Changes among Israeli Youth Movements: A Structural Analysis Based on Kahane's Code of Informality

ERIC Educational Resources Information Center

Cohen, Erik H.

2015-01-01

Multi-dimensional data analysis tools are applied to Reuven Kahane's data on the informality of youth organizations, yielding a graphic portrayal of Kahane's code of informality. This structure helps address questions of the whether the eight structural components exhaustively cover the field without redundancy. Further, the structure is used to…

EFFECTS OF LASER RADIATION ON MATTER. LASER PLASMA: Laser—ultrasonic formation of melts of high-speed tool steels

NASA Astrophysics Data System (ADS)

Gureev, D. M.

1994-09-01

A study was made of the influence of ultrasonic vibrations on the processes of heat and mass transfer, and of structure formation during ultrafast crystallisation of laser melts of T1 high-speed tool steel. Acoustic flows which appeared in laser melts effectively smoothed out the temperature inhomogeneities and flattened the relief of the molten surface even when the laser radiation acted for just ~1 ms. The transformation of the mechanical energy of ultrasonic vibrations into heat increased the depth of the laser melt baths and suppressed crack formation. The observed changes in the structural and phase composition appeared as a change in the microhardness of the solidified laser melts. The geometry of coupling of ultrasound into a laser melt influenced the changes in the microhardness, suggesting a need for a more detailed analysis of the structure formation processes in the course of ultrafast crystallisation of laser melts in an ultrasonic field.

Effect of crumb cellular structure characterized by image analysis on cake softness.

PubMed

Dewaest, Marine; Villemejane, Cindy; Berland, Sophie; Neron, Stéphane; Clement, Jérôme; Verel, Aliette; Michon, Camille

2018-06-01

Sponge cake is a cereal product characterized by an aerated crumb and appreciated for its softness. When formulating such product, it is interesting to be able to characterize the crumb structure using image analysis and to bring knowledge about the effects of the crumb cellular structure on its mechanical properties which contribute to softness. An image analysis method based on mathematical morphology was adapted from the one developed for bread crumb. In order to evaluate its ability to discriminate cellular structures, series of cakes were prepared using two rather similar emulsifiers but also using flours with different aging times before use. The mechanical properties of the crumbs of these different cakes were also characterized. It allowed a cell structure classification taking into account cell size and homogeneity, but also cell wall thickness and the number of holes in the walls. Interestingly, the cellular structure differences had a larger impact on the aerated crumb Young modulus than the wall firmness. Increasing the aging time of flour before use leads to the production of firmer crumbs due to coarser and inhomogeneous cellular structures. Changing the composition of the emulsifier may change the cellular structure and, depending on the type of the structural changes, have an impact on the firmness of the crumb. Cellular structure rather than cell wall firmness was found to impact cake crumb firmness. The new fast and automated tool for cake crumb structure analysis allows detecting quickly any change in cell size or homogeneity but also cell wall thickness and number of holes in the walls (openness degree). To obtain a softer crumb, it seems that options are to decrease the cell size and the cell wall thickness and/or to increase the openness degree. It is then possible to easily evaluate the effects of ingredients (flour composition, emulsifier …) or change in the process on the crumb structure and thus its softness. Moreover, this image analysis is a very efficient tool for quality control. © 2017 Wiley Periodicals, Inc.

The Readiness to Change for Bariatric Surgery Assessment Tool: Validity, Factor Structure, and Reliability.

PubMed

Carlson, Susan M S

2017-11-01

Currently, there is no guideline or standard of practice for performing the psychiatric/psychological evaluation that is a requirement for approval for bariatric surgery. The Readiness to Change for Bariatric Surgery Assessment Tool (RCB-SAT) establishes a means for psychiatric evaluators to objectively assess the patient's cognition, beliefs, and motivation around the bariatric diet and lifestyle changes. Development of a clinical decision-making tool for assessing readiness to change in bariatric patients will be useful regarding The Strategic Plan for NIH Obesity Research. The strategic plan outlines 6 overarching themes, with the last 3 centering around creation of such a clinical decision-making tool to assess a bariatric patient's readiness to change: evaluate promising strategies for obesity prevention and treatment in realworld settings and diverse populations, harness technology and tools to advance obesity research and improve health care delivery, and facilitate integration of research results into community programs and medical practice (National Institutes of Health, 2011). The pilot tool was administered to 153 potential bariatric patients, with 61 patients completing the survey a second time. Face and content validity of the items were established through an expert review process. Principle axis factoring by means of varimax rotation with Kaiser normalization identified 15 items loading on 3 factors associated with Prochaska and DiClemente's transtheoretical model of health behavior change: precontemplation, contemplation, and action (DiClemente & Prochaska, 1998). Test-retest reliability was also established for the tool. The proposed RCB-SAT demonstrates potential for assessing a patient's readiness to change regarding the bariatric diet and lifestyle.

Digital Tools for Algebra Education: Criteria and Evaluation

ERIC Educational Resources Information Center

Bokhove, Christian; Drijvers, Paul

2010-01-01

In the Netherlands, as in many other countries, the algebraic expertise of students graduating from secondary education is an issue. The use of digital tools for algebra education is expected to change epistemologies, activity structures and student achievement. Therefore, a study was set up to investigate in what way the use of ICT in upper…

Analysis about diamond tool wear in nano-metric cutting of single crystal silicon using molecular dynamics method

NASA Astrophysics Data System (ADS)

Wang, Zhiguo; Liang, Yingchun; Chen, Mingjun; Tong, Zhen; Chen, Jiaxuan

2010-10-01

Tool wear not only changes its geometry accuracy and integrity, but also decrease machining precision and surface integrity of workpiece that affect using performance and service life of workpiece in ultra-precision machining. Scholars made a lot of experimental researches and stimulant analyses, but there is a great difference on the wear mechanism, especially on the nano-scale wear mechanism. In this paper, the three-dimensional simulation model is built to simulate nano-metric cutting of a single crystal silicon with a non-rigid right-angle diamond tool with 0 rake angle and 0 clearance angle by the molecular dynamics (MD) simulation approach, which is used to investigate the diamond tool wear during the nano-metric cutting process. A Tersoff potential is employed for the interaction between carbon-carbon atoms, silicon-silicon atoms and carbon-silicon atoms. The tool gets the high alternating shear stress, the tool wear firstly presents at the cutting edge where intension is low. At the corner the tool is splitted along the {1 1 1} crystal plane, which forms the tipping. The wear at the flank face is the structure transformation of diamond that the diamond structure transforms into the sheet graphite structure. Owing to the tool wear the cutting force increases.

Qualitative evaluation of the implementation of the Interdisciplinary Management Tool: a reflective tool to enhance interdisciplinary teamwork using Structured, Facilitated Action Research for Implementation.

PubMed

Nancarrow, Susan A; Smith, Tony; Ariss, Steven; Enderby, Pamela M

2015-07-01

Reflective practice is used increasingly to enhance team functioning and service effectiveness; however, there is little evidence of its use in interdisciplinary teams. This paper presents the qualitative evaluation of the Interdisciplinary Management Tool (IMT), an evidence-based change tool designed to enhance interdisciplinary teamwork through structured team reflection. The IMT incorporates three components: an evidence-based resource guide; a reflective implementation framework based on Structured, Facilitated Action Research for Implementation methodology; and formative and summative evaluation components. The IMT was implemented with intermediate care teams supported by independent facilitators in England. Each intervention lasted 6 months and was evaluated over a 12-month period. Data sources include interviews, a focus group with facilitators, questionnaires completed by team members and documentary feedback from structured team reports. Data were analysed qualitatively using the Framework approach. The IMT was implemented with 10 teams, including 253 staff from more than 10 different disciplines. Team challenges included lack of clear vision; communication issues; limited career progression opportunities; inefficient resource use; need for role clarity and service development. The IMT successfully engaged staff in the change process, and resulted in teams developing creative strategies to address the issues identified. Participants valued dedicated time to focus on the processes of team functioning; however, some were uncomfortable with a focus on teamwork at the expense of delivering direct patient care. The IMT is a relatively low-cost, structured, reflective way to enhance team function. It empowers individuals to understand and value their own, and others' roles and responsibilities within the team; identify barriers to effective teamwork, and develop and implement appropriate solutions to these. To be successful, teams need protected time to take for reflection, and executive support to be able to broker changes that are beyond the scope of the team. © 2014 John Wiley & Sons Ltd.

Participants' evaluation of a group-based organisational assessment tool in Danish general practice: the Maturity Matrix.

PubMed

Buch, Martin Sandberg; Edwards, Adrian; Eriksson, Tina

2009-01-01

The Maturity Matrix is a group-based formative self-evaluation tool aimed at assessing the degree of organisational development in general practice and providing a starting point for local quality improvement. Earlier studies of the Maturity Matrix have shown that participants find the method a useful way of assessing their practice's organisational development. However, little is known about participants' views on the resulting efforts to implement intended changes. To explore users' perspectives on the Maturity Matrix method, the facilitation process, and drivers and barriers for implementation of intended changes. Observation of two facilitated practice meetings, 17 semi-structured interviews with participating general practitioners (GPs) or their staff, and mapping of reasons for continuing or quitting the project. General practices in Denmark Main outcomes: Successful change was associated with: a clearly identified anchor person within the practice, a shared and regular meeting structure, and an external facilitator who provides support and counselling during the implementation process. Failure to implement change was associated with: a high patient-related workload, staff or GP turnover (that seemed to affect small practices more), no clearly identified anchor person or anchor persons who did not do anything, no continuous support from an external facilitator, and no formal commitment to working with agreed changes. Future attempts to improve the impact of the Maturity Matrix, and similar tools for quality improvement, could include: (a) attention to matters of variation caused by practice size, (b) systematic counselling on barriers to implementation and support to structure the change processes, (c) a commitment from participants that goes beyond participation in two-yearly assessments, and (d) an anchor person for each identified goal who takes on the responsibility for improvement in practice.

Structure and vulnerability of Pacific Northwest tidal wetlands – A summary of wetland climate change research by the Western Ecology Division, U.S. EPA

USGS Publications Warehouse

Folger, Christina L; Lee, Henry; Janousek, Christopher N.; Reusser, Deborah A.

2014-01-01

Climate change poses a serious threat to the tidal wetlands of the Pacific Northwest (PNW) region of the U.S. In response to this threat, scientists at the Western Ecology Division of the U.S. EPA at and the Western Fisheries Research Center of the U.S. Geological Survey, along with other partners, initiated a series of studies on the structure and vulnerability of tidal wetlands to climate change. One research thrust was to evaluate community structure of PNW marshes, experimentally assess the vulnerability of marsh plants to inundation and salinity stress (as would happen with sea level rise), and evaluate the utility of the National Wetland Inventory (NWI) classification system. Another research thrust was to develop tools that provide insights into possible impacts of climate change. This effort included enhancing the Sea Level Affecting Marshes Model (SLAMM) to predict the effects of sea level rise on submerged aquatic vegetation (Zostera marina) distributions, evaluating changes in river flow into coastal estuaries in response to precipitation changes, and synthesizing Pacific Coast estuary, watershed, and climate data in a downloadable tool. Because the research resulting from these efforts was published in multiple venues, we summarized them in this document. We anticipate that future research efforts by the U.S. EPA will continue with a focus on climate change impacts on a regional scale.

A comparison of selected diversity, similarity, and biotic indices for detecting changes in benthic-invertebrate community structure and stream quality

USGS Publications Warehouse

Lydy, M.J.; Crawford, Charles G.; Frey, J.W.

2000-01-01

Implementation of advanced wastewater treatment at the two municipal wastewater-treatment plants for Indianapolis, Indiana, resulted in substantial improvement in the quality of the receiving stream and significant changes in the benthic-invertebrate community. Diversity, similarity, and biotic indices were compared to determine which indices best reflected changes in the composition of the biota in the river. None of the indices perfectly reflected the changes in river quality or community structure. Similarity indices, especially percentage similarity, exhibit the most promise of the three classes of indices. Diversity indices were least useful, wrongly indicating that water quality deteriorated after the upgrade of the wastewater-treatment plants. The most descriptive tool in analyzing the data was the percentage of Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa present. Using a mixture of indices and other analytical tools, such as EPT, in the analysis of biological data will ensure the most effective investigations of water quality.

Student Destination Surveys: Design and Development of an Instrument for Use by TAFE Agencies.

ERIC Educational Resources Information Center

Walsh, Lynne

The development of the student destination survey instrument was a response to an identified need for a tool to measure the effectiveness of Technical and Further Education (TAFE) programs in Australia. The requirement was for a tool that was flexible in accommodating changing course structures and consistent across state and territory boundaries.…

Interviewing Baltimore Older Adults about Food System Change: Oral History as a Teaching Tool

ERIC Educational Resources Information Center

Neff, Roni A.; Laestadius, Linnea I.; DiMauro, Susan; Palmer, Anne M.

2017-01-01

Urban food systems have changed considerably over the past half century. Older adults' descriptions of place-based, personal food system history can help inform student learning and may contribute to expert understanding of food system change. Structural and social shifts in food purchasing and consumption contribute to diet-related disease and…

Strategy, Structure and Quality Service: Developing School Wide Quality Improvement.

ERIC Educational Resources Information Center

Murgatroyd, Stephen

1991-01-01

Builds on earlier contributions to the literature on educational leadership and total quality management in education. Introduces two new tools--the service guarantee and the House of Quality, placing them in the context of strategic marketing, structural change, and other total quality management methods. (19 references) (MLH)

NOTE: Characterization of cirrhosis and hepatocellular carcinoma using low-angle x-ray scattering signatures of serum

NASA Astrophysics Data System (ADS)

Elshemey, Wael M.; Desouky, Omar S.; Mohammed, Mohammed S.; Elsayed, Anwar A.; El-houseini, Motawa E.

2003-09-01

The diagnosis of hepatocellular carcinoma (HCC) usually occurs at late stages in the disease when there are few effective treatment options. The measurement of the concentration of tumour markers in the serum of patients is a complementary tool frequently used for the interpretation of diagnostic imaging results. It is also used as a prognostic tool for the detection of cancer. Unfortunately, the sensitivity of tumour markers is still low and many times it yields normal results for cirrhotic and HCC patients. In the current work, the detection possibility of the structural changes in serum proteins accompanying cirrhosis and HCC is investigated using a low-angle x-ray scattering (LAXS) technique. The results show that there are significant differences in the LAXS profiles of cirrhosis and HCC lyophilized serum samples compared to normal. The changes in shape, total counts and position of the first scattering peak at 4.8°, which was previously reported to be sensitive to the structural changes in protein, showed the most characteristic deviations from normal serum. The present results are promising and would offer a potentially helpful complementary tool for monitoring cirrhosis and HCC.

Effectiveness of structured multidisciplinary rounding in acute care units on length of stay and satisfaction of patients and staff: a quantitative systematic review.

PubMed

Mercedes, Angela; Fairman, Precillia; Hogan, Lisa; Thomas, Rexi; Slyer, Jason T

2016-07-01

Consistent, concise and timely communication between a multidisciplinary team of healthcare providers, patients and families is necessary for the delivery of quality care. Structured multidisciplinary rounding (MDR) using a structured communication tool may positively impact length of stay (LOS) and satisfaction of patients and staff by improving communication, coordination and collaboration among the healthcare team. To evaluate the effectiveness of structured MDR using a structured communication tool in acute care units on LOS and satisfaction of patients and staff. Adult patients admitted to acute care units and healthcare providers who provide direct care for adult patients hospitalized in in-patient acute care units. The implementation of structured MDR utilizing a structured communication tool to enhance and/or guide communication. Quasi-experimental studies and descriptive studies. Length of stay, patient satisfaction and staff satisfaction. The comprehensive search strategy aimed to find relevant published and unpublished quantitative English language studies from the inception of each database searched through June 30, 2015. Databases searched include Cumulative Index to Nursing and Allied Health Literature, PubMed, Excerpta Medica Database, Health Source, Cochrane Central Register of Controlled Trials and Scopus. A search of gray literature was also performed. All reviewers independently evaluated the included studies for methodological quality using critical appraisal tools from the Joanna Briggs Institute (JBI). Data related to the methods, participants, interventions and findings were extracted using a standardized data extraction tool from the JBI. Due to clinical and methodological heterogeneity in the interventions and outcome measures of the included studies, statistical meta-analysis was not possible. Results are presented in narrative form. Eight studies were included, three quasi-experimental studies and five descriptive studies of quality improvement projects. In the three quasi-experimental studies, one had a statistically significant decrease (p = 0.01), one no change (p = 0.1) and one had an increase (p = 0.03) in LOS; in the two descriptive studies, one had a statistically significant decrease (p = 0.02) and the other reported a trend toward reduced LOS. Two studies evaluated patient satisfaction, one showed no change (p = 0.76) and one showed a trend toward increased patient satisfaction at 12 months. Six studies demonstrated an improvement in staff satisfaction (p < 0.05) after implementation of structured MDR. The evidence suggests that MDR utilizing a structured communication tool may have contributed to an improvement in staff satisfaction. There was inconclusive evidence to support the use of structured MDR to improve LOS or patient satisfaction. The use of a structured communication tool during MDR is one means to facilitate communication and collaboration, thus improving satisfaction among the multidisciplinary team. More rigorous research using higher level study designs on larger samples of diverse patient populations is needed to further evaluate the effectiveness of structured MDR on patient care outcomes and satisfaction of patients and providers.

Diagnostic approaches for diabetic cardiomyopathy and myocardial fibrosis

PubMed Central

Maya, Lisandro; Villarreal, Francisco J.

2009-01-01

In diabetes mellitus, alterations in cardiac structure/function in the absence of ischemic heart disease, hypertension or other cardiac pathologies is termed diabetic cardiomyopathy. In the United States, the prevalence of diabetes mellitus continues to rise and the disease currently affects about 8% of the general population. Hence, it is imperative the use of appropriate diagnostic strategies for diabetic cardiomyopathy, which may help correctly identify the disease at early stages and implement suitable corrective therapies. Currently, there is no single diagnostic method for the identification of diabetic cardiomyopathy. Diabetic cardiomyopathy is known to induce changes in cardiac structure such as, myocardial hypertrophy, fibrosis and fat droplet deposition. Early changes in cardiac function are typically manifested as abnormal diastolic function that with time leads to loss of contractile function. Echocardiography based methods currently stands as the preferred diagnostic approach for diabetic cardiomyopathy, due to its wide availability and economical use. In addition to conventional techniques, magnetic resonance imaging and spectroscopy along with contrast agents are now leading new approaches in the diagnosis of myocardial fibrosis, and cardiac and hepatic metabolic changes. These strategies can be complemented with serum biomarkers so they can offer a clear picture as to diabetes-induced changes in cardiac structure/function even at very early stages of the disease. This review article intends to provide a summary of experimental and routine tools currently available to diagnose diabetic cardiomyopathy induced changes in cardiac structure/function. These tools can be reliably used in either experimental models of diabetes or for clinical applications. PMID:19595694

Spirituality: A Tool for Learning, Change and Adaptation of Elderly in Changing Indian Family

ERIC Educational Resources Information Center

Kumari, Shikha; Sharma, Alka

2018-01-01

Globalisation as a worldwide integrating force leads to changes in the social structures, values and mindsets of people. Parents raise their children expecting they would take care of them in old age but the globalised economy has given rise to a materialistic culture in which children migrate to other cities or countries. Parents accept this in…

Adaptation Design Tool for Climate-Smart Management of Coral Reefs and Other Natural Resources.

PubMed

West, Jordan M; Courtney, Catherine A; Hamilton, Anna T; Parker, Britt A; Gibbs, David A; Bradley, Patricia; Julius, Susan H

2018-06-22

Scientists and managers of natural resources have recognized an urgent need for improved methods and tools to enable effective adaptation of management measures in the face of climate change. This paper presents an Adaptation Design Tool that uses a structured approach to break down an otherwise overwhelming and complex process into tractable steps. The tool contains worksheets that guide users through a series of design considerations for adapting their planned management actions to be more climate-smart given changing environmental stressors. Also provided with other worksheets is a framework for brainstorming new adaptation options in response to climate threats not yet addressed in the current plan. Developed and tested in collaboration with practitioners in Hawai'i and Puerto Rico using coral reefs as a pilot ecosystem, the tool and associated reference materials consist of worksheets, instructions and lessons-learned from real-world examples. On the basis of stakeholder feedback from expert consultations during tool development, we present insights and recommendations regarding how to maximize tool efficiency, gain the greatest value from the thought process, and deal with issues of scale and uncertainty. We conclude by reflecting on how the tool advances the theory and practice of assessment and decision-making science, informs higher level strategic planning, and serves as a platform for a systematic, transparent and inclusive process to tackle the practical implications of climate change for management of natural resources.

Design Change Model for Effective Scheduling Change Propagation Paths

NASA Astrophysics Data System (ADS)

Zhang, Hai-Zhu; Ding, Guo-Fu; Li, Rong; Qin, Sheng-Feng; Yan, Kai-Yin

2017-09-01

Changes in requirements may result in the increasing of product development project cost and lead time, therefore, it is important to understand how requirement changes propagate in the design of complex product systems and be able to select best options to guide design. Currently, a most approach for design change is lack of take the multi-disciplinary coupling relationships and the number of parameters into account integrally. A new design change model is presented to systematically analyze and search change propagation paths. Firstly, a PDS-Behavior-Structure-based design change model is established to describe requirement changes causing the design change propagation in behavior and structure domains. Secondly, a multi-disciplinary oriented behavior matrix is utilized to support change propagation analysis of complex product systems, and the interaction relationships of the matrix elements are used to obtain an initial set of change paths. Finally, a rough set-based propagation space reducing tool is developed to assist in narrowing change propagation paths by computing the importance of the design change parameters. The proposed new design change model and its associated tools have been demonstrated by the scheduling change propagation paths of high speed train's bogie to show its feasibility and effectiveness. This model is not only supportive to response quickly to diversified market requirements, but also helpful to satisfy customer requirements and reduce product development lead time. The proposed new design change model can be applied in a wide range of engineering systems design with improved efficiency.

Structured illumination microscopy as a diagnostic tool for nephrotic disease

NASA Astrophysics Data System (ADS)

Nylk, Jonathan; Pullman, James M.; Campbell, Elaine C.; Gunn-Moore, Frank J.; Prystowsky, Michael B.; Dholakia, Kishan

2017-02-01

Nephrotic disease is a group of debilitating and sometimes lethal diseases affecting kidney function, specifically the loss of ability to retain vital proteins in the blood while smaller molecules are removed through filtration into the urine. Treatment routes are often dictated by microscopic analysis of kidney biopsies. Podocytes within the glomeruli of the kidney have many interdigitating projections (foot processes), which form the main filtration system. Nephrotic disease is characterised by the loss of this tightly interdigitating substructure and its observation by electron microscopy (EM) is necessitated as these structures are typically 250 500nm wide, with 40nm spacing. Diagnosis by EM is both expensive and time consuming; it can take up to one week to complete the preparation, imaging, and analysis of a single sample. We propose structured illumination microscopy (SIM) as an alternative, optical diagnostic tool. Our results show that SIM can resolve the structure of fluorescent probes tagged to podocin, a protein localised to the periphery of the podocyte foot processes. Three-dimensional podocin maps were acquired in healthy tissue and tissue from patients diagnosed with two different nephrotic disease states; minimal change disease and membranous nephropathy. These structures correlated well with EM images of the same structure. Preparation, imaging, and analysis could be achieved in several hours. Additionally, the volumetric information of the SIM images revealed morphological changes in disease states not observed by EM. This evidence supports the use of SIM as a diagnostic tool for nephrotic disease and can potentially reduce the time and cost per diagnosis.

Atomic Force Microscopy Studies on DNA Structural Changes Induced by Vincristine Sulfate and Aspirin

NASA Astrophysics Data System (ADS)

Zhu, Yi; Zeng, Hu; Xie, Jianming; Ba, Long; Gao, Xiang; Lu, Zuhong

2004-04-01

We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.

Interactive graphic editing tools in bioluminescent imaging simulation

NASA Astrophysics Data System (ADS)

Li, Hui; Tian, Jie; Luo, Jie; Wang, Ge; Cong, Wenxiang

2005-04-01

It is a challenging task to accurately describe complicated biological tissues and bioluminescent sources in bioluminescent imaging simulation. Several graphic editing tools have been developed to efficiently model each part of the bioluminescent simulation environment and to interactively correct or improve the initial models of anatomical structures or bioluminescent sources. There are two major types of graphic editing tools: non-interactive tools and interactive tools. Geometric building blocks (i.e. regular geometric graphics and superquadrics) are applied as non-interactive tools. To a certain extent, complicated anatomical structures and bioluminescent sources can be approximately modeled by combining a sufficient large number of geometric building blocks with Boolean operators. However, those models are too simple to describe the local features and fine changes in 2D/3D irregular contours. Therefore, interactive graphic editing tools have been developed to facilitate the local modifications of any initial surface model. With initial models composed of geometric building blocks, interactive spline mode is applied to conveniently perform dragging and compressing operations on 2D/3D local surface of biological tissues and bioluminescent sources inside the region/volume of interest. Several applications of the interactive graphic editing tools will be presented in this article.

Investigation of Conceptual Change about Double-Slit Interference in Secondary School Physics

ERIC Educational Resources Information Center

Kocakulah, Mustafa Sabri; Kural, Mehmet

2010-01-01

In this study, whether or not constructivist teaching of double-slit interference of light has a positive effect on the secondary school students' conceptual change is examined. An achievement test, a conceptual understanding test and semi-structured interviews were used as data collection tools in this mixed methods research. Experimental group…

Health goal priming as a situated intervention tool: how to benefit from nonconscious motivational routes to health behaviour.

PubMed

Papies, Esther K

2016-12-01

Recent research has shown the limited effects of intentions on behaviour, so that novel methods to facilitate behaviour change are needed that do not rely on conscious intentions. Here, it is argued that nonintentional effects on health behaviour, such as the effects of habits, impulses, and nonconscious goals, occur through the activation of cognitive structures by specific situations. Interventions should therefore be situated to change these effects, either by changing the critical cognitive structures (training interventions), or by changing which cognitive structures get activated (cueing interventions). The current article presents this framework for situated interventions, as well as examples of interventions of each type. Then, it introduces goal priming as a cueing intervention tool to activate health goals and thus facilitate healthier behaviour, even in tempting situations that typically activate short-term hedonic goals. Following a review of empirical evidence, five principles for the effective application of health goal primes are proposed, namely (1) to target individuals who value the primed goals, (2) by activating their specific motivation, (3) through effective cues (4) that attract attention at the right time. Finally, (5) an effective goal-directed behaviour needs to be known and accessible to the primed individual. These principles are illustrated with examples of different health behaviours in order to facilitate their application for successful behaviour change.

Health goal priming as a situated intervention tool: how to benefit from nonconscious motivational routes to health behaviour

PubMed Central

Papies, Esther K.

2016-01-01

ABSTRACT Recent research has shown the limited effects of intentions on behaviour, so that novel methods to facilitate behaviour change are needed that do not rely on conscious intentions. Here, it is argued that nonintentional effects on health behaviour, such as the effects of habits, impulses, and nonconscious goals, occur through the activation of cognitive structures by specific situations. Interventions should therefore be situated to change these effects, either by changing the critical cognitive structures (training interventions), or by changing which cognitive structures get activated (cueing interventions). The current article presents this framework for situated interventions, as well as examples of interventions of each type. Then, it introduces goal priming as a cueing intervention tool to activate health goals and thus facilitate healthier behaviour, even in tempting situations that typically activate short-term hedonic goals. Following a review of empirical evidence, five principles for the effective application of health goal primes are proposed, namely (1) to target individuals who value the primed goals, (2) by activating their specific motivation, (3) through effective cues (4) that attract attention at the right time. Finally, (5) an effective goal-directed behaviour needs to be known and accessible to the primed individual. These principles are illustrated with examples of different health behaviours in order to facilitate their application for successful behaviour change. PMID:27144729

Probing and controlling terahertz-driven structural dynamics with surface sensitivity

DOE PAGES

Bowlan, Pamela Renee; Bowlan, J.; Trugman, S. A.; ...

2017-03-17

Intense, single-cycle terahertz (THz) pulses are powerful tools to understand and control material properties through low-energy resonances, such as phonons. Combining this with optical second harmonic generation (SHG) makes it possible to observe the resulting ultrafast structural changes with surface sensitivity. This makes SHG an ideal method to probe phonon dynamics in topological insulators (TI), materials with unique surface transport properties. Here, we resonantly excite a phonon mode in the TI Bi 2Se 3with THz pulses and use SHG to separate the resulting symmetry changes at the surface from the bulk. Furthermore, we coherently control the lattice vibrations with amore » pair of THz pulses. Lastly, our work demonstrates a versatile, table-top tool to probe and control phonon dynamics in a range of systems, particularly at surfaces and interfaces.« less

Informing Hospital Change Processes through Visualization and Simulation: A Case Study at a Children's Emergency Clinic.

PubMed

Persson, Johanna; Dalholm, Elisabeth Hornyánszky; Johansson, Gerd

2014-01-01

To demonstrate the use of visualization and simulation tools in order to involve stakeholders and inform the process in hospital change processes, illustrated by an empirical study from a children's emergency clinic. Reorganization and redevelopment of a hospital is a complex activity that involves many stakeholders and demands. Visualization and simulation tools have proven useful for involving practitioners and eliciting relevant knowledge. More knowledge is desired about how these tools can be implemented in practice for hospital planning processes. A participatory planning process including practitioners and researchers was executed over a 3-year period to evaluate a combination of visualization and simulation tools to involve stakeholders in the planning process and to elicit knowledge about needs and requirements. The initial clinic proposal from the architect was discarded as a result of the empirical study. Much general knowledge about the needs of the organization was extracted by means of the adopted tools. Some of the tools proved to be more accessible than others for the practitioners participating in the study. The combination of tools added value to the process by presenting information in alternative ways and eliciting questions from different angles. Visualization and simulation tools inform a planning process (or other types of change processes) by providing the means to see beyond present demands and current work structures. Long-term involvement in combination with accessible tools is central for creating a participatory setting where the practitioners' knowledge guides the process. © 2014 Vendome Group, LLC.

Experimental resource pulses influence social-network dynamics and the potential for information flow in tool-using crows

PubMed Central

St Clair, James J. H.; Burns, Zackory T.; Bettaney, Elaine M.; Morrissey, Michael B.; Otis, Brian; Ryder, Thomas B.; Fleischer, Robert C.; James, Richard; Rutz, Christian

2015-01-01

Social-network dynamics have profound consequences for biological processes such as information flow, but are notoriously difficult to measure in the wild. We used novel transceiver technology to chart association patterns across 19 days in a wild population of the New Caledonian crow—a tool-using species that may socially learn, and culturally accumulate, tool-related information. To examine the causes and consequences of changing network topology, we manipulated the environmental availability of the crows' preferred tool-extracted prey, and simulated, in silico, the diffusion of information across field-recorded time-ordered networks. Here we show that network structure responds quickly to environmental change and that novel information can potentially spread rapidly within multi-family communities, especially when tool-use opportunities are plentiful. At the same time, we report surprisingly limited social contact between neighbouring crow communities. Such scale dependence in information-flow dynamics is likely to influence the evolution and maintenance of material cultures. PMID:26529116

Visual simulations of forest wildlife habitat structure, change, and landscape context in New England

Treesearch

Richard M. DeGraaf; Anna M. Lester; Mariko Yamasaki; William B. Leak

2007-01-01

Visualization is a powerful tool for depicting projections of forest structure and landscape conditions, for communicating habitat management practices, and for providing a landscape context to private landowners and to those concerned with public land management. Recent advances in visualization technology, especially in graphics quality, ease of use, and relative...

Direct protein photoinduced conformational changes using porphyrins.

NASA Astrophysics Data System (ADS)

Brancaleon, Lorenzo; Silva, Ivan; Fernandez, Nicholas; Johnson, Eric; Sansone, Samuel

2008-03-01

Most proteins functions depend on the interaction with other ligands. These interactions depend on uniquely structured binding sites formed by the folding of the proteins. Ligands can often prompt intended as well as ``accidental'' protein structural changes. One can foresee that the ability to prompt and control post-translational protein folding could be a powerful tool to investigate protein folding mechanisms but also to inhibit certain proteins or induce new properties to proteins. One possible way to produce such structural disruption is the combination of light and photoactive ligands. This option has been investigated in recent years by exploiting photoisomerization and other properties of non-physiological dyes. We used an alternative approach which uses porphyrins as the ``triggers'' of structural changes. The advantage of porphyrins is that they can be found naturally in living cells. The photophysical properties of porphyrins can induce local as well as long range effects on the structure of the bound protein. Porphyrins are known to produce structural changes in porphyrin-specific proteins, however the novelty of our results is that we demonstrated that these dyes can also produce structural changes in non-porphyrin-specific globular proteins. We will present an overview of our research to-date in this field and its potential applications.

The combined use of analytical tools for exploring tetanus toxin and tetanus toxoid structures.

PubMed

Bayart, Caroline; Peronin, Sébastien; Jean, Elisa; Paladino, Joseph; Talaga, Philippe; Borgne, Marc Le

2017-06-01

Aldehyde detoxification is a process used to convert toxin into toxoid for vaccine applications. In the case of tetanus toxin (TT), formaldehyde is used to obtain the tetanus toxoid (TTd), which is used either for the tetanus vaccine or as carrier protein in conjugate vaccines. Several studies have already been conducted to better understand the exact mechanism of this detoxification. Those studies led to the identification of a number of formaldehyde-induced modifications on lab scale TTd samples. To obtain greater insights of the changes induced by formaldehyde, we used three industrial TTd batches to identify repeatable modifications in the detoxification process. Our strategy was to combine seven analytical tools to map these changes. Mass spectrometry (MS), colorimetric test and amino acid analysis (AAA) were used to study modifications on amino acids. SDS-PAGE, asymmetric flow field flow fractionation (AF4), fluorescence spectroscopy and circular dichroism (CD) were used to study formaldehyde modifications on the whole protein structure. We identified 41 formaldehyde-induced modifications across the 1315 amino acid primary sequence of TT. Of these, five modifications on lysine residues were repeatable across TTd batches. Changes in protein conformation were also observed using SDS-PAGE, AF4 and CD techniques. Each analytical tool brought a piece of information regarding formaldehyde induced-modifications, and all together, these methods provided a comprehensive overview of the structural changes that occurred with detoxification. These results could be the first step leading to site-directed TT mutagenesis studies that may enable the production of a non-toxic equivalent protein without using formaldehyde. Copyright © 2017 Elsevier B.V. All rights reserved.

Sonic Boom Research at NASA Dryden: Objectives and Flight Results from the Lift and Nozzle Change Effects on Tail Shock (LaNCETS) Project

NASA Technical Reports Server (NTRS)

Moes, Timothy R.

2009-01-01

The principal objective of the Supersonics Project is to develop and validate multidisciplinary physics-based predictive design, analysis and optimization capabilities for supersonic vehicles. For aircraft, the focus will be on eliminating the efficiency, environmental and performance barriers to practical supersonic flight. Previous flight projects found that a shaped sonic boom could propagate all the way to the ground (F-5 SSBD experiment) and validated design tools for forebody shape modifications (F-5 SSBD and Quiet Spike experiments). The current project, Lift and Nozzle Change Effects on Tail Shock (LaNCETS) seeks to obtain flight data to develop and validate design tools for low-boom tail shock modifications. Attempts will be made to alter the shock structure of NASA's NF-15B TN/837 by changing the lift distribution by biasing the canard positions, changing the plume shape by under- and over-expanding the nozzles, and changing the plume shape using thrust vectoring. Additional efforts will measure resulting shocks with a probing aircraft (F-15B TN/836) and use the results to validate and update predictive tools. Preliminary flight results are presented and are available to provide truth data for developing and validating the CFD tools required to design low-boom supersonic aircraft.

Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil*

PubMed Central

Zhang, Shu-ying; Wang, Qing-feng; Wan, Rui; Xie, Shu-guang

2011-01-01

Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene clone library analysis. The two bimolecular tools revealed a large shift of bacterial community structure after anthracene amendment and subsequent biodegradation. Genera Methylophilus, Mesorhizobium, and Terrimonas had potential links to anthracene biodegradation, suggesting a consortium playing an active role. PMID:21887852

Soak Up the Rain New England Webinar Series: National ...

EPA Pesticide Factsheets

Presenters will provide an introduction to the most recent EPA green infrastructure tools to R1 stakeholders; and their use in making decisions about implementing green infrastructure. We will discuss structuring your green infrastructure decision, finding appropriate information and tools, evaluating options and selecting the right Best Management Practices mix for your needs.WMOST (Watershed Management Optimization Support Tool)- for screening a wide range of practices for cost-effectiveness in achieving watershed or water utilities management goals.GIWiz (Green Infrastructure Wizard)- a web application connecting communities to EPA Green Infrastructure tools and resources.Opti-Tool-designed to assist in developing technically sound and optimized cost-effective Stormwater management plans. National Stormwater Calculator- a desktop application for estimating the impact of land cover change and green infrastructure controls on stormwater runoff. DASEES-GI (Decision Analysis for a Sustainable Environment, Economy, and Society) – a framework for linking objectives and measures with green infrastructure methods. Presenters will provide an introduction to the most recent EPA green infrastructure tools to R1 stakeholders; and their use in making decisions about implementing green infrastructure. We will discuss structuring your green infrastructure decision, finding appropriate information and tools, evaluating options and selecting the right Best Management Pr

An intelligent advisor for the design manager

NASA Technical Reports Server (NTRS)

Rogers, James L.; Padula, Sharon L.

1989-01-01

A design problem is viewed as a complex system divisible into modules. Before the design of a complex system can begin, much time and money are spent in determining the couplings among modules and the presence of iterative loops. This is important because the design manager must know how to group the modules into substems and how to assign subsystems to design teams so that changes in one subsystem will have predictable effects on other subsystems. Determining these subsystems is not an easy, straightforward process and often important couplings are overlooked. Moreover, the planning task must be repeated as new information becomes available or as the design specifications change. The purchase of this research effort is to develop a knowledge-based tool to act as an intelligent advisor for the design manager. This tool identifies the subsystems of a complex design problem, orders them into a well-structured format, and marks the couplings among the subsystems to facilitate the use of multilevel tools. The tool was tested in the decomposition of the COFS (Control of Flexible Structures) mast design which has about 50 modules. This test indicated that this type of approach could lead to a substantial savings by organizing and displaying a complex problem as a sequence of subsystems easily divisible among design teams.

Interplay between past market correlation structure changes and future volatility outbursts.

PubMed

Musmeci, Nicoló; Aste, Tomaso; Di Matteo, T

2016-11-18

We report significant relations between past changes in the market correlation structure and future changes in the market volatility. This relation is made evident by using a measure of "correlation structure persistence" on correlation-based information filtering networks that quantifies the rate of change of the market dependence structure. We also measured changes in the correlation structure by means of a "metacorrelation" that measures a lagged correlation between correlation matrices computed over different time windows. Both methods show a deep interplay between past changes in correlation structure and future changes in volatility and we demonstrate they can anticipate market risk variations and this can be used to better forecast portfolio risk. Notably, these methods overcome the curse of dimensionality that limits the applicability of traditional econometric tools to portfolios made of a large number of assets. We report on forecasting performances and statistical significance of both methods for two different equity datasets. We also identify an optimal region of parameters in terms of True Positive and False Positive trade-off, through a ROC curve analysis. We find that this forecasting method is robust and it outperforms logistic regression predictors based on past volatility only. Moreover the temporal analysis indicates that methods based on correlation structural persistence are able to adapt to abrupt changes in the market, such as financial crises, more rapidly than methods based on past volatility.

Interplay between past market correlation structure changes and future volatility outbursts

NASA Astrophysics Data System (ADS)

Musmeci, Nicoló; Aste, Tomaso; Di Matteo, T.

2016-11-01

We report significant relations between past changes in the market correlation structure and future changes in the market volatility. This relation is made evident by using a measure of “correlation structure persistence” on correlation-based information filtering networks that quantifies the rate of change of the market dependence structure. We also measured changes in the correlation structure by means of a “metacorrelation” that measures a lagged correlation between correlation matrices computed over different time windows. Both methods show a deep interplay between past changes in correlation structure and future changes in volatility and we demonstrate they can anticipate market risk variations and this can be used to better forecast portfolio risk. Notably, these methods overcome the curse of dimensionality that limits the applicability of traditional econometric tools to portfolios made of a large number of assets. We report on forecasting performances and statistical significance of both methods for two different equity datasets. We also identify an optimal region of parameters in terms of True Positive and False Positive trade-off, through a ROC curve analysis. We find that this forecasting method is robust and it outperforms logistic regression predictors based on past volatility only. Moreover the temporal analysis indicates that methods based on correlation structural persistence are able to adapt to abrupt changes in the market, such as financial crises, more rapidly than methods based on past volatility.

Interplay between past market correlation structure changes and future volatility outbursts

PubMed Central

Musmeci, Nicoló; Aste, Tomaso; Di Matteo, T.

2016-01-01

We report significant relations between past changes in the market correlation structure and future changes in the market volatility. This relation is made evident by using a measure of “correlation structure persistence” on correlation-based information filtering networks that quantifies the rate of change of the market dependence structure. We also measured changes in the correlation structure by means of a “metacorrelation” that measures a lagged correlation between correlation matrices computed over different time windows. Both methods show a deep interplay between past changes in correlation structure and future changes in volatility and we demonstrate they can anticipate market risk variations and this can be used to better forecast portfolio risk. Notably, these methods overcome the curse of dimensionality that limits the applicability of traditional econometric tools to portfolios made of a large number of assets. We report on forecasting performances and statistical significance of both methods for two different equity datasets. We also identify an optimal region of parameters in terms of True Positive and False Positive trade-off, through a ROC curve analysis. We find that this forecasting method is robust and it outperforms logistic regression predictors based on past volatility only. Moreover the temporal analysis indicates that methods based on correlation structural persistence are able to adapt to abrupt changes in the market, such as financial crises, more rapidly than methods based on past volatility. PMID:27857144

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

ERIC Educational Resources Information Center

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

2014-01-01

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

Monitoring and evaluation of strategic change programme implementation-Lessons from a case analysis.

PubMed

Neumann, Jan; Robson, Andrew; Sloan, Diane

2018-02-01

This study considered the monitoring and evaluation of a large-scale and domestic and global strategic change programme implementation. It considers the necessary prerequisites to overcome challenges and barriers that prevent systematic and effective monitoring and evaluation to take place alongside its operationalisation. The work involves a case study based on a major industrial company from the energy sector. The change programme makes particular reference to changes in business models, business processes, organisation structures as well as Enterprise Resource Planning infrastructure. The case study focussed on the summative evaluation of the programme post-implementation. This assessment involved 25 semi-structured interviews with employees across a range of managerial strata capturing more than 65 roles within the change programme at both local and global levels. Data relating to their perception of evaluation effectiveness and shortcomings were analysed by means of template analysis. The study identifies responsibilities for executing an evaluation alongside various methods and tools that are appropriate, thereby focussing on the "Who" (roles, responsibility for particular activities) and "How" (methods and tools) rather than "What" to monitor and evaluate. The findings are presented generically so they offer new insights and transferability for practitioners involved in managing strategic change and its associated evaluation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Method and apparatus for suppressing regenerative instability and related chatter in machine tools

DOEpatents

Segalman, Daniel J.; Redmond, James M.

2001-01-01

Methods of and apparatuses for mitigating chatter vibrations in machine tools or components thereof. Chatter therein is suppressed by periodically or continuously varying the stiffness of the cutting tool (or some component of the cutting tool), and hence the resonant frequency of the cutting tool (or some component thereof). The varying of resonant frequency of the cutting tool can be accomplished by modulating the stiffness of the cutting tool, the cutting tool holder, or any other component of the support for the cutting tool. By periodically altering the impedance of the cutting tool assembly, chatter is mitigated. In one embodiment, a cyclic electric (or magnetic) field is applied to the spindle quill which contains an electro-rheological (or magneto-rheological) fluid. The variable yield stress in the fluid affects the coupling of the spindle to the machine tool structure, changing the natural frequency of oscillation. Altering the modal characteristics in this fashion disrupts the modulation of current tool vibrations with previous tool vibrations recorded on the workpiece surface.

Method and apparatus for suppressing regenerative instability and related chatter in machine tools

DOEpatents

Segalman, Daniel J.; Redmond, James M.

1999-01-01

Methods of and apparatuses for mitigating chatter vibrations in machine tools or components thereof. Chatter therein is suppressed by periodically or continuously varying the stiffness of the cutting tool (or some component of the cutting tool), and hence the resonant frequency of the cutting tool (or some component thereof). The varying of resonant frequency of the cutting tool can be accomplished by modulating the stiffness of the cutting tool, the cutting tool holder, or any other component of the support for the cutting tool. By periodically altering the impedance of the cutting tool assembly, chatter is mitigated. In one embodiment, a cyclic electric (or magnetic) field is applied to the spindle quill which contains an electro-rheological (or magneto-rheological) fluid. The variable yield stress in the fluid affects the coupling of the spindle to the machine tool structure, changing the natural frequency of oscillation. Altering the modal characteristics in this fashion disrupts the modulation of current tool vibrations with previous tool vibrations recorded on the workpiece surface.

Structural and functional plasticity of dendritic spines – root or result of behavior?

PubMed Central

Gipson, Cassandra D.; Olive, M. Foster

2016-01-01

Dendritic spines are multifunctional integrative units of the nervous system and are highly diverse and dynamic in nature. Both internal and external stimuli influence dendritic spine density and morphology on the order of minutes. It is clear that the structural plasticity of dendritic spines is related to changes in synaptic efficacy, learning and memory, and other cognitive processes. However, it is currently unclear whether structural changes in dendritic spines are primary instigators of changes in specific behaviors, a consequence of behavioral changes, or both. In this review, we first review the basic structure and function of dendritic spines in the brain, as well as laboratory methods to characterize and quantify morphological changes in dendritic spines. We then discuss the existing literature on the temporal and functional relationship between changes in dendritic spines in specific brain regions and changes in specific behaviors mediated by those regions. Although technological advancements have allowed us to better understand the functional relevance of structural changes in dendritic spines that are influenced by environmental stimuli, the role of spine dynamics as an underlying driver or consequence of behavior still remains elusive. We conclude that while it is likely that structural changes in dendritic spines are both instigators and results of behavioral changes, improved research tools and methods are needed to experimentally and directly manipulate spine dynamics in order to more empirically delineate the relationship between spine structure and behavior. PMID:27561549

Tool for simplifying the complex interactions within resilient communities

NASA Astrophysics Data System (ADS)

Stwertka, C.; Albert, M. R.; White, K. D.

2016-12-01

In recent decades, scientists have observed and documented impacts from climate change that will impact multiple sectors, will be impacted by decisions from multiple sectors, and will change over time. This complex human-engineered system has a large number of moving, interacting parts, which are interdependent and evolve over time towards their purpose. Many of the existing resilience frameworks and vulnerability frameworks focus on interactions between the domains, but do not include the structure of the interactions. We present an engineering systems approach to investigate the structural elements that influence a community's ability to be resilient. In this presentation we will present and analyze four common methods for building community resilience, utilizing our common framework. For several existing case studies we examine the stress points in the system and identify the impacts on the outcomes from the case studies. In ongoing research we will apply our system tool to a new case in the field.

eMovie: a storyboard-based tool for making molecular movies.

PubMed

Hodis, Eran; Schreiber, Gideon; Rother, Kristian; Sussman, Joel L

2007-05-01

The 3D structures of macromolecules are difficult to grasp and also to communicate. By their nature, movies or animations are particularly useful for highlighting key features by offering a 'guided tour' of structures and conformation changes. However, high-quality movies are rarely seen because they are currently difficult and time consuming to make. By adopting the traditional movie 'storyboard' concept, which gives guidance and direction to filming, eMovie makes the creation of lengthy molecular animations much easier. This tool is a plug-in for the open-source molecular graphics program PyMOL, and enables experts and novices alike to produce informative and high-quality molecular animations.

The impact of CmapTools utilization towards students' conceptual change on optics topic

NASA Astrophysics Data System (ADS)

Rofiuddin, Muhammad Rifqi; Feranie, Selly

2017-05-01

Science teachers need to help students identify their prior ideas and modify them based on scientific knowledge. This process is called as conceptual change. One of essential tools to analyze students' conceptual change is by using concept map. Concept Maps are graphical representations of knowledge that are comprised of concepts and the relationships between them. Constructing concept map is implemented by adapting the role of technology to support learning process, as it is suitable with Educational Ministry Regulation No.68 year 2013. Institute for Human and Machine Cognition (IHMC) has developed CmapTools, a client-server software for easily construct and visualize concept maps. This research aims to investigate secondary students' conceptual change after experiencing five-stage conceptual teaching model by utilizing CmapTools in learning Optics. Weak experimental method through one group pretest-posttest design is implemented in this study to collect preliminary and post concept map as qualitative data. Sample was taken purposively of 8th grade students (n= 22) at one of private schools Bandung, West Java. Conceptual change based on comparison of preliminary and post concept map construction is assessed based on rubric of concept map scoring and structure. Results shows significance conceptual change differences at 50.92 % that is elaborated into concept map element such as prepositions and hierarchical level in high category, cross links in medium category and specific examples in low category. All of the results are supported with the students' positive response towards CmapTools utilization that indicates improvement of motivation, interest, and behavior aspect towards Physics lesson.

Visualizing Morphological Changes of Abscission Zone Cells in Arabidopsis by Scanning Electron Microscope.

PubMed

Shi, Chun-Lin; Butenko, Melinka A

2018-01-01

Scanning electron microscope (SEM) is a type of electron microscope which produces detailed images of surface structures. It has been widely used in plants and animals to study cellular structures. Here, we describe a detailed protocol to prepare samples of floral abscission zones (AZs) for SEM, as well as further image analysis. We show that it is a powerful tool to detect morphologic changes at the cellular level during the course of abscission in wild-type plants and to establish the details of phenotypic alteration in abscission mutants.

Fuels planning: science synthesis and integration; forest structure and fire hazard fact sheet 03: visualizing forest structure and fuels

Treesearch

Rocky Mountain Research Station USDA Forest Service

2004-01-01

The software described in this fact sheet provides managers with tools for visualizing forest and fuels information. Computer-based landscape simulations can help visualize stand and landscape conditions and the effects of different management treatments and fuel changes over time. These visualizations can assist forest planning by considering a range of management...

Understanding and quantifying urban forest structure, functions, and value

Treesearch

David J. Nowak; Daniel E. Crane; Jeffrey T. Walton; Daniel B. Twardus; John F. Dwyer

2002-01-01

Trees in urban areas can have a significant impact on human health and the environment. Unfortunately, there is relatively little data about the structure, health, functions, and long-term changes in this important resource. In the United States, a number of efforts are underway to assess urban forest attributes at the local to national scales. In addition, tools are...

Resolution of structural heterogeneity in dynamic crystallography.

PubMed

Ren, Zhong; Chan, Peter W Y; Moffat, Keith; Pai, Emil F; Royer, William E; Šrajer, Vukica; Yang, Xiaojing

2013-06-01

Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.

G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures.

PubMed

Solomon, Oz; Kunik, Vered; Simon, Amos; Kol, Nitzan; Barel, Ortal; Lev, Atar; Amariglio, Ninette; Somech, Raz; Rechavi, Gidi; Eyal, Eran

2016-08-26

Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Structural information however is still not routinely exploited during this evaluation process. The main reasons can be attributed to the partial structural coverage of the human proteome and the lack of tools which conveniently convert genomic positions, which are the frequent output of genomic pipelines, to proteins and structure coordinates. We present G23D, a tool for conversion of human genomic coordinates to protein coordinates and protein structures. G23D allows mapping of genomic positions/variants on evolutionary related (and not only identical) protein three dimensional (3D) structures as well as on theoretical models. By doing so it significantly extends the space of variants for which structural insight is feasible. To facilitate interpretation of the variant consequence, pathogenic variants, functional sites and polymorphism sites are displayed on protein sequence and structure diagrams alongside the input variants. G23D also provides modeling of the mutant structure, analysis of intra-protein contacts and instant access to functional predictions and predictions of thermo-stability changes. G23D is available at http://www.sheba-cancer.org.il/G23D . G23D extends the fraction of variants for which structural analysis is applicable and provides better and faster accessibility for structural data to biologists and geneticists who routinely work with genomic information.

RNA2DMut: a web tool for the design and analysis of RNA structure mutations.

PubMed

Moss, Walter N

2018-03-01

With the widespread application of high-throughput sequencing, novel RNA sequences are being discovered at an astonishing rate. The analysis of function, however, lags behind. In both the cis - and trans -regulatory functions of RNA, secondary structure (2D base-pairing) plays essential regulatory roles. In order to test RNA function, it is essential to be able to design and analyze mutations that can affect structure. This was the motivation for the creation of the RNA2DMut web tool. With RNA2DMut, users can enter in RNA sequences to analyze, constrain mutations to specific residues, or limit changes to purines/pyrimidines. The sequence is analyzed at each base to determine the effect of every possible point mutation on 2D structure. The metrics used in RNA2DMut rely on the calculation of the Boltzmann structure ensemble and do not require a robust 2D model of RNA structure for designing mutations. This tool can facilitate a wide array of uses involving RNA: for example, in designing and evaluating mutants for biological assays, interrogating RNA-protein interactions, identifying key regions to alter in SELEX experiments, and improving RNA folding and crystallization properties for structural biology. Additional tools are available to help users introduce other mutations (e.g., indels and substitutions) and evaluate their effects on RNA structure. Example calculations are shown for five RNAs that require 2D structure for their function: the MALAT1 mascRNA, an influenza virus splicing regulatory motif, the EBER2 viral noncoding RNA, the Xist lncRNA repA region, and human Y RNA 5. RNA2DMut can be accessed at https://rna2dmut.bb.iastate.edu/. © 2018 Moss; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

MRI tools for assessment of microstructure and nephron function of the kidney.

PubMed

Xie, Luke; Bennett, Kevin M; Liu, Chunlei; Johnson, G Allan; Zhang, Jeff Lei; Lee, Vivian S

2016-12-01

MRI can provide excellent detail of renal structure and function. Recently, novel MR contrast mechanisms and imaging tools have been developed to evaluate microscopic kidney structures including the tubules and glomeruli. Quantitative MRI can assess local tubular function and is able to determine the concentrating mechanism of the kidney noninvasively in real time. Measuring single nephron function is now a near possibility. In parallel to advancing imaging techniques for kidney microstructure is a need to carefully understand the relationship between the local source of MRI contrast and the underlying physiological change. The development of these imaging markers can impact the accurate diagnosis and treatment of kidney disease. This study reviews the novel tools to examine kidney microstructure and local function and demonstrates the application of these methods in renal pathophysiology. Copyright © 2016 the American Physiological Society.

Amorphous Metal Polysulfides: Electrode Materials with Unique Insertion/Extraction Reactions.

PubMed

Sakuda, Atsushi; Ohara, Koji; Fukuda, Katsutoshi; Nakanishi, Koji; Kawaguchi, Tomoya; Arai, Hajime; Uchimoto, Yoshiharu; Ohta, Toshiaki; Matsubara, Eiichiro; Ogumi, Zempachi; Okumura, Toyoki; Kobayashi, Hironori; Kageyama, Hiroyuki; Shikano, Masahiro; Sakaebe, Hikari; Takeuchi, Tomonari

2017-07-05

A unique charge/discharge mechanism of amorphous TiS 4 is reported. Amorphous transition metal polysulfide electrodes exhibit anomalous charge/discharge performance and should have a unique charge/discharge mechanism: neither the typical intercalation/deintercalation mechanism nor the conversion-type one, but a mixture of the two. Analyzing the mechanism of such electrodes has been a challenge because fewer tools are available to examine the "amorphous" structure. It is revealed that the electrode undergoes two distinct structural changes: (i) the deformation and formation of S-S disulfide bonds and (ii) changes in the coordination number of titanium. These structural changes proceed continuously and concertedly for Li insertion/extraction. The results of this study provide a novel and unique model of amorphous electrode materials with significantly larger capacities.

High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE

PubMed Central

Majoros, William H.; Campbell, Michael S.; Holt, Carson; DeNardo, Erin K.; Ware, Doreen; Allen, Andrew S.; Yandell, Mark; Reddy, Timothy E.

2017-01-01

Abstract Motivation: The accurate interpretation of genetic variants is critical for characterizing genotype–phenotype associations. Because the effects of genetic variants can depend strongly on their local genomic context, accurate genome annotations are essential. Furthermore, as some variants have the potential to disrupt or alter gene structure, variant interpretation efforts stand to gain from the use of individualized annotations that account for differences in gene structure between individuals or strains. Results: We describe a suite of software tools for identifying possible functional changes in gene structure that may result from sequence variants. ACE (‘Assessing Changes to Exons’) converts phased genotype calls to a collection of explicit haplotype sequences, maps transcript annotations onto them, detects gene-structure changes and their possible repercussions, and identifies several classes of possible loss of function. Novel transcripts predicted by ACE are commonly supported by spliced RNA-seq reads, and can be used to improve read alignment and transcript quantification when an individual-specific genome sequence is available. Using publicly available RNA-seq data, we show that ACE predictions confirm earlier results regarding the quantitative effects of nonsense-mediated decay, and we show that predicted loss-of-function events are highly concordant with patterns of intolerance to mutations across the human population. ACE can be readily applied to diverse species including animals and plants, making it a broadly useful tool for use in eukaryotic population-based resequencing projects, particularly for assessing the joint impact of all variants at a locus. Availability and Implementation: ACE is written in open-source C ++ and Perl and is available from geneprediction.org/ACE Contact: myandell@genetics.utah.edu or tim.reddy@duke.edu Supplementary information: Supplementary information is available at Bioinformatics online. PMID:28011790

High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.

PubMed

Majoros, William H; Campbell, Michael S; Holt, Carson; DeNardo, Erin K; Ware, Doreen; Allen, Andrew S; Yandell, Mark; Reddy, Timothy E

2017-05-15

The accurate interpretation of genetic variants is critical for characterizing genotype-phenotype associations. Because the effects of genetic variants can depend strongly on their local genomic context, accurate genome annotations are essential. Furthermore, as some variants have the potential to disrupt or alter gene structure, variant interpretation efforts stand to gain from the use of individualized annotations that account for differences in gene structure between individuals or strains. We describe a suite of software tools for identifying possible functional changes in gene structure that may result from sequence variants. ACE ('Assessing Changes to Exons') converts phased genotype calls to a collection of explicit haplotype sequences, maps transcript annotations onto them, detects gene-structure changes and their possible repercussions, and identifies several classes of possible loss of function. Novel transcripts predicted by ACE are commonly supported by spliced RNA-seq reads, and can be used to improve read alignment and transcript quantification when an individual-specific genome sequence is available. Using publicly available RNA-seq data, we show that ACE predictions confirm earlier results regarding the quantitative effects of nonsense-mediated decay, and we show that predicted loss-of-function events are highly concordant with patterns of intolerance to mutations across the human population. ACE can be readily applied to diverse species including animals and plants, making it a broadly useful tool for use in eukaryotic population-based resequencing projects, particularly for assessing the joint impact of all variants at a locus. ACE is written in open-source C ++ and Perl and is available from geneprediction.org/ACE. myandell@genetics.utah.edu or tim.reddy@duke.edu. Supplementary information is available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Implementation of a competency assessment tool for agency nurses working in an acute paediatric setting.

PubMed

Hennerby, Cathy; Joyce, Pauline

2011-03-01

This paper reports on the implementation of a competency assessment tool for registered general agency nurses working in an acute paediatric setting, using a change management framework. The increased number of registered general agency nurses working in an acute children's hospital alerted concerns around their competency in working with children. These concerns were initially raised via informal complaints about 'near misses', parental dissatisfaction, perceived competency weaknesses and rising cost associated with their use. [Young's (2009) Journal of Organisational Change, 22, 524-548] nine-stage change framework was used to guide the implementation of the competency assessment tool within a paediatric acute care setting. The ongoing success of the initiative, from a nurse manager's perspective, relies on structured communication with the agency provider before employing competent agency nurses. Sustainability of the change will depend on nurse managers' persistence in attending the concerns of those resisting the change while simultaneously supporting those championing the change. These key communication and supporting roles highlight the pivotal role held by nurse managers, as gate keepers, in safe-guarding children while in hospital. Leadership qualities of nurse managers will also be challenged in continuing to manage and drive the change where resistance might prevail. © 2011 The Authors. Journal compilation © 2011 Blackwell Publishing Ltd.

Framework for architecture-independent run-time reconfigurable applications

NASA Astrophysics Data System (ADS)

Lehn, David I.; Hudson, Rhett D.; Athanas, Peter M.

2000-10-01

Configurable Computing Machines (CCMs) have emerged as a technology with the computational benefits of custom ASICs as well as the flexibility and reconfigurability of general-purpose microprocessors. Significant effort from the research community has focused on techniques to move this reconfigurability from a rapid application development tool to a run-time tool. This requires the ability to change the hardware design while the application is executing and is known as Run-Time Reconfiguration (RTR). Widespread acceptance of run-time reconfigurable custom computing depends upon the existence of high-level automated design tools. Such tools must reduce the designers effort to port applications between different platforms as the architecture, hardware, and software evolves. A Java implementation of a high-level application framework, called Janus, is presented here. In this environment, developers create Java classes that describe the structural behavior of an application. The framework allows hardware and software modules to be freely mixed and interchanged. A compilation phase of the development process analyzes the structure of the application and adapts it to the target platform. Janus is capable of structuring the run-time behavior of an application to take advantage of the memory and computational resources available.

Impact of an Information Technology-Enabled Initiative on the Quality of Prostate Multiparametric MRI Reports

PubMed Central

Silveira, Patricia C.; Dunne, Ruth; Sainani, Nisha I.; Lacson, Ronilda; Silverman, Stuart G.; Tempany, Clare M.; Khorasani, Ramin

2015-01-01

Rationale and Objectives Assess the impact of implementing a structured report template and a computer-aided diagnosis (CAD) tool on the quality of prostate multiparametric MRI (mp-MRI) reports. Materials and Methods Institutional Review Board approval was obtained for this HIPAA-compliant study performed at an academic medical center. The study cohort included all prostate mp-MRI reports (n=385) finalized 6 months before and after implementation of a structured report template and a CAD tool (collectively the IT tools) integrated into the PACS workstation. Primary outcome measure was quality of prostate mp-MRI reports. An expert panel of our institution’s subspecialty trained abdominal radiologists defined prostate mp-MRI report quality as optimal, satisfactory or unsatisfactory based on documentation of 9 variables. Reports were reviewed to extract the predefined quality variables and determine whether the IT tools were used to create each report. Chi-square and Student’s t-tests were used to compare report quality before and after implementation of IT tools. Results The overall proportion of optimal or satisfactory reports increased from 29.8% (47/158) to 53.3% (121/227) (p<0.001) after implementing the IT tools. While the proportion of optimal or satisfactory reports increased among reports generated using at least one of the IT tools (47/158=[29.8%] vs. 105/161=[65.2%]; p<0.001), there was no change in quality among reports generated without use of the IT tools (47/158=[29.8%] vs. 16/66=[24.2%]; p=0.404). Conclusion The use of a structured template and CAD tool improved the quality of prostate mp-MRI reports compared to free-text report format and subjective measurement of contrast enhancement kinetic curve. PMID:25863794

[New methods for the evaluation of bone quality. Assessment of bone structural property using imaging.

PubMed

Ito, Masako

Structural property of bone includes micro- or nano-structural property of the trabecular and cortical bone, and macroscopic geometry. Radiological technique is useful to analyze the bone structural property;multi-detector row CT(MDCT)or high-resolution peripheral QCT(HR-pQCT)is available to analyze human bone in vivo . For the analysis of hip geometry, CT-based hip structure analysis(HSA)is available as well as DXA-based HSA. These structural parameters are related to biomechanical property, and these assessment tools provide information of pathological changes or the effects of anti-osteoporotic agents on bone.

Improving educational environment in medical colleges through transactional analysis practice of teachers.

PubMed

Rajan, Marina; Chacko, Thomas

2012-01-01

 A FAIMER (Foundation for Advancement in International Medical Education and Research) fellow organized a comprehensive faculty development program to improve faculty awareness resulting in changed teaching practices and better teacher student relationships using Transactional Analysis (TA). Practicing TA tools help development of 'awareness' about intrapersonal and interpersonal processes. To improve self-awareness among medical educators.To bring about self-directed change in practices among medical educators.To assess usefulness of TA tools for the same.  An experienced trainer conducted a basic course (12 hours) in TA for faculty members. The PAC model of personality structure, functional fluency model of personal functioning, stroke theory on motivation, passivity and script theories of adult functional styles were taught experientially with examples from the Medical Education Scenario. Self-reported improvement in awareness and changes in practices were assessed immediately after, at three months, and one year after training.  The mean improvement in self-'awareness' is 13.3% (95% C.I 9.3-17.2) among nineteen participants. This persists one year after training. Changes in practices within a year include, collecting feedback, new teaching styles and better relationship with students.  These findings demonstrate sustainable and measurable improvement in self-awareness by practice of TA tools. Improvement in self-'awareness' of faculty resulted in self-directed changes in teaching practices. Medical faculty has judged the TA tools effective for improving self-awareness leading to self-directed changes.

Improving educational environment in medical colleges through transactional analysis practice of teachers

PubMed Central

Rajan, Marina

2012-01-01

Context: A FAIMER (Foundation for Advancement in International Medical Education and Research) fellow organized a comprehensive faculty development program to improve faculty awareness resulting in changed teaching practices and better teacher student relationships using Transactional Analysis (TA). Practicing TA tools help development of ‘awareness’ about intrapersonal and interpersonal processes. Objectives: To improve self-awareness among medical educators.To bring about self-directed change in practices among medical educators.To assess usefulness of TA tools for the same. Methods: An experienced trainer conducted a basic course (12 hours) in TA for faculty members. The PAC model of personality structure, functional fluency model of personal functioning, stroke theory on motivation, passivity and script theories of adult functional styles were taught experientially with examples from the Medical Education Scenario. Self-reported improvement in awareness and changes in practices were assessed immediately after, at three months, and one year after training. Findings: The mean improvement in self-'awareness' is 13.3% (95% C.I 9.3-17.2) among nineteen participants. This persists one year after training. Changes in practices within a year include, collecting feedback, new teaching styles and better relationship with students. Discussion and Conclusions: These findings demonstrate sustainable and measurable improvement in self-awareness by practice of TA tools. Improvement in self-'awareness' of faculty resulted in self-directed changes in teaching practices. Medical faculty has judged the TA tools effective for improving self-awareness leading to self-directed changes. PMID:24358808

Organizational and technological insight as important factors for successful implementation of IT.

PubMed

Nikula, R E

1999-01-01

Politicians and hospital management in Sweden and Denmark focus on IT and especially Electronic Patient Record, EPR as a tool for changes that will lead to better economy as well as better quality and service to the patients. These changes are not direct effects of the new medium for patient records but indirect effects due to the possibilities embedded in the new technology. To ensure that the implementation is successful, i.e. leads to changes in organization structure and workflow, we need tools to prepare clinicians and management. The focus of this paper is the individual insight in technology and organization and it proposes a model to assess and categorize the possibilities of individuals and groups to participate in and make an implementation process powerful.

Probing the Complexities of Structural Changes in Layered Oxide Cathode Materials for Li-Ion Batteries during Fast Charge-Discharge Cycling and Heating.

PubMed

Hu, Enyuan; Wang, Xuelong; Yu, Xiqian; Yang, Xiao-Qing

2018-02-20

The rechargeable lithium-ion battery (LIB) is the most promising energy storage system to power electric vehicles with high energy density and long cycling life. However, in order to meet customers' demands for fast charging, the power performances of current LIBs need to be improved. From the cathode aspect, layer-structured cathode materials are widely used in today's market and will continue to play important roles in the near future. The high rate capability of layered cathode materials during charging and discharging is critical to the power performance of the whole cell and the thermal stability is closely related to the safety issues. Therefore, the in-depth understanding of structural changes of layered cathode materials during high rate charging/discharging and the thermal stability during heating are essential in developing new materials and improving current materials. Since structural changes take place from the atomic level to the whole electrode level, combination of characterization techniques covering multilength scales is quite important. In many cases, this means using comprehensive tools involving diffraction, spectroscopy, and imaging to differentiate the surface from the bulk and to obtain structural/chemical information with different levels of spatial resolution. For example, hard X-ray spectroscopy can yield the bulk information and soft X-ray spectroscopy can give the surface information; X-ray based imaging techniques can obtain spatial resolution of tens of nanometers, and electron-based microcopy can go to angstroms. In addition to challenges associated with different spatial resolution, the dynamic nature of structural changes during high rate cycling and heating requires characterization tools to have the capability of collecting high quality data in a time-resolved fashion. Thanks to the advancement in synchrotron based techniques and high-resolution electron microscopy, high temporal and spatial resolutions can now be achieved. In this Account, we focus on the recent works studying kinetic and thermal properties of layer-structured cathode materials, especially the structural changes during high rate cycling and the thermal stability during heating. Advanced characterization techniques relating to the rate capability and thermal stability will be introduced. The different structure evolution behavior of cathode materials cycled at high rate will be compared with that cycled at low rate. Different response of individual transition metals and the inhomogeneity in chemical distribution will be discussed. For the thermal stability, the relationship between structural changes and oxygen release will be emphatically pointed out. In all these studies being reviewed, advanced characterization techniques are critically applied to reveal complexities at multiscale in layer-structured cathode materials.

Patient- and Caregiver-Reported Assessment Tools for Palliative Care: Summary of the 2017 Agency for Healthcare Research and Quality Technical Brief.

PubMed

Aslakson, Rebecca A; Dy, Sydney M; Wilson, Renee F; Waldfogel, Julie; Zhang, Allen; Isenberg, Sarina R; Blair, Alex; Sixon, Joshua; Lorenz, Karl A; Robinson, Karen A

2017-12-01

Assessment tools are data collection instruments that are completed by or with patients or caregivers and which collect data at the individual patient or caregiver level. The objectives of this study are to 1) summarize palliative care assessment tools completed by or with patients or caregivers and 2) identify needs for future tool development and evaluation. We completed 1) a systematic review of systematic reviews; 2) a supplemental search of previous reviews and Web sites, and/or 3) a targeted search for primary articles when no tools existed in a domain. Paired investigators screened search results, assessed risk of bias, and abstracted data. We organized tools by domains from the National Consensus Project Clinical Practice Guidelines for Palliative Care and selected the most relevant, recent, and highest quality systematic review for each domain. We included 10 systematic reviews and identified 152 tools (97 from systematic reviews and 55 from supplemental sources). Key gaps included no systematic review for pain and few tools assessing structural, cultural, spiritual, or ethical/legal domains, or patient-reported experience with end-of-life care. Psychometric information was available for many tools, but few studies evaluated responsiveness (sensitivity to change) and no studies compared tools. Few to no tools address the spiritual, ethical, or cultural domains or patient-reported experience with end-of-life care. While some data exist on psychometric properties of tools, the responsiveness of different tools to change and/or comparisons between tools have not been evaluated. Future research should focus on developing or testing tools that address domains for which few tools exist, evaluating responsiveness, and comparing tools. Copyright © 2017 American Academy of Hospice and Palliative Medicine. All rights reserved.

The Challenge: Overcoming the Pitfalls.

ERIC Educational Resources Information Center

Lozier, G. Gregory; Teeter, Deborah J.

1993-01-01

Some organizations are having difficulty with the Total Quality Management (TQM) approach. Problems appear to come from reliance on prepackaged TQM programs, large-scale, diffuse implementation, mass training programs, measurement paralysis, overemphasis on tools, process selection, outmoded reward structures, and simplistic views of change and…

Multi-agent electricity market modeling with EMCAS.

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

North, M.; Macal, C.; Conzelmann, G.

2002-09-05

Electricity systems are a central component of modern economies. Many electricity markets are transitioning from centrally regulated systems to decentralized markets. Furthermore, several electricity markets that have recently undergone this transition have exhibited extremely unsatisfactory results, most notably in California. These high stakes transformations require the introduction of largely untested regulatory structures. Suitable tools that can be used to test these regulatory structures before they are applied to real systems are required. Multi-agent models can provide such tools. To better understand the requirements such as tool, a live electricity market simulation was created. This experience helped to shape the developmentmore » of the multi-agent Electricity Market Complex Adaptive Systems (EMCAS) model. To explore EMCAS' potential, several variations of the live simulation were created. These variations probed the possible effects of changing power plant outages and price setting rules on electricity market prices.« less

Research resource: Update and extension of a glycoprotein hormone receptors web application.

PubMed

Kreuchwig, Annika; Kleinau, Gunnar; Kreuchwig, Franziska; Worth, Catherine L; Krause, Gerd

2011-04-01

The SSFA-GPHR (Sequence-Structure-Function-Analysis of Glycoprotein Hormone Receptors) database provides a comprehensive set of mutation data for the glycoprotein hormone receptors (covering the lutropin, the FSH, and the TSH receptors). Moreover, it provides a platform for comparison and investigation of these homologous receptors and helps in understanding protein malfunctions associated with several diseases. Besides extending the data set (> 1100 mutations), the database has been completely redesigned and several novel features and analysis tools have been added to the web site. These tools allow the focused extraction of semiquantitative mutant data from the GPHR subtypes and different experimental approaches. Functional and structural data of the GPHRs are now linked interactively at the web interface, and new tools for data visualization (on three-dimensional protein structures) are provided. The interpretation of functional findings is supported by receptor morphings simulating intramolecular changes during the activation process, which thus help to trace the potential function of each amino acid and provide clues to the local structural environment, including potentially relocated spatial counterpart residues. Furthermore, double and triple mutations are newly included to allow the analysis of their functional effects related to their spatial interrelationship in structures or homology models. A new important feature is the search option and data visualization by interactive and user-defined snake-plots. These new tools allow fast and easy searches for specific functional data and thereby give deeper insights in the mechanisms of hormone binding, signal transduction, and signaling regulation. The web application "Sequence-Structure-Function-Analysis of GPHRs" is accessible on the internet at http://www.ssfa-gphr.de/.

Frequency analysis for modulation-enhanced powder diffraction.

PubMed

Chernyshov, Dmitry; Dyadkin, Vadim; van Beek, Wouter; Urakawa, Atsushi

2016-07-01

Periodic modulation of external conditions on a crystalline sample with a consequent analysis of periodic diffraction response has been recently proposed as a tool to enhance experimental sensitivity for minor structural changes. Here the intensity distributions for both a linear and nonlinear structural response induced by a symmetric and periodic stimulus are analysed. The analysis is further extended for powder diffraction when an external perturbation changes not only the intensity of Bragg lines but also their positions. The derived results should serve as a basis for a quantitative modelling of modulation-enhanced diffraction data measured in real conditions.

Effects of scale and logging on landscape structure in a forest mosaic.

PubMed

Leimgruber, P; McShea, W J; Schnell, G D

2002-03-01

Landscape structure in a forest mosaic changes with spatial scale (i.e. spatial extent) and thresholds may occur where structure changes markedly. Forest management alters landscape structure and may affect the intensity and location of thresholds. Our purpose was to examine landscape structure at different scales to determine thresholds where landscape structure changes markedly in managed forest mosaics of the Appalachian Mountains in the eastern United States. We also investigated how logging influences landscape structure and whether these management activities change threshold values. Using threshold and autocorrelation analyses, we found that thresholds in landscape indices exist at 400, 500, and 800 m intervals from the outer edge of management units in our study region. For landscape indices that consider all landcover categories, such as dominance and contagion, landscape structure and thresholds did not change after logging occurred. Measurements for these overall landscape indices were strongly influenced by midsuccessional deciduous forest, the most common landcover category in the landscape. When restricting analyses for mean patch size and percent cover to individual forest types, thresholds for early-successional forests changed after logging. However, logging changed the landscape structure at small spatial scale, but did not alter the structure of the entire forest mosaic. Previous forest management may already have increased the heterogeneity of the landscape beyond the point where additional small cuts alter the overall structure of the forest. Because measurements for landscape indices yield very different results at different spatial scales, it is important first to identify thresholds in order to determine the appropriate scales for landscape ecological studies. We found that threshold and autocorrelation analyses were simple but powerful tools for the detection of appropriate scales in the managed forest mosaic under study.

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

PubMed

Egri-Nagy, Attila; Nehaniv, Chrystopher L

2008-01-01

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

The STAR score: a method for auditing clinical records

PubMed Central

Tuffaha, H

2012-01-01

INTRODUCTION Adequate medical note keeping is critical in delivering high quality healthcare. However, there are few robust tools available for the auditing of notes. The aim of this paper was to describe the design, validation and implementation of a novel scoring tool to objectively assess surgical notes. METHODS An initial ‘path finding’ study was performed to evaluate the quality of note keeping using the CRABEL scoring tool. The findings prompted the development of the Surgical Tool for Auditing Records (STAR) as an alternative. STAR was validated using inter-rater reliability analysis. An audit cycle of surgical notes using STAR was performed. The results were analysed and a structured form for the completion of surgical notes was introduced to see if the quality improved in the next audit cycle using STAR. An education exercise was conducted and all participants said the exercise would change their practice, with 25% implementing major changes. RESULTS Statistical analysis of STAR showed that it is reliable (Cronbach’s a = 0.959). On completing the audit cycle, there was an overall increase in the STAR score from 83.344% to 97.675% (p<0.001) with significant improvements in the documentation of the initial clerking from 59.0% to 96.5% (p<0.001) and subsequent entries from 78.4% to 96.1% (p<0.001). CONCLUSIONS The authors believe in the value of STAR as an effective, reliable and reproducible tool. Coupled with the application of structured forms to note keeping, it can significantly improve the quality of surgical documentation and can be implemented universally. PMID:22613300

Necessity of creating digital tools to ensure efficiency of technical means

NASA Astrophysics Data System (ADS)

Rakov, V. I.; Zakharova, O. V.

2018-05-01

The authors estimated the problems of functioning of technical objects. The article notes that the increasing complexity of automation systems may lead to an increase of the redundant resource in proportion to the number of components and relationships in the system, and to the need of the redundant resource constant change that can make implementation of traditional structures with redundancy unnecessarily costly (Standby System, Fault Tolerance, High Availability). It proposes the idea of creating digital tools to ensure efficiency of technical facilities.

Multiplex social ecological network analysis reveals how social changes affect community robustness more than resource depletion.

PubMed

Baggio, Jacopo A; BurnSilver, Shauna B; Arenas, Alex; Magdanz, James S; Kofinas, Gary P; De Domenico, Manlio

2016-11-29

Network analysis provides a powerful tool to analyze complex influences of social and ecological structures on community and household dynamics. Most network studies of social-ecological systems use simple, undirected, unweighted networks. We analyze multiplex, directed, and weighted networks of subsistence food flows collected in three small indigenous communities in Arctic Alaska potentially facing substantial economic and ecological changes. Our analysis of plausible future scenarios suggests that changes to social relations and key households have greater effects on community robustness than changes to specific wild food resources.

Study of structural change in volcanic and geothermal areas using seismic tomography

NASA Astrophysics Data System (ADS)

Mhana, Najwa; Foulger, Gillian; Julian, Bruce; peirce, Christine

2014-05-01

Long Valley caldera is a large silicic volcano. It has been in a state of volcanic and seismic unrest since 1978. Farther escalation of this unrest could pose a threat to the 5,000 residents and the tens of thousands of tourists who visit the area. We have studied the crustal structure beneath 28 km X 16 km area using seismic tomography. We performed tomographic inversions for the years 2009 and 2010 with a view to differencing it with the 1997 result to look for structural changes with time and whether repeat tomography is a capable of determining the changes in structure in volcanic and geothermal reservoirs. Thus, it might provide a useful tool to monitoring physical changes in volcanoes and exploited geothermal reservoirs. Up to 600 earthquakes, selected from the best-quality events, were used for the inversion. The inversions were performed using program simulps12 [Thurber, 1983]. Our initial results show that changes in both V p and V s were consistent with the migration of CO2 into the upper 2 km or so. Our ongoing work will also invert pairs of years simultaneously using a new program, tomo4d [Julian and Foulger, 2010]. This program inverts for the differences in structure between two epochs so it can provide a more reliable measure of structural change than simply differencing the results of individual years.

Techniques for assessing the socio-economic effects of vehicle mileage fees.

DOT National Transportation Integrated Search

2008-06-01

The purpose of this study was to develop tools for assessing the distributional effects of alternative highway user fees for light vehicles : in Oregon. The analysis focused on a change from the current gasoline tax to a VMT fee structure for collect...

CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels.

PubMed

Kartasalo, Kimmo; Pölönen, Risto-Pekka; Ojala, Marisa; Rasku, Jyrki; Lekkala, Jukka; Aalto-Setälä, Katriina; Kallio, Pasi

2015-10-26

Orientation and the degree of isotropy are important in many biological systems such as the sarcomeres of cardiomyocytes and other fibrillar structures of the cytoskeleton. Image based analysis of such structures is often limited to qualitative evaluation by human experts, hampering the throughput, repeatability and reliability of the analyses. Software tools are not readily available for this purpose and the existing methods typically rely at least partly on manual operation. We developed CytoSpectre, an automated tool based on spectral analysis, allowing the quantification of orientation and also size distributions of structures in microscopy images. CytoSpectre utilizes the Fourier transform to estimate the power spectrum of an image and based on the spectrum, computes parameter values describing, among others, the mean orientation, isotropy and size of target structures. The analysis can be further tuned to focus on targets of particular size at cellular or subcellular scales. The software can be operated via a graphical user interface without any programming expertise. We analyzed the performance of CytoSpectre by extensive simulations using artificial images, by benchmarking against FibrilTool and by comparisons with manual measurements performed for real images by a panel of human experts. The software was found to be tolerant against noise and blurring and superior to FibrilTool when analyzing realistic targets with degraded image quality. The analysis of real images indicated general good agreement between computational and manual results while also revealing notable expert-to-expert variation. Moreover, the experiment showed that CytoSpectre can handle images obtained of different cell types using different microscopy techniques. Finally, we studied the effect of mechanical stretching on cardiomyocytes to demonstrate the software in an actual experiment and observed changes in cellular orientation in response to stretching. CytoSpectre, a versatile, easy-to-use software tool for spectral analysis of microscopy images was developed. The tool is compatible with most 2D images and can be used to analyze targets at different scales. We expect the tool to be useful in diverse applications dealing with structures whose orientation and size distributions are of interest. While designed for the biological field, the software could also be useful in non-biological applications.

Eulerian frequency analysis of structural vibrations from high-speed video

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

Venanzoni, Andrea; Siemens Industry Software NV, Interleuvenlaan 68, B-3001 Leuven; De Ryck, Laurent

An approach for the analysis of the frequency content of structural vibrations from high-speed video recordings is proposed. The techniques and tools proposed rely on an Eulerian approach, that is, using the time history of pixels independently to analyse structural motion, as opposed to Lagrangian approaches, where the motion of the structure is tracked in time. The starting point is an existing Eulerian motion magnification method, which consists in decomposing the video frames into a set of spatial scales through a so-called Laplacian pyramid [1]. Each scale — or level — can be amplified independently to reconstruct a magnified motionmore » of the observed structure. The approach proposed here provides two analysis tools or pre-amplification steps. The first tool provides a representation of the global frequency content of a video per pyramid level. This may be further enhanced by applying an angular filter in the spatial frequency domain to each frame of the video before the Laplacian pyramid decomposition, which allows for the identification of the frequency content of the structural vibrations in a particular direction of space. This proposed tool complements the existing Eulerian magnification method by amplifying selectively the levels containing relevant motion information with respect to their frequency content. This magnifies the displacement while limiting the noise contribution. The second tool is a holographic representation of the frequency content of a vibrating structure, yielding a map of the predominant frequency components across the structure. In contrast to the global frequency content representation of the video, this tool provides a local analysis of the periodic gray scale intensity changes of the frame in order to identify the vibrating parts of the structure and their main frequencies. Validation cases are provided and the advantages and limits of the approaches are discussed. The first validation case consists of the frequency content retrieval of the tip of a shaker, excited at selected fixed frequencies. The goal of this setup is to retrieve the frequencies at which the tip is excited. The second validation case consists of two thin metal beams connected to a randomly excited bar. It is shown that the holographic representation visually highlights the predominant frequency content of each pixel and locates the global frequencies of the motion, thus retrieving the natural frequencies for each beam.« less

Developments to the Sylvan stand structure model to describe wood quality changes in southern bottomland hardwood forests because of forest management

Treesearch

Ian R. Scott

2009-01-01

Growth models can produce a wealth of detailed information that is often very difficult to perceive because it is frequently presented either as summary tables, stand view or landscape view visualizations. We have developed new tools for use with the Sylvan model (Larsen 1994) that allow the analysis of wood-quality changes as a consequence of forest management....

The interplay between climate change, forests, and disturbances.

PubMed

Dale, V H; Joyce, L A; McNulty, S; Neilson, R P

2000-11-15

Climate change affects forests both directly and indirectly through disturbances. Disturbances are a natural and integral part of forest ecosystems, and climate change can alter these natural interactions. When disturbances exceed their natural range of variation, the change in forest structure and function may be extreme. Each disturbance affects forests differently. Some disturbances have tight interactions with the species and forest communities which can be disrupted by climate change. Impacts of disturbances and thus of climate change are seen over a board spectrum of spatial and temporal scales. Future observations, research, and tool development are needed to further understand the interactions between climate change and forest disturbances.

Balancing stability and flexibility in adaptive governance: an ...

EPA Pesticide Factsheets

Adaptive governance must work “on the ground,” that is, it must operate through structures and procedures that the people it governs perceive to be legitimate and fair, as well as incorporating processes and substantive goals that are effective in allowing social-ecological systems (SESs) to adapt to climate change and other impacts. To address the continuing and accelerating alterations that climate change is bringing to SESs, adaptive governance generally will require more flexibility than prior governance institutions have often allowed. However, to function as good governance, adaptive governance must pay real attention to the problem of how to balance this increased need for flexibility with continuing governance stability so that it can foster adaptation to change without being perceived or experienced as perpetually destabilizing, disruptive, and unfair. Flexibility and stability serve different purposes in governance, and a variety of tools exist to strike different balances between them while still preserving the governance institution’s legitimacy among the people governed. After reviewing those purposes and the implications of climate change for environmental governance, we examine psychological insights into the structuring of adaptive governance and the variety of legal tools available to incorporate those insights into adaptive governance regimes. Because the substantive goals of governance systems will differ among specific systems, we do no

Modelling of robotic work cells using agent based-approach

NASA Astrophysics Data System (ADS)

Sękala, A.; Banaś, W.; Gwiazda, A.; Monica, Z.; Kost, G.; Hryniewicz, P.

2016-08-01

In the case of modern manufacturing systems the requirements, both according the scope and according characteristics of technical procedures are dynamically changing. This results in production system organization inability to keep up with changes in a market demand. Accordingly, there is a need for new design methods, characterized, on the one hand with a high efficiency and on the other with the adequate level of the generated organizational solutions. One of the tools that could be used for this purpose is the concept of agent systems. These systems are the tools of artificial intelligence. They allow assigning to agents the proper domains of procedures and knowledge so that they represent in a self-organizing system of an agent environment, components of a real system. The agent-based system for modelling robotic work cell should be designed taking into consideration many limitations considered with the characteristic of this production unit. It is possible to distinguish some grouped of structural components that constitute such a system. This confirms the structural complexity of a work cell as a specific production system. So it is necessary to develop agents depicting various aspects of the work cell structure. The main groups of agents that are used to model a robotic work cell should at least include next pattern representatives: machine tool agents, auxiliary equipment agents, robots agents, transport equipment agents, organizational agents as well as data and knowledge bases agents. In this way it is possible to create the holarchy of the agent-based system.

Analysis of real-time vibration data

USGS Publications Warehouse

Safak, E.

2005-01-01

In recent years, a few structures have been instrumented to provide continuous vibration data in real time, recording not only large-amplitude motions generated by extreme loads, but also small-amplitude motions generated by ambient loads. The main objective in continuous recording is to track any changes in structural characteristics, and to detect damage after an extreme event, such as an earthquake or explosion. The Fourier-based spectral analysis methods have been the primary tool to analyze vibration data from structures. In general, such methods do not work well for real-time data, because real-time data are mainly composed of ambient vibrations with very low amplitudes and signal-to-noise ratios. The long duration, linearity, and the stationarity of ambient data, however, allow us to utilize statistical signal processing tools, which can compensate for the adverse effects of low amplitudes and high noise. The analysis of real-time data requires tools and techniques that can be applied in real-time; i.e., data are processed and analyzed while being acquired. This paper presents some of the basic tools and techniques for processing and analyzing real-time vibration data. The topics discussed include utilization of running time windows, tracking mean and mean-square values, filtering, system identification, and damage detection.

Importance of polarity change in the electrical discharge machining

NASA Astrophysics Data System (ADS)

Schulze, H.-P.

2017-10-01

The polarity change in the electrical discharge machining is still a problem and is often performed completely unmotivated or randomly. The polarity must be designated primarily, i.e. the anodic part must be clearly assigned to the tool or the workpiece. Normally, the polarity of the workpiece electrode is named. In paper, will be shown which determine fundamental causes the structural behavior of the cathode and anode, and when it makes sense to change the polarity. The polarity change is primarily dependent on the materials that are used as cathode and anode. This distinction must be made if there are pure metals or complex materials. Secondary of the polarity change is also affected by the process energy source (PES) and the supply line. The polarity change is mostly influenced by the fact that the removal is to be maximized on the workpiece while the tool is minimal removal (wear) occur. A second factor that makes a polarity change needed is the use of electrical discharge in combination with other machining methods, such as electrochemical machining (ECM).

Dynamically variable negative stiffness structures.

PubMed

Churchill, Christopher B; Shahan, David W; Smith, Sloan P; Keefe, Andrew C; McKnight, Geoffrey P

2016-02-01

Variable stiffness structures that enable a wide range of efficient load-bearing and dexterous activity are ubiquitous in mammalian musculoskeletal systems but are rare in engineered systems because of their complexity, power, and cost. We present a new negative stiffness-based load-bearing structure with dynamically tunable stiffness. Negative stiffness, traditionally used to achieve novel response from passive structures, is a powerful tool to achieve dynamic stiffness changes when configured with an active component. Using relatively simple hardware and low-power, low-frequency actuation, we show an assembly capable of fast (<10 ms) and useful (>100×) dynamic stiffness control. This approach mitigates limitations of conventional tunable stiffness structures that exhibit either small (<30%) stiffness change, high friction, poor load/torque transmission at low stiffness, or high power active control at the frequencies of interest. We experimentally demonstrate actively tunable vibration isolation and stiffness tuning independent of supported loads, enhancing applications such as humanoid robotic limbs and lightweight adaptive vibration isolators.

Measuring changes in chemistry, composition, and molecular structure within hair fibers by infrared and Raman spectroscopic imaging.

PubMed

Zhang, Guojin; Senak, Laurence; Moore, David J

2011-05-01

Spatially resolved infrared (IR) and Raman images are acquired from human hair cross sections or intact hair fibers. The full informational content of these spectra are spatially correlated to hair chemistry, anatomy, and structural organization through univariate and multivariate data analysis. Specific IR and Raman images from untreated human hair describing the spatial dependence of lipid and protein distribution, protein secondary structure, lipid chain conformational order, and distribution of disulfide cross-links in hair protein are presented in this study. Factor analysis of the image plane acquired with IR microscopy in hair sections, permits delineation of specific micro-regions within the hair. These data indicate that both IR and Raman imaging of molecular structural changes in a specific region of hair will prove to be valuable tools in the understanding of hair structure, physiology, and the effect of various stresses upon its integrity.

Use of standardized multidimensional evaluation tools and the emergence of the case manager's professional identity in France.

PubMed

Nugue, Mathilde; De Stampa, Matthieu; Couturier, Yves; Somme, Dominique

2012-01-01

In France, the national public health plan proposes a group of innovations including the initiation of case management for older adults in complex situations, particularly those with cognitive disorders. In this context, public authorities asked case managers to use a standardized multidimensional evaluation tool. The results of a qualitative study on the pertinence of such a tool relative to the emergence of this new professional field are described. Early use of an evaluation tool seems to be linked to the emergence of a new professional identity for recently recruited case managers. Factors determining the strength of this link are training tool standardization, computerization, and local structure's involvement. Our results contribute to identifying one of the ways by which professional identity can be changed to become a case manager.

Atomic view of the histidine environment stabilizing higher-pH conformations of pH-dependent proteins

PubMed Central

Valéry, Céline; Deville-Foillard, Stéphanie; Lefebvre, Christelle; Taberner, Nuria; Legrand, Pierre; Meneau, Florian; Meriadec, Cristelle; Delvaux, Camille; Bizien, Thomas; Kasotakis, Emmanouil; Lopez-Iglesias, Carmen; Gall, Andrew; Bressanelli, Stéphane; Le Du, Marie-Hélène; Paternostre, Maïté; Artzner, Franck

2015-01-01

External stimuli are powerful tools that naturally control protein assemblies and functions. For example, during viral entry and exit changes in pH are known to trigger large protein conformational changes. However, the molecular features stabilizing the higher pH structures remain unclear. Here we elucidate the conformational change of a self-assembling peptide that forms either small or large nanotubes dependent on the pH. The sub-angstrom high-pH peptide structure reveals a globular conformation stabilized through a strong histidine-serine H-bond and a tight histidine-aromatic packing. Lowering the pH induces histidine protonation, disrupts these interactions and triggers a large change to an extended β-sheet-based conformation. Re-visiting available structures of proteins with pH-dependent conformations reveals both histidine-containing aromatic pockets and histidine-serine proximity as key motifs in higher pH structures. The mechanism discovered in this study may thus be generally used by pH-dependent proteins and opens new prospects in the field of nanomaterials. PMID:26190377

Describing Technological Paradigm Transitions: A Methodological Exploration.

ERIC Educational Resources Information Center

Wallace, Danny P.; Van Fleet, Connie

1997-01-01

Presents a humorous treatment of the "sessio taurino" (or humanistic inquiry) technique for describing changes in technological models. The fundamental tool of "sessio taurino" is a loosely-structured event known as the session, which is of indeterminate length, involves a flexible number of participants, and utilizes a…

Schools as Agencies of Social Criticism.

ERIC Educational Resources Information Center

Ferree, George

1989-01-01

Posits that schools must help students evaluate their culture and seek social change where warranted. Analyzes features of rationality in the mandate that schools provide students with tools for reasoned, logical, and unpartisan social criticism. Suggests that radical theorists have not clearly proposed to schools rational structures for…

Protein engineering and its applications in food industry.

PubMed

Kapoor, Swati; Rafiq, Aasima; Sharma, Savita

2017-07-24

Protein engineering is a young discipline that has been branched out from the field of genetic engineering. Protein engineering is based on the available knowledge about the proteins structure/function(s), tools/instruments, software, bioinformatics database, available cloned gene, knowledge about available protein, vectors, recombinant strains and other materials that could lead to change in the protein backbone. Protein produced properly from genetic engineering process means a protein that is able to fold correctly and to do particular function(s) efficiently even after being subjected to engineering practices. Protein is modified through its gene or chemically. However, modification of protein through gene is easier. There is no specific limitation of Protein Engineering tools; any technique that can lead to change the protein constituent of amino acid and result in the modification of protein structure/function is in the frame of Protein Engineering. Meanwhile, there are some common tools used to reach a specific target. More active industrial and pharmaceutical based proteins have been invented by the field of Protein Engineering to introduce new function as well as to change its interaction with surrounding environment. A variety of protein engineering applications have been reported in the literature. These applications range from biocatalysis for food and industry to environmental, medical and nanobiotechnology applications. Successful combinations of various protein engineering methods had led to successful results in food industries and have created a scope to maintain the quality of finished product after processing.

Using vibrational molecular spectroscopy to reveal association of steam-flaking induced carbohydrates molecular structural changes with grain fractionation, biodigestion and biodegradation

NASA Astrophysics Data System (ADS)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-04-01

Advanced vibrational molecular spectroscopy has been developed as a rapid and non-destructive tool to reveal intrinsic molecular structure conformation of biological tissues. However, this technique has not been used to systematically study flaking induced structure changes at a molecular level. The objective of this study was to use vibrational molecular spectroscopy to reveal association between steam flaking induced CHO molecular structural changes in relation to grain CHO fractionation, predicted CHO biodegradation and biodigestion in ruminant system. The Attenuate Total Reflectance Fourier-transform Vibrational Molecular Spectroscopy (ATR-Ft/VMS) at SRP Key Lab of Molecular Structure and Molecular Nutrition, Ministry of Agriculture Strategic Research Chair Program (SRP, University of Saskatchewan) was applied in this study. The fractionation, predicted biodegradation and biodigestion were evaluated using the Cornell Net Carbohydrate Protein System. The results show that: (1) The steam flaking induced significant changes in CHO subfractions, CHO biodegradation and biodigestion in ruminant system. There were significant differences between non-processed (raw) and steam flaked grain corn (P < .01); (2) The ATR-Ft/VMS molecular technique was able to detect the processing induced CHO molecular structure changes; (3) Induced CHO molecular structure spectral features are significantly correlated (P < .05) to CHO subfractions, CHO biodegradation and biodigestion and could be applied to potentially predict CHO biodegradation (R2 = 0.87, RSD = 0.74, P < .01) and intestinal digestible undegraded CHO (R2 = 0.87, RSD = 0.24, P < .01). In summary, the processing induced molecular CHO structure changes in grain corn could be revealed by the ATR-Ft/VMS vibrational molecular spectroscopy. These molecular structure changes in grain were potentially associated with CHO biodegradation and biodigestion.

Effect of pin tool design on the material flow of dissimilar AA7075-AA6061 friction stir welds

NASA Astrophysics Data System (ADS)

Hasan, Mohammed M.; Ishak, M.; Rejab, M. R. M.

2017-10-01

Tool design is the most influential aspect in the friction stir welding (FSW) technology. Influence of pin tool geometry on material flow pattern are studied in this work during the FSW of dissimilar AA7075 and AA6061 aluminium alloys. Three truncated pin tool profiles (threaded, threaded with single flat, and unthreaded with single flat) were used to prepare the weldments. The workpieces were joined using a custom-made clamping system under 1100 rpm of spindle speed, 300 mm/min of traverse rate and 3° of tilt angle. The metallographic analysis showed that defect-free welds can be produced using the three pin tools with significant changes in the mixing stir zone structure. The results declared that the introducing of the flat on the cone of the probe deviates the pattern of the onion rings without changing the chemical composition of the created layers. This in turn improves the hardness distribution and tensile strength of the welded joint. It was also noted that both heat affected zone (HAZ) and thermal-mechanical affected zone (TMAZ) are similar in composition to their corresponding base materials (BM).

Augmented Endoscopic Images Overlaying Shape Changes in Bone Cutting Procedures.

PubMed

Nakao, Megumi; Endo, Shota; Nakao, Shinichi; Yoshida, Munehito; Matsuda, Tetsuya

2016-01-01

In microendoscopic discectomy for spinal disorders, bone cutting procedures are performed in tight spaces while observing a small portion of the target structures. Although optical tracking systems are able to measure the tip of the surgical tool during surgery, the poor shape information available during surgery makes accurate cutting difficult, even if preoperative computed tomography and magnetic resonance images are used for reference. Shape estimation and visualization of the target structures are essential for accurate cutting. However, time-varying shape changes during cutting procedures are still challenging issues for intraoperative navigation. This paper introduces a concept of endoscopic image augmentation that overlays shape changes to support bone cutting procedures. This framework handles the history of the location of the measured drill tip as a volume label and visualizes the remains to be cut overlaid on the endoscopic image in real time. A cutting experiment was performed with volunteers, and the feasibility of this concept was examined using a clinical navigation system. The efficacy of the cutting aid was evaluated with respect to the shape similarity, total moved distance of a cutting tool, and required cutting time. The results of the experiments showed that cutting performance was significantly improved by the proposed framework.

Understanding and planning ecological restoration of plant-pollinator networks.

PubMed

Devoto, Mariano; Bailey, Sallie; Craze, Paul; Memmott, Jane

2012-04-01

Theory developed from studying changes in the structure and function of communities during natural or managed succession can guide the restoration of particular communities. We constructed 30 quantitative plant-flower visitor networks along a managed successional gradient to identify the main drivers of change in network structure. We then applied two alternative restoration strategies in silico (restoring for functional complementarity or redundancy) to data from our early successional plots to examine whether different strategies affected the restoration trajectories. Changes in network structure were explained by a combination of age, tree density and variation in tree diameter, even when variance explained by undergrowth structure was accounted for first. A combination of field data, a network approach and numerical simulations helped to identify which species should be given restoration priority in the context of different restoration targets. This combined approach provides a powerful tool for directing management decisions, particularly when management seeks to restore or conserve ecosystem function. © 2012 Blackwell Publishing Ltd/CNRS.

Sensor-Only System Identification for Structural Health Monitoring of Advanced Aircraft

NASA Technical Reports Server (NTRS)

Kukreja, Sunil L.; Bernstein, Dennis S.

2012-01-01

Environmental conditions, cyclic loading, and aging contribute to structural wear and degradation, and thus potentially catastrophic events. The challenge of health monitoring technology is to determine incipient changes accurately and efficiently. This project addresses this challenge by developing health monitoring techniques that depend only on sensor measurements. Since actively controlled excitation is not needed, sensor-to-sensor identification (S2SID) provides an in-flight diagnostic tool that exploits ambient excitation to provide advance warning of significant changes. S2SID can subsequently be followed up by ground testing to localize and quantify structural changes. The conceptual foundation of S2SID is the notion of a pseudo-transfer function, where one sensor is viewed as the pseudo-input and another is viewed as the pseudo-output, is approach is less restrictive than transmissibility identification and operational modal analysis since no assumption is made about the locations of the sensors relative to the excitation.

Brainstem Involvement as a Cause of Central Sleep Apnea: Pattern of Microstructural Cerebral Damage in Patients with Cerebral Microangiopathy

PubMed Central

Duning, Thomas; Deppe, Michael; Brand, Eva; Stypmann, Jörg; Becht, Charlotte; Heidbreder, Anna; Young, Peter

2013-01-01

Background The exact underlying pathomechanism of central sleep apnea with Cheyne-Stokes respiration (CSA-CSR) is still unclear. Recent studies have demonstrated an association between cerebral white matter changes and CSA. A dysfunction of central respiratory control centers in the brainstem was suggested by some authors. Novel MR-imaging analysis tools now allow far more subtle assessment of microstructural cerebral changes. The aim of this study was to investigate whether and what severity of subtle structural cerebral changes could lead to CSA-CSR, and whether there is a specific pattern of neurodegenerative changes that cause CSR. Therefore, we examined patients with Fabry disease (FD), an inherited, lysosomal storage disease. White matter lesions are early and frequent findings in FD. Thus, FD can serve as a "model disease" of cerebral microangiopathy to study in more detail the impact of cerebral lesions on central sleep apnea. Patients and Methods Genetically proven FD patients (n = 23) and age-matched healthy controls (n = 44) underwent a cardio-respiratory polysomnography and brain MRI at 3.0 Tesla. We applied different MR-imaging techniques, ranging from semiquantitative measurement of white matter lesion (WML) volumes and automated calculation of brain tissue volumes to VBM of gray matter and voxel-based diffusion tensor imaging (DTI) analysis. Results In 5 of 23 Fabry patients (22%) CSA-CSR was detected. Voxel-based DTI analysis revealed widespread structural changes in FD patients when compared to the healthy controls. When calculated as a separate group, DTI changes of CSA-CSR patients were most prominent in the brainstem. Voxel-based regression analysis revealed a significant association between CSR severity and microstructural DTI changes within the brainstem. Conclusion Subtle microstructural changes in the brainstem might be a neuroanatomical correlate of CSA-CSR in patients at risk of WML. DTI is more sensitive and specific than conventional structural MRI and other advanced MR analyses tools in demonstrating these abnormalities. PMID:23637744

Molecular dynamics simulation analysis of the effect of T790M mutation on epidermal growth factor receptor protein architecture in non-small cell lung carcinoma.

PubMed

Peng, Xiao-Nu; Wang, Jing; Zhang, Wei

2017-08-01

Non-small cell lung cancer etiology and its treatment failure are due to epidermal growth factor receptor (EGFR) kinase domain mutations at amino acid position 790. The mutational change from threonine to methionine at position 790 (T790M) is responsible for tyrosine kinase inhibition failure. Using molecular dynamic simulation, the present study investigated the architectural changes occurring at the atomic scale. The 50-nsec runs using a GROMOS force field for wild-type and mutant EGFR's kinase domains were investigated for contrasting variations using Gromacs inbuilt tools. The adenosine triphosphate binding domain and the active site of EGFR were studied extensively in order to understand the structural changes. All the parameters investigated in the present study revealed considerable changes in the studied structures, and the knowledge gained from this may be used to develop novel kinase inhibitors that will be effective irrespective of the structural alterations in kinase domain.

On the Vertical Structure of Seasonal, Interannual and Intraseasonal Flows

DTIC Science & Technology

1992-12-01

regions. Extensive use is made of a primitive equation (PE) model, as a diagnostic tool, to explore the extent to which tropical heating might influence ...vertical modes, while Wiin-Nielsen (1971a and b) studied the time 2 behaviour of long waves for various vertical structures. More recent investigations...nonlinear three-leve PE model, are used to determine the influence of tropical heating on extratropica wave response. In Chapter 4, the interannual changes

Prescribed fire as the minimum tool for wilderness forest and fire regime restoration: a case study from the Sierra Nevada, California

Treesearch

MaryBeth Keifer; Nathan L. Stephenson; Jeff Manley

2000-01-01

Changes in forest structure were monitored in areas treated with prescribed fire in Sequoia and Kings Canyon National Parks. Five years after the initial prescribed fires, tree density was reduced by 61% in the giant sequoia-mixed conifer forest, with the greatest reduction in the smaller trees. This post-burn forest structure falls within the range that may have been...

Investigation of the subcellular architecture of L7 neurons of Aplysia californica using magnetic resonance microscopy (MRM) at 7.8 microns.

PubMed

Lee, Choong H; Flint, Jeremy J; Hansen, Brian; Blackband, Stephen J

2015-06-10

Magnetic resonance microscopy (MRM) is a non-invasive diagnostic tool which is well-suited to directly resolve cellular structures in ex vivo and in vitro tissues without use of exogenous contrast agents. Recent advances in its capability to visualize mammalian cellular structure in intact tissues have reinvigorated analytical interest in aquatic cell models whose previous findings warrant up-to-date validation of subcellular components. Even if the sensitivity of MRM is less than other microscopic technologies, its strength lies in that it relies on the same image contrast mechanisms as clinical MRI which make it a unique tool for improving our ability to interpret human diagnostic imaging through high resolution studies of well-controlled biological model systems. Here, we investigate the subcellular MR signal characteristics of isolated cells of Aplysia californica at an in-plane resolution of 7.8 μm. In addition, direct correlation and positive identification of subcellular architecture in the cells is achieved through well-established histology. We hope this methodology will serve as the groundwork for studying pathophysiological changes through perturbation studies and allow for development of disease-specific cellular modeling tools. Such an approach promises to reveal the MR contrast changes underlying cellular mechanisms in various human diseases, for example in ischemic stroke.

Efficient simulation of press hardening process through integrated structural and CFD analyses

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

Palaniswamy, Hariharasudhan; Mondalek, Pamela; Wronski, Maciek

Press hardened steel parts are being increasingly used in automotive structures for their higher strength to meet safety standards while reducing vehicle weight to improve fuel consumption. However, manufacturing of sheet metal parts by press hardening process to achieve desired properties is extremely challenging as it involves complex interaction of plastic deformation, metallurgical change, thermal distribution, and fluid flow. Numerical simulation is critical for successful design of the process and to understand the interaction among the numerous process parameters to control the press hardening process in order to consistently achieve desired part properties. Until now there has been no integratedmore » commercial software solution that can efficiently model the complete process from forming of the blank, heat transfer between the blank and tool, microstructure evolution in the blank, heat loss from tool to the fluid that flows through water channels in the tools. In this study, a numerical solution based on Altair HyperWorks® product suite involving RADIOSS®, a non-linear finite element based structural analysis solver and AcuSolve®, an incompressible fluid flow solver based on Galerkin Least Square Finite Element Method have been utilized to develop an efficient solution for complete press hardening process design and analysis. RADIOSS is used to handle the plastic deformation, heat transfer between the blank and tool, and microstructure evolution in the blank during cooling. While AcuSolve is used to efficiently model heat loss from tool to the fluid that flows through water channels in the tools. The approach is demonstrated through some case studies.« less

Capturing structure and function in an embryonic heart with biophotonic tools

PubMed Central

Karunamuni, Ganga H.; Gu, Shi; Ford, Matthew R.; Peterson, Lindsy M.; Ma, Pei; Wang, Yves T.; Rollins, Andrew M.; Jenkins, Michael W.; Watanabe, Michiko

2014-01-01

Disturbed cardiac function at an early stage of development has been shown to correlate with cellular/molecular, structural as well as functional cardiac anomalies at later stages culminating in the congenital heart defects (CHDs) that present at birth. While our knowledge of cellular and molecular steps in cardiac development is growing rapidly, our understanding of the role of cardiovascular function in the embryo is still in an early phase. One reason for the scanty information in this area is that the tools to study early cardiac function are limited. Recently developed and adapted biophotonic tools may overcome some of the challenges of studying the tiny fragile beating heart. In this chapter, we describe and discuss our experience in developing and implementing biophotonic tools to study the role of function in heart development with emphasis on optical coherence tomography (OCT). OCT can be used for detailed structural and functional studies of the tubular and looping embryo heart under physiological conditions. The same heart can be rapidly and quantitatively phenotyped at early and again at later stages using OCT. When combined with other tools such as optical mapping (OM) and optical pacing (OP), OCT has the potential to reveal in spatial and temporal detail the biophysical changes that can impact mechanotransduction pathways. This information may provide better explanations for the etiology of the CHDs when interwoven with our understanding of morphogenesis and the molecular pathways that have been described to be involved. Future directions for advances in the creation and use of biophotonic tools are discussed. PMID:25309451

The Effects of Video Games on Cognition and Brain Structure: Potential Implications for Neuropsychiatric Disorders.

PubMed

Shams, Tahireh A; Foussias, George; Zawadzki, John A; Marshe, Victoria S; Siddiqui, Ishraq; Müller, Daniel J; Wong, Albert H C

2015-09-01

Video games are now a ubiquitous form of entertainment that has occasionally attracted negative attention. Video games have also been used to test cognitive function, as therapeutic interventions for neuropsychiatric disorders, and to explore mechanisms of experience-dependent structural brain changes. Here, we review current research on video games published from January 2011 to April 2014 with a focus on studies relating to mental health, cognition, and brain imaging. Overall, there is evidence that specific types of video games can alter brain structure or improve certain aspects of cognitive functioning. Video games can also be useful as neuropsychological assessment tools. While research in this area is still at a very early stage, there are interesting results that encourage further work in this field, and hold promise for utilizing this technology as a powerful therapeutic and experimental tool.

Parametric Dependencies in Aero-Elastic, Articulated, Flapping Flight

NASA Astrophysics Data System (ADS)

Willis, D. J.; Persson, P.; Peraire, J.; Breuer, K. S.

2006-11-01

Aero-elastic coupling and wing articulation both play a vital role in the generation of lift and propulsion in birds, bats and fish. We present results from a computational study that employs several tools of varying fidelity to explore the role of flexible structures on the performance and efficiency of bird and bat flight mechanics. The tools (both 2-D and 3-D) include a Wake only ``Betz'' analysis following the work of Hall, Pigott and Hall (J. Aircaft, 1998), a potential flow model coupled to a free-vortex wake (Willis, Peraire & White, AIAA 2005-0854), and lastly, a discontinuous Galerkin solver (Persson & Peraire, AIAA 2006-0113) for the full Navier-Stokes equations. Structural models include springs, beams and membranes to represent compliant biological structures. The results demonstrate the changes in efficiency that can be achieved by different parametric variations in the flight behavior, including the effects of increasing kinematic degrees of freedom (e.g. articulated wings) and the effect of compliance in wing and skeletal structures.

Dynamic Weather Routes Architecture Overview

NASA Technical Reports Server (NTRS)

Eslami, Hassan; Eshow, Michelle

2014-01-01

Dynamic Weather Routes Architecture Overview, presents the high level software architecture of DWR, based on the CTAS software framework and the Direct-To automation tool. The document also covers external and internal data flows, required dataset, changes to the Direct-To software for DWR, collection of software statistics, and the code structure.

The Decision Tree: A Tool for Achieving Behavioral Change.

ERIC Educational Resources Information Center

Saren, Dru

1999-01-01

Presents a "Decision Tree" process for structuring team decision making and problem solving about specific student behavioral goals. The Decision Tree involves a sequence of questions/decisions that can be answered in "yes/no" terms. Questions address reasonableness of the goal, time factors, importance of the goal, responsibilities, safety,…

Feasibility of using a bacteriophage-based structural color sensor for screening the geographical origins of agricultural products

NASA Astrophysics Data System (ADS)

Seol, Daun; Moon, Jong-Sik; Lee, Yujin; Han, Jiye; Jang, Daeil; Kang, Dong-Jin; Moon, Jiyoung; Jang, Eunjin; Oh, Jin-Woo; Chung, Hoeil

2018-05-01

An M13 bacteriophage-based color sensor, which can change its structural color upon interaction with a gaseous molecule, was evaluated as a screening tool for the discrimination of the geographical origins of three different agricultural products (garlic, onion, and perilla). Exposure of the color sensor to sample odors induced the self-assembled M13 bacteriophage bundles to swell by the interaction of amino acid residues (repeating units of four glutamates) on the bacteriophage with the odor components, resulting in a change in the structural color of the sensor. When the sensor was exposed to the odors of garlic and onion samples, the RGB color changes were considerable because of the strong interactions of the odor components such as disulfides with the glutamate residues on the sensor. Although the patterns of the color variations were generally similar between the domestic and imported samples, some degrees of dissimilarities in their intensities were also observed. Although the magnitude of color change decreased for perilla, the color change patterns between the two groups were somewhat different. With the acquired RGB data, a support vector machine was employed to distinguish the domestic and imported samples, and the resulting accuracies in the measurements of garlic, onion, and perilla samples were 94.1, 88.7, and 91.6%, respectively. The differences in the concentrations of the odor components between both groups and/or the presence of specific components exclusively in the odor of one group allowed the color sensor-based discrimination. The demonstrated color sensor was thus shown to be a potentially versatile and simple as an on-site screening tool. Strategies able to further improve the sensor performance were also discussed.

Feasibility of using a bacteriophage-based structural color sensor for screening the geographical origins of agricultural products.

PubMed

Seol, Daun; Moon, Jong-Sik; Lee, Yujin; Han, Jiye; Jang, Daeil; Kang, Dong-Jin; Moon, Jiyoung; Jang, Eunjin; Oh, Jin-Woo; Chung, Hoeil

2018-05-15

An M13 bacteriophage-based color sensor, which can change its structural color upon interaction with a gaseous molecule, was evaluated as a screening tool for the discrimination of the geographical origins of three different agricultural products (garlic, onion, and perilla). Exposure of the color sensor to sample odors induced the self-assembled M13 bacteriophage bundles to swell by the interaction of amino acid residues (repeating units of four glutamates) on the bacteriophage with the odor components, resulting in a change in the structural color of the sensor. When the sensor was exposed to the odors of garlic and onion samples, the RGB color changes were considerable because of the strong interactions of the odor components such as disulfides with the glutamate residues on the sensor. Although the patterns of the color variations were generally similar between the domestic and imported samples, some degrees of dissimilarities in their intensities were also observed. Although the magnitude of color change decreased for perilla, the color change patterns between the two groups were somewhat different. With the acquired RGB data, a support vector machine was employed to distinguish the domestic and imported samples, and the resulting accuracies in the measurements of garlic, onion, and perilla samples were 94.1, 88.7, and 91.6%, respectively. The differences in the concentrations of the odor components between both groups and/or the presence of specific components exclusively in the odor of one group allowed the color sensor-based discrimination. The demonstrated color sensor was thus shown to be a potentially versatile and simple as an on-site screening tool. Strategies able to further improve the sensor performance were also discussed. Copyright © 2018. Published by Elsevier B.V.

Chimeras of Channelrhodopsin-1 and -2 from Chlamydomonas reinhardtii Exhibit Distinctive Light-induced Structural Changes from Channelrhodopsin-2*

PubMed Central

Inaguma, Asumi; Tsukamoto, Hisao; Kato, Hideaki E.; Kimura, Tetsunari; Ishizuka, Toru; Oishi, Satomi; Yawo, Hiromu; Nureki, Osamu; Furutani, Yuji

2015-01-01

Channelrhodopsin-2 (ChR2) from the green alga Chlamydomonas reinhardtii functions as a light-gated cation channel that has been developed as an optogenetic tool to stimulate specific nerve cells in animals and control their behavior by illumination. The molecular mechanism of ChR2 has been extensively studied by a variety of spectroscopic methods, including light-induced difference Fourier transform infrared (FTIR) spectroscopy, which is sensitive to structural changes in the protein upon light activation. An atomic structure of channelrhodopsin was recently determined by x-ray crystallography using a chimera of channelrhodopsin-1 (ChR1) and ChR2. Electrophysiological studies have shown that ChR1/ChR2 chimeras are less desensitized upon continuous illumination than native ChR2, implying that there are some structural differences between ChR2 and chimeras. In this study, we applied light-induced difference FTIR spectroscopy to ChR2 and ChR1/ChR2 chimeras to determine the molecular basis underlying these functional differences. Upon continuous illumination, ChR1/ChR2 chimeras exhibited structural changes distinct from those in ChR2. In particular, the protonation state of a glutamate residue, Glu-129 (Glu-90 in ChR2 numbering), in the ChR chimeras is not changed as dramatically as in ChR2. Moreover, using mutants stabilizing particular photointermediates as well as time-resolved measurements, we identified some differences between the major photointermediates of ChR2 and ChR1/ChR2 chimeras. Taken together, our data indicate that the gating and desensitizing processes in ChR1/ChR2 chimeras are different from those in ChR2 and that these differences should be considered in the rational design of new optogenetic tools based on channelrhodopsins. PMID:25796616

Chimeras of channelrhodopsin-1 and -2 from Chlamydomonas reinhardtii exhibit distinctive light-induced structural changes from channelrhodopsin-2.

PubMed

Inaguma, Asumi; Tsukamoto, Hisao; Kato, Hideaki E; Kimura, Tetsunari; Ishizuka, Toru; Oishi, Satomi; Yawo, Hiromu; Nureki, Osamu; Furutani, Yuji

2015-05-01

Channelrhodopsin-2 (ChR2) from the green alga Chlamydomonas reinhardtii functions as a light-gated cation channel that has been developed as an optogenetic tool to stimulate specific nerve cells in animals and control their behavior by illumination. The molecular mechanism of ChR2 has been extensively studied by a variety of spectroscopic methods, including light-induced difference Fourier transform infrared (FTIR) spectroscopy, which is sensitive to structural changes in the protein upon light activation. An atomic structure of channelrhodopsin was recently determined by x-ray crystallography using a chimera of channelrhodopsin-1 (ChR1) and ChR2. Electrophysiological studies have shown that ChR1/ChR2 chimeras are less desensitized upon continuous illumination than native ChR2, implying that there are some structural differences between ChR2 and chimeras. In this study, we applied light-induced difference FTIR spectroscopy to ChR2 and ChR1/ChR2 chimeras to determine the molecular basis underlying these functional differences. Upon continuous illumination, ChR1/ChR2 chimeras exhibited structural changes distinct from those in ChR2. In particular, the protonation state of a glutamate residue, Glu-129 (Glu-90 in ChR2 numbering), in the ChR chimeras is not changed as dramatically as in ChR2. Moreover, using mutants stabilizing particular photointermediates as well as time-resolved measurements, we identified some differences between the major photointermediates of ChR2 and ChR1/ChR2 chimeras. Taken together, our data indicate that the gating and desensitizing processes in ChR1/ChR2 chimeras are different from those in ChR2 and that these differences should be considered in the rational design of new optogenetic tools based on channelrhodopsins. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Assisted Migration as a Management Tool in Coastal Ecosystems Threatened by Climate Change

DTIC Science & Technology

2016-04-30

upslope migration, the changes in community structure did not include establishment of downslope species. Instead, disturbed assemblages remained...concerns. Pages 134- 141 in Susan I. Cerulean and R. Todd Engstrom, eds. Fire in wetlands: a management perspective. Proceedings of the Tall Timbers Fire...Ecology Conference, No. 19. Tall Timbers Research Station, Tallahassee, FL. Pivovaroff, A. L., C. Swift, L. L. Battaglia, B. Kunz, W. J. Platt, and

Quantification of microscopic surface features of single point diamond turned optics with subsequent chemical polishing

NASA Astrophysics Data System (ADS)

Cardenas, Nelson; Kyrish, Matthew; Taylor, Daniel; Fraelich, Margaret; Lechuga, Oscar; Claytor, Richard; Claytor, Nelson

2015-03-01

Electro-Chemical Polishing is routinely used in the anodizing industry to achieve specular surface finishes of various metals products prior to anodizing. Electro-Chemical polishing functions by leveling the microscopic peaks and valleys of the substrate, thereby increasing specularity and reducing light scattering. The rate of attack is dependent of the physical characteristics (height, depth, and width) of the microscopic structures that constitute the surface finish. To prepare the sample, mechanical polishing such as buffing or grinding is typically required before etching. This type of mechanical polishing produces random microscopic structures at varying depths and widths, thus the electropolishing parameters are determined in an ad hoc basis. Alternatively, single point diamond turning offers excellent repeatability and highly specific control of substrate polishing parameters. While polishing, the diamond tool leaves behind an associated tool mark, which is related to the diamond tool geometry and machining parameters. Machine parameters such as tool cutting depth, speed and step over can be changed in situ, thus providing control of the spatial frequency of the microscopic structures characteristic of the surface topography of the substrate. By combining single point diamond turning with subsequent electro-chemical etching, ultra smooth polishing of both rotationally symmetric and free form mirrors and molds is possible. Additionally, machining parameters can be set to optimize post polishing for increased surface quality and reduced processing times. In this work, we present a study of substrate surface finish based on diamond turning tool mark spatial frequency with subsequent electro-chemical polishing.

Balancing stability and flexibility in adaptive governance: An analysis of tools available in U.S. environmental law

USGS Publications Warehouse

Kundis Craig, Robin; Garmestani, Ahjond S.; Allen, Craig R.; Arnold, Craig Anthony (Tony); Birge, Hannah E.; DeCaro, Daniel A.; Fremier, Alexander K.; Gosnell, Hannah; Schlager, Edella

2017-01-01

Adaptive governance must work “on the ground,” that is, it must operate through structures and procedures that the people it governs perceive to be legitimate and fair, as well as incorporating processes and substantive goals that are effective in allowing social-ecological systems (SESs) to adapt to climate change and other impacts. To address the continuing and accelerating alterations that climate change is bringing to SESs, adaptive governance generally will require more flexibility than prior governance institutions have often allowed. However, to function as good governance, adaptive governance must pay real attention to the problem of how to balance this increased need for flexibility with continuing governance stability so that it can foster adaptation to change without being perceived or experienced as perpetually destabilizing, disruptive, and unfair. Flexibility and stability serve different purposes in governance, and a variety of tools exist to strike different balances between them while still preserving the governance institution’s legitimacy among the people governed. After reviewing those purposes and the implications of climate change for environmental governance, we examine psychological insights into the structuring of adaptive governance and the variety of legal tools available to incorporate those insights into adaptive governance regimes. Because the substantive goals of governance systems will differ among specific systems, we do not purport to comment on what the normative or substantive goals of law should be. Instead, we conclude that attention to process and procedure (including participation), as well as increased use of substantive standards (instead of rules), may allow an increased level of substantive flexibility to operate with legitimacy and fairness, providing the requisite levels of psychological, social, and economic stability needed for communities to adapt successfully to the Anthropocene.

Balancing stability and flexibility in adaptive governance: an analysis of tools available in U.S. environmental law.

PubMed

Craig, Robin Kundis; Garmestani, Ahjond S; Allen, Craig R; Arnold, Craig Anthony Tony; Birgé, Hannah; DeCaro, Daniel A; Fremier, Alexander K; Gosnell, Hannah; Schlager, Edella

2017-06-30

Adaptive governance must work "on the ground," that is, it must operate through structures and procedures that the people it governs perceive to be legitimate and fair, as well as incorporating processes and substantive goals that are effective in allowing social-ecological systems (SESs) to adapt to climate change and other impacts. To address the continuing and accelerating alterations that climate change is bringing to SESs, adaptive governance generally will require more flexibility than prior governance institutions have often allowed. However, to function as good governance, adaptive governance must pay real attention to the problem of how to balance this increased need for flexibility with continuing governance stability so that it can foster adaptation to change without being perceived or experienced as perpetually destabilizing, disruptive, and unfair. Flexibility and stability serve different purposes in governance, and a variety of tools exist to strike different balances between them while still preserving the governance institution's legitimacy among the people governed. After reviewing those purposes and the implications of climate change for environmental governance, we examine psychological insights into the structuring of adaptive governance and the variety of legal tools available to incorporate those insights into adaptive governance regimes. Because the substantive goals of governance systems will differ among specific systems, we do not purport to comment on what the normative or substantive goals of law should be. Instead, we conclude that attention to process and procedure (including participation), as well as increased use of substantive standards (instead of rules), may allow an increased level of substantive flexibility to operate with legitimacy and fairness, providing the requisite levels of psychological, social, and economic stability needed for communities to adapt successfully to the Anthropocene.

Biodiversity evaluation in tropical agricultural systems - How will rubber cultivation and land use change effect species diversity in SW China

NASA Astrophysics Data System (ADS)

Cotter, M.; Grenz, J.; Sauerborn, J.

2012-04-01

The Greater Mekong Subregion is a known hotspot of biodiversity, which faces drastic changes due to human impact particularly with regard to infrastructure and economy. Within the framework of the Sino-German research project "Living Landscapes China" (LILAC), we have developed a biodiversity evaluation tool based on the combination of approaches from landscape ecology with detailed empirical data on species diversity and habitat characteristics of tropical plant and arthropod communities in a Geographical Information System. We use field ecological data to assess different spatial and qualitative aspects of the diversity and spatial distribution of species throughout the research area, a watershed in south-western Yunnan province, PR China. In addition, scenarios on the impact of land use change have been analyzed and compared in order to highlight the implications these possible future scenarios would have on species diversity within the research area. The aim of the presented tool is to provide scientists and policy makers who have to evaluate the consequences of scenarios of future land use with information on the current and likely future state of biodiversity in their research area or administrative region. This will enable them to assess the likely impacts of land use changes on structural and ecological diversity and allow for informed land use planning. The methodology developed for this tool can also be applied outside of the Greater Mekong Subregion, as the model structure allows for an easy adaption to other research areas and challenges, be it oil palm production in Southeast Asia or small scale farming in central Africa or the Amazon basin.

Understanding Global Change: Tools for exploring Earth processes and biotic change through time

NASA Astrophysics Data System (ADS)

Bean, J. R.; White, L. D.; Berbeco, M.

2014-12-01

Teaching global change is one of the great pedagogical challenges of our day because real understanding entails integrating a variety of concepts from different scientific subject areas, including chemistry, physics, and biology, with a variety of causes and impacts in the past, present, and future. With the adoption of the Next Generation Science Standards, which emphasize climate change and other human impacts on natural systems, there has never been a better time to provide instructional support to educators on these topics. In response to this clear need, the University of California Museum of Paleontology, in collaboration with the National Center for Science Education, developed a new web resource for teachers and students titled "Understanding Global Change" (UGC) that introduces the drivers and impacts of global change. This website clarifies the connections among deep time, modern Earth system processes, and anthropogenic influences, and provides K-16 instructors with a wide range of easy-to-use tools, strategies, and lesson plans for communicating these important concepts regarding global change and the basic Earth systems processes. In summer 2014, the UGC website was field-tested during a workshop with 25 K-12 teachers and science educators. Feedback from participants helped the UGC team develop and identify pedagogically sound lesson plans and instructional tools on global change. These resources are accessible through UGC's searchable database, are aligned with NGSS and Common Core, and are categorized by grade level, subject, and level of inquiry-based instruction (confirmation, structured, guided, open). Providing a range of content and tools at levels appropriate for teachers is essential because our initial needs assessment found that educators often feel that they lack the content knowledge and expertise to address complex, but relevant global change issues, such as ocean acidification and deforestation. Ongoing needs assessments and surveys of teacher confidence when teaching global change content will continue to drive UGC resource development as the site expands in the future.

Pedestrian Evacuation Analysis for Tsunami Hazards

NASA Astrophysics Data System (ADS)

Jones, J. M.; Ng, P.; Wood, N. J.

2014-12-01

Recent catastrophic tsunamis in the last decade, as well as the 50th anniversary of the 1964 Alaskan event, have heightened awareness of the threats these natural hazards present to large and increasing coastal populations. For communities located close to the earthquake epicenter that generated the tsunami, strong shaking may also cause significant infrastructure damage, impacting the road network and hampering evacuation. There may also be insufficient time between the earthquake and first wave arrival to rely on a coordinated evacuation, leaving at-risk populations to self-evacuate on foot and across the landscape. Emergency managers evaluating these coastal risks need tools to assess the evacuation potential of low-lying areas in order to discuss mitigation options, which may include vertical evacuation structures to provide local safe havens in vulnerable communities. The U.S. Geological Survey has developed the Pedestrian Evacuation Analyst software tool for use by researchers and emergency managers to assist in the assessment of a community's evacuation potential by modeling travel times across the landscape and producing both maps of travel times and charts of population counts with corresponding times. The tool uses an anisotropic (directionally dependent) least cost distance model to estimate evacuation potential and allows for the variation of travel speed to measure its effect on travel time. The effectiveness of vertical evacuation structures on evacuation time can also be evaluated and compared with metrics such as travel time maps showing each structure in place and graphs displaying the percentage change in population exposure for each structure against the baseline. Using the tool, travel time maps and at-risk population counts have been generated for some coastal communities of the U.S. Pacific Northwest and Alaska. The tool can also be used to provide valuable decision support for tsunami vertical evacuation siting.

HRTEM low dose: the unfold of the morphed graphene, from amorphous carbon to morphed graphenes.

PubMed

Calderon, H A; Okonkwo, A; Estrada-Guel, I; Hadjiev, V G; Alvarez-Ramírez, F; Robles Hernández, F C

We present experimental evidence under low-dose conditions transmission electron microscopy for the unfolding of the evolving changes in carbon soot during mechanical milling. The milled soot shows evolving changes as a function of the milling severity or time. Those changes are responsible for the transformation from amorphous carbon to graphenes, graphitic carbon, and highly ordered structures such as morphed graphenes, namely Rh6 and Rh6-II. The morphed graphenes are corrugated layers of carbon with cross-linked covalently nature and sp 2 - or sp 3 -type allotropes. Electron microscopy and numerical simulations are excellent complementary tools to identify those phases. Furthermore, the TEAM 05 microscope is an outstanding tool to resolve the microstructure and prevent any damage to the sample. Other characterization techniques such as XRD, Raman, and XPS fade to convey a true identification of those phases because the samples are usually blends or mixes of the mentioned phases.

A crystallographic perspective on sharing data and knowledge

NASA Astrophysics Data System (ADS)

Bruno, Ian J.; Groom, Colin R.

2014-10-01

The crystallographic community is in many ways an exemplar of the benefits and practices of sharing data. Since the inception of the technique, virtually every published crystal structure has been made available to others. This has been achieved through the establishment of several specialist data centres, including the Cambridge Crystallographic Data Centre, which produces the Cambridge Structural Database. Containing curated structures of small organic molecules, some containing a metal, the database has been produced for almost 50 years. This has required the development of complex informatics tools and an environment allowing expert human curation. As importantly, a financial model has evolved which has, to date, ensured the sustainability of the resource. However, the opportunities afforded by technological changes and changing attitudes to sharing data make it an opportune moment to review current practices.

OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data

PubMed Central

2014-01-01

There is an ever increasing resource in terms of both structural information and activity data for many protein targets. In this paper we describe OOMMPPAA, a novel computational tool designed to inform compound design by combining such data. OOMMPPAA uses 3D matched molecular pairs to generate 3D ligand conformations. It then identifies pharmacophoric transformations between pairs of compounds and associates them with their relevant activity changes. OOMMPPAA presents this data in an interactive application providing the user with a visual summary of important interaction regions in the context of the binding site. We present validation of the tool using openly available data for CDK2 and a GlaxoSmithKline data set for a SAM-dependent methyl-transferase. We demonstrate OOMMPPAA’s application in optimizing both potency and cell permeability and use OOMMPPAA to highlight nuanced and cross-series SAR. OOMMPPAA is freely available to download at http://oommppaa.sgc.ox.ac.uk/OOMMPPAA/. PMID:25244105

Some uses of wavelets for imaging dynamic processes in live cochlear structures

NASA Astrophysics Data System (ADS)

Boutet de Monvel, J.

2007-09-01

A variety of image and signal processing algorithms based on wavelet filtering tools have been developed during the last few decades, that are well adapted to the experimental variability typically encountered in live biological microscopy. A number of processing tools are reviewed, that use wavelets for adaptive image restoration and for motion or brightness variation analysis by optical flow computation. The usefulness of these tools for biological imaging is illustrated in the context of the restoration of images of the inner ear and the analysis of cochlear motion patterns in two and three dimensions. I also report on recent work that aims at capturing fluorescence intensity changes associated with vesicle dynamics at synaptic zones of sensory hair cells. This latest application requires one to separate the intensity variations associated with the physiological process under study from the variations caused by motion of the observed structures. A wavelet optical flow algorithm for doing this is presented, and its effectiveness is demonstrated on artificial and experimental image sequences.

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

Raymond, David W.; Blankenship, Douglas A.; Buerger, Stephen

The dynamic stability of deep drillstrings is challenged by an inability to impart controllability with ever-changing conditions introduced by geology, depth, structural dynamic properties and operating conditions. A multi-organizational LDRD project team at Sandia National Laboratories successfully demonstrated advanced technologies for mitigating drillstring vibrations to improve the reliability of drilling systems used for construction of deep, high-value wells. Using computational modeling and dynamic substructuring techniques, the benefit of controllable actuators at discrete locations in the drillstring is determined. Prototype downhole tools were developed and evaluated in laboratory test fixtures simulating the structural dynamic response of a deep drillstring. A laboratory-basedmore » drilling applicability demonstration was conducted to demonstrate the benefit available from deployment of an autonomous, downhole tool with self-actuation capabilities in response to the dynamic response of the host drillstring. A concept is presented for a prototype drilling tool based upon the technical advances. The technology described herein is the subject of U.S. Patent Application No. 62219481, entitled "DRILLING SYSTEM VIBRATION SUPPRESSION SYSTEMS AND METHODS", filed September 16, 2015.« less

Mechanical Anisotropy and Pressure Induced Structural Changes in Piroxicam Crystals Probed by In Situ Indentation and Raman Spectroscopy

NASA Astrophysics Data System (ADS)

Manimunda, Praveena; Hintsala, Eric; Asif, Syed; Mishra, Manish Kumar

2017-01-01

The ability to correlate mechanical and chemical characterization techniques in real time is both lacking and powerful tool for gaining insights into material behavior. This is demonstrated through use of a novel nanoindentation device equipped with Raman spectroscopy to explore the deformation-induced structural changes in piroxicam crystals. Mechanical anisotropy was observed in two major faces ( 0bar{1}1 ) and (011), which are correlated to changes in the interlayer interaction from in situ Raman spectra recorded during indentation. The results of this study demonstrate the considerable potential of an in situ Raman nanoindentation instrument for studying a variety of topics, including stress-induced phase transformation mechanisms, mechanochemistry, and solid state reactivity under mechanical forces that occur in molecular and pharmaceutical solids.

Bridging the gap between individual-level risk for HIV and structural determinants: using root cause analysis in strategic planning.

PubMed

Willard, Nancy; Chutuape, Kate; Stines, Stephanie; Ellen, Jonathan M

2012-01-01

HIV prevention efforts have expanded beyond individual-level interventions to address structural determinants of risk. Coalitions have been an important vehicle for addressing similar intractable and deeply rooted health-related issues. A root cause analysis process may aid coalitions in identifying fundamental, structural-level contributors to risk and in identifying appropriate solutions. For this article, strategic plans for 13 coalitions were analyzed both before and after a root cause analysis approach was applied to determine the coalitions' strategic plans potential impact and comprehensiveness. After root cause analysis, strategic plans trended toward targeting policies and practices rather than on single agency programmatic changes. Plans expanded to target multiple sectors and several changes within sectors to penetrate deeply into a sector or system. Findings suggest that root cause analysis may be a viable tool to assist coalitions in identifying structural determinants and possible solutions for HIV risk.

Freeform manufacturing of a microoptical lens array on a steep curved substrate by use of a voice coil fast tool servo.

PubMed

Scheiding, Sebastian; Yi, Allen Y; Gebhardt, Andreas; Li, Lei; Risse, Stefan; Eberhardt, Ramona; Tünnermann, Andreas

2011-11-21

We report what is to our knowledge the first approach to diamond turn microoptical lens array on a steep curved substrate by use of a voice coil fast tool servo. In recent years ultraprecision machining has been employed to manufacture accurate optical components with 3D structure for beam shaping, imaging and nonimaging applications. As a result, geometries that are difficult or impossible to manufacture using lithographic techniques might be fabricated using small diamond tools with well defined cutting edges. These 3D structures show no rotational symmetry, but rather high frequency asymmetric features thus can be treated as freeform geometries. To transfer the 3D surface data with the high frequency freeform features into a numerical control code for machining, the commonly piecewise differentiable surfaces are represented as a cloud of individual points. Based on this numeric data, the tool radius correction is calculated to account for the cutting-edge geometry. Discontinuities of the cutting tool locations due to abrupt slope changes on the substrate surface are bridged using cubic spline interpolation.When superimposed with the trajectory of the rotationally symmetric substrate the complete microoptical geometry in 3D space is established. Details of the fabrication process and performance evaluation are described. © 2011 Optical Society of America

CMS Configuration Editor: GUI based application for user analysis job

NASA Astrophysics Data System (ADS)

de Cosa, A.

2011-12-01

We present the user interface and the software architecture of the Configuration Editor for the CMS experiment. The analysis workflow is organized in a modular way integrated within the CMS framework that organizes in a flexible way user analysis code. The Python scripting language is adopted to define the job configuration that drives the analysis workflow. It could be a challenging task for users, especially for newcomers, to develop analysis jobs managing the configuration of many required modules. For this reason a graphical tool has been conceived in order to edit and inspect configuration files. A set of common analysis tools defined in the CMS Physics Analysis Toolkit (PAT) can be steered and configured using the Config Editor. A user-defined analysis workflow can be produced starting from a standard configuration file, applying and configuring PAT tools according to the specific user requirements. CMS users can adopt this tool, the Config Editor, to create their analysis visualizing in real time which are the effects of their actions. They can visualize the structure of their configuration, look at the modules included in the workflow, inspect the dependences existing among the modules and check the data flow. They can visualize at which values parameters are set and change them according to what is required by their analysis task. The integration of common tools in the GUI needed to adopt an object-oriented structure in the Python definition of the PAT tools and the definition of a layer of abstraction from which all PAT tools inherit.

Adult and Lifelong Learning as Tools for Organisational Adaptation and Change Management

ERIC Educational Resources Information Center

Laitinen, Ilpo

2015-01-01

Significant structural reforms of public administration are commencing in Finland from 2017. Firstly, municipalities and cities are being combined into larger entities. Secondly, five social-welfare and healthcare regions are to be created, with that level being responsible for arranging services in this field. Thirdly, the City of Helsinki is…

The Hard Work of Interpretation: The National Politics of PISA Reception in Hungary and Romania

ERIC Educational Resources Information Center

Neumann, Eszter; Kiss, Adel; Fejes, Ildiko

2012-01-01

This article discusses the dynamic interaction between global policy and knowledge flows and two post-communist education systems--Hungary and Romania--with special attention to the appropriation of post-bureaucratic regulation tools and the structural changes enhanced by the knowledge transmitted by the Programme for International Student…

Informing the improvement of forest products durability using small angle neutron scattering

Treesearch

Nayomi Plaza Rodriguez; Sai Venkatesh Pingali; Shuo Qian; William T. Heller; Joseph E. Jakes

2016-01-01

A better understanding of how wood nanostructure swells with moisture is needed to accelerate the development of forest products with enhanced moisture durability. Despite its suitability to study nanostructures, small angle neutron scattering (SANS) remains an underutilized tool in forest products research. Nanoscale moisture-induced structural changes in intact and...

Clinical governance and operations management methodologies.

PubMed

Davies, C; Walley, P

2000-01-01

The clinical governance mechanism, introduced since 1998 in the UK National Health Service (NHS), aims to deliver high quality care with efficient, effective and cost-effective patient services. Scally and Donaldson recognised that new approaches are needed, and operations management techniques comprise potentially powerful methodologies in understanding the process of care, which can be applied both within and across professional boundaries. This paper summarises four studies in hospital Trusts which took approaches to improving process that were different from and less structured than business process re-engineering (BPR). The problems were then amenable to change at a relatively low cost and short timescale, producing significant improvement to patient care. This less structured approach to operations management avoided incurring overhead costs of large scale and costly change such as new information technology (IT) systems. The most successful changes were brought about by formal tools to control quantity, content and timing of changes.

How to implement a new strategy without disrupting your organization.

PubMed

Kaplan, Robert S; Norton, David P

2006-03-01

Throughout most of modern busi ness history, corporations have attempted to unlock value by matching their structures to their strategies: Centralization by function. Decentralization by product category or geographic region. Matrix organizations that attempt both at once. Virtual organizations. Networked organizations. Velcro organizations. But none of these approaches has worked very well. Restructuring churn is expensive, and new structures often create new organizational problems that are as troublesome as the ones they try to solve. It takes time for employees to adapt to them, they create legacy systems that refuse to die, and a great deal of tacit knowledge gets lost in the process. Given the costs and difficulties involved in finding structural ways to unlock value, it's fair to raise the question: Is structural change the right tool for the job? The answer is usually no, Kaplan and Norton contend. It's far less disruptive to choose an organizational design that works without major conflicts and then design a customized strategic system to align that structure to the strategy. A management system based on the balanced scorecard framework is the best way to align strategy and structure, the authors suggest. Managers can use the tools of the framework to drive their unit's performance: strategy maps to define and communicate the company's value proposition and the scorecard to implement and monitor the strategy. In this article, the originators of the balanced scorecard describe how two hugely different organizations--DuPont and the Royal Canadian Mounted Police-used corporate scorecards and strategy maps organized around strategic themes to realize the enormous value that their portfolios of assets, people, and skills represented. As a result, they did not have to endure a painful series of changes that simply replaced one rigid structure with another.

Perspectives and reflections on the practice of behaviour change communication for infant and young child feeding.

PubMed

Pelto, Gretel H; Martin, Stephanie L; van Liere, Marti J; Fabrizio, Cecilia S

2016-04-01

Behaviour change communication (BCC) is a critical component of infant and young child feeding (IYCF) interventions. In this study we asked BCC practitioners working in low- and middle-income countries to participate in an examination of BCC practice. We focus here on results of their personal reflections related to larger issues of practice. We used a combination of iterative triangulation and snowball sampling procedures to obtain a sample of 29 BCC professionals. Major themes include (1) participants using tools and guidelines to structure their work, and many consider their organisation's tools to be their most important contribution to the field; (2) they value research to facilitate programme design and implementation; (3) half felt research needed to increase; (4) they have a strong commitment to respecting cultural beliefs and culturally appropriate programming; (5) they are concerned about lack of a strong theoretical foundation for their work. Based on participants' perspectives and the authors' reflections, we identified the following needs: (1) conducting a systematic examination of the alternative theoretical structures that are available for nutrition BCC, followed by a review of the evidence base and suggestions for future programmatic research to fill the gaps in knowledge; (2) developing a checklist of common patterns to facilitate efficiency in formative research; (3) developing an analytic compendium of current IYCF BCC guidelines and tools; (4) developing tools and guidelines that cover the full programme process, including use of innovative channels to support 'scaling up nutrition'; and (5) continued support for programmes of proven effectiveness. © 2015 John Wiley & Sons Ltd.

Method for detecting the signature of noise-induced structures in spatiotemporal data sets: an application to excitable media

NASA Astrophysics Data System (ADS)

Huett, Marc-Thorsten

2003-05-01

We formulate mathematical tools for analyzing spatiotemporal data sets. The tools are based on nearest-neighbor considerations similar to cellular automata. One of the analysis tools allows for reconstructing the noise intensity in a data set and is an appropriate method for detecting a variety of noise-induced phenomena in spatiotemporal data. The functioning of these methods is illustrated on sample data generated with the forest fire model and with networks of nonlinear oscillators. It is seen that these methods allow the characterization of spatiotemporal stochastic resonance (STSR) in experimental data. Application of these tools to biological spatiotemporal patterns is discussed. For one specific example, the slime mold Dictyostelium discoideum, it is seen, how transitions between different patterns are clearly marked by changes in the spatiotemporal observables.

Climate-induced changes in lake ecosystem structure inferred from coupled neo- and paleoecological approaches

USGS Publications Warehouse

Saros, Jasmine E.; Stone, Jeffery R.; Pederson, Gregory T.; Slemmons, Krista; Spanbauer, Trisha; Schliep, Anna; Cahl, Douglas; Williamson, Craig E.; Engstrom, Daniel R.

2015-01-01

Over the 20th century, surface water temperatures have increased in many lake ecosystems around the world, but long-term trends in the vertical thermal structure of lakes remain unclear, despite the strong control that thermal stratification exerts on the biological response of lakes to climate change. Here we used both neo- and paleoecological approaches to develop a fossil-based inference model for lake mixing depths and thereby refine understanding of lake thermal structure change. We focused on three common planktonic diatom taxa, the distributions of which previous research suggests might be affected by mixing depth. Comparative lake surveys and growth rate experiments revealed that these species respond to lake thermal structure when nitrogen is sufficient, with species optima ranging from shallower to deeper mixing depths. The diatom-based mixing depth model was applied to sedimentary diatom profiles extending back to 1750 AD in two lakes with moderate nitrate concentrations but differing climate settings. Thermal reconstructions were consistent with expected changes, with shallower mixing depths inferred for an alpine lake where treeline has advanced, and deeper mixing depths inferred for a boreal lake where wind strength has increased. The inference model developed here provides a new tool to expand and refine understanding of climate-induced changes in lake ecosystems.

Narrative change, narrative stability, and structural constraint: The case of prisoner reentry narratives

PubMed Central

Harding, David J.; Dobson, Cheyney C.; Wyse, Jessica J. B.; Morenoff, Jeffrey D.

2016-01-01

Cultural sociologists and other social scientists have increasingly used the concept of narrative as a theoretical tool to understand how individuals make sense of the links between their past, present, and future, how individuals construct social identities from cultural building blocks, and how culture shapes social action and individual behavior. Despite its richness, we contend that the narratives literature has yet to grapple with narrative change and stability when structural constraints or barriers challenge personal narratives and narrative identities. Particularly for marginalized groups, the potential incompatibility of personal narratives with daily experiences raises questions about the capacity of narratives to influence behavior and decision-making. In this study we draw on prospective longitudinal data on the reentry narratives and narrative identities of former prisoners to understand how narratives do and not change when confronted with contradictory experiences and structural constraints. We identify and describe the processes generating narrative change and stability among our subjects. These findings inform a framework for studying narrative change and stability based on four factors: the content of the narrative itself, the structural circumstances experienced by the individual, the institutional contexts in which the individual is embedded, and the social networks in which the individual is embedded. PMID:28316785

Distal Sensorimotor Neuropathy: Improvements in Diagnosis

PubMed Central

Vas, Prashanth R. J.; Sharma, Sanjeev; Rayman, Gerry

2015-01-01

Neurological complications of diabetes are common, affecting up to 50% of people with diabetes. In these patients, diabetic sensorimotor neuropathy (DSPN) is by far the most frequent complication. Detecting DSPN has traditionally been a clinical exercise that is based on signs and symptoms. However, the appearance of morphometric and neurophysiological techniques along with composite scoring systems and new screening tools has induced a paradigm change in the detection and stratification of DSPN and our understanding of its natural history and etiopathogenesis. These newer techniques have provided further evidence that changes in small nerve fiber structure and function precede large fiber changes in diabetes. Although useful, the challenge for the use of these new techniques will be their sensitivity and specificity when widely adopted and ultimately, their ability to demonstrate improvement when pathogenic mechanisms are corrected. Concurrently, we have also witnessed an emergence of simpler screening tools or methods that are mainly aimed at quicker detection of large fiber neuropathy in the outpatient setting. In this review, we have focused on techniques and tools that receive particular attention in the current literature, their use in research and potential use in the clinical environment. PMID:26676660

Linking Science and Management in an Interactive Geospatial, Mutli-Criterion, Structured Decision Support Framework: Use Case Studies of the "Future Forests Geo-visualization and Decision Support Tool

NASA Astrophysics Data System (ADS)

Pontius, J.; Duncan, J.

2017-12-01

Land managers are often faced with balancing management activities to accomplish a diversity of management objectives, in systems faced with many stress agents. Advances in ecosystem modeling provide a rich source of information to inform management. Coupled with advances in decision support techniques and computing capabilities, interactive tools are now accessible for a broad audience of stakeholders. Here we present one such tool designed to capture information on how climate change may impact forested ecosystems, and how that impact varies spatially across the landscape. This tool integrates empirical models of current and future forest structure and function in a structured decision framework that allows users to customize weights for multiple management objectives and visualize suitability outcomes across the landscape. Combined with climate projections, the resulting products allow stakeholders to compare the relative success of various management objectives on a pixel by pixel basis and identify locations where management outcomes are most likely to be met. Here we demonstrate this approach with the integration of several of the preliminary models developed to map species distributions, sugar maple health, forest fragmentation risk and hemlock vulnerability to hemlock woolly adelgid under current and future climate scenarios. We compare three use case studies with objective weightings designed to: 1) Identify key parcels for sugarbush conservation and management, 2) Target state lands that may serve as hemlock refugia from hemlock woolly adelgid induced mortality, and 3) Examine how climate change may alter the success of managing for both sugarbush and hemlock across privately owned lands. This tool highlights the value of flexible models that can be easily run with customized weightings in a dynamic, integrated assessment that allows users to hone in on their potentially complex management objectives, and to visualize and prioritize locations across the landscape. It also demonstrates the importance of including climate considerations for long-term management. This merging of scientific knowledge with the diversity of stakeholder needs is an important step towards using science to inform management and policy decisions.

Dynamically variable negative stiffness structures

PubMed Central

Churchill, Christopher B.; Shahan, David W.; Smith, Sloan P.; Keefe, Andrew C.; McKnight, Geoffrey P.

2016-01-01

Variable stiffness structures that enable a wide range of efficient load-bearing and dexterous activity are ubiquitous in mammalian musculoskeletal systems but are rare in engineered systems because of their complexity, power, and cost. We present a new negative stiffness–based load-bearing structure with dynamically tunable stiffness. Negative stiffness, traditionally used to achieve novel response from passive structures, is a powerful tool to achieve dynamic stiffness changes when configured with an active component. Using relatively simple hardware and low-power, low-frequency actuation, we show an assembly capable of fast (<10 ms) and useful (>100×) dynamic stiffness control. This approach mitigates limitations of conventional tunable stiffness structures that exhibit either small (<30%) stiffness change, high friction, poor load/torque transmission at low stiffness, or high power active control at the frequencies of interest. We experimentally demonstrate actively tunable vibration isolation and stiffness tuning independent of supported loads, enhancing applications such as humanoid robotic limbs and lightweight adaptive vibration isolators. PMID:26989771

Assessing the role of learning devices and geovisualisation tools for collective action in natural resource management: Experiences from Vietnam.

PubMed

Castella, Jean-Christophe

2009-02-01

In northern Vietnam uplands the successive policy reforms that accompanied agricultural decollectivisation triggered very rapid changes in land use in the 1990s. From a centralized system of natural resource management, a multitude of individual strategies emerged which contributed to new production interactions among farming households, changes in landscape structures, and conflicting strategies among local stakeholders. Within this context of agrarian transition, learning devices can help local communities to collectively design their own course of action towards sustainable natural resource management. This paper presents a collaborative approach combining a number of participatory methods and geovisualisation tools (e.g., spatially explicit multi-agent models and role-playing games) with the shared goal to analyse and represent the interactions between: (i) decision-making processes by individual farmers based on the resource profiles of their farms; (ii) the institutions which regulate resource access and usage; and (iii) the biophysical and socioeconomic environment. This methodological pathway is illustrated by a case study in Bac Kan Province where it successfully led to a communication platform on natural resource management. In a context of rapid socioeconomic changes, learning devices and geovisualisation tools helped embed the participatory approach within a process of community development. The combination of different tools, each with its own advantages and constraints, proved highly relevant for supporting collective natural resource management.

Multivariate Analysis of Two-Dimensional 1H, 13C Methyl NMR Spectra of Monoclonal Antibody Therapeutics To Facilitate Assessment of Higher Order Structure.

PubMed

Arbogast, Luke W; Delaglio, Frank; Schiel, John E; Marino, John P

2017-11-07

Two-dimensional (2D) 1 H- 13 C methyl NMR provides a powerful tool to probe the higher order structure (HOS) of monoclonal antibodies (mAbs), since spectra can readily be acquired on intact mAbs at natural isotopic abundance, and small changes in chemical environment and structure give rise to observable changes in corresponding spectra, which can be interpreted at atomic resolution. This makes it possible to apply 2D NMR spectral fingerprinting approaches directly to drug products in order to systematically characterize structure and excipient effects. Systematic collections of NMR spectra are often analyzed in terms of the changes in specifically identified peak positions, as well as changes in peak height and line widths. A complementary approach is to apply principal component analysis (PCA) directly to the matrix of spectral data, correlating spectra according to similarities and differences in their overall shapes, rather than according to parameters of individually identified peaks. This is particularly well-suited for spectra of mAbs, where some of the individual peaks might not be well resolved. Here we demonstrate the performance of the PCA method for discriminating structural variation among systematic sets of 2D NMR fingerprint spectra using the NISTmAb and illustrate how spectral variability identified by PCA may be correlated to structure.

Do structural changes (eg, collagen/matrix) explain the response to therapeutic exercises in tendinopathy: a systematic review.

PubMed

Drew, Benjamin T; Smith, Toby O; Littlewood, Chris; Sturrock, Ben

2014-06-01

Previous reviews have highlighted the benefit of loaded therapeutic exercise in the treatment of tendinopathy. Changes in observable structural outcomes have been suggested as a possible explanation for this response to therapeutic exercise. However, the mechanism for the efficacy of therapeutic exercise remains unclear. To systematically review the relationship between the observable structural change and clinical outcomes following therapeutic exercise. An electronic search of AMED, CiNAHL, Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, PEDro and SPORTDiscus was undertaken from their inception to June 2012. Any study design that incorporated observable structural outcomes and clinical outcomes when assessing the effect of therapeutic exercise on participants with tendinopathy. Included studies were appraised for risk of bias using the tool developed by the Cochrane Back Review Group. Due to heterogeneity of studies, a qualitative synthesis was undertaken. Twenty articles describing 625 patients were included. Overall, there is a strong evidence to refute any observable structural change as an explanation for the response to therapeutic exercise when treated by eccentric exercise training. Moderate evidence does exist to support the response of heavy-slow resistance training (HSR). The available literature does not support observable structural change as an explanation for the response of therapeutic exercise except for some support from HSR. Future research should focus on indentifying other explanations including neural, biochemical and myogenic changes. Registered with PROSPERO, registration number CRD42011001638. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Increased variability in ApcMin/+ intestinal tissue can be measured with microultrasound

NASA Astrophysics Data System (ADS)

Fatehullah, A.; Sharma, S.; Newton, I. P.; Langlands, A. J.; Lay, H.; Nelson, S. A.; McMahon, R. K.; McIlvenny, N.; Appleton, P. L.; Cochran, S.; Näthke, I. S.

2016-07-01

Altered tissue structure is a feature of many disease states and is usually measured by microscopic methods, limiting analysis to small areas. Means to rapidly and quantitatively measure the structure and organisation of large tissue areas would represent a major advance not just for research but also in the clinic. Here, changes in tissue organisation that result from heterozygosity in Apc, a precancerous situation, are comprehensively measured using microultrasound and three-dimensional high-resolution microscopy. Despite its normal appearance in conventionally examined cross-sections, both approaches revealed a significant increase in the variability of tissue organisation in Apc heterozygous tissue. These changes preceded the formation of aberrant crypt foci or adenoma. Measuring these premalignant changes using microultrasound provides a potential means to detect microscopically abnormal regions in large tissue samples, independent of visual examination or biopsies. Not only does this provide a powerful tool for studying tissue structure in experimental settings, the ability to detect and monitor tissue changes by microultrasound could be developed into a powerful adjunct to screening endoscopy in the clinic.

Nanoparticle-Based and Bioengineered Probes and Sensors to Detect Physiological and Pathological Biomarkers in Neural Cells

PubMed Central

Maysinger, Dusica; Ji, Jeff; Hutter, Eliza; Cooper, Elis

2015-01-01

Nanotechnology, a rapidly evolving field, provides simple and practical tools to investigate the nervous system in health and disease. Among these tools are nanoparticle-based probes and sensors that detect biochemical and physiological properties of neurons and glia, and generate signals proportionate to physical, chemical, and/or electrical changes in these cells. In this context, quantum dots (QDs), carbon-based structures (C-dots, grapheme, and nanodiamonds) and gold nanoparticles are the most commonly used nanostructures. They can detect and measure enzymatic activities of proteases (metalloproteinases, caspases), ions, metabolites, and other biomolecules under physiological or pathological conditions in neural cells. Here, we provide some examples of nanoparticle-based and genetically engineered probes and sensors that are used to reveal changes in protease activities and calcium ion concentrations. Although significant progress in developing these tools has been made for probing neural cells, several challenges remain. We review many common hurdles in sensor development, while highlighting certain advances. In the end, we propose some future directions and ideas for developing practical tools for neural cell investigations, based on the maxim “Measure what is measurable, and make measurable what is not so” (Galileo Galilei). PMID:26733793

Analysis and control on changeable wheel tool system of hybrid grinding and polishing machine tool for blade finishing

NASA Astrophysics Data System (ADS)

He, Qiuwei; Lv, Xingming; Wang, Xin; Qu, Xingtian; Zhao, Ji

2017-01-01

Blade is the key component in the energy power equipment of turbine, aircraft engines and so on. Researches on the process and equipment for blade finishing become one of important and difficult point. To control precisely tool system of developed hybrid grinding and polishing machine tool for blade finishing, the tool system with changeable wheel for belt polishing is analyzed in this paper. Firstly, the belt length and wrap angle of each wheel in different position of tension wheel swing angle in the process of changing wheel is analyzed. The reasonable belt length is calculated by using MATLAB, and relationships between wrap angle of each wheel and cylinder expansion amount of contact wheel are obtained. Then, the control system for changeable wheel tool structure is developed. Lastly, the surface roughness of blade finishing is verified by experiments. Theoretical analysis and experimental results show that reasonable belt length and wheel wrap angle can be obtained by proposed analysis method, the changeable wheel tool system can be controlled precisely, and the surface roughness of blade after grinding meets the design requirements.

Influence of the axial rotation angle on tool mark striations.

PubMed

Garcia, Derrel Louis; Pieterman, René; Baiker, Martin

2017-10-01

A tool's axial rotation influences the geometric properties of a tool mark. The larger the axial rotation angle, the larger the compression of structural details like striations. This complicates comparing tool marks at different axial rotations. Using chisels, tool marks were made from 0° to 75° axial rotation and compared using an automated approach Baiker et al. [10]. In addition, a 3D topographic surface of a chisel was obtained to generate virtual tool marks and to test whether the axial rotation angle of a mark could be predicted. After examination of the tool mark and chisel data-sets it was observed that marks lose information with increasing rotation due to the change in relative distance between geometrical details on the tool and the disappearance of smaller details. The similarity and repeatability were high for comparisons between marks with no difference in axial rotation, but decreasing with increased rotation angle from 0° to 75°. With an increasing difference in the rotation angles, the tool marks had to be corrected to account for the different compression factors between them. For compression up to 7.5%, this was obtained automatically by the tool mark alignment method. For larger compression, manually re-sizing the marks to the uncompressed widths at 0° rotation before the alignment was found suitable for successfully comparing even large differences in axial rotation. The similarity and repeatability were decreasing however, with increasing degree of re-sizing. The quality was assessed by determining the similarity at different detail levels within a tool mark. With an axial rotation up to 75°, tool marks were found to reliably represent structural details down to 100μm. The similarity of structural details below 100μm was dependent on the angle, with the highest similarity at small rotation angles and the lowest similarity at large rotation angles. Filtering to remove the details below 100μm lead to consistently higher similarity between tool marks at all angles and allowed for a comparison of marks up to 75° axial rotation. Finally, generated virtual tool mark profiles with an axial rotation were compared to experimental tool marks. The similarity between virtual and experimental tool marks remained high up to 60° rotation after which it decreased due to the loss in quality in both marks. Predicting the rotation angle is possible under certain conditions up to 45° rotation with an accuracy of 2.667±0.577° rotation. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis and design of nonlinear resonances via singularity theory

NASA Astrophysics Data System (ADS)

Cirillo, G. I.; Habib, G.; Kerschen, G.; Sepulchre, R.

2017-03-01

Bifurcation theory and continuation methods are well-established tools for the analysis of nonlinear mechanical systems subject to periodic forcing. We illustrate the added value and the complementary information provided by singularity theory with one distinguished parameter. While tracking bifurcations reveals the qualitative changes in the behaviour, tracking singularities reveals how structural changes are themselves organised in parameter space. The complementarity of that information is demonstrated in the analysis of detached resonance curves in a two-degree-of-freedom system.

Use of prescribed burning for restoration and maintenance of ecological conditions: Predicting and managing fire injury and tree mortality

Treesearch

Kevin Ryan; E. Rigolot; F. C. Rego; H. Botelho; J. A. Vega; P. M. Fernandes; T. M. Sofronova

2010-01-01

Throughout Earth’s history fire has been a major disturbance factor in many terrestrial ecosystems. Fire is man’s first tool. It was used for a host of cultural purposes to modify stand structure and species composition as well as landscape pattern and process. Changes in climate and land use are leading to changes in vegetation and the frequency and severity of modern...

Tools and Functions of Reconfigurable Colloidal Assembly.

PubMed

Solomon, Michael J

2018-02-19

We review work in reconfigurable colloidal assembly, a field in which rapid, back-and-forth transitions between the equilibrium states of colloidal self-assembly are accomplished by dynamic manipulation of the size, shape, and interaction potential of colloids, as well as the magnitude and direction of the fields applied to them. It is distinguished from the study of colloidal phase transitions by the centrality of thermodynamic variables and colloidal properties that are time switchable; by the applicability of these changes to generate transitions in assembled colloids that may be spatially localized; and by its incorporation of the effects of generalized potentials due to, for example, applied electric and magnetic fields. By drawing upon current progress in the field, we propose a matrix classification of reconfigurable colloidal systems based on the tool used and function performed by reconfiguration. The classification distinguishes between the multiple means by which reconfigurable assembly can be accomplished (i.e., the tools of reconfiguration) and the different kinds of structural transitions that can be achieved by it (i.e., the functions of reconfiguration). In the first case, the tools of reconfiguration can be broadly classed as (i) those that control the colloidal contribution to the system entropy-as through volumetric and/or shape changes of the particles; (ii) those that control the internal energy of the colloids-as through manipulation of colloidal interaction potentials; and (iii) those that control the spatially resolved potential energy that is imposed on the colloids-as through the introduction of field-induced phoretic mechanisms that yield colloidal displacement and accumulation. In the second case, the functions of reconfiguration include reversible: (i) transformation between different phases-including fluid, cluster, gel, and crystal structures; (ii) manipulation of the spacing between colloids in crystals and clusters; and (iii) translation, rotation, or shape-change of finite-size objects self-assembled from colloids. With this classification in hand, we correlate the current limits on the spatiotemporal scales for reconfigurable colloidal assembly and identify a set of future research challenges.

Quantitative Analysis of Nucleic Acid Stability with Ligands Under High Pressure to Design Novel Drugs Targeting G-Quadruplexes.

PubMed

Takahashi, Shuntaro; Sugimoto, Naoki

2017-09-18

Nucleic acids (DNA and RNA) can form various non-canonical structures. Because some serious diseases are caused by the conformational change of G-quadruplex DNA structures, the development of ligands that bind and stabilize G-quadruplex DNA is of interest to the field of nucleic acid chemistry. Volumetric changes (ΔV) in the biomolecular reaction include the structural change of biomolecules and hydration behaviors, which provide information about the tertiary interaction between G-quadruplex DNA and ligands. Thus, it is valuable to investigate ΔV values to understand the mechanism of interaction between non-canonical structures and their ligands. This unit describes methods that can be used to quantitatively analyze the interaction between G-quadruplex DNA and ligands by using high-pressure UV melting. The combination of thermodynamic parameters (ΔG, ΔH, ΔS, and ΔV) is a powerful tool to elucidate the mechanism of ligand binding to G-quadruplex without real structural analysis by NMR and X-ray spectroscopy, and gives useful information to design novel drugs. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

STRUCTURAL AND CONNECTOMIC NEUROIMAGING FOR THE PERSONALIZED STUDY OF LONGITUDINAL ALTERATIONS IN CORTICAL SHAPE, THICKNESS AND CONNECTIVITY AFTER TRAUMATIC BRAIN INJURY

PubMed Central

Irimia, A.; Goh, S.-Y. M.; Torgerson, C. M.; Vespa, P. M.; Van Horn, J. D.

2014-01-01

The integration of longitudinal brain structure analysis with neurointensive care strategies continues to be a substantial difficulty facing the traumatic brain injury (TBI) research community. For patient-tailored case analysis, it remains challenging to establish how lesion profile modulates longitudinal changes in cortical structure and connectivity, as well as how these changes lead to behavioral, cognitive and neural dysfunction. Additionally, despite the clinical potential of morphometric and connectomic studies, few analytic tools are available for their study in TBI. Here we review the state of the art in structural and connectomic neuroimaging for the study of TBI and illustrate a set of recently-developed, patient-tailored approaches for the study of TBI-related brain atrophy and alterations in morphometry as well as inter-regional connectivity. The ability of such techniques to quantify how injury modulates longitudinal changes in cortical shape, structure and circuitry is highlighted. Quantitative approaches such as these can be used to assess and monitor the clinical condition and evolution of TBI victims, and can have substantial translational impact, especially when used in conjunction with measures of neuropsychological function. PMID:24844173

Excitation-Energy Transfer Paths from Tryptophans to Coordinated Copper Ions in Engineered Azurins: a Source of Observables for Monitoring Protein Structural Changes

NASA Astrophysics Data System (ADS)

Di Rocco, Giulia; Bernini, Fabrizio; Borsari, Marco; Martinelli, Ilaria; Bortolotti, Carlo Augusto; Battistuzzi, Gianantonio; Ranieri, Antonio; Caselli, Monica; Sola, Marco; Ponterini, Glauco

2016-09-01

The intrinsic fluorescence of recombinant proteins offers a powerful tool to detect and characterize structural changes induced by chemical or biological stimuli. We show that metal-ion binding to a hexahistidine tail can significantly broaden the range of such structurally sensitive fluorescence observables. Bipositive metal-ions as Cu2+, Ni2+ and Zn2+ bind 6xHis-tag azurin and its 6xHis-tagged R129W and W48A-R129W mutants with good efficiency and, thereby, quench their intrinsic fluorescence. Due to a much more favourable spectral overlap, the 6xHis-tag/Cu2+ complex(es) are the most efficient quenchers of both W48 and W129 emissions. Based on simple Förster-type dependence of energy-transfer efficiency on donor/acceptor distance, we can trace several excitation-energy transfer paths across the protein structure. Unexpected lifetime components in the azurin 6xHis-tag/Cu2+ complex emission decays reveal underneath complexity in the conformational landscape of these systems. The new tryptophan emission quenching paths provide additional signals for detecting and identifying protein structural changes.

Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

PubMed

Otero, Toribio F

2017-01-18

In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (E a ), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. E a , k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

Investigating ion channel conformational changes using voltage clamp fluorometry.

PubMed

Talwar, Sahil; Lynch, Joseph W

2015-11-01

Ion channels are membrane proteins whose functions are governed by conformational changes. The widespread distribution of ion channels, coupled with their involvement in most physiological and pathological processes and their importance as therapeutic targets, renders the elucidation of these conformational mechanisms highly compelling from a drug discovery perspective. Thanks to recent advances in structural biology techniques, we now have high-resolution static molecular structures for members of the major ion channel families. However, major questions remain to be resolved about the conformational states that ion channels adopt during activation, drug modulation and desensitization. Patch-clamp electrophysiology has long been used to define ion channel conformational states based on functional criteria. It achieves this by monitoring conformational changes at the channel gate and cannot detect conformational changes occurring in regions distant from the gate. Voltage clamp fluorometry involves labelling cysteines introduced into domains of interest with environmentally sensitive fluorophores and inferring structural rearrangements from voltage or ligand-induced fluorescence changes. Ion channel currents are monitored simultaneously to verify the conformational status. By defining real time conformational changes in domains distant from the gate, this technique provides unexpected new insights into ion channel structure and function. This review aims to summarise the methodology and highlight recent innovative applications of this powerful technique. This article is part of the Special Issue entitled 'Fluorescent Tools in Neuropharmacology'. Copyright © 2015 Elsevier Ltd. All rights reserved.

GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations

PubMed Central

Bachega, José Fernando R.; Timmers, Luís Fernando S.M.; Assirati, Lucas; Bachega, Leonardo R.; Field, Martin J.; Wymore, Troy

2014-01-01

Hybrid quantum chemical (QC)/molecular mechanical (MM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions, that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use we have developed an open-source graphical plug-in, GTKDynamo, that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations. PMID:24137667

Historical changes in the structure and functioning of the benthic community in the lagoon of Venice

NASA Astrophysics Data System (ADS)

Pranovi, Fabio; Da Ponte, Filippo; Torricelli, Patrizia

2008-03-01

One of the main challenges in environmental management is how to manage the dynamics of natural environments. In this context, having information about historical changes of the structure of the biological communities could represent a useful tool to improve management strategies, contributing to refine the policy objectives, since it gives reference states with which to compare the present. The Venice lagoon represents an interesting case study, since it is a highly dynamic, but sensitive, environment which requires the adoption of prudent management. In its recent history the lagoon ecosystem has been exposed to different kinds of disturbance, from the discharge of pollutants and nutrients, to the invasion of alien species and the exploitation of its biological resources by using highly impacting fishing gears. The analysis of available data about the macro-benthic community, from 1935 to 2004, allows the description of changes of the community structure over almost 70 years, showing a sharp decrease in its diversity. In order to obtain information about its functioning, it is necessary to know how these changes have affected processes at the community and system level. In shallow water ecosystems, as the control is mainly due to the benthic compartment, variations in the structure of the benthic community can induce modifications in processes at different hierarchical levels. The trophic structure analysis has revealed major changes during the period; from a well-assorted structure in 1935, to an herbivore-detritivore dominated one in the 1990s, and finally to a filter feeder dominated structure during the last decade. This has produced variations in the secondary production and it has induced modifications in the type of the ecosystem control. These changes are discussed in the light of the dynamics of the main driving forces.

3D printing in chemical engineering and catalytic technology: structured catalysts, mixers and reactors.

PubMed

Parra-Cabrera, Cesar; Achille, Clement; Kuhn, Simon; Ameloot, Rob

2018-01-02

Computer-aided fabrication technologies combined with simulation and data processing approaches are changing our way of manufacturing and designing functional objects. Also in the field of catalytic technology and chemical engineering the impact of additive manufacturing, also referred to as 3D printing, is steadily increasing thanks to a rapidly decreasing equipment threshold. Although still in an early stage, the rapid and seamless transition between digital data and physical objects enabled by these fabrication tools will benefit both research and manufacture of reactors and structured catalysts. Additive manufacturing closes the gap between theory and experiment, by enabling accurate fabrication of geometries optimized through computational fluid dynamics and the experimental evaluation of their properties. This review highlights the research using 3D printing and computational modeling as digital tools for the design and fabrication of reactors and structured catalysts. The goal of this contribution is to stimulate interactions at the crossroads of chemistry and materials science on the one hand and digital fabrication and computational modeling on the other.

GoPros™ as an underwater photogrammetry tool for citizen science

PubMed Central

David, Peter A.; Dupont, Sally F.; Mathewson, Ciaran P.; O’Neill, Samuel J.; Powell, Nicholas N.; Williamson, Jane E.

2016-01-01

Citizen science can increase the scope of research in the marine environment; however, it suffers from necessitating specialized training and simplified methodologies that reduce research output. This paper presents a simplified, novel survey methodology for citizen scientists, which combines GoPro imagery and structure from motion to construct an ortho-corrected 3D model of habitats for analysis. Results using a coral reef habitat were compared to surveys conducted with traditional snorkelling methods for benthic cover, holothurian counts, and coral health. Results were comparable between the two methods, and structure from motion allows the results to be analysed off-site for any chosen visual analysis. The GoPro method outlined in this study is thus an effective tool for citizen science in the marine environment, especially for comparing changes in coral cover or volume over time. PMID:27168973

GoPros™ as an underwater photogrammetry tool for citizen science.

PubMed

Raoult, Vincent; David, Peter A; Dupont, Sally F; Mathewson, Ciaran P; O'Neill, Samuel J; Powell, Nicholas N; Williamson, Jane E

2016-01-01

Citizen science can increase the scope of research in the marine environment; however, it suffers from necessitating specialized training and simplified methodologies that reduce research output. This paper presents a simplified, novel survey methodology for citizen scientists, which combines GoPro imagery and structure from motion to construct an ortho-corrected 3D model of habitats for analysis. Results using a coral reef habitat were compared to surveys conducted with traditional snorkelling methods for benthic cover, holothurian counts, and coral health. Results were comparable between the two methods, and structure from motion allows the results to be analysed off-site for any chosen visual analysis. The GoPro method outlined in this study is thus an effective tool for citizen science in the marine environment, especially for comparing changes in coral cover or volume over time.

Looking for Broken TAD Boundaries and Changes on DNA Interactions: Clinical Guide to 3D Chromatin Change Analysis in Complex Chromosomal Rearrangements and Chromothripsis.

PubMed

Yauy, Kevin; Gatinois, Vincent; Guignard, Thomas; Sati, Satish; Puechberty, Jacques; Gaillard, Jean Baptiste; Schneider, Anouck; Pellestor, Franck

2018-01-01

Apparition of next-generation sequencing (NGS) was a breakthrough on knowledge of genome structure. Bioinformatic tools are a key point to analyze this huge amount of data from NGS and characterize the three-dimensional organization of chromosomes. This chapter describes usage of different browsers to explore publicly available online data and to search for possible 3D chromatin changes involved during complex chromosomal rearrangements as chromothripsis. Their pathogenic impact on clinical phenotype and gene misexpression can also be evaluated with annotated databases.

Dynamic Response of Composite Structures Underwater

DTIC Science & Technology

2013-09-01

then run and the desired data was viewed in CFD-post of the CFX tool. The ANSYS model illustrates the changing concavity of the beam along its...OF ABSTRACT Unclassified 20. LIMITATION OF ABSTRACT UU NSN 7540-01-280-5500 Standard Form 298 (Rev. 2-89) Prescribed by ANSI Std. 239-18...41 Figure 36. ANSYS Beam Displacement

Negotiating the Conflicts: Reexamining the Structure and Function of Reflection in Science Teacher Learning

ERIC Educational Resources Information Center

Danielowich, Robert

2007-01-01

Many researchers and teacher educators propose that reflection is an important way teachers can think about changing their views and practices. The hierarchical constructs used to describe reflection, however, are often interpreted in ways that promote reflection as a "tool" teachers use to elevate their views and practices toward ideal "end…

Changing Places: A Cross-Language Perspective on Frequency and Family Size in Dutch and Hebrew

ERIC Educational Resources Information Center

Moscoso del Prado Martin, Fermin; Deutsch, Avital; Frost, Ram; Schreuder, Robert; De Jong, Nivja H.; Baayen, R. Harald

2005-01-01

This study uses the morphological family size effect as a tool for exploring the degree of isomorphism in the networks of morphologically related words in the Hebrew and Dutch mental lexicon. Hebrew and Dutch are genetically unrelated, and they structure their morphologically complex words in very different ways. Two visual lexical decision…

Mobile Learning: New Tools Flying in the Face of the Same Old Schooling

ERIC Educational Resources Information Center

Berge, Zane L.

2013-01-01

Currently mobile learning is making headlines in the educational press as a possible path for transforming education, just like it has significantly changed communication in business and society generally. Technology in American schools has a decades-long history of failure compared with its use outside schooling. Until the structure and political…

Effects of Metric Change on Workers’ Tools and Training.

DTIC Science & Technology

1981-07-01

understanding of the metric system, and particularly a lack of fluency in converting customary measurements to metric measuremerts, may increase the...assembly, installing, and repairing occupations 84 Painting, plastering, waterproofing, cementing , and related occupations 85 Excavating, grading... cementing , and related occupations 85 Excavating, grading, paving, and related occupations 86 Construction occupations, n.e.c. 89 Structural work

New Technologies as a Tool for Changing Academic Communities in the Global Context

ERIC Educational Resources Information Center

Jankowska, Dorota; Tanas, Maciej

2016-01-01

It has been defined that knowledge society emerges at the end of the twentieth century as the socio-economic structure characteristic for developed societies in which unlike in industrial societies, the dominant sector of economy is services and the largest social group is the "men of knowledge". It has been indicated that the…

Building "Consciousness and Legacies": Integrating Community, Critical, and Classical Knowledge Bases in a Precalculus Class

ERIC Educational Resources Information Center

Gutierrez, Rodrigo Jorge

2013-01-01

Grounded in Freire's (1970) notion that the purpose of education in an unjust society is to bring about equality and justice, Critical Mathematics (CM) scholars consider mathematics to be a tool to understand, critique, and change the world by deconstructing power structures that marginalize certain groups. In particular, Gutstein's (2006)…

The G-factor as a tool to learn more about bone structure and function.

PubMed

Zerath, E

1999-07-01

In normal life on earth, the locomotor system is exposed to two types of stimulation: gravity (passive stimulation) and motion (active stimulation). Both permanently combine, and the interactions between locomotion and gravity induce an overall recruitment which is repeated daily and maintains the bone tissue structure within the range of constraints to which it is adapted. This range is one of the basic hypotheses underlying the mechanical concepts of bone structure control, and it has been considered as logical to assume that weightlessness of spaceflight should produce bone loss since astronauts are outside of the terrestrial gravitational field of forces, no longer relying on muscular work to change positions or move. But, thirty years after the first changes in phospho-calcium metabolism were observed in astronauts after spaceflight, current knowledge does not provide a full understanding of this pathogeny, and prove the G-factor is now considered as an essential component of the experimental tools available to study bone physiology. The study of the physiology of bone tissue usually consists in the investigation of its two fundamental roles, i.e. reservoir of inorganic elements (calcium, phosphorus, magnesium) and mechanical support for soft tissues. Together with the combined action of muscles, tendons, and ligaments, this support permits motion and locomotion. These two functions rely on a sophisticated bone tissue architecture, and on the adaptability of this structure, with modeling and remodeling processes, themselves associated with the coupled activity of specialized bone cell populations.

Implementation strategies to promote community-engaged efforts to counter tobacco marketing at the point of sale.

PubMed

Leeman, Jennifer; Myers, Allison; Grant, Jennifer C; Wangen, Mary; Queen, Tara L

2017-09-01

The US tobacco industry spends $8.2 billion annually on marketing at the point of sale (POS), a practice known to increase tobacco use. Evidence-based policy interventions (EBPIs) are available to reduce exposure to POS marketing, and nationwide, states are funding community-based tobacco control partnerships to promote local enactment of these EBPIs. Little is known, however, about what implementation strategies best support community partnerships' success enacting EBPI. Guided by Kingdon's theory of policy change, Counter Tools provides tools, training, and other implementation strategies to support community partnerships' performance of five core policy change processes: document local problem, formulate policy solutions, engage partners, raise awareness of problems and solutions, and persuade decision makers to enact new policy. We assessed Counter Tools' impact at 1 year on (1) partnership coordinators' self-efficacy, (2) partnerships' performance of core policy change processes, (3) community progress toward EBPI enactment, and (4) salient contextual factors. Counter Tools provided implementation strategies to 30 partnerships. Data on self-efficacy were collected using a pre-post survey. Structured interviews assessed performance of core policy change processes. Data also were collected on progress toward EBPI enactment and contextual factors. Analysis included descriptive and bivariate statistics and content analysis. Following 1-year exposure to implementation strategies, coordinators' self-efficacy increased significantly. Partnerships completed the greatest proportion of activities within the "engage partners" and "document local problem" core processes. Communities made only limited progress toward policy enactment. Findings can inform delivery of implementation strategies and tests of their effects on community-level efforts to enact EBPIs.

Protein conformation determines the sensibility to high pressure treatment of infectious scrapie prions.

PubMed

Heindl, Philipp; García, Avelina Fernández; Butz, Peter; Pfaff, Eberhard; Tauscher, Bernhard

2006-03-01

Application of high pressure can be used for gentle pasteurizing of food, minimizing undesirable alterations such as vitamin losses and changes in taste and color. In addition, pressure has become a useful tool for investigating structural changes in proteins. Treatments of proteins with high pressure can reveal conformations that are not obtainable by other physical variables like temperature, since pressure favors structural transitions accompanied with smaller volumes. Here, we discuss both the potential use of high pressure to inactivate infectious TSE material and the application of this thermodynamic parameter for the investigation of prion folding. This review summarizes our findings on the effects of pressure on the structure of native infectious scrapie prions in hamster brain homogenates and on the structure of infectious prion rods isolated from diseased hamsters brains. Native prions were found to be pressure sensitive, whereas isolated prions revealed an extreme pressure-resistant structure. The discussion will be focused on the different pressure behavior of these prion isoforms, which points out differences in the protein structure that have not been taken into consideration before.

Structure of poly(ethylene glycol)-modified horseradish peroxidase in organic solvents: infrared amide I spectral changes upon protein dehydration are largely caused by protein structural changes and not by water removal per se.

PubMed Central

Al-Azzam, Wasfi; Pastrana, Emil A; Ferrer, Yancy; Huang, Qing; Schweitzer-Stenner, Reinhard; Griebenow, Kai

2002-01-01

Fourier transform infrared (FTIR) spectroscopy has emerged as a powerful tool to guide the development of stable lyophilized protein formulations by providing information on the structure of proteins in amorphous solids. The underlying assumption is that IR spectral changes in the amide I and III region upon protein dehydration are caused by protein structural changes. However, it has been claimed that amide I IR spectral changes could be the result of water removal per se. Here, we investigated whether such claims hold true. The structure of horseradish peroxidase (HRP) and poly(ethylene glycol)-modified HRP (HRP-PEG) has been investigated under various conditions (in aqueous solution, the amorphous dehydrated state, and dissolved/suspended in toluene and benzene) by UV-visible (UV-Vis), FTIR, and resonance Raman spectroscopy. The resonance Raman and UV-Vis spectra of dehydrated HRP-PEG dissolved in neat toluene or benzene were very similar to that of HRP in aqueous buffer, and thus the heme environment (heme iron spin, coordination, and redox state) was essentially the same under both conditions. Therefore, the three-dimensional structure of HRP-PEG dissolved in benzene and toluene was similar to that in aqueous solution. The amide I IR spectra of HRP-PEG in aqueous buffer and of dehydrated HRP-PEG dissolved in neat benzene and toluene were also very similar, and the secondary structure compositions (percentages of alpha-helices and beta-sheets) were within the standard error the same. These results are irreconcilable with recent claims that water removal per se could cause substantial amide I IR spectral changes (M. van de Weert, P.I. Haris, W.E. Hennink, and D.J. Crommelin. 2001. Anal. Biochem. 297:160-169). On the contrary, amide I IR spectral changes upon protein dehydration are caused by perturbations in the secondary structure. PMID:12496131

Moodle 2.0: Shifting from a Learning Toolkit to a Open Learning Platform

NASA Astrophysics Data System (ADS)

Alier, Marc; Casañ, María José; Piguillem, Jordi

Learning Management Systems (LMS) have reached a plateau of maturity in features, application to teaching practices and wide adoption by learning institutions. But the Web 2.0 carries new kinds of tools, services and ways of using the web; personally and socially. Some educators and learners have started to advocate for a new approach to frame one's learning sources, from the LMS course space towards Personal Learning Environments (PLE). But PLE's are characterized by its absence of structure, just what is provided by open standards and mashup techniques. Based on 5 years of participative observation research, this article explains the changes in architecture performed on the second version of Moodle, why did these changes happen and what should be the next steps so Moodle can shift from being a learning tool to a true open learning platform.

DataRocket: Interactive Visualisation of Data Structures

NASA Astrophysics Data System (ADS)

Parkes, Steve; Ramsay, Craig

2010-08-01

CodeRocket is a software engineering tool that provides cognitive support to the software engineer for reasoning about a method or procedure and for documenting the resulting code [1]. DataRocket is a software engineering tool designed to support visualisation and reasoning about program data structures. DataRocket is part of the CodeRocket family of software tools developed by Rapid Quality Systems [2] a spin-out company from the Space Technology Centre at the University of Dundee. CodeRocket and DataRocket integrate seamlessly with existing architectural design and coding tools and provide extensive documentation with little or no effort on behalf of the software engineer. Comprehensive, abstract, detailed design documentation is available early on in a project so that it can be used for design reviews with project managers and non expert stakeholders. Code and documentation remain fully synchronised even when changes are implemented in the code without reference to the existing documentation. At the end of a project the press of a button suffices to produce the detailed design document. Existing legacy code can be easily imported into CodeRocket and DataRocket to reverse engineer detailed design documentation making legacy code more manageable and adding substantially to its value. This paper introduces CodeRocket. It then explains the rationale for DataRocket and describes the key features of this new tool. Finally the major benefits of DataRocket for different stakeholders are considered.

An Engineering Tool for the Prediction of Internal Dielectric Charging

NASA Astrophysics Data System (ADS)

Rodgers, D. J.; Ryden, K. A.; Wrenn, G. L.; Latham, P. M.; Sorensen, J.; Levy, L.

1998-11-01

A practical internal charging tool has been developed. It provides an easy-to-use means for satellite engineers to predict whether on-board dielectrics are vulnerable to electrostatic discharge in the outer radiation belt. The tool is designed to simulate irradiation of single-dielectric planar or cylindrical structures with or without shielding. Analytical equations are used to describe current deposition in the dielectric. This is fast and gives charging currents to sufficient accuracy given the uncertainties in other aspects of the problem - particularly material characteristics. Time-dependent internal electric fields are calculated, taking into account the effect on conductivity of electric field, dose rate and temperature. A worst-case model of electron fluxes in the outer belt has been created specifically for the internal charging problem and is built into the code. For output, the tool gives a YES or NO decision on the susceptibility of the structure to internal electrostatic breakdown and if necessary, calculates the required changes to bring the system below the breakdown threshold. A complementary programme of laboratory irradiations has been carried out to validate the tool. The results for Epoxy-fibreglass samples show that the code models electric field realistically for a wide variety of shields, dielectric thicknesses and electron spectra. Results for Teflon samples indicate that some further experimentation is required and the radiation-induced conductivity aspects of the code have not been validated.

Classification of processes involved in sharing individual participant data from clinical trials.

PubMed

Ohmann, Christian; Canham, Steve; Banzi, Rita; Kuchinke, Wolfgang; Battaglia, Serena

2018-01-01

Background: In recent years, a cultural change in the handling of data from research has resulted in the strong promotion of a culture of openness and increased sharing of data. In the area of clinical trials, sharing of individual participant data involves a complex set of processes and the interaction of many actors and actions. Individual services/tools to support data sharing are available, but what is missing is a detailed, structured and comprehensive list of processes/subprocesses involved and tools/services needed. Methods : Principles and recommendations from a published data sharing consensus document are analysed in detail by a small expert group. Processes/subprocesses involved in data sharing are identified and linked to actors and possible services/tools. Definitions are adapted from the business process model and notation (BPMN) and applied in the analysis. Results: A detailed and comprehensive list of individual processes/subprocesses involved in data sharing, structured according to 9 main processes, is provided. Possible tools/services to support these processes/subprocesses are identified and grouped according to major type of support. Conclusions: The list of individual processes/subprocesses and tools/services identified is a first step towards development of a generic framework or architecture for sharing of data from clinical trials. Such a framework is strongly needed to give an overview of how various actors, research processes and services could form an interoperable system for data sharing.

Classification of processes involved in sharing individual participant data from clinical trials

PubMed Central

Ohmann, Christian; Canham, Steve; Banzi, Rita; Kuchinke, Wolfgang; Battaglia, Serena

2018-01-01

Background: In recent years, a cultural change in the handling of data from research has resulted in the strong promotion of a culture of openness and increased sharing of data. In the area of clinical trials, sharing of individual participant data involves a complex set of processes and the interaction of many actors and actions. Individual services/tools to support data sharing are available, but what is missing is a detailed, structured and comprehensive list of processes/subprocesses involved and tools/services needed. Methods: Principles and recommendations from a published data sharing consensus document are analysed in detail by a small expert group. Processes/subprocesses involved in data sharing are identified and linked to actors and possible services/tools. Definitions are adapted from the business process model and notation (BPMN) and applied in the analysis. Results: A detailed and comprehensive list of individual processes/subprocesses involved in data sharing, structured according to 9 main processes, is provided. Possible tools/services to support these processes/subprocesses are identified and grouped according to major type of support. Conclusions: The list of individual processes/subprocesses and tools/services identified is a first step towards development of a generic framework or architecture for sharing of data from clinical trials. Such a framework is strongly needed to give an overview of how various actors, research processes and services could form an interoperable system for data sharing. PMID:29623192

Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing.

PubMed

Waryah, Charlene Babra; Moses, Colette; Arooj, Mahira; Blancafort, Pilar

2018-01-01

The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications. Three different molecular platforms for epigenetic editing have been developed: zinc finger proteins (ZFs), transcription activator-like effectors (TALEs), and the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins. These platforms serve as custom DNA-binding domains (DBDs), which are fused to epigenetic modifying domains to manipulate epigenetic marks at specific sites in the genome. The addition and/or removal of epigenetic modifications reconfigures local chromatin structure, with the potential to provoke long-lasting changes in gene transcription. Here we summarize the molecular structure and mechanism of action of ZF, TALE, and CRISPR platforms and describe their applications for the locus-specific manipulation of the epigenome. The advantages and disadvantages of each platform will be discussed with regard to genomic specificity, potency in regulating gene expression, and reprogramming cell phenotypes, as well as ease of design, construction, and delivery. Finally, we outline potential applications for these tools in molecular biology and biomedicine and identify possible barriers to their future clinical implementation.

Classification and assessment tools for structural motif discovery algorithms.

PubMed

Badr, Ghada; Al-Turaiki, Isra; Mathkour, Hassan

2013-01-01

Motif discovery is the problem of finding recurring patterns in biological data. Patterns can be sequential, mainly when discovered in DNA sequences. They can also be structural (e.g. when discovering RNA motifs). Finding common structural patterns helps to gain a better understanding of the mechanism of action (e.g. post-transcriptional regulation). Unlike DNA motifs, which are sequentially conserved, RNA motifs exhibit conservation in structure, which may be common even if the sequences are different. Over the past few years, hundreds of algorithms have been developed to solve the sequential motif discovery problem, while less work has been done for the structural case. In this paper, we survey, classify, and compare different algorithms that solve the structural motif discovery problem, where the underlying sequences may be different. We highlight their strengths and weaknesses. We start by proposing a benchmark dataset and a measurement tool that can be used to evaluate different motif discovery approaches. Then, we proceed by proposing our experimental setup. Finally, results are obtained using the proposed benchmark to compare available tools. To the best of our knowledge, this is the first attempt to compare tools solely designed for structural motif discovery. Results show that the accuracy of discovered motifs is relatively low. The results also suggest a complementary behavior among tools where some tools perform well on simple structures, while other tools are better for complex structures. We have classified and evaluated the performance of available structural motif discovery tools. In addition, we have proposed a benchmark dataset with tools that can be used to evaluate newly developed tools.

Giant Pressure-Induced Enhancement of Seebeck Coefficient and Thermoelectric Efficiency in SnTe

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

Baker, Jason; Kumar, Ravhi; Park, Changyong

The thermoelectric properties of polycrystalline SnTe have been measured up to 4.5 GPa at 330 K. SnTe shows an enormous enhancement in Seebeck coefficient, greater than 200 % after 3 GPa, which correlates to a known pressure-induced structural phase transition that is observed through simultaneous in situ X-ray diffraction measurement. We also measured electrical resistance and relative changes to the thermal conductivity, enabling the determination of relative changes in the dimensionless figure of merit (ZT), which increases dramatically after 3 GPa, reaching 350 % of the lowest pressure ZT value. Our results demonstrate a fundamental relationship between structure and thermoelectricmore » behaviours and suggest that pressure is an effective tool to control them.« less

Giant Pressure-Induced Enhancement of Seebeck Coefficient and Thermoelectric Efficiency in SnTe

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

Baker, Jason; Kumar, Ravhi; Park, Changyong

The thermoelectric properties of polycrystalline SnTe have been measured up to 4.5 GPa at 330 K. SnTe shows an enormous enhancement in Seebeck coefficient, greater than 200 % after 3 GPa, which correlates to a known pressure-induced structural phase transition that is observed through simultaneous in situ X-ray diffraction measurement. Electrical resistance and relative changes to the thermal conductivity were also measured, enabling the determination of relative changes in the dimensionless figure of merit (ZT), which increases dramatically after 3 GPa, reaching 350 % of the lowest pressure ZT value. The results demonstrate a fundamental relationship between structure and thermoelectricmore » behaviours and suggest that pressure is an effective tool to control them.« less

Giant Pressure-Induced Enhancement of Seebeck Coefficient and Thermoelectric Efficiency in SnTe

DOE PAGES

Baker, Jason; Kumar, Ravhi; Park, Changyong; ...

2017-10-30

The thermoelectric properties of polycrystalline SnTe have been measured up to 4.5 GPa at 330 K. SnTe shows an enormous enhancement in Seebeck coefficient, greater than 200 % after 3 GPa, which correlates to a known pressure-induced structural phase transition that is observed through simultaneous in situ X-ray diffraction measurement. We also measured electrical resistance and relative changes to the thermal conductivity, enabling the determination of relative changes in the dimensionless figure of merit (ZT), which increases dramatically after 3 GPa, reaching 350 % of the lowest pressure ZT value. Our results demonstrate a fundamental relationship between structure and thermoelectricmore » behaviours and suggest that pressure is an effective tool to control them.« less

Toward the application of ecological concepts in EU coastal water management.

PubMed

de Jonge, Victor N

2007-01-01

The EU Water Framework Directive demands the protection of the functioning and the structure of our aquatic ecosystems. The defined means to realize this goal are: (1) optimization of the habitat providing conditions and (2) optimizing the water quality. The effects of the measures on the structure and functioning of the aquatic ecosystems then has to be assessed and judged. The available tool to do this is 'monitoring'. The present monitoring activities in The Netherlands cover target monitoring and trend monitoring. This is insufficient to meet the requirements of the EU. It is, given the EU demands, the ongoing budget reductions in The Netherlands and an increasing flow of unused new ecological concepts and theories (e.g. new theoretical insights related to resource competition theory, intermediate disturbance hypothesis and tools to judge the system quality like ecological network analysis) suggested to reconsider the present monitoring tasks among governmental services (final responsibility for the program and logistic support) and the academia (data analyses, data interpretation and development of concepts suitable for ecosystem modelling and tools to judge the quality of our ecosystems). This will lead to intensified co-operation between both arena's and consequently increased exchange of knowledge and ideas. Suggestions are done to extend the Dutch monitoring by surveillance monitoring and to change the focus from 'station oriented' to 'area oriented' without changing the operational aspects and its costs. The extended data sets will allow proper calibration and validation of developed dynamic ecosystem models which is not possible now. The described 'cost-effective' change in the environmental monitoring will also let biological and ecological theories play the pivotal role they should play in future integrated environmental management.

Climate Impact and GIS Education Using Realistic Applications of Data.gov Thematic Datasets in a Structured Lesson-Based Workbook

NASA Astrophysics Data System (ADS)

Amirazodi, S.; Griffin, R.; Bugbee, K.; Ramachandran, R.; Weigel, A. M.

2016-12-01

This project created a workbook which teaches Earth Science education undergraduate and graduate students through guided in-class activities and take-home assignments organized around climate topics which use GIS to teach key geospatial analysis techniques and cartography skills. The workbook is structured to the White House's Data.gov climate change themes, which include Coastal Flooding, Ecosystem Vulnerability, Energy Infrastructure, Arctic, Food Resilience, Human Health, Transportation, Tribal Nations, Water. Each theme provides access to framing questions, associated data, interactive tools, and further reading (e.g. the US Climate Resilience Toolkit and National Climate Assessment). Lessons make use of the respective theme's available resources. The structured thematic approach is designed to encourage independent exploration. The goal is to teach climate concepts and concerns, GIS techniques and approaches, and effective cartographic representation and communication of results; and foster a greater awareness of publically available resources and datasets. To reach more audiences more effectively, a two level approach was used. Level 1 serves as an introductory study and relies on only freely available interactive tools to reach audiences with fewer resources and less familiarity. Level 2 presents a more advanced case study, and focuses on supporting common commercially available tool use and real-world analysis techniques.

An operational structured decision making framework for ...

EPA Pesticide Factsheets

Pressure to develop an operational framework for decision makers to employ the concepts of ecosystem goods and services for assessing changes to human well-being has been increasing since these concepts gained widespread notoriety after the Millennium Ecosystem Assessment Report. Many conceptual frameworks have been proposed, but most do not propose methodologies and tools to make this approach to decision making implementable. Building on common components of existing conceptual frameworks for ecosystem services and human well-being assessment we apply a structured decision making approach to develop a standardized operational framework and suggest tools and methods for completing each step. The structured decision making approach consists of six steps: 1) Clarify the Decision Context 2) Define Objectives and Evaluation Criteria 3) Develop Alternatives 4) Estimate Consequences 5) Evaluate Trade-Offs and Select and 6) Implement and Monitor. These six steps include the following activities, and suggested tools, when applied to ecosystem goods and services and human well-being conceptual frameworks: 1) Characterization of decision specific human beneficiaries using the Final Ecosystem Goods and Services (FEGS) approach and Classification System (FEGS-CS) 2) Determine beneficiaries’ relative priorities for human well-being domains in the Human Well-Being Index (HWBI) through stakeholder engagement and identify beneficiary-relevant metrics of FEGS using the Nat

Climate Impact and GIS Education Using Realistic Applications of Data.gov Thematic Datasets in a Structured Lesson-Based Workbook

NASA Technical Reports Server (NTRS)

Amirazodi, Sara; Griffin, Robert; Bugbee, Kaylin; Ramachandran, Rahul; Weigel, Amanda

2016-01-01

This project created a workbook which teaches Earth Science to undergraduate and graduate students through guided in-class activities and take-home assignments organized around climate topics which use GIS to teach key geospatial analysis techniques and cartography skills. The workbook is structured to the White House's Data.gov climate change themes, which include Coastal Flooding, Ecosystem Vulnerability, Energy Infrastructure, Arctic, Food Resilience, Human Health, Transportation, Tribal Nations, and Water. Each theme provides access to framing questions, associated data, interactive tools, and further reading (e.g. The US Climate Resilience Toolkit and National Climate Assessment). Lessons make use of the respective theme's available resources. The structured thematic approach is designed to encourage independent exploration. The goal is to teach climate concepts and concerns, GIS techniques and approaches, and effective cartographic representation and communication results; and foster a greater awareness of publicly available resources and datasets. To reach more audiences more effectively, a two level approach was used. Level 1 serves as an introductory study and relies on only freely available interactive tools to reach audiences with fewer resources and less familiarity. Level 2 presents a more advanced case study, and focuses on supporting common commercially available tool use and real-world analysis techniques.

A Probabilistic Approach to Model Update

NASA Technical Reports Server (NTRS)

Horta, Lucas G.; Reaves, Mercedes C.; Voracek, David F.

2001-01-01

Finite element models are often developed for load validation, structural certification, response predictions, and to study alternate design concepts. In rare occasions, models developed with a nominal set of parameters agree with experimental data without the need to update parameter values. Today, model updating is generally heuristic and often performed by a skilled analyst with in-depth understanding of the model assumptions. Parameter uncertainties play a key role in understanding the model update problem and therefore probabilistic analysis tools, developed for reliability and risk analysis, may be used to incorporate uncertainty in the analysis. In this work, probability analysis (PA) tools are used to aid the parameter update task using experimental data and some basic knowledge of potential error sources. Discussed here is the first application of PA tools to update parameters of a finite element model for a composite wing structure. Static deflection data at six locations are used to update five parameters. It is shown that while prediction of individual response values may not be matched identically, the system response is significantly improved with moderate changes in parameter values.

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

Suresh, Niraj; Stephens, Sean A.; Adams, Lexor

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to climate change and forest management. Quantitative size information on roots in their native environment is invaluable for studying root growth and environmental processes involving the plant. X ray computed tomography (XCT) has been demonstrated to be an effective tool for in situ root scanning and analysis. Our group at the Environmental Molecular Sciences Laboratory (EMSL) has developed an XCT-based tool to image and quantitatively analyze plant root structures in their native soil environment. XCT data collected on amore » Prairie dropseed (Sporobolus heterolepis) specimen was used to visualize its root structure. A combination of open-source software RooTrak and DDV were employed to segment the root from the soil, and calculate its isosurface, respectively. Our own computer script named 3DRoot-SV was developed and used to calculate root volume and surface area from a triangular mesh. The process utilizing a unique combination of tools, from imaging to quantitative root analysis, including the 3DRoot-SV computer script, is described.« less

When structure affects function--the need for partial volume effect correction in functional and resting state magnetic resonance imaging studies.

PubMed

Dukart, Juergen; Bertolino, Alessandro

2014-01-01

Both functional and also more recently resting state magnetic resonance imaging have become established tools to investigate functional brain networks. Most studies use these tools to compare different populations without controlling for potential differences in underlying brain structure which might affect the functional measurements of interest. Here, we adapt a simulation approach combined with evaluation of real resting state magnetic resonance imaging data to investigate the potential impact of partial volume effects on established functional and resting state magnetic resonance imaging analyses. We demonstrate that differences in the underlying structure lead to a significant increase in detected functional differences in both types of analyses. Largest increases in functional differences are observed for highest signal-to-noise ratios and when signal with the lowest amount of partial volume effects is compared to any other partial volume effect constellation. In real data, structural information explains about 25% of within-subject variance observed in degree centrality--an established resting state connectivity measurement. Controlling this measurement for structural information can substantially alter correlational maps obtained in group analyses. Our results question current approaches of evaluating these measurements in diseased population with known structural changes without controlling for potential differences in these measurements.

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales.

PubMed

Rueckl, Martin; Lenzi, Stephen C; Moreno-Velasquez, Laura; Parthier, Daniel; Schmitz, Dietmar; Ruediger, Sten; Johenning, Friedrich W

2017-01-01

The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca 2+ -imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca 2+ imaging datasets, particularly when these have been acquired at different spatial scales.

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales

PubMed Central

Rueckl, Martin; Lenzi, Stephen C.; Moreno-Velasquez, Laura; Parthier, Daniel; Schmitz, Dietmar; Ruediger, Sten; Johenning, Friedrich W.

2017-01-01

The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca2+-imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca2+ imaging datasets, particularly when these have been acquired at different spatial scales. PMID:28706482

Multi-model approach to assess the impact of climate change on runoff

NASA Astrophysics Data System (ADS)

Dams, J.; Nossent, J.; Senbeta, T. B.; Willems, P.; Batelaan, O.

2015-10-01

The assessment of climate change impacts on hydrology is subject to uncertainties related to the climate change scenarios, stochastic uncertainties of the hydrological model and structural uncertainties of the hydrological model. This paper focuses on the contribution of structural uncertainty of hydrological models to the overall uncertainty of the climate change impact assessment. To quantify the structural uncertainty of hydrological models, four physically based hydrological models (SWAT, PRMS and a semi- and fully distributed version of the WetSpa model) are set up for a catchment in Belgium. Each model is calibrated using four different objective functions. Three climate change scenarios with a high, mean and low hydrological impact are statistically perturbed from a large ensemble of climate change scenarios and are used to force the hydrological models. This methodology allows assessing and comparing the uncertainty introduced by the climate change scenarios with the uncertainty introduced by the hydrological model structure. Results show that the hydrological model structure introduces a large uncertainty on both the average monthly discharge and the extreme peak and low flow predictions under the climate change scenarios. For the low impact climate change scenario, the uncertainty range of the mean monthly runoff is comparable to the range of these runoff values in the reference period. However, for the mean and high impact scenarios, this range is significantly larger. The uncertainty introduced by the climate change scenarios is larger than the uncertainty due to the hydrological model structure for the low and mean hydrological impact scenarios, but the reverse is true for the high impact climate change scenario. The mean and high impact scenarios project increasing peak discharges, while the low impact scenario projects increasing peak discharges only for peak events with return periods larger than 1.6 years. All models suggest for all scenarios a decrease of the lowest flows, except for the SWAT model with the mean hydrological impact climate change scenario. The results of this study indicate that besides the uncertainty introduced by the climate change scenarios also the hydrological model structure uncertainty should be taken into account in the assessment of climate change impacts on hydrology. To make it more straightforward and transparent to include model structural uncertainty in hydrological impact studies, there is a need for hydrological modelling tools that allow flexible structures and methods to validate model structures in their ability to assess impacts under unobserved future climatic conditions.

Multidimensional Ultrasound Imaging of the Wrist: Changes of Shape and Displacement of the Median Nerve and Tendons in Carpal Tunnel Syndrome

PubMed Central

Filius, Anika; Scheltens, Marjan; Bosch, Hans G.; van Doorn, Pieter A.; Stam, Henk J.; Hovius, Steven E.R.; Amadio, Peter C.; Selles, Ruud W.

2015-01-01

Dynamics of structures within the carpal tunnel may alter in carpal tunnel syndrome (CTS) due to fibrotic changes and increased carpal tunnel pressure. Ultrasound can visualize these potential changes, making ultrasound potentially an accurate diagnostic tool. To study this, we imaged the carpal tunnel of 113 patients and 42 controls. CTS severity was classified according to validated clinical and nerve conduction study (NCS) classifications. Transversal and longitudinal displacement and shape (changes) were calculated for the median nerve, tendons and surrounding tissue. To predict diagnostic value binary logistic regression modeling was applied. Reduced longitudinal nerve displacement (p≤0.019), increased nerve cross-sectional area (p≤0.006) and perimeter (p≤0.007), and a trend of relatively changed tendon displacements were seen in patients. Changes were more convincing when CTS was classified as more severe. Binary logistic modeling to diagnose CTS using ultrasound showed a sensitivity of 70-71% and specificity of 80-84%. In conclusion, CTS patients have altered dynamics of structures within the carpal tunnel. PMID:25865180

Lake Michigan offshore ecosystem structure and food web changes from 1987 to 2008

USGS Publications Warehouse

Rogers, Mark W.; Bunnell, David B.; Madenjian, Charles P.; Warner, David M.

2014-01-01

Ecosystems undergo dynamic changes owing to species invasions, fisheries management decisions, landscape modifications, and nutrient inputs. At Lake Michigan, new invaders (e.g., dreissenid mussels (Dreissena spp.), spiny water flea (Bythotrephes longimanus), round goby (Neogobius melanostomus)) have proliferated and altered energy transfer pathways, while nutrient concentrations and stocking rates to support fisheries have changed. We developed an ecosystem model to describe food web structure in 1987 and ran simulations through 2008 to evaluate changes in biomass of functional groups, predator consumption, and effects of recently invading species. Keystone functional groups from 1987 were identified as Mysis, burbot (Lota lota), phytoplankton, alewife (Alosa pseudoharengus), nonpredatory cladocerans, and Chinook salmon (Oncorhynchus tshawytscha). Simulations predicted biomass reductions across all trophic levels and predicted biomasses fit observed trends for most functional groups. The effects of invasive species (e.g., dreissenid grazing) increased across simulation years, but were difficult to disentangle from other changes (e.g., declining offshore nutrient concentrations). In total, our model effectively represented recent changes to the Lake Michigan ecosystem and provides an ecosystem-based tool for exploring future resource management scenarios.

The nuclear lamina promotes telomere aggregation and centromere peripheral localization during senescence of human mesenchymal stem cells.

PubMed

Raz, Vered; Vermolen, Bart J; Garini, Yuval; Onderwater, Jos J M; Mommaas-Kienhuis, Mieke A; Koster, Abraham J; Young, Ian T; Tanke, Hans; Dirks, Roeland W

2008-12-15

Ex vivo, human mesenchymal stem cells (hMSCs) undergo spontaneous cellular senescence after a limited number of cell divisions. Intranuclear structures of the nuclear lamina were formed in senescent hMSCs, which are identified by the presence of Hayflick-senescence-associated factors. Notably, spatial changes in lamina shape were observed before the Hayflick senescence-associated factors, suggesting that the lamina morphology can be used as an early marker to identify senescent cells. Here, we applied quantitative image-processing tools to study the changes in nuclear architecture during cell senescence. We found that centromeres and telomeres colocalised with lamina intranuclear structures, which resulted in a preferred peripheral distribution in senescent cells. In addition, telomere aggregates were progressively formed during cell senescence. Once formed, telomere aggregates showed colocalization with gamma-H2AX but not with TERT, suggesting that telomere aggregates are sites of DNA damage. We also show that telomere aggregation is associated with lamina intranuclear structures, and increased telomere binding to lamina proteins is found in cells expressing lamina mutants that lead to increases in lamina intranuclear structures. Moreover, three-dimensional image processing revealed spatial overlap between telomere aggregates and lamina intranuclear structures. Altogether, our data suggest a mechanical link between changes in lamina spatial organization and the formation of telomere aggregates during senescence of hMSCs, which can possibly contribute to changes in nuclear activity during cell senescence.

In vivo, label-free, three-dimensional quantitative imaging of liver surface using multi-photon microscopy

NASA Astrophysics Data System (ADS)

Zhuo, Shuangmu; Yan, Jie; Kang, Yuzhan; Xu, Shuoyu; Peng, Qiwen; So, Peter T. C.; Yu, Hanry

2014-07-01

Various structural features on the liver surface reflect functional changes in the liver. The visualization of these surface features with molecular specificity is of particular relevance to understanding the physiology and diseases of the liver. Using multi-photon microscopy (MPM), we have developed a label-free, three-dimensional quantitative and sensitive method to visualize various structural features of liver surface in living rat. MPM could quantitatively image the microstructural features of liver surface with respect to the sinuosity of collagen fiber, the elastic fiber structure, the ratio between elastin and collagen, collagen content, and the metabolic state of the hepatocytes that are correlative with the pathophysiologically induced changes in the regions of interest. This study highlights the potential of this technique as a useful tool for pathophysiological studies and possible diagnosis of the liver diseases with further development.

Engineered control of enzyme structural dynamics and function.

PubMed

Boehr, David D; D'Amico, Rebecca N; O'Rourke, Kathleen F

2018-04-01

Enzymes undergo a range of internal motions from local, active site fluctuations to large-scale, global conformational changes. These motions are often important for enzyme function, including in ligand binding and dissociation and even preparing the active site for chemical catalysis. Protein engineering efforts have been directed towards manipulating enzyme structural dynamics and conformational changes, including targeting specific amino acid interactions and creation of chimeric enzymes with new regulatory functions. Post-translational covalent modification can provide an additional level of enzyme control. These studies have not only provided insights into the functional role of protein motions, but they offer opportunities to create stimulus-responsive enzymes. These enzymes can be engineered to respond to a number of external stimuli, including light, pH, and the presence of novel allosteric modulators. Altogether, the ability to engineer and control enzyme structural dynamics can provide new tools for biotechnology and medicine. © 2018 The Protein Society.

Distortion and Residual Stress Control in Integrally Stiffened Structure Produced by Direct Metal Deposition

NASA Technical Reports Server (NTRS)

Lin, Shih-Yung; Hoffman, Eric K.; Domack, Marcia S.

2007-01-01

2-D thermo-mechanical model developed to characterize distortion and residual stresses in integral structure produced by DMD. Demonstrated as a tool to guide experimental development of DMD fabrication process for aero structures. Distortion and residual stresses are local to deposit. Most distortion develops during deposition of the first few layers; Little change in distortion or residual stresses after fifth deposit layer Most of distortion is localized just beneath the build. Thicker build plates and the use of build lands results in greatest decrease in levels of distortion. Pre-straining shown to reduce distortion. Difficult to implement, particularly for complex stiffener arrays. Clamp position has complex effect on distortion and stresses. Overall distortion reduced with decreasing clamp clearance. Larger clamp clearances induce bending. Use of pre-heat and active cooling show minor influence on panel distortion. Generate changes in thermal gradients in the build plate.

In vivo, label-free, three-dimensional quantitative imaging of liver surface using multi-photon microscopy

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

Zhuo, Shuangmu, E-mail: shuangmuzhuo@gmail.com, E-mail: hanry-yu@nuhs.edu.sg; Institute of Laser and Optoelectronics Technology, Fujian Normal University, Fuzhou 350007; Yan, Jie

2014-07-14

Various structural features on the liver surface reflect functional changes in the liver. The visualization of these surface features with molecular specificity is of particular relevance to understanding the physiology and diseases of the liver. Using multi-photon microscopy (MPM), we have developed a label-free, three-dimensional quantitative and sensitive method to visualize various structural features of liver surface in living rat. MPM could quantitatively image the microstructural features of liver surface with respect to the sinuosity of collagen fiber, the elastic fiber structure, the ratio between elastin and collagen, collagen content, and the metabolic state of the hepatocytes that are correlativemore » with the pathophysiologically induced changes in the regions of interest. This study highlights the potential of this technique as a useful tool for pathophysiological studies and possible diagnosis of the liver diseases with further development.« less

Changes in composition, ecology and structure of high-mountain vegetation: a re-visitation study over 42 years.

PubMed

Evangelista, Alberto; Frate, Ludovico; Carranza, Maria Laura; Attorre, Fabio; Pelino, Giovanni; Stanisci, Angela

2016-01-27

High-mountain ecosystems are increasingly threatened by climate change, causing biodiversity loss, habitat degradation and landscape modifications. However, very few detailed studies have focussed on plant biodiversity in the high mountains of the Mediterranean. In this study, we investigated the long-term changes that have occurred in the composition, structure and ecology of high-mountain vegetation in the central Apennines (Majella) over the last 42 years. We performed a re-visitation study, using historical and newly collected vegetation data to explore which ecological and structural features have been the most successful in coping with climatic changes. Vegetation changes were analysed by comparing geo-referenced phytosociological relevés collected in high-mountain habitats (dolines, gentle slopes and ridges) on the Majella massif in 1972 and in 2014. Composition analysis was performed by detrended correspondence analysis, followed by an analysis of similarities for statistical significance assessment and by similarity percentage procedure (SIMPER) for identifying which species indicate temporal changes. Changes in ecological and structural indicators were analysed by a permutational multivariate analysis of variance, followed by a post hoc comparison. Over the last 42 years, clear floristic changes and significant ecological and structural variations occurred. We observed a significant increase in the thermophilic and mesonitrophilic plant species and an increment in the frequencies of hemicryptophytes. This re-visitation study in the Apennines agrees with observations in other alpine ecosystems, providing new insights for a better understanding of the effects of global change on Mediterranean high-mountain biodiversity. The observed changes in floristic composition, the thermophilization process and the shift towards a more nutrient-demanding vegetation are likely attributable to the combined effect of higher temperatures and the increase in soil nutrients triggered by global change. The re-visitation approach adopted herein represents a powerful tool for studying climate-related changes in sensitive high-mountain habitats. Published by Oxford University Press on behalf of the Annals of Botany Company.

The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures

USGS Publications Warehouse

Allen, J.P.; Atekwana, E.A.; Duris, J.W.; Werkema, D.D.; Rossbach, S.

2007-01-01

The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueousphase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.

Operando XRD studies as a tool for determination of transport parameters of mobile ions in electrode materials

NASA Astrophysics Data System (ADS)

Kondracki, Łukasz; Kulka, Andrzej; Świerczek, Konrad; Ziąbka, Magdalena; Molenda, Janina

2017-11-01

In this work a detailed operando XRD investigations of structural properties of LixMn2O4 manganese spinel are shown to be a complementary, successful method of determination of diffusion coefficient D and surface exchange coefficient k in the working electrode. Kinetics of lithium ions transport are estimated on the basis of rate of structural changes of the cathode material during a relaxation stage after a high current charge, i.e. during structural relaxation of the material. The presented approach seems to be applicable as a complementary method of determination of transport coefficients for all intercalation-type electrode materials.

Amplitude and phase beam shaping for highest sensitivity in sidewall angle detection.

PubMed

Cisotto, Luca; Paul Urbach, H

2017-01-01

In integrated circuits manufacturing, specific structures are used as tools to evaluate the quality of the lithographic process, and the shape of these structures is often described by a few parameters, of which in particular the sidewall angle suffers from considerable inaccuracies. Using scalar diffraction theory, we investigate whether a properly shaped cylindrically focused probing beam could increase the ability to detect tiny changes in this angle in the case of a cliff-like structure, modeled as a phase object. This paper describes the theoretical formulation used to calculate the optimized beam and compares its performance with the case of a focused plane wave.

Plastinated fetus: 3D CT scan (VRT) evaluation.

PubMed

Tiwari, Shilpi; Nandlal, B; Shama Sundar, N M

2012-01-01

The intent of this study was to evaluate the effect of plastination on the morphology and structure of stored organs, to find out how much accuracy a plastinated specimen has, and to look into the changes that occurred because of plastination. A human fetus of gestational age 24 weeks was plastinated, and 3D CT scan evaluation of the fetus was done. The results showed normal, well-defined, clearly identifiable organs, with no alteration in morphology and structure of organs. In our opinion, plastinated specimens are better way of visualization of morphology and structure of stored organs, which is a useful tool for teaching as well as for research purposes.

Influence of pH on the Structure and Function of Kiwi Pectin Methylesterase Inhibitor.

PubMed

Bonavita, Alessandro; Carratore, Vitale; Ciardiello, Maria Antonietta; Giovane, Alfonso; Servillo, Luigi; D'Avino, Rossana

2016-07-27

Pectin methylesterase is a pectin modifying enzyme that plays a key role in plant physiology. It is also an important quality-related enzyme in plant-based food products. The pectin methylesterase inhibitor (PMEI) from kiwifruit inhibits this enzyme activity and is widely used as an efficient tool for research purposes and also recommended in the context of fruit and vegetable processing. Using several methodologies of protein biochemistry, including circular dichroism and fluorescence spectroscopy, chemical modifications, direct protein-sequencing, enzyme activity, and bioinformatics analysis of the crystal structure, this study demonstrates that conformational changes occur in kiwi PMEI by the pH rising over 6.0 bringing about structure loosening, exposure, and cleavage of a natively buried disulfide bond, unfolding and aggregation, ultimately determining the loss of ability of kiwi PMEI to bind and inhibit PME. pH-induced structural changes are prevented when PMEI is already engaged in complex or is in a solution of high ionic strength.

Suppression of superconductivity and structural phase transitions under pressure in tetragonal FeS

DOE PAGES

Lai, Xiaofang; Liu, Ying; Lu, Xujie; ...

2016-08-08

Pressure is a powerful tool to study iron-based superconductors. Here, we report systematic high-pressure transport and structural characterizations of the newly discovered superconductor FeS. It is found that superconductor FeS (tetragonal) partly transforms to a hexagonal structure at 0.4 GPa, and then completely transforms to an orthorhombic phase at 7.4 GPa and finally to a monoclinic phase above 9.0 GPa. The superconducting transition temperature of tetragonal FeS was gradually depressed by pressure, different from the case in tetragonal FeSe. With pressure increasing, the S-Fe-S angles only slightly change but the anion height deviates farther from 1.38 Å. This change ofmore » anion height, together with the structural instability under pressure, should be closely related to the suppression of superconductivity. We also observed an anomalous metal-semiconductor transition at 6.0 GPa and an unusual increased resistance with further compression above 9.6 GPa. The former can be ascribed to the tetragonal-orthorhombic structural phase transition, and the latter to the electronic structure changes of the high-pressure monoclinic phase. Lastly, a phase diagram of tetragonal FeS as functions of pressure and temperature was mapped out for the first time, which will shed new light on understanding of the structure and physics of the superconducting FeS.« less

Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC.

PubMed

Pucci, Fabrizio; Bourgeas, Raphaël; Rooman, Marianne

2016-03-18

The accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to predict the change in melting temperature ΔTm upon point mutations, given the protein structure and, when available, the melting temperature Tm of the wild-type protein. The key ingredients of our model structure are standard and temperature-dependent statistical potentials, which are combined with the help of an artificial neural network. The model structure was chosen on the basis of a detailed thermodynamic analysis of the system. The parameters of the model were identified on a set of more than 1,600 mutations with experimentally measured ΔTm. The performance of our method was tested using a strict 5-fold cross-validation procedure, and was found to be significantly superior to that of competing methods. We obtained a root mean square deviation between predicted and experimental ΔTm values of 4.2 °C that reduces to 2.9 °C when ten percent outliers are removed. A webserver-based tool is freely available for non-commercial use at soft.dezyme.com.

Computer constructed imagery of distant plasma interaction boundaries

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

Grenstadt, E.W.; Schurr, H.D.; Tsugawa, R.K.

1982-01-01

Computer constructed sketches of plasma boundaries arising from the interaction between the solar wind and the magnetosphere can serve as both didactic and research tools. In particular, the structure of the earth's bow shock can be represented as a nonuniform surfce according to the instantaneous orientation of the IMF, and temporal changes in structural distribution can be modeled as a sequence of sketches based on observed sequences of spacecraft-based measurements. Viewed rapidly, such a sequence of sketches can be the basis for representation of plasma processes by computer animation.

Reliability and Validity of the Dutch Version of the Behavioural Status Index: A Nurse-Rated Forensic Assessment Tool

ERIC Educational Resources Information Center

Chakhssi, Farid; de Ruiter, Corine; Bernstein, David

2010-01-01

The Behavioural Status Index (BEST-Index) has been introduced into Dutch forensic psychiatry to measure change in risk level of future violence. The BEST-Index is a structured observational measure that assesses aggressive behavior, degree of insight, social skills, self-care, and work and leisure skills during inpatient treatment. Thus far,…

Using Corporate Tools for Organizational Development to Affect Cultural and Structural Change in the Academy: Gallup Impact Planning at the University of Nebraska-Lincoln

ERIC Educational Resources Information Center

Latta, Gail F.

2006-01-01

External pressures have transformed academic life, shattering the roles and relationships that created a sense of community. Increasingly the challenges of fostering an engaged workforce in these institutions mirror the corporate world. Leaders at UNL have adapted Gallup's organizational development strategy to improve faculty engagement and…

Mind the Gap: Physical Education and Health and the Frame Factor Theory as a Tool for Analysing Educational Settings

ERIC Educational Resources Information Center

Lundvall, Suzanne; Meckbach, Jane

2008-01-01

Background: On a normative level as a subject physical education and health seems to adjust rapidly to changes in society, whereas at the practical level it seems receptive to limiting factors such as time, facilities and dominating inherited practices. How can the structuring components and processes relating to the shaping, transformation and…

Leading Learning Organizations through Transformational Change: Making the Case for Blended Learning

ERIC Educational Resources Information Center

Boone, Joyce

2015-01-01

Purpose: There are two conditions that threaten to derail the American education system as we know it: the poor state of the US economy in America and the less than effective structure of the American education system. Researchers and practitioners are searching to identify tools and strategies that can help to restore confidence in the soundness…

In-situ, Real-Time Monitoring of Mechanical and Chemical Structure Changes in a V2O5 Battery Electrode Using a MEMS Optical Sensor

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

Jung, H.; Gerasopoulos, K.; Gnerlich, Markus

This work presents the first demonstration of a MEMS optical sensor for in-situ, real-time monitoring of both mechanical and chemical structure evolutions in a V2O5 lithium-ion battery (LIB) cathode during battery operation. A reflective membrane forms one side of a Fabry-Perot (FP) interferometer, while the other side is coated with V2O5 and exposed to electrolyte in a half-cell LIB. Using one microscope and two laser sources, both the induced membrane deflection and the corresponding Raman intensity changes are observed during lithium cycling. Results are in good agreement with the expected mechanical behavior and disorder change of the V2O5 layers, highlightingmore » the significant potential of MEMS as enabling tools for advanced scientific investigations.« less

Evolution of the Human Nervous System Function, Structure, and Development.

PubMed

Sousa, André M M; Meyer, Kyle A; Santpere, Gabriel; Gulden, Forrest O; Sestan, Nenad

2017-07-13

The nervous system-in particular, the brain and its cognitive abilities-is among humans' most distinctive and impressive attributes. How the nervous system has changed in the human lineage and how it differs from that of closely related primates is not well understood. Here, we consider recent comparative analyses of extant species that are uncovering new evidence for evolutionary changes in the size and the number of neurons in the human nervous system, as well as the cellular and molecular reorganization of its neural circuits. We also discuss the developmental mechanisms and underlying genetic and molecular changes that generate these structural and functional differences. As relevant new information and tools materialize at an unprecedented pace, the field is now ripe for systematic and functionally relevant studies of the development and evolution of human nervous system specializations. Copyright © 2017 Elsevier Inc. All rights reserved.

Conformational rearrangements in the transmembrane domain of CNGA1 channels revealed by single-molecule force spectroscopy

NASA Astrophysics Data System (ADS)

Maity, Sourav; Mazzolini, Monica; Arcangeletti, Manuel; Valbuena, Alejandro; Fabris, Paolo; Lazzarino, Marco; Torre, Vincent

2015-05-01

Cyclic nucleotide-gated (CNG) channels are activated by binding of cyclic nucleotides. Although structural studies have identified the channel pore and selectivity filter, conformation changes associated with gating remain poorly understood. Here we combine single-molecule force spectroscopy (SMFS) with mutagenesis, bioinformatics and electrophysiology to study conformational changes associated with gating. By expressing functional channels with SMFS fingerprints in Xenopus laevis oocytes, we were able to investigate gating of CNGA1 in a physiological-like membrane. Force spectra determined that the S4 transmembrane domain is mechanically coupled to S5 in the closed state, but S3 in the open state. We also show there are multiple pathways for the unfolding of the transmembrane domains, probably caused by a different degree of α-helix folding. This approach demonstrates that CNG transmembrane domains have dynamic structure and establishes SMFS as a tool for probing conformational change in ion channels.

Pre-evaluation and interactive editing of B-spline and GERBS curves and surfaces

NASA Astrophysics Data System (ADS)

Laksâ, Arne

2017-12-01

Interactive computer based geometry editing is very useful for designers and artists. Our goal has been to develop useful tools for geometry editing in a way that increases the ability for creative design. When we interactively editing geometry, we want to see the change happening gradually and smoothly on the screen. Pre-evaluation is a tool for increasing the speed of the graphics when doing interactive affine operation on control points and control surfaces. It is then possible to add details on surfaces, and change shape in a smooth and continuous way. We use pre-evaluation on basis functions, on blending functions and on local surfaces. Pre-evaluation can be made hierarchi-cally and is thus useful for local refinements. Sampling and plotting of curves, surfaces and volumes can today be handled by the GPU and it is therefore important to have a structured organization and updating system to be able to make interactive editing as smooth and user friendly as possible. In the following, we will show a structure for pre-evaluation and an optimal organisation of the computation and we will show the effect of implementing both of these techniques.

Das Bremerhavener Grundwasser im Klimawandel - Eine FREEWAT-Fallstudie

NASA Astrophysics Data System (ADS)

Panteleit, Björn; Jensen, Sven; Seiter, Katherina; Siebert, Yvonne

2018-01-01

A 3D structural model was created for the state of Bremen based on an extensive borehole database. Parameters were assigned to the model by interpretation and interpolation of the borehole descriptions. This structural model was transferred into a flow model via the FREEWAT platform, an open-source plug-in of the free QGIS software, with connection to the MODFLOW code. This groundwater management tool is intended for long-term use. As a case study for the FREEWAT Project, possible effects of climate change on groundwater levels in the Bremerhaven area have been simulated. In addition to the calibration year 2010, scenarios with a sea-level rise and decreasing groundwater recharge were simulated for the years 2040, 2070 and 2100. In addition to seawater intrusion in the coastal area, declining groundwater levels are also a concern. Possibilities for future groundwater management already include active control of the water level of a lake and the harbor basin. With the help of a focused groundwater monitoring program based on the model results, the planned flow model can become an important forecasting tool for groundwater management within the framework of the planned continuous model management and for representing the effects of changing climatic conditions and mitigation measures.

The growth of partnerships to support patient safety practice adoption.

PubMed

Mendel, Peter; Damberg, Cheryl L; Sorbero, Melony E S; Varda, Danielle M; Farley, Donna O

2009-04-01

To document the numbers and types of interorganizational partnerships within the national patient safety domain, changes over time in these networks, and their potential for disseminating patient safety knowledge and practices. Self-reported information gathered from representatives of national-level organizations active in promoting patient safety. Social network analysis was used to examine the structure and composition of partnership networks and changes between 2004 and 2006. Two rounds of structured telephone interviews (n=35 organizations in 2004 and 55 in 2006). Patient safety partnerships expanded between 2004 and 2006. The average number of partnerships per interviewed organization increased 40 percent and activities per reported partnership increased over 50 percent. Partnerships increased in all activity domains, particularly dissemination and tools development. Fragmentation of the overall partnership network decreased and potential for information flow increased. Yet network centralization increased, suggesting vulnerability to partnership failure if key participants disengage. Growth in partnerships signifies growing strength in the capacity to disseminate and implement patient safety advancements in the U.S. health care system. The centrality of AHRQ in these networks of partnerships bodes well for its leadership role in disseminating information, tools, and practices generated by patient safety research projects.

Atomic force microscopy as an advanced tool in neuroscience

PubMed Central

Jembrek, Maja Jazvinšćak; Šimić, Goran; Hof, Patrick R.; Šegota, Suzana

2015-01-01

This review highlights relevant issues about applications and improvements of atomic force microscopy (AFM) toward a better understanding of neurodegenerative changes at the molecular level with the hope of contributing to the development of effective therapeutic strategies for neurodegenerative illnesses. The basic principles of AFM are briefly discussed in terms of evaluation of experimental data, including the newest PeakForce Quantitative Nanomechanical Mapping (QNM) and the evaluation of Young’s modulus as the crucial elasticity parameter. AFM topography, revealed in imaging mode, can be used to monitor changes in live neurons over time, representing a valuable tool for high-resolution detection and monitoring of neuronal morphology. The mechanical properties of living cells can be quantified by force spectroscopy as well as by new AFM. A variety of applications are described, and their relevance for specific research areas discussed. In addition, imaging as well as non-imaging modes can provide specific information, not only about the structural and mechanical properties of neuronal membranes, but also on the cytoplasm, cell nucleus, and particularly cytoskeletal components. Moreover, new AFM is able to provide detailed insight into physical structure and biochemical interactions in both physiological and pathophysiological conditions. PMID:28123795

Structures composing protein domains.

PubMed

Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

2013-08-01

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

EXPECT: Explicit Representations for Flexible Acquisition

NASA Technical Reports Server (NTRS)

Swartout, BIll; Gil, Yolanda

1995-01-01

To create more powerful knowledge acquisition systems, we not only need better acquisition tools, but we need to change the architecture of the knowledge based systems we create so that their structure will provide better support for acquisition. Current acquisition tools permit users to modify factual knowledge but they provide limited support for modifying problem solving knowledge. In this paper, the authors argue that this limitation (and others) stem from the use of incomplete models of problem-solving knowledge and inflexible specification of the interdependencies between problem-solving and factual knowledge. We describe the EXPECT architecture which addresses these problems by providing an explicit representation for problem-solving knowledge and intent. Using this more explicit representation, EXPECT can automatically derive the interdependencies between problem-solving and factual knowledge. By deriving these interdependencies from the structure of the knowledge-based system itself EXPECT supports more flexible and powerful knowledge acquisition.

A novel approach of deposition for uniform diamond films on circular saw blades

NASA Astrophysics Data System (ADS)

Hongxiu, ZHOU; Boya, YUAN; Jilei, LYU; Nan, JIANG

2017-11-01

Uniform diamond films are highly desirable for cutting industries, due to their high performance and long lifetime used on cutting tools. Nevertheless, they are difficult to obtain on cutting tools with complicated shapes, greatly limiting the applications of diamond films. In this study, a novel approach of deposition for uniform diamond films is proposed, on circular saw blades made of cemented carbide using reflectors of brass sheets. Diamond films are deposited using hot filament chemical vapor deposition (HFCVD). A novel concave structure of brass sheets is designed and fabricated, improving the distribution of temperature field, and overcoming the disadvantages of the conventional HFCVD systems. This increases the energy efficiency of use without changing the structure and increasing the cost of HFCVD. The grains are refined and the intensities of diamond peaks are strengthened obviously, which is confirmed by scanning electron microscopy and Raman spectra respectively.

Analysis of Vaginal Microbicide Film Hydration Kinetics by Quantitative Imaging Refractometry

PubMed Central

Rinehart, Matthew; Grab, Sheila; Rohan, Lisa; Katz, David; Wax, Adam

2014-01-01

We have developed a quantitative imaging refractometry technique, based on holographic phase microscopy, as a tool for investigating microscopic structural changes in water-soluble polymeric materials. Here we apply the approach to analyze the structural degradation of vaginal topical microbicide films due to water uptake. We implemented transmission imaging of 1-mm diameter film samples loaded into a flow chamber with a 1.5×2 mm field of view. After water was flooded into the chamber, interference images were captured and analyzed to obtain high resolution maps of the local refractive index and subsequently the volume fraction and mass density of film material at each spatial location. Here, we compare the hydration dynamics of a panel of films with varying thicknesses and polymer compositions, demonstrating that quantitative imaging refractometry can be an effective tool for evaluating and characterizing the performance of candidate microbicide film designs for anti-HIV drug delivery. PMID:24736376

Analysis of vaginal microbicide film hydration kinetics by quantitative imaging refractometry.

PubMed

Rinehart, Matthew; Grab, Sheila; Rohan, Lisa; Katz, David; Wax, Adam

2014-01-01

We have developed a quantitative imaging refractometry technique, based on holographic phase microscopy, as a tool for investigating microscopic structural changes in water-soluble polymeric materials. Here we apply the approach to analyze the structural degradation of vaginal topical microbicide films due to water uptake. We implemented transmission imaging of 1-mm diameter film samples loaded into a flow chamber with a 1.5×2 mm field of view. After water was flooded into the chamber, interference images were captured and analyzed to obtain high resolution maps of the local refractive index and subsequently the volume fraction and mass density of film material at each spatial location. Here, we compare the hydration dynamics of a panel of films with varying thicknesses and polymer compositions, demonstrating that quantitative imaging refractometry can be an effective tool for evaluating and characterizing the performance of candidate microbicide film designs for anti-HIV drug delivery.

Second harmonic generation imaging as a potential tool for staging pregnancy and predicting preterm birth

NASA Astrophysics Data System (ADS)

Akins, Meredith L.; Luby-Phelps, Katherine; Mahendroo, Mala

2010-03-01

We use second harmonic generation (SHG) microscopy to assess changes in collagen structure of murine cervix during cervical remodeling of normal pregnancy and in a preterm birth model. Visual inspection of SHG images revealed substantial changes in collagen morphology throughout normal gestation. SHG images collected in both the forward and backward directions were analyzed quantitatively for changes in overall mean intensity, forward to backward intensity ratio, collagen fiber size, and porosity. Changes in mean SHG intensity and intensity ratio take place in early pregnancy, suggesting that submicroscopic changes in collagen fibril size and arrangement occur before macroscopic changes become evident. Fiber size progressively increased from early to late pregnancy, while pores between collagen fibers became larger and farther apart. Analysis of collagen features in premature cervical remodeling show that changes in collagen structure are dissimilar from normal remodeling. The ability to quantify multiple morphological features of collagen that characterize normal cervical remodeling and distinguish abnormal remodeling in preterm birth models supports future studies aimed at development of SHG endoscopic devices for clinical assessment of collagen changes during pregnancy in women and for predicting risk of preterm labor which occurs in 12.5% of all pregnancies.

Structure and software tools of AIDA.

PubMed

Duisterhout, J S; Franken, B; Witte, F

1987-01-01

AIDA consists of a set of software tools to allow for fast development and easy-to-maintain Medical Information Systems. AIDA supports all aspects of such a system both during development and operation. It contains tools to build and maintain forms for interactive data entry and on-line input validation, a database management system including a data dictionary and a set of run-time routines for database access, and routines for querying the database and output formatting. Unlike an application generator, the user of AIDA may select parts of the tools to fulfill his needs and program other subsystems not developed with AIDA. The AIDA software uses as host language the ANSI-standard programming language MUMPS, an interpreted language embedded in an integrated database and programming environment. This greatly facilitates the portability of AIDA applications. The database facilities supported by AIDA are based on a relational data model. This data model is built on top of the MUMPS database, the so-called global structure. This relational model overcomes the restrictions of the global structure regarding string length. The global structure is especially powerful for sorting purposes. Using MUMPS as a host language allows the user an easy interface between user-defined data validation checks or other user-defined code and the AIDA tools. AIDA has been designed primarily for prototyping and for the construction of Medical Information Systems in a research environment which requires a flexible approach. The prototyping facility of AIDA operates terminal independent and is even to a great extent multi-lingual. Most of these features are table-driven; this allows on-line changes in the use of terminal type and language, but also causes overhead. AIDA has a set of optimizing tools by which it is possible to build a faster, but (of course) less flexible code from these table definitions. By separating the AIDA software in a source and a run-time version, one is able to write implementation-specific code which can be selected and loaded by a special source loader, being part of the AIDA software. This feature is also accessible for maintaining software on different sites and on different installations.

Going beyond the identification of change facilitators to effectively implement a new model of services: lessons learned from a case example in paediatric rehabilitation.

PubMed

Camden, Chantal; Swaine, Bonnie; Tétreault, Sylvie; Carrière, Monique

2011-01-01

To identify facilitators and barriers to service reorganization, how they evolved and interacted to influence change during the implementation of a new service delivery model of paediatric rehabilitation. Over 3 years, different stakeholders responded to SWOT questionnaires (n = 139) and participated in focus groups (n = 19) and telephone interviews (n = 13). A framework based on socio constructivist theories made sense of the data. Facilitators related to the programme's structure (e.g. funding), the actors (e.g. willingness to test the new service model) and the change management process (e.g. participative approach). Some initial facilitators became barriers (e.g. leadership lacked at the end), while other barriers emerged (e.g. lack of tools). Understanding factor interactions requires examining the multiple actors' intentions, actions and consequences and their relations with structural elements. Analysing facilitators and barriers helped better understand the change processes, but this must be followed by concrete actions to successfully implement new paediatric rehabilitation models.

Noninvasive optical coherence tomography monitoring of structure and hydration changes of human corneas in different preservation media

NASA Astrophysics Data System (ADS)

Wu, Yicong; Clarke, Dominic; Mathew, Aby; Nicoud, Ian; Li, Xingde

2011-02-01

The influence of different tissue preservation (a test solution under development and a standard storage solution) on human cornea morphology, refractive index and hydration was assessed noninvasively by ultrahigh-resolution optical coherence tomography (OCT) over time. For 28 days' or 15 days' storage in the preservation media, corneas in the two media exhibited different structural changes with different onset times including epithelial desquamation, edema-induced cornea thickening and change in tissue refractive index. It was found that the variation of the group refractive index over time was only about 2%, while 25% variation of hydration was observed in the storage and subsequent return to normothermic conditions in both preservation media. The results suggest the two media involved different but correlated preservation mechanisms. This study demonstrates that the noncontact, noninvasive, and high-resolution OCT is a powerful tool for noninvasive characterization of tissue morphological changes and hydration process and for assessment of the effects of preservation media on stored tissue integrity. Engineers.

Correlated Light and Electron Microscopy/Electron Tomography of Mitochondria In Situ

PubMed Central

Perkins, Guy A.; Sun, Mei G.; Frey, Terrence G.

2009-01-01

Three-dimensional light microscopy and three-dimensional electron microscopy (electron tomography) separately provide very powerful tools to study cellular structure and physiology, including the structure and physiology of mitochondria. Fluorescence microscopy allows one to study processes in live cells with specific labels and stains that follow the movement of labeled proteins and changes within cellular compartments but does not have sufficient resolution to define the ultrastructure of intracellular organelles such as mitochondria. Electron microscopy and electron tomography provide the highest resolution currently available to study mitochondrial ultrastructure but cannot follow processes in living cells. We describe the combination of these two techniques in which fluorescence confocal microscopy is used to study structural and physiologic changes in mitochondria within apoptotic HeLa cells to define the apoptotic timeframe. Cells can then be selected at various stages of the apoptotic timeframe for examination at higher resolution by electron microscopy and electron tomography. This is a form of “virtual” 4-dimensional electron microscopy that has revealed interesting structural changes in the mitochondria of HeLa cells during apoptosis. The same techniques can be applied, with modification, to study other dynamic processes within cells in other experimental contexts. PMID:19348881

Structural features and properties of the laser-deposited nickel alloy layer on a KhV4F tool steel after heat treatment

NASA Astrophysics Data System (ADS)

Shcherbakov, V. S.; Dikova, Ts. D.; Stavrev, D. S.

2017-07-01

The study and application of the materials that are stable in the temperature range up to 1000°C are necessary to repair forming dies operating in this range. Nickel-based alloys can be used for this purpose. The structural state of a nickel alloy layer deposited onto a KhV4F tool steel and then heat treated is investigated. KhV4F tool steel (RF GOST) samples are subjected to laser deposition using a pulsed Nd:YAG laser. A nickel-based material (0.02C-73.8Ni-2.5Nb-19.5Cr-1.9Fe-2.8Mn) is employed for laser deposition. After laser deposition, the samples are subjected to heat treatment at 400°C for 5 h, 600°C for 1 h, 800°C for 1 h, and 1000°C for 1 h. The microstructure, the phase composition, and the microhardness of the deposited layer are studied. The structure of the initial deposited layer has relatively large grains (20-40 μm in size). The morphology is characterized by a cellular-dendritic structure in the transition zone. The following two structural constituents with a characteristic dendritic structure are revealed: a supersaturated nickel-based γ solid solution and a chromium-based bcc α solid solution. In the initial state and after heat treatment, the hardness of the deposited material (210-240 HV 0.1) is lower than the hardness of the base material (400-440 HV 0.1). Only after heat treatment at 600°C for 1 h, the hardness increases to 240-250 HV0.1. Structure heredity in the form of a dendritic morphology is observed at temperatures of 400, 600, and 800°C. The following sharp change in the structural state is detected upon heat treatment at 1000°C for 1 h: the dendritic morphology changes into a typical α + γ crystalline structure. The hardness of the base material decreases significantly to 160-180 HV 0.1. The low hardness of the deposited layer implies the use of the layer material in limited volume to repair the forming surfaces of dies and molds for die casting. However, the high ductility of the deposited layer of the nickel-based material is a prerequisite for a high stability under thermocycling loading conditions.

Providing Context for Complexity: Using Infographics and Conceptual Models to Teach Global Change Processes

NASA Astrophysics Data System (ADS)

Bean, J. R.; White, L. D.

2015-12-01

Understanding modern and historical global changes requires interdisciplinary knowledge of the physical and life sciences. The Understanding Global Change website from the UC Museum of Paleontology will use a focal infographic that unifies diverse content often taught in separate K-12 science units. This visualization tool provides scientists with a structure for presenting research within the broad context of global change, and supports educators with a framework for teaching and assessing student understanding of complex global change processes. This new approach to teaching the science of global change is currently being piloted and refined based on feedback from educators and scientists in anticipation of a 2016 website launch. Global change concepts are categorized within the infographic as causes of global change (e.g., burning of fossil fuels, volcanism), ongoing Earth system processes (e.g., ocean circulation, the greenhouse effect), and the changes scientists measure in Earth's physical and biological systems (e.g., temperature, extinctions/radiations). The infographic will appear on all website content pages and provides a template for the creation of flowcharts, which are conceptual models that allow teachers and students to visualize the interdependencies and feedbacks among processes in the atmosphere, hydrosphere, biosphere, and geosphere. The development of this resource is timely given that the newly adopted Next Generation Science Standards emphasize cross-cutting concepts, including model building, and Earth system science. Flowchart activities will be available on the website to scaffold inquiry-based lessons, determine student preconceptions, and assess student content knowledge. The infographic has already served as a learning and evaluation tool during professional development workshops at UC Berkeley, Stanford University, and the Smithsonian National Museum of Natural History. At these workshops, scientists and educators used the infographic to highlight how their research and activities reinforce conceptual links among global change topics. Pre- and post-workshop assessment results and responses to questionnaires have guided the refinement of classroom activities and assessment tools utilizing flowcharts as models for global change processes.

Mapping local anisotropy axis for scattering media using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Guo, Yihong; He, Yonghong; Ma, Hui

2014-03-01

Mueller matrix imaging techniques can be used to detect the micro-structure variations of superficial biological tissues, including the sizes and shapes of cells, the structures in cells, and the densities of the organelles. Many tissues contain anisotropic fibrous micro-structures, such as collagen fibers, elastin fibers, and muscle fibers. Changes of these fibrous structures are potentially good indicators for some pathological variations. In this paper, we propose a quantitative analysis technique based on Mueller matrix for mapping local anisotropy axis of scattering media. By conducting both experiments on silk sample and Monte Carlo simulation based on the sphere-cylinder scattering model (SCSM), we extract anisotropy axis parameters from different backscattering Mueller matrix elements. Moreover, we testify the possible applications of these parameters for biological tissues. The preliminary experimental results of human cancerous samples show that, these parameters are capable to map the local axis of fibers. Since many pathological changes including early stage cancers affect the well aligned structures for tissues, the experimental results indicate that these parameters can be used as potential tools in clinical applications for biomedical diagnosis purposes.

Information structure and organisation in change of shift reports: An observational study of nursing hand-offs in a Paediatric Intensive Care Unit.

PubMed

Foster-Hunt, Tara; Parush, Avi; Ellis, Jacqueline; Thomas, Margot; Rashotte, Judy

2015-06-01

Patient hand-offs involve the exchange of critical information. Ineffective hand-offs can result in reduced patient safety by leading to wrong treatment, delayed diagnoses or other outcomes that can negatively affect the healthcare system. The objectives of this study were to uncover the structure of the information conveyed during patient hand-offs and look for principles characterising the organisation of the information. With an observational study approach, data was gathered during the morning and evening nursing change of shift hand-offs in a Paediatric Intensive Care Unit. Content analysis identified a common meta-structure used for information transfer that contained categories with varying degrees of information integration and the repetition of high consequence information. Differences were found in the organisation of the hand-off structures, and these varied as a function of nursing experience. The findings are discussed in terms of the potential benefits of computerised tools which utilise standardised structure for information transfer and the implications for future education and critical care skill acquisition. Copyright © 2014 Elsevier Ltd. All rights reserved.

Correlative nanoscale imaging of actin filaments and their complexes

NASA Astrophysics Data System (ADS)

Sharma, Shivani; Zhu, Huanqi; Grintsevich, Elena E.; Reisler, Emil; Gimzewski, James K.

2013-06-01

Actin remodeling is an area of interest in biology in which correlative microscopy can bring a new way to analyze protein complexes at the nanoscale. Advances in EM, X-ray diffraction, fluorescence, and single molecule techniques have provided a wealth of information about the modulation of the F-actin structure and its regulation by actin binding proteins (ABPs). Yet, there are technological limitations of these approaches to achieving quantitative molecular level information on the structural and biophysical changes resulting from ABPs interaction with F-actin. Fundamental questions about the actin structure and dynamics and how these determine the function of ABPs remain unanswered. Specifically, how local and long-range structural and conformational changes result in ABPs induced remodeling of F-actin needs to be addressed at the single filament level. Advanced, sensitive and accurate experimental tools for detailed understanding of ABP-actin interactions are much needed. This article discusses the current understanding of nanoscale structural and mechanical modulation of F-actin by ABPs at the single filament level using several correlative microscopic techniques, focusing mainly on results obtained by Atomic Force Microscopy (AFM) analysis of ABP-actin complexes.

Three dimensional electron microscopy and in silico tools for macromolecular structure determination

PubMed Central

Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

2013-01-01

Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it. PMID:27092033

Probing the Complexities of Structural Changes in Layered Oxide Cathode Materials for Li-Ion Batteries during Fast Charge–Discharge Cycling and Heating

DOE PAGES

Hu, Enyuan; Wang, Xuelong; Yu, Xiqian; ...

2018-01-19

The rechargeable lithium-ion battery (LIB) is the most promising energy storage system to power electric vehicles with high energy density and long cycling life. However, in order to meet customers’ demands for fast charging, the power performances of current LIBs need to be improved. From the cathode aspect, layer-structured cathode materials are widely used in today’s market and will continue to play important roles in the near future. The high rate capability of layered cathode materials during charging and discharging is critical to the power performance of the whole cell and the thermal stability is closely related to the safetymore » issues. Therefore, the in-depth understanding of structural changes of layered cathode materials during high rate charging/discharging and the thermal stability during heating are essential in developing new materials and improving current materials. Since structural changes take place from the atomic level to the whole electrode level, combination of characterization techniques covering multilength scales is quite important. Finally, in many cases, this means using comprehensive tools involving diffraction, spectroscopy, and imaging to differentiate the surface from the bulk and to obtain structural/chemical information with different levels of spatial resolution.« less

Simulation of controllable permeation in PNIPAAm coated membranes

NASA Astrophysics Data System (ADS)

Ehrenhofer, Adrian; Wallmersperger, Thomas; Richter, Andreas

2016-04-01

Membranes separate fluid compartments and can comprise transport structures for selective permeation. In biology, channel proteins are specialized in their atomic structure to allow transport of specific compounds (selectivity). Conformational changes in protein structure allow the control of the permeation abilities by outer stimuli (gating). In polymeric membranes, the selectivity is due to electrostatic or size-exclusion. It can thus be controlled by size variation or electric charges. Controllable permeation can be useful to determine particle-size distributions in continuous flow, e.g. in microfluidics and biomedicine to gain cell diameter profiles in blood. The present approach uses patterned polyethylene terephthalate (PET) membranes with hydrogel surface coating for permeation control by size-exclusion. The thermosensitive hydrogel poly(N-isopropylacrylamide) (PNIPAAm) is structured with a cross-shaped pore geometry. A change in the temperature of the water flow through the membrane leads to a pore shape variation. The temperature dependent behavior of PNIPAAm can be numerically modeled with a temperature expansion model, where the swelling and deswelling is depicted by temperature dependent expansion coefficients. In the present study, the free swelling behavior was implemented to the Finite Element tool ABAQUS for the complex composite structure of the permeation control membrane. Experimental values of the geometry characteristics were derived from microscopy images with the tool Image J and compared to simulation results. Numerical simulations using the derived thermo-mechanical model for different pore geometries (circular, rectangle, cross and triangle) were performed. With this study, we show that the temperature expansion model with values from the free swelling behavior can be used to adequately predict the deformation behavior of the complex membrane system. The predictions can be used to optimize the behavior of the membrane pores and the overall performance of the smart membrane.

Resolution of structural heterogeneity in dynamic crystallography

PubMed Central

Ren, Zhong; Chan, Peter W. Y.; Moffat, Keith; Pai, Emil F.; Royer, William E.; Šrajer, Vukica; Yang, Xiaojing

2013-01-01

Dynamic behavior of proteins is critical to their function. X-­ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic ‘structural changes’ are often indirectly inferred from ‘structural differences’ by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods. PMID:23695239

Mechanical Response Analysis of Long-life Asphalt Pavement Structure of Yunluo High-speed on the Semi-rigid Base

NASA Astrophysics Data System (ADS)

Liu, Feng; Wu, Chuanhai; Xu, Xinquan; Li, Hao; Wang, Zhixiang

2018-01-01

In order to grasp the rule of the strain change of the semi-rigid asphalt pavement structure under the FWD load and provide a reliable theoretical and practical basis for the design of the pavement structure, based on the test section of Guangdong Yunluo expressway, taking FWD as the loading tool, by using the finite element analysis software ANSYS, the internal variation rules of each pavement structural layer were obtained. Based on the results of the theoretical analysis, the measured strain sensor was set up in the corresponding layer of the pavement structure, and the strain test plan was determined. Based on the analysis of the strain data obtained from several structural layers and field monitoring, the rationality of the type pavement structure and the strain test scheme were verified, so as to provide useful help for the design and the maintenance of the pavement structure.

Advanced Usage of Vehicle Sketch Pad for CFD-Based Conceptual Design

NASA Technical Reports Server (NTRS)

Ordaz, Irian; Li, Wu

2013-01-01

Conceptual design is the most fluid phase of aircraft design. It is important to be able to perform large scale design space exploration of candidate concepts that can achieve the design intent to avoid more costly configuration changes in later stages of design. This also means that conceptual design is highly dependent on the disciplinary analysis tools to capture the underlying physics accurately. The required level of analysis fidelity can vary greatly depending on the application. Vehicle Sketch Pad (VSP) allows the designer to easily construct aircraft concepts and make changes as the design matures. More recent development efforts have enabled VSP to bridge the gap to high-fidelity analysis disciplines such as computational fluid dynamics and structural modeling for finite element analysis. This paper focuses on the current state-of-the-art geometry modeling for the automated process of analysis and design of low-boom supersonic concepts using VSP and several capability-enhancing design tools.

The effect of defocusing on spot diameter when ablate the silicon surface by femtosecond laser

NASA Astrophysics Data System (ADS)

Luo, Xinkai; Li, Wei; Wu, Tengfei; Wang, Yu; Zhu, Zhenyu

2018-02-01

Femtosecond laser has been demonstrated to be a prominent tool to manufacture micro scale structure. In the processing, the focusing lens is usually used as the concentrated tool to assemble the original beam to the tiny spot to provide enough energy for ablation. What is more, different focal length means the diverse scale of the focused spot. In common use, various sizes of the spot are required to adjust to the multifarious profiles and substituting the focus lens is the general method. There is no doubt that changing the lens is a fussy job and frequent replacing the lens may cause the lack of stability. In this paper, we report the defocus of the lens to modify the scale of the spot and it is proved to be an effective way to vary the diameter of the focused spot without changing the focus lens.

Studies in electron phenomena in MOS structures: The pulsed C-V method. M.S. Thesis. Abstract Only

NASA Technical Reports Server (NTRS)

Kaplan, G.

1983-01-01

The pulse hysteresis capacitance voltage (C-V) provides a straight forward technique for measuring the change of various charges in MOS structures and a tool for investigating the kinetics of various electron phenomena is developed and described. The method can be used for measuring the energy distribution and kinetics of surface states with the resolution of about 1/5 x 10 to the -9 power cm eV. Some transients in an MOS structure, particularly, the thermal generation of minority charge carriers via surface states and the relaxation of minority charge carriers supplied from the inversion layer outside the MOS structure are theoretically investigated. Analytical expressions which clearly present the physics of those electron phenomena are derived.

Multiscale molecular dynamics simulations of rotary motor proteins.

PubMed

Ekimoto, Toru; Ikeguchi, Mitsunori

2018-04-01

Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

Visual Basic, Excel-based fish population modeling tool - The pallid sturgeon example

USGS Publications Warehouse

Moran, Edward H.; Wildhaber, Mark L.; Green, Nicholas S.; Albers, Janice L.

2016-02-10

The model presented in this report is a spreadsheet-based model using Visual Basic for Applications within Microsoft Excel (http://dx.doi.org/10.5066/F7057D0Z) prepared in cooperation with the U.S. Army Corps of Engineers and U.S. Fish and Wildlife Service. It uses the same model structure and, initially, parameters as used by Wildhaber and others (2015) for pallid sturgeon. The difference between the model structure used for this report and that used by Wildhaber and others (2015) is that variance is not partitioned. For the model of this report, all variance is applied at the iteration and time-step levels of the model. Wildhaber and others (2015) partition variance into parameter variance (uncertainty about the value of a parameter itself) applied at the iteration level and temporal variance (uncertainty caused by random environmental fluctuations with time) applied at the time-step level. They included implicit individual variance (uncertainty caused by differences between individuals) within the time-step level.The interface developed for the model of this report is designed to allow the user the flexibility to change population model structure and parameter values and uncertainty separately for every component of the model. This flexibility makes the modeling tool potentially applicable to any fish species; however, the flexibility inherent in this modeling tool makes it possible for the user to obtain spurious outputs. The value and reliability of the model outputs are only as good as the model inputs. Using this modeling tool with improper or inaccurate parameter values, or for species for which the structure of the model is inappropriate, could lead to untenable management decisions. By facilitating fish population modeling, this modeling tool allows the user to evaluate a range of management options and implications. The goal of this modeling tool is to be a user-friendly modeling tool for developing fish population models useful to natural resource managers to inform their decision-making processes; however, as with all population models, caution is needed, and a full understanding of the limitations of a model and the veracity of user-supplied parameters should always be considered when using such model output in the management of any species.

Friction Stir Welding of Metal Matrix Composites for use in aerospace structures

NASA Astrophysics Data System (ADS)

Prater, Tracie

2014-01-01

Friction Stir Welding (FSW) is a relatively nascent solid state joining technique developed at The Welding Institute (TWI) in 1991. The process was first used at NASA to weld the super lightweight external tank for the Space Shuttle. Today FSW is used to join structural components of the Delta IV, Atlas V, and Falcon IX rockets as well as the Orion Crew Exploration Vehicle. A current focus of FSW research is to extend the process to new materials which are difficult to weld using conventional fusion techniques. Metal Matrix Composites (MMCs) consist of a metal alloy reinforced with ceramics and have a very high strength to weight ratio, a property which makes them attractive for use in aerospace and defense applications. MMCs have found use in the space shuttle orbiter's structural tubing, the Hubble Space Telescope's antenna mast, control surfaces and propulsion systems for aircraft, and tank armors. The size of MMC components is severely limited by difficulties encountered in joining these materials using fusion welding. Melting of the material results in formation of an undesirable phase (formed when molten Aluminum reacts with the reinforcement) which leaves a strength depleted region along the joint line. Since FSW occurs below the melting point of the workpiece material, this deleterious phase is absent in FSW-ed MMC joints. FSW of MMCs is, however, plagued by rapid wear of the welding tool, a consequence of the large discrepancy in hardness between the steel tool and the reinforcement material. This work characterizes the effect of process parameters (spindle speed, traverse rate, and length of joint) on the wear process. Based on the results of these experiments, a phenomenological model of the wear process was constructed based on the rotating plug model for FSW. The effectiveness of harder tool materials (such as Tungsten Carbide, high speed steel, and tools with diamond coatings) to combat abrasive wear is explored. In-process force, torque, and vibration signals are analyzed to assess the feasibility of on-line monitoring of tool shape changes as a result of wear (an advancement which would eliminate the need for off-line evaluation of tool condition during joining). Monitoring, controlling, and reducing tool wear in FSW of MMCs is essential to the implementation of these materials in structures (such as launch vehicles) where they would be of maximum benefit.

Voltage-Gated Channel Mechanosensitivity: Fact or Friction?

PubMed Central

Morris, Catherine E.

2011-01-01

The heart is a continually active pulsatile fluid pump. It generates appropriate forces by precisely timed and spaced engagement of its contractile machinery. Largely, it makes its own control signals, the most crucial of which are precisely timed and spaced fluxes of ions across the sarcolemma, achieved by the timely opening and closing of diverse voltage-gated channels (VGC). VGCs have four voltage sensors around a central ion-selective pore that opens and closes under the influence of membrane voltage. Operation of any VGC is secondarily tuned by the mechanical state (i.e., structure) of the bilayer in which it is embedded. Rates of opening and closing, in other words, vary with bilayer structure. Thus, in the intensely mechanical environment of the myocardium and its vasculature, VGCs kinetics might be routinely modulated by reversible and irreversible nano-scale changes in bilayer structure. If subtle bilayer deformations are routine in the pumping heart, VGCs could be subtly transducing bilayer mechanical signals, thereby tuning cardiac rhythmicity, collectively contributing to mechano-electric feedback. Reversible bilayer deformations would be expected with changing shear flows and tissue distension, while irreversible bilayer restructuring occurs with ischemia, inflammation, membrane remodeling, etc. I suggest that tools now available could be deployed to help probe whether/how the inherent mechanosensitivity of VGCs – an attribute substantially reflecting the dependence of voltage sensor stability on bilayer structure – contributes to cardiac rhythmicity. Chief among these tools are voltage sensor toxins (whose inhibitory efficacy varies with the mechanical state of bilayer) and arrhythmia-inducing VGC mutants with distinctive mechano-phenotypes. PMID:21660289

Integration of community structure data reveals observable effects below sediment guideline thresholds in a large estuary.

PubMed

Tremblay, Louis A; Clark, Dana; Sinner, Jim; Ellis, Joanne I

2017-09-20

The sustainable management of estuarine and coastal ecosystems requires robust frameworks due to the presence of multiple physical and chemical stressors. In this study, we assessed whether ecological health decline, based on community structure composition changes along a pollution gradient, occurred at levels below guideline threshold values for copper, zinc and lead. Canonical analysis of principal coordinates (CAP) was used to characterise benthic communities along a metal contamination gradient. The analysis revealed changes in benthic community distribution at levels below the individual guideline values for the three metals. These results suggest that field-based measures of ecological health analysed with multivariate tools can provide additional information to single metal guideline threshold values to monitor large systems exposed to multiple stressors.

Evolution and inheritance of animal mitochondrial DNA: rules and exceptions.

PubMed

Ladoukakis, Emmanuel D; Zouros, Eleftherios

2017-12-01

Mitochondrial DNA (mtDNA) has been studied intensely for "its own" merit. Its role for the function of the cell and the organism remains a fertile field, its origin and evolution is an indispensable part of the evolution of life and its interaction with the nuclear DNA is among the most important cases of genome synergism and co-evolution. Also, mtDNA was proven one of the most useful tools in population genetics and molecular phylogenetics. In this article we focus on animal mtDNA and discuss briefly how our views about its structure, function and transmission have changed, how these changes affect the information we have accumulated through its use in the fields of phylogeny and population structure and what are the most important questions that remain open for future research.

Young macaques (Macaca fascicularis) preferentially bias attention towards closer, older, and better tool users.

PubMed

Tan, Amanda W Y; Hemelrijk, Charlotte K; Malaivijitnond, Suchinda; Gumert, Michael D

2018-05-12

Examining how animals direct social learning during skill acquisition under natural conditions, generates data for examining hypotheses regarding how transmission biases influence cultural change in animal populations. We studied a population of macaques on Koram Island, Thailand, and examined model-based biases during interactions by unskilled individuals with tool-using group members. We first compared the prevalence of interactions (watching, obtaining food, object exploration) and proximity to tool users during interactions, in developing individuals (infants, juveniles) versus mature non-learners (adolescents, adults), to provide evidence that developing individuals are actively seeking information about tool use from social partners. All infants and juveniles, but only 49% of mature individuals carried out interacted with tool users. Macaques predominantly obtained food by scrounging or stealing, suggesting maximizing scrounging opportunities motivates interactions with tool users. However, while interactions by adults was limited to obtaining food, young macaques and particularly infants also watched tool users and explored objects, indicating additional interest in tool use itself. We then ran matrix correlations to identify interaction biases, and what attributes of tool users influenced these. Biases correlated with social affiliation, but macaques also preferentially targeted tool users that potentially increase scrounging and learning opportunities. Results suggest that social structure may constrain social learning, but the motivation to bias interactions towards tool users to maximize feeding opportunities may also socially modulate learning by facilitating close proximity to better tool users, and further interest in tool-use actions and materials, especially during development.

Surgical tool detection and tracking in retinal microsurgery

NASA Astrophysics Data System (ADS)

Alsheakhali, Mohamed; Yigitsoy, Mehmet; Eslami, Abouzar; Navab, Nassir

2015-03-01

Visual tracking of surgical instruments is an essential part of eye surgery, and plays an important role for the surgeons as well as it is a key component of robotics assistance during the operation time. The difficulty of detecting and tracking medical instruments in-vivo images comes from its deformable shape, changes in brightness, and the presence of the instrument shadow. This paper introduces a new approach to detect the tip of surgical tool and its width regardless of its head shape and the presence of the shadows or vessels. The approach relies on integrating structural information about the strong edges from the RGB color model, and the tool location-based information from L*a*b color model. The probabilistic Hough transform was applied to get the strongest straight lines in the RGB-images, and based on information from the L* and a*, one of these candidates lines is selected as the edge of the tool shaft. Based on that line, the tool slope, the tool centerline and the tool tip could be detected. The tracking is performed by keeping track of the last detected tool tip and the tool slope, and filtering the Hough lines within a box around the last detected tool tip based on the slope differences. Experimental results demonstrate the high accuracy achieved in term of detecting the tool tip position, the tool joint point position, and the tool centerline. The approach also meets the real time requirements.

ASTROS: A multidisciplinary automated structural design tool

NASA Technical Reports Server (NTRS)

Neill, D. J.

1989-01-01

ASTROS (Automated Structural Optimization System) is a finite-element-based multidisciplinary structural optimization procedure developed under Air Force sponsorship to perform automated preliminary structural design. The design task is the determination of the structural sizes that provide an optimal structure while satisfying numerous constraints from many disciplines. In addition to its automated design features, ASTROS provides a general transient and frequency response capability, as well as a special feature to perform a transient analysis of a vehicle subjected to a nuclear blast. The motivation for the development of a single multidisciplinary design tool is that such a tool can provide improved structural designs in less time than is currently needed. The role of such a tool is even more apparent as modern materials come into widespread use. Balancing conflicting requirements for the structure's strength and stiffness while exploiting the benefits of material anisotropy is perhaps an impossible task without assistance from an automated design tool. Finally, the use of a single tool can bring the design task into better focus among design team members, thereby improving their insight into the overall task.

Constraints on interpretations structural trap in 4 dimensions

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

Kelsch, K.D.; Kowalik, W.S.; Kluth, C.F.

1995-04-01

Interpretation of the geometry of the structural hydrocarbon trap continues to be one of the fundamental risks in exploration for, and production of, hydrocarbons. New geometric and computer tools are being developed to improve those interpretations by allowing the incremental restoration of structures in three dimensions. This adds powerful constraints on the structural interpretation because it requires that the interpretation be rational and consistent not only for the structure in the line of one cross section at the present time, but also for all moments during its development in 3 dimensions. It is possible to gather information, such as juxtapositionmore » of different reservoir units through time to evaluate the development of seals or leaks with respect to trap formation and to maturation and migration of hydrocarbons. In addition, software is available to produce interactive 3D images of the data that allow the interpreter to see the 4D restoration as it proceeds, but also to change the viewing orientation. This allows the interpreter to {open_quotes}move{close_quotes} through the restoration and examine areas critical for the interpretation as the restoration proceeds while viewing in 3D. While some of these tools are still under development, we have applied them successfully to model and real data sets.« less

Instituting a standards-based K--12 science curriculum supplement program at the National Institutes of Health: A case study

NASA Astrophysics Data System (ADS)

Witherly, Jeffre

Research on student achievement indicates the U.S. K-12 education system is not adequately preparing American students to compete in the 21st century global economy in the areas of science and mathematics. Congress has asked the scientific entities of the federal government to help increase K-12 science learning by creating standards-based learning tools for science classrooms as part of a "voluntary curriculum." One problem facing federal entities, such as the National Institutes of Health (NIH), is the need to create science-learning tools that conform to the National Science Education Standards (NSES) for curriculum materials and, therefore, are standards-based and applicable to the K-12 curriculum. This case study sought to better understand the change process at one federal agency as it went from producing K-12 learning tools that were educational in nature to a program that produced K-12 standards-based learning tools: the NIH Science Curriculum Supplement Program (NIH SCSP). The NIH SCSP was studied to gain insight into how this change in educational approach occurred, what factors enabled or inhibited the change process, and what the long-term benefits of the NIH SCSP are to the NIH. Kurt Lewin's three-step theory of change guided data gathering and data analysis. Semi-structured interviews and programmatic document review served as the major data gathering sources. Details describing the process of organizational change at the NIH were revealed during analysis of these data following the coding of interview transcripts and written record documents. The study found the process of change at the NIH proceeded in a manner generally predicted by the Lewinian change model. Enablers to the change were cost-sharing with individual institutes, support of senior leadership, and crediting the role of individual institutes prominently in each supplement. The cost of creating a supplement was reported as the single inhibitor to the program. This case study yielded a detailed description of the process of change at this federal institution that may offer valuable insights to similar federal organizations confronting educational change. The study may also contribute to the existing body of knowledge regarding the process of organizational change in a federal setting.

Understanding the structure and structural degradation mechanisms in high-voltage lithium-ion battery cathode oxides. A review of materials diagnostics

DOE PAGES

Mohanty, Debasish; Li, Jianlin; Nagpure, Shrikant C; ...

2015-12-21

Materials diagnostic techniques are the principal tools used in the development of low-cost, high-performance electrodes for next-generation lithium-based energy storage technologies. Also, this review highlights the importance of materials diagnostic techniques in unraveling the structure and the structural degradation mechanisms in high-voltage, high-capacity oxides that have the potential to be implemented in high-energy-density lithium-ion batteries for transportation that can use renewable energy and is less-polluting than today. The rise in CO 2 concentration in the earth’s atmosphere due to the use of petroleum products in vehicles and the dramatic increase in the cost of gasoline demand the replacement of currentmore » internal combustion engines in our vehicles with environmentally friendly, carbon free systems. Therefore, vehicles powered fully/partially by electricity are being introduced into today’s transportation fleet. As power requirements in all-electric vehicles become more demanding, lithium-ion battery (LiB) technology is now the potential candidate to provide higher energy density. Moreover, discovery of layered high-voltage lithium-manganese–rich (HV-LMR) oxides has provided a new direction toward developing high-energy-density LiBs because of their ability to deliver high capacity (~250 mA h/g) and to be operated at high operating voltage (~4.7 V). Unfortunately, practical use of HV-LMR electrodes is not viable because of structural changes in the host oxide during operation that can lead to fundamental and practical issues. This article provides the current understanding on the structure and structural degradation pathways in HV-LMR oxides, and manifests the importance of different materials diagnostic tools to unraveling the key mechanism(s). Furthermore, the fundamental insights reported, might become the tools to manipulate the chemical and/or structural aspects of HV-LMR oxides for low cost, high-energy-density LiB applications.« less

Anatomical guidance for functional near-infrared spectroscopy: AtlasViewer tutorial

PubMed Central

Aasted, Christopher M.; Yücel, Meryem A.; Cooper, Robert J.; Dubb, Jay; Tsuzuki, Daisuke; Becerra, Lino; Petkov, Mike P.; Borsook, David; Dan, Ippeita; Boas, David A.

2015-01-01

Abstract. Functional near-infrared spectroscopy (fNIRS) is an optical imaging method that is used to noninvasively measure cerebral hemoglobin concentration changes induced by brain activation. Using structural guidance in fNIRS research enhances interpretation of results and facilitates making comparisons between studies. AtlasViewer is an open-source software package we have developed that incorporates multiple spatial registration tools to enable structural guidance in the interpretation of fNIRS studies. We introduce the reader to the layout of the AtlasViewer graphical user interface, the folder structure, and user files required in the creation of fNIRS probes containing sources and detectors registered to desired locations on the head, evaluating probe fabrication error and intersubject probe placement variability, and different procedures for estimating measurement sensitivity to different brain regions as well as image reconstruction performance. Further, we detail how AtlasViewer provides a generic head atlas for guiding interpretation of fNIRS results, but also permits users to provide subject-specific head anatomies to interpret their results. We anticipate that AtlasViewer will be a valuable tool in improving the anatomical interpretation of fNIRS studies. PMID:26157991

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.

Video Clips for Youtube: Collaborative Video Creation as an Educational Concept for Knowledge Acquisition and Attitude Change Related to Obesity Stigmatization

ERIC Educational Resources Information Center

Zahn, Carmen; Schaeffeler, Norbert; Giel, Katrin Elisabeth; Wessel, Daniel; Thiel, Ansgar; Zipfel, Stephan; Hesse, Friedrich W.

2014-01-01

Mobile phones and advanced web-based video tools have pushed forward new paradigms for using video in education: Today, students can readily create and broadcast their own digital videos for others and create entirely new patterns of video-based information structures for modern online-communities and multimedia environments. This paradigm shift…

Relating fire-caused change in forest structure to remotely sensed estimates of fire severity

Treesearch

Jamie M. Lydersen; Brandon M. Collins; Jay D. Miller; Danny L. Fry; Scott L. Stephens

2016-01-01

Fire severity maps are an important tool for understanding fire effects on a landscape. The relative differenced normalized burn ratio (RdNBR) is a commonly used severity index in California forests, and is typically divided into four categories: unchanged, low, moderate, and high. RdNBR is often calculated twice--from images collected the year of the fire (initial...

Humans and Autonomy: Implications of Shared Decision Making for Military Operations

DTIC Science & Technology

2017-01-01

and machine learning transparency are identified as future research opportunities. 15. SUBJECT TERMS autonomy, human factors, intelligent agents...network as either the mission changes or an agent becomes disabled (DSB 2012). Fig. 2 Control structures for human agent teams. Robots without tools... learning (ML) algorithms monitor progress. However, operators have final executive authority; they are able to tweak the plan or choose an option

Mediation Game When the Conflict Can Be Fun to Learn--A Legal Skill Learning Tool: The Integration of Knowledge Management, Learning Theory and Serious Game Concept

ERIC Educational Resources Information Center

Luengvilai, Chainarong; Yodmongkol, Pitipong

2016-01-01

Legal justice in Thailand has been shifted to restorative justice for reasons. But Thai law schools have not been changed to promote lawyering skill learning opportunities due to various obstacles and limitations caused by existing legal educational policies, law curriculum's structure, knowledgeable instructors, and learners' characteristics. As…

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.

PubMed

Furnham, Nicholas; Dawson, Natalie L; Rahman, Syed A; Thornton, Janet M; Orengo, Christine A

2016-01-29

Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology. Over 100 years of detailed biochemistry studies, combined with the large volumes of sequence and protein structural data now available, means that we are able to perform large-scale analyses to address this question. Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, linking the changes observed in functions during evolution to changes in reaction chemistry. Many superfamilies show changes in function at some level, although one function often dominates one superfamily. We use quantitative measures of changes in reaction chemistry to reveal the various types of chemical changes occurring during evolution and to exemplify these by detailed examples. Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. Some superfamilies have changed the reactions they perform without changing catalytic machinery. In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery. Interestingly, in some superfamilies, relatives perform similar functions but with different catalytic machineries. This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Manufacturing Challenges Associated with the Use of Metal Matrix Composites in Aerospace Structures

NASA Technical Reports Server (NTRS)

Prater, Tracie

2014-01-01

Metal Matrix Composites (MMCs) consist of a metal alloy reinforced with ceramic particles or fibers. These materials possess a very high strength to weight ratio, good resistance to impact and wear, and a number of other properties which make them attractive for use in aerospace and defense applications. MMCs have found use in the space shuttle orbiter's structural tubing, the Hubble Space Telescope's antenna mast, control surfaces and propulsion systems for aircraft, and tank armors. The size of MMC components is severely limited by difficulties encountered in joining these materials using fusion welding. Melting of the material results in formation of an undesirable phase (formed when molten Aluminum reacts with the reinforcement) which leaves a strength depleted region along the joint line. Friction Stir Welding (FSW) is a relatively nascent solid state joining technique developed at The Welding Institute (TWI) in 1991. The process was first used at NASA to weld the super lightweight external tank for the Space Shuttle. Today FSW is used to join structural components of the Delta IV, Atlas V, and Falcon IX rockets as well as NASA's Orion Crew Exploration Vehicle and Space Launch System. A current focus of FSW research is to extend the process to new materials, such as MMCs, which are difficult to weld using conventional fusion techniques. Since Friction Stir Welding occurs below the melting point of the workpiece material, this deleterious phase is absent in FSW-ed MMC joints. FSW of MMCs is, however, plagued by rapid wear of the welding tool, a consequence of the large discrepancy in hardness between the steel tool and the reinforcement material. This chapter summarizes the challenges encountered when joining MMCs to themselves or to other materials in structures. Specific attention is paid to the influence of process variables in Friction Stir Welding on the wear process characterizes the effect of process parameters (spindle speed, traverse rate, and length of joint) on the wear process. A phenomenological model of the wear process was constructed based on the rotating plug model of Friction Stir Welding. The effectiveness of harder tool materials (such as Tungsten Carbide, high speed steel, and tools with diamond coatings) to combat abrasive wear is also explored. In-process force, torque, and vibration signals are analyzed to assess the feasibility of in situ monitoring of tool shape changes as a result of wear (an advancement which would eliminate the need for off-line evaluation of tool condition during joining). Monitoring, controlling, and reducing tool wear in FSW of MMCs is essential to implementation of these materials in structures (such as launch vehicles) where they would be of maximum benefit. The work presented here is extendable to machining of MMCs, where wear of the tool is also a limiting factor.

Magnetic resonance imaging can accurately assess the long-term progression of knee structural changes in experimental dog osteoarthritis.

PubMed

Boileau, C; Martel-Pelletier, J; Abram, F; Raynauld, J-P; Troncy, E; D'Anjou, M-A; Moreau, M; Pelletier, J-P

2008-07-01

Osteoarthritis (OA) structural changes take place over decades in humans. MRI can provide precise and reliable information on the joint structure and changes over time. In this study, we investigated the reliability of quantitative MRI in assessing knee OA structural changes in the experimental anterior cruciate ligament (ACL) dog model of OA. OA was surgically induced by transection of the ACL of the right knee in five dogs. High resolution three dimensional MRI using a 1.5 T magnet was performed at baseline, 4, 8 and 26 weeks post surgery. Cartilage volume/thickness, cartilage defects, trochlear osteophyte formation and subchondral bone lesion (hypersignal) were assessed on MRI images. Animals were killed 26 weeks post surgery and macroscopic evaluation was performed. There was a progressive and significant increase over time in the loss of knee cartilage volume, the cartilage defect and subchondral bone hypersignal. The trochlear osteophyte size also progressed over time. The greatest cartilage loss at 26 weeks was found on the tibial plateaus and in the medial compartment. There was a highly significant correlation between total knee cartilage volume loss or defect and subchondral bone hypersignal, and also a good correlation between the macroscopic and the MRI findings. This study demonstrated that MRI is a useful technology to provide a non-invasive and reliable assessment of the joint structural changes during the development of OA in the ACL dog model. The combination of this OA model with MRI evaluation provides a promising tool for the evaluation of new disease-modifying osteoarthritis drugs (DMOADs).

Integration of Full Tensor Gravity and Z-Axis Tipper Electromagnetic Passive Low Frequency EM Instruments for Simultaneous Data Acquisition - Final Technical Report

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

Wieberg, Scott

Ground gravity is a common and useful tool for geothermal exploration. Gravity surveys map density changes in the subsurface that may be caused by tectonic deformation such as faulting, fracturing, plutonism, volcanism, hydrothermal alteration, etc. Full Tensor Gravity Gradient (FTG) data has been used for over a decade in both petroleum and mining exploration to map changes in density associated with geologic structure. Measuring the gravity gradient, rather than the gravity field, provides significantly higher resolution data. Modeling studies have shown FTG data to be a viable tool for geothermal exploration, but no FTG data had been acquired for geothermalmore » applications to date. Electromagnetic methods have been used for geothermal exploration for some time. The Z-Axis Tipper Electromagnetic (ZTEM) was a newer technology that had found success in mapping deep conductivity changes for mining applications. ZTEM had also been used in limited tests for geothermal exploration. This newer technology provided the ability to cost effectively map large areas whilst detailing the electrical properties of the geological structures at depths. The ZTEM is passive and it uses naturally occurring audio frequency magnetic (AFMAG) signals as the electromagnetic triggering source. These geophysical methods were to be tested over a known geothermal site to determine whether or not the data provided the information required for accurately interpreting the subsurface geologic structure associated with a geothermal deposit. After successful acquisition and analysis of the known source area, an additional survey of a “greenfield” area was to be completed. The final step was to develop a combined interpretation model and determine if the combination produced a higher confident geophysical model compared to models developed using each of the technologies individually.« less

The Feeding Practices and Structure Questionnaire (FPSQ-28): A parsimonious version validated for longitudinal use from 2 to 5 years.

PubMed

Jansen, Elena; Williams, Kate E; Mallan, Kimberley M; Nicholson, Jan M; Daniels, Lynne A

2016-05-01

Prospective studies and intervention evaluations that examine change over time assume that measurement tools measure the same construct at each occasion. In the area of parent-child feeding practices, longitudinal measurement properties of the questionnaires used are rarely verified. To ascertain that measured change in feeding practices reflects true change rather than change in the assessment, structure, or conceptualisation of the constructs over time, this study examined longitudinal measurement invariance of the Feeding Practices and Structure Questionnaire (FPSQ) subscales (9 constructs; 40 items) across 3 time points. Mothers participating in the NOURISH trial reported their feeding practices when children were aged 2, 3.7, and 5 years (N = 404). Confirmatory Factor Analysis (CFA) within a structural equation modelling framework was used. Comparisons of initial cross-sectional models followed by longitudinal modelling of subscales, resulted in the removal of 12 items, including two redundant or poorly performing subscales. The resulting 28-item FPSQ-28 comprised 7 multi-item subscales: Reward for Behaviour, Reward for Eating, Persuasive Feeding, Overt Restriction, Covert Restriction, Structured Meal Setting and Structured Meal Timing. All subscales showed good fit over 3 time points and each displayed at least partial scalar (thresholds equal) longitudinal measurement invariance. We recommend the use of a separate single item indicator to assess the family meal setting. This is the first study to examine longitudinal measurement invariance in a feeding practices questionnaire. Invariance was established, indicating that the subscales of the shortened FPSQ-28 can be used with mothers to validly assess change in 7 feeding constructs in samples of children aged 2-5 years of age. Copyright © 2016 Elsevier Ltd. All rights reserved.

NNDC Tools and Publications

Science.gov Websites

Site Index NNDC Tools and Publications Nuclear Structure and Decay Tools Nuclear Reaction Tools Nuclear Structure and Decay Tools 2016 Atomic Mass Evaluation Atomic mass evaluation, by Wang, Audi values as a function of gamma energy and multipolarity. Calculations based on I.M. Band and S. Raman

Implementation of structure-mapping inference by event-file binding and action planning: a model of tool-improvisation analogies.

PubMed

Fields, Chris

2011-03-01

Structure-mapping inferences are generally regarded as dependent upon relational concepts that are understood and expressible in language by subjects capable of analogical reasoning. However, tool-improvisation inferences are executed by members of a variety of non-human primate and other species. Tool improvisation requires correctly inferring the motion and force-transfer affordances of an object; hence tool improvisation requires structure mapping driven by relational properties. Observational and experimental evidence can be interpreted to indicate that structure-mapping analogies in tool improvisation are implemented by multi-step manipulation of event files by binding and action-planning mechanisms that act in a language-independent manner. A functional model of language-independent event-file manipulations that implement structure mapping in the tool-improvisation domain is developed. This model provides a mechanism by which motion and force representations commonly employed in tool-improvisation structure mappings may be sufficiently reinforced to be available to inwardly directed attention and hence conceptualization. Predictions and potential experimental tests of this model are outlined.

Exploring the effect of at-risk case management compensation on hospital pay-for-performance outcomes: tools for change.

PubMed

Granata, Randy L; Hamilton, Karen

2015-01-01

Acute care nurse case managers are charged with compliance oversight, managing throughput, and ensuring safe care transitions. Leveraging the roles of nurse case managers and social workers during care transitions translates into improved fiscal performance under the Affordable Care Act. This article aims to equip leaders in the field of case management with tools to facilitate the alignment of case management systems with hospital pay-for-performance measures. A quality improvement project was implemented at a hospital in south Alabama to examine the question: for acute care case managers, what is the effect of key performance indictors using an at-risk compensation model in comparison to past nonincentive models on hospital readmissions, lengths of stay, and patient satisfaction surrounding the discharge process. Inpatient acute care hospital. The implementation of an at-risk compensation model using key performance indicators, Lean Six Sigma methodology, and Creative Health Care Management's Relationship-Based Care framework demonstrated reduced length of stay, hospital readmissions, and improved patient experiences. Regulatory changes and new models of reimbursement in the acute care environment have created the perfect storm for case management leaders. Hospital fiscal performance is dependent on effective case management processes and the ability to optimize scarce resources. The quality improvement project aimed to further align case management systems and structures with hospital pay-for-performance measures. Tools for change were presented to assist leaders with the change acceleration process.

Building Training Curricula for Accelerating the Use of NOAA Climate Products and Tools

NASA Astrophysics Data System (ADS)

Timofeyeva-Livezey, M. M.; Meyers, J. C.; Stevermer, A.; Abshire, W. E.; Beller-Simms, N.; Herring, D.

2016-12-01

The National Oceanic and Atmospheric Administration (NOAA) plays a leading role in U.S. intergovernmental efforts on the Climate Data Initiative and the Climate Resilience Toolkit (CRT). CRT (http://toolkit.climate.gov/) is a valuable resource that provides tools, information, and subject matter expertise to decision makers in various sectors, such as agriculture, water resources and transportation, to help them build resilience to our changing climate. In order to make best use of the toolkit and all the resources within it, a training component is critical. The training section helps building users' understanding of the data, science, and impacts of climate variability and change. CRT identifies five steps in building resilience that includes use of appropriate tools to support decision makers depending on their needs. One tool that can be potentially integrated into CRT is NOAA's Local Climate Analysis Tool (LCAT), which provides access to trusted NOAA data and scientifically-sound analysis techniques for doing regional and local climate studies on climate variability and climate change. However, in order for LCAT to be used effectively, we have found an iterative learning approach using specific examples to train users. For example, for LCAT application in analysis of water resources, we use existing CRT case studies for Arizona and Florida water supply users. The Florida example demonstrates primary sensitivity to climate variability impacts, whereas the Arizona example takes into account longer- term climate change. The types of analyses included in LCAT are time series analysis of local climate and the estimated rate of change in the local climate. It also provides a composite analysis to evaluate the relationship between local climate and climate variability events such as El Niño Southern Oscillation, the Pacific North American Index, and other modes of climate variability. This paper will describe the development of a training module for use of LCAT and its integration into CRT. An iterative approach was used that incorporates specific examples of decision making while working with subject matter experts within the water supply community. The recommended strategy is to use a "stepping stone" learning structure to build users knowledge of best practices for use of LCAT.

Improved glucose-neopentyl glycol (GNG) amphiphiles for membrane protein solubilization and stabilization.

PubMed

Cho, Kyung Ho; Bae, Hyoung Eun; Das, Manabendra; Gellman, Samuel H; Chae, Pil Seok

2014-02-01

Membrane proteins are inherently amphipathic and undergo dynamic conformational changes for proper function within native membranes. Maintaining the functional structures of these biomacromolecules in aqueous media is necessary for structural studies but difficult to achieve with currently available tools, thus necessitating the development of novel agents with favorable properties. This study introduces several new glucose-neopentyl glycol (GNG) amphiphiles and reveals some agents that display favorable behaviors for the solubilization and stabilization of a large, multi-subunit membrane protein assembly. Furthermore, a detergent structure-property relationship that could serve as a useful guideline for the design of novel amphiphiles is discussed. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Detailed electromagnetic simulation for the structural color of butterfly wings.

PubMed

Lee, R Todd; Smith, Glenn S

2009-07-20

Many species of butterflies exhibit interesting optical phenomena due to structural color. The physical reason for this color is subwavelength features on the surface of a single scale. The exposed surface of a scale is covered with a ridge structure. The fully three-dimensional, periodic, finite-difference time-domain method is used to create a detailed electromagnetic model of a generic ridge. A novel method for presenting the three-dimensional observed color pattern is developed. Using these tools, the change in color that is a result of varying individual features of the scale is explored. Computational models are developed that are similar to three butterflies: Morpho rhetenor, Troides magellanus, and Ancyluris meliboeus.

RNA-SSPT: RNA Secondary Structure Prediction Tools.

PubMed

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

RNA-SSPT: RNA Secondary Structure Prediction Tools

PubMed Central

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes. PMID:24250115

Present and future of membrane protein structure determination by electron crystallography.

PubMed

Ubarretxena-Belandia, Iban; Stokes, David L

2010-01-01

Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This chapter describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins. Copyright © 2010 Elsevier Inc. All rights reserved.

Present and future of membrane protein structure determination by electron crystallography

PubMed Central

Ubarretxena-Belandia, Iban; Stokes, David L.

2011-01-01

Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This review describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins. PMID:21115172

Culture as a predictor of resistance to change: a study of competing values in a psychiatric nursing context.

PubMed

Johansson, Catrin; Åström, Sture; Kauffeldt, Anders; Helldin, Lars; Carlström, Eric

2014-02-01

It is well known that a conservative organizational culture can hinder the implementation of new organizational models. Prior to introducing something new it is important to identify the culture within the organization. This paper sets out to detect the feasibility of reform in a psychiatric clinic in a Swedish hospital prior to implementation of a new working method - a structured tool based on the International Classification of Functioning Disability and Health. A survey consisting of two instruments - an organizational values questionnaire (OVQ) and a resistance to change scale (RTC) - was distributed to registered and assistant nurses at the clinic. The association between the organizational subcultures and resistance to change was investigated with regression analysis. The results revealed that the dominating cultures in the outpatient centers and hospital wards were characterized by human relation properties such as flexibility, cohesion, belongingness, and trust. The mean resistance to change was low, but the subscale of cognitive rigidity was dominant, reflecting a tendency to avoid alternative ideas and perspectives. An instrument like the one employed in the study could be a useful tool for diagnosing the likelihood of extensive and costly interventions. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Anticipative management for coral reef ecosystem services in the 21st century.

PubMed

Rogers, Alice; Harborne, Alastair R; Brown, Christopher J; Bozec, Yves-Marie; Castro, Carolina; Chollett, Iliana; Hock, Karlo; Knowland, Cheryl A; Marshell, Alyssa; Ortiz, Juan C; Razak, Tries; Roff, George; Samper-Villarreal, Jimena; Saunders, Megan I; Wolff, Nicholas H; Mumby, Peter J

2015-02-01

Under projections of global climate change and other stressors, significant changes in the ecology, structure and function of coral reefs are predicted. Current management strategies tend to look to the past to set goals, focusing on halting declines and restoring baseline conditions. Here, we explore a complementary approach to decision making that is based on the anticipation of future changes in ecosystem state, function and services. Reviewing the existing literature and utilizing a scenario planning approach, we explore how the structure of coral reef communities might change in the future in response to global climate change and overfishing. We incorporate uncertainties in our predictions by considering heterogeneity in reef types in relation to structural complexity and primary productivity. We examine 14 ecosystem services provided by reefs, and rate their sensitivity to a range of future scenarios and management options. Our predictions suggest that the efficacy of management is highly dependent on biophysical characteristics and reef state. Reserves are currently widely used and are predicted to remain effective for reefs with high structural complexity. However, when complexity is lost, maximizing service provision requires a broader portfolio of management approaches, including the provision of artificial complexity, coral restoration, fish aggregation devices and herbivore management. Increased use of such management tools will require capacity building and technique refinement and we therefore conclude that diversification of our management toolbox should be considered urgently to prepare for the challenges of managing reefs into the 21st century. © 2014 John Wiley & Sons Ltd.

Damage detection of civil infrastructures with piezoelectric oscillator sensors

NASA Astrophysics Data System (ADS)

Roh, Y. R.; Kim, D. Y.; Park, S. H.; Yun, C. B.

2006-03-01

Many researches have been reported on the condition monitoring of civil infrastructures by means of piezoelectric sensors. Most of them made use of the impedance change of the piezoelectric device in relation to the creation of internal damages to the structure. The impedance measurement is a well accepted method in the piezoelectric sensor area, and has been proved by many authors to be useful for civil structure diagnosis. However, the impedance measurement normally requires sophisticated equipment and analysis technology. For more general and wide application of the piezoelectric diagnosis tool, a new methodology is desired to overcome the limitations of the impedance measurement. This paper presents the feasibility of a piezoelectric oscillator sensor to detect the damages in civil infrastructures. The oscillator sensor is composed of an electronic feedback oscillator circuit and a piezoelectric thickness mode vibrator to be attached to the structure of interest. Damage to the structure causes a change in the impedance spectrum of the structure, which results in a corresponding change of the resonant frequency of the structure. The oscillator sensors can instantly detect the frequency change in a very simple manner. Feasibility of the piezoelectric oscillator sensor was verified in this work with a sample aluminum plate where artificial cracks of different depth were imposed in sequence. Validity of the measurement was confirmed through comparison of the experimental data with the results of finite element analyses of the plate with cracks. Performance of the oscillator sensor was also compared with that of its conventional counterpart, i.e. impedance measurement, to manifest the superiority of the oscillator sensor.

Prediction Of Tensile And Shear Strength Of Friction Surfaced Tool Steel Deposit By Using Artificial Neural Networks

NASA Astrophysics Data System (ADS)

Manzoor Hussain, M.; Pitchi Raju, V.; Kandasamy, J.; Govardhan, D.

2018-04-01

Friction surface treatment is well-established solid technology and is used for deposition, abrasion and corrosion protection coatings on rigid materials. This novel process has wide range of industrial applications, particularly in the field of reclamation and repair of damaged and worn engineering components. In this paper, we present the prediction of tensile and shear strength of friction surface treated tool steel using ANN for simulated results of friction surface treatment. This experiment was carried out to obtain tool steel coatings of low carbon steel parts by changing contribution process parameters essentially friction pressure, rotational speed and welding speed. The simulation is performed by a 33-factor design that takes into account the maximum and least limits of the experimental work performed with the 23-factor design. Neural network structures, such as the Feed Forward Neural Network (FFNN), were used to predict tensile and shear strength of tool steel sediments caused by friction.

Visualizing the Geography of the Diseases of China: Western Disease Maps from Analytical Tools to Tools of Empire, Sovereignty, and Public Health Propaganda, 1878-1929.

PubMed

Hanson, Marta

2017-09-01

Argument This article analyzes for the first time the earliest western maps of diseases in China spanning fifty years from the late 1870s to the end of the 1920s. The 24 featured disease maps present a visual history of the major transformations in modern medicine from medical geography to laboratory medicine wrought on Chinese soil. These medical transformations occurred within new political formations from the Qing dynasty (1644-1911) to colonialism in East Asia (Hong Kong, Taiwan, Manchuria, Korea) and hypercolonialism within China (Tianjin, Shanghai, Amoy) as well as the new Republican Chinese nation state (1912-49). As a subgenre of persuasive graphics, physicians marshaled disease maps for various rhetorical functions within these different political contexts. Disease maps in China changed from being mostly analytical tools to functioning as tools of empire, national sovereignty, and public health propaganda legitimating new medical concepts, public health interventions, and political structures governing over human and non-human populations.

Applications of picosecond lasers and pulse-bursts in precision manufacturing

NASA Astrophysics Data System (ADS)

Knappe, Ralf

2012-03-01

Just as CW and quasi-CW lasers have revolutionized the materials processing world, picosecond lasers are poised to change the world of micromachining, where lasers outperform mechanical tools due to their flexibility, reliability, reproducibility, ease of programming, and lack of mechanical force or contamination to the part. Picosecond lasers are established as powerful tools for micromachining. Industrial processes like micro drilling, surface structuring and thin film ablation benefit from a process, which provides highest precision and minimal thermal impact for all materials. Applications such as microelectronics, semiconductor, and photovoltaic industries use picosecond lasers for maximum quality, flexibility, and cost efficiency. The range of parts, manufactured with ps lasers spans from microscopic diamond tools over large printing cylinders with square feet of structured surface. Cutting glass for display and PV is a large application, as well. With a smart distribution of energy into groups of ps-pulses at ns-scale separation (known as burst mode) ablation rates can be increased by one order of magnitude or more for some materials, also providing a better surface quality under certain conditions. The paper reports on the latest results of the laser technology, scaling of ablation rates, and various applications in ps-laser micromachining.

Probing the onset of structural instabilities as a tool for detection of staling of dairy milk: A permittivity and conductivity study

NASA Astrophysics Data System (ADS)

Madhurima, V.; Harindran, Aswini

2018-05-01

Dairy milk is a worldwide drink and a versatile raw material for food industries too. The major issue regarding dairy milk is their contamination by micro-organisms and subsequent spoiling. Pasteurization and sealed packing are used to minimize this contamination. The presence of pathogenic micro-organisms like psychrotrophs, reduces the pH of fresh milk by fermenting the lactose into lactic acid leading to the spoiling of milk. While there are various tests to check the spoilage of milk, there is no unique test to detect the onset of the complex dynamics of spoilage. There have been some studies on the dielectric properties of dairy milk but the primary method of identification of freshness of milk is through the measurement of pH. In this study, broadband dielectric spectroscopy is used as a tool to probe the spoiling of milk and that provides the information about the structural changes of milk during spoilage. The gamma dispersion explains the influence of free water content which is found to be a sensitive tool to probe the onset of milk spoilage process. The observations here are further backed by studies on the particle size and zeta potential.

GCView: the genomic context viewer for protein homology searches

PubMed Central

Grin, Iwan; Linke, Dirk

2011-01-01

Genomic neighborhood can provide important insights into evolution and function of a protein or gene. When looking at operons, changes in operon structure and composition can only be revealed by looking at the operon as a whole. To facilitate the analysis of the genomic context of a query in multiple organisms we have developed Genomic Context Viewer (GCView). GCView accepts results from one or multiple protein homology searches such as BLASTp as input. For each hit, the neighboring protein-coding genes are extracted, the regions of homology are labeled for each input and the results are presented as a clear, interactive graphical output. It is also possible to add more searches to iteratively refine the output. GCView groups outputs by the hits for different proteins. This allows for easy comparison of different operon compositions and structures. The tool is embedded in the framework of the Bioinformatics Toolkit of the Max-Planck Institute for Developmental Biology (MPI Toolkit). Job results from the homology search tools inside the MPI Toolkit can be forwarded to GCView and results can be subsequently analyzed by sequence analysis tools. Results are stored online, allowing for later reinspection. GCView is freely available at http://toolkit.tuebingen.mpg.de/gcview. PMID:21609955

Can new passenger cars reduce pedestrian lower extremity injury? A review of geometrical changes of front-end design before and after regulatory efforts.

PubMed

Nie, Bingbing; Zhou, Qing

2016-10-02

Pedestrian lower extremity represents the most frequently injured body region in car-to-pedestrian accidents. The European Directive concerning pedestrian safety was established in 2003 for evaluating pedestrian protection performance of car models. However, design changes have not been quantified since then. The goal of this study was to investigate front-end profiles of representative passenger car models and the potential influence on pedestrian lower extremity injury risk. The front-end styling of sedans and sport utility vehicles (SUV) released from 2008 to 2011 was characterized by the geometrical parameters related to pedestrian safety and compared to representative car models before 2003. The influence of geometrical design change on the resultant risk of injury to pedestrian lower extremity-that is, knee ligament rupture and long bone fracture-was estimated by a previously developed assessment tool assuming identical structural stiffness. Based on response surface generated from simulation results of a human body model (HBM), the tool provided kinematic and kinetic responses of pedestrian lower extremity resulted from a given car's front-end design. Newer passenger cars exhibited a "flatter" front-end design. The median value of the sedan models provided 87.5 mm less bottom depth, and the SUV models exhibited 94.7 mm less bottom depth. In the lateral impact configuration similar to that in the regulatory test methods, these geometrical changes tend to reduce the injury risk of human knee ligament rupture by 36.6 and 39.6% based on computational approximation. The geometrical changes did not significantly influence the long bone fracture risk. The present study reviewed the geometrical changes in car front-ends along with regulatory concerns regarding pedestrian safety. A preliminary quantitative benefit of the lower extremity injury reduction was estimated based on these geometrical features. Further investigation is recommended on the structural changes and inclusion of more accident scenarios.

Is it worth changing pattern recognition methods for structural health monitoring?

NASA Astrophysics Data System (ADS)

Bull, L. A.; Worden, K.; Cross, E. J.; Dervilis, N.

2017-05-01

The key element of this work is to demonstrate alternative strategies for using pattern recognition algorithms whilst investigating structural health monitoring. This paper looks to determine if it makes any difference in choosing from a range of established classification techniques: from decision trees and support vector machines, to Gaussian processes. Classification algorithms are tested on adjustable synthetic data to establish performance metrics, then all techniques are applied to real SHM data. To aid the selection of training data, an informative chain of artificial intelligence tools is used to explore an active learning interaction between meaningful clusters of data.

Heat treatment stabilizes welded aluminum jigs and tool structures

NASA Technical Reports Server (NTRS)

Mehnert, R. S.

1966-01-01

Heat treatment processes, applied after welding but before machining, imparts above normal stability to welded aluminum jigs and tool structures. Weight saving will not be realized in these tools if rigidity equal to that of a comparable steel tool is required.

Quality assurance planning for lunar Mars exploration

NASA Technical Reports Server (NTRS)

Myers, Kay

1991-01-01

A review is presented of the tools and techniques required to meet the challenge of total quality in the goal of traveling to Mars and returning to the moon. One program used by NASA to ensure the integrity of baselined requirements documents is configuration management (CM). CM is defined as an integrated management process that documents and identifies the functional and physical characteristics of a facility's systems, structures, computer software, and components. It also ensures that changes to these characteristics are properly assessed, developed, approved, implemented, verified, recorded, and incorporated into the facility's documentation. Three principal areas are discussed that will realize significant efficiencies and enhanced effectiveness, change assessment, change avoidance, and requirements management.

MICRO- AND NANOSCALE MEASUREMENT METHODS FOR PHASE CHANGE HEAT TRANSFER ON PLANAR AND STRUCTURED SURFACES

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

Buongiorno, J; Cahill, DG; Hidrovo, CH

2014-07-23

In this opinion piece, we discuss recent advances in experimental methods for characterizing phase change heat transfer. We begin with a survey of techniques for high-resolution measurements of temperature and heat flux at the solid surface and in the working fluid. Next, we focus on diagnostic tools for boiling heat transfer and describe techniques for visualizing the temperature and velocity fields, as well as measurements at the single bubble level. Finally, we discuss techniques to probe the kinetics of vapor formation within a few molecular layers of the interface. We conclude with our outlook for future progress in experimental methodsmore » for phase change heat transfer.« less

Using CASE tools to write engineering specifications

NASA Astrophysics Data System (ADS)

Henry, James E.; Howard, Robert W.; Iveland, Scott T.

1993-08-01

There are always a wide variety of obstacles to writing and maintaining engineering documentation. To combat these problems, documentation generation can be linked to the process of engineering development. The same graphics and communication tools used for structured system analysis and design (SSA/SSD) also form the basis for the documentation. The goal is to build a living document, such that as an engineering design changes, the documentation will `automatically' revise. `Automatic' is qualified by the need to maintain textual descriptions associated with the SSA/SSD graphics, and the need to generate new documents. This paper describes a methodology and a computer aided system engineering toolset that enables a relatively seamless transition into document generation for the development engineering team.

Using scenario analysis to determine managed care strategy.

PubMed

Krentz, S E; Gish, R S

2000-09-01

In today's volatile healthcare environment, traditional planning tools are inadequate to guide financial managers of provider organizations in developing managed care strategies. These tools often disregard the uncertainty surrounding market forces such as employee benefit structure, the future of Medicare managed care, and the impact of consumer behavior. Scenario analysis overcomes this limitation by acknowledging the uncertain healthcare environment and articulating a set of plausible alternative futures, thus supplying financial executives with the perspective to craft strategies that can improve the market position of their organizations. By being alert for trigger points that might signal the rise of a specific scenario, financial managers can increase their preparedness for changes in market forces.

Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins.

PubMed

Tamiola, Kamil; Mulder, Frans A A

2012-10-01

NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are available and idiosyncratic sensitivity of backbone chemical shifts to structural information is treated in a sensible manner. In the present paper, we describe methods to detect structural protein changes from chemical shifts, and present an online tool [ncSPC (neighbour-corrected Structural Propensity Calculator)], which unites aspects of several current approaches. Examples of structural propensity calculations are given for two well-characterized systems, namely the binding of α-synuclein to micelles and light activation of photoactive yellow protein. These examples spotlight the great power of NMR chemical shift analysis for the quantitative assessment of protein disorder at the atomic level, and further our understanding of biologically important problems.

Analyzing the Structure and Content of Public Health Messages

PubMed Central

Morrison, Frances P.; Kukafka, Rita; Johnson, Stephen B.

2005-01-01

Background Health messages are crucial to the field of public health in effecting behavior change, but little research is available to assist writers in composing the overall structure of a message. In order to develop software to assist individuals in constructing effective messages, the structure of existing health messages must be understood, and an appropriate method for analyzing health message structure developed. Methods 72 messages from expert sources were used for development of the method, which was then tested for reproducibility using ten randomly selected health messages. Four raters analyzed the messages and inter-coder agreement was calculated. Results A method for analyzing the structure of the messages was developed using sublanguage analysis and discourse analysis. Overall kappa between four coders was 0.69. Conclusion A novel framework for characterizing health message structure and a method for analyzing messages appears to be reproducible and potentially useful for creating an authoring tool. PMID:16779098

doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS.

PubMed

Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector; Rissanen, Sami; Lolicato, Fabio; Róg, Tomasz; Vattulainen, Ilpo

2017-10-23

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell-cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS.

Structure preserving noise and dissipation in the Toda lattice

NASA Astrophysics Data System (ADS)

Arnaudon, Alexis

2018-05-01

In this paper, we use Flaschka’s change of variables of the open Toda lattice and its interpretation in terms of the group structure of the LU factorisation as a coadjoint motion on a certain dual of the Lie algebra to implement a structure preserving noise and dissipation. Both preserve the structure of the coadjoint orbit, that is the space of symmetric tri-diagonal matrices and arise as a new type of multiplicative noise and nonlinear dissipation of the Toda lattice. We investigate some of the properties of these deformations and, in particular, the continuum limit as a stochastic Burger equation with a nonlinear viscosity. This work is meant to be exploratory, and open more questions that we can answer with simple mathematical tools and without numerical simulations.

Study of Silicon/silicon, Silicon/silicon Dioxide, and Metal-Oxide

NASA Astrophysics Data System (ADS)

Leung, To Chi

A variable-energy positron beam is used to study Si/Si, Si/SiO_2, and metal-oxide -semiconductor (MOS) structures. The capability of depth resolution and the remarkable sensitivity to defects have made the positron annihilation technique a unique tool in detecting open-volume defects in the newly innovated low temperature (300^circC) molecular-beam-epitaxy (MBE) Si/Si. These two features of the positron beam have further shown its potential role in the study of the Si/SiO_2. Distinct annihilation characteristics has been observed at the interface and has been studied as a function of the sample growth conditions, annealing (in vacuum), and hydrogen exposure. The MOS structure provides an effective way to study the electrical properties of the Si/SiO_2 interface as a function of applied bias voltage. The annihilation characteristics show a large change as the device condition is changed from accumulation to inversion. The effect of forming gas (FG) anneal is studied using positron annihilation and the result is compared with capacitance-voltage (C -V) measurements. The reduction in the number of interface states is found correlated with the changes in the positron spectra. The present study shows the importance of the positron annihilation technique as a non-contact, non-destructive, and depth-sensitive characterization tool to study the Si-related systems, in particular, the Si/SiO_2 interface which is of crucial importance in semiconductor technology, and fundamental understanding of the defects responsible for degradation of the electrical properties.

SEADS 3.0 Sectoral Energy/Employment Analysis and Data System

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

Roop, Joseph M.; Anderson, David A.; Schultz, Robert W.

2007-12-17

SEADS 3.0, the Sectoral Energy/Employment Analysis and Data System, is a revision and upgrading of SEADS--PC, a software package designed for the analysis of policy that could be described by modifying final demands of consumer, businesses, or governments (Roop, et al., 1995). If a question can be formulated so that implications can be translated into changes in final demands for goods and services, then SEADS 3.0 provides a quick and easy tool to assess preliminary impacts. And SEADS 3.0 should be considered just that: a quick and easy way to get preliminary results. Often a thorough answer, even to suchmore » a simple question as, “What would be the effect on U. S. energy use and employment if the Federal Government doubled R&D expenditures?” requires a more sophisticated analytical framework than the input-output structure embedded in SEADS 3.0. This tool uses a static, input-output model to assess the impacts of changes in final demands on first industry output, then employment and energy use. The employment and energy impacts are derived by multiplying the industry outputs (derived from the changed final demands) by industry-specific energy and employment coefficients. The tool also allows for the specification of regional or state employment impacts, though this option is not available for energy impacts.« less

[Cross-cultural adaptation and psychometric tests of a self-efficacy scale and an adherence scale for French adolescents with Type 1 diabetes

PubMed

Colson, Sébastien; Coté, José; Collombier, Madeleine; Debout, Christophe; Bonnel, Galadriel; Reynaud, Rachel; Lagouanelle-Simeoni, Marie-Claude

2016-12-01

Introduction : many structured educational programs, using the concept of self-efficacy, have been studied in English-speaking countries. Background : tools were developed in English to assess this concept along with treatment adherence. However, there seems to be no French version of these tools in scientific literature. Aim : to adapt the tools to the French language and to test the psychometric properties of the Self-Efficacy for Diabetes Self-Management (SEDM) and the Diabetes Self-Management Profile (DSMP). Methods : a cross-cultural adaptation of the SEDM and DSMP in French was performed. The psychometric properties were tested in a pilot study that took place between January 1st and December 31st, 2015. Results : Cronbach’s alpha coefficient of SEDM in French was 0.84, test-retest reliability 0.80 and sensitivity to change was moderate. The Cronbach’s alpha and sensitivity to change of the French DSMP were low, and the test-retest was 0.71. Discussion and conclusions : the first results of the psychometric properties of French SEDM were rather encouraging. The use of the French version of DSMP seems compromised in terms of psychometric properties and the opinion of the participants.

Quantifying Biomass and Bare Earth Changes from the Hayman Fire Using Multi-temporal Lidar

NASA Astrophysics Data System (ADS)

Stoker, J. M.; Kaufmann, M. R.; Greenlee, S. K.

2007-12-01

Small-footprint multiple-return lidar data collected in the Cheesman Lake property prior to the 2002 Hayman fire in Colorado provided an excellent opportunity to evaluate Lidar as a tool to predict and analyze fire effects on both soil erosion and overstory structure. Re-measuring this area and applying change detection techniques allowed for analyses at a high level of detail. Our primary objectives focused on the use of change detection techniques using multi-temporal lidar data to: (1) evaluate the effectiveness of change detection to identify and quantify areas of erosion or deposition caused by post-fire rain events and rehab activities; (2) identify and quantify areas of biomass loss or forest structure change due to the Hayman fire; and (3) examine effects of pre-fire fuels and vegetation structure derived from lidar data on patterns of burn severity. While we were successful in identifying areas where changes occurred, the original error bounds on the variation in actual elevations made it difficult, if not misleading to quantify volumes of material changed on a per pixel basis. In order to minimize these variations in the two datasets, we investigated several correction and co-registration methodologies. The lessons learned from this project highlight the need for a high level of flight planning and understanding of errors in a lidar dataset in order to correctly estimate and report quantities of vertical change. Directly measuring vertical change using only lidar without ancillary information can provide errors that could make quantifications confusing, especially in areas with steep slopes.

Formation of graded vanadium oxide (V-O compound) under strong gravitational field

NASA Astrophysics Data System (ADS)

Khandaker, Jahirul Islam; Tokuda, Makoto; Ogata, Yudai; Januszko, Kamila; Nishiyama, Tadao; Yoshiasa, Akira; Mashimo, Tsutomu

2015-05-01

Sedimentation of atoms induced under strong gravitational field gives a tool for controlling elemental compositions in condensed matter. We performed a strong-gravity experiment (0.397 × 106 G at 400 °C for 24 h) on a V2O5 polycrystal using the high-temperature ultracentrifuge to examine the composition change and further the structure change. The graded composition structure of V and O was formed along gravity direction, where V increases and O decreases with gravity. It was found by the x-ray diffraction and Raman scattering method that VO2 and V2O3 phases appeared and the amounts increased, while one of the V2O5 phase decreased gradually along gravity direction. The X-ray absorption near edge structure spectra analysis identified the chemical valency decrease (+5 to +3). The UV-Vis absorption spectroscopy addressed the shifting in center of major absorption peak to longer wavelength (red shift) with the increase in gravitational field. The tail absorption peak (band gap 2.09 eV) at strong gravity region in the graded structure showed transparent conductive oxide.

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

Hu, Enyuan; Wang, Xuelong; Yu, Xiqian

The rechargeable lithium-ion battery (LIB) is the most promising energy storage system to power electric vehicles with high energy density and long cycling life. However, in order to meet customers’ demands for fast charging, the power performances of current LIBs need to be improved. From the cathode aspect, layer-structured cathode materials are widely used in today’s market and will continue to play important roles in the near future. The high rate capability of layered cathode materials during charging and discharging is critical to the power performance of the whole cell and the thermal stability is closely related to the safetymore » issues. Therefore, the in-depth understanding of structural changes of layered cathode materials during high rate charging/discharging and the thermal stability during heating are essential in developing new materials and improving current materials. Since structural changes take place from the atomic level to the whole electrode level, combination of characterization techniques covering multilength scales is quite important. Finally, in many cases, this means using comprehensive tools involving diffraction, spectroscopy, and imaging to differentiate the surface from the bulk and to obtain structural/chemical information with different levels of spatial resolution.« less

Development of Metallic Sensory Alloys

NASA Technical Reports Server (NTRS)

Wallace Terryl A.; Newman, John A.; Horne, Michael R.; Messick, Peter L.

2010-01-01

Existing nondestructive evaluation (NDE) technologies are inherently limited by the physical response of the structural material being inspected and are therefore not generally effective at the identification of small discontinuities, making the detection of incipient damage extremely difficult. One innovative solution to this problem is to enhance or complement the NDE signature of structural materials to dramatically improve the ability of existing NDE tools to detect damage. To address this need, a multifunctional metallic material has been developed that can be used in structural applications. The material is processed to contain second phase sensory particles that significantly improve the NDE response, enhancing the ability of conventional NDE techniques to detect incipient damage both during and after flight. Ferromagnetic shape-memory alloys (FSMAs) are an ideal material for these sensory particles as they undergo a uniform and repeatable change in both magnetic properties and crystallographic structure (martensitic transformation) when subjected to strain and/or temperature changes which can be detected using conventional NDE techniques. In this study, the use of a ferromagnetic shape memory alloy (FSMA) as the sensory particles was investigated.

Participatory Culture as a Model for How New Media Technologies Can Change Public Schools. WCER Working Paper No. 2016-7

ERIC Educational Resources Information Center

Halverson, Rich; Kallio, Julie; Hackett, Sarah; Halverson, Erica

2016-01-01

Students who have mastered the ability to create their own learning environments have an advantage over students who rely on traditional environments to structure their learning. Students who understand how to use new tools for school learning typically do not pick up these skills at school--they learn from the habits of parents and peers who work…

4D-SFM Photogrammetry for Monitoring Sediment Dynamics in a Debris-Flow Catchment: Software Testing and Results Comparison

NASA Astrophysics Data System (ADS)

Cucchiaro, S.; Maset, E.; Fusiello, A.; Cazorzi, F.

2018-05-01

In recent years, the combination of Structure-from-Motion (SfM) algorithms and UAV-based aerial images has revolutionised 3D topographic surveys for natural environment monitoring, offering low-cost, fast and high quality data acquisition and processing. A continuous monitoring of the morphological changes through multi-temporal (4D) SfM surveys allows, e.g., to analyse the torrent dynamic also in complex topography environment like debris-flow catchments, provided that appropriate tools and procedures are employed in the data processing steps. In this work we test two different software packages (3DF Zephyr Aerial and Agisoft Photoscan) on a dataset composed of both UAV and terrestrial images acquired on a debris-flow reach (Moscardo torrent - North-eastern Italian Alps). Unlike other papers in the literature, we evaluate the results not only on the raw point clouds generated by the Structure-from- Motion and Multi-View Stereo algorithms, but also on the Digital Terrain Models (DTMs) created after post-processing. Outcomes show differences between the DTMs that can be considered irrelevant for the geomorphological phenomena under analysis. This study confirms that SfM photogrammetry can be a valuable tool for monitoring sediment dynamics, but accurate point cloud post-processing is required to reliably localize geomorphological changes.

Identifying socio-ecological networks in rural-urban gradients: Diagnosis of a changing cultural landscape.

PubMed

Arnaiz-Schmitz, C; Schmitz, M F; Herrero-Jáuregui, C; Gutiérrez-Angonese, J; Pineda, F D; Montes, C

2018-01-15

Socio-ecological systems maintain reciprocal interactions between biophysical and socioeconomic structures. As a result of these interactions key essential services for society emerge. Urban expansion is a direct driver of land change and cause serious shifts in socio-ecological relationships and the associated lifestyles. The framework of rural-urban gradients has proved to be a powerful tool for ecological research about urban influences on ecosystems and on sociological issues related to social welfare. However, to date there has not been an attempt to achieve a classification of municipalities in rural-urban gradients based on socio-ecological interactions. In this paper, we developed a methodological approach that allows identifying and classifying a set of socio-ecological network configurations in the Region of Madrid, a highly dynamic cultural landscape considered one of the European hotspots in urban development. According to their socio-ecological links, the integrated model detects four groups of municipalities, ordered along a rural-urban gradient, characterized by their degree of biophysical and socioeconomic coupling and different indicators of landscape structure and social welfare. We propose the developed model as a useful tool to improve environmental management schemes and land planning from a socio-ecological perspective, especially in territories subject to intense urban transformations and loss of rurality. Copyright © 2017 Elsevier B.V. All rights reserved.

Measuring grassland structure for recovery of grassland species at risk

NASA Astrophysics Data System (ADS)

Guo, Xulin; Gao, Wei; Wilmshurst, John

2005-09-01

An action plan for recovering species at risk (SAR) depends on an understanding of the plant community distribution, vegetation structure, quality of the food source and the impact of environmental factors such as climate change at large scale and disturbance at small scale, as these are fundamental factors for SAR habitat. Therefore, it is essential to advance our knowledge of understanding the SAR habitat distribution, habitat quality and dynamics, as well as developing an effective tool for measuring and monitoring SAR habitat changes. Using the advantages of non-destructive, low cost, and high efficient land surface vegetation biophysical parameter characterization, remote sensing is a potential tool for helping SAR recovery action. The main objective of this paper is to assess the most suitable techniques for using hyperspectral remote sensing to quantify grassland biophysical characteristics. The challenge of applying remote sensing in semi-arid and arid regions exists simply due to the lower biomass vegetation and high soil exposure. In conservation grasslands, this problem is enhanced because of the presence of senescent vegetation. Results from this study demonstrated that hyperspectral remote sensing could be the solution for semi-arid grassland remote sensing applications. Narrow band raw data and derived spectral vegetation indices showed stronger relationships with biophysical variables compared to the simulated broad band vegetation indices.

Graphite fiber reinforced structure for supporting machine tools

DOEpatents

Knight, Jr., Charles E.; Kovach, Louis; Hurst, John S.

1978-01-01

Machine tools utilized in precision machine operations require tool support structures which exhibit minimal deflection, thermal expansion and vibration characteristics. The tool support structure of the present invention is a graphite fiber reinforced composite in which layers of the graphite fibers or yarn are disposed in a 0/90.degree. pattern and bonded together with an epoxy resin. The finished composite possesses a low coefficient of thermal expansion and a substantially greater elastic modulus, stiffness-to-weight ratio, and damping factor than a conventional steel tool support utilized in similar machining operations.

Investigating local degradation and thermal stability of charged nickel-based cathode materials through real-time electron microscopy.

PubMed

Hwang, Sooyeon; Kim, Seung Min; Bak, Seong-Min; Cho, Byung-Won; Chung, Kyung Yoon; Lee, Jeong Yong; Chang, Wonyoung; Stach, Eric A

2014-09-10

In this work, we take advantage of in situ transmission electron microscopy (TEM) to investigate thermally induced decomposition of the surface of Li(x)Ni(0.8)Co(0.15)Al(0.05)O2 (NCA) cathode materials that have been subjected to different states of charge (SOC). While uncharged NCA is stable up to 400 °C, significant changes occur in charged NCA with increasing temperature. These include the development of surface porosity and changes in the oxygen K-edge electron energy loss spectra, with pre-edge peaks shifting to higher energy losses. These changes are closely related to O2 gas released from the structure, as well as to phase changes of NCA from the layered structure to the disordered spinel structure, and finally to the rock-salt structure. Although the temperatures where these changes initiate depend strongly on the state of charge, there also exist significant variations among particles with the same state of charge. Notably, when NCA is charged to x = 0.33 (the charge state that is the practical upper limit voltage in most applications), the surfaces of some particles undergo morphological and oxygen K-edge changes even at temperatures below 100 °C, a temperature that electronic devices containing lithium ion batteries (LIB) can possibly see during normal operation. Those particles that experience these changes are likely to be extremely unstable and may trigger thermal runaway at much lower temperatures than would be usually expected. These results demonstrate that in situ heating experiments are a unique tool not only to study the general thermal behavior of cathode materials but also to explore particle-to-particle variations, which are sometimes of critical importance in understanding the performance of the overall system.

Dynamically Tunable Cell Culture Platforms for Tissue Engineering and Mechanobiology

PubMed Central

Uto, Koichiro; Tsui, Jonathan H.; DeForest, Cole A.; Kim, Deok-Ho

2016-01-01

Human tissues are sophisticated ensembles of many distinct cell types embedded in the complex, but well-defined, structures of the extracellular matrix (ECM). Dynamic biochemical, physicochemical, and mechano-structural changes in the ECM define and regulate tissue-specific cell behaviors. To recapitulate this complex environment in vitro, dynamic polymer-based biomaterials have emerged as powerful tools to probe and direct active changes in cell function. The rapid evolution of polymerization chemistries, structural modulation, and processing technologies, as well as the incorporation of stimuli-responsiveness, now permit synthetic microenvironments to capture much of the dynamic complexity of native tissue. These platforms are comprised not only of natural polymers chemically and molecularly similar to ECM, but those fully synthetic in origin. Here, we review recent in vitro efforts to mimic the dynamic microenvironment comprising native tissue ECM from the viewpoint of material design. We also discuss how these dynamic polymer-based biomaterials are being used in fundamental cell mechanobiology studies, as well as towards efforts in tissue engineering and regenerative medicine. PMID:28522885

First-principles calculations of K-shell X-ray absorption spectra for warm dense nitrogen

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

Li, Zi; Zhang, Shen; Kang, Wei

2016-05-15

X-ray absorption spectrum is a powerful tool for atomic structure detection on warm dense matter. Here, we perform first-principles molecular dynamics and X-ray absorption spectrum calculations on warm dense nitrogen along a Hugoniot curve. From the molecular dynamics trajectory, the detailed atomic structures are examined for each thermodynamical condition. The K-shell X-ray absorption spectrum is calculated, and its changes with temperature and pressure along the Hugoniot curve are discussed. The warm dense nitrogen systems may contain isolated nitrogen atoms, N{sub 2} molecules, and nitrogen clusters, which show quite different contributions to the total X-ray spectrum due to their different electronmore » density of states. The changes of X-ray spectrum along the Hugoniot curve are caused by the different nitrogen structures induced by the temperature and the pressure. Some clear signatures on X-ray spectrum for different thermodynamical conditions are pointed out, which may provide useful data for future X-ray experiments.« less

Tensor methods for parameter estimation and bifurcation analysis of stochastic reaction networks

PubMed Central

Liao, Shuohao; Vejchodský, Tomáš; Erban, Radek

2015-01-01

Stochastic modelling of gene regulatory networks provides an indispensable tool for understanding how random events at the molecular level influence cellular functions. A common challenge of stochastic models is to calibrate a large number of model parameters against the experimental data. Another difficulty is to study how the behaviour of a stochastic model depends on its parameters, i.e. whether a change in model parameters can lead to a significant qualitative change in model behaviour (bifurcation). In this paper, tensor-structured parametric analysis (TPA) is developed to address these computational challenges. It is based on recently proposed low-parametric tensor-structured representations of classical matrices and vectors. This approach enables simultaneous computation of the model properties for all parameter values within a parameter space. The TPA is illustrated by studying the parameter estimation, robustness, sensitivity and bifurcation structure in stochastic models of biochemical networks. A Matlab implementation of the TPA is available at http://www.stobifan.org. PMID:26063822

Tensor methods for parameter estimation and bifurcation analysis of stochastic reaction networks.

PubMed

Liao, Shuohao; Vejchodský, Tomáš; Erban, Radek

2015-07-06

Stochastic modelling of gene regulatory networks provides an indispensable tool for understanding how random events at the molecular level influence cellular functions. A common challenge of stochastic models is to calibrate a large number of model parameters against the experimental data. Another difficulty is to study how the behaviour of a stochastic model depends on its parameters, i.e. whether a change in model parameters can lead to a significant qualitative change in model behaviour (bifurcation). In this paper, tensor-structured parametric analysis (TPA) is developed to address these computational challenges. It is based on recently proposed low-parametric tensor-structured representations of classical matrices and vectors. This approach enables simultaneous computation of the model properties for all parameter values within a parameter space. The TPA is illustrated by studying the parameter estimation, robustness, sensitivity and bifurcation structure in stochastic models of biochemical networks. A Matlab implementation of the TPA is available at http://www.stobifan.org.

The Career and Work Adaptability Questionnaire (CWAQ): a first contribution to its validation.

PubMed

Nota, Laura; Ginevra, Maria Cristina; Soresi, Salvatore

2012-12-01

Over the last decade, occupational changes have the rapidly changing job market has begun to demand that people more actively construct their professional lives and acquire career adaptability. The aim of the present study was to develop a specific, new instrument, "Career and Work Adaptability", to assess degree of adaptability in adolescents planning their futures. We conducted three studies, the first of which aimed to formulate the instrument's items and to verify its factor structure; the second study confirmed the instrument's multidimensional structure and evaluated its discriminant validity; the third study was conducted to verify the factorial structure's across-gender invariance and to evaluate its stability over time. Our results showed that the instrument is an effective and multidimensional instrument for accurately measuring career adaptability. Specifically, it can serve as a useful vocational guidance tool in analyzing adolescents' career adaptability. Copyright © 2012 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

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

Weisz, Daniel A.; Gross, Michael L.; Pakrasi, Himadri B.

Photosystem II (PSII) is a photosynthetic membrane-protein complex that undergoes an intricate, tightly regulated cycle of assembly, damage, and repair. The available crystal structures of cyanobacterial PSII are an essential foundation for understanding PSII function, but nonetheless provide a snapshot only of the active complex. To study aspects of the entire PSII life-cycle, mass spectrometry (MS) has emerged as a powerful tool that can be used in conjunction with biochemical techniques. In this article, we present the MS-based approaches that are used to study PSII composition, dynamics, and structure, and review the information about the PSII life-cycle that has beenmore » gained by these methods. This information includes the composition of PSII subcomplexes, discovery of accessory PSII proteins, identification of post-translational modifications and quantification of their changes under various conditions, determination of the binding site of proteins not observed in PSII crystal structures, conformational changes that underlie PSII functions, and identification of water and oxygen channels within PSII. Lastly, we conclude with an outlook for the opportunity of future MS contributions to PSII research.« less

Strong nonadditivity as a key structure-activity relationship feature: distinguishing structural changes from assay artifacts.

PubMed

Kramer, Christian; Fuchs, Julian E; Liedl, Klaus R

2015-03-23

Nonadditivity in protein-ligand affinity data represents highly instructive structure-activity relationship (SAR) features that indicate structural changes and have the potential to guide rational drug design. At the same time, nonadditivity is a challenge for both basic SAR analysis as well as many ligand-based data analysis techniques such as Free-Wilson Analysis and Matched Molecular Pair analysis, since linear substituent contribution models inherently assume additivity and thus do not work in such cases. While structural causes for nonadditivity have been analyzed anecdotally, no systematic approaches to interpret and use nonadditivity prospectively have been developed yet. In this contribution, we lay the statistical framework for systematic analysis of nonadditivity in a SAR series. First, we develop a general metric to quantify nonadditivity. Then, we demonstrate the non-negligible impact of experimental uncertainty that creates apparent nonadditivity, and we introduce techniques to handle experimental uncertainty. Finally, we analyze public SAR data sets for strong nonadditivity and use recourse to the original publications and available X-ray structures to find structural explanations for the nonadditivity observed. We find that all cases of strong nonadditivity (ΔΔpKi and ΔΔpIC50 > 2.0 log units) with sufficient structural information to generate reasonable hypothesis involve changes in binding mode. With the appropriate statistical basis, nonadditivity analysis offers a variety of new attempts for various areas in computer-aided drug design, including the validation of scoring functions and free energy perturbation approaches, binding pocket classification, and novel features in SAR analysis tools.

i-Tree: Tools to assess and manage structure, function, and value of community forests

NASA Astrophysics Data System (ADS)

Hirabayashi, S.; Nowak, D.; Endreny, T. A.; Kroll, C.; Maco, S.

2011-12-01

Trees in urban communities can mitigate many adverse effects associated with anthropogenic activities and climate change (e.g. urban heat island, greenhouse gas, air pollution, and floods). To protect environmental and human health, managers need to make informed decisions regarding urban forest management practices. Here we present the i-Tree suite of software tools (www.itreetools.org) developed by the USDA Forest Service and their cooperators. This software suite can help urban forest managers assess and manage the structure, function, and value of urban tree populations regardless of community size or technical capacity. i-Tree is a state-of-the-art, peer-reviewed Windows GUI- or Web-based software that is freely available, supported, and continuously refined by the USDA Forest Service and their cooperators. Two major features of i-Tree are 1) to analyze current canopy structures and identify potential planting spots, and 2) to estimate the environmental benefits provided by the trees, such as carbon storage and sequestration, energy conservation, air pollution removal, and storm water reduction. To cover diverse forest topologies, various tools were developed within the i-Tree suite: i-Tree Design for points (individual trees), i-Tree Streets for lines (street trees), and i-Tree Eco, Vue, and Canopy (in the order of complexity) for areas (community trees). Once the forest structure is identified with these tools, ecosystem services provided by trees can be estimated with common models and protocols, and reports in the form of texts, charts, and figures are then created for users. Since i-Tree was developed with a client/server architecture, nationwide data in the US such as location-related parameters, weather, streamflow, and air pollution data are stored in the server and retrieved to a user's computer at run-time. Freely available remote-sensed images (e.g. NLCD and Google maps) are also employed to estimate tree canopy characteristics. As the demand for i-Tree grows internationally, environmental databases from more countries will be coupled with the software suite. Two more i-Tree applications, i-Tree Forecast and i-Tree Landscape are now under development. i-Tree Forecast simulates canopy structures for up to 100 years based on planting and mortality rates and adds capabilities for other i-Tree applications to estimate the benefits of future canopy scenarios. While most i-Tree applications employ a spatially lumped approach, i-Tree landscape employs a spatially distributed approach that allows users to map changes in canopy cover and ecosystem services through time and space. These new i-Tree tools provide an advanced platform for urban managers to assess the impact of current and future urban forests. i-Tree allows managers to promote effective urban forest management and sound arboricultural practices by providing information for advocacy and planning, baseline data for making informed decisions, and standardization for comparisons with other communities.

Decay extent evaluation of wood degraded by a fungal community using NIRS: application for ecological engineering structures used for natural hazard mitigation

NASA Astrophysics Data System (ADS)

Baptiste Barré, Jean; Bourrier, Franck; Bertrand, David; Rey, Freddy

2015-04-01

Ecological engineering corresponds to the design of efficient solutions for protection against natural hazards such as shallow landslides and soil erosion. In particular, bioengineering structures can be composed of a living part, made of plants, cuttings or seeds, and an inert part, a timber logs structure. As wood is not treated by preservatives, fungal degradation can occur from the start of the construction. It results in wood strength loss, which practitioners try to evaluate with non-destructive tools (NDT). Classical NDT are mainly based on density measurements. However, the fungal activity reduces the mechanical properties (modulus of elasticity - MOE) well before well before a density change could be measured. In this context, it would be useful to provide a tool for assessing the residual mechanical strength at different decay stages due to a fungal community. Near-infrared spectroscopy (NIRS) can be used for that purpose, as it can allow evaluating wood mechanical properties as well as wood chemical changes due to brown and white rots. We monitored 160 silver fir samples (30x30x6000mm) from green state to different levels of decay. The degradation process took place in a greenhouse and samples were inoculated with silver fir decayed debris in order to accelerate the process. For each sample, we calculated the normalized bending modulus of elasticity loss (Dw moe) and defined it as decay extent. Near infrared spectra collected from both green and decayed ground samples were corrected by the subtraction of baseline offset. Spectra of green samples were averaged into one mean spectrum and decayed spectra were subtracted from the mean spectrum to calculate the absorption loss. Partial least square regression (PLSR) has been performed between the normalized MOE loss Dw moe (0 < Dw moe < 1) and the absorption loss, with a correlation coefficient R² equal to 0.85. Finally, the prediction of silver fir biodegradation rate by NIRS was significant (RMSEP = 0.13). This tool improves the evaluation accuracy of wood decay extent in the context of ecological engineering structures used for natural hazard mitigation.

Diffusion tensor image segmentation of the cerebrum provides a single measure of cerebral small vessel disease severity related to cognitive change.

PubMed

Williams, Owen A; Zeestraten, Eva A; Benjamin, Philip; Lambert, Christian; Lawrence, Andrew J; Mackinnon, Andrew D; Morris, Robin G; Markus, Hugh S; Charlton, Rebecca A; Barrick, Thomas R

2017-01-01

Cerebral small vessel disease (SVD) is the primary cause of vascular cognitive impairment and is associated with decline in executive function (EF) and information processing speed (IPS). Imaging biomarkers are needed that can monitor and identify individuals at risk of severe cognitive decline. Recently there has been interest in combining several magnetic resonance imaging (MRI) markers of SVD into a unitary score to describe disease severity. Here we apply a diffusion tensor image (DTI) segmentation technique (DSEG) to describe SVD related changes in a single unitary score across the whole cerebrum, to investigate its relationship with cognitive change over a three-year period. 98 patients (aged 43-89) with SVD underwent annual MRI scanning and cognitive testing for up to three years. DSEG provides a vector of 16 discrete segments describing brain microstructure of healthy and/or damaged tissue. By calculating the scalar product of each DSEG vector in reference to that of a healthy ageing control we generate an angular measure (DSEG θ ) describing the patients' brain tissue microstructural similarity to a disease free model of a healthy ageing brain. Conventional MRI markers of SVD brain change were also assessed including white matter hyperintensities, cerebral atrophy, incident lacunes, cerebral-microbleeds, and white matter microstructural damage measured by DTI histogram parameters. The impact of brain change on cognition was explored using linear mixed-effects models. Post-hoc sample size analysis was used to assess the viability of DSEG θ as a tool for clinical trials. Changes in brain structure described by DSEG θ were related to change in EF and IPS ( p  < 0.001) and remained significant in multivariate models including other MRI markers of SVD as well as age, gender and premorbid IQ. Of the conventional markers, presence of new lacunes was the only marker to remain a significant predictor of change in EF and IPS in the multivariate models ( p  = 0.002). Change in DSEG θ was also related to change in all other MRI markers ( p  < 0.017), suggesting it may be used as a surrogate marker of SVD damage across the cerebrum. Sample size estimates indicated that fewer patients would be required to detect treatment effects using DSEG θ compared to conventional MRI and DTI markers of SVD severity. DSEG θ is a powerful tool for characterising subtle brain change in SVD that has a negative impact on cognition and remains a significant predictor of cognitive change when other MRI markers of brain change are accounted for. DSEG provides an automatic segmentation of the whole cerebrum that is sensitive to a range of SVD related structural changes and successfully predicts cognitive change. Power analysis shows DSEG θ has potential as a monitoring tool in clinical trials. As such it may provide a marker of SVD severity from a single imaging modality (i.e. DTIs).

Molecular ecological network analyses.

PubMed

Deng, Ye; Jiang, Yi-Huei; Yang, Yunfeng; He, Zhili; Luo, Feng; Zhou, Jizhong

2012-05-30

Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA). The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.

Reconstructing Late Holocene North Atlantic atmospheric circulation changes using functional paleoclimate networks

NASA Astrophysics Data System (ADS)

Franke, Jasper G.; Werner, Johannes P.; Donner, Reik V.

2017-11-01

Obtaining reliable reconstructions of long-term atmospheric circulation changes in the North Atlantic region presents a persistent challenge to contemporary paleoclimate research, which has been addressed by a multitude of recent studies. In order to contribute a novel methodological aspect to this active field, we apply here evolving functional network analysis, a recently developed tool for studying temporal changes of the spatial co-variability structure of the Earth's climate system, to a set of Late Holocene paleoclimate proxy records covering the last two millennia. The emerging patterns obtained by our analysis are related to long-term changes in the dominant mode of atmospheric circulation in the region, the North Atlantic Oscillation (NAO). By comparing the time-dependent inter-regional linkage structures of the obtained functional paleoclimate network representations to a recent multi-centennial NAO reconstruction, we identify co-variability between southern Greenland, Svalbard, and Fennoscandia as being indicative of a positive NAO phase, while connections from Greenland and Fennoscandia to central Europe are more pronounced during negative NAO phases. By drawing upon this correspondence, we use some key parameters of the evolving network structure to obtain a qualitative reconstruction of the NAO long-term variability over the entire Common Era (last 2000 years) using a linear regression model trained upon the existing shorter reconstruction.

Atomic Scale Structure-Chemistry Relationships at Oxide Catalyst Surfaces and Interfaces

NASA Astrophysics Data System (ADS)

McBriarty, Martin E.

Oxide catalysts are integral to chemical production, fuel refining, and the removal of environmental pollutants. However, the atomic-scale phenomena which lead to the useful reactive properties of catalyst materials are not sufficiently understood. In this work, the tools of surface and interface science and electronic structure theory are applied to investigate the structure and chemical properties of catalytically active particles and ultrathin films supported on oxide single crystals. These studies focus on structure-property relationships in vanadium oxide, tungsten oxide, and mixed V-W oxides on the surfaces of alpha-Al2O3 and alpha-Fe2O 3 (0001)-oriented single crystal substrates, two materials with nearly identical crystal structures but drastically different chemical properties. In situ synchrotron X-ray standing wave (XSW) measurements are sensitive to changes in the atomic-scale geometry of single crystal model catalyst surfaces through chemical reaction cycles, while X-ray photoelectron spectroscopy (XPS) reveals corresponding chemical changes. Experimental results agree with theoretical calculations of surface structures, allowing for detailed electronic structure investigations and predictions of surface chemical phenomena. The surface configurations and oxidation states of V and W are found to depend on the coverage of each, and reversible structural shifts accompany chemical state changes through reduction-oxidation cycles. Substrate-dependent effects suggest how the choice of oxide support material may affect catalytic behavior. Additionally, the structure and chemistry of W deposited on alpha-Fe 2O3 nanopowders is studied using X-ray absorption fine structure (XAFS) measurements in an attempt to bridge single crystal surface studies with real catalysts. These investigations of catalytically active material surfaces can inform the rational design of new catalysts for more efficient and sustainable chemistry.

Investigating and Promoting Trainee Science Teachers' Conceptual Change of the Nature of Science with Digital Dialogue Games `InterLoc'

NASA Astrophysics Data System (ADS)

Mansour, Nasser; Wegerif, Rupert; Skinner, Nigel; Postlethwaite, Keith; Hetherington, Lindsay

2016-10-01

The purpose of this study is to explore how an online-structured dialogue environment supported (OSDE) collaborative learning about the nature of science among a group of trainee science teachers in the UK. The software used (InterLoc) is a linear text-based tool, designed to support structured argumentation with openers and `dialogue moves'. A design-based research approach was used to investigate multiple sessions using InterLoc with 65 trainee science teachers. Five participants who showed differential conceptual change in terms of their Nature of Science (NOS) views were purposively selected and closely followed throughout the study by using key event recall interviews. Initially, the majority of participants held naïve views of NOS. Substantial and favourable changes in these views were evident as a result of the OSDE. An examination of the development of the five participants' NOS views indicated that the effectiveness of the InterLoc discussions was mediated by cultural, cognitive, and experiential factors. The findings suggest that InterLoc can be effective in promoting reflection and conceptual change.

Italian public health care organizations: specialization, institutional deintegration, and public networks relationships.

PubMed

Del Vecchio, Mario; De Pietro, Carlo

2011-01-01

The Italian National Health Service (INHS) has undergone profound changes over the past three decades. With establishment of the INHS in 1978--a tax-based public health care system with universal coverage--one of the underlying principles was integration. The recognition of health and health care as requiring integrated answers led to the creation of a single public organization, the Local Health Unit, responsible for the health status of the population of its catchment area. At the beginning of the 1990s, the scenario radically changed. The creation of hospital trusts, the development of quasi-market mechanisms and management control tools, the adoption of a prospective payment system for reimbursing health care providers--all were signs of deintegration and institutional unbundling. Two structural changes have deeply sustained this deintegration: patients' empowerment and the increased possibilities for outsourcing practices. In more recent years, a new reintegration effort has occurred, often led by regional governments and based on institutional cooperation and network relationships. However, the earlier structural changes require innovative approaches and solutions if public health care organizations want to retain their leading role.

A comparative genomic hybridization approach to study gene copy number variations among Chinese hamster cell lines.

PubMed

Vishwanathan, Nandita; Bandyopadhyay, Arpan; Fu, Hsu-Yuan; Johnson, Kathryn C; Springer, Nathan M; Hu, Wei-Shou

2017-08-01

Chinese Hamster Ovary (CHO) cells are aneuploid in nature. The genome of recombinant protein producing CHO cell lines continuously undergoes changes in its structure and organization. We analyzed nine cell lines, including parental cell lines, using a comparative genomic hybridization (CGH) array focused on gene-containing regions. The comparison of CGH with copy-number estimates from sequencing data showed good correlation. Hierarchical clustering of the gene copy number variation data from CGH data revealed the lineage relationships between the cell lines. On analyzing the clones of a clonal population, some regions with altered genomic copy number status were identified indicating genomic changes during passaging. A CGH array is thus an effective tool in quantifying genomic alterations in industrial cell lines and can provide insights into the changes in the genomic structure during cell line derivation and long term culture. Biotechnol. Bioeng. 2017;114: 1903-1908. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Modeling small cell lung cancer (SCLC) biology through deterministic and stochastic mathematical models.

PubMed

Salgia, Ravi; Mambetsariev, Isa; Hewelt, Blake; Achuthan, Srisairam; Li, Haiqing; Poroyko, Valeriy; Wang, Yingyu; Sattler, Martin

2018-05-25

Mathematical cancer models are immensely powerful tools that are based in part on the fractal nature of biological structures, such as the geometry of the lung. Cancers of the lung provide an opportune model to develop and apply algorithms that capture changes and disease phenotypes. We reviewed mathematical models that have been developed for biological sciences and applied them in the context of small cell lung cancer (SCLC) growth, mutational heterogeneity, and mechanisms of metastasis. The ultimate goal is to develop the stochastic and deterministic nature of this disease, to link this comprehensive set of tools back to its fractalness and to provide a platform for accurate biomarker development. These techniques may be particularly useful in the context of drug development research, such as combination with existing omics approaches. The integration of these tools will be important to further understand the biology of SCLC and ultimately develop novel therapeutics.

NASA Engineering and Technology Advancement Office: A proposal to the administrator

NASA Technical Reports Server (NTRS)

Schulze, Norman R.

1993-01-01

NASA has continually had problems with cost, schedule, performance, reliability, quality, and safety aspects in programs. Past solutions have not provided the answers needed, and a major change is needed in the way of doing business. A new approach is presented for consideration. These problems are all engineering matters, and therefore, require engineering solutions. Proper engineering tools are needed to fix engineering problems. Headquarters is responsible for providing the management structure to support programs with appropriate engineering tools. A guide to define those tools and an approach for putting them into place is provided. Recommendations include establishing a new Engineering and Technology Advancement Office, requesting a review of this proposal by the Administrator since this subject requires a top level decision. There has been a wide peer review conducted by technical staff at Headquarters, the Field Installations, and others in industry as discussed.

Spring-back simulation of unidirectional carbon/epoxy L- shaped laminate composites manufactured through autoclave processing

NASA Astrophysics Data System (ADS)

Nasir, M. N. M.; Mezeix, L.; Aminanda, Y.; Seman, M. A.; Rivai, A.; Ali, K. M.

2016-02-01

This paper presents an original method in predicting the spring-back for composite aircraft structures using non-linear Finite Element Analysis (FEA) and is an extension of the previous accompanying study on flat geometry samples. Firstly, unidirectional prepreg lay-up samples are fabricated on moulds with different corner angles (30°, 45° and 90°) and the effect on spring-back deformation are observed. Then, the FEA model that was developed in the previous study on flat samples is utilized. The model maintains the physical mechanisms of spring-back such as ply stretching and tool-part interface properties with the additional mechanism in the corner effect and geometrical changes in the tool, part and the tool-part interface components. The comparative study between the experimental data and FEA results show that the FEA model predicts adequately the spring-back deformation within the range of corner angle tested.

Cause-and-effect mapping of critical events.

PubMed

Graves, Krisanne; Simmons, Debora; Galley, Mark D

2010-06-01

Health care errors are routinely reported in the scientific and public press and have become a major concern for most Americans. In learning to identify and analyze errors health care can develop some of the skills of a learning organization, including the concept of systems thinking. Modern experts in improving quality have been working in other high-risk industries since the 1920s making structured organizational changes through various frameworks for quality methods including continuous quality improvement and total quality management. When using these tools, it is important to understand systems thinking and the concept of processes within organization. Within these frameworks of improvement, several tools can be used in the analysis of errors. This article introduces a robust tool with a broad analytical view consistent with systems thinking, called CauseMapping (ThinkReliability, Houston, TX, USA), which can be used to systematically analyze the process and the problem at the same time. Copyright 2010 Elsevier Inc. All rights reserved.

Clinical peer review program self-evaluation for US hospitals.

PubMed

Edwards, Marc T

2010-01-01

Prior research has shown wide variation in clinical peer review program structure, process, governance, and perceived effectiveness. This study sought to validate the utility of a Peer Review Program Self-Evaluation Tool as a potential guide to physician and hospital leaders seeking greater program value. Data from 330 hospitals show that the total score from the self-evaluation tool is strongly associated with perceived quality impact. Organizational culture also plays a significant role. When controlling for these factors, there was no evidence of benefit from a multispecialty review process. Physicians do not generally use reliable methods to measure clinical performance. A high rate of change since 2007 has not produced much improvement. The Peer Review Program Self-Evaluation Tool reliably differentiates hospitals along a continuum of perceived program performance. The full potential of peer review as a process to improve the quality and safety of care has yet to be realized.

Stereometric parameters change vs. Topographic Change Analysis (TCA) agreement in Heidelberg Retina Tomography III (HRT-3) early detection of clinical significant glaucoma progression.

PubMed

Dascalu, A M; Cherecheanu, A P; Stana, D; Voinea, L; Ciuluvica, R; Savlovschi, C; Serban, D

2014-01-01

to investigate the sensitivity and specificity of the stereometric parameters change analysis vs. Topographic Change Analysis in early detection of glaucoma progression. 81 patients with POAG were monitored for 4 years (GAT monthly, SAP at every 6 months, optic disc photographs and HRT3 yearly). The exclusion criteria were other optic disc or retinal pathology; topographic standard deviation (TSD>30; inter-test variation of reference height>25 μm. The criterion for structural progression was the following: at least 20 adjacent super-pixels with a clinically significant decrease in height (>5%). 16 patients of the total 81 presented structural progression on TCA. The most useful stereometric parameters for the early detection of glaucoma progression were the following: Rim Area change (sensitivity 100%, specificity 74.2% for a "cut-off " value of -0.05), C/D Area change (sensitivity 85.7%, specificity 71.5% for a "cut off " value of 0.02), C/D linear change (sensitivity 85.7%, specificity 71.5% for a "cut-off " value of 0.02), Rim Volume change (sensitivity 71.4%, specificity 88.8% for a "cut-off " value of -0.04). RNFL Thickness change (<0) was highly sensitive (82%), but less specific for glaucoma progression (45,2%). Changes of the other stereometric parameters have a limited diagnostic value for the early detection of glaucoma progression. TCA is a valuable tool for the assessment of the structural progression in glaucoma patients and its inter-test variability is low. On long-term, the quantitative analysis according to stereometric parameters change is also very important. The most relevant parameters to detect progression are RA, C/D Area, Linear C/D and RV.

Virtual Learning and Instructional Tools: Perfecting the Weekly Roadmap

ERIC Educational Resources Information Center

Cicco, Gina

2015-01-01

This article will provide details on the importance of providing structure within an online graduate counseling course in the form of a weekly roadmap tool. There are various instructional tools that may be useful in providing students with differing levels of structure, to meet their learning style preferences for structural stimuli (Cicco,…

Acoustic emission from single point machining: Part 2, Signal changes with tool wear

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

Heiple, C.R.; Carpenter, S.H.; Armentrout, D.L.

1989-01-01

Changes in acoustic emission signal characteristics with tool wear were monitored during single point machining of 4340 steel and Ti-6Al-4V heat treated to several strength levels, 606l-T6 aluminum, 304 stainless steel, 17-4PH stainless steel, 410 stainless steel, lead, and teflon. No signal characteristic changed in the same way with tool wear for all materials tested. A single change in a particular AE signal characteristic with tool wear valid for all materials probably does not exist. Nevertheless, changes in various signal characteristic with wear for a given material may be sufficient to be used to monitor tool wear.

GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline.

PubMed

Thanki, Anil S; Soranzo, Nicola; Haerty, Wilfried; Davey, Robert P

2018-03-01

Gene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological, and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL, and HomoloGene, to identify gene families and visualize syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries among multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences, provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families. A certain amount of expertise is required to configure and run the Ensembl Compara GeneTrees pipeline via command line. Therefore, we converted this pipeline into a Galaxy workflow, called GeneSeqToFamily, and provided additional functionality. This workflow uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow. GeneSeqToFamily represents the Ensembl GeneTrees pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxy's user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualize the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project.

The "Transport Specificity Ratio": a structure-function tool to search the protein fold for loci that control transition state stability in membrane transport catalysis

PubMed Central

King, Steven C

2004-01-01

Background In establishing structure-function relationships for membrane transport proteins, the interpretation of phenotypic changes can be problematic, owing to uncertainties in protein expression levels, sub-cellular localization, and protein-folding fidelity. A dual-label competitive transport assay called "Transport Specificity Ratio" (TSR) analysis has been developed that is simple to perform, and circumvents the "expression problem," providing a reliable TSR phenotype (a constant) for comparison to other transporters. Results Using the Escherichia coli GABA (4-aminobutyrate) permease (GabP) as a model carrier, it is demonstrated that the TSR phenotype is largely independent of assay conditions, exhibiting: (i) indifference to the particular substrate concentrations used, (ii) indifference to extreme changes (40-fold) in transporter expression level, and within broad limits (iii) indifference to assay duration. The theoretical underpinnings of TSR analysis predict all of the above observations, supporting that TSR has (i) applicability in the analysis of membrane transport, and (ii) particular utility in the face of incomplete information on protein expression levels and initial reaction rate intervals (e.g., in high-throughput screening situations). The TSR was used to identify gab permease (GabP) variants that exhibit relative changes in catalytic specificity (kcat/Km) for [14C]GABA (4-aminobutyrate) versus [3H]NA (nipecotic acid). Conclusions The TSR phenotype is an easily measured constant that reflects innate molecular properties of the transition state, and provides a reliable index of the difference in catalytic specificity that a carrier exhibits toward a particular pair of substrates. A change in the TSR phenotype, called a Δ(TSR), represents a specificity shift attributable to underlying changes in the intrinsic substrate binding energy (ΔGb) that translocation catalysts rely upon to decrease activation energy (). TSR analysis is therefore a structure-function tool that enables parsimonious scanning for positions in the protein fold that couple to the transition state, creating stability and thereby serving as functional determinants of catalytic power (efficiency, or specificity). PMID:15548327

Developing bioproxies of past ocean ecosystem change through compound-specific stable isotope analysis of proteinaceous deep-sea corals.

NASA Astrophysics Data System (ADS)

McMahon, K.; Williams, B.; Mccarthy, M. D.; Etnoyer, P. J.

2015-12-01

Our understanding of current and future ocean conditions is framed by our ability to reconstruct past changes in ecosystem structure and function recorded in paleoarchives. One such archive, proteinaceous deep-sea corals, act as "living sediment traps" with the potential to greatly improve our ability to reconstruct long-term, high-resolution biogeochemical records of export production. Compound-specific stable isotope analysis (CSIA) of individual amino acids (AAs) in deep-sea corals has provided highly detailed new tools to reconstruct changes in both plankton community composition and sources of nitrogen. However, to realize the full potential of CSIA in deep-sea corals, it is critical to better understand the link between the biogeochemical signatures of deep-sea coral polyp tissue and diagenetically resistant proteinaceous skeletal material. We conducted the first detailed comparison of δ13C and δ15N values for individual AAs between tissue and skeleton for three deep-sea coral genera (Primnoa, Isidella, and Kulamanamana). For δ13C values, we found minimal offsets in both essential and non-essential AAs across genera, strongly supporting coral skeleton AA fingerprinting as a new tool to reconstruct plankton community structure. Similarly, there was no significant offset in source AA δ15N values between tissue and skeleton, supporting the use of Phe δ15N as a proxy for baseline nitrogen sources. However, and rather unexpectedly, we found that the d15N values of the trophic AA group were consistently 3-4‰ lighter in skeleton than polyp tissue for all three genera. We hypothesize that this may reflect a partitioning of either N flux or pathways associated with AA transamination between polyp and skeleton tissues. This offset leads to an underestimate of trophic position using current CSIA-based calculations. Overall, our work strongly supports the applicability of CSIA in proteinaceous deep-sea corals to reconstruct past changes in biogeochemical cycling and plankton community dynamics. However, it also indicates that a new correction factor will be required to reconstruct accurate records of change in plankton trophic structure.

Simulation study of reticle enhancement technology applications for 157-nm lithography

NASA Astrophysics Data System (ADS)

Schurz, Dan L.; Flack, Warren W.; Karklin, Linard

2002-03-01

The acceleration of the International Technology Roadmap for Semiconductors (ITRS) is placing significant pressure on the industry's infrastructure, particularly the lithography equipment. As recently as 1997, there was no optical solution offered past the 130 nm design node. The current roadmap has the 65 nm node (reduced from 70 nm) pulled in one year to 2007. Both 248 nm and 193 nm wavelength lithography tools will be pushed to their practical resolution limits in the near term. Very high numerical aperture (NA) 193 nm exposure tools in conjunction with resolution enhancement techniques (RET) will postpone the requirement for 157 nm lithography in manufacturing. However, ICs produced at 70 nm design rules with manufacturable k 1 values will require that 157 nm wavelength lithography tools incorporate the same RETs utilized in 248nm, and 193 nm tools. These enhancements will include Alternating Phase Shifting Masks (AltPSM) and Optical Proximity Correction (OPC) on F 2 doped quartz reticle substrates. This study investigates simulation results when AltPSM is applied to sub-100 nm test patterns in 157 nm lithography in order to maintain Critical Dimension (CD) control for both nested and isolated geometries. Aerial image simulations are performed for a range of numerical apertures, chrome regulators, gate pitches and gate widths. The relative performance for phase shifted versus binary structures is also compared. Results are demonstrated in terms of aerial image contrast and process window changes. The results clearly show that a combination of high NA and RET is necessary to achieve usable process windows for 70 nm line/space structures. In addition, it is important to consider two-dimensional proximity effects for sub-100 nm gate structures.

Imbalance between Goals and Organizational Structure in Primary Health Care in Iran- a Systematic Review.

PubMed

Zanganeh Baygi, Mehdi; Seyedin, Hesam

2013-07-01

In recent years, the main focus of health sector reforms in Iran is the family physician and referral system plan. Fundamental changes in the goals and strategies, has increased the necessity of the need to reform the organizational structure. This study tries to review and summarize all cases about the organizational structure of Iran and its challenges in primary health care system. This study was a systematic review of published and grey literature. We searched the relevant databases, bibliography of related papers, and laws, using appropriate search strategies and key words. The CASP tool was used by two experts to evaluate the quality of retrieved papers and inconsistencies were resolved by discussion. After removal of duplicate citations, a total of 52 titles were identified through database searching, among which 30 met the inclusion criteria. Considering the research quality criteria, 14 papers were recognized qualified, which were categorized into two groups of: articles and policies. The results showed ineffectiveness of the current organizational structure at different level. The majority of the papers recommend performing reforms in the system because of changes in goals and strategies. Also, some suggest an appropriate information system to be designed in the current structures. Centralization and delegation process are the main discussions for the studies. Because of fundamental changes in goals and strategies, reforms in the organizational structure of primary health system in Iran especially in peripheral levels are highly recommended.

Hydrophobic core malleability of a de novo designed three-helix bundle protein.

PubMed

Walsh, S T; Sukharev, V I; Betz, S F; Vekshin, N L; DeGrado, W F

2001-01-12

De novo protein design provides a tool for testing the principles that stabilize the structures of proteins. Recently, we described the design and structure determination of alpha(3)D, a three-helix bundle protein with a well-packed hydrophobic core. Here, we test the malleability and adaptability of this protein's structure by mutating a small, Ala residue (A60) in its core to larger, hydrophobic side-chains, Leu and Ile. Such changes introduce strain into the structures of natural proteins, and therefore generally destabilize the native state. By contrast, these mutations were slightly stabilizing ( approximately 1.5 kcal mol(-1)) to the tertiary structure of alpha(3)D. The value of DeltaC(p) for unfolding of these mutants was not greatly affected relative to wild-type, indicating that the change in solvent accessibility for unfolding was similar. However, two-dimensional heteronuclear single quantum coherence spectra indicate that the protein adjusts to the introduction of steric bulk in different ways. A60L-alpha(3)D showed serious erosion in the dispersion of both the amide backbone as well as the side-chain methyl chemical shifts. By contrast, A60I-alpha(3)D showed excellent dispersion of the backbone resonances, and selective changes in dispersion of the aliphatic side-chains proximal to the site of mutation. Together, these data suggest that alpha(3)D, although folded into a unique three-dimensional structure, is nevertheless more malleable and flexible than most natural, native proteins. Copyright 2001 Academic Press.

Wear-Induced Changes in FSW Tool Pin Profile: Effect of Process Parameters

NASA Astrophysics Data System (ADS)

Sahlot, Pankaj; Jha, Kaushal; Dey, G. K.; Arora, Amit

2018-06-01

Friction stir welding (FSW) of high melting point metallic (HMPM) materials has limited application due to tool wear and relatively short tool life. Tool wear changes the profile of the tool pin and adversely affects weld properties. A quantitative understanding of tool wear and tool pin profile is crucial to develop the process for joining of HMPM materials. Here we present a quantitative wear study of H13 steel tool pin profile for FSW of CuCrZr alloy. The tool pin profile is analyzed at multiple traverse distances for welding with various tool rotational and traverse speeds. The results indicate that measured wear depth is small near the pin root and significantly increases towards the tip. Near the pin tip, wear depth increases with increase in tool rotational speed. However, change in wear depth near the pin root is minimal. Wear depth also increases with decrease in tool traverse speeds. Tool pin wear from the bottom results in pin length reduction, which is greater for higher tool rotational speeds, and longer traverse distances. The pin profile changes due to wear and result in root defect for long traverse distance. This quantitative understanding of tool wear would be helpful to estimate tool wear, optimize process parameters, and tool pin shape during FSW of HMPM materials.

doGlycans–Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

PubMed Central

2017-01-01

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell–cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS. PMID:28906114

Three-dimensional mapping of the local interstellar medium with composite data

NASA Astrophysics Data System (ADS)

Capitanio, L.; Lallement, R.; Vergely, J. L.; Elyajouri, M.; Monreal-Ibero, A.

2017-10-01

Context. Three-dimensional maps of the Galactic interstellar medium are general astrophysical tools. Reddening maps may be based on the inversion of color excess measurements for individual target stars or on statistical methods using stellar surveys. Three-dimensional maps based on diffuse interstellar bands (DIBs) have also been produced. All methods benefit from the advent of massive surveys and may benefit from Gaia data. Aims: All of the various methods and databases have their own advantages and limitations. Here we present a first attempt to combine different datasets and methods to improve the local maps. Methods: We first updated our previous local dust maps based on a regularized Bayesian inversion of individual color excess data by replacing Hipparcos or photometric distances with Gaia Data Release 1 values when available. Secondly, we complemented this database with a series of ≃5000 color excess values estimated from the strength of the λ15273 DIB toward stars possessing a Gaia parallax. The DIB strengths were extracted from SDSS/APOGEE spectra. Third, we computed a low-resolution map based on a grid of Pan-STARRS reddening measurements by means of a new hierarchical technique and used this map as the prior distribution during the inversion of the two other datasets. Results: The use of Gaia parallaxes introduces significant changes in some areas and globally increases the compactness of the structures. Additional DIB-based data make it possible to assign distances to clouds located behind closer opaque structures and do not introduce contradictory information for the close structures. A more realistic prior distribution instead of a plane-parallel homogeneous distribution helps better define the structures. We validated the results through comparisons with other maps and with soft X-ray data. Conclusions: Our study demonstrates that the combination of various tracers is a potential tool for more accurate maps. An online tool makes it possible to retrieve maps and reddening estimations. Our online tool is available at http://stilism.obspm.fr

A Multirate Control Strategy to the Slow Sensors Problem: An Interactive Simulation Tool for Controller Assisted Design

PubMed Central

Salt, Julián; Cuenca, Ángel; Palau, Francisco; Dormido, Sebastián

2014-01-01

In many control applications, the sensor technology used for the measurement of the variable to be controlled is not able to maintain a restricted sampling period. In this context, the assumption of regular and uniform sampling pattern is questionable. Moreover, if the control action updating can be faster than the output measurement frequency in order to fulfill the proposed closed loop behavior, the solution is usually a multirate controller. There are some known aspects to be careful of when a multirate system (MR) is going to be designed. The proper multiplicity between input-output sampling periods, the proper controller structure, the existence of ripples and others issues need to be considered. A useful way to save time and achieve good results is to have an assisted computer design tool. An interactive simulation tool to deal with MR seems to be the right solution. In this paper this kind of simulation application is presented. It allows an easy understanding of the performance degrading or improvement when changing the multirate sampling pattern parameters. The tool was developed using Sysquake, a Matlab-like language with fast execution and powerful graphic facilities. It can be delivered as an executable. In the paper a detailed explanation of MR treatment is also included and the design of four different MR controllers with flexible structure to be adapted to different schemes will also be presented. The Smith's predictor in these MR schemes is also explained, justified and used when time delays appear. Finally some interesting observations achieved using this interactive tool are included. PMID:24583971

Control/structure interaction conceptual design tool

NASA Technical Reports Server (NTRS)

Briggs, Hugh C.

1990-01-01

The JPL Control/Structure Interaction Program is developing new analytical methods for designing micro-precision spacecraft with controlled structures. One of these, the Conceptual Design Tool, will illustrate innovative new approaches to the integration of multi-disciplinary analysis and design methods. The tool will be used to demonstrate homogeneity of presentation, uniform data representation across analytical methods, and integrated systems modeling. The tool differs from current 'integrated systems' that support design teams most notably in its support for the new CSI multi-disciplinary engineer. The design tool will utilize a three dimensional solid model of the spacecraft under design as the central data organization metaphor. Various analytical methods, such as finite element structural analysis, control system analysis, and mechanical configuration layout, will store and retrieve data from a hierarchical, object oriented data structure that supports assemblies of components with associated data and algorithms. In addition to managing numerical model data, the tool will assist the designer in organizing, stating, and tracking system requirements.

Review of current status of smart structures and integrated systems

NASA Astrophysics Data System (ADS)

Chopra, Inderjit

1996-05-01

A smart structure involves distributed actuators and sensors, and one or more microprocessors that analyze the responses from the sensors and use distributed-parameter control theory to command the actuators to apply localized strains to minimize system response. A smart structure has the capability to respond to a changing external environment (such as loads or shape change) as well as to a changing internal environment (such as damage or failure). It incorporates smart actuators that allow the alteration of system characteristics (such as stiffness or damping) as well as of system response (such as strain or shape) in a controlled manner. Many types of actuators and sensors are being considered, such as piezoelectric materials, shape memory alloys, electrostrictive materials, magnetostrictive materials, electro- rheological fluids and fiber optics. These can be integrated with main load-carrying structures by surface bonding or embedding without causing any significant changes in the mass or structural stiffness of the system. Numerous applications of smart structures technology to various physical systems are evolving to actively control vibration, noise, aeroelastic stability, damping, shape and stress distribution. Applications range from space systems, fixed-wing and rotary-wing aircraft, automotive, civil structures and machine tools. Much of the early development of smart structures methodology was driven by space applications such as vibration and shape control of large flexible space structures, but now wider applications are envisaged for aeronautical and other systems. Embedded or surface-bonded smart actuators on an airplane wing or helicopter blade will induce alteration of twist/camber of airfoil (shape change), that in turn will cause variation of lift distribution and may help to control static and dynamic aeroelastic problems. Applications of smart structures technology to aerospace and other systems are expanding rapidly. Major barriers are: actuator stroke, reliable data base of smart material characteristics, non-availability of robust distributed parameter control strategies, and non-existent mathematical modeling of smart systems. The objective of this paper is to review the state-of-the-art of smart actuators and sensors and integrated systems and point out the needs for future research.

Graph distance for complex networks

NASA Astrophysics Data System (ADS)

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

2016-10-01

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

Preface -2017EMRS-Fall-symposium W: Stress, structure and stoichiometry effects on the properties of nanomaterials IV

NASA Astrophysics Data System (ADS)

Sánchez, Florencio; Craciun, Valentin

2018-07-01

Research on nanomaterials and nanostructures is continuing to grow at a rapid pace as they are used in many important devices like transistors, sensors, MEMS or components of modern tools for diagnosis and treatment in medicine. The functional properties of the materials used in these devices depend on their microstructure, and can be finely tuned using physical and chemical synthesis or various processing techniques that change the structure, composition, morphology and defects type and concentration. The investigation of stress, stoichiometry, phase structure and defects at atomic level is necessary to understand, model and further optimize the electric, magnetic, optical and mechanical properties of the nanosystems and for engineers to design new, better and more reliable devices.

Aeroelastic Tailoring of Transport Aircraft Wings: State-of-the-Art and Potential Enabling Technologies

NASA Technical Reports Server (NTRS)

Jutte, Christine; Stanford, Bret K.

2014-01-01

This paper provides a brief overview of the state-of-the-art for aeroelastic tailoring of subsonic transport aircraft and offers additional resources on related research efforts. Emphasis is placed on aircraft having straight or aft swept wings. The literature covers computational synthesis tools developed for aeroelastic tailoring and numerous design studies focused on discovering new methods for passive aeroelastic control. Several new structural and material technologies are presented as potential enablers of aeroelastic tailoring, including selectively reinforced materials, functionally graded materials, fiber tow steered composite laminates, and various nonconventional structural designs. In addition, smart materials and structures whose properties or configurations change in response to external stimuli are presented as potential active approaches to aeroelastic tailoring.

Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes.

PubMed

Freeman, Noam S; Moore, Curtis E; Wilhelmsson, L Marcus; Tor, Yitzhak

2016-06-03

Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure.

Use of an automated decision support tool optimizes clinicians' ability to interpret and appropriately respond to structured self-monitoring of blood glucose data.

PubMed

Rodbard, Helena W; Schnell, Oliver; Unger, Jeffrey; Rees, Christen; Amstutz, Linda; Parkin, Christopher G; Jelsovsky, Zhihong; Wegmann, Nathan; Axel-Schweitzer, Matthias; Wagner, Robin S

2012-04-01

We evaluated the impact of an automated decision support tool (DST) on clinicians' ability to identify glycemic abnormalities in structured self-monitoring of blood glucose (SMBG) data and then make appropriate therapeutic changes based on the glycemic patterns observed. In this prospective, randomized, controlled, multicenter study, 288 clinicians (39.6% family practice physicians, 37.9% general internal medicine physicians, and 22.6% nurse practitioners) were randomized to structured SMBG alone (STG; n = 72); structured SMBG with DST (DST; n = 72); structured SMBG with an educational DVD (DVD; n = 72); and structured SMBG with DST and the educational DVD (DST+DVD; n = 72). Clinicians analyzed 30 patient cases (type 2 diabetes), identified the primary abnormality, and selected the most appropriate therapy. A total of 222 clinicians completed all 30 patient cases with no major protocol deviations. Significantly more DST, DVD, and DST+DVD clinicians correctly identified the glycemic abnormality and selected the most appropriate therapeutic option compared with STG clinicians: 49, 51, and 55%, respectively, vs. 33% (all P < 0.0001) with no significant differences among DST, DVD, and DST+DVD clinicians. Use of structured SMBG, combined with the DST, the educational DVD, or both, enhances clinicians' ability to correctly identify significant glycemic patterns and make appropriate therapeutic decisions to address those patterns. Structured testing interventions using either the educational DVD or the DST are equally effective in improving data interpretation and utilization. The DST provides a viable alternative when comprehensive education is not feasible, and it may be integrated into medical practices with minimal training.

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template

PubMed Central

Christensen, Signe; Horowitz, Scott; Bardwell, James C.A.; Olsen, Johan G.; Willemoës, Martin; Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Winther, Jakob R.

2017-01-01

Despite the development of powerful computational tools, the full-sequence design of proteins still remains a challenging task. To investigate the limits and capabilities of computational tools, we conducted a study of the ability of the program Rosetta to predict sequences that recreate the authentic fold of thioredoxin. Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each. For experimental evaluation, we chose six sequences from each of the eight templates by objective criteria. The 48 selected sequences were evaluated based on their progressive ability to (1) produce soluble protein in Escherichia coli and (2) yield stable monomeric protein, and (3) on the ability of the stable, soluble proteins to adopt the target fold. Of the 48 designs, we were able to synthesize 32, 20 of which resulted in soluble protein. Of these, only two were sufficiently stable to be purified. An X-ray crystal structure was solved for one of the designs, revealing a close resemblance to the target structure. We found a significant difference among the eight template structures to realize the above three criteria despite their high structural similarity. Thus, in order to improve the success rate of computational full-sequence design methods, we recommend that multiple template structures are used. Furthermore, this study shows that special care should be taken when optimizing the geometry of a structure prior to computational design when using a method that is based on rigid conformations. PMID:27659562

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.

PubMed

Johansson, Kristoffer E; Tidemand Johansen, Nicolai; Christensen, Signe; Horowitz, Scott; Bardwell, James C A; Olsen, Johan G; Willemoës, Martin; Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Winther, Jakob R

2016-10-23

Despite the development of powerful computational tools, the full-sequence design of proteins still remains a challenging task. To investigate the limits and capabilities of computational tools, we conducted a study of the ability of the program Rosetta to predict sequences that recreate the authentic fold of thioredoxin. Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each. For experimental evaluation, we chose six sequences from each of the eight templates by objective criteria. The 48 selected sequences were evaluated based on their progressive ability to (1) produce soluble protein in Escherichia coli and (2) yield stable monomeric protein, and (3) on the ability of the stable, soluble proteins to adopt the target fold. Of the 48 designs, we were able to synthesize 32, 20 of which resulted in soluble protein. Of these, only two were sufficiently stable to be purified. An X-ray crystal structure was solved for one of the designs, revealing a close resemblance to the target structure. We found a significant difference among the eight template structures to realize the above three criteria despite their high structural similarity. Thus, in order to improve the success rate of computational full-sequence design methods, we recommend that multiple template structures are used. Furthermore, this study shows that special care should be taken when optimizing the geometry of a structure prior to computational design when using a method that is based on rigid conformations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods

PubMed Central

2012-01-01

High-dimensional gene expression data provide a rich source of information because they capture the expression level of genes in dynamic states that reflect the biological functioning of a cell. For this reason, such data are suitable to reveal systems related properties inside a cell, e.g., in order to elucidate molecular mechanisms of complex diseases like breast or prostate cancer. However, this is not only strongly dependent on the sample size and the correlation structure of a data set, but also on the statistical hypotheses tested. Many different approaches have been developed over the years to analyze gene expression data to (I) identify changes in single genes, (II) identify changes in gene sets or pathways, and (III) identify changes in the correlation structure in pathways. In this paper, we review statistical methods for all three types of approaches, including subtypes, in the context of cancer data and provide links to software implementations and tools and address also the general problem of multiple hypotheses testing. Further, we provide recommendations for the selection of such analysis methods. Reviewers This article was reviewed by Arcady Mushegian, Byung-Soo Kim and Joel Bader. PMID:23227854

Subcortical volumetric changes across the adult lifespan: subregional thalamic atrophy accounts for age-related sensorimotor performance declines.

PubMed

Serbruyns, Leen; Leunissen, Inge; Huysmans, Toon; Cuypers, Koen; Meesen, Raf L; van Ruitenbeek, Peter; Sijbers, Jan; Swinnen, Stephan P

2015-04-01

Even though declines in sensorimotor performance during healthy aging have been documented extensively, its underlying neural mechanisms remain unclear. Here, we explored whether age-related subcortical atrophy plays a role in sensorimotor performance declines, and particularly during bimanual manipulative performance (Purdue Pegboard Test). The thalamus, putamen, caudate and pallidum of 91 participants across the adult lifespan (ages 20-79 years) were automatically segmented. In addition to studying age-related changes in the global volume of each subcortical structure, local deformations within these structures, indicative of subregional volume changes, were assessed by means of recently developed shape analyses. Results showed widespread age-related global and subregional atrophy, as well as some notable subregional expansion. Even though global atrophy failed to explain the observed performance declines with aging, shape analyses indicated that atrophy in left and right thalamic subregions, specifically subserving connectivity with the premotor, primary motor and somatosensory cortical areas, mediated the relation between aging and performance decline. It is concluded that subregional volume assessment by means of shape analyses offers a sensitive tool with high anatomical resolution in the search for specific age-related associations between brain structure and behavior. Copyright © 2015 Elsevier Ltd. All rights reserved.

AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation.

PubMed

Masso, Majid; Vaisman, Iosif I

2014-01-01

The AUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins upon single residue substitutions, developed by combining structure-based features with trained statistical learning models. Three of the predictors evaluate changes to protein stability upon mutation, each complementing a distinct experimental approach. Two additional classifiers are available, one for predicting activity changes due to residue replacements and the other for determining the disease potential of mutations associated with nonsynonymous single nucleotide polymorphisms (nsSNPs) in human proteins. These five command-line driven tools, as well as all the supporting programs, complement those that run our AUTO-MUTE web-based server. Nevertheless, all the codes have been rewritten and substantially altered for the new portable software, and they incorporate several new features based on user feedback. Included among these upgrades is the ability to perform three highly requested tasks: to run "big data" batch jobs; to generate predictions using modified protein data bank (PDB) structures, and unpublished personal models prepared using standard PDB file formatting; and to utilize NMR structure files that contain multiple models.

Atomic structure and pressure-induced phase transformations in a phase-change alloy

NASA Astrophysics Data System (ADS)

Xu, Ming

Phase-change materials exist in at least two phases under the ambient condition. One is the amorphous state and another is crystalline phase. These two phases have vastly different physical properties, such as electrical conductivity, optical reflectivity, mass density, thermal conductivity, etc. The distinct physical properties and the fast transformation between amorphous and crystalline phases render these materials the ability to store information. For example, the DVD and the Blue-ray discs take advantage of the optical reflectivity contrast, and the newly developed solid-state memories make use of the large conductivity difference. In addition, both the amorphous and crystalline phases in phase-change memories (PCMs) are very stable at room temperature, and they are easy to be scaled up in the production of devices with large storage density. All these features make phase-change materials the ideal candidates for the next-generation memories. Despite of the fast development of these new memory materials in industry, many fundamental physics problems underlying these interesting materials are still not fully resolved. This thesis is aiming at solving some of the key issues in phase-change materials. Most of phase-change materials are composed of Ge-Sb-Te constituents. Among all these Ge-Sb-Te based materials, Ge2Sb2Te5 (GST) has the best performance and has been frequently studied as a prototypical phase-change material. The first and foremost issue is the structure of the two functioning phases. In this thesis, we investigate the unique atomic structure and bonding nature of amorphous GST (a-GST) and crystalline GST ( c-GST), using ab initio tools and X-ray diffraction (XRD) methods. Their local structures and bonding scenarios are then analyzed using electronic structure calculations. In order to gain insight into the fast phase transformation mechanism, we also carried out a series of high-pressure experiments on GST. Several new polymorphs and their transformations have been revealed under high pressure via in situ XRD and in situ electrical resistivity measurements. The mechanisms of the structural and property changes have been uncovered via ab initio molecular dynamics simulations.

A new approach for structural health monitoring by applying anomaly detection on strain sensor data

NASA Astrophysics Data System (ADS)

Trichias, Konstantinos; Pijpers, Richard; Meeuwissen, Erik

2014-03-01

Structural Health Monitoring (SHM) systems help to monitor critical infrastructures (bridges, tunnels, etc.) remotely and provide up-to-date information about their physical condition. In addition, it helps to predict the structure's life and required maintenance in a cost-efficient way. Typically, inspection data gives insight in the structural health. The global structural behavior, and predominantly the structural loading, is generally measured with vibration and strain sensors. Acoustic emission sensors are more and more used for measuring global crack activity near critical locations. In this paper, we present a procedure for local structural health monitoring by applying Anomaly Detection (AD) on strain sensor data for sensors that are applied in expected crack path. Sensor data is analyzed by automatic anomaly detection in order to find crack activity at an early stage. This approach targets the monitoring of critical structural locations, such as welds, near which strain sensors can be applied during construction and/or locations with limited inspection possibilities during structural operation. We investigate several anomaly detection techniques to detect changes in statistical properties, indicating structural degradation. The most effective one is a novel polynomial fitting technique, which tracks slow changes in sensor data. Our approach has been tested on a representative test structure (bridge deck) in a lab environment, under constant and variable amplitude fatigue loading. In both cases, the evolving cracks at the monitored locations were successfully detected, autonomously, by our AD monitoring tool.

Acoustic emission from single point machining: Part 2, Signal changes with tool wear. Revised

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

Heiple, C.R.; Carpenter, S.H.; Armentrout, D.L.

1989-12-31

Changes in acoustic emission signal characteristics with tool wear were monitored during single point machining of 4340 steel and Ti-6Al-4V heat treated to several strength levels, 606l-T6 aluminum, 304 stainless steel, 17-4PH stainless steel, 410 stainless steel, lead, and teflon. No signal characteristic changed in the same way with tool wear for all materials tested. A single change in a particular AE signal characteristic with tool wear valid for all materials probably does not exist. Nevertheless, changes in various signal characteristic with wear for a given material may be sufficient to be used to monitor tool wear.

Integrated Aerodynamic/Structural/Dynamic Analyses of Aircraft with Large Shape Changes

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.; Chwalowski, Pawel; Horta, Lucas G.; Piatak, David J.; McGowan, Anna-Maria R.

2007-01-01

The conceptual and preliminary design processes for aircraft with large shape changes are generally difficult and time-consuming, and the processes are often customized for a specific shape change concept to streamline the vehicle design effort. Accordingly, several existing reports show excellent results of assessing a particular shape change concept or perturbations of a concept. The goal of the current effort was to develop a multidisciplinary analysis tool and process that would enable an aircraft designer to assess several very different morphing concepts early in the design phase and yet obtain second-order performance results so that design decisions can be made with better confidence. The approach uses an efficient parametric model formulation that allows automatic model generation for systems undergoing radical shape changes as a function of aerodynamic parameters, geometry parameters, and shape change parameters. In contrast to other more self-contained approaches, the approach utilizes off-the-shelf analysis modules to reduce development time and to make it accessible to many users. Because the analysis is loosely coupled, discipline modules like a multibody code can be easily swapped for other modules with similar capabilities. One of the advantages of this loosely coupled system is the ability to use the medium-to high-fidelity tools early in the design stages when the information can significantly influence and improve overall vehicle design. Data transfer among the analysis modules are based on an accurate and automated general purpose data transfer tool. In general, setup time for the integrated system presented in this paper is 2-4 days for simple shape change concepts and 1-2 weeks for more mechanically complicated concepts. Some of the key elements briefly described in the paper include parametric model development, aerodynamic database generation, multibody analysis, and the required software modules as well as examples for a telescoping wing, a folding wing, and a bat-like wing.

An Ecosystem Service Evaluation Tool to Support Ridge-to-Reef Management and Conservation in Hawaii

NASA Astrophysics Data System (ADS)

Oleson, K.; Callender, T.; Delevaux, J. M. S.; Falinski, K. A.; Htun, H.; Jin, G.

2014-12-01

Faced with increasing anthropogenic stressors and diverse stakeholders, local managers are adopting a ridge-to-reef and multi-objective management approach to restore declining coral reef health state. An ecosystem services framework, which integrates ecological indicators and stakeholder values, can foster more applied and integrated research, data collection, and modeling, and thus better inform the decision-making process and realize decision outcomes grounded in stakeholders' values. Here, we describe a research program that (i) leverages remotely sensed and empirical data to build an ecosystem services-based decision-support tool geared towards ridge-to-reef management; and (ii) applies it as part of a structured, value-based decision-making process to inform management in west Maui, a NOAA coral reef conservation priority site. The tool links terrestrial and marine biophysical models in a spatially explicit manner to quantify and map changes in ecosystem services delivery resulting from management actions, projected climate change impacts, and adaptive responses. We couple model outputs with localized valuation studies to translate ecosystem service outcomes into benefits and their associated socio-cultural and/or economic values. Managers can use this tool to run scenarios during their deliberations to evaluate trade-offs, cost-effectiveness, and equity implications of proposed policies. Ultimately, this research program aims at improving the effectiveness, efficiency, and equity outcomes of ecosystem-based management. This presentation will describe our approach, summarize initial results from the terrestrial modeling and economic valuations for west Maui, and highlight how this decision support tool benefits managers in west Maui.

Energy Monitoring and Targeting as diagnosis; Applying work analysis to adapt a statistical change detection strategy using representation aiding

NASA Astrophysics Data System (ADS)

Hilliard, Antony

Energy Monitoring and Targeting is a well-established business process that develops information about utility energy consumption in a business or institution. While M&T has persisted as a worthwhile energy conservation support activity, it has not been widely adopted. This dissertation explains M&T challenges in terms of diagnosing and controlling energy consumption, informed by a naturalistic field study of M&T work. A Cognitive Work Analysis of M&T identifies structures that diagnosis can search, information flows un-supported in canonical support tools, and opportunities to extend the most popular tool for MM&T: Cumulative Sum of Residuals (CUSUM) charts. A design application outlines how CUSUM charts were augmented with a more contemporary statistical change detection strategy, Recursive Parameter Estimates, modified to better suit the M&T task using Representation Aiding principles. The design was experimentally evaluated in a controlled M&T synthetic task, and was shown to significantly improve diagnosis performance.

Development of Adaptive Management Tools to Guide Habitat Allocations for At-Risk Species

DTIC Science & Technology

2014-01-01

Results indicated that the mating system assumptions can have a large impact on the ability of the model to approximate data collected in the field...indicated that strength of habitat preferences during dispersal for juvenile and subadult male dispersal also significantly impacted model fit. Certainly...the influence of habitat loss, as these structural (or geometric) changes are often confounded in real landscapes, the impact of fragmentation is

Comprehensive surface treatment of high-speed steel tool

NASA Astrophysics Data System (ADS)

Fedorov, Sergey V.; Aleshin, Sergey V.; Swe, Min Htet; Abdirova, Raushan D.; Kapitanov, Alexey V.; Egorov, Sergey B.

2018-03-01

One of the promising directions of hardening of high-speed steel tool is the creation on their surface of the layered structures with the gradient of physic-chemical properties between the wear-resistant coatings to the base material. Among the methods of such surface modification, a special process takes place based on the use of pulsed high-intensity charged particle beams. The high speed of heating and cooling allows structural-phase transformations in the surface layer, which cannot be realized in a stationary mode. The treatment was conducted in a RITM-SP unit, which constitutes a combination of a source of low-energy high-current electron beams "RITM" and two magnetron spraying systems on a single vacuum chamber. The unit enables deposition of films on the surface of the desired product and subsequent liquid-phase mixing of materials of the film and the substrate by an intense pulse electron beam. The article discusses features of the structure of the subsurface layer of high-speed steel M2, modified by surface alloying of a low-energy high-current electron beam, and its effect on the wear resistance of the tool when dry cutting hard to machine Nickel alloy. A significant decrease of intensity of wear of high-speed steel with combined treatment happens due to the displacement of the zone of wear and decrease the radius of rounding of the cutting edge because of changes in conditions of interaction with the material being treated.

Structural Embeddings: Mechanization with Method

NASA Technical Reports Server (NTRS)

Munoz, Cesar; Rushby, John

1999-01-01

The most powerful tools for analysis of formal specifications are general-purpose theorem provers and model checkers, but these tools provide scant methodological support. Conversely, those approaches that do provide a well-developed method generally have less powerful automation. It is natural, therefore, to try to combine the better-developed methods with the more powerful general-purpose tools. An obstacle is that the methods and the tools often employ very different logics. We argue that methods are separable from their logics and are largely concerned with the structure and organization of specifications. We, propose a technique called structural embedding that allows the structural elements of a method to be supported by a general-purpose tool, while substituting the logic of the tool for that of the method. We have found this technique quite effective and we provide some examples of its application. We also suggest how general-purpose systems could be restructured to support this activity better.

Detecting correlation changes in multivariate time series: A comparison of four non-parametric change point detection methods.

PubMed

Cabrieto, Jedelyn; Tuerlinckx, Francis; Kuppens, Peter; Grassmann, Mariel; Ceulemans, Eva

2017-06-01

Change point detection in multivariate time series is a complex task since next to the mean, the correlation structure of the monitored variables may also alter when change occurs. DeCon was recently developed to detect such changes in mean and\\or correlation by combining a moving windows approach and robust PCA. However, in the literature, several other methods have been proposed that employ other non-parametric tools: E-divisive, Multirank, and KCP. Since these methods use different statistical approaches, two issues need to be tackled. First, applied researchers may find it hard to appraise the differences between the methods. Second, a direct comparison of the relative performance of all these methods for capturing change points signaling correlation changes is still lacking. Therefore, we present the basic principles behind DeCon, E-divisive, Multirank, and KCP and the corresponding algorithms, to make them more accessible to readers. We further compared their performance through extensive simulations using the settings of Bulteel et al. (Biological Psychology, 98 (1), 29-42, 2014) implying changes in mean and in correlation structure and those of Matteson and James (Journal of the American Statistical Association, 109 (505), 334-345, 2014) implying different numbers of (noise) variables. KCP emerged as the best method in almost all settings. However, in case of more than two noise variables, only DeCon performed adequately in detecting correlation changes.

Development of designed site-directed pseudopeptide-peptido-mimetic immunogens as novel minimal subunit-vaccine candidates for malaria.

PubMed

Lozano, José Manuel; Lesmes, Liliana P; Carreño, Luisa F; Gallego, Gina M; Patarroyo, Manuel Elkin

2010-12-06

Synthetic vaccines constitute the most promising tools for controlling and preventing infectious diseases. When synthetic immunogens are designed from the pathogen native sequences, these are normally poorly immunogenic and do not induce protection, as demonstrated in our research. After attempting many synthetic strategies for improving the immunogenicity properties of these sequences, the approach consisting of identifying high binding motifs present in those, and then performing specific changes on amino-acids belonging to such motifs, has proven to be a workable strategy. In addition, other strategies consisting of chemically introducing non-natural constraints to the backbone topology of the molecule and modifying the α-carbon asymmetry are becoming valuable tools to be considered in this pursuit. Non-natural structural constraints to the peptide backbone can be achieved by introducing peptide bond isosters such as reduced amides, partially retro or retro-inverso modifications or even including urea motifs. The second can be obtained by strategically replacing L-amino-acids with their enantiomeric forms for obtaining both structurally site-directed designed immunogens as potential vaccine candidates and their Ig structural molecular images, both having immuno-therapeutic effects for preventing and controlling malaria.

Chemical Sensor Array Response Modeling Using Quantitative Structure-Activity Relationships Technique

NASA Astrophysics Data System (ADS)

Shevade, Abhijit V.; Ryan, Margaret A.; Homer, Margie L.; Zhou, Hanying; Manfreda, Allison M.; Lara, Liana M.; Yen, Shiao-Pin S.; Jewell, April D.; Manatt, Kenneth S.; Kisor, Adam K.

We have developed a Quantitative Structure-Activity Relationships (QSAR) based approach to correlate the response of chemical sensors in an array with molecular descriptors. A novel molecular descriptor set has been developed; this set combines descriptors of sensing film-analyte interactions, representing sensor response, with a basic analyte descriptor set commonly used in QSAR studies. The descriptors are obtained using a combination of molecular modeling tools and empirical and semi-empirical Quantitative Structure-Property Relationships (QSPR) methods. The sensors under investigation are polymer-carbon sensing films which have been exposed to analyte vapors at parts-per-million (ppm) concentrations; response is measured as change in film resistance. Statistically validated QSAR models have been developed using Genetic Function Approximations (GFA) for a sensor array for a given training data set. The applicability of the sensor response models has been tested by using it to predict the sensor activities for test analytes not considered in the training set for the model development. The validated QSAR sensor response models show good predictive ability. The QSAR approach is a promising computational tool for sensing materials evaluation and selection. It can also be used to predict response of an existing sensing film to new target analytes.

[Rating scales based on the phenomenological and structural approach].

PubMed

Schiltz, L

2006-01-01

A current tendency of research in clinical psychology consists in using an integrated quantitative and qualitative methodology. This approach is especially suited to the study of the therapeutic intervention where the researcher is himself part of the situation he is investigating. As to the tools of research, the combination of the semi-structured clinical interview, of psychometric scales and projective tests has proved to be pertinent to describe the multidimensional and fluctuating reality of the therapeutic relationship and the changes induced by it in the two partners. In arts therapeutic research the investigation of the artistic production or of the free expression of people may complete the psychometric and projective tools. The concept of "expressive test" is currently being used to characterise this method. In this context, the development of rating scales, based on the phenomenological and structural or holistic approach allows us making the link between qualitative analysis and quantification, leading to the use of inferential statistics, providing that we remain at the nominal or ordinal level of measurement. We are explaining the principle of construction of these rating scales and we are illustrating our practice with some examples drawn from studies we realized in clinical psychology.

A systematic review on popularity, application and characteristics of protein secondary structure prediction tools.

PubMed

Kashani-Amin, Elaheh; Tabatabaei-Malazy, Ozra; Sakhteman, Amirhossein; Larijani, Bagher; Ebrahim-Habibi, Azadeh

2018-02-27

Prediction of proteins' secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple secondary structure prediction (SSP) options is challenging. The current study is an insight onto currently favored methods and tools, within various contexts. A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of 209 studies were finally found eligible to extract data. Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating a SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. This study provides a comprehensive insight about the recent usage of SSP tools which could be helpful for selecting a proper tool's choice. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

p3d--Python module for structural bioinformatics.

PubMed

Fufezan, Christian; Specht, Michael

2009-08-21

High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

Climate Adaptation is About More Than Climate: Value-Driven Science Delivery

NASA Astrophysics Data System (ADS)

Swanston, C.

2015-12-01

Efforts to deliver relevant scientific information and tools to diverse stakeholders have dramatically increased in recent years with the intention of promoting climate change adaptation. Much work has been done to understand the barriers to action, but these largely overlook the need to frame the discussion in terms of stakeholder values and co-create innovative solutions that meet their individual needs. A partnership-based effort in the upper Midwest and Northeast called the Climate Change Response Framework (CCRF; www.forestadaptation.org) ensures relevance, breadth, and credibility of its products through stakeholder inclusion at all levels. The fundamental role of the CCRF is to help people meet their land stewardship goals while minimizing climate risk. This represents a subtle but important shift in focus to people and their values, as opposed to climate change and its effects. The CCRF uses a climate planning tool, the Adaptation Workbook (www.adaptationworkbook.org), along with ecosystem vulnerability assessments and a diverse "menu" of adaptation approaches to generate site-specific adaptation actions that meet explicit conservation objectives. These tools are integrated into an Adaptation Planning and Practices workshop that leads organizations through this structured process of designing adaptation tactics for their projects and plans. All of these tools were developed with stakeholders, or in response to their direct and continuing feedback. The CCRF has involved thousands of people and over 100 organizations, published six ecoregional vulnerability assessments with more than 130 authors, and generated more than 125 intentional adaptation demonstrations in real-world land management projects on federal, state, tribal, county, conservancy, and private lands. The CCRF contributes strongly to the USDA Regional Climate Hubs, working on the applied end of the continuum of climate services occupied by providers such as the CSCs, LCCs, RISAs, and RCCs.

Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course.

PubMed

Jaswal, Sheila S; O'Hara, Patricia B; Williamson, Patrick L; Springer, Amy L

2013-01-01

Because understanding the structure of biological macromolecules is critical to understanding their function, students of biochemistry should become familiar not only with viewing, but also with generating and manipulating structural representations. We report a strategy from a one-semester undergraduate biochemistry course to integrate use of structural representation tools into both laboratory and homework activities. First, early in the course we introduce the use of readily available open-source software for visualizing protein structure, coincident with modules on amino acid and peptide bond properties. Second, we use these same software tools in lectures and incorporate images and other structure representations in homework tasks. Third, we require a capstone project in which teams of students examine a protein-nucleic acid complex and then use the software tools to illustrate for their classmates the salient features of the structure, relating how the structure helps explain biological function. To ensure engagement with a range of software and database features, we generated a detailed template file that can be used to explore any structure, and that guides students through specific applications of many of the software tools. In presentations, students demonstrate that they are successfully interpreting structural information, and using representations to illustrate particular points relevant to function. Thus, over the semester students integrate information about structural features of biological macromolecules into the larger discussion of the chemical basis of function. Together these assignments provide an accessible introduction to structural representation tools, allowing students to add these methods to their biochemical toolboxes early in their scientific development. © 2013 by The International Union of Biochemistry and Molecular Biology.

Spline-Screw Payload-Fastening System

NASA Technical Reports Server (NTRS)

Vranish, John M.

1994-01-01

Payload handed off securely between robot and vehicle or structure. Spline-screw payload-fastening system includes mating female and male connector mechanisms. Clockwise (or counter-clockwise) rotation of splined male driver on robotic end effector causes connection between robot and payload to tighten (or loosen) and simultaneously causes connection between payload and structure to loosen (or tighten). Includes mechanisms like those described in "Tool-Changing Mechanism for Robot" (GSC-13435) and "Self-Aligning Mechanical and Electrical Coupling" (GSC-13430). Designed for use in outer space, also useful on Earth in applications needed for secure handling and secure mounting of equipment modules during storage, transport, and/or operation. Particularly useful in machine or robotic applications.

Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI

NASA Astrophysics Data System (ADS)

Alba, Josephine; Marcaida, Maria Jose; Prieto, Jesus; Montoya, Guillermo; Molina, Rafael; D'Abramo, Marco

2017-12-01

I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target sequences, thus providing potential tools for genome manipulation. Working towards this particular application, many efforts have been made to generate mesophilic variants of I-DmoI that function at lower temperatures than the wild-type. Here, we report a structural and computational analysis of two I-DmoI mesophilic mutants. Despite very limited structural variations between the crystal structures of these variants and the wild-type, a different dynamical behaviour near the cleavage sites is observed. In particular, both the dynamics of the water molecules and the protein perturbation effect on the cleavage site correlate well with the changes observed in the experimental enzymatic activity.

Application of carbide cutting tools with nano-structured multilayer composite coatings for turning austenitic steels, type 16Cr-10NI

NASA Astrophysics Data System (ADS)

Vereschaka, Alexey; Migranov, Mars; Oganyan, Gaik; Sotova, Catherine S.; Batako, Andre

2018-03-01

This paper addresses the challenges of increasing the efficiency of the machining of austenitic stainless steels AISI 321 and S31600 by application of cutting tools with multilayer composite nano-structured coatings. The main mechanical properties and internal structures of the coatings under study (hardness, adhesion strength in the "coating-substrate" system) were investigated, and their chemical compositions were analyzed. The conducted research of tool life and nature of wear of carbide tools with the investigated coatings during turning of the above mentioned steels showed that the application of those coatings increases the tool life by up to 2.5 times. In addition, the use of a cutting tool with coatings allows machining at higher cutting speeds. It was also found that the use of a tool with multilayer composite nano-structured coating (Zr,Nb)N-(Zr,Al,Nb)N ensures better results compared with not only monolithic coating TiN, but also with nano-structured coatings Ti-TiN-(Ti,Al)N and (Zr,Nb)N-(Cr,Zr,Nb,Al)N. The mechanism of failure of the coatings under study was also investigated.

Using competences and competence tools in workforce development.

PubMed

Green, Tess; Dickerson, Claire; Blass, Eddie

The NHS Knowledge and Skills Framework (KSF) has been a driving force in the move to competence-based workforce development in the NHS. Skills for Health has developed national workforce competences that aim to improve behavioural performance, and in turn increase productivity. This article describes five projects established to test Skills for Health national workforce competences, electronic tools and products in different settings in the NHS. Competences and competence tools were used to redesign services, develop job roles, identify skills gaps and develop learning programmes. Reported benefits of the projects included increased clarity and a structured, consistent and standardized approach to workforce development. Findings from the evaluation of the tools were positive in terms of their overall usefulness and provision of related training/support. Reported constraints of using the competences and tools included issues relating to their availability, content and organization. It is recognized that a highly skilled and flexible workforce is important to the delivery of high-quality health care. These projects suggest that Skills for Health competences can be used as a 'common currency' in workforce development in the UK health sector. This would support the need to adapt rapidly to changing service needs.

Predicting functional divergence in protein evolution by site-specific rate shifts

NASA Technical Reports Server (NTRS)

Gaucher, Eric A.; Gu, Xun; Miyamoto, Michael M.; Benner, Steven A.

2002-01-01

Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.

Emergent mechanics of biological structures

PubMed Central

Dumont, Sophie; Prakash, Manu

2014-01-01

Mechanical force organizes life at all scales, from molecules to cells and tissues. Although we have made remarkable progress unraveling the mechanics of life's individual building blocks, our understanding of how they give rise to the mechanics of larger-scale biological structures is still poor. Unlike the engineered macroscopic structures that we commonly build, biological structures are dynamic and self-organize: they sculpt themselves and change their own architecture, and they have structural building blocks that generate force and constantly come on and off. A description of such structures defies current traditional mechanical frameworks. It requires approaches that account for active force-generating parts and for the formation of spatial and temporal patterns utilizing a diverse array of building blocks. In this Perspective, we term this framework “emergent mechanics.” Through examples at molecular, cellular, and tissue scales, we highlight challenges and opportunities in quantitatively understanding the emergent mechanics of biological structures and the need for new conceptual frameworks and experimental tools on the way ahead. PMID:25368421

Architectural Improvements and New Processing Tools for the Open XAL Online Model

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

Allen, Christopher K; Pelaia II, Tom; Freed, Jonathan M

The online model is the component of Open XAL providing accelerator modeling, simulation, and dynamic synchronization to live hardware. Significant architectural changes and feature additions have been recently made in two separate areas: 1) the managing and processing of simulation data, and 2) the modeling of RF cavities. Simulation data and data processing have been completely decoupled. A single class manages all simulation data while standard tools were developed for processing the simulation results. RF accelerating cavities are now modeled as composite structures where parameter and dynamics computations are distributed. The beam and hardware models both maintain their relative phasemore » information, which allows for dynamic phase slip and elapsed time computation.« less

Rate Change Graph Technology: Absolute Value Point Methodology

NASA Astrophysics Data System (ADS)

Strickland, Ken; Duvernois, Michael

2011-10-01

Absolute Value Point Methodology (AVPM) is a new theoretical tool for science research centered on Rate Change Graph Technology (RCGT). The modeling techniques of AVPM surpass conventional methods by extending the geometrical rules of mathematics. Exact geometrical structures of matter and energy become clearer revealing new ways to compile advanced data. RCGT mechanics is realized from geometrical intersections that are the result of plotting changing value vs. changing geometry. RCGT methods ignore size and value to perform an objective analysis in geometry. Value and size are then re-introduced back into the analytical system for a clear and concise solution. Available AVPM applications reveal that a massive amount of data from the Big Bang to vast super-clusters is untouched by human thought. Once scientists learn to design tools from RCGT Mechanics, new and formidable approaches to experimentation and theory may lead to new discoveries. In the creation of AVPM, it has become apparent there is a particle-world that exists between strings and our familiar universe. These unrealized particles in their own nature exhibit inflation like properties and may be the progenitor of the implements of our universe. Thus space, time, energy, motion, space-time and gravity are born from its existence and decay. This announcement will be the beginning of many new ideas from the study of RCGT mechanics.

An interactive tool for outdoor computer controlled cultivation of microalgae in a tubular photobioreactor system.

PubMed

Dormido, Raquel; Sánchez, José; Duro, Natividad; Dormido-Canto, Sebastián; Guinaldo, María; Dormido, Sebastián

2014-03-06

This paper describes an interactive virtual laboratory for experimenting with an outdoor tubular photobioreactor (henceforth PBR for short). This virtual laboratory it makes possible to: (a) accurately reproduce the structure of a real plant (the PBR designed and built by the Department of Chemical Engineering of the University of Almería, Spain); (b) simulate a generic tubular PBR by changing the PBR geometry; (c) simulate the effects of changing different operating parameters such as the conditions of the culture (pH, biomass concentration, dissolved O2, inyected CO2, etc.); (d) simulate the PBR in its environmental context; it is possible to change the geographic location of the system or the solar irradiation profile; (e) apply different control strategies to adjust different variables such as the CO2 injection, culture circulation rate or culture temperature in order to maximize the biomass production; (f) simulate the harvesting. In this way, users can learn in an intuitive way how productivity is affected by any change in the design. It facilitates the learning of how to manipulate essential variables for microalgae growth to design an optimal PBR. The simulator has been developed with Easy Java Simulations, a freeware open-source tool developed in Java, specifically designed for the creation of interactive dynamic simulations.

An Interactive Tool for Outdoor Computer Controlled Cultivation of Microalgae in a Tubular Photobioreactor System

PubMed Central

Dormido, Raquel; Sánchez, José; Duro, Natividad; Dormido-Canto, Sebastián; Guinaldo, María; Dormido, Sebastián

2014-01-01

This paper describes an interactive virtual laboratory for experimenting with an outdoor tubular photobioreactor (henceforth PBR for short). This virtual laboratory it makes possible to: (a) accurately reproduce the structure of a real plant (the PBR designed and built by the Department of Chemical Engineering of the University of Almería, Spain); (b) simulate a generic tubular PBR by changing the PBR geometry; (c) simulate the effects of changing different operating parameters such as the conditions of the culture (pH, biomass concentration, dissolved O2, inyected CO2, etc.); (d) simulate the PBR in its environmental context; it is possible to change the geographic location of the system or the solar irradiation profile; (e) apply different control strategies to adjust different variables such as the CO2 injection, culture circulation rate or culture temperature in order to maximize the biomass production; (f) simulate the harvesting. In this way, users can learn in an intuitive way how productivity is affected by any change in the design. It facilitates the learning of how to manipulate essential variables for microalgae growth to design an optimal PBR. The simulator has been developed with Easy Java Simulations, a freeware open-source tool developed in Java, specifically designed for the creation of interactive dynamic simulations. PMID:24662450

Addressing Neuroplastic Changes in Distributed Areas of the Nervous System Associated With Chronic Musculoskeletal Disorders.

PubMed

Pelletier, René; Higgins, Johanne; Bourbonnais, Daniel

2015-11-01

Present interventions utilized in musculoskeletal rehabilitation are guided, in large part, by a biomedical model where peripheral structural injury is believed to be the sole driver of the disorder. There are, however, neurophysiological changes across different areas of the peripheral and central nervous systems, including peripheral receptors, dorsal horn of the spinal cord, brain stem, sensorimotor cortical areas, and the mesolimbic and prefrontal areas associated with chronic musculoskeletal disorders, including chronic low back pain, osteoarthritis, and tendon injuries. These neurophysiological changes appear not only to be a consequence of peripheral structural injury but also to play a part in the pathophysiology of chronic musculoskeletal disorders. Neurophysiological changes are consistent with a biopsychosocial formulation reflecting the underlying mechanisms associated with sensory and motor findings, psychological traits, and perceptual changes associated with chronic musculoskeletal conditions. These changes, therefore, have important implications in the clinical manifestation, pathophysiology, and treatment of chronic musculoskeletal disorders. Musculoskeletal rehabilitation professionals have at their disposal tools to address these neuroplastic changes, including top-down cognitive-based interventions (eg, education, cognitive-behavioral therapy, mindfulness meditation, motor imagery) and bottom-up physical interventions (eg, motor learning, peripheral sensory stimulation, manual therapy) that induce neuroplastic changes across distributed areas of the nervous system and affect outcomes in patients with chronic musculoskeletal disorders. Furthermore, novel approaches such as the use of transcranial direct current stimulation and repetitive transcranial magnetic stimulation may be utilized to help renormalize neurological function. Comprehensive treatment addressing peripheral structural injury as well as neurophysiological changes occurring across distributed areas of the nervous system may help to improve outcomes in patients with chronic musculoskeletal disorders. © 2015 American Physical Therapy Association.

Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy

PubMed Central

Woodside, Michael T.; Block, Steven M.

2015-01-01

Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate. PMID:24895850

Applying Structural Systems Thinking to Frame Perspectives on Social Work Innovation.

PubMed

Stringfellow, Erin J

2017-03-01

Innovation will be key to the success of the Grand Challenges Initiative in social work. A structural systems framework based in system dynamics could be useful for considering how to advance innovation. Diagrams using system dynamics conventions were developed to link common themes across concept papers written by social work faculty members and graduate students ( N = 19). Transdisciplinary teams and ethical partnerships with communities and practitioners will be needed to responsibly develop high-quality innovative solutions. A useful next step would be to clarify to what extent factors that could "make or break" these partnerships arise from within versus outside of the field of social work and how this has changed over time. Advancing innovation in social work will mean making decisions in a complex, ever-changing system. Principles and tools from methods that account for complexity, such as system dynamics, can help improve this decision-making process.

Applying Structural Systems Thinking to Frame Perspectives on Social Work Innovation

PubMed Central

Stringfellow, Erin J.

2017-01-01

Objective Innovation will be key to the success of the Grand Challenges Initiative in social work. A structural systems framework based in system dynamics could be useful for considering how to advance innovation. Method Diagrams using system dynamics conventions were developed to link common themes across concept papers written by social work faculty members and graduate students (N = 19). Results Transdisciplinary teams and ethical partnerships with communities and practitioners will be needed to responsibly develop high-quality innovative solutions. A useful next step would be to clarify to what extent factors that could “make or break” these partnerships arise from within versus outside of the field of social work and how this has changed over time. Conclusions Advancing innovation in social work will mean making decisions in a complex, ever-changing system. Principles and tools from methods that account for complexity, such as system dynamics, can help improve this decision-making process. PMID:28298877

High-speed atomic force microscopy combined with inverted optical microscopy for studying cellular events

PubMed Central

Suzuki, Yuki; Sakai, Nobuaki; Yoshida, Aiko; Uekusa, Yoshitsugu; Yagi, Akira; Imaoka, Yuka; Ito, Shuichi; Karaki, Koichi; Takeyasu, Kunio

2013-01-01

A hybrid atomic force microscopy (AFM)-optical fluorescence microscopy is a powerful tool for investigating cellular morphologies and events. However, the slow data acquisition rates of the conventional AFM unit of the hybrid system limit the visualization of structural changes during cellular events. Therefore, high-speed AFM units equipped with an optical/fluorescence detection device have been a long-standing wish. Here we describe the implementation of high-speed AFM coupled with an optical fluorescence microscope. This was accomplished by developing a tip-scanning system, instead of a sample-scanning system, which operates on an inverted optical microscope. This novel device enabled the acquisition of high-speed AFM images of morphological changes in individual cells. Using this instrument, we conducted structural studies of living HeLa and 3T3 fibroblast cell surfaces. The improved time resolution allowed us to image dynamic cellular events. PMID:23823461

High-speed atomic force microscopy combined with inverted optical microscopy for studying cellular events.

PubMed

Suzuki, Yuki; Sakai, Nobuaki; Yoshida, Aiko; Uekusa, Yoshitsugu; Yagi, Akira; Imaoka, Yuka; Ito, Shuichi; Karaki, Koichi; Takeyasu, Kunio

2013-01-01

A hybrid atomic force microscopy (AFM)-optical fluorescence microscopy is a powerful tool for investigating cellular morphologies and events. However, the slow data acquisition rates of the conventional AFM unit of the hybrid system limit the visualization of structural changes during cellular events. Therefore, high-speed AFM units equipped with an optical/fluorescence detection device have been a long-standing wish. Here we describe the implementation of high-speed AFM coupled with an optical fluorescence microscope. This was accomplished by developing a tip-scanning system, instead of a sample-scanning system, which operates on an inverted optical microscope. This novel device enabled the acquisition of high-speed AFM images of morphological changes in individual cells. Using this instrument, we conducted structural studies of living HeLa and 3T3 fibroblast cell surfaces. The improved time resolution allowed us to image dynamic cellular events.

Multi-scale Modeling of Radiation Damage: Large Scale Data Analysis

NASA Astrophysics Data System (ADS)

Warrier, M.; Bhardwaj, U.; Bukkuru, S.

2016-10-01

Modification of materials in nuclear reactors due to neutron irradiation is a multiscale problem. These neutrons pass through materials creating several energetic primary knock-on atoms (PKA) which cause localized collision cascades creating damage tracks, defects (interstitials and vacancies) and defect clusters depending on the energy of the PKA. These defects diffuse and recombine throughout the whole duration of operation of the reactor, thereby changing the micro-structure of the material and its properties. It is therefore desirable to develop predictive computational tools to simulate the micro-structural changes of irradiated materials. In this paper we describe how statistical averages of the collision cascades from thousands of MD simulations are used to provide inputs to Kinetic Monte Carlo (KMC) simulations which can handle larger sizes, more defects and longer time durations. Use of unsupervised learning and graph optimization in handling and analyzing large scale MD data will be highlighted.

Measuring Maladaptive Cognitions in Complicated Grief: Introducing the Typical Beliefs Questionnaire

PubMed Central

Skritskaya, Natalia A.; Mauro, Christine; Olonoff, Matthew; Qiu, Xin; Duncan, Sarah; Wang, Yuanjia; Duan, Naihua; Lebowitz, Barry; Reynolds, Charles F.; Simon, Naomi M.; Zisook, Sidney; Shear, M. Katherine

2016-01-01

Objectives Maladaptive cognitions related to loss are thought to contribute to development of complicated grief and are crucial to address in treatment, but tools available to assess them are limited. This paper introduces the Typical Beliefs Questionnaire (TBQ), a 25-item self-report instrument to assess cognitions that interfere with adaptation to loss. Design Study participants completed an assessment battery during their initial evaluation and again after completing treatment at 20 weeks. Test-retest reliability was assessed on a subsample of the participants who did not show change in complicated grief severity after the first four weeks of treatment. To examine latent structure of the TBQ, an exploratory factor analysis (EFA) was performed. Setting Academic medical centers in Boston, New York, Pittsburgh and San Diego from 2010–2014. Participants 394 bereaved adults who met criteria for complicated grief. Measurements The TBQ along with assessments of complicated grief symptoms and related avoidance, depression symptoms, functional impairment, and perceived social support. Results The TBQ exhibited good internal consistency (α= .82) and test-retest reliability (n=105; ICC= .74). EFA indicated a five-factor structure: “Protesting the Death,” “Negative Thoughts About the World,” “Needing the Person,” “Less Grief is Wrong” and “Grieving Too Much.” The total score and all factors showed sensitivity to change with treatment. Conclusions This new tool allows a clinician to quickly and reliably ascertain presence of specific maladaptive cognitions related to complicated grief, and subsequently, to use the information to aid a diagnostic assessment, to structure the treatment, and to measure treatment outcomes. PMID:27793576

Is the learning value of workplace-based assessment being realised? A qualitative study of trainer and trainee perceptions and experiences.

PubMed

Barrett, Aileen; Galvin, Rose; Scherpbier, Albert J J A; Teunissen, Pim W; O'Shaughnessy, Ann; Horgan, Mary

2017-03-01

Workplace-based assessments (WBAs) were originally intended to inform learning and development by structuring effective observation-based feedback. The success of this innovation has not yet been established due in part to the widely varied tools, implementation strategies and research approaches. Using a conceptual framework of experience, trajectories and reifications in workplace learning, we aimed to explore trainer and trainee experiences and perceptions of the learning value of WBAs. Trainers and trainees who had used at least one WBA in the previous year were invited to participate in semistructured interviews for this phenomenological study. We used a template analysis method to explore and compare the experiences of the two groups, using the emergent themes to develop an understanding of the impact of these experiences on perceptions of learning value. Nine trainers and eight trainees participated in the study. Common themes emerged among the two groups around issues of responsibility and engagement along with (mis)understandings of the purpose of the individual tools. Trainer-specific themes emerged related to the concurrent implementation of a new e-portfolio and perceptions of increased workload. Trainees associated WBA with a training structure support value but could not translate experiences into learning values. WBAs provide trainees with a justified reason to approach trainers for feedback. WBAs, however, are not being reified as the formative assessments originally intended. A culture change may be required to change the focus of WBA research and reconceptualise this set of tools and methods as a workplace learning practice . 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/.

Use of Standardized Assessment Tools to Improve the Effectiveness of Palliative Care Rounds: A Quality Improvement Initiative.

PubMed

Spaner, Donna; Caraiscos, Valerie B; Muystra, Christina; Furman, Margaret Lynn; Zaltz-Dubin, Jodi; Wharton, Marilyn; Whitehead, Katherine

Optimal care for patients in the palliative care setting requires effective clinical teamwork. Communication may be challenging for health-care workers from different disciplines. Daily rounds are one way for clinical teams to share information and develop care plans for patients. The objective of this initiative was to improve the structure and process of daily palliative care rounds by incorporating the use of standardized tools and improved documentation into the meeting. We chose a quality improvement (QI) approach to address this initiative. Our aims were to increase the use of assessment tools when discussing patient care in rounds and to improve the documentation and accessibility of important information in the health record, including goals of care. This QI initiative used a preintervention and postintervention comparison of the outcome measures of interest. The initiative was tested in a palliative care unit (PCU) over a 22-month period from April 2014 to January 2016. Participants were clinical staff in the PCU. Data collected after the completion of several plan-do-study-act cycles showed increased use and incorporation of the Edmonton Symptom Assessment System and Palliative Performance Scale into patient care discussions as well as improvement in inclusion of goals of care into the patient plan of care. Our findings demonstrate that the effectiveness of daily palliative care rounds can be improved by incorporating the use of standard assessment tools and changes into the meeting structure to better focus and direct patient care discussions.

Validation of the Italian version of the HSE Indicator Tool.

PubMed

Magnavita, N

2012-06-01

An Italian version of the Health & Safety Executive's (HSE) Management Standards Revised Indicator Tool (MS-RIT) has been used to monitor the working conditions that may lead to stress. To initially examine the factor structure of the Italian version of the MS-RIT, in comparison with the original UK tool, and to investigate its validity and reliability; second, to study the association between occupational stress and psychological distress. Workers from 17 companies self-completed the MS-RIT and the General Health Questionnaire used to measure the psychological distress while they waited for their periodic examination at the workplace. Factor analysis was employed to ascertain whether the Italian version maintained the original subdivision into seven scales. Odds ratios were calculated to estimate the risk of impairment associated with exposure to stress at the workplace. In total, 748 workers participated; the response rate was 91%. The factor structure of the Italian MS-RIT corresponded partially to the original UK version. The 'demand', 'control', 'role', ' relationship' and 'colleague-support' scales were equivalent to the UK ones. A principal factor, termed ' elasticity', incorporated the UK 'management-support' and 'change' scales. Reliability analysis of the sub-scales revealed Cronbach's alpha values ranging from 0.75 to 0.86. Our findings confirmed the usefulness of the Italian version of the HSE MS-RIT in stress control.

Update on HCDstruct - A Tool for Hybrid Wing Body Conceptual Design and Structural Optimization

NASA Technical Reports Server (NTRS)

Gern, Frank H.

2015-01-01

HCDstruct is a Matlab® based software tool to rapidly build a finite element model for structural optimization of hybrid wing body (HWB) aircraft at the conceptual design level. The tool uses outputs from a Flight Optimization System (FLOPS) performance analysis together with a conceptual outer mold line of the vehicle, e.g. created by Vehicle Sketch Pad (VSP), to generate a set of MSC Nastran® bulk data files. These files can readily be used to perform a structural optimization and weight estimation using Nastran’s® Solution 200 multidisciplinary optimization solver. Initially developed at NASA Langley Research Center to perform increased fidelity conceptual level HWB centerbody structural analyses, HCDstruct has grown into a complete HWB structural sizing and weight estimation tool, including a fully flexible aeroelastic loads analysis. Recent upgrades to the tool include the expansion to a full wing tip-to-wing tip model for asymmetric analyses like engine out conditions and dynamic overswings, as well as a fully actuated trailing edge, featuring up to 15 independently actuated control surfaces and twin tails. Several example applications of the HCDstruct tool are presented.

Tooling Foam for Structural Composite Applications

NASA Technical Reports Server (NTRS)

DeLay, Tom; Smith, Brett H.; Ely, Kevin; MacArthur, Doug

1998-01-01

Tooling technology applications for composite structures fabrication have been expanded at MSFC's Productivity Enhancement Complex (PEC). Engineers from NASA/MSFC and Lockheed Martin Corporation have developed a tooling foam for use in composite materials processing and manufacturing that exhibits superior thermal and mechanical properties in comparison with other tooling foam materials. This tooling foam is also compatible with most preimpregnated composite resins such as epoxy, bismaleimide, phenolic and their associated cure cycles. MARCORE tooling foam has excellent processability for applications requiring either integral or removable tooling. It can also be tailored to meet the requirements for composite processing of parts with unlimited cross sectional area. A shelf life of at least six months is easily maintained when components are stored between 50F - 70F. The MARCORE tooling foam system is a two component urethane-modified polyisocyanurate, high density rigid foam with zero ozone depletion potential. This readily machineable, lightweight tooling foam is ideal for composite structures fabrication and is dimensionally stable at temperatures up to 350F and pressures of 100 psi.

Assessing local capacity to expand rural breast cancer screening and patient navigation: An iterative mixed-method tool.

PubMed

Inrig, Stephen J; Higashi, Robin T; Tiro, Jasmin A; Argenbright, Keith E; Lee, Simon J Craddock

2017-04-01

Despite federal funding for breast cancer screening, fragmented infrastructure and limited organizational capacity hinder access to the full continuum of breast cancer screening and clinical follow-up procedures among rural-residing women. We proposed a regional hub-and-spoke model, partnering with local providers to expand access across North Texas. We describe development and application of an iterative, mixed-method tool to assess county capacity to conduct community outreach and/or patient navigation in a partnership model. Our tool combined publicly-available quantitative data with qualitative assessments during site visits and semi-structured interviews. Application of our tool resulted in shifts in capacity designation in 10 of 17 county partners: 8 implemented local outreach with hub navigation; 9 relied on the hub for both outreach and navigation. Key factors influencing capacity: (1) formal linkages between partner organizations; (2) inter-organizational relationships; (3) existing clinical service protocols; (4) underserved populations. Qualitative data elucidate how our tool captured these capacity changes. Our capacity assessment tool enabled the hub to establish partnerships with county organizations by tailoring support to local capacity and needs. Absent a vertically integrated provider network for preventive services in these rural counties, our tool facilitated a virtually integrated regional network to extend access to breast cancer screening to underserved women. Copyright © 2016 Elsevier Ltd. All rights reserved.

Numerical Simulation with Experimental Validation of the Draping Behavior of Woven Fabrics

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

Rodgers, William; Pasupuleti, Praveen; Zhao, Selina

Woven fabric composites are extensively used in molding complex geometrical shapes due to their high conformability compared to other fabrics. Preforming is an important step in the overall process. In this step, the two-dimensional fabric is draped to become the three-dimensional shape of the part prior to resin injection. During preforming, the orientation of the tows may change significantly compared to the initial orientations. Accurate prediction of the tow orientations after molding is important for evaluating the structural performance of the final part. This paper investigates the fiber angle changes for carbon fiber woven fabrics during draping over a truncatedmore » pyramid tool designed and fabricated at the General Motors Research Labs. This aspect of study is a subset of the broad study conducted under the purview of a Department of Energy project funded to GM in developing state of the art computational tools for integrated manufacturing and structural performance prediction of carbon fiber composites. Fabric bending, picture frame testing, and bias-extension evaluations were carried out to determine the material parameters for these fabrics. The PAM-FORM computer program was used to model the draping behavior of these fabrics. Following deformation, fiber angle changes at different locations on the truncated pyramid were measured experimentally. The predicted angles matched the experimental results well as measured along the centerline and at several different locations on the deformed fabric. Details of the test methods used as well as the numerical results with various simulation parameters will be provided.« less

The general alcoholics anonymous tools of recovery: the adoption of 12-step practices and beliefs.

PubMed

Greenfield, Brenna L; Tonigan, J Scott

2013-09-01

Working the 12 steps is widely prescribed for Alcoholics Anonymous (AA) members although the relative merits of different methods for measuring step work have received minimal attention and even less is known about how step work predicts later substance use. The current study (1) compared endorsements of step work on an face-valid or direct measure, the Alcoholics Anonymous Inventory (AAI), with an indirect measure of step work, the General Alcoholics Anonymous Tools of Recovery (GAATOR); (2) evaluated the underlying factor structure of the GAATOR and changes in step work over time; (3) examined changes in the endorsement of step work over time; and (4) investigated how, if at all, 12-step work predicted later substance use. New AA affiliates (N = 130) completed assessments at intake, 3, 6, and 9 months. Significantly more participants endorsed step work on the GAATOR than on the AAI for nine of the 12 steps. An exploratory factor analysis revealed a two-factor structure for the GAATOR comprising behavioral step work and spiritual step work. Behavioral step work did not change over time, but was predicted by having a sponsor, while Spiritual step work decreased over time and increases were predicted by attending 12-step meetings or treatment. Behavioral step work did not prospectively predict substance use. In contrast, spiritual step work predicted percent days abstinent. Behavioral step work and spiritual step work appear to be conceptually distinct components of step work that have distinct predictors and unique impacts on outcomes. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Quantitative assessment of lung ventilation and microstructure in an animal model of idiopathic pulmonary fibrosis using hyperpolarized gas MRI.

PubMed

Stephen, Michael J; Emami, Kiarash; Woodburn, John M; Chia, Elaine; Kadlecek, Stephen; Zhu, Jianliang; Pickup, Stephen; Ishii, Masaru; Rizi, Rahim R; Rossman, Milton

2010-11-01

The use of hyperpolarized (3)He magnetic resonance imaging as a quantitative lung imaging tool has progressed rapidly in the past decade, mostly in the assessment of the airway diseases chronic obstructive pulmonary disease and asthma. This technique has shown potential to assess both structural and functional information in healthy and diseased lungs. In this study, the regional measurements of structure and function were applied to a bleomycin rat model of interstitial lung disease. Male Sprague-Dawley rats (weight, 300-350 g) were administered intratracheal bleomycin. After 3 weeks, apparent diffusion coefficient and fractional ventilation were measured by (3)He magnetic resonance imaging and pulmonary function testing using a rodent-specific plethysmography chamber. Sensitized and healthy animals were then compared using threshold analysis to assess the potential sensitivity of these techniques to pulmonary abnormalities. No significant changes were observed in total lung volume and compliance between the two groups. Airway resistance elevated and forced expiratory volume significantly declined in the 3-week bleomycin rats, and fractional ventilation was significantly decreased compared to control animals (P < .0004). The apparent diffusion coefficient of (3)He showed a smaller change but still a significant decrease in 3-week bleomycin animals (P < .05). Preliminary results suggest that quantitative (3)He magnetic resonance imaging can be a sensitive and noninvasive tool to assess changes in an animal interstitial lung disease model. This technique may be useful for longitudinal animal studies and also in the investigation of human interstitial lung diseases. Copyright © 2010 AUR. Published by Elsevier Inc. All rights reserved.

Epigenomics in cancer management

PubMed Central

Costa, Fabricio F

2010-01-01

The identification of all epigenetic modifications implicated in gene expression is the next step for a better understanding of human biology in both normal and pathological states. This field is referred to as epigenomics, and it is defined as epigenetic changes (ie, DNA methylation, histone modifications and regulation by noncoding RNAs such as microRNAs) on a genomic scale rather than a single gene. Epigenetics modulate the structure of the chromatin, thereby affecting the transcription of genes in the genome. Different studies have already identified changes in epigenetic modifications in a few genes in specific pathways in cancers. Based on these epigenetic changes, drugs against different types of tumors were developed, which mainly target epimutations in the genome. Examples include DNA methylation inhibitors, histone modification inhibitors, and small molecules that target chromatin-remodeling proteins. However, these drugs are not specific, and side effects are a major problem; therefore, new DNA sequencing technologies combined with epigenomic tools have the potential to identify novel biomarkers and better molecular targets to treat cancers. The purpose of this review is to discuss current and emerging epigenomic tools and to address how these new technologies may impact the future of cancer management. PMID:21188117

Gaining Insight of Fetal Brain Development with Diffusion MRI and Histology

PubMed Central

Huang, Hao; Vasung, Lana

2013-01-01

Human brain is extraordinarily complex and yet its origin is a simple tubular structure. Its development during the fetal period is characterized by a series of accurately organized events which underlie the mechanisms of dramatic structural changes during fetal development. Revealing detailed anatomy at different stages of human fetal brain development provides insight on understanding not only this highly ordered process, but also the neurobiological foundations of cognitive brain disorders such as mental retardation, autism, schizophrenia, bipolar and language impairment. Diffusion tensor imaging (DTI) and histology are complementary tools which are capable of delineating the fetal brain structures at both macroscopic and microscopic level. In this review, the structural development of the fetal brains has been characterized with DTI and histology. Major components of the fetal brain, including cortical plate, fetal white matter and cerebral wall layer between the ventricle and subplate, have been delineated with DTI and histology. Anisotropic metrics derived from DTI were used to quantify the microstructural changes during the dynamic process of human fetal cortical development and prenatal development of other animal models. Fetal white matter pathways have been traced with DTI-based tractography to reveal growth patterns of individual white matter tracts and corticocortical connectivity. These detailed anatomical accounts of the structural changes during fetal period may provide the clues of detecting developmental and cognitive brain disorders at their early stages. The anatomical information from DTI and histology may also provide reference standards for diagnostic radiology of premature newborns. PMID:23796901

Managing changes in distributed biomedical ontologies using hierarchical distributed graph transformation.

PubMed

Shaban-Nejad, Arash; Haarslev, Volker

2015-01-01

The issue of ontology evolution and change management is inadequately addressed by available tools and algorithms, mostly due to the lack of suitable knowledge representation formalisms to deal with temporal abstract notations and the overreliance on human factors. Also most of the current approaches have been focused on changes within the internal structure of ontologies and interactions with other existing ontologies have been widely neglected. In our research, after revealing and classifying some of the common alterations in a number of popular biomedical ontologies, we present a novel agent-based framework, Represent, Legitimate and Reproduce (RLR), to semi-automatically manage the evolution of bio-ontologies, with emphasis on the FungalWeb Ontology, with minimal human intervention. RLR assists and guides ontology engineers through the change management process in general and aids in tracking and representing the changes, particularly through the use of category theory and hierarchical graph transformation.

Business change process, creativity and the brain: a practitioner's reflective account with suggestions for future research.

PubMed

Yeats, Rowena M; Yeats, Martyn F

2007-11-01

Resolution of a critical organizational problem requires the use of carefully selected techniques. This is the work of a management consultant: facilitating a business change process in an organizational setting. Here, an account is provided of a practitioner's reflections on one such case study that demonstrates a structure for a business change process. The reflective account highlights certain affective states and social behaviors that were extracted from participants during the business change process. These affective states and social behaviors are mediated by specific neural networks in the brain that are activated during organizational intervention. By breaking down the process into the affective states and social behaviors highlighted, cognitive neuroscience can be a useful tool for investigating the neural substrates of such intervention. By applying a cognitive neuroscience approach to examine organizational change, it is possible to converge on a greater understanding of the neural substrates of everyday social behavior.

Adapting inland fisheries management to a changing climate

USGS Publications Warehouse

Paukert, Craig P.; Glazer, Bob A.; Hansen, Gretchen J. A.; Irwin, Brian J.; Jacobson, Peter C.; Kershner, Jeffrey L.; Shuter, Brian J.; Whitney, James E.; Lynch, Abigail J.

2016-01-01

Natural resource decision makers are challenged to adapt management to a changing climate while balancing short-term management goals with long-term changes in aquatic systems. Adaptation will require developing resilient ecosystems and resilient management systems. Decision makers already have tools to develop or ensure resilient aquatic systems and fisheries such as managing harvest and riparian zones. Because fisheries management often interacts with multiple stakeholders, adaptation strategies involving fisheries managers and other partners focused on land use, policy, and human systems, coupled with long-term monitoring, are necessary for resilient systems. We show how agencies and organizations are adapting to a changing climate in Minnesota and Ontario lakes and Montana streams. We also present how the Florida Fish and Wildlife Commission created a management structure to develop adaptation strategies. These examples demonstrate how organizations and agencies can cope with climate change effects on fishes and fisheries through creating resilient management and ecological systems.

Mechanics and energetics in tool manufacture and use: a synthetic approach.

PubMed

Wang, Liyu; Brodbeck, Luzius; Iida, Fumiya

2014-11-06

Tool manufacture and use are observed not only in humans but also in other animals such as mammals, birds and insects. Manufactured tools are used for biomechanical functions such as effective control of fluids and small solid objects and extension of reaching. These tools are passive and used with gravity and the animal users' own energy. From the perspective of evolutionary biology, manufactured tools are extended phenotypes of the genes of the animal and exhibit phenotypic plasticity. This incurs energetic cost of manufacture as compared to the case with a fixed tool. This paper studies mechanics and energetics aspects of tool manufacture and use in non-human beings. Firstly, it investigates possible mechanical mechanisms of the use of passive manufactured tools. Secondly, it formulates the energetic cost of manufacture and analyses when phenotypic plasticity benefits an animal tool maker and user. We take a synthetic approach and use a controlled physical model, i.e. a robot arm. The robot is capable of additively manufacturing scoop and gripper structures from thermoplastic adhesives to pick and place fluid and solid objects, mimicking primates and birds manufacturing tools for a similar function. We evaluate the effectiveness of tool use in pick-and-place and explain the mechanism for gripper tools picking up solid objects with a solid-mechanics model. We propose a way to formulate the energetic cost of tool manufacture that includes modes of addition and reshaping, and use it to analyse the case of scoop tools. Experiment results show that with a single motor trajectory, the robot was able to effectively pick and place water, rice grains, a pebble and a plastic box with a scoop tool or gripper tools that were manufactured by itself. They also show that by changing the dimension of scoop tools, the energetic cost of tool manufacture and use could be reduced. The work should also be interesting for engineers to design adaptive machines. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Mechanics and energetics in tool manufacture and use: a synthetic approach

PubMed Central

Wang, Liyu; Brodbeck, Luzius; Iida, Fumiya

2014-01-01

Tool manufacture and use are observed not only in humans but also in other animals such as mammals, birds and insects. Manufactured tools are used for biomechanical functions such as effective control of fluids and small solid objects and extension of reaching. These tools are passive and used with gravity and the animal users' own energy. From the perspective of evolutionary biology, manufactured tools are extended phenotypes of the genes of the animal and exhibit phenotypic plasticity. This incurs energetic cost of manufacture as compared to the case with a fixed tool. This paper studies mechanics and energetics aspects of tool manufacture and use in non-human beings. Firstly, it investigates possible mechanical mechanisms of the use of passive manufactured tools. Secondly, it formulates the energetic cost of manufacture and analyses when phenotypic plasticity benefits an animal tool maker and user. We take a synthetic approach and use a controlled physical model, i.e. a robot arm. The robot is capable of additively manufacturing scoop and gripper structures from thermoplastic adhesives to pick and place fluid and solid objects, mimicking primates and birds manufacturing tools for a similar function. We evaluate the effectiveness of tool use in pick-and-place and explain the mechanism for gripper tools picking up solid objects with a solid-mechanics model. We propose a way to formulate the energetic cost of tool manufacture that includes modes of addition and reshaping, and use it to analyse the case of scoop tools. Experiment results show that with a single motor trajectory, the robot was able to effectively pick and place water, rice grains, a pebble and a plastic box with a scoop tool or gripper tools that were manufactured by itself. They also show that by changing the dimension of scoop tools, the energetic cost of tool manufacture and use could be reduced. The work should also be interesting for engineers to design adaptive machines. PMID:25209405

Winds of Change Blowing for Wind Farm Research with NREL's SOWFA Tool |

Science.gov Websites

News | NREL Winds of Change Blowing for Wind Farm Research with NREL's SOWFA Tool Winds of Change Blowing for Wind Farm Research with NREL's SOWFA Tool April 1, 2016 Before the Energy Department's that researchers all over the world could embrace. Now, the winds of change are blowing. SOWFA is a

Environmental corrections of a dual-induction logging while drilling tool in vertical wells

NASA Astrophysics Data System (ADS)

Kang, Zhengming; Ke, Shizhen; Jiang, Ming; Yin, Chengfang; Li, Anzong; Li, Junjian

2018-04-01

With the development of Logging While Drilling (LWD) technology, dual-induction LWD logging is not only widely applied in deviated wells and horizontal wells, but it is used commonly in vertical wells. Accordingly, it is necessary to simulate the response of LWD tools in vertical wells for logging interpretation. In this paper, the investigation characteristics, the effects of the tool structure, skin effect and drilling environment of a dual-induction LWD tool are simulated by the three-dimensional (3D) finite element method (FEM). In order to closely simulate the actual situation, real structure of the tool is taking into account. The results demonstrate that the influence of the background value of the tool structure can be eliminated. The values of deducting the background of a tool structure and analytical solution have a quantitative agreement in homogeneous formations. The effect of measurement frequency could be effectively eliminated by chart of skin effect correction. In addition, the measurement environment, borehole size, mud resistivity, shoulder bed, layer thickness and invasion, have an effect on the true resistivity. To eliminate these effects, borehole correction charts, shoulder bed correction charts and tornado charts are computed based on real tool structure. Based on correction charts, well logging data can be corrected automatically by a suitable interpolation method, which is convenient and fast. Verified with actual logging data in vertical wells, this method could obtain the true resistivity of formation.

Blended near-optimal tools for flexible water resources decision making

NASA Astrophysics Data System (ADS)

Rosenberg, David

2015-04-01

State-of-the-art systems analysis techniques focus on efficiently finding optimal solutions. Yet an optimal solution is optimal only for the static modelled issues and managers often seek near-optimal alternatives that address un-modelled or changing objectives, preferences, limits, uncertainties, and other issues. Early on, Modelling to Generate Alternatives (MGA) formalized near-optimal as performance within a tolerable deviation from the optimal objective function value and identified a few maximally-different alternatives that addressed select un-modelled issues. This paper presents new stratified, Monte Carlo Markov Chain sampling and parallel coordinate plotting tools that generate and communicate the structure and full extent of the near-optimal region to an optimization problem. Plot controls allow users to interactively explore region features of most interest. Controls also streamline the process to elicit un-modelled issues and update the model formulation in response to elicited issues. Use for a single-objective water quality management problem at Echo Reservoir, Utah identifies numerous and flexible practices to reduce the phosphorus load to the reservoir and maintain close-to-optimal performance. Compared to MGA, the new blended tools generate more numerous alternatives faster, more fully show the near-optimal region, help elicit a larger set of un-modelled issues, and offer managers greater flexibility to cope in a changing world.

3-dimensional free standing micro-structures by proton beam writing of Su 8-silver nanoParticle polymeric composite

NASA Astrophysics Data System (ADS)

Igbenehi, H.; Jiguet, S.

2012-09-01

Proton beam lithography a maskless direct-write lithographic technique (well suited for producing 3-Dimensional microstructures in a range of resist and semiconductor materials) is demonstrated as an effective tool in the creation of electrically conductive freestanding micro-structures in an Su 8 + Nano Silver polymer composite. The structures produced show non-ohmic conductivity and fit the percolation theory conduction model of tunneling of separated nanoparticles. Measurements show threshold switching and a change in conductivity of at least 4 orders of magnitude. The predictable range of protons in materials at a given energy is exploited in the creation of high aspect ratio, free standing micro-structures, made from a commercially available SU8 Silver nano-composite (GMC3060 form Gersteltec Inc. a negative tone photo-epoxy with added metallic nano-particles(Silver)) to create films with enhanced electrical properties when exposed and cured. Nano-composite films are directly written on with a finely focused MeV accelerated Proton particle beam. The energy loss of the incident proton beams in the target polymer nano- composite film is concentrated at the end of its range, where damage occurs; changing the chemistry of the nano-composite film via an acid initiated polymerization - creating conduction paths. Changing the energy of the incident beams provide exposed regions with different penetration and damage depth - exploited in the demonstrated cantilever microstructure.

Fractal lacunarity of trabecular bone and magnetic resonance imaging: New perspectives for osteoporotic fracture risk assessment

PubMed Central

Zaia, Annamaria

2015-01-01

Osteoporosis represents one major health condition for our growing elderly population. It accounts for severe morbidity and increased mortality in postmenopausal women and it is becoming an emerging health concern even in aging men. Screening of the population at risk for bone degeneration and treatment assessment of osteoporotic patients to prevent bone fragility fractures represent useful tools to improve quality of life in the elderly and to lighten the related socio-economic impact. Bone mineral density (BMD) estimate by means of dual-energy X-ray absorptiometry is normally used in clinical practice for osteoporosis diagnosis. Nevertheless, BMD alone does not represent a good predictor of fracture risk. From a clinical point of view, bone microarchitecture seems to be an intriguing aspect to characterize bone alteration patterns in aging and pathology. The widening into clinical practice of medical imaging techniques and the impressive advances in information technologies together with enhanced capacity of power calculation have promoted proliferation of new methods to assess changes of trabecular bone architecture (TBA) during aging and osteoporosis. Magnetic resonance imaging (MRI) has recently arisen as a useful tool to measure bone structure in vivo. In particular, high-resolution MRI techniques have introduced new perspectives for TBA characterization by non-invasive non-ionizing methods. However, texture analysis methods have not found favor with clinicians as they produce quite a few parameters whose interpretation is difficult. The introduction in biomedical field of paradigms, such as theory of complexity, chaos, and fractals, suggests new approaches and provides innovative tools to develop computerized methods that, by producing a limited number of parameters sensitive to pathology onset and progression, would speed up their application into clinical practice. Complexity of living beings and fractality of several physio-anatomic structures suggest fractal analysis as a promising approach to quantify morpho-functional changes in both aging and pathology. In this particular context, fractal lacunarity seems to be the proper tool to characterize TBA texture as it is able to describe both discontinuity of bone network and sizes of bone marrow spaces, whose changes are an index of bone fracture risk. In this paper, an original method of MRI texture analysis, based on TBA fractal lacunarity is described and discussed in the light of new perspectives for early diagnosis of osteoporotic fractures. PMID:25793162

Changes of Metabolomic Profile in Helianthus annuus under Exposure to Chromium(VI) Studied by capHPLC-ESI-QTOF-MS and MS/MS

PubMed Central

Gonzalez Ibarra, Alan Alexander; Wrobel, Kazimierz; Yanez Barrientos, Eunice; Corrales Escobosa, Alma Rosa; Gutierrez Corona, J. Felix; Enciso Donis, Israel

2017-01-01

The application of capHPLC-ESI-QTOF-MS and MS/MS to study the impact of Cr(VI) on metabolites profile in Helianthus annuus is reported. Germinated seeds were grown hydroponically in the presence of Cr(VI) (25 mgCr/L) and root extracts of the exposed and control plants were analyzed by untargeted metabolomic approach. The main goal was to detect which metabolite groups were mostly affected by Cr(VI) stress; two data analysis tools (ProfileAnalysis, Bruker, and online XCMS) were used under criteria of intensity threshold 5 · 104 cps, fold change ≥ 5, and p ≤ 0.01, yielding precursor ions. Molecular formulas were assigned based on data processing with two computational tools (SIRIUS and MS-Finder); annotation of candidate structures was performed by database search using CSI:FingerID and MS-Finder. Even though ultimate identification has not been achieved, it was demonstrated that secondary metabolism became activated under Cr(VI) stress. Among 42 candidate compounds returned from database search for seven molecular formulas, ten structures corresponded to isocoumarin derivatives and eleven were sesquiterpenes or sesquiterpene lactones; three benzofurans and four glycoside or pyrane derivatives of phenolic compounds were also suggested. To gain further insight on the effect of Cr(VI) in sunflower, isocoumarins and sesquiterpenes were selected as the target compounds for future study. PMID:29359067

The perceived personal control (PPC) questionnaire: reliability and validity in a sample from the United Kingdom.

PubMed

McAllister, Marion; Wood, Alex M; Dunn, Graham; Shiloh, Shoshana; Todd, Chris

2012-02-01

Outcome measures are important assessment tools to evaluate clinical genetics services. Research suggests that perceived personal control (PPC) is an outcome valued by clinical genetics patients and clinicians. The PPC scale was developed in Hebrew to capture three dimensions of PPC: Cognitive, decisional, and behavioral control. This article reports on the first psychometric validation of the English translation of the PPC scale. Previous research has shown that the Hebrew and Dutch translations have good psychometric properties. However, the psychometric properties of the English translation have not been tested, and there is disagreement about the factor structure, with implications for how to score the measure. A total of 395 patients attending a clinical genetics appointment in the United Kingdom completed several measures at baseline, and a further 241 also completed measures at 2-4 weeks follow-up. The English language PPC has (a) a one-factor structure, (b) convergent validity with internal health locus of control (IHLC), satisfaction with life (SWL), depression, and authenticity, (c) high internal consistency (α = 0.83), and (d) sensitivity to change, being able to identify moderate changes in PPC following clinic attendance (Cohen's d = 0.40). These properties suggest the English language PPC measure is a useful tool for both clinical genetics research and for use as a Patient Reported Outcome Measure (PROM) in service evaluation. Copyright © 2011 Wiley Periodicals, Inc.

Development and Validation of a Self-reported Questionnaire for Measuring Internet Search Dependence

PubMed Central

Wang, Yifan; Wu, Lingdan; Zhou, Hongli; Xu, Jiaojing; Dong, Guangheng

2016-01-01

Internet search has become the most common way that people deal with issues and problems in everyday life. The wide use of Internet search has largely changed the way people search for and store information. There is a growing interest in the impact of Internet search on users’ affect, cognition, and behavior. Thus, it is essential to develop a tool to measure the changes in psychological characteristics as a result of long-term use of Internet search. The aim of this study is to develop a Questionnaire on Internet Search Dependence (QISD) and test its reliability and validity. We first proposed a preliminary structure and items of the QISD based on literature review, supplemental investigations, and interviews. And then, we assessed the psychometric properties and explored the factor structure of the initial version via exploratory factor analysis (EFA). The EFA results indicated that four dimensions of the QISD were very reliable, i.e., habitual use of Internet search, withdrawal reaction, Internet search trust, and external storage under Internet search. Finally, we tested the factor solution obtained from EFA through confirmatory factor analysis (CFA). The results of CFA confirmed that the four dimensions model fits the data well. In all, this study suggests that the 12-item QISD is of high reliability and validity and can serve as a preliminary tool to measure the features of Internet search dependence. PMID:28066753

Development and Validation of a Self-reported Questionnaire for Measuring Internet Search Dependence.

PubMed

Wang, Yifan; Wu, Lingdan; Zhou, Hongli; Xu, Jiaojing; Dong, Guangheng

2016-01-01

Internet search has become the most common way that people deal with issues and problems in everyday life. The wide use of Internet search has largely changed the way people search for and store information. There is a growing interest in the impact of Internet search on users' affect, cognition, and behavior. Thus, it is essential to develop a tool to measure the changes in psychological characteristics as a result of long-term use of Internet search. The aim of this study is to develop a Questionnaire on Internet Search Dependence (QISD) and test its reliability and validity. We first proposed a preliminary structure and items of the QISD based on literature review, supplemental investigations, and interviews. And then, we assessed the psychometric properties and explored the factor structure of the initial version via exploratory factor analysis (EFA). The EFA results indicated that four dimensions of the QISD were very reliable, i.e., habitual use of Internet search, withdrawal reaction, Internet search trust, and external storage under Internet search. Finally, we tested the factor solution obtained from EFA through confirmatory factor analysis (CFA). The results of CFA confirmed that the four dimensions model fits the data well. In all, this study suggests that the 12-item QISD is of high reliability and validity and can serve as a preliminary tool to measure the features of Internet search dependence.

[Cellular mechanisms of neuroplasticity].

PubMed

Bergado-Rosado, J A; Almaguer-Melian, W

To present a unified vision of the principal known mechanisms of neuroplasticity, emphasizing their universality. The concept of the central nervous system as an immutable entity has been considerably modified during the second half of the 20th century. Neuroplasticity, that is the ability of the brain regarding change and repair is expressed in different ways, from functional modifications of existing structures to the formation, by growth and proliferation, of new structures and neurons. This study considers the molecular and cellular mechanisms of neuroplastic phenomena and classifies them into two main groups: plasticity due to growth, including the mechanisms of axonal regeneration, collateralization and reactive synaptogenesis; and functional plasticity, which includes changes in the efficacy of synaptic transmission such as long-term potentiation and the activation of silent synapses. We also describe some of the relations of neuroplastic phenomena with disease of the central nervous system, together with examples of physiological, physical and pharmacological factors which may be used in future as therapeutic tools to stimulate and modulate neuroplasticity. Neuroplastic mechanisms show a high degree of phylogenetic and ontogenetic conservation. They are important both in the genesis of disorders and disease of the nervous system and for its repair after different types of damage and trauma. Modulation of neuroplastic mechanisms by physical and chemical agents would appear to be one of the most powerful therapeutic tools of restorative neurology.

A flexible, multi-faceted, multi-media approach to teaching climate change to non-STEM majors

NASA Astrophysics Data System (ADS)

De Roo, R. D.; Liemohn, M. W.

2011-12-01

The University of Michigan offers a 100-level course entitled, "Our Changing Atmosphere," often taken to fulfill the natural science distribution credit requirement by up to 200 students in non-technical majors per term. This course covers the properties and structure of the atmosphere and how they are changing, emphasizing the global climate and climate change. After a brief introduction to atmospheric basics, highlights from Earth's climate history are presented, followed by modern-day changes to climate, such as air pollution, stratospheric ozone depletion, and global warming. The current format of the course relies heavily on Lecturebook, Lecturetools, and C-tools as online electronic resources for the class. The textbook for the course is managed through Lecturebook, which also provides hyperlinked text and hundreds of built-in questions for homework sets and student review. The recitation lessons are uploaded to Lecturebook, which allows for interactive question-and-answer sessions during class in multiple formats. The University of Michigan's C-tools environment is also used for email distribution and archiving, additional resource postings, and as a backup to these other two websites. The structure of the class permits different instructors to emphasize different facets of climate, and to employ different instructional techniques. For example, the textbook differs depending on the term the course is offered. One of us emphasizes good-vs-bad science usage via video, sound clip, or PDF posting on a weather or climate related topic in every lecture. Good-v-bad science usage of climate topics in research, media reporting, and casual conversation are all discussed by the students and included in the examinations. The other instructor emphasizes the findings of the IPCC, employs hands-on activities in lecture and eschews exams in favor of collaborative homework assignments. The assignments include qualitative and quantitative analyses of climate topics and the exploration of model predictions under differing assumptions.

Correlating Petrophysical Well Logs Using Fractal-based Analysis to Identify Changes in the Signal Complexity Across Neutron, Density, Dipole Sonic, and Gamma Ray Tool Types

NASA Astrophysics Data System (ADS)

Matthews, L.; Gurrola, H.

2015-12-01

Typical petrophysical well log correlation is accomplished by manual pattern recognition leading to subjective correlations. The change in character in a well log is dependent upon the change in the response of the tool to lithology. The petrophysical interpreter looks for a change in one log type that would correspond to the way a different tool responds to the same lithology. To develop an objective way to pick changes in well log characteristics, we adapt a method of first arrival picking used in seismic data to analyze changes in the character of well logs. We chose to use the fractal method developed by Boschetti et al[1] (1996). This method worked better than we expected and we found similar changes in the fractal dimension across very different tool types (sonic vs density vs gamma ray). We reason the fractal response of the log is not dependent on the physics of the tool response but rather the change in the complexity of the log data. When a formation changes physical character in time or space the recorded magnitude in tool data changes complexity at the same time even if the original tool response is very different. The relative complexity of the data regardless of the tool used is dependent upon the complexity of the medium relative to tool measurement. The relative complexity of the recorded magnitude data changes as a tool transitions from one character type to another. The character we are measuring is the roughness or complexity of the petrophysical curve. Our method provides a way to directly compare different log types based on a quantitative change in signal complexity. For example, using changes in data complexity allow us to correlate gamma ray suites with sonic logs within a well and then across to an adjacent well with similar signatures. Our method creates reliable and automatic correlations to be made in data sets beyond the reasonable cognitive limits of geoscientists in both speed and consistent pattern recognition. [1] Fabio Boschetti, Mike D. Dentith, and Ron D. List, (1996). A fractal-based algorithm for detecting first arrivals on seismic traces. Geophysics, Vol.61, No.4, P. 1095-1102.

Structural comparison of nickel electrodes and precursor phases

NASA Technical Reports Server (NTRS)

Cornilsen, Bahne C.; Shan, Xiaoyin; Loyselle, Patricia

1989-01-01

A summary of previous Raman spectroscopic results and a discussion of important structural differences in the various phases of active mass and active mass precurors are presented. Raman spectra provide unique signatures for these phases, and allow one to distinguish each phase, even when the compound is amorphous to X-rays (i.e., does not scatter X-rays because of a lack of order and/or small particle size). The structural changes incurred during formation, charge and discharge, cobalt addition, and aging will be discussed and related to electrode properties. Important structural differences include NiO2 layer stacking, nonstoichiometry (especially cation-deficit nonstoichiometry), disorder, dopant content, and water content. The results indicate that optimal nickel active mass is non-close packed and nonstoichiometric. The formation process transforms precursor phases into this structure. Therefore, the precursor disorder, or lack thereof, influences this final active mass structure and the rate of formation. Aging processes induce structural change which is believed to be detrimental. The role of cobalt addition can be appreciated in terms of structures favored or stabilized by the dopant. In recent work, the in situ Raman technique to characterize the critical structural parameters was developed. An in situ method relates structure, electrochemistry, and preparation. In situ Raman spectra of cells during charge and discharge, either during cyclic voltammetry or under constant current conditions were collected. With the structure-preparation knowledge and the in situ Raman tool, it will be possible to define the structure-property-preparation relations in more detail. This instrumentation has application to a variety of electrode systems.

Decay of interspecific avian flock networks along a disturbance gradient in Amazonia.

PubMed

Mokross, Karl; Ryder, Thomas B; Côrtes, Marina Corrêa; Wolfe, Jared D; Stouffer, Philip C

2014-02-07

Our understanding of how anthropogenic habitat change shapes species interactions is in its infancy. This is in large part because analytical approaches such as network theory have only recently been applied to characterize complex community dynamics. Network models are a powerful tool for quantifying how ecological interactions are affected by habitat modification because they provide metrics that quantify community structure and function. Here, we examine how large-scale habitat alteration has affected ecological interactions among mixed-species flocking birds in Amazonian rainforest. These flocks provide a model system for investigating how habitat heterogeneity influences non-trophic interactions and the subsequent social structure of forest-dependent mixed-species bird flocks. We analyse 21 flock interaction networks throughout a mosaic of primary forest, fragments of varying sizes and secondary forest (SF) at the Biological Dynamics of Forest Fragments Project in central Amazonian Brazil. Habitat type had a strong effect on network structure at the levels of both species and flock. Frequency of associations among species, as summarized by weighted degree, declined with increasing levels of forest fragmentation and SF. At the flock level, clustering coefficients and overall attendance positively correlated with mean vegetation height, indicating a strong effect of habitat structure on flock cohesion and stability. Prior research has shown that trophic interactions are often resilient to large-scale changes in habitat structure because species are ecologically redundant. By contrast, our results suggest that behavioural interactions and the structure of non-trophic networks are highly sensitive to environmental change. Thus, a more nuanced, system-by-system approach may be needed when thinking about the resiliency of ecological networks.

MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids.

PubMed

Andreini, Claudia; Cavallaro, Gabriele; Rosato, Antonio; Valasatava, Yana

2013-11-25

We developed a new software tool, MetalS(2), for the structural alignment of Minimal Functional Sites (MFSs) in metal-binding biological macromolecules. MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. On our example data sets, MetalS(2) unveiled structural similarities that other programs for protein structure comparison do not consistently point out and overall identified a larger number of structurally similar MFSs. MetalS(2) supports the comparison of MFSs harboring different metals and/or with different nuclearity and is available both as a stand-alone program and a Web tool ( http://metalweb.cerm.unifi.it/tools/metals2/).

Engine System Loads Development for the Fastrac 60K Flight Engine

NASA Technical Reports Server (NTRS)

Frady, Greg; Christensen, Eric R.; Mims, Katherine; Harris, Don; Parks, Russell; Brunty, Joseph

2000-01-01

Early implementation of structural dynamics finite element analyses for calculation of design loads is considered common design practice for high volume manufacturing industries such as automotive and aeronautical industries. However, with the rarity of rocket engine development programs starts, these tools are relatively new to the design of rocket engines. In the new Fastrac engine program, the focus has been to reduce the cost to weight ratio; current structural dynamics analysis practices were tailored in order to meet both production and structural design goals. Perturbation of rocket engine design parameters resulted in a number of Fastrac load cycles necessary to characterize the impact due to mass and stiffness changes. Evolution of loads and load extraction methodologies, parametric considerations and a discussion of load path sensitivities are discussed.

Farm, household, and farmer characteristics associated with changes in management practices and technology adoption among dairy smallholders.

PubMed

Martínez-García, Carlos Galdino; Ugoretz, Sarah Janes; Arriaga-Jordán, Carlos Manuel; Wattiaux, Michel André

2015-02-01

This study explored whether technology adoption and changes in management practices were associated with farm structure, household, and farmer characteristics and to identify processes that may foster productivity and sustainability of small-scale dairy farming in the central highlands of Mexico. Factor analysis of survey data from 44 smallholders identified three factors-related to farm size, farmer's engagement, and household structure-that explained 70 % of cumulative variance. The subsequent hierarchical cluster analysis yielded three clusters. Cluster 1 included the most senior farmers with fewest years of education but greatest years of experience. Cluster 2 included farmers who reported access to extension, cooperative services, and more management changes. Cluster 2 obtained 25 and 35 % more milk than farmers in clusters 1 and 3, respectively. Cluster 3 included the youngest farmers, with most years of education and greatest availability of family labor. Access to a network and membership in a community of peers appeared as important contributors to success. Smallholders gravitated towards easy to implement technologies that have immediate benefits. Nonusers of high investment technologies found them unaffordable because of cost, insufficient farm size, and lack of knowledge or reliable electricity. Multivariate analysis may be a useful tool in planning extension activities and organizing channels of communication to effectively target farmers with varying needs, constraints, and motivations for change and in identifying farmers who may exemplify models of change for others who manage farms that are structurally similar but performing at a lower level.

Probing the CZTS/CdS heterojunction utilizing photoelectrochemistry and x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Turnbull, Matthew J.; Vaccarello, Daniel; Wong, Jonathan; Yiu, Yun Mui; Sham, Tsun-Kong; Ding, Zhifeng

2018-04-01

The importance of renewable resources is becoming more and more influential on research due to the depletion of fossil fuels. Cost-effective ways of harvesting solar energy should also be at the forefront of these investigations. Cu2ZnSnS4 (CZTS) solar cells are well within the frame of these goals, and a thorough understanding of how they are made and processed synthetically is crucial. The CZTS/CdS heterojunction was examined using photoelectrochemistry and synchrotron radiation (SR) spectroscopy. These tools provided physical insights into this interface that was formed by the electrophoretic deposition of CZTS nanocrystals and chemical bath deposition (CBD) of CdS for the respective films. It was discovered that CBD induced a change in the local and long range environment of the Zn in the CZTS lattice, which was detrimental to the photoresponse. X-ray absorption near-edge structures and extended X-ray absorption fine structures (EXAFSs) of the junction showed that this change was at an atomic level and was associated with the coordination of oxygen to zinc. This was confirmed through FEFF fitting of the EXAFS and through IR spectroscopy. It was found that this change in both photoresponse and the Zn coordination can be reversed with the use of low temperature annealing. Investigating CZTS through SR techniques provides detailed structural information of minor changes from the zinc perspective.

Unusual infrared absorption increases in photo-degraded organic films

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

Shah, Satvik; Biswas, Rana; Koschny, Thomas

Degradation is among the most pressing problems facing organic materials, occurring through ingress of moisture and oxygen, and light exposure. We determine the nanoscale pathways underlying degradation by light-soaking organic films in an environmental chamber, and performing infrared spectroscopy, to identify atomic bonding changes. We utilize as a prototype the low band gap PTB7-PCBM blend. Films light-soaked in the presence of oxygen show unusual increased absorption at 1727 cm –1 attributable to increased C=O modes, and a broad increase at 3240 cm –1 attributable to hydroxyl (O–H) groups bonded within the organic matrix. Films exposed to oxygen in the dark,more » or light-soaked in an inert atmosphere, do not exhibit significant absorption changes, suggesting simultaneous exposure of oxygen and light that creates singlet excited oxygen is the detrimental factor. Our ab initio electronic structure simulations interpret these by oxidation at the α-C site of the alkyl chains in PTB7, with an irreversible rupture of the alkyl chain and formation of new C=O and C–O–H conformations at the α-C. Infrared spectroscopy coupled with ab initio simulation can provide a powerful tool for quantifying photo-structural atomic bonding changes. As a result, understanding nanoscale light-induced structural changes will open avenues to designing more stable organic materials for organic electronics.« less

Unusual infrared absorption increases in photo-degraded organic films

DOE PAGES

Shah, Satvik; Biswas, Rana; Koschny, Thomas; ...

2017-06-05

Degradation is among the most pressing problems facing organic materials, occurring through ingress of moisture and oxygen, and light exposure. We determine the nanoscale pathways underlying degradation by light-soaking organic films in an environmental chamber, and performing infrared spectroscopy, to identify atomic bonding changes. We utilize as a prototype the low band gap PTB7-PCBM blend. Films light-soaked in the presence of oxygen show unusual increased absorption at 1727 cm –1 attributable to increased C=O modes, and a broad increase at 3240 cm –1 attributable to hydroxyl (O–H) groups bonded within the organic matrix. Films exposed to oxygen in the dark,more » or light-soaked in an inert atmosphere, do not exhibit significant absorption changes, suggesting simultaneous exposure of oxygen and light that creates singlet excited oxygen is the detrimental factor. Our ab initio electronic structure simulations interpret these by oxidation at the α-C site of the alkyl chains in PTB7, with an irreversible rupture of the alkyl chain and formation of new C=O and C–O–H conformations at the α-C. Infrared spectroscopy coupled with ab initio simulation can provide a powerful tool for quantifying photo-structural atomic bonding changes. As a result, understanding nanoscale light-induced structural changes will open avenues to designing more stable organic materials for organic electronics.« less

Code Analysis and Refactoring with Clang Tools, Version 0.1

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

Kelley, Timothy M.

2016-12-23

Code Analysis and Refactoring with Clang Tools is a small set of example code that demonstrates techniques for applying tools distributed with the open source Clang compiler. Examples include analyzing where variables are used and replacing old data structures with standard structures.

A Review on the Bioinformatics Tools for Neuroimaging

PubMed Central

MAN, Mei Yen; ONG, Mei Sin; Mohamad, Mohd Saberi; DERIS, Safaai; SULONG, Ghazali; YUNUS, Jasmy; CHE HARUN, Fauzan Khairi

2015-01-01

Neuroimaging is a new technique used to create images of the structure and function of the nervous system in the human brain. Currently, it is crucial in scientific fields. Neuroimaging data are becoming of more interest among the circle of neuroimaging experts. Therefore, it is necessary to develop a large amount of neuroimaging tools. This paper gives an overview of the tools that have been used to image the structure and function of the nervous system. This information can help developers, experts, and users gain insight and a better understanding of the neuroimaging tools available, enabling better decision making in choosing tools of particular research interest. Sources, links, and descriptions of the application of each tool are provided in this paper as well. Lastly, this paper presents the language implemented, system requirements, strengths, and weaknesses of the tools that have been widely used to image the structure and function of the nervous system. PMID:27006633

Lymph Node Metastases Optical Molecular Diagnostic and Radiation Therapy

DTIC Science & Technology

2017-03-01

structures and not molecular functions. The one tool commonly used for metastases imaging is nuclear medicine. Positron emission tomography, PET, is...be visualized at a relevant stage., largely because most imaging is based upon structures and not molecular functions. But there are no tools to...system suitable for imaging signals from in small animals on the standard radiation therapy tools. (3) To evaluate the limits on structural , metabolic

Automated extraction of chemical structure information from digital raster images

PubMed Central

Park, Jungkap; Rosania, Gus R; Shedden, Kerby A; Nguyen, Mandee; Lyu, Naesung; Saitou, Kazuhiro

2009-01-01

Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research articles. PMID:19196483

Tools and perspectives for a unified approach to understanding microbial ecology in the critical zone

NASA Astrophysics Data System (ADS)

Gallery, R. E.; Aronson, E. L.; Fairbanks, D.; Murphy, M. A.; Rich, V. I.; Hart, S. C.

2015-12-01

Microbial communities that control nutrient transformation and storage in ecosystems are themselves influenced by landscape topography and vegetative cover. Globally, disturbances such as fires and insect outbreaks are increasing in frequency and severity with enormous impacts on global carbon cycling. The resiliency of soil microbial communities to these heterogeneous disturbances determines rates of nutrient transformations as well as ecosystem structure and recovery. Natural and anthropogenic disturbances are a common thread throughout Critical Zone Observatories and ecosystems in general. Using the 2013 Thompson Ridge Fire in the Jemez River Basin CZO as a case study, we examine the effect of a wildfire disturbance regime on successional changes in soil microbiota and ecosystem fluxes across a landscape with high topographic variation. We find that, layered over the topographic controls of hotspots of biogeochemical activity, fire alters organic substrate quality, microbial biomass, community structure, and activity. For example, fire increases soil pH, which is commonly found as an explanatory variable describing bacterial community structure. Soil microbes excrete exoenzymes to decompose polymers and acquire nutrients, and these activities can indicate changing microbial function or soil quality. In these mixed conifer forests, we find shifts from carbon to nitrogen-dominated exoenzyme activities in burned forests with alkaline soils, suggesting shifts of microbial taxa and function that correspond with recovering soil microbial biomass. More generally we ask - what combination of tools and perspectives is needed to fully understand soil microbial ecology and biogeochemistry of the critical zone? Results from an NSF Science Across Virtual Institutes (SAVI) CZO Network Biogeochemistry Workshop highlight the importance of incorporating a standard suite of microbial activity and community assays along with soil biogeochemical and flux measurements to enable comparisons across the broader CZO network. These characterizations would provide regional microbial function and biodiversity data in a standardized framework that can be used to enable more effective management and valuation of critical zone services and inform projections under global change scenarios.

Surface Spectroscopic Signatures of Mechanical Deformation in HDPE.

PubMed

Averett, Shawn C; Stanley, Steven K; Hanson, Joshua J; Smith, Stacey J; Patterson, James E

2018-01-01

High-density polyethylene (HDPE) has been extensively studied, both as a model for semi-crystalline polymers and because of its own industrial utility. During cold drawing, crystalline regions of HDPE are known to break up and align with the direction of tensile load. Structural changes due to deformation should also manifest at the surface of the polymer, but until now, a detailed molecular understanding of how the surface responds to mechanical deformation has been lacking. This work establishes a precedent for using vibrational sum-frequency generation (VSFG) spectroscopy to investigate changes in the molecular-level structure of the surface of HDPE after cold drawing. X-ray diffraction (XRD) was used to confirm that the observed surface behavior corresponds to the expected bulk response. Before tensile loading, the VSFG spectra indicate that there is significant variability in the surface structure and tilt of the methylene groups away from the surface normal. After deformation, the VSFG spectroscopic signatures are notably different. These changes suggest that hydrocarbon chains at the surface of visibly necked HDPE are aligned with the direction of loading, while the associated methylene groups are oriented with the local C 2 v symmetry axis roughly parallel to the surface normal. Small amounts of unaltered material are also found at the surface of necked HDPE, with the relative amount of unaltered material decreasing as the amount of deformation increases. Aspects of the nonresonant SFG response in the transition zone between necked and undeformed polymer provide additional insight into the deformation process and may provide the first indication of mechanical deformation. Nonlinear surface spectroscopy can thus be used as a noninvasive and nondestructive tool to probe the stress history of a HPDE sample in situations where X-ray techniques are not available or not applicable. Vibrational sum-frequency generation thus has great potential as a platform for material state awareness (MSA) and should be considered as part of a broader suite of tools for such applications.

An illustrated anatomical ontology of the developing mouse lower urogenital tract

PubMed Central

Georgas, Kylie M.; Armstrong, Jane; Keast, Janet R.; Larkins, Christine E.; McHugh, Kirk M.; Southard-Smith, E. Michelle; Cohn, Martin J.; Batourina, Ekatherina; Dan, Hanbin; Schneider, Kerry; Buehler, Dennis P.; Wiese, Carrie B.; Brennan, Jane; Davies, Jamie A.; Harding, Simon D.; Baldock, Richard A.; Little, Melissa H.; Vezina, Chad M.; Mendelsohn, Cathy

2015-01-01

Malformation of the urogenital tract represents a considerable paediatric burden, with many defects affecting the lower urinary tract (LUT), genital tubercle and associated structures. Understanding the molecular basis of such defects frequently draws on murine models. However, human anatomical terms do not always superimpose on the mouse, and the lack of accurate and standardised nomenclature is hampering the utility of such animal models. We previously developed an anatomical ontology for the murine urogenital system. Here, we present a comprehensive update of this ontology pertaining to mouse LUT, genital tubercle and associated reproductive structures (E10.5 to adult). Ontology changes were based on recently published insights into the cellular and gross anatomy of these structures, and on new analyses of epithelial cell types present in the pelvic urethra and regions of the bladder. Ontology changes include new structures, tissue layers and cell types within the LUT, external genitalia and lower reproductive structures. Representative illustrations, detailed text descriptions and molecular markers that selectively label muscle, nerves/ganglia and epithelia of the lower urogenital system are also presented. The revised ontology will be an important tool for researchers studying urogenital development/malformation in mouse models and will improve our capacity to appropriately interpret these with respect to the human situation. PMID:25968320

An illustrated anatomical ontology of the developing mouse lower urogenital tract.

PubMed

Georgas, Kylie M; Armstrong, Jane; Keast, Janet R; Larkins, Christine E; McHugh, Kirk M; Southard-Smith, E Michelle; Cohn, Martin J; Batourina, Ekatherina; Dan, Hanbin; Schneider, Kerry; Buehler, Dennis P; Wiese, Carrie B; Brennan, Jane; Davies, Jamie A; Harding, Simon D; Baldock, Richard A; Little, Melissa H; Vezina, Chad M; Mendelsohn, Cathy

2015-05-15

Malformation of the urogenital tract represents a considerable paediatric burden, with many defects affecting the lower urinary tract (LUT), genital tubercle and associated structures. Understanding the molecular basis of such defects frequently draws on murine models. However, human anatomical terms do not always superimpose on the mouse, and the lack of accurate and standardised nomenclature is hampering the utility of such animal models. We previously developed an anatomical ontology for the murine urogenital system. Here, we present a comprehensive update of this ontology pertaining to mouse LUT, genital tubercle and associated reproductive structures (E10.5 to adult). Ontology changes were based on recently published insights into the cellular and gross anatomy of these structures, and on new analyses of epithelial cell types present in the pelvic urethra and regions of the bladder. Ontology changes include new structures, tissue layers and cell types within the LUT, external genitalia and lower reproductive structures. Representative illustrations, detailed text descriptions and molecular markers that selectively label muscle, nerves/ganglia and epithelia of the lower urogenital system are also presented. The revised ontology will be an important tool for researchers studying urogenital development/malformation in mouse models and will improve our capacity to appropriately interpret these with respect to the human situation. © 2015. Published by The Company of Biologists Ltd.

Engineering Proteins for Thermostability with iRDP Web Server

PubMed Central

Ghanate, Avinash; Ramasamy, Sureshkumar; Suresh, C. G.

2015-01-01

Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements. PMID:26436543

Engineering Proteins for Thermostability with iRDP Web Server.

PubMed

Panigrahi, Priyabrata; Sule, Manas; Ghanate, Avinash; Ramasamy, Sureshkumar; Suresh, C G

2015-01-01

Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements.

Advanced structural analysis of nanoporous materials by thermal response measurements.

PubMed

Oschatz, Martin; Leistner, Matthias; Nickel, Winfried; Kaskel, Stefan

2015-04-07

Thermal response measurements based on optical adsorption calorimetry are presented as a versatile tool for the time-saving and profound characterization of the pore structure of porous carbon-based materials. This technique measures the time-resolved temperature change of an adsorbent during adsorption of a test gas. Six carbide and carbon materials with well-defined nanopore architecture including micro- and/or mesopores are characterized by thermal response measurements based on n-butane and carbon dioxide as the test gases. With this tool, the pore systems of the model materials can be clearly distinguished and accurately analyzed. The obtained calorimetric data are correlated with the adsorption/desorption isotherms of the materials. The pore structures can be estimated from a single experiment due to different adsorption enthalpies/temperature increases in micro- and mesopores. Adsorption/desorption cycling of n-butane at 298 K/1 bar with increasing desorption time allows to determine the pore structure of the materials in more detail due to different equilibration times. Adsorption of the organic test gas at selected relative pressures reveals specific contributions of particular pore systems to the increase of the temperature of the samples and different adsorption mechanisms. The use of carbon dioxide as the test gas at 298 K/1 bar provides detailed insights into the ultramicropore structure of the materials because under these conditions the adsorption of this test gas is very sensitive to the presence of pores smaller than 0.7 nm.

Global value chains: Building blocks and network dynamics

NASA Astrophysics Data System (ADS)

Tsekeris, Theodore

2017-12-01

The paper employs measures and tools from complex network analysis to enhance the understanding and interpretation of structural characteristics pertaining to the Global Value Chains (GVCs) during the period 1995-2011. The analysis involves the country, sector and country-sector value chain networks to identify main drivers of structural change. The results indicate significant intertemporal changes, mirroring the increased globalization in terms of network size, strength and connectivity. They also demonstrate higher clustering and increased concentration of the most influential countries and country-sectors relative to all others in the GVC network, with the geographical dimension to prevail over the sectoral dimension in the formation of value chains. The regionalization and less hierarchical organization drive country-sector production sharing, while the sectoral value chain network has become more integrated and more competitive over time. The findings suggest that the impact of country-sector policies and/or shocks may vary with the own-group and network-wide influence of each country, take place in multiple geographical scales, as GVCs have a block structure, and involve time dynamics.

The use of advanced mass spectrometry to dissect the life-cycle of photosystem II

DOE PAGES

Weisz, Daniel A.; Gross, Michael L.; Pakrasi, Himadri B.

2016-05-10

Photosystem II (PSII) is a photosynthetic membrane-protein complex that undergoes an intricate, tightly regulated cycle of assembly, damage, and repair. The available crystal structures of cyanobacterial PSII are an essential foundation for understanding PSII function, but nonetheless provide a snapshot only of the active complex. To study aspects of the entire PSII life-cycle, mass spectrometry (MS) has emerged as a powerful tool that can be used in conjunction with biochemical techniques. In this article, we present the MS-based approaches that are used to study PSII composition, dynamics, and structure, and review the information about the PSII life-cycle that has beenmore » gained by these methods. This information includes the composition of PSII subcomplexes, discovery of accessory PSII proteins, identification of post-translational modifications and quantification of their changes under various conditions, determination of the binding site of proteins not observed in PSII crystal structures, conformational changes that underlie PSII functions, and identification of water and oxygen channels within PSII. Lastly, we conclude with an outlook for the opportunity of future MS contributions to PSII research.« less

Structural impact analysis of missense SNPs present in the uroguanylin gene by long-term molecular dynamics simulations.

PubMed

Marcolino, Antonio C S; Porto, William F; Pires, Állan S; Franco, Octavio L; Alencar, Sérgio A

2016-12-07

The guanylate cyclase activator 2B, also known as uroguanylin, is part of the guanylin peptide family, which includes peptides such as guanylin and lymphoguanylin. The guanylin peptides could be related to sodium absorption inhibition and water secretion induction and their dysfunction may be related to various pathologies such as chronic renal failure, congestive heart failure and nephrotic syndrome. Besides, uroguanylin point mutations have been associated with essential hypertension. However, currently there are no studies on the impact of missense SNPs on uroguanylin structure. This study applied in silico SNP impact prediction tools to evaluate the impact of uroguanylin missense SNPs and to filter those considered as convergent deleterious, which were then further analyzed through long-term molecular dynamics simulations of 1μs of duration. The simulations suggested that all missense SNPs considered as convergent deleterious caused some kind of structural change to the uroguanylin peptide. Additionally, four of these SNPs were also shown to cause modifications in peptide flexibility, possibly resulting in functional changes. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Effect of Solution Thermal History on Chicken Egg White Lysozyme Nucleation

NASA Technical Reports Server (NTRS)

Burke, Michael W.; Judge, Russell A.; Pusey, Marc L.

2001-01-01

Proteins are highly flexible molecules and often exhibit defined conformational changes in response to changes in the ambient temperature. Chicken egg white lysozyme has been previously shown to undergo an apparent structural change when warmed above the tetragonal/orthorhombic phase transition temperature. This is reflected by a change in the habit of the tetragonal and orthorhombic crystals so formed. In this study, we show that possible conformational changes induced by heating are stable and apparently non-reversible by simple cooling. Exposure of protein solutions to temperatures above the phase change transition temperature, before combining with precipitant solution to begin crystallization, reduces final crystal numbers. Protein that is briefly warmed to 37 C, then cooled shows no sign of reversal to the unheated nucleation behavior even after storage for four weeks at 4 C. The change in nucleation behavior of tetragonal lysozyme crystals, attributed to a structural shift, occurs faster the greater the exposure to temperature above the equi-solubility point for the two phases. Heating for 2 hours at 48 C reduces crystal numbers by 20 fold in comparison to the same solution heated for the same time at 30 C. Thermal treatment of solutions is therefore a possible tool to reduce crystal numbers and increase crystal size. The effects of a protein's previous thermal history are now shown to be a potentially critical factor in subsequent macromolecule crystal nucleation and growth studies.

The Effect of Solution Thermal History on Chicken Egg White Lysozyme Nucleation

NASA Technical Reports Server (NTRS)

Burke, Michael W.; Judge, Russell A.; Pusey, Marc L.; Rose, M. Franklin (Technical Monitor)

2000-01-01

Proteins are highly flexible molecules and often exhibit defined conformational changes in response to changes in the ambient temperature. Chicken egg white lysozyme has been previously shown to undergo an apparent structural change when warmed above the tetragonal/orthorhombic phase transition temperature. This is reflected by a change in the habit of the tetragonal and orthorhombic crystals so formed. In this study we show that possible conformational changes induced by heating are stable and apparently non- reversible by simple cooling. Exposure of protein solutions to temperatures above the phase change transition temperature, before combining with precipitant solution to begin crystallization, reduces final crystal numbers. Protein that is briefly warmed to 37 C, then cooled shows no sign of reversal to the unheated nucleation behavior even after storage for 4 weeks at 4 C. The change in nucleation behavior of tetragonal lysozyme crystals, attributed to a structural shift, occurs faster the greater the exposure to temperature above the equi-solubility point for the two phases. Heating for 2 h at 48 C reduces crystal numbers by 20 fold in comparison to the same solution heated for the same time at 30 C. Thermal treatment of solutions is therefore a possible tool to reduce crystal numbers and increase crystal size. The effects of a protein's previous thermal history are now shown to be a potentially critical factor in subsequent macromolecule crystal nucleation and growth studies.

Does research through Structured Operational Research and Training (SORT IT) courses impact policy and practice?

PubMed Central

Shewade, H. D.; Tripathy, J. P.; Guillerm, N.; Tayler-Smith, K.; Berger, S. Dar; Bissell, K.; Reid, A. J.; Zachariah, R.; Harries, A. D.

2016-01-01

Setting: Structured Operational Research and Training Initiative (SORT IT) courses are well known for their output, with nearly 90% of participants completing the course and publishing in scientific journals. Objective: We assessed the impact of research papers on policy and practice that resulted from six SORT IT courses initiated between July 2012 and March 2013. Design: This was a cross-sectional study involving e-mail-based, self-administered questionnaires and telephone/skype/in-person responses from first and/or senior co-authors of course papers. A descriptive content analysis of the responses was performed and categorised into themes. Results: Of 72 participants, 63 (88%) completed the course. Course output included 81 submitted papers, of which 76 (94%) were published. Of the 81 papers assessed, 45 (55%) contributed to a change in policy and/or practice: 29 contributed to government policy/practice change (20 at national, 4 at subnational and 5 at hospital level), 11 to non-government organisational policy change and 5 to reinforcing existing policy. The changes ranged from modifications of monitoring and evaluation tools, to redrafting of national guidelines, to scaling up existing policies. Conclusion: More than half of the SORT IT course papers contributed to a change in policy and/or practice. Future assessments should include more robust and independent verification of the reported change(s) with all stakeholders. PMID:27051612

NASTRAN as an analytical research tool for composite mechanics and composite structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Sinclair, J. H.; Sullivan, T. L.

1976-01-01

Selected examples are described in which NASTRAN is used as an analysis research tool for composite mechanics and for composite structural components. The examples were selected to illustrate the importance of using NASTRAN as an analysis tool in this rapidly advancing field.

Meaningful learning: The essential factor for conceptual change in limited or inappropriate propositional hierarchies leading to empowerment of learners

NASA Astrophysics Data System (ADS)

Novak, Joseph D.

2002-07-01

The construction and reconstruction of meanings by learners requires that they actively seek to integrate new knowledge with knowledge already in their cognitive structure. Ausubel's assimilation theory of cognitive learning has been shown to be effective in guiding research and instructional design to facilitate meaningful learning (Ausubel, The psychology of meaningful verbal learning, New York: Grune and Stratton, 1963; Educational psychology: A cognitive view, New York: Holt, Rinehart and Winston, 1968; The acquisition and retention of knowledge, Dordrecht: Kluwer, 2000). Gowin's Vee heuristic has been employed effectively to aid teachers and students in understanding the constructed nature of knowledge (Gowin, Educating, Ithaca, NY: Cornell University Press, 1981). Situated learning occurs when learning is by rote or at a lower level of meaningful learning. Concept mapping has been used effectively to aid meaningful learning with resulting modification of student's knowledge structures. When these knowledge structures are limited or faulty in some way, they may be referred to as Limited or Inappropriate Propositional Hierarchies (LIPH's). Conceptual change, or more accurately conceptual reconstrution, requires meaningful learning to modify LIPH's. Collaborative group learning facilitates meaningful learning and new knowledge construction. World-wide economic changes are forcing major changes in business and industry placing a premium on the power and value of knowledge and new knowledge production. These changes require changes in school and university education that centers on the nature and power of meaningful learning. New computer tools are available to facilitate teaching activities targeted at modifying LIPH's, and aiding meaningful learning in general.

An analytical method for predicting the geometrical and optical properties of the human lens under accommodation

PubMed Central

Sheil, Conor J.; Bahrami, Mehdi; Goncharov, Alexander V.

2014-01-01

We present an analytical method to describe the accommodative changes in the human crystalline lens. The method is based on the geometry-invariant lens model, in which the gradient-index (GRIN) iso-indicial contours are coupled to the external shape. This feature ensures that any given number of iso-indicial contours does not change with accommodation, which preserves the optical integrity of the GRIN structure. The coupling also enables us to define the GRIN structure if the radii and asphericities of the external lens surfaces are known. As an example, the accommodative changes in lenticular radii and central thickness were taken from the literature, while the asphericities of the external surfaces were derived analytically by adhering to the basic physical conditions of constant lens volume and its axial position. The resulting changes in lens geometry are consistent with experimental data, and the optical properties are in line with expected values for optical power and spherical aberration. The aim of the paper is to provide an anatomically and optically accurate lens model that is valid for 3 mm pupils and can be used as a new tool for better understanding of accommodation. PMID:24877022

An analytical method for predicting the geometrical and optical properties of the human lens under accommodation.

PubMed

Sheil, Conor J; Bahrami, Mehdi; Goncharov, Alexander V

2014-05-01

We present an analytical method to describe the accommodative changes in the human crystalline lens. The method is based on the geometry-invariant lens model, in which the gradient-index (GRIN) iso-indicial contours are coupled to the external shape. This feature ensures that any given number of iso-indicial contours does not change with accommodation, which preserves the optical integrity of the GRIN structure. The coupling also enables us to define the GRIN structure if the radii and asphericities of the external lens surfaces are known. As an example, the accommodative changes in lenticular radii and central thickness were taken from the literature, while the asphericities of the external surfaces were derived analytically by adhering to the basic physical conditions of constant lens volume and its axial position. The resulting changes in lens geometry are consistent with experimental data, and the optical properties are in line with expected values for optical power and spherical aberration. The aim of the paper is to provide an anatomically and optically accurate lens model that is valid for 3 mm pupils and can be used as a new tool for better understanding of accommodation.

Understanding the Differential Selectivity of Arrestins toward the Phosphorylation State of the Receptor.

PubMed

Sensoy, Ozge; Moreira, Irina S; Morra, Giulia

2016-09-21

Proteins in the arrestin family exhibit a conserved structural fold that nevertheless allows for significant differences in their selectivity for G-protein coupled receptors (GPCRs) and their phosphorylation states. To reveal the mechanism of activation that prepares arrestin for selective interaction with GPCRs, and to understand the basis for these differences, we used unbiased molecular dynamics simulations to compare the structural and dynamic properties of wild type Arr1 (Arr1-WT), Arr3 (Arr3-WT), and a constitutively active Arr1 mutant, Arr1-R175E, characterized by a perturbation of the phosphate recognition region called "polar core". We find that in our simulations the mutant evolves toward a conformation that resembles the known preactivated structures of an Arr1 splice-variant, and the structurally similar phosphopeptide-bound Arr2-WT, while this does not happen for Arr1-WT. Hence, we propose an activation allosteric mechanism connecting the perturbation of the polar core to a global conformational change, including the relative reorientation of N- and C-domains, and the emergence of electrostatic properties of putative binding surfaces. The underlying local structural changes are interpreted as markers of the evolution of an arrestin structure toward an active-like conformation. Similar activation related changes occur in Arr3-WT in the absence of any perturbation of the polar core, suggesting that this system could spontaneously visit preactivated states in solution. This hypothesis is proposed to explain the lower selectivity of Arr3 toward nonphosphorylated receptors. Moreover, by elucidating the allosteric mechanism underlying activation, we identify functionally critical regions on arrestin structure that can be targeted with drugs or chemical tools for functional modulation.

Game changer: the topology of creativity.

PubMed

de Vaan, Mathijs; Stark, David; Vedres, Balazs

2015-01-01

This article examines the sociological factors that explain why some creative teams are able to produce game changers--cultural products that stand out as distinctive while also being critically recognized as outstanding. The authors build on work pointing to structural folding--the network property of a cohesive group whose membership overlaps with that of another cohesive group. They hypothesize that the effects of structural folding on game changing success are especially strong when overlapping groups are cognitively distant. Measuring social distance separately from cognitive distance and distinctiveness independently from critical acclaim, the authors test their hypothesis about structural folding and cognitive diversity by analyzing team reassembly for 12,422 video games and the career histories of 139,727 video game developers. When combined with cognitive distance, structural folding channels and mobilizes a productive tension of rules, roles, and codes that promotes successful innovation. In addition to serving as pipes and prisms, network ties are also the source of tools and tensions.

Quantitative Subsurface Atomic Structure Fingerprint for 2D Materials and Heterostructures by First-Principles-Calibrated Contact-Resonance Atomic Force Microscopy.

PubMed

Tu, Qing; Lange, Björn; Parlak, Zehra; Lopes, Joao Marcelo J; Blum, Volker; Zauscher, Stefan

2016-07-26

Interfaces and subsurface layers are critical for the performance of devices made of 2D materials and heterostructures. Facile, nondestructive, and quantitative ways to characterize the structure of atomically thin, layered materials are thus essential to ensure control of the resultant properties. Here, we show that contact-resonance atomic force microscopy-which is exquisitely sensitive to stiffness changes that arise from even a single atomic layer of a van der Waals-adhered material-is a powerful experimental tool to address this challenge. A combined density functional theory and continuum modeling approach is introduced that yields sub-surface-sensitive, nanomechanical fingerprints associated with specific, well-defined structure models of individual surface domains. Where such models are known, this information can be correlated with experimentally obtained contact-resonance frequency maps to reveal the (sub)surface structure of different domains on the sample.

RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins.

PubMed

Hirsh, Layla; Paladin, Lisanna; Piovesan, Damiano; Tosatto, Silvio C E

2018-05-09

RepeatsDB-lite (http://protein.bio.unipd.it/repeatsdb-lite) is a web server for the prediction of repetitive structural elements and units in tandem repeat (TR) proteins. TRs are a widespread but poorly annotated class of non-globular proteins carrying heterogeneous functions. RepeatsDB-lite extends the prediction to all TR types and strongly improves the performance both in terms of computational time and accuracy over previous methods, with precision above 95% for solenoid structures. The algorithm exploits an improved TR unit library derived from the RepeatsDB database to perform an iterative structural search and assignment. The web interface provides tools for analyzing the evolutionary relationships between units and manually refine the prediction by changing unit positions and protein classification. An all-against-all structure-based sequence similarity matrix is calculated and visualized in real-time for every user edit. Reviewed predictions can be submitted to RepeatsDB for review and inclusion.

Parameterized centrality metric for network analysis

NASA Astrophysics Data System (ADS)

Ghosh, Rumi; Lerman, Kristina

2011-06-01

A variety of metrics have been proposed to measure the relative importance of nodes in a network. One of these, alpha-centrality [P. Bonacich, Am. J. Sociol.0002-960210.1086/228631 92, 1170 (1987)], measures the number of attenuated paths that exist between nodes. We introduce a normalized version of this metric and use it to study network structure, for example, to rank nodes and find community structure of the network. Specifically, we extend the modularity-maximization method for community detection to use this metric as the measure of node connectivity. Normalized alpha-centrality is a powerful tool for network analysis, since it contains a tunable parameter that sets the length scale of interactions. Studying how rankings and discovered communities change when this parameter is varied allows us to identify locally and globally important nodes and structures. We apply the proposed metric to several benchmark networks and show that it leads to better insights into network structure than alternative metrics.

Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy.

PubMed

Kekilli, Demet; Dworkowski, Florian S N; Pompidor, Guillaume; Fuchs, Martin R; Andrew, Colin R; Antonyuk, Svetlana; Strange, Richard W; Eady, Robert R; Hasnain, S Samar; Hough, Michael A

2014-05-01

It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularly when applied in situ at macromolecular crystallography beamlines, allow spectroscopic investigations of redox and ligand states and the identification of reaction intermediates in protein crystals during the collection of structural data. Single-crystal resonance Raman spectroscopy was carried out in combination with macromolecular crystallography on Swiss Light Source beamline X10SA using cytochrome c' from Alcaligenes xylosoxidans. This allowed the fingerprinting and validation of different redox and ligand states, identification of vibrational modes and identification of intermediates together with monitoring of radiation-induced changes. This combined approach provides a powerful tool to obtain complementary data and correctly assign the true oxidation and ligand state(s) in redox-protein crystals.

The evolution of structured illumination microscopy in studies of HIV.

PubMed

Marno, Kelly; Al'Zoubi, Lara; Pearson, Matthew; Posch, Markus; McKnight, Áine; Wheeler, Ann P

2015-10-15

The resolution limit of conventional light microscopy has proven to be limiting for many biological structures such as viruses including Human immunodeficiency virus (HIV). Individual HIV virions are impossible to study using confocal microscopy as they are well below the 200 nm resolution limit of conventional light microscopes. Structured illumination microscopy (SIM) allows a twofold enhancement in image resolution compared to standard widefield illumination and so provides an excellent tool for study of HIV. Viral capsids (CAs) vary between 110 and 146 nm so this study challenges the performance of SIM microscopes. SIM microscopy was first developed in 2000, commercialised in 2007 and rapidly developed. Here we present the changes in capabilities of the SIM microscopes for study of HIV localisation as the instrumentation for structured illumination microscopy has evolved over the past 8 years. Copyright © 2015. Published by Elsevier Inc.

Diversification and cumulative evolution in New Caledonian crow tool manufacture.

PubMed Central

Hunt, Gavin R; Gray, Russell D

2003-01-01

Many animals use tools but only humans are generally considered to have the cognitive sophistication required for cumulative technological evolution. Three important characteristics of cumulative technological evolution are: (i) the diversification of tool design; (ii) cumulative change; and (iii) high-fidelity social transmission. We present evidence that crows have diversified and cumulatively changed the design of their pandanus tools. In 2000 we carried out an intensive survey in New Caledonia to establish the geographical variation in the manufacture of these tools. We documented the shapes of 5550 tools from 21 sites throughout the range of pandanus tool manufacture. We found three distinct pandanus tool designs: wide tools, narrow tools and stepped tools. The lack of ecological correlates of the three tool designs and their different, continuous and overlapping geographical distributions make it unlikely that they evolved independently. The similarities in the manufacture method of each design further suggest that pandanus tools have gone through a process of cumulative change from a common historical origin. We propose a plausible scenario for this rudimentary cumulative evolution. PMID:12737666

Clarity versus complexity: land-use modeling as a practical tool for decision-makers

USGS Publications Warehouse

Sohl, Terry L.; Claggett, Peter

2013-01-01

The last decade has seen a remarkable increase in the number of modeling tools available to examine future land-use and land-cover (LULC) change. Integrated modeling frameworks, agent-based models, cellular automata approaches, and other modeling techniques have substantially improved the representation of complex LULC systems, with each method using a different strategy to address complexity. However, despite the development of new and better modeling tools, the use of these tools is limited for actual planning, decision-making, or policy-making purposes. LULC modelers have become very adept at creating tools for modeling LULC change, but complicated models and lack of transparency limit their utility for decision-makers. The complicated nature of many LULC models also makes it impractical or even impossible to perform a rigorous analysis of modeling uncertainty. This paper provides a review of land-cover modeling approaches and the issues causes by the complicated nature of models, and provides suggestions to facilitate the increased use of LULC models by decision-makers and other stakeholders. The utility of LULC models themselves can be improved by 1) providing model code and documentation, 2) through the use of scenario frameworks to frame overall uncertainties, 3) improving methods for generalizing key LULC processes most important to stakeholders, and 4) adopting more rigorous standards for validating models and quantifying uncertainty. Communication with decision-makers and other stakeholders can be improved by increasing stakeholder participation in all stages of the modeling process, increasing the transparency of model structure and uncertainties, and developing user-friendly decision-support systems to bridge the link between LULC science and policy. By considering these options, LULC science will be better positioned to support decision-makers and increase real-world application of LULC modeling results.

Real time software tools and methodologies

NASA Technical Reports Server (NTRS)

Christofferson, M. J.

1981-01-01

Real time systems are characterized by high speed processing and throughput as well as asynchronous event processing requirements. These requirements give rise to particular implementations of parallel or pipeline multitasking structures, of intertask or interprocess communications mechanisms, and finally of message (buffer) routing or switching mechanisms. These mechanisms or structures, along with the data structue, describe the essential character of the system. These common structural elements and mechanisms are identified, their implementation in the form of routines, tasks or macros - in other words, tools are formalized. The tools developed support or make available the following: reentrant task creation, generalized message routing techniques, generalized task structures/task families, standardized intertask communications mechanisms, and pipeline and parallel processing architectures in a multitasking environment. Tools development raise some interesting prospects in the areas of software instrumentation and software portability. These issues are discussed following the description of the tools themselves.

Transportation Resilience Tools from the U.S. Department of Transportation

NASA Astrophysics Data System (ADS)

Snow, C.; Rodehorst, B.; Miller, R.; Choate, A.; Hyman, R.; Kafalenos, R.; Beucler, B.

2014-12-01

The U.S. Department of Transportation (U.S. DOT) and ICF International have been working to develop tools and resources to help state departments of transportation (DOTs) and metropolitan planning organizations (MPOs) prepare for the impacts of climate change. U.S. DOT recently released a set of climate change and extreme weather tools for state DOTs and MPOs that address key challenges they have faced in increasing their climate change resilience. The tools were developed under the U.S. DOT Gulf Coast Study, Phase 2. The CMIP Climate Data Processing Tool provides an easy way for users to gather and process downscaled climate model data at the local level, and "translates" that data into information relevant to transportation engineers and planners. The Vulnerability Assessment Scoring Tool (VAST), provides a step-by-step approach for users to assess their vulnerability to climate change in a transparent, cost-effective way. The Transportation Climate Change Sensitivity Matrix provides detailed information on how 11 different climate stressors may affect transportation infrastructure and operations. These tools significantly advance the state of the practice for transportation agencies to respond to climate change impacts, and beta-versions have been used successfully by several state DOTs and MPOs. This presentation will focus on these tools, examples of how they can be applied within transportation agencies, and opportunities to apply the lessons learned from the tools—or even the tools themselves—beyond the transportation sector, including as part of the national Climate Resilience Toolkit.

Preoperative evaluation of patients with squamous cell carcinoma of the oral cavity: fluorine-18 fluorodeoxyglucose positron emission tomography/computed tomography and ultrasonography versus histopathology.

PubMed

Sugawara, Chieko; Takahashi, Akira; Kubo, Michiko; Otsuka, Hideki; Ishimaru, Naozumi; Miyamoto, Youji; Honda, Eiichi

2012-10-01

The purpose of this retrospective study was to compare fluorine-18 fluorodeoxyglucose positron emission tomography/computed tomography (PET/CT) and ultrasonography (US) in the staging of patients with squamous cell carcinoma of the oral cavity. We compared preoperative evaluations regarding lymph nodes using PET/CT, US, and both methods. The cutoff for the maximum standardized uptake value (SUV(max)) in PET/CT was set at 2.7 by a receiver operating characteristic analysis that was based on the histopathological diagnosis. US was used to examine internal structural changes on B-mode and hilar vascularity on power Doppler. The performance of PET/CT and US in combination was better than that of each modality separately. However, there were histopathological changes that could not be detected on PET/CT or US. PET/CT could not detect nodes with necrotic or cystic changes. US could not detect lymph nodes that did not have abnormal structures. PET/CT and US are complementary tools to evaluate preoperative patients. Copyright © 2012 Elsevier Inc. All rights reserved.

From structure to function, via dynamics

NASA Astrophysics Data System (ADS)

Stetter, O.; Soriano, J.; Geisel, T.; Battaglia, D.

2013-01-01

Neurons in the brain are wired into a synaptic network that spans multiple scales, from local circuits within cortical columns to fiber tracts interconnecting distant areas. However, brain function require the dynamic control of inter-circuit interactions on time-scales faster than synaptic changes. In particular, strength and direction of causal influences between neural populations (described by the so-called directed functional connectivity) must be reconfigurable even when the underlying structural connectivity is fixed. Such directed functional influences can be quantified resorting to causal analysis of time-series based on tools like Granger Causality or Transfer Entropy. The ability to quickly reorganize inter-areal interactions is a chief requirement for performance in a changing natural environment. But how can manifold functional networks stem "on demand" from an essentially fixed structure? We explore the hypothesis that the self-organization of neuronal synchronous activity underlies the control of brain functional connectivity. Based on simulated and real recordings of critical neuronal cultures in vitro, as well as on mean-field and spiking network models of interacting brain areas, we have found that "function follows dynamics", rather than structure. Different dynamic states of a same structural network, characterized by different synchronization properties, are indeed associated to different functional digraphs (functional multiplicity). We also highlight the crucial role of dynamics in establishing a structure-to-function link, by showing that whenever different structural topologies lead to similar dynamical states, than the associated functional connectivities are also very similar (structural degeneracy).

Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures.

PubMed

Schloss, Patrick D; Handelsman, Jo

2006-10-01

The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furthermore, current tests of community structure do not indicate the similarity of the communities but only report the probability of a statistical hypothesis. Here we present a computer program, SONS, which implements nonparametric estimators for the fraction and richness of OTUs shared between two communities.

A New Glaucoma Severity Score Combining Structural and Functional Defects.

PubMed

Wachtl, J; Töteberg-Harms, M; Frimmel, S; Kniestedt, C

2017-04-01

Background In order to assess glaucoma severity and to compare the success of surgical and medical therapy and study outcomes, an objective and independent staging tool is necessary. A combination of information from both structural and functional testing is probably the best approach to stage glaucomatous damage. There has been no universally accepted standard for glaucoma staging. The aim of this study was to develop a Glaucoma Severity Score (GSS) for objective assessment of a patient's glaucoma severity, combining both functional and structural information. Materials and methods The Glaucoma Severity Score includes the following 3 criteria: superior and inferior Retinal Nerve Fibre Layer (RNFL) thickness, perimetric mean defect (MD), and agreement of anatomical and perimetric defects, as assessed by two glaucoma specialists. The specialists defined a staging tool for each of the 3 criteria in a consensus process, assigning specific characteristics to a scale value between 0 and 2 or 0 and 3, respectively. The GSS ranges between 0 and 10 points. In a prospective observational study, the data of 112 glaucoma patients were assessed independently by the two specialists according to this staging tool. Results The GSS was applied to 112 eyes and patients (59.8 % female) with a mean age of 66.3 ± 13.1 years. Mean GSS was 4.73 points. Cohen's kappa coefficient was determined to measure inter-rater agreement between glaucoma specialists for the third criterion. With κ = 0.83, the agreement was very good. Thus, all 3 criteria of the GSS may be regarded as objective. Conclusions The Glaucoma Severity Score is an objective tool, combining both structural and functional characteristics, and permitting comparison of different patients, populations and studies. The Glaucoma Severity Score has proven effective in the objective assessment of 112 glaucoma patients and is relatively user-friendly in clinical practice. A comparative study of the GSS with the results of the FORUM® Glaucoma Workplace (Carl Zeiss Meditec AG, Jena, Germany) will be the next step. If outcomes match, the Glaucoma Severity Score can be accepted as a promising tool to stage glaucoma and monitor changes objectively in patients when comparing glaucoma progression in study analyses. Georg Thieme Verlag KG Stuttgart · New York.

Quantitative Imaging of Scattering Changes Associated With Epithelial Proliferation, Necrosis and Fibrosis in Tumors Using Microsampling Reflectance Spectroscopy

PubMed Central

Krishnaswamy, Venkataramanan; Hoopes, P. Jack; Samkoe, Kimberley S.; O'Hara, Julia A.; Hasan, Tayyaba; Pogue, Brian W.

2010-01-01

Highly localized reflectance measurements can be used to directly quantify scatter changes in tissues. This study presents a microsampling approach that is used to raster scan tumors to extract parameters believed to be related to the tissue ultra-structure. A confocal reflectance imager was developed to examine scatter changes across pathologically distinct regions within tumor tissues. Tissue sections from two murine tumors, AsPC-1 pancreas tumor and the Mat-LyLu Dunning prostate tumor, were imaged. After imaging, histopathology-guided region-of-interest studies of the images allowed analysis of the variations in scattering resulting from differences in tissue ultra-structure. On average, the median scatter power of tumor cells with high proliferation index was about 26% less compared to tumor cells with low proliferation index (LPI). Necrosis exhibited the lowest scatter power signature across all the tissue types considered, with about 55% lower median scatter power than LPI tumor cells. Additionally, the level and maturity of the tumor's fibroplastic response was found to influence the scatter signal. This approach to scatter visualization of tissue ultra-structure in situ could provide a unique tool for guiding surgical resection, but this kind of interpretation into what the signal means relative to the pathology is required before proceeding to clinical studies. PMID:19256692

The upper-mantle transition zone beneath the Chile-Argentina flat subduction zone

NASA Astrophysics Data System (ADS)

Bagdo, Paula; Bonatto, Luciana; Badi, Gabriela; Piromallo, Claudia

2016-04-01

The main objective of the present work is the study of the upper mantle structure of the western margin of South America (between 26°S and 36°S) within an area known as the Chile-Argentina flat subduction zone. For this purpose, we use teleseismic records from temporary broad band seismic stations that resulted from different seismic experiments carried out in South America. This area is characterized by on-going orogenic processes and complex subduction history that have profoundly affected the underlying mantle structure. The detection and characterization of the upper mantle seismic discontinuities are useful to understand subduction processes and the dynamics of mantle convection; this is due to the fact that they mark changes in mantle composition or phase changes in mantle minerals that respond differently to the disturbances caused by mantle convection. The discontinuities at a depth of 410 km and 660 km, generally associated to phase changes in olivine, vary in width and depth as a result of compositional and temperature anomalies. As a consequence, these discontinuities are an essential tool to study the thermal and compositional structure of the mantle. Here, we analyze the upper-mantle transition zone discontinuities at a depth of 410 km and 660 km as seen from Pds seismic phases beneath the Argentina-Chile flat subduction.

Structure-guided design and functional characterization of an artificial red light-regulated guanylate/adenylate cyclase for optogenetic applications.

PubMed

Etzl, Stefan; Lindner, Robert; Nelson, Matthew D; Winkler, Andreas

2018-06-08

Genetically targeting biological systems to control cellular processes with light is the concept of optogenetics. Despite impressive developments in this field, underlying molecular mechanisms of signal transduction of the employed photoreceptor modules are frequently not sufficiently understood to rationally design new optogenetic tools. Here, we investigate the requirements for functional coupling of red light-sensing phytochromes with non-natural enzymatic effectors by creating a series of constructs featuring the Deinococcus radiodurans bacteriophytochrome linked to a Synechocystis guanylate/adenylate cyclase. Incorporating characteristic structural elements important for cyclase regulation in our designs, we identified several red light-regulated fusions with promising properties. We provide details of one light-activated construct with low dark-state activity and high dynamic range that outperforms previous optogenetic tools in vitro and expands our in vivo toolkit, as demonstrated by manipulation of Caenorhabditis elegans locomotor activity. The full-length crystal structure of this phytochrome-linked cyclase revealed molecular details of photoreceptor-effector coupling, highlighting the importance of the regulatory cyclase element. Analysis of conformational dynamics by hydrogen-deuterium exchange in different functional states enriched our understanding of phytochrome signaling and signal integration by effectors. We found that light-induced conformational changes in the phytochrome destabilize the coiled-coil sensor-effector linker, which releases the cyclase regulatory element from an inhibited conformation, increasing cyclase activity of this artificial system. Future designs of optogenetic functionalities may benefit from our work, indicating that rational considerations for the effector improve the rate of success of initial designs to obtain optogenetic tools with superior properties. © 2018 Etzl et al.

N-Glycan Structure Annotation of Glycopeptides Using a Linearized Glycan Structure Database (GlyDB)

PubMed Central

Ren, Jian Min; Rejtar, Tomas; Li, Lingyun; Karger, Barry L.

2008-01-01

While glycoproteins are abundant in nature, and changes in glycosylation occur in cancer and other diseases, glycoprotein characterization remains a challenge due to the structural complexity of the biopolymers. This paper presents a general strategy, termed GlyDB, for glycan structure annotation of N-linked glycopeptides from tandem mass spectra in the LC-MS analysis of proteolytic digests of glycoproteins. The GlyDB approach takes advantage of low-energy collision induced dissociation of N-linked glycopeptides that preferentially cleaves the glycosidic bonds while the peptide backbone remains intact. A theoretical glycan structure database derived from biosynthetic rules for N-linked glycans was constructed employing a novel representation of branched glycan structures consisting of multiple linear sequences. The commonly used peptide identification program, Sequest, could then be utilized to assign experimental tandem mass spectra to individual glycoforms. Analysis of synthetic glycopeptides and well-characterized glycoproteins demonstrate that the GlyDB approach can be a useful tool for annotation of glycan structures and for selection of a limited number of potential glycan structure candidates for targeted validation. PMID:17625816

Quantitative Restoration of the Evolution of Mantle Structures Using Data Assimilation

NASA Astrophysics Data System (ADS)

Ismail-Zadeh, A.; Schubert, G.; Tsepelev, I.

2008-12-01

Rapid progress in imaging deep Earth structures and in studies of physical and chemical properties of mantle rocks facilitates research in assimilation of data related to mantle dynamics. We present a quantitative approach to assimilation of geophysical and geodetic data, which allows for incorporating observations and unknown initial conditions for mantle temperature and flow into a three-dimensional dynamic model in order to determine the initial conditions in the geological past. Once the conditions are determined the evolution of mantle structures can be restore backward in time. We apply data assimilation techniques to model the evolution of mantle plumes and lithospheric slabs. We show that the geometry of the mantle structures changes with time diminishing the degree of surface curvature of the structures, because the heat conduction smoothes the complex thermal surfaces of mantle bodies with time. Present seismic tomography images of mantle structures do not allow definition of the sharp shapes of these structures. Assimilation of mantle temperature and flow to the geological past instead provides a quantitative tool to restore thermal shapes of prominent structures in the past from their diffusive shapes at present.

From Worker Health To Citizen Health: Moving Upstream

PubMed Central

Sepulveda, Martin-Jose

2014-01-01

New rapid growth economies, urbanization, health systems crises and “big data” are causing fundamental changes in social structures and systems including health. These forces for change have significant consequences for occupational and environmental medicine and will challenge the specialty to think beyond workers and workplaces as the principal locus of innovation for health and performance. These trends are placing great emphasis on upstream strategies for addressing the complex systems dynamics of the social determinants of health. The need to engage systems in communities for healthier workforces is a shift in orientation from worker and workplace centric to citizen and community centric. This change for occupational and environmental medicine requires extending systems approaches in the workplace to communities which are systems of systems and which require different skills, data, tools and partnerships. PMID:24284749

From worker health to citizen health: moving upstream.

PubMed

Sepulveda, Martin-Jose

2013-12-01

New rapid growth economies, urbanization, health systems crises, and "big data" are causing fundamental changes in social structures and systems, including health. These forces for change have significant consequences for occupational and environmental medicine and will challenge the specialty to think beyond workers and workplaces as the principal locus of innovation for health and performance. These trends are placing great emphasis on upstream strategies for addressing the complex systems dynamics of the social determinants of health. The need to engage systems in communities for healthier workforces is a shift in orientation from worker and workplace centric to citizen and community centric. This change for occupational and environmental medicine requires extending systems approaches in the workplace to communities that are systems of systems and that require different skills, data, tools, and partnerships.

Investigations on the change of texture of plant cells due to preservative treatments by digital holographic microscopy

NASA Astrophysics Data System (ADS)

Vora, Priyanka; Anand, Arun

2014-10-01

Texture change is observed in preserved fruits and vegetables. Responsible factors for texture change during preservative treatments are cell morphology, cell wall structure, cell turger, water content and some biochemical components, and also the environmental conditions. Digital Holographic microscopy (DHM) is a quantitative phase contrast imaging technique, which provides three dimensional optical thickness profiles of transparent specimen. Using DHM the morphology of plant cells preserved by refrigeration or stored in vinegar or in sodium chloride can be obtained. This information about the spatio-temporal evolution of optical volume and thickness can be an important tool in area of food processing. Also from the three dimensional images, the texture of the cell can be retrieved and can be investigated under varying conditions.

Biology and Medicine Division annual report, 1987

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

Not Available

Modern biology is characterized by rapid change. The development of new tools and the results derived from their application to various biological systems require significant shifts in our concepts and the strategies that are adopted to analyze and elucidate mechanisms. In parallel with exciting new scientific developments our organizational structure and programmatic emphases have altered. These changes and developments have enabled the life sciences at LBL to be better positioned to create and respond to new opportunities. The work summarized in this annual report reflects a vital multifaceted research program that is in the vanguard of the areas represented. Wemore » are committed to justifying the confidence expressed by LBL through the new mission statement and reorganizational changes designed to give greater prominence to the life sciences.« less

Whither managerialism in the Italian National Health Service?

PubMed

Anessi-Pessina, Eugenio; Cantù, Elena

2006-01-01

In the last decade, the Italian National Health Service has been characterized by the introduction of managerial concepts and techniques, according to the New Public Management paradigm. Recently, these reforms have been increasingly criticized. This article examines the implementation of managerialism in an attempt to evaluate its overall achievements and shortcomings. Overall, managerialism seems to have made good progress: managerial skills are improving; several management tools have been adapted to health-care and public-sector peculiarities; health-care organizations have adopted a wide range of technical solutions to fit their specific needs. At the same time, managerial innovations have often focused on structures as opposed to processes, on the way the organization looks as opposed to the way it works, on the tools it has as opposed to those it actually needs and uses. We thus suggest that research, training and policy-making should stop focusing on the technical features and theoretical virtues of specific tools and should redirect their emphasis on change management.

Fourier transform-infrared spectroscopy as a diagnostic tool for mosquito coil smoke inhalation toxicity in Swiss Albino mice

NASA Astrophysics Data System (ADS)

Anusha, Chidambaram; Sankar, Renu; Varunkumar, Krishnamoorthy; Sivasindhuja, Gnanasambantham; Ravikumar, Vilwanathan

2017-12-01

The goal of this study is to establish Fourier transform-infrared (FTIR) spectroscopy as a diagnostic tool for allethrin-based mosquito coil smoke inhalation induced toxicity in mice. Primarily, we confirmed mosquito coil smoke inhalation toxicity in mice via reduced the body, organ weight and major vital organ tissue morphological structure changes. Furthermore, FTIR spectra was collected from control and mosquito coil smoke inhalation (8 h per day for 30 days) mice various tissues like liver, kidney, lung, heart and brain, to investigate the functional groups and their corresponding biochemical content variations. The FTIR spectra result shown major bio macromolecules such as protein and lipid functional peaks were shifted (decreased) in the mosquito coil smoke inhalation group as compared to control. The drastic peak shift was noticed in the liver, kidney followed by lung and brain. It is therefore concluded that the FTIR spectroscopy can be a successful detection tool in mosquito coil smoke inhalation toxicity.

Validation of the Mobile Information Software Evaluation Tool (MISET) With Nursing Students.

PubMed

Secco, M Loretta; Furlong, Karen E; Doyle, Glynda; Bailey, Judy

2016-07-01

This study evaluated the Mobile Information Software Evaluation Tool (MISET) with a sample of Canadian undergraduate nursing students (N = 240). Psychometric analyses determined how well the MISET assessed the extent that nursing students find mobile device-based information resources useful and supportive of learning in the clinical and classroom settings. The MISET has a valid three-factor structure with high explained variance (74.7%). Internal consistency reliabilities were high for the MISET total (.90) and three subscales: Usefulness/Helpfulness, Information Literacy Support, and Use of Evidence-Based Sources (.87 to .94). Construct validity evidence included significantly higher mean total MISET, Helpfulness/Usefulness, and Information Literacy Support scores for senior students and those with higher computer competence. The MISET is a promising tool to evaluate mobile information technologies and information literacy support; however, longitudinal assessment of changes in scores over time would determine scale sensitivity and responsiveness. [J Nurs Educ. 2016;55(7):385-390.]. Copyright 2016, SLACK Incorporated.

Computational Tools for Allosteric Drug Discovery: Site Identification and Focus Library Design.

PubMed

Huang, Wenkang; Nussinov, Ruth; Zhang, Jian

2017-01-01

Allostery is an intrinsic phenomenon of biological macromolecules involving regulation and/or signal transduction induced by a ligand binding to an allosteric site distinct from a molecule's active site. Allosteric drugs are currently receiving increased attention in drug discovery because drugs that target allosteric sites can provide important advantages over the corresponding orthosteric drugs including specific subtype selectivity within receptor families. Consequently, targeting allosteric sites, instead of orthosteric sites, can reduce drug-related side effects and toxicity. On the down side, allosteric drug discovery can be more challenging than traditional orthosteric drug discovery due to difficulties associated with determining the locations of allosteric sites and designing drugs based on these sites and the need for the allosteric effects to propagate through the structure, reach the ligand binding site and elicit a conformational change. In this study, we present computational tools ranging from the identification of potential allosteric sites to the design of "allosteric-like" modulator libraries. These tools may be particularly useful for allosteric drug discovery.

Using the NASTRAN Thermal Analyzer to simulate a flight scientific instrument package

NASA Technical Reports Server (NTRS)

Lee, H.-P.; Jackson, C. E., Jr.

1974-01-01

The NASTRAN Thermal Analyzer has proven to be a unique and useful tool for thermal analyses involving large and complex structures where small, thermally induced deformations are critical. Among its major advantages are direct grid point-to-grid point compatibility with large structural models; plots of the model that may be generated for both conduction and boundary elements; versatility of applying transient thermal loads especially to repeat orbital cycles; on-line printer plotting of temperatures and rate of temperature changes as a function of time; and direct matrix input to solve linear differential equations on-line. These features provide a flexibility far beyond that available in most finite-difference thermal analysis computer programs.

Characterizing TPS Microstructure: A Review of Some techniques

NASA Technical Reports Server (NTRS)

Gasch, Matthew; Stackpole, Mairead; Agrawal, Parul; Chavez-Garcie, Jose

2011-01-01

I. When seeking to understand ablator microstructure and morphology there are several useful techniques A. SEM 1) Visual characteriza3on at various length scales. 2) Chemical mapping by backscatter or x-ray highlights areas of interest. 3) Combined with other techniques (density, weight change, chemical analysis) SEM is a powerful tool to aid in explaining thermo/structural data. B. ASAP. 1) Chemical characteriza3on at various length scales. 2) Chemical mapping of pore structure by gas adsorption. 3) Provides a map of pore size vs. pore volume. 4) Provided surface area of exposed TPS. II. Both methods help characterize and understand how ablators react with other chemical species and provides insight into how they oxidize.

Fluorescent probes for exploring plant cell wall deconstruction: a review.

PubMed

Paës, Gabriel

2014-07-03

Plant biomass is a potential resource of chemicals, new materials and biofuels that could reduce our dependency on fossil carbon, thus decreasing the greenhouse effect. However, due to its chemical and structural complexity, plant biomass is recalcitrant to green biological transformation by enzymes, preventing the establishment of integrated bio-refineries. In order to gain more knowledge in the architecture of plant cell wall to facilitate their deconstruction, many fluorescent probes bearing various fluorophores have been devised and used successfully to reveal the changes in structural motifs during plant biomass deconstruction, and the molecular interactions between enzymes and plant cell wall polymers. Fluorescent probes are thus relevant tools to explore plant cell wall deconstruction.

Human factors in operations design

NASA Technical Reports Server (NTRS)

Chafin, R. L.

1982-01-01

The manner in which organizations develop their organizational structure is considered, taking into account an example in which the environment changes for an older organization. In such cases, it would be preferable to have some theoretical foundation on which to base the restructuring of the organization to meet new environmental needs. A description is given of a theoretic foundation based on the principles of Differentiation/Integration and Procedural/Knowledge based operations. The organizational design principle of Differentiation and Integration has been presented by Lawrence and Lorsch (1969). The differentiation/integration processes are related to the organizational structures presented in studies concerning NASA Deep Space Network (DSN) operations. The principles presented provide valuable tools for analyzing operations organization.

Early changes in coronary artery wall structure detected by microcomputed tomography in experimental hypercholesterolemia.

PubMed

Zhu, Xiang-Yang; Bentley, Michael D; Chade, Alejandro R; Ritman, Erik L; Lerman, Amir; Lerman, Lilach O

2007-09-01

Changes in the structure of the artery wall commence shortly after exposure to cardiovascular risk factors, such as hypercholesterolemia (HC), but may be difficult to detect. The ability to study vascular wall structure could be helpful in evaluation of the factors that instigate atherosclerosis and its pathomechanisms. The present study tested the hypothesis that early morphological changes in coronary arteries of hypercholesterolemic (HC) pigs can be detected using the novel X-ray contrast agent OsO(4) and three-dimensional micro-computed tomography (CT). Two groups of pigs were studied after they were fed a normal or an HC (2% cholesterol) diet for 12 wk. Hearts were harvested, coronary arteries were injected with 1% OsO(4) solution, and cardiac samples (6-mum-thick) were scanned by micro-CT. Layers of the epicardial coronary artery wall, early lesions, and perivascular OsO(4) accumulation were determined. Leakage of OsO(4) from myocardial microvessels was used to assess vascular permeability, which was correlated with immunoreactivity of vascular endothelial growth factor in corresponding histological cross sections. OsO(4) enhanced the visualization of coronary artery wall layers and facilitated detection of early lesions in HC in longitudinal tomographic sections of vascular segments. Increased density of perivascular OsO(4) in HC was correlated with increased vascular endothelial growth factor expression and suggested increased microvascular permeability. The use of OsO(4) as a contrast agent in micro-CT allows three-dimensional visualization of coronary artery wall structure, early lesion formation, and changes in vascular permeability. Therefore, this technique can be a useful tool in atherosclerosis research.

Scientific developments ISFD3

USGS Publications Warehouse

Schropp, M.H.I.; Soong, T.W.

2006-01-01

Highlights, trends, and consensus from the 63 papers submitted to the Scientific Developments theme of the Third International Symposium on Flood Defence (ISFD) are presented. Realizing that absolute protection against flooding can never be guaranteed, trends in flood management have shifted: (1) from flood protection to flood-risk management, (2) from reinforcing structural protection to lowering flood levels, and (3) to sustainable management through integrated problem solving. Improved understanding of watershed responses, climate changes, applications of GIS and remote-sensing technologies, and advanced analytical tools appeared to be the driving forces for renewing flood-risk management strategies. Technical competence in integrating analytical tools to form the basin wide management systems are demonstrated by several large, transnation models. However, analyses from social-economic-environmental points of view are found lag in general. ?? 2006 Taylor & Francis Group.

Natural Products in the Discovery of Agrochemicals.

PubMed

Loiseleur, Olivier

2017-12-01

Natural products have a long history of being used as, or serving as inspiration for, novel crop protection agents. Many of the discoveries in agrochemical research in the last decades have their origin in a wide range of natural products from a variety of sources. In light of the continuing need for new tools to address an ever-changing array of fungal, weed and insect pests, new agricultural practices and evolving regulatory requirements, the needs for new agrochemical tools remains as critical as ever. In that respect, nature continues to be an important source for novel chemical structures and biological mechanisms to be applied for the development of pest control agents. Here we review several of the natural products and their derivatives which contributed to shape crop protection research in past and present.

Influence of tool shape on lattice rearrangement under loading conditions reproducing friction stir welding

NASA Astrophysics Data System (ADS)

Konovalenko, Ivan S.; Konovalenko, Igor S.

2015-10-01

Metal behavior under loading conditions that reproduce friction stir welding was studied on the atomic scale. Calculations were conducted based on molecular dynamics simulation with potentials calculated within the embedded atom method. The loading of the interface between two crystallites, whose structure corresponded to aluminum alloy 2024, was simulated by the motion of a cone-shaped tool along the interface with constant angular and translational velocities. The motion of the rotating tool causes fracture of the workpiece crystal structure with subsequent mixing of surface atoms of the interfacing crystallites. It is shown that the resistance force acting on the moving tool from the workpiece and the process of structural defect formation in the workpiece depend on the tool shape.