a Lynch Syndrome Patient: A Case Report

PubMed Central

Campos, Sara; Amaro, Pedro; Cunha, Inês; Fraga, João; Cipriano, Maria Augusta; Tomé, Luís

2017-01-01

Introduction Lynch syndrome (LS), the most common hereditary colorectal cancer syndrome, is characterized by mutations in mismatch repair (MMR) genes leading to an increased cancer risk, namely colorectal cancer. Case In the context of surveillance colonoscopy, a 40-mm flat lesion (0-IIa+b, Paris classification) was identified and submitted to piecemeal mucosal endoscopic resection in a 64-year-old LS patient with an MLH1 germline mutation (262delATC) and two previous segmental resections due to metachronous colorectal cancer. Pathology raised the suspicion of superficial submucosal invasive carcinoma with poor differentiation. Immunochemistry showed heterogeneous MLH1 expression and PMS2 loss. In a short-term follow-up colonoscopy, another 30-mm advanced carcinoma was identified. The patient was referred to surgery. Conclusion This case raises several issues: (1) the potentially fast tumorigenesis and progression to carcinoma in LS and implications for endoscopic screening and surveillance; (2) pitfalls in the interpretation of MMR proteins immunochemistry; (3) the role of endoscopic resection in LS. PMID:29255760

Perceived barriers to effective implementation of public reporting of hospital performance data in Australia: a qualitative study.

PubMed

Canaway, Rachel; Bismark, Marie; Dunt, David; Kelaher, Margaret

2017-06-07

Public reporting of government funded (public) hospital performance data was mandated in Australia in 2011. Studies suggest some benefit associated with such public reporting, but also considerable scope to improve reporting systems. In 2015, a purposive sample of 41 expert informants were interviewed, representing consumer, provider and purchasers perspectives across Australia's public and private health sectors, to ascertain expert opinion on the utility and impact of public reporting of health service performance. Qualitative data was thematically analysed with a focus on reporting perceived strengths and barriers to public reporting of hospital performance data (PR). Many more weaknesses and barriers to PR were identified than strengths. Barriers were: conceptual (unclear objective, audience and reporting framework); systems-level (including lack of consumer choice, lack of consumer and clinician involvement, jurisdictional barriers, lack of mandate for private sector reporting); technical and resource related (including data complexity, lack of data relevance consistency, rigour); and socio-cultural (including provider resistance to public reporting, poor consumer health literacy, lack of consumer empowerment). Perceptions of the Australian experience of PR highlight important issues in its implementation that can provide lessons for Australia and elsewhere. A considerable weakness of PR in Australia is that the public are often not considered its major audience, resulting in information ineffectually framed to meet the objective of PR informing consumer decision-making about treatment options. Greater alignment is needed between the primary objective of PR, its audience and audience needs; more than one system of PR might be necessary to meet different audience needs and objectives. Further research is required to assess objectively the potency of the barriers to PR suggested by our panel of informants.

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

Webb, Aaron P.; Carlson, Charles T.; Weaver, William T.

A mask alignment system for providing precise and repeatable alignment between ion implantation masks and workpieces. The system includes a mask frame having a plurality of ion implantation masks loosely connected thereto. The mask frame is provided with a plurality of frame alignment cavities, and each mask is provided with a plurality of mask alignment cavities. The system further includes a platen for holding workpieces. The platen may be provided with a plurality of mask alignment pins and frame alignment pins configured to engage the mask alignment cavities and frame alignment cavities, respectively. The mask frame can be lowered ontomore » the platen, with the frame alignment cavities moving into registration with the frame alignment pins to provide rough alignment between the masks and workpieces. The mask alignment cavities are then moved into registration with the mask alignment pins, thereby shifting each individual mask into precise alignment with a respective workpiece.« less

Needs and barriers to improve the collaboration in oral anticoagulant therapy: a qualitative study

PubMed Central

2011-01-01

Background Oral anticoagulant therapy (OAT) involves many health care disciplines. Even though collaboration between care professionals is assumed to improve the quality of OAT, very little research has been done into the practice of OAT management to arrange and manage the collaboration. This study aims to identify the problems in collaboration experienced by the care professionals involved, the solutions they proposed to improve collaboration, and the barriers they encountered to the implementation of these solutions. Methods In the Netherlands, intensive follow-up of OAT is provided by specialized anticoagulant clinics (ACs). Sixty-eight semi-structured face-to-face interviews were conducted with 103 professionals working at an AC. These semi-structured interviews were transcribed verbatim and analysed inductively. Wagner's chronic care model (CCM) and Cabana's framework for improvement were used to categorize the results. Results AC professionals experienced three main bottlenecks in collaboration: lack of knowledge (mostly of other professionals), lack of consensus on OAT, and limited information exchange between professionals. They mentioned several solutions to improve collaboration, especially solutions of CCM's decision support component (i.e. education, regular meetings, and agreements and protocols). Education is considered a prerequisite for the successful implementation of other proposed solutions such as developing a multidisciplinary protocol and changing the allocation of tasks. The potential of the health care organization to improve collaboration seemed to be underestimated by professionals. They experienced several barriers to the successful implementation of the proposed solutions. Most important barriers were the lack motivation of non-AC professionals and lack of time to establish collaboration. Conclusions This study revealed that the collaboration in OAT is limited by a lack of knowledge, a lack of consensus, and a limited information exchange. Education was identified as the best way to improve collaboration and considered a prerequisite for a successful implementation of other proposed solutions. Hence, the implementation sequence is of importance in order to improve the collaboration successfully. First step is to establish alignment regarding collaboration with all involved professionals to encounter the lack of motivation of non-AC professionals and lack of time. PMID:22192088

Polar cap particle precipitation and aurora: Review and commentary

NASA Astrophysics Data System (ADS)

Newell, Patrick T.; Liou, Kan; Wilson, Gordon R.

2009-02-01

Polar rain has a beautiful set of symmetry properties, individually established, but not previously discussed collectively, which can be organized by a single unifying principle. The key polar rain properties are favored hemisphere (controlled by the interplanetary magnetic field Bx), dawn/dusk gradient (IMF By), merging rate (IMF Bz or more generally d[Phi]MP/dt), nightside/dayside gradient, and seasonal effect. We argue that all five properties involve variants on a single theme: the further downstream a field line exits the magnetosphere (or less directly points toward the solar wind electron heat flux), the weaker the polar rain. This effect is the result of the requirements of charge quasi-neutrality, and because the ion thermal velocity declines and the tailward ion bulk flow velocity rises moving down tail from the frontside magnetopause. Polar cap arcs (or more properly, high-latitude sun-aligned arcs) are largely complementary to the polar rain, occurring most frequently when the dayside merging rate is low, and thus when polar rain is weak. Sun-aligned arcs are often considered as originating either in the polar rain or the expansion of the plasma sheet into the polar cap. In fact three quite distinct types of sun-aligned high-latitude arcs exist, two common, and one rare. One type of arc occurs as intensifications of the polar rain, and is common, but weak, typically <0.1 ergs/cm2 s, and lacks associated ion precipitation. A second category of Sun-aligned arcs with energy flux >0.1 ergs/cm2 s usually occurs adjacent to the auroral oval, and includes ion precipitation. The plasma regime of these common, and at times intense, arcs is often distinct from the oval which they abut. Convection alone does not specify the open/closed nature of these arcs, because multiple narrow convection reversals are common around such arcs, and the arcs themselves can be embedded within flows that are either sunward or anti-sunward. These observational facts do not neatly fit into either a plasma sheet origin or a polar rain origin (e.g., the necessity to abut the auroral oval, and the presence of ions does not fit the properties of polar rain, which can in any event be nearly absent for northward interplanetary magnetic field). One theory is that such arcs are associated with merging tailward of the cusp. Both of these common types of sun-aligned arcs fade within about 30 min of a southward IMF turning. The third, and rarest, category of sun-aligned arcs are intense, well detached from the auroral oval, contain plasma sheet origin ion precipitation as well as electrons, and persist for hours after a southward turning. These intense detached sun-aligned arcs can rapidly cross the polar cap, sometimes multiple times. Most events discussed in the literature as "theta-aurora" do not fit into this category (for example, although they may appear detached in images, they abut the oval in particle data, and do not have the persistence of detached events under southward IMF turnings). It is possible that no single theory can account for all three types of sun-aligned arcs. Solar energetic particle (SEP) events are at times used to demarcate polar cap open/closed boundaries. Although this works at times, examples exist where this method fails (e.g., very quiet conditions for which SEP reaches below L=4), and the method should be used with caution. Finally, it is shown that, although it is rare, the polar cap can at times completely close.

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

PubMed Central

2010-01-01

Background Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. Results This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. Conclusions Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service. PMID:21034504

Membranes with highly ordered straight nanopores by selective swelling of fast perpendicularly aligned block copolymers.

PubMed

Yin, Jun; Yao, Xueping; Liou, Jiun-You; Sun, Wei; Sun, Ya-Sen; Wang, Yong

2013-11-26

Membranes with uniform, straight nanopores have important applications in diverse fields, but their application is limited by the lack of efficient producing methods with high controllability. In this work, we reported on an extremely simple and efficient strategy to produce such well-defined membranes. We demonstrated that neutral solvents were capable of annealing amphiphilic block copolymer (BCP) films of polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP) with thicknesses up to 600 nm to the perpendicular orientation within 1 min. Annealing in neutral solvents was also effective to the perpendicular alignment of block copolymers with very high molecular weights, e.g., 362 000 Da. Remarkably, simply by immersing the annealed BCP films in hot ethanol followed by drying in air, the originally dense BCP films were nondestructively converted into porous membranes containing highly ordered, straight nanopores traversing the entire thickness of the membrane (up to 1.1 μm). Grazing incident small-angle X-ray spectroscopy confirmed the hexagonal ordering of the nanopores over large areas. We found that the overflow of P2VP chains from their reservoir P2VP cylinders and the deformation of the PS matrix in the swelling process contributed to the transformation of the solid P2VP cylinders to empty straight pores. The pore diameters can be tuned by either changing the swelling temperatures or depositing thin layers of metal oxides on the preformed membranes via atomic layer deposition with a subnanometer accuracy. To demonstrate the application of the obtained porous membranes, we used them as templates and produced centimeter-scale arrays of aligned nanotubes of metal oxides with finely tunable wall thicknesses.

A protocol to correct for intra- and interspecific variation in tail hair growth to align isotope signatures of segmentally cut tail hair to a common time line.

PubMed

Burnik Šturm, Martina; Pukazhenthi, Budhan; Reed, Dolores; Ganbaatar, Oyunsaikhan; Sušnik, Stane; Haymerle, Agnes; Voigt, Christian C; Kaczensky, Petra

2015-06-15

In recent years, segmental stable isotope analysis of hair has been a focus of research in animal dietary ecology and migration. To correctly assign tail hair segments to seasons or even Julian dates, information on tail hair growth rates is a key parameter, but is lacking for most species. We (a) reviewed the literature on tail hair growth rates in mammals; b) made own measurements of three captive equid species; (c) measured δ(2)H, δ(13)C and δ(15)N values in sequentially cut tail hairs of three sympatric, free-ranging equids from the Mongolian Gobi, using isotope ratio mass spectrometry (IRMS); and (d) collected environmental background data on seasonal variation by measuring δ(2)H values in precipitation by IRMS and by compiling pasture productivity measured by remote sensing via the normalized difference vegetation index (NDVI). Tail hair growth rates showed significant inter- and intra-specific variation making temporal alignment problematic. In the Mongolian Gobi, high seasonal variation of δ(2)H values in precipitation results in winter lows and summer highs of δ(2)H values of available water sources. In water-dependent equids, this seasonality is reflected in the isotope signatures of sequentially cut tails hairs. In regions which are subject to strong seasonal patterns we suggest identifying key isotopes which show strong seasonal variation in the environment and can be expected to be reflected in the animal tissue. The known interval between the maxima and minima of these isotope values can then be used to correctly temporally align the segmental stable isotope signature for each individual animal. © 2015 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd.

A protocol to correct for intra- and interspecific variation in tail hair growth to align isotope signatures of segmentally cut tail hair to a common time line

PubMed Central

Burnik Šturm, Martina; Pukazhenthi, Budhan; Reed, Dolores; Ganbaatar, Oyunsaikhan; Sušnik, Stane; Haymerle, Agnes; Voigt, Christian C; Kaczensky, Petra

2015-01-01

Rationale In recent years, segmental stable isotope analysis of hair has been a focus of research in animal dietary ecology and migration. To correctly assign tail hair segments to seasons or even Julian dates, information on tail hair growth rates is a key parameter, but is lacking for most species. Methods We (a) reviewed the literature on tail hair growth rates in mammals; b) made own measurements of three captive equid species; (c) measured δ2H, δ13C and δ15N values in sequentially cut tail hairs of three sympatric, free-ranging equids from the Mongolian Gobi, using isotope ratio mass spectrometry (IRMS); and (d) collected environmental background data on seasonal variation by measuring δ2H values in precipitation by IRMS and by compiling pasture productivity measured by remote sensing via the normalized difference vegetation index (NDVI). Results Tail hair growth rates showed significant inter- and intra-specific variation making temporal alignment problematic. In the Mongolian Gobi, high seasonal variation of δ2H values in precipitation results in winter lows and summer highs of δ2H values of available water sources. In water-dependent equids, this seasonality is reflected in the isotope signatures of sequentially cut tails hairs. Conclusions In regions which are subject to strong seasonal patterns we suggest identifying key isotopes which show strong seasonal variation in the environment and can be expected to be reflected in the animal tissue. The known interval between the maxima and minima of these isotope values can then be used to correctly temporally align the segmental stable isotope signature for each individual animal. © 2015 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd. PMID:26044272

High School Science Teachers' Receptivity to the Next Generation Science Standards: An Examination of Discipline Specific Factors

NASA Astrophysics Data System (ADS)

Shapiro, Lesley Jacqueline

The Next Generation Science Standards (NGSS), are the biggest change to American science education since the National Science Education Standards (NSES) were published. While inquiry was central to the NSES, science assessment largely addressed factual knowledge acquisition. The NGSS represent a significant practical change for teachers as they mark a return to the ideals specified in the National Science Education Standards (NSES) and Benchmarks for Science Literacy. The purpose of this explanatory sequential, mixed-methods study was to identify and compare the factors that influenced high school science teachers' receptivity to the curricular shifts necessitated by the adoption of the NGSS. The survey data identified three factors as significant predictors of teacher receptivity: teachers' non-monetary cost-benefit analysis, alignment between the NGSS and their current teaching style, and concerns about student readiness. To understand how these factors operate in the classroom, both receptive and non-receptive teachers were interviewed. In terms of cost-benefit analysis, all teachers agree that time is a significant cost. This includes the time it takes to adapt lessons to the NGSS, and the time it takes to teach in a way that integrates the three parts of the NGSS which are the practices of science and engineering, the crosscutting concepts, and the disciplinary core ideas. In terms of alignment between their teaching style and the NGSS, teachers talked about the lack of examples of what NGSS-aligned instruction looks like and the dearth of accessible high quality professional development. Finally, concerns about students' readiness focused on both inadequate preparation for college-level science coursework and deficits in science instruction in the lower grades.

ALMA Reveals Transition of Polarization Pattern with Wavelength in HL Tau’s Disk

NASA Astrophysics Data System (ADS)

Stephens, Ian W.; Yang, Haifeng; Li, Zhi-Yun; Looney, Leslie W.; Kataoka, Akimasa; Kwon, Woojin; Fernández-López, Manuel; Hull, Charles L. H.; Hughes, Meredith; Segura-Cox, Dominique; Mundy, Lee; Crutcher, Richard; Rao, Ramprasad

2017-12-01

The mechanism for producing polarized emission from protostellar disks at (sub)millimeter wavelengths is currently uncertain. Classically, polarization is expected from non-spherical grains aligned with the magnetic field. Recently, two alternatives have been suggested. One polarization mechanism is caused by self-scattering from dust grains of sizes comparable with the wavelength, while the other mechanism is due to grains aligned with their short axes along the direction of radiation anisotropy. The latter has recently been shown as a likely mechanism for causing the dust polarization detected in HL Tau at 3.1 mm. In this paper, we present ALMA polarization observations of HL Tau for two more wavelengths: 870 μm and 1.3 mm. The morphology at 870 μm matches the expectation for self-scattering, while that at 1.3 mm shows a mix between self-scattering and grains aligned with the radiation anisotropy. The observations cast doubt on the ability of (sub)millimeter continuum polarization to probe disk magnetic fields for at least HL Tau. By showing two distinct polarization morphologies at 870 μm and 3.1 mm and a transition between the two at 1.3 mm, this paper provides definitive evidence that the dominant (sub)millimeter polarization mechanism transitions with wavelength. In addition, if the polarization at 870 μm is due to scattering, the lack of polarization asymmetry along the minor axis of the inclined disk implies that the large grains responsible for the scattering have already settled into a geometrically thin layer, and the presence of asymmetry along the major axis indicates that the HL Tau disk is not completely axisymmetric.

Favourable outcome of posterior decompression and stabilization in lordosis for cervical spondylotic myelopathy: the spinal cord "back shift" concept.

PubMed

Denaro, Vincenzo; Longo, Umile Giuseppe; Berton, Alessandra; Salvatore, Giuseppe; Denaro, Luca

2015-11-01

Surgical management of patients with multilevel CSM aims to decompress the spinal cord and restore the normal sagittal alignment. The literature lacks of high level evidences about the best surgical approach. Posterior decompression and stabilization in lordosis allows spinal cord back shift, leading to indirect decompression of the anterior spinal cord. The purpose of this study was to investigate the efficacy of posterior decompression and stabilization in lordosis for multilevel CSM. 36 out of 40 patients were clinically assessed at a mean follow-up of 5, 7 years. Outcome measures included EMS, mJOA Score, NDI and SF-12. Patients were asked whether surgery met their expectations and if they would undergo the same surgery again. Bone graft fusion, instrumental failure and cervical curvature were evaluated. Spinal cord back shift was measured and correlation with EMS and mJOA score recovery rate was analyzed. All scores showed a significative improvement (p < 0.001), except the SF12-MCS (p > 0.05). Ninety percent of patients would undergo the same surgery again. There was no deterioration of the cervical alignment, posterior grafted bones had completely fused and there were no instrument failures. The mean spinal cord back shift was 3.9 mm (range 2.5-4.5 mm). EMS and mJOA recovery rates were significantly correlated with the postoperative posterior cord migration (P < 0.05). Posterior decompression and stabilization in lordosis is a valuable procedure for patients affected by multilevel CSM, leading to significant clinical improvement thanks to the spinal cord back shift. Postoperative lordotic alignment of the cervical spine is a key factor for successful treatment.

Health sector operational planning and budgeting processes in Kenya-"never the twain shall meet".

PubMed

Tsofa, Benjamin; Molyneux, Sassy; Goodman, Catherine

2016-07-01

Operational planning is considered an important tool for translating government policies and strategic objectives into day-to-day management activities. However, developing countries suffer from persistent misalignment between policy, planning and budgeting. The Medium Term Expenditure Framework (MTEF) was introduced to address this misalignment. Kenya adopted the MTEF in the early 2000s, and in 2005, the Ministry of Health adopted the Annual Operational Plan process to adapt the MTEF to the health sector. This study assessed the degree to which the health sector Annual Operational Plan process in Kenya has achieved alignment between planning and budgeting at the national level, using document reviews, participant observation and key informant interviews. We found that the Kenyan health sector was far from achieving planning and budgeting alignment. Several factors contributed to this problem including weak Ministry of Health stewardship and institutionalized separation between planning and budgeting processes; a rapidly changing planning and budgeting environment; lack of reliable data to inform target setting and poor participation by key stakeholders in the process including a top-down approach to target setting. We conclude that alignment is unlikely to be achieved without consideration of the specific institutional contexts and the power relationships between stakeholders. In particular, there is a need for institutional integration of the planning and budgeting processes into a common cycle and framework with common reporting lines and for improved data and local-level input to inform appropriate and realistic target setting. © 2015 The Authors. International Journal of Health Planning and Management published by John Wiley & Sons, Ltd. © 2015 The Authors. International Journal of Health Planning and Management published by John Wiley & Sons, Ltd.

COACH: profile-profile alignment of protein families using hidden Markov models.

PubMed

Edgar, Robert C; Sjölander, Kimmen

2004-05-22

Alignments of two multiple-sequence alignments, or statistical models of such alignments (profiles), have important applications in computational biology. The increased amount of information in a profile versus a single sequence can lead to more accurate alignments and more sensitive homolog detection in database searches. Several profile-profile alignment methods have been proposed and have been shown to improve sensitivity and alignment quality compared with sequence-sequence methods (such as BLAST) and profile-sequence methods (e.g. PSI-BLAST). Here we present a new approach to profile-profile alignment we call Comparison of Alignments by Constructing Hidden Markov Models (HMMs) (COACH). COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM. We compare the alignment accuracy of COACH with two recently published methods: Yona and Levitt's prof_sim and Sadreyev and Grishin's COMPASS. On two sets of reference alignments selected from the FSSP database, we find that COACH is able, on average, to produce alignments giving the best coverage or the fewest errors, depending on the chosen parameter settings. COACH is freely available from www.drive5.com/lobster

Template-based structure modeling of protein-protein interactions

PubMed Central

Szilagyi, Andras; Zhang, Yang

2014-01-01

The structure of protein-protein complexes can be constructed by using the known structure of other protein complexes as a template. The complex structure templates are generally detected either by homology-based sequence alignments or, given the structure of monomer components, by structure-based comparisons. Critical improvements have been made in recent years by utilizing interface recognition and by recombining monomer and complex template libraries. Encouraging progress has also been witnessed in genome-wide applications of template-based modeling, with modeling accuracy comparable to high-throughput experimental data. Nevertheless, bottlenecks exist due to the incompleteness of the proteinprotein complex structure library and the lack of methods for distant homologous template identification and full-length complex structure refinement. PMID:24721449

Treatment of Class III malocclusion in a young adult patient: a case report.

PubMed

Kiran, B H Jyothi; Kumar, Prashanth; Ravi, S; Shivalinga, B M; Bhagyalaxmi; Pradeep; Kudagi, Vishal

2012-01-01

This article describes the treatment of a young adult male with a concave profile, skeletal class III malocclusion because of a prognathic mandible and proclined upper incisors. The therapy included stages: 1. Pre-surgical orthodontics involving leveling and aligning of upper and lower arches, protraction of lower molars and retraction of upper incisors; 2. Surgical phase involving BSSO with mandibular setback and 3. Post-surgical orthodontics for finishing and detailing. The treatment lasted 23 months and improved facial esthetics significantly The treatment resulted in a functional occlusion with a lack of lateral cuspid guidance that could be accepted considering the difficulty of the case. Over jet and overbite are within norms.

Plagioclase-dominated Seismic Anisotropy in the Basin and Range Lower Crust

NASA Astrophysics Data System (ADS)

Bernard, R. E.; Behr, W. M.

2017-12-01

Observations of seismic anisotropy have the ability to provide important information on deformation and structures within the lithosphere. While the mechanisms controlling seismic anisotropy in the upper mantle are fairly well understood (i.e., olivine "lattice preferred orientation" or LPO), less is known about the minerals and structures controlling regional lower crustal anisotropy. We use lower crustal xenoliths from young cinder cones in the eastern Mojave/western Basin and Range to investigate mineral LPOs and their effect on seismic anisotropy. Lower crustal gabbros were collected from two areas roughly 80 km apart — the Cima and Deadman Lake Volcanic Fields. Lower crustal fabrics measured using EBSD are dominated by LPOs in plagioclase associated with both plastic deformation and magmatic flow. In all fabric types, plagioclase LPOs produce seismic fast axes oriented perpendicular to the foliation plane. This is in contrast to mantle peridotite xenoliths from the same locations, which preserve olivine LPOs with fast axes aligned parallel to the foliation plane. The orthogonal orientations of mantle and lower crustal fast axes relative to foliation implies that even where fabric development in both layers is coeval and kinematically compatible, their measured anisotropies can be perpendicular to each other, therefore appearing anti-correlated when measured seismically. Furthermore, our observation of plagioclase-dominated LPO and negligible concentrations of mica is at odds with the common assumption that lower crustal anisotropy is dominated by micaceous minerals, whose slow axes reliably align parallel to lineation or flow. In contrast, our data show that for plagioclase, fast axes align perpendicular to flow and the slow axes are variably aligned within the foliation plane. Therefore, for a crustal section dominated by plagioclase LPO with assumed horizontal foliation, there would be a vertical rather than a horizontal axis of symmetry, resulting in a lack of azimuthal anisotropy and minimal shear wave splitting for vertically propagating waves. Crustal seismic studies in this type of setting may only be able to identify crustal flow planes, but not flow directions. These findings may be generally applicable to regions of significant mafic volcanism and lower crustal magmatic underplating.

Thickness-independent capacitance of vertically aligned liquid-crystalline MXenes

DOE PAGES

Xia, Yu; Mathis, Tyler S.; Zhao, Meng -Qiang; ...

2018-05-16

The scalable and sustainable manufacture of thick electrode films with high energy and power densities is critical for the large-scale storage of electrochemical energy for application in transportation and stationary electric grids. Two-dimensional nanomaterials have become the predominant choice of electrode material in the pursuit of high energy and power densities owing to their large surface-area-to-volume ratios and lack of solid-state diffusion. However, traditional electrode fabrication methods often lead to restacking of two-dimensional nanomaterials, which limits ion transport in thick films and results in systems in which the electrochemical performance is highly dependent on the thickness of the film. Strategiesmore » for facilitating ion transport—such as increasing the interlayer spacing by intercalation or introducing film porosity by designing nanoarchitectures—result in materials with low volumetric energy storage as well as complex and lengthy ion transport paths that impede performance at high charge–discharge rates. Vertical alignment of two-dimensional flakes enables directional ion transport that can lead to thickness-independent electrochemical performances in thick films. However, so far only limited success has been reported, and the mitigation of performance losses remains a major challenge when working with films of two-dimensional nanomaterials with thicknesses that are near to or exceed the industrial standard of 100 micrometres. Here we demonstrate electrochemical energy storage that is independent of film thickness for vertically aligned two-dimensional titanium carbide (Ti 3C 2T x), a material from the MXene family (two-dimensional carbides and nitrides of transition metals (M), where X stands for carbon or nitrogen). The vertical alignment was achieved by mechanical shearing of a discotic lamellar liquid-crystal phase of Ti 3C 2T x. The resulting electrode films show excellent performance that is nearly independent of film thickness up to 200 micrometres, which makes them highly attractive for energy storage applications. In conclusion, the self-assembly approach presented here is scalable and can be extended to other systems that involve directional transport, such as catalysis and filtration.« less

Thickness-independent capacitance of vertically aligned liquid-crystalline MXenes

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

Xia, Yu; Mathis, Tyler S.; Zhao, Meng -Qiang

The scalable and sustainable manufacture of thick electrode films with high energy and power densities is critical for the large-scale storage of electrochemical energy for application in transportation and stationary electric grids. Two-dimensional nanomaterials have become the predominant choice of electrode material in the pursuit of high energy and power densities owing to their large surface-area-to-volume ratios and lack of solid-state diffusion. However, traditional electrode fabrication methods often lead to restacking of two-dimensional nanomaterials, which limits ion transport in thick films and results in systems in which the electrochemical performance is highly dependent on the thickness of the film. Strategiesmore » for facilitating ion transport—such as increasing the interlayer spacing by intercalation or introducing film porosity by designing nanoarchitectures—result in materials with low volumetric energy storage as well as complex and lengthy ion transport paths that impede performance at high charge–discharge rates. Vertical alignment of two-dimensional flakes enables directional ion transport that can lead to thickness-independent electrochemical performances in thick films. However, so far only limited success has been reported, and the mitigation of performance losses remains a major challenge when working with films of two-dimensional nanomaterials with thicknesses that are near to or exceed the industrial standard of 100 micrometres. Here we demonstrate electrochemical energy storage that is independent of film thickness for vertically aligned two-dimensional titanium carbide (Ti 3C 2T x), a material from the MXene family (two-dimensional carbides and nitrides of transition metals (M), where X stands for carbon or nitrogen). The vertical alignment was achieved by mechanical shearing of a discotic lamellar liquid-crystal phase of Ti 3C 2T x. The resulting electrode films show excellent performance that is nearly independent of film thickness up to 200 micrometres, which makes them highly attractive for energy storage applications. In conclusion, the self-assembly approach presented here is scalable and can be extended to other systems that involve directional transport, such as catalysis and filtration.« less

Global health initiatives in Africa - governance, priorities, harmonisation and alignment.

PubMed

Mwisongo, Aziza; Nabyonga-Orem, Juliet

2016-07-18

The advent of global health initiatives (GHIs) has changed the landscape and architecture of health financing in low and middle income countries, particularly in Africa. Over the last decade, the African Region has realised improvements in health outcomes as a result of interventions implemented by both governments and development partners. However, alignment and harmonisation of partnerships and GHIs are still difficult in the African countries with inadequate capacity for their effective coordination. Both published and grey literature was reviewed to understand the governance, priorities, harmonisation and alignment of GHIs in the African Region; to synthesise the knowledge and highlight the persistent challenges; and to identify gaps for future research. GHI governance structures are often separate from those of the countries in which they operate. Their divergent funding channels and modalities may have contributed to the failure of governments to track their resources. There is also evidence that basically, earmarking and donor conditions drive funding allocations regardless of countries' priorities. Although studies cite the lack of harmonisation of GHI priorities with national strategies, evidence shows improvements in that area over time. GHIs have used several strategies and mechanisms to involve the private sector. These have widened the pool of health service policy-makers and providers to include groups such as civil society organisations (CSOs), with both positive and negative implications. GHI strategies such as co-financing by countries as a condition for support have been positive in achieving sustainability of interventions. GHI approaches have not changed substantially over the years but there has been evolution in terms of donor funding and conditions. GHIs still largely operate in a vertical manner, bypassing country systems; they compete for the limited human resources; they influence country policies; and they are not always harmonised with other donors. To maximise returns on GHI support, there is need to ensure that their approaches are more comprehensive as opposed to being selective; to improve GHI country level governance and alignment with countries' changing epidemiologic profiles; and to strengthen their involvement of CSOs.

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

PubMed

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both single and multi-domain comparisons. The CAB-align software is freely available to academic users as stand-alone software at http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Publications.html.

IUS prerelease alignment

NASA Technical Reports Server (NTRS)

Evans, F. A.

1978-01-01

Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

Standing sagittal alignment of the whole axial skeleton with reference to the gravity line in humans.

PubMed

Hasegawa, Kazuhiro; Okamoto, Masashi; Hatsushikano, Shun; Shimoda, Haruka; Ono, Masatoshi; Homma, Takao; Watanabe, Kei

2017-05-01

Human beings stand upright with the chain of balance beginning at the feet, progressing to the lower limbs (ankles, knees, hip joints, pelvis), each of the spinal segments, and then ending at the cranium to achieve horizontal gaze and balance using minimum muscle activity. The details of the alignment and balance of the chain, however, are not clearly understood, due to the lack of information regarding the three-dimensional (3D) orientation of all bony elements in relation to the gravity line (GL). We performed a clinical study to clarify the standing sagittal alignment of whole axial skeletons in reference to the GL using the EOS slot-scanning 3D X-ray imaging system with simultaneous force plate measurement in a healthy human population. The GL was defined as a vertical line drawn through the centre of vertical pressure measured by the force plate. The present study yielded a complete set of physiological alignment measurements of the standing axial skeleton from the database of 136 healthy subjects (a mean age of 39.7 years, 20-69 years; men: 40, women: 96). The mean offset of centre of the acoustic meati from the GL was 0.0 cm. The offset of the cervical and thoracic vertebrae was posterior to the GL with the apex of thoracic kyphosis at T7, 5.0 cm posterior to the GL. The sagittal alignment changed to lordosis at the level of L2. The apex of the lumbar lordosis was L4, 0.6 cm anterior to the GL, and the centre of the base of the sacrum (CBS) was just posterior to the GL. The hip axis (HA) was 1.4 cm anterior to the GL. The knee joint was 2.4 cm posterior and the ankle joint was 4.8 cm posterior to the GL. L4-, L5- and the CBS-offset in subjects in the age decades of 40s, 50s and 60s were significantly posterior to those of subjects in their 20s. The L5- and CBS-offset in subjects in their 50s and 60s were also significantly posterior to those in subjects in their 30s. HA was never posterior to the GL. In the global alignment, there was a positive correlation between offset of C7 vertebra from the sagittal vertical axis (a vertical line drawn through the posterior superior corner of the sacrum in the sagittal plane) and age, but no correlation was detected between the centre of the acoustic meati-GL offset and age. Cervical lordosis (CL), pelvic tilt (PT), pelvic incidence, hip extension, knee flexion and ankle dorsiflexion increased significantly with age. Our results revealed that aging induces trunk stooping, but the global alignment is compensated for by an increase in the CL, PT and knee flexion, with the main function of CL and PT to maintain a horizontal gaze in a healthy population. © 2017 The Authors Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical Society.

LOCAL GOVERNMENT AND COMMUNITY LEADERS' PERSPECTIVES ON CHILD HEALTH AND MORTALITY AND INEQUITY ISSUES IN RURAL EASTERN INDONESIA.

PubMed

Pardosi, Jerico Franciscus; Parr, Nick; Muhidin, Salut

2017-01-01

Since 2001 a decentralization policy has increased the responsibility placed on local government for improving child health in Indonesia. This paper explores local government and community leaders' perspectives on child health in a rural district in Indonesia, using a qualitative approach. Focus group discussions were held in May 2013. The issues probed relate to health personnel skills and motivation, service availability, the influence of traditional beliefs, and health care and gender inequity. The participants identify weak leadership, inefficient health management and inadequate child health budgets as important issues. The lack of health staff in rural areas is seen as the reason for promoting the use of traditional birth attendants. Midwifery graduates and village midwives are perceived as lacking motivation to work in rural areas. Some local traditions are seen as detrimental to child health. Husbands provide little support to their wives. These results highlight the need for a harmonization and alignment of the efforts of local government agencies and local community leaders to address child health care and gender inequity issues.

Placental labyrinth formation in mice requires endothelial FLRT2/UNC5B signaling.

PubMed

Tai-Nagara, Ikue; Yoshikawa, Yusuke; Numata, Naoko; Ando, Tomofumi; Okabe, Keisuke; Sugiura, Yuki; Ieda, Masaki; Takakura, Nobuyuki; Nakagawa, Osamu; Zhou, Bin; Okabayashi, Koji; Suematsu, Makoto; Kitagawa, Yuko; Bastmeyer, Martin; Sato, Kohji; Klein, Rüdiger; Navankasattusas, Sutip; Li, Dean Y; Yamagishi, Satoru; Kubota, Yoshiaki

2017-07-01

The placental labyrinth is the interface for gas and nutrient exchange between the embryo and the mother; hence its proper development is essential for embryogenesis. However, the molecular mechanism underlying development of the placental labyrinth, particularly in terms of its endothelial organization, is not well understood. Here, we determined that fibronectin leucine-rich transmembrane protein 2 (FLRT2), a repulsive ligand of the UNC5 receptor family for neurons, is unexpectedly expressed in endothelial cells specifically in the placental labyrinth. Mice lacking FLRT2 in endothelial cells exhibited embryonic lethality at mid-gestation, with systemic congestion and hypoxia. Although they lacked apparent deformities in the embryonic vasculature and heart, the placental labyrinths of these embryos exhibited aberrant alignment of endothelial cells, which disturbed the feto-maternal circulation. Interestingly, this vascular deformity was related to endothelial repulsion through binding to the UNC5B receptor. Our results suggest that the proper organization of the placental labyrinth depends on coordinated inter-endothelial repulsion, which prevents uncontrolled layering of the endothelium. © 2017. Published by The Company of Biologists Ltd.

End-to-End ASR-Free Keyword Search From Speech

NASA Astrophysics Data System (ADS)

Audhkhasi, Kartik; Rosenberg, Andrew; Sethy, Abhinav; Ramabhadran, Bhuvana; Kingsbury, Brian

2017-12-01

End-to-end (E2E) systems have achieved competitive results compared to conventional hybrid hidden Markov model (HMM)-deep neural network based automatic speech recognition (ASR) systems. Such E2E systems are attractive due to the lack of dependence on alignments between input acoustic and output grapheme or HMM state sequence during training. This paper explores the design of an ASR-free end-to-end system for text query-based keyword search (KWS) from speech trained with minimal supervision. Our E2E KWS system consists of three sub-systems. The first sub-system is a recurrent neural network (RNN)-based acoustic auto-encoder trained to reconstruct the audio through a finite-dimensional representation. The second sub-system is a character-level RNN language model using embeddings learned from a convolutional neural network. Since the acoustic and text query embeddings occupy different representation spaces, they are input to a third feed-forward neural network that predicts whether the query occurs in the acoustic utterance or not. This E2E ASR-free KWS system performs respectably despite lacking a conventional ASR system and trains much faster.

Prospects for progress on health inequalities in England in the post-primary care trust era: professional views on challenges, risks and opportunities.

PubMed

Turner, Daniel; Salway, Sarah; Mir, Ghazala; Ellison, George T H; Skinner, John; Carter, Lynne; Bostan, Bushara

2013-03-26

Addressing health inequalities remains a prominent policy objective of the current UK government, but current NHS reforms involve a significant shift in roles and responsibilities. Clinicians are now placed at the heart of healthcare commissioning through which significant inequalities in access, uptake and impact of healthcare services must be addressed. Questions arise as to whether these new arrangements will help or hinder progress on health inequalities. This paper explores the perspectives of experienced healthcare professionals working within the commissioning arena; many of whom are likely to remain key actors in this unfolding scenario. Semi-structured interviews were conducted with 42 professionals involved with health and social care commissioning at national and local levels. These included representatives from the Department of Health, Primary Care Trusts, Strategic Health Authorities, Local Authorities, and third sector organisations. In general, respondents lamented the lack of progress on health inequalities during the PCT commissioning era, where strong policy had not resulted in measurable improvements. However, there was concern that GP-led commissioning will fare little better, particularly in a time of reduced spending. Specific concerns centred on: reduced commitment to a health inequalities agenda; inadequate skills and loss of expertise; and weakened partnership working and engagement. There were more mixed opinions as to whether GP commissioners would be better able than their predecessors to challenge large provider trusts and shift spend towards prevention and early intervention, and whether GPs' clinical experience would support commissioning action on inequalities. Though largely pessimistic, respondents highlighted some opportunities, including the potential for greater accountability of healthcare commissioners to the public and more influential needs assessments via emergent Health & Wellbeing Boards. There is doubt about the ability of GP commissioners to take clearer action on health inequalities than PCTs have historically achieved. Key actors expect the contribution from commissioning to address health inequalities to become even more piecemeal in the new arrangements, as it will be dependent upon the interest and agency of particular individuals within the new commissioning groups to engage and influence a wider range of stakeholders.

Sub-Saharan red cell antigen phenotypes and glucose-6-phosphate dehydrogenase deficiency variants in French Guiana.

PubMed

Petit, Florence; Bailly, Pascal; Chiaroni, Jacques; Mazières, Stéphane

2016-06-07

The treatment of Plasmodium vivax infections requires the use of primaquine, which can lead to severe haemolysis in glucose-6-phosphate dehydrogenase (G6PD)-deficient individuals. However, most of the Latin American countries, which are still endemic for vivax malaria, lack information on the distribution of G6PD deficiency (G6PDd). No survey has been performed so far in French Guiana. Herein, 80 individuals of the French Guianan Noir Marron population were scrutinized for red cell surface antigens of six blood group systems (ABO, Rh, Kell, Kidd, Duffy and MNS) and G6PD genetic polymorphisms. First, the sub-Saharan origin of the red cell phenotypes was assessed in relation with the literature. Then, given that the main sub-Saharan G6PDd variants are expected to be encountered, only the G6PD sequences of exons 4, 5, 6 and 9 were screened. This work aims at appraising the G6PD gene variation in this population, and thus, contributing to the G6PD piecemeal information in Latin America. Ninety-seven percent (97 %) of the red cells are Fy(a- b-), either D+ C- E- c+ e+ or D+ C+ E- c+ e+ and 44 % exhibited the Fya-/Jkb-/S- combined phenotype. Noteworthy is the detection of the G6PD(Val68Met) variant characterized by c.202G > A transition, G6PD(Asn126Asp) variant characterized by c.376A>G transition and G6PD(Asp181Val) variant characterized by c.542A>T transversion of the G6PD gene in 22.5 % of the sample, characteristic of the A(-(202)), A and Santamaria G6PDd variants, respectively. French Guianan Noir Marron population represents a pool of Rh-D antigen positive, Duffy-negative and G6PD-deficient erythrocytes, the latter accounting for one in every eight persons. The present study provides the first community-based estimation of the frequency of G6PDd polymorphisms in French Guiana. These results contribute to the G6PD genetic background information puzzle in Latin America.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

PubMed

Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

Books Noted

NASA Astrophysics Data System (ADS)

Walsh, Edward J.

1999-10-01

The Colloidal Domain: Where Physics, Chemistry, Biology, and Technology Meet, 2nd edition

D. Fennell Evans and Hakan Wennerstroem. Advances in Interfacial Engineering Series. Wiley-VCH: New York, 1999. xl + 632 pp. ISBN 0-471-24247-0. 89.95.

Commercial Nuclear Power: Assuring Safety for the Future

Charles B. Ramsey and Mohammed Modarres. Wiley-Interscience: New York, 1998. xxviii + 508 pp. ISBN 0-471-29186-2. 79.95.

Advances in Medicinal Chemistry, Vol. 4

Bruce E. Maryanoff and Allen B. Reitz, Eds. JAI Press: Stamford, CT, 1999. ISBN 1-7623-0064-7. 109.50.

Advances in Strained and Interesting Organic Molecules, Vol. 7

Brian Halton, Ed. JAI Press: Stamford, CT, 1999. xii + 259 pp. ISBN 0-7623-0530-4. 109.50.

Advances in Electron Transfer Chemistry, Vol. 6

Patrick S. Mariano, Ed. JAI Press: Stamford, CT, 1999. x + 171 pp. ISBN 0-7623-0213-5. 109.50.

Automating Science and Engineering Laboratories with Visual Basic

Mark F. Russo and Martin M. Echols. Wiley-Interscience Series on Laboratory Automation. Wiley-Interscience: New York, 1999. xx + 355 pp. ISBN 0-471-25493-2. 49.95.

Plantwide Process Control

Kelvin T. Erickson and John L. Hedrick. Wiley Series in Chemical Engineering. Wiley-Interscience: New York, 1999. xii + 547 pp. ISBN 0-471-17835-7. 89.95.

Heme Peroxidases

H. Brian Dunford. Wiley-VCH: New York, 1999. xiii + 507 pp. ISBN 0-471-24244-6. 195.00.

Industrial Ecology: Environmental Chemistry and Hazardous Wastes

Stanley E. Manahan. Lewis: Boca Raton, FL, 1999. 318 pp. ISBN 1-56670-381-6. 69.95.

Reviews in Computational Chemistry, Vol. 13

Kenny B. Lipkowitz and Donald B. Boyd. Wiley-VCH: New York, 1999. xxxiii + 426 pp. ISBN 0-471-33135-x. 135.00.

Surfaces, Interfaces, and Colloids: Principles and Applications, 2nd edition

Drew Myers. Wiley-VCH: New York, 1999. xx + 501 pp. ISBN 0-471-33060-4. 94.95.

Onium Ions

George A. Olah, Kenneth K. Laali, Qi Wang, and G. K. Surya Prakash. Wiley-Interscience: New York, 1998. xv + 509 pp. ISBN 0-471-14877-6. 110.00.

Environmental Soil and Water Chemistry: Principles and Applications V. P. Evangelou. Wiley-Interscience: New York, 1998. xix + 564 pp. ISBN 0-471-16515-8. 79.95.

1001 Chemicals in Everyday Products, 2nd edition

Grace Ross Lewis. Wiley-Interscience: New York, 1999. x + 388 pp. ISBN 0-471-29212-5. 39.95.

Organic Coatings: Science and Technology, 2nd edition

Zeno W. Wicks Jr., Frank N. Jones, and S. Peter Pappas. Wiley-Interscience: New York, 1999. xxi + 630 pp. ISBN 0-471-24507-0. 125.00.

Progress in Inorganic Chemistry, Vol. 48

Kenneth D. Karlin, Ed. Wiley-Interscience: New York, 1999. vi + 603 pp. ISBN 0-471-32623-2. 145.00.

Occupational Biomechanics, 3rd edition

Don B. Chaffin, Gunnar B. Andersson, and Bernard J. Martin. Wiley-Interscience: New York, 1999. xvii + 579 pp. ISBN 0-471-24697-2. 69.95.

Advances in Photochemistry, Vol. 25

Douglas C. Neckers, David H. Volman, and Gunther Von Bünau. Wiley-Interscience: New York, 1999. xi + 238 pp. ISBN 0-471-32708-5. 110.00.

Distillation

Johann G. Stichlmair and James R. Fair. Wiley-VCH: New York, 1998. xiii + 524 pp. ISBN 0-471-25241-7. 94.95.

Ammonia - Principles and Industrial Practice

Maz Appl. Wiley-VCH: New York, 1999. ix + 301 pp. ISBN 3-527-29593-3. 160.00.

Precursor-Derived Ceramics: Synthesis, Structure, and High-Temperature Mechanical Properties

Fritz Aldinger, Fumihiro Wakai, and Joachim Bill, Eds. Wiley-VCH: New York, 1999. xv + 298 pp. ISBN 3-527-29814-2. 180.00.

Advances in Sonochemisty, Vol. 5

Timothy J. Mason. JAI Press: Stamford, CT, 1999. xi + 311 pp. ISBN 0-7623-0331-x. 109.50.

Fluid Metals: The Liquid-Vapor Transition of Metals

Friedrich Hensel and William W. Warren Jr. Princeton University Press: Princeton, NJ. 1999. xvii + 243 pp. ISBN 0-691-05830-x. 69.50.

Direct Phasing in Crystallography: Fundamentals and Applications

Carmelo Giacovazzo. Oxford University Press: New York, 1999. xxiii + 767 pp. ISBN 0-19-850072-6. 140.00.

Practical Environmental Analysis

M. Radojevic and V. N. Bashkin. Royal Society of Chemistry: Cambridge, UK. 1999. xx + 466 pp. ISBN 0-85404-594-5. £32.00.

Advances in Dendritic Macromolecules, Vol. 4 George R. Newkome, Ed. JAI Press: Stamford, CT, 1999. x + 207 pp. ISBN 0-7623-0347-6. 109.50.

Advances in Quantitative Structure-Property Relationships, Vol. 2

Marvin Charton. JAI Press: Stamford, CT, 1999. ix + 257 pp. ISBN 0-7623-0067-1. 109.50.

Pesticide Residues in Foods: Methods, Techniques, and Regulations

W. George Fong, H. Anson Moye, James N. Seiber, and John P. Toth. Chemical Analysis, Vol. 151.Wiley-Interscience: New York, 1999. xiv + 358 pp. ISBN 0-471-57400-7. $84.95.

A novel approach to multiple sequence alignment using hadoop data grids.

PubMed

Sudha Sadasivam, G; Baktavatchalam, G

2010-01-01

Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences.

Fabrication of high temperature superconductors

DOEpatents

Balachandran, Uthamalingam; Dorris, Stephen E.; Ma, Beihai; Li, Meiya

2003-06-17

A method of forming a biaxially aligned superconductor on a non-biaxially aligned substrate substantially chemically inert to the biaxially aligned superconductor comprising is disclosed. A non-biaxially aligned substrate chemically inert to the superconductor is provided and a biaxially aligned superconductor material is deposited directly on the non-biaxially aligned substrate. A method forming a plume of superconductor material and contacting the plume and the non-biaxially aligned substrate at an angle greater than 0.degree. and less than 90.degree. to deposit a biaxially aligned superconductor on the non-biaxially aligned substrate is also disclosed. Various superconductors and substrates are illustrated.

Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

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

Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.

2015-11-01

Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangularmore » AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.« less

Unified Alignment of Protein-Protein Interaction Networks.

PubMed

Malod-Dognin, Noël; Ban, Kristina; Pržulj, Nataša

2017-04-19

Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.

Accelerating large-scale protein structure alignments with graphics processing units

PubMed Central

2012-01-01

Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU. PMID:22357132

AlignMe—a membrane protein sequence alignment web server

PubMed Central

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

NASA Astrophysics Data System (ADS)

Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

2016-03-01

Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

Viral phylogenomics using an alignment-free method: A three-step approach to determine optimal length of k-mer

DOE PAGES

Zhang, Qian; Jun, Se -Ran; Leuze, Michael; ...

2017-01-19

The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral tree of life . However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conservedmore » proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. Lastly, the resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses.« less

Viral phylogenomics using an alignment-free method: A three-step approach to determine optimal length of k-mer

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

Zhang, Qian; Jun, Se -Ran; Leuze, Michael

The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral tree of life . However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conservedmore » proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. Lastly, the resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses.« less

THE STELLAR SPHEROID, THE DISK, AND THE DYNAMICS OF THE COSMIC WEB

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

Domínguez-Tenreiro, R.; Obreja, A.; Brook, C. B.

Models of the advanced stages of gravitational instability predict that baryons that form the stellar populations of current galaxies at z = 0 displayed a web-like structure at high z, as part of the cosmic web (CW). We explore details of these predictions using cosmological hydrodynamical simulations. When the stellar populations of the spheroid and disk components of simulated late-type galaxies are traced back separately to high zs we found CW-like structures where spheroid progenitors are more evolved than disk progenitors. The distinction between the corresponding stellar populations, as driven by their specific angular momentum content j, can be explainedmore » in terms of the CW evolution, extended to two processes occurring at lower z. First, the spheroid progenitors strongly lose j at collapse, which contrasts with the insignificant j loss of the disk progenitors. The second is related to the lack of alignment, at assembly, between the spheroid-to-be material and the already settled proto-disk, in contrast to the alignment of disk-to-be material, in some cases resulting from circumgalactic, disk-induced gravitational torques. The different final outcomes of these low-z processes have their origins in the different initial conditions driven by the CW dynamics.« less

The ``listener'' in the modeling of speech prosody

NASA Astrophysics Data System (ADS)

Kohler, Klaus J.

2004-05-01

Autosegmental-metrical modeling of speech prosody is principally speaker-oriented. The production of pitch patterns, in systematic lab speech experiments as well as in spontaneous speech corpora, is analyzed in f0 tracings, from which sequences of H(igh) and L(ow) are abstracted. The perceptual relevance of these pitch categories in the transmission from speakers to listeners is largely not conceptualized; thus their modeling in speech communication lacks an essential component. In the metalinguistic task of labeling speech data with the annotation system ToBI, the ``listener'' plays a subordinate role as well: H and L, being suggestive of signal values, are allocated with reference to f0 curves and little or no concern for perceptual classification by the trained labeler. The seriousness of this theoretical gap in the modeling of speech prosody is demonstrated by experimental data concerning f0-peak alignment. A number of papers in JASA have dealt with this topic from the point of synchronizing f0 with the vocal tract time course in acoustic output. However, perceptual experiments within the Kiel intonation model show that ``early,'' ``medial'' and ``late'' peak alignments need to be defined perceptually and that in doing so microprosodic variation has to be filtered out from the surface signal.

ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes

PubMed Central

Otto, Thomas Dan; Catanho, Marcos; Tristão, Cristian; Bezerra, Márcia; Fernandes, Renan Mathias; Elias, Guilherme Steinberger; Scaglia, Alexandre Capeletto; Bovermann, Bill; Berstis, Viktors; Lifschitz, Sergio; de Miranda, Antonio Basílio; Degrave, Wim

2010-01-01

Motivation: Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith–Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid™, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach. Availability: The database can be accessed through http://proteinworlddb.org Contact: otto@fiocruz.br PMID:20089515

[Barriers to the normalization of telemedicine in a healthcare system model based on purchasing of healthcare services using providers' contracts].

PubMed

Roig, Francesc; Saigí, Francesc

2011-01-01

Despite the clear political will to promote telemedicine and the large number of initiatives, the incorporation of this modality in clinical practice remains limited. The objective of this study was to identify the barriers perceived by key professionals who actively participate in the design and implementation of telemedicine in a healthcare system model based on purchasing of healthcare services using providers' contracts. We performed a qualitative study based on data from semi-structured interviews with 17 key informants belonging to distinct Catalan health organizations. The barriers identified were grouped in four areas: technological, organizational, human and economic. The main barriers identified were changes in the healthcare model caused by telemedicine, problems with strategic alignment, resistance to change in the (re)definition of roles, responsibilities and new skills, and lack of a business model that incorporates telemedicine in the services portfolio to ensure its sustainability. In addition to suitable management of change and of the necessary strategic alignment, the definitive normalization of telemedicine in a mixed healthcare model based on purchasing of healthcare services using providers' contracts requires a clear and stable business model that incorporates this modality in the services portfolio and allows healthcare organizations to obtain reimbursement from the payer. 2010 SESPAS. Published by Elsevier Espana. All rights reserved.

Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer

PubMed Central

Zhang, Qian; Jun, Se-Ran; Leuze, Michael; Ussery, David; Nookaew, Intawat

2017-01-01

The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral “tree of life”. However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. The resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses. PMID:28102365

Innovating information-delivery for potential clinical trials participants. What do patients want from multi-media resources?

PubMed

Shneerson, Catherine; Windle, Richard; Cox, Karen

2013-01-01

To discover whether the provision of clinical trials information via a multi-media platform could better meet the needs, preferences and practices of potential cancer trial participants. A mixed qualitative and quantitative questionnaire was delivered to 72 participants from cancer support groups to elicit views on the provision and design features of multimedia resources in delivering clinical trials information. Perceived lack of information is an expressed barrier to clinical trials participation. Multimedia resources were viewed positively as a way to address this barrier by most potential clinical trials participants; in particular by helping to align information to individual needs, promote active engagement with information, and by allowing more control of the learning experience. Whilst text remained the most valued attribute of any resource, other highly rated attributes included the resource being simple to use, easily accessible, having a clear focus, incorporating examples and visual aids, and being interactive. Provision of support for the learning resource was also rated highly. As in other areas, such as education, multimedia resources may enhance the delivery and acceptance of information regarding clinical trials. Better alignment of information may have a positive impact on recruitment and retention into clinical trials. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Design for human factors (DfHF): a grounded theory for integrating human factors into production design processes.

PubMed

Village, Judy; Searcy, Cory; Salustri, Filipo; Patrick Neumann, W

2015-01-01

The 'design for human factors' grounded theory explains 'how' human factors (HF) went from a reactive, after-injury programme in safety, to being proactively integrated into each step of the production design process. In this longitudinal case study collaboration with engineers and HF Specialists in a large electronics manufacturer, qualitative data (e.g. meetings, interviews, observations and reflections) were analysed using a grounded theory methodology. The central tenet in the theory is that when HF Specialists acclimated to the engineering process, language and tools, and strategically aligned HF to the design and business goals of the organisation, HF became a means to improve business performance. This led to engineers 'pulling' HF Specialists onto their team. HF targets were adopted into engineering tools to communicate HF concerns quantitatively, drive continuous improvement, visibly demonstrate change and lead to benchmarking. Senior management held engineers accountable for HF as a key performance indicator, thus integrating HF into the production design process. Practitioner Summary: Research and practice lack explanations about how HF can be integrated early in design of production systems. This three-year case study and the theory derived demonstrate how ergonomists changed their focus to align with design and business goals to integrate HF into the design process.

Texture analysis of radiometric signatures of new sea ice forming in Arctic leads

NASA Technical Reports Server (NTRS)

Eppler, Duane T.; Farmer, L. Dennis

1991-01-01

Analysis of 33.6-GHz, high-resolution, passive microwave images suggests that new sea ice accumulating in open leads is characterized by a unique textural signature which can be used to discriminate new ice forming in this environment from adjacent surfaces of similar radiometric temperature. Ten training areas were selected from the data set, three of which consisted entirely of first-year ice, four entirely of multilayer ice, and three of new ice in open leads in the process of freezing. A simple gradient operator was used to characterize the radiometric texture in each training region in terms of the degree to which radiometric gradients are oriented. New ice in leads has a sufficiently high proportion of well-oriented features to distinguish it uniquely from first-year ice and multiyear ice. The predominance of well-oriented features probably reflects physical processes by which new ice accumulates in open leads. Banded structures, which are evident in aerial photographs of new ice, apparently give rise to the radiometric signature observed, in which the trend of brightness temperature gradients is aligned parallel to lead trends. First-year ice and multiyear ice, which have been subjected to a more random growth and process history, lack this banded structure and therefore are characterized by signatures in which well-aligned elements are less dominant.

A Method for Functional Task Alignment Analysis of an Arthrocentesis Simulator.

PubMed

Adams, Reid A; Gilbert, Gregory E; Buckley, Lisa A; Nino Fong, Rodolfo; Fuentealba, I Carmen; Little, Erika L

2018-05-16

During simulation-based education, simulators are subjected to procedures composed of a variety of tasks and processes. Simulators should functionally represent a patient in response to the physical action of these tasks. The aim of this work was to describe a method for determining whether a simulator does or does not have sufficient functional task alignment (FTA) to be used in a simulation. Potential performance checklist items were gathered from published arthrocentesis guidelines and aggregated into a performance checklist using Lawshe's method. An expert panel used this performance checklist and an FTA analysis questionnaire to evaluate a simulator's ability to respond to the physical actions required by the performance checklist. Thirteen items, from a pool of 39, were included on the performance checklist. Experts had mixed reviews of the simulator's FTA and its suitability for use in simulation. Unexpectedly, some positive FTA was found for several tasks where the simulator lacked functionality. By developing a detailed list of specific tasks required to complete a clinical procedure, and surveying experts on the simulator's response to those actions, educators can gain insight into the simulator's clinical accuracy and suitability. Unexpected of positive FTA ratings of function deficits suggest that further revision of the survey method is required.

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.

PubMed

Kaczor-Urbanowicz, Karolina Elzbieta; Kim, Yong; Li, Feng; Galeev, Timur; Kitchen, Rob R; Gerstein, Mark; Koyano, Kikuye; Jeong, Sung-Hee; Wang, Xiaoyan; Elashoff, David; Kang, So Young; Kim, Su Mi; Kim, Kyoung; Kim, Sung; Chia, David; Xiao, Xinshu; Rozowsky, Joel; Wong, David T W

2018-01-01

Analysis of RNA sequencing (RNA-Seq) data in human saliva is challenging. Lack of standardization and unification of the bioinformatic procedures undermines saliva's diagnostic potential. Thus, it motivated us to perform this study. We applied principal pipelines for bioinformatic analysis of small RNA-Seq data of saliva of 98 healthy Korean volunteers including either direct or indirect mapping of the reads to the human genome using Bowtie1. Analysis of alignments to exogenous genomes by another pipeline revealed that almost all of the reads map to bacterial genomes. Thus, salivary exRNA has fundamental properties that warrant the design of unique additional steps while performing the bioinformatic analysis. Our pipelines can serve as potential guidelines for processing of RNA-Seq data of human saliva. Processing and analysis results of the experimental data generated by the exceRpt (v4.6.3) small RNA-seq pipeline (github.gersteinlab.org/exceRpt) are available from exRNA atlas (exrna-atlas.org). Alignment to exogenous genomes and their quantification results were used in this paper for the analyses of small RNAs of exogenous origin. dtww@ucla.edu. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Human iPSC-derived myocardium-on-chip with capillary-like flow for personalized medicine.

PubMed

Ellis, Bradley W; Acun, Aylin; Can, U Isik; Zorlutuna, Pinar

2017-03-01

The heart wall tissue, or the myocardium, is one of the main targets in cardiovascular disease prevention and treatment. Animal models have not been sufficient in mimicking the human myocardium as evident by the very low clinical translation rates of cardiovascular drugs. Additionally, current in vitro models of the human myocardium possess several shortcomings such as lack of physiologically relevant co-culture of myocardial cells, lack of a 3D biomimetic environment, and the use of non-human cells. In this study, we address these shortcomings through the design and manufacture of a myocardium-on-chip (MOC) using 3D cell-laden hydrogel constructs and human induced pluripotent stem cell (hiPSC) derived myocardial cells. The MOC utilizes 3D spatially controlled co-culture of hiPSC derived cardiomyocytes (iCMs) and hiPSC derived endothelial cells (iECs) integrated among iCMs as well as in capillary-like side channels, to better mimic the microvasculature seen in native myocardium. We first fully characterized iCMs using immunostaining, genetic, and electrochemical analysis and iECs through immunostaining and alignment analysis to ensure their functionality, and then seeded these cells sequentially into the MOC device. We showed that iECs could be cultured within the microfluidic device without losing their phenotypic lineage commitment, and align with the flow upon physiological level shear stresses. We were able to incorporate iCMs within the device in a spatially controlled manner with the help of photocrosslinkable polymers. The iCMs were shown to be viable and functional within the device up to 7 days, and were integrated with the iECs. The iCMs and iECs in this study were derived from the same hiPSC cell line, essentially mimicking the myocardium of an individual human patient. Such devices are essential for personalized medicine studies where the individual drug response of patients with different genetic backgrounds can be tested in a physiologically relevant manner.

Is There an Enabling Environment for Nutrition-Sensitive Agriculture in East Africa? Stakeholder Perspectives From Ethiopia, Kenya, and Uganda.

PubMed

Hodge, Judith; Herforth, Anna; Gillespie, Stuart; Beyero, Mesfin; Wagah, Margaret; Semakula, Richard

2015-12-01

There is growing recognition that "nutrition-sensitive" development is necessary to ensure nutrition security and reduce malnutrition. While agriculture has the potential to be a strong driver of malnutrition reduction and serves as the main source of livelihood for approximately two-thirds of East Africa's population, its potential to reduce malnutrition is currently not being realized. Leveraging Agriculture for Nutrition in East Africa is a research study based in Ethiopia, Kenya, and Uganda that seeks to understand the enabling environment necessary for optimizing the contribution of the food and agriculture sector to nutrition outcomes. Its objectives were to explore stakeholder perceptions of nutrition-agriculture linkages, of political and institutional challenges and opportunities, of evidence that is available and influential for policy making, and of key issues with regard to capacity. Open-ended and semistructured interviews were conducted with 53 stakeholders from government, civil society, donors, United Nations organizations, private sector, and research/academic institutions in Ethiopia, Kenya, and Uganda in 2014. Although policy opportunities and contexts are different between the 3 countries, stakeholders identified similar barriers to greater action, including a narrow focus on solely market-oriented and staple crop production, a lack of clarity and incentives within the agriculture sector about improving nutrition and how to translate policy into action, and lack of capacity in human and financial resources. Many actions to improve the nutrition sensitivity of agriculture were mentioned, including crop diversification, value chain activities and improved market access, nutrition education, and reduction in time and labor costs to women. Many opportunities exist to strengthen the impact of agriculture on nutrition in East Africa, but stronger formulation and implementation of policies will require adequate human resources, funds, timely data on the context, sector alignment on priority actions, and alignment on a framework or indicators for accountability. © The Author(s) 2015.

Comparative Effect of Physicomechanical and Biomolecular Cues on Zone-Specific Chondrogenic Differentiation of Mesenchymal Stem Cells

PubMed Central

Moeinzadeh, Seyedsina; Shariati, Seyed Ramin Pajoum; Jabbari, Esmaiel

2016-01-01

Current tissue engineering approaches to regeneration of articular cartilage rarely restore the tissue to its normal state because the generated tissue lacks the intricate zonal organization of the native cartilage. Zonal regeneration of articular cartilage is hampered by the lack of knowledge for the relation between physical, mechanical, and biomolecular cues and zone-specific chondrogenic differentiation of progenitor cells. This work investigated in 3D the effect of TGF-β1, zone-specific growth factors, optimum matrix stiffness, and adding nanofibers on the expression of chondrogenic markers specific to the superficial, middle, and calcified zones of articular cartilage by the differentiating human mesenchymal stem cells (hMSCs). Growth factors included BMP-7, IGF-1, and hydroxyapatite (HA) for the superficial, middle, and calcified zones, respectively; optimum matrix stiffness was 80 kPa, 2.1 MPa, and 320 MPa; and nanofibers were aligned horizontal, random, and perpendicular to the gel surface. hMSCs with zone-specific cell densities were encapsulated in engineered hydrogels and cultured with or without TGF-β1, zone-specific growth factor, optimum matrix modulus, and fiber addition and cultured in basic chondrogenic medium. The expression of encapsulated cells was measured by mRNA, protein, and biochemical analysis. Results indicated that zone-specific matrix stiffness had a dominating effect on chondrogenic differentiation of hMSCs to the superficial and calcified zone phenotypes. Addition of aligned nanofibers parallel to the direction of gel surface significantly enhanced expression of Col II in the superficial zone chondrogenic differentiation of hMSCs. Conversely, biomolecular factor IGF-1 in combination with TGF-β1 had a dominating effect on the middle zone chondrogenic differentiation of hMSCs. Results of this work could potentially lead to the development of multilayer grafts mimicking the zonal organization of articular cartilage. PMID:27038568

Sanger and Next-Generation Sequencing data for characterization of CTL epitopes in archived HIV-1 proviral DNA.

PubMed

Tumiotto, Camille; Riviere, Lionel; Bellecave, Pantxika; Recordon-Pinson, Patricia; Vilain-Parce, Alice; Guidicelli, Gwenda-Line; Fleury, Hervé

2017-01-01

One of the strategies for curing viral HIV-1 is a therapeutic vaccine involving the stimulation of cytotoxic CD8-positive T cells (CTL) that are Human Leucocyte Antigen (HLA)-restricted. The lack of efficiency of previous vaccination strategies may have been due to the immunogenic peptides used, which could be different from a patient's virus epitopes and lead to a poor CTL response. To counteract this lack of specificity, conserved epitopes must be targeted. One alternative is to gather as many data as possible from a large number of patients on their HIV-1 proviral archived epitope variants, taking into account their genetic background to select the best presented CTL epitopes. In order to process big data generated by Next-Generation Sequencing (NGS) of the DNA of HIV-infected patients, we have developed a software package called TutuGenetics. This tool combines an alignment derived either from Sanger or NGS files, HLA typing, target gene and a CTL epitope list as input files. It allows automatic translation after correction of the alignment obtained between the HxB2 reference and the reads, followed by automatic calculation of the MHC IC50 value for each epitope variant and the HLA allele of the patient by using NetMHCpan 3.0, resulting in a csv file as output result. We validated this new tool by comparing Sanger and NGS (454, Roche) sequences obtained from the proviral DNA of patients at success of ART included in the Provir Latitude 45 study and showed a 90% correlation between the quantitative results of NGS and Sanger. This automated analysis combined with complementary samples should yield more data regarding the archived CTL epitopes according to the patients' HLA alleles and will be useful for screening epitopes that in theory are presented efficiently to the HLA groove, thus constituting promising immunogenic peptides for a therapeutic vaccine.

Human iPSC-derived myocardium-on-chip with capillary-like flow for personalized medicine

PubMed Central

Ellis, Bradley W.; Acun, Aylin; Can, U. Isik; Zorlutuna, Pinar

2017-01-01

The heart wall tissue, or the myocardium, is one of the main targets in cardiovascular disease prevention and treatment. Animal models have not been sufficient in mimicking the human myocardium as evident by the very low clinical translation rates of cardiovascular drugs. Additionally, current in vitro models of the human myocardium possess several shortcomings such as lack of physiologically relevant co-culture of myocardial cells, lack of a 3D biomimetic environment, and the use of non-human cells. In this study, we address these shortcomings through the design and manufacture of a myocardium-on-chip (MOC) using 3D cell-laden hydrogel constructs and human induced pluripotent stem cell (hiPSC) derived myocardial cells. The MOC utilizes 3D spatially controlled co-culture of hiPSC derived cardiomyocytes (iCMs) and hiPSC derived endothelial cells (iECs) integrated among iCMs as well as in capillary-like side channels, to better mimic the microvasculature seen in native myocardium. We first fully characterized iCMs using immunostaining, genetic, and electrochemical analysis and iECs through immunostaining and alignment analysis to ensure their functionality, and then seeded these cells sequentially into the MOC device. We showed that iECs could be cultured within the microfluidic device without losing their phenotypic lineage commitment, and align with the flow upon physiological level shear stresses. We were able to incorporate iCMs within the device in a spatially controlled manner with the help of photocrosslinkable polymers. The iCMs were shown to be viable and functional within the device up to 7 days, and were integrated with the iECs. The iCMs and iECs in this study were derived from the same hiPSC cell line, essentially mimicking the myocardium of an individual human patient. Such devices are essential for personalized medicine studies where the individual drug response of patients with different genetic backgrounds can be tested in a physiologically relevant manner. PMID:28396709

MaxAlign: maximizing usable data in an alignment.

PubMed

Gouveia-Oliveira, Rodrigo; Sackett, Peter W; Pedersen, Anders G

2007-08-28

The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

Phenotypic interactions between tree hosts and invasive forest pathogens in the light of globalization and climate change

PubMed Central

2016-01-01

Invasive pathogens can cause considerable damage to forest ecosystems. Lack of coevolution is generally thought to enable invasive pathogens to bypass the defence and/or recognition systems in the host. Although mostly true, this argument fails to predict intermittent outcomes in space and time, underlining the need to include the roles of the environment and the phenotype in host–pathogen interactions when predicting disease impacts. We emphasize the need to consider host–tree imbalances from a phenotypic perspective, considering the lack of coevolutionary and evolutionary history with the pathogen and the environment, respectively. We describe how phenotypic plasticity and plastic responses to environmental shifts may become maladaptive when hosts are faced with novel pathogens. The lack of host–pathogen and environmental coevolution are aligned with two global processes currently driving forest damage: globalization and climate change, respectively. We suggest that globalization and climate change act synergistically, increasing the chances of both genotypic and phenotypic imbalances. Short moves on the same continent are more likely to be in balance than if the move is from another part of the world. We use Gremmeniella abietina outbreaks in Sweden to exemplify how host–pathogen phenotypic interactions can help to predict the impacts of specific invasive and emergent diseases. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’. PMID:28080981

Phenotypic interactions between tree hosts and invasive forest pathogens in the light of globalization and climate change.

PubMed

Stenlid, Jan; Oliva, Jonàs

2016-12-05

Invasive pathogens can cause considerable damage to forest ecosystems. Lack of coevolution is generally thought to enable invasive pathogens to bypass the defence and/or recognition systems in the host. Although mostly true, this argument fails to predict intermittent outcomes in space and time, underlining the need to include the roles of the environment and the phenotype in host-pathogen interactions when predicting disease impacts. We emphasize the need to consider host-tree imbalances from a phenotypic perspective, considering the lack of coevolutionary and evolutionary history with the pathogen and the environment, respectively. We describe how phenotypic plasticity and plastic responses to environmental shifts may become maladaptive when hosts are faced with novel pathogens. The lack of host-pathogen and environmental coevolution are aligned with two global processes currently driving forest damage: globalization and climate change, respectively. We suggest that globalization and climate change act synergistically, increasing the chances of both genotypic and phenotypic imbalances. Short moves on the same continent are more likely to be in balance than if the move is from another part of the world. We use Gremmeniella abietina outbreaks in Sweden to exemplify how host-pathogen phenotypic interactions can help to predict the impacts of specific invasive and emergent diseases.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'. © 2016 The Author(s).

System and method for 2D workpiece alignment

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

Weaver, William T.; Carlson, Charles T.; Smith, Scott A.

2015-07-14

A carrier capable of holding one or more workpieces is disclosed. The carrier includes movable projections located along the sides of each cell in the carrier. This carrier, in conjunction with a separate alignment apparatus, aligns each workpiece within its respective cell against several alignment pins, using a multiple step alignment process to guarantee proper positioning of the workpiece in the cell. First, the workpieces are moved toward one side of the cell. Once the workpieces have been aligned against this side, the workpieces are then moved toward an adjacent orthogonal side such that the workpieces are aligned to twomore » sides of the cell. Once aligned, the workpiece is held in place by the projections located along each side of each cell. In addition, the alignment pins are also used to align the associated mask, thereby guaranteeing that the mask is properly aligned to the workpiece.« less

The power of change: interpersonal attraction as a function of attitude similarity and attitude alignment.

PubMed

Reid, Chelsea A; Davis, Jody L; Green, Jeffrey D

2013-01-01

Does attitude alignment predict attraction? Would you like a stranger more who shifts her/his attitudes to more closely align with yours? In pairs, participants (N = 77) discussed social issues about which they disagreed and received false feedback on whether the partner engaged in attitude alignment (shifted her/his attitudes toward the participant's attitude) following discussion. Participants also received false feedback about the proportion of similarity to the partner on a set of issues (i.e., 25%, 50%, or 75%). Participants reported greater attraction to partners who engaged in attitude alignment and who were more similar. Moreover, similarity and attitude alignment interacted. Similarity predicted attraction when attitude alignment did not occur, but did not predict attraction when attitude alignment did occur. Finally, partner attitude alignment led to participant attitude alignment, and perceived reasoning ability mediated the attitude alignment-attraction relationship.

Aligned Single Wall Carbon Nanotube Polymer Composites Using an Electric Field

NASA Technical Reports Server (NTRS)

Park, Cheol; Wiklinson, John; Banda, Sumanth; Ounaies, Zoubeida; Wise, Kristopher E.; Sauti, Godfrey; Lillehei, Peter T.; Harrison, Joycelyn S.

2005-01-01

While high shear alignment has been shown to improve the mechanical properties of single wall carbon nanotubes (SWNT)-polymer composites, it is difficult to control and often results in degradation of the electrical and dielectric properties of the composite. Here, we report a novel method to actively align SWNTs in a polymer matrix, which allows for control over the degree of alignment of SWNTs without the side effects of shear alignment. In this process, SWNTs are aligned via field-induced dipolar interactions among the nanotubes under an AC electric field in a liquid matrix followed by immobilization by photopolymerization while maintaining the electric field. Alignment of SWNTs was controlled as a function of magnitude, frequency, and application time of the applied electric field. The degree of SWNT alignment was assessed using optical microscopy and polarized Raman spectroscopy and the morphology of the aligned nanocomposites was investigated by high resolution scanning electron microscopy. The structure of the field induced aligned SWNTs is intrinsically different from that of shear aligned SWNTs. In the present work, SWNTs are not only aligned along the field, but also migrate laterally to form thick, aligned SWNT percolative columns between the electrodes. The actively aligned SWNTs amplify the electrical and dielectric properties in addition to improving the mechanical properties of the composite. All of these properties of the aligned nanocomposites exhibited anisotropic characteristics, which were controllable by tuning the applied field conditions.

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

PubMed

Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

2009-07-01

The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

Image-based quantification of fiber alignment within electrospun tissue engineering scaffolds is related to mechanical anisotropy.

PubMed

Fee, Timothy; Downs, Crawford; Eberhardt, Alan; Zhou, Yong; Berry, Joel

2016-07-01

It is well documented that electrospun tissue engineering scaffolds can be fabricated with variable degrees of fiber alignment to produce scaffolds with anisotropic mechanical properties. Several attempts have been made to quantify the degree of fiber alignment within an electrospun scaffold using image-based methods. However, these methods are limited by the inability to produce a quantitative measure of alignment that can be used to make comparisons across publications. Therefore, we have developed a new approach to quantifying the alignment present within a scaffold from scanning electron microscopic (SEM) images. The alignment is determined by using the Sobel approximation of the image gradient to determine the distribution of gradient angles with an image. This data was fit to a Von Mises distribution to find the dispersion parameter κ, which was used as a quantitative measure of fiber alignment. We fabricated four groups of electrospun polycaprolactone (PCL) + Gelatin scaffolds with alignments ranging from κ = 1.9 (aligned) to κ = 0.25 (random) and tested our alignment quantification method on these scaffolds. It was found that our alignment quantification method could distinguish between scaffolds of different alignments more accurately than two other published methods. Additionally, the alignment parameter κ was found to be a good predictor the mechanical anisotropy of our electrospun scaffolds. The ability to quantify fiber alignment within and make direct comparisons of scaffold fiber alignment across publications can reduce ambiguity between published results where cells are cultured on "highly aligned" fibrous scaffolds. This could have important implications for characterizing mechanics and cellular behavior on aligned tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1680-1686, 2016. © 2016 Wiley Periodicals, Inc.

Aligning for accountable care: Strategic practices for change in accountable care organizations.

PubMed

Hilligoss, Brian; Song, Paula H; McAlearney, Ann Scheck

Alignment within accountable care organizations (ACOs) is crucial if these new entities are to achieve their lofty goals. However, the concept of alignment remains underexamined, and we know little about the work entailed in creating alignment. The aim of this study was to develop the concept of aligning by identifying and describing the strategic practices administrators use to align the structures, processes, and behaviors of their organizations and individual providers in pursuit of accountable care. We conducted 2-year qualitative case studies of four ACOs that have assumed full risk for the costs and quality of care for defined populations. Five strategic aligning practices were used by all four ACOs. Informing both aligns providers' understandings with the goals and value proposition of the ACO and aligns the providers' attention with the drivers of performance. Involving both aligns ACO leaders' understandings with the realities facing providers and aligns the policies of the ACO with the needs of providers. Enhancing both aligns the operations of individual provider practices with the operations of the ACO and aligns the trust of providers with the ACO. Motivating aligns what providers value with the goals of the ACO. Finally, evolving is a metapractice of learning and adapting that guides the execution of the other four practices. Our findings suggest that there are second-order cognitive (e.g., understandings and attention) and cultural (e.g., trust and values) levels of alignment, as well as a first-order operational level (organizational structures, processes, and incentives). A well-aligned organization may require ongoing repositioning at each of these levels, as well as attention to both cooperative and coordinative dimensions of alignment. Implications for research and practice are discussed.

Using structure to explore the sequence alignment space of remote homologs.

PubMed

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

Intrinsic alignments of galaxies in the EAGLE and cosmo-OWLS simulations

NASA Astrophysics Data System (ADS)

Velliscig, Marco; Cacciato, Marcello; Schaye, Joop; Hoekstra, Henk; Bower, Richard G.; Crain, Robert A.; van Daalen, Marcel P.; Furlong, Michelle; McCarthy, I. G.; Schaller, Matthieu; Theuns, Tom

2015-12-01

We report results for the alignments of galaxies in the EAGLE and cosmo-OWLS hydrodynamical cosmological simulations as a function of galaxy separation (-1 ≤ log10(r/[ h-1 Mpc]) ≤ 2) and halo mass (10.7 ≤ log10(M200/[h-1 M⊙]) ≤ 15). We focus on two classes of alignments: the orientations of galaxies with respect to either the directions to, or the orientations of, surrounding galaxies. We find that the strength of the alignment is a strongly decreasing function of the distance between galaxies. For galaxies hosted by the most massive haloes in our simulations the alignment can remain significant up to ˜100 Mpc. Galaxies hosted by more massive haloes show stronger alignment. At a fixed halo mass, more aspherical or prolate galaxies exhibit stronger alignments. The spatial distribution of satellites is anisotropic and significantly aligned with the major axis of the main host halo. The major axes of satellite galaxies, when all stars are considered, are preferentially aligned towards the centre of the main host halo. The predicted projected direction-orientation alignment, ɛg+(rp), is in broad agreement with recent observations. We find that the orientation-orientation alignment is weaker than the orientation-direction alignment on all scales. Overall, the strength of galaxy alignments depends strongly on the subset of stars that are used to measure the orientations of galaxies and it is always weaker than the alignment of dark matter haloes. Thus, alignment models that use halo orientation as a direct proxy for galaxy orientation overestimate the impact of intrinsic galaxy alignments.

Alignment method for parabolic trough solar concentrators

DOEpatents

Diver, Richard B [Albuquerque, NM

2010-02-23

A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation.

PubMed

Sharma, Virag; Hiller, Michael

2017-08-21

Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0.75 substitutions per neutral site, like human and other non-placental vertebrates, benefit from increased sensitivity. To systematically test if increased sensitivity improves comparative gene annotations, we built a multiple alignment of 144 vertebrate genomes and used this alignment to map human genes to the other 143 vertebrates with CESAR. We found that higher alignment sensitivity substantially improves the completeness of comparative gene annotations by adding on average 2382 and 7440 novel exons and 117 and 317 novel genes for mammalian and non-mammalian species, respectively. Our results suggest a more sensitive alignment strategy that should generally be used for genome alignments between distantly-related species. Our 144-vertebrate genome alignment and the comparative gene annotations (https://bds.mpi-cbg.de/hillerlab/144VertebrateAlignment_CESAR/) are a valuable resource for comparative genomics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.

PubMed

Hashemifar, Somaye; Xu, Jinbo

2014-09-01

High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene

PubMed Central

2017-01-01

The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data. We use a taxonomic gold standard to compare the accuracy of alignment-free phylogenetic inference with that of common microbiome-wide phylogenetic inference pipelines based on PyNAST and MUSCLE alignments with FastTree and RAxML. We re-simulate fecal communities from Human Microbiome Project data to evaluate the performance of the methods on datasets with properties of real data. Our comparisons show that alignment-free methods are not inferior to alignment-based methods in giving accurate and robust phylogenic trees. Moreover, consensus ensembles of alignment-free phylogenies are superior to those built from alignment-based methods in their ability to highlight community differences in low power settings. In addition, the overall running times of alignment-based and alignment-free phylogenetic inference are comparable. Taken together our empirical results suggest that alignment-free methods provide a viable approach for microbiome-wide phylogenetic inference. PMID:29136663

Evaluating patient and stakeholder engagement in research: moving from theory to practice.

PubMed

Esmail, Laura; Moore, Emily; Rein, Alison

2015-03-01

Despite the growing demand for research that engages stakeholders, there is limited evidence in the literature to demonstrate its value - or return on investment. This gap indicates a general lack of evaluation of engagement activities. To adequately inform engagement activities, we need to further investigate the dividends of engaged research, and how to evaluate these effects. This paper synthesizes the literature on hypothesized impacts of engagement, shares what has been evaluated and identifies steps needed to reduce the gap between engagement's promises and the underlying evidence supporting its practice. This assessment provides explicit guidance for better alignment of engagement's promised benefits with evaluation efforts and identifies specific areas for development of evaluative measures and better reporting processes.

Direct evidence of a role for heterochromatin in meiotic chromosome segregation.

PubMed

Dernburg, A F; Sedat, J W; Hawley, R S

1996-07-12

We have investigated the mechanism that enables achiasmate chromosomes to segregate from each other at meiosis I in D. melanogaster oocytes. Using novel cytological methods, we asked whether nonexchange chromosomes are paired prior to disjunction. Our results show that the heterochromatin of homologous chromosomes remains associated throughout prophase until metaphase I regardless of whether they undergo exchange, suggesting that homologous recognition can lead to segregation even in the absence of chiasmata. However, partner chromosomes lacking homology do not pair prior to disjunction. Furthermore, euchromatic synapsis is not maintained throughout prophase. These observations provide a physical demonstration that homologous and heterologous achiasmate segregations occur by different mechanisms and establish a role for heterochromatin in maintaining the alignment of chromosomes during meiosis.

Effect of tow alignment on the mechanical performance of 3D woven textile composites

NASA Technical Reports Server (NTRS)

Norman, Timothy L.; Allison, Patti; Baldwin, Jack W.; Gracias, Brian K.; Seesdorf, Dave

1993-01-01

Three-dimensional (3D) woven preforms are currently being considered for use as primary structural components. Lack of technology to properly manufacture, characterize and predict mechanical properties, and predict damage mechanisms leading to failure are problems facing designers of textile composite materials. Two material systems with identical specifications but different manufacturing approaches are investigated. One manufacturing approach resulted in an irregular (nonuniform) preform geometry. The other approach yielded the expected preform geometry (uniform). The objectives are to compare the mechanical properties of the uniform and nonuniform angle interlock 3D weave constructions. The effect of adding layers of laminated tape to the outer surfaces of the textile preform is also examined. Damage mechanisms are investigated and test methods are evaluated.

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Health care's new game changer. Thinking like a health plan.

PubMed

Eggbeer, Bill; Bowers, Krista

2014-10-01

The transition for hospitals from having only a provider's perspective to thinking more like a health plan will require strategic alignment on four fronts: Health plan alignment. Hospital and physician alignment. Leadership alignment. Organizational alignment.

Iterative non-sequential protein structural alignment.

PubMed

Salem, Saeed; Zaki, Mohammed J; Bystroff, Christopher

2009-06-01

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.

Electric-field-induced flow-aligning state in a nematic liquid crystal.

PubMed

Fatriansyah, Jaka Fajar; Orihara, Hiroshi

2015-04-01

The response of shear stress to a weak ac electric field as a probe is measured in a nematic liquid crystal under shear flow and dc electric fields. Two states with different responses are clearly observed when the dc electric field is changed at a constant shear rate: the flow aligning and non-flow aligning states. The director lies in the shear plane in the flow aligning state and out of the plane in the non-flow aligning state. Through application of dc electric field, the non-flow aligning state can be changed to the flow aligning state. In the transition from the flow aligning state to the non-flow aligning state, it is found that the response increases and the relaxation time becomes longer. Here, the experimental results in the flow aligning state are discussed on the basis of the Ericksen-Leslie theory.

Alignment of the femoral component in a mobile-bearing unicompartmental knee arthroplasty: a study in 10 cadaver femora.

PubMed

Kort, N P; van Raay, J J A M; Thomassen, B J W

2007-08-01

Use of an intramedullary rod is advised for the alignment of the femoral component of an Oxford phase-III prosthesis. There are users moving toward extramedullary alignment, which is merely an indicator of frustration with accuracy of intramedullary alignment. The results of our study with 10 cadaver femora demonstrate that use of a short and long intramedullary femoral rod may result in excessive flexion alignment error of the femoral component. Understanding of the extramedullary alignment possibility and experience with the visual alignment of the femoral drill guide is essential toward minimizing potential errors in the alignment of the femoral component.

Desktop aligner for fabrication of multilayer microfluidic devices.

PubMed

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-07-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm(-1). To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

Desktop aligner for fabrication of multilayer microfluidic devices

PubMed Central

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-01-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

Iterative refinement of structure-based sequence alignments by Seed Extension

PubMed Central

Kim, Changhoon; Tai, Chin-Hsien; Lee, Byungkook

2009-01-01

Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence alignment procedures still mis-align substantial numbers of residues. In order to correct such errors, we previously explored the possibility of replacing the residue-based dynamic programming algorithm in structure alignment procedures with the Seed Extension algorithm, which does not use a gap penalty. Here, we describe a new procedure called RSE (Refinement with Seed Extension) that iteratively refines a structure-based sequence alignment. Results RSE uses SE (Seed Extension) in its core, which is an algorithm that we reported recently for obtaining a sequence alignment from two superimposed structures. The RSE procedure was evaluated by comparing the correctly aligned fractions of residues before and after the refinement of the structure-based sequence alignments produced by popular programs. CE, DaliLite, FAST, LOCK2, MATRAS, MATT, TM-align, SHEBA and VAST were included in this analysis and the NCBI's CDD root node set was used as the reference alignments. RSE improved the average accuracy of sequence alignments for all programs tested when no shift error was allowed. The amount of improvement varied depending on the program. The average improvements were small for DaliLite and MATRAS but about 5% for CE and VAST. More substantial improvements have been seen in many individual cases. The additional computation times required for the refinements were negligible compared to the times taken by the structure alignment programs. Conclusion RSE is a computationally inexpensive way of improving the accuracy of a structure-based sequence alignment. It can be used as a standalone procedure following a regular structure-based sequence alignment or to replace the traditional iterative refinement procedures based on residue-level dynamic programming algorithm in many structure alignment programs. PMID:19589133

Torsional stress impedance and magneto-impedance in (Co0.95Fe0.05)72.5 Si12.5B15 amorphous wire with helical induced anisotropy

NASA Astrophysics Data System (ADS)

Blanco, J. M.; Zhukov, A. P.; González, J.

1999-12-01

The magneto-impedance effect icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/ZH = [Z(H)-Z(Hmax)]/Z(Hmax) has been measured in (Fe0.95Co0.05)72.5B15Si12.5 wire under torsion stress, icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> (torsion angle per unit length) with axial magnetic field (H) as parameter. Without stress (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)H(H) dependence has a non-monotonous shape with first an increase of total impedance Z and then a decrease, i.e. shows a maximum at certain axial magnetic field Hm. It was found that the torsion stress dependence of electrical impedance (torsion impedance), (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> = [Z(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>)-Z(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>max)]/Z(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>max), has asymmetric character with a clear maximum at torsion angle, icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> around 7icons/Journals/Common/pi" ALT="pi" ALIGN="TOP"/> rad m-1 in as-cast wire, while (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> reaches a maximum around 170%. Thermal treatments under torsion stress (without and with a previous annealing stage) develop a helical anisotropy on the amorphous wire, which drastically modifies the (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> response. Such treatments were carried out by using current annealing which resulted in a drastic increase of the maximum (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> up to 225%, and a change of torsion dependence of icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z with a tendency to a finally symmetric dependence of (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/>(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>). The maximum (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> ratio, (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> m, was obtained under torsion stress of icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> = 20icons/Journals/Common/pi" ALT="pi" ALIGN="TOP"/> rad m-1 (in a torsion annealed sample) and = 11 rad m-1 (with pre-annealing and torsion annealing). Observed dependences were explained taking into account the frozen-in magneto-elastic anisotropy owing to the internal stress distribution during the fabrication process, the helical anisotropies induced by the torsion strain and that developed by thermal treatment under torsion stress (torsion annealing). The differences in the shape and intensity of the maximum ( Z/Z) m between the torsion annealed and pre-annealed and torsion annealed samples should be ascribed to the visco-elastic character of the helical anisotropy induced by torsion stress.

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

PubMed

Chapais, Bernard

2013-01-01

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

National health insurance reconsidered: dilemmas and opportunities.

PubMed

Battistella, R M; Weil, T P

1989-01-01

Changing social and economic constraints are precipitating a reformulation of the role of government in the provision of social welfare services. The authors conclude that government intervention in the health sector is bound to expand rather than contract because centralization is the key to reconciling otherwise divergent political demands for spending controls and greater equality of access to quality care for the increasing number of uninsured or underinsured persons. In the past eight years, the federal government has unleashed competitive market principles that have had negative side effects on the nation's health services. Payers, providers, and consumers will likely seek to protect themselves by forming coalitions, as happened recently in Massachusetts where the law now requires employers to provide minimum health insurance benefits to their employees. Escalating pressures to correct the damages from short-term piecemeal solutions to problems of health finance and delivery will provide the chief dynamic for universal health insurance in the United States. New economic, social, and political realities suggest, however, an eclectic strategy for attaining this goal that bears little resemblance to the conventional wisdom that guided health policy throughout the postwar period.

Towards On-Line Services Based on a Holistic Analysis of Human Activities

NASA Technical Reports Server (NTRS)

Clancey, William J.

2004-01-01

Very often computer scientists view computerization of services in terms of the logistics of human-machine interaction, including establishing a contract, accessing records, and of course designing an interface. But this analysis often moves too quickly to tactical details, failing to frame the entire service in human terms, and not recognizing the mutual learning required to define and relate goals, constraints, and the personalized value of available services. In particular, on-line services that "computerize communication" can be improved by constructing an activity model of what the person is trying to do, not just filtering, comparing, and selling piece-meal services. For example, from the customer s perspective the task of an on-line travel service is not merely to establish confirmed reservations, but to have a complete travel plan, usually integrating many days of transportation, lodging, and recreation into a happy experience. The task of the travel agent is not merely "ticketing", but helping the customer understand what they want and providing services that will connect everything together in an enjoyable way.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

PubMed

Kyrpides, Nikos C; Hugenholtz, Philip; Eisen, Jonathan A; Woyke, Tanja; Göker, Markus; Parker, Charles T; Amann, Rudolf; Beck, Brian J; Chain, Patrick S G; Chun, Jongsik; Colwell, Rita R; Danchin, Antoine; Dawyndt, Peter; Dedeurwaerdere, Tom; DeLong, Edward F; Detter, John C; De Vos, Paul; Donohue, Timothy J; Dong, Xiu-Zhu; Ehrlich, Dusko S; Fraser, Claire; Gibbs, Richard; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Jansson, Janet K; Keasling, Jay D; Knight, Rob; Labeda, David; Lapidus, Alla; Lee, Jung-Sook; Li, Wen-Jun; Ma, Juncai; Markowitz, Victor; Moore, Edward R B; Morrison, Mark; Meyer, Folker; Nelson, Karen E; Ohkuma, Moriya; Ouzounis, Christos A; Pace, Norman; Parkhill, Julian; Qin, Nan; Rossello-Mora, Ramon; Sikorski, Johannes; Smith, David; Sogin, Mitch; Stevens, Rick; Stingl, Uli; Suzuki, Ken-Ichiro; Taylor, Dorothea; Tiedje, Jim M; Tindall, Brian; Wagner, Michael; Weinstock, George; Weissenbach, Jean; White, Owen; Wang, Jun; Zhang, Lixin; Zhou, Yu-Guang; Field, Dawn; Whitman, William B; Garrity, George M; Klenk, Hans-Peter

2014-08-01

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

Correction of gynecomastia through a single puncture incision.

PubMed

Mentz, Henry A; Ruiz-Razura, Amado; Newall, German; Patronella, Christopher K; Miniel, Laura A

2007-01-01

In men, the development of feminized breasts may cause significant emotional distress and embarrassment, particularly in young men and adolescents. Unfortunately, gynecomastia responds poorly to diet and exercise, and conventional corrective surgery may produce large stigmatizing areolar or chest scars and a flattened or concave chest. In 2004, board-certified plastic surgeons performed 16,275 corrective procedures, and in 2005 there was a 17% increase, according to The American Society of Plastic Surgeons (ASPS) procedural statistics. This report describes a surgical approach for removal of both glandular and adipose tissue using a small 3-mm areolar stab wound incision and a piecemeal glandular resection to correct gynecomastia with minimal and imperceptible external scarring. Pectoral etching of the chest and suction lipectomy are performed simultaneously to enhance and define the thoracic musculature and further virilize the upper thorax. Excellent results have been obtained with minimal complications. The authors present their experience with more than 200 consecutive cases over the past 4 years. They are very optimistic with these results because they have obtained a high degree of patient satisfaction.

Thermodynamics of Highly Concentrated Aqueous Electrolytes: Based on Boltzmann's eponymous equation

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

Ally, Moonis Raza

This sharply focused book invites the reader to explore the chemical thermodynamics of highly concentrated aqueous electrolytes from a different vantage point than traditional methods. The book's foundation is deeply rooted in Ludwig Boltzmann's eponymous equation. The pathway from micro to macro thermodynamics is explained heuristically, in a step-by-step approach. Concepts and mathematical formalism are explained in detail to captivate and maintain interest as the algebra twists and turns. Every significant result is derived in a lucid and piecemeal fashion. Application of the theory is exemplified with examples. It is amazing to realize that Boltamann's simple equation contains sufficient informationmore » from which such an elaborate theory can emerge. This book is suitable for undergraduate and graduate level classes in chemical engineering, chemistry, geochemistry, environmental sciences, and those studying aerosol particles in the troposphere. Students interested in understanding how thermodynamic theories may be developed would be inspired by the methodology. The author wishes that readers get as much excitement reading this book as he did writing it.« less

The compulsory psychiatric regime in Hong Kong: Constitutional and ethical perspectives.

PubMed

Cheung, Daisy

This article examines the compulsory psychiatric regime in Hong Kong. Under section 36 of the Mental Health Ordinance, which authorises long-term detention of psychiatric patients, a District Judge is required to countersign the form filled out by the registered medical practitioners in order for the detention to be valid. Case law, however, has shown that the role of the District Judge is merely administrative. This article suggests that, as it currently stands, the compulsory psychiatric regime in Hong Kong is unconstitutional because it fails the proportionality test. In light of this conclusion, the author proposes two solutions to deal with the issue, by common law or by legislative reform. The former would see an exercise of discretion by the courts read into section 36, while the latter would involve piecemeal reform of the relevant provisions to give the courts an explicit discretion to consider substantive issues when reviewing compulsory detention applications. The author argues that these solutions would introduce effective judicial supervision into the compulsory psychiatric regime and safeguard against abuse of process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Avoiding piecemeal research on participation in cervical cancer screening: the advantages of a social identity framework

PubMed Central

Tribe, Candice; Webb, Janine

2012-01-01

Abstract Background  Cervical cancer screening research has predominantly focused on one type of participation, namely compliance with medical recommendations, and has largely ignored other types of participation. While there is some research that has taken a different approach, findings in this research area are not well integrated under a theoretical framework. Objective  The aim of this study is to show how consideration of a broader definition of participation and better integration of the theoretical conceptualization of participation in cervical cancer screening are both possible and desirable to enable a better understanding of women’s experiences of cervical cancer screening specifically and to improve women’s health generally. Main Conclusion  It is suggested that alternative types of participation in cervical cancer screening warrant further investigation and that a social identity theoretical approach offers one way of integrating such conceptualizations of participation. The paper also argues for more explicit consideration of the role of social processes and of the variables, such as power, social identity and relational justice, which are involved in participation in cervical cancer screening. PMID:22646802

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

PubMed Central

Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A.; Woyke, Tanja; Göker, Markus; Parker, Charles T.; Amann, Rudolf; Beck, Brian J.; Chain, Patrick S. G.; Chun, Jongsik; Colwell, Rita R.; Danchin, Antoine; Dawyndt, Peter; Dedeurwaerdere, Tom; DeLong, Edward F.; Detter, John C.; De Vos, Paul; Donohue, Timothy J.; Dong, Xiu-Zhu; Ehrlich, Dusko S.; Fraser, Claire; Gibbs, Richard; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Jansson, Janet K.; Keasling, Jay D.; Knight, Rob; Labeda, David; Lapidus, Alla; Lee, Jung-Sook; Li, Wen-Jun; MA, Juncai; Markowitz, Victor; Moore, Edward R. B.; Morrison, Mark; Meyer, Folker; Nelson, Karen E.; Ohkuma, Moriya; Ouzounis, Christos A.; Pace, Norman; Parkhill, Julian; Qin, Nan; Rossello-Mora, Ramon; Sikorski, Johannes; Smith, David; Sogin, Mitch; Stevens, Rick; Stingl, Uli; Suzuki, Ken-ichiro; Taylor, Dorothea; Tiedje, Jim M.; Tindall, Brian; Wagner, Michael; Weinstock, George; Weissenbach, Jean; White, Owen; Wang, Jun; Zhang, Lixin; Zhou, Yu-Guang; Field, Dawn; Whitman, William B.; Garrity, George M.; Klenk, Hans-Peter

2014-01-01

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment. PMID:25093819

Morphometric synaptology of a whole neuron profile using a semiautomatic interactive computer system.

PubMed

Saito, K; Niki, K

1983-07-01

We propose a new method of dealing with morphometric synaptology that processes all synapses and boutons around the HRP marked neuron on a large composite electron micrograph, rather than a qualitative or a piecemeal quantitative study of a particular synapse and/or bouton that is not positioned on the surface of the neuron. This approach requires the development of both neuroanatomical procedures, by which a specific whole neuronal profile is identified, and valuable specialized tools, which support the collection and analysis of a great volume of morphometric data from composite electron micrographs, in order to reduce the burden of the morphologist. The present report is also concerned with the total and reliable semi-automatic interactive computer system for gathering and analyzing morphometric data that has been under development in our laboratory. A morphologist performs the pattern recognition portion by using a large-sized tablet digitizer and a menu-sheet command, and the system registers the various morphometric values of many different neurons and performs statistical analysis. Some examples of morphometric measurements and analysis show the usefulness and efficiency of the proposed system and method.

The use of Coca-Cola in the management of bolus obstruction in benign oesophageal stricture.

PubMed Central

Karanjia, N. D.; Rees, M.

1993-01-01

Oesophageal stricture is a complication of oesophageal reflux and may itself be complicated by bolus obstruction. We reviewed the records of patients presenting with dysphagia and who were found to have benign oesophageal strictures. We studied the outcome of bolus obstruction in 13 episodes affecting eight patients. In six episodes Coca-Cola was administered on the day before endoscopy, and in all these patients the bolus had cleared. In seven episodes nothing was administered before endoscopy, and in all seven a bolus was evident at endoscopy. In five of these seven the bolus was removed piecemeal and in each of these instances the endoscope had to be passed between two and five times. In the remaining two instances the procedure was abandoned and the patients returned to the ward for the administration of Coca-Cola. At subsequent endoscopy these patients were found to be clear of any bolus. These results suggest that the administration of Coca-Cola (or other aerated drinks) may clear a bolus in the acutely obstructed oesophagus. PMID:8476194

Networking for rare diseases: a necessity for Europe.

PubMed

Aymé, S; Schmidtke, J

2007-12-01

Most rare diseases are life-threatening and chronically debilitating conditions, and the vast majority of them are genetically determined. Their individually low prevalence requires special combined efforts to address them so as to improve diagnosis, care and prevention. Though it is difficult to develop a public health policy specific to each rare disease, it is possible to have a global rather than a piecemeal approach in the areas of scientific and biomedical research, drug research and development, industry policy, information and training, social benefits, hospitalisation and outpatient care. In the recent past, several initiatives at EU and Member States levels have been taken and proved efficient in developing suitable solutions which are now having a positive impact on the quality of life of patients. These initiatives are presented here. They include the establishment of Orphanet, a database of rare diseases and orphan drugs providing an encyclopedia of rare diseases and a directory of associated expert services, the funding of research networks to boost the collaboration between research teams, as well as the funding of networks of clinical centres of reference to better serve the patients and contribute to developing clinical research.

Marketing alcohol to young people: implications for industry regulation and research policy.

PubMed

Jackson, M C; Hastings, G; Wheeler, C; Eadie, D; Mackintosh, A M

2000-12-01

This paper focuses on the marketing of alcohol to young people in the United Kingdom, but the lessons that emerge have international significance. Alcohol is a global enterprise and recent consolidation means that it is controlled by a decreasing number of expanding multi-nationals. Alcohol companies are able to allocate significant resources to researching consumer preferences, developing new products and promoting them on an international level. Recent years have seen a growth in the value that youth culture attaches to brand labels and symbols and a move away from the healthy-living ethos. The alcohol industry's response to these trends has been to design alcoholic beverages that appeal to young people, using well-informed and precisely targeted marketing strategies. This has led to growing concerns about the implications for public health and a demand for tighter controls to regulate alcohol marketing practices. In the United Kingdom, controls on alcohol are piecemeal and reactive and the current system of voluntary regulation appears ineffective. This paper argues for more research to establish current industry practice and inform the development of a comprehensive regulatory structure and system of monitoring.

Reverse alignment "mirror image" visualization as a laparoscopic training tool improves task performance.

PubMed

Dunnican, Ward J; Singh, T Paul; Ata, Ashar; Bendana, Emma E; Conlee, Thomas D; Dolce, Charles J; Ramakrishnan, Rakesh

2010-06-01

Reverse alignment (mirror image) visualization is a disconcerting situation occasionally faced during laparoscopic operations. This occurs when the camera faces back at the surgeon in the opposite direction from which the surgeon's body and instruments are facing. Most surgeons will attempt to optimize trocar and camera placement to avoid this situation. The authors' objective was to determine whether the intentional use of reverse alignment visualization during laparoscopic training would improve performance. A standard box trainer was configured for reverse alignment, and 34 medical students and junior surgical residents were randomized to train with either forward alignment (DIRECT) or reverse alignment (MIRROR) visualization. Enrollees were tested on both modalities before and after a 4-week structured training program specific to their modality. Student's t test was used to determine differences in task performance between the 2 groups. Twenty-one participants completed the study (10 DIRECT, 11 MIRROR). There were no significant differences in performance time between DIRECT or MIRROR participants during forward or reverse alignment initial testing. At final testing, DIRECT participants had improved times only in forward alignment performance; they demonstrated no significant improvement in reverse alignment performance. MIRROR participants had significant time improvement in both forward and reverse alignment performance at final testing. Reverse alignment imaging for laparoscopic training improves task performance for both reverse alignment and forward alignment tasks. This may be translated into improved performance in the operating room when faced with reverse alignment situations. Minimal lab training can account for drastic adaptation to this environment.

Photoresist thin-film effects on alignment process capability

NASA Astrophysics Data System (ADS)

Flores, Gary E.; Flack, Warren W.

1993-08-01

Two photoresists were selected for alignment characterization based on their dissimilar coating properties and observed differences on alignment capability. The materials are Dynachem OFPR-800 and Shipley System 8. Both photoresists were examined on two challenging alignment levels in a submicron CMOS process, a nitride level and a planarized second level metal. An Ultratech Stepper model 1500 which features a darkfield alignment system with a broadband green light for alignment signal detection was used for this project. Initially, statistically designed linear screening experiments were performed to examine six process factors for each photoresist: viscosity, spin acceleration, spin speed, spin time, softbake time, and softbake temperature. Using the results derived from the screening experiments, a more thorough examination of the statistically significant process factors was performed. A full quadratic experimental design was conducted to examine viscosity, spin speed, and spin time coating properties on alignment. This included a characterization of both intra and inter wafer alignment control and alignment process capability. Insight to the different alignment behavior is analyzed in terms of photoresist material properties and the physical nature of the alignment detection system.

A Polar Initial Alignment Algorithm for Unmanned Underwater Vehicles

PubMed Central

Yan, Zheping; Wang, Lu; Wang, Tongda; Zhang, Honghan; Zhang, Xun; Liu, Xiangling

2017-01-01

Due to its highly autonomy, the strapdown inertial navigation system (SINS) is widely used in unmanned underwater vehicles (UUV) navigation. Initial alignment is crucial because the initial alignment results will be used as the initial SINS value, which might affect the subsequent SINS results. Due to the rapid convergence of Earth meridians, there is a calculation overflow in conventional initial alignment algorithms, making conventional initial algorithms are invalid for polar UUV navigation. To overcome these problems, a polar initial alignment algorithm for UUV is proposed in this paper, which consists of coarse and fine alignment algorithms. Based on the principle of the conical slow drift of gravity, the coarse alignment algorithm is derived under the grid frame. By choosing the velocity and attitude as the measurement, the fine alignment with the Kalman filter (KF) is derived under the grid frame. Simulation and experiment are realized among polar, conventional and transversal initial alignment algorithms for polar UUV navigation. Results demonstrate that the proposed polar initial alignment algorithm can complete the initial alignment of UUV in the polar region rapidly and accurately. PMID:29168735

Relation between film character and wafer alignment: critical alignment issues on HV device for VLSI manufacturing

NASA Astrophysics Data System (ADS)

Lo, Yi-Chuan; Lee, Chih-Hsiung; Lin, Hsun-Peng; Peng, Chiou-Shian

1998-06-01

Several continuous splits for wafer alignment target topography conditions to improve epitaxy film alignment were applied. The alignment evaluation among former layer pad oxide thickness (250 angstrom - 500 angstrom), drive oxide thickness (6000 angstrom - 10000 angstrom), nitride film thickness (600 angstrom - 1500 angstrom), initial oxide etch (fully wet etch, fully dry etch and dry plus wet etch) will be split to this experiment. Also various epitaxy deposition recipe such as: epitaxy source (SiHCl2 or SiCHCl3) and growth rate (1.3 micrometer/min approximately 2.0 micrometer/min) will be used to optimize the process window for alignment issue. All the reflectance signal and cross section photography of alignment target during NIKON stepper alignment process will be examined. Experimental results show epitaxy recipe plays an important role to wafer alignment. Low growth rate with good performance conformity epitaxy lead to alignment target avoid washout, pattern shift and distortion. All the results (signal monitor and film character) combined with NIKON's stepper standard laser scanning alignment system will be discussed in this paper.

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

PubMed

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

Toward a view-oriented approach for aligning RDF-based biomedical repositories.

PubMed

Anguita, A; García-Remesal, M; de la Iglesia, D; Graf, N; Maojo, V

2015-01-01

This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". The need for complementary access to multiple RDF databases has fostered new lines of research, but also entailed new challenges due to data representation disparities. While several approaches for RDF-based database integration have been proposed, those focused on schema alignment have become the most widely adopted. All state-of-the-art solutions for aligning RDF-based sources resort to a simple technique inherited from legacy relational database integration methods. This technique - known as element-to-element (e2e) mappings - is based on establishing 1:1 mappings between single primitive elements - e.g. concepts, attributes, relationships, etc. - belonging to the source and target schemas. However, due to the intrinsic nature of RDF - a representation language based on defining tuples < subject, predicate, object > -, one may find RDF elements whose semantics vary dramatically when combined into a view involving other RDF elements - i.e. they depend on their context. The latter cannot be adequately represented in the target schema by resorting to the traditional e2e approach. These approaches fail to properly address this issue without explicitly modifying the target ontology, thus lacking the required expressiveness for properly reflecting the intended semantics in the alignment information. To enhance existing RDF schema alignment techniques by providing a mechanism to properly represent elements with context-dependent semantics, thus enabling users to perform more expressive alignments, including scenarios that cannot be adequately addressed by the existing approaches. Instead of establishing 1:1 correspondences between single primitive elements of the schemas, we propose adopting a view-based approach. The latter is targeted at establishing mapping relationships between RDF subgraphs - that can be regarded as the equivalent of views in traditional databases -, rather than between single schema elements. This approach enables users to represent scenarios defined by context-dependent RDF elements that cannot be properly represented when adopting the currently existing approaches. We developed a software tool implementing our view-based strategy. Our tool is currently being used in the context of the European Commission funded p-medicine project, targeted at creating a technological framework to integrate clinical and genomic data to facilitate the development of personalized drugs and therapies for cancer, based on the genetic profile of the patient. We used our tool to integrate different RDF-based databases - including different repositories of clinical trials and DICOM images - using the Health Data Ontology Trunk (HDOT) ontology as the target schema. The importance of database integration methods and tools in the context of biomedical research has been widely recognized. Modern research in this area - e.g. identification of disease biomarkers, or design of personalized therapies - heavily relies on the availability of a technical framework to enable researchers to uniformly access disparate repositories. We present a method and a tool that implement a novel alignment method specifically designed to support and enhance the integration of RDF-based data sources at schema (metadata) level. This approach provides an increased level of expressiveness compared to other existing solutions, and allows solving heterogeneity scenarios that cannot be properly represented using other state-of-the-art techniques.

How genome complexity can explain the difficulty of aligning reads to genomes.

PubMed

Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

2015-01-01

Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.

Aligned Layers of Silver Nano-Fibers.

PubMed

Golovin, Andrii B; Stromer, Jeremy; Kreminska, Liubov

2012-02-01

We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polarization of transmitted light. The aligned layers of silver nano-fibers might be used in optics, microwave applications, and organic electronics.