Declining Financial Capacity in Mild Cognitive Impairment: A Six-Year Longitudinal Study.

PubMed

Martin, Roy C; Gerstenecker, Adam; Triebel, Kristen L; Falola, Michael; McPherson, Tarrant; Cutter, Gary; Marson, Daniel C

2018-03-31

To investigate financial skill decline over a 6-year period in persons with mild cognitive impairment (MCI) presumed due to Alzheimer's disease (AD). Study participants were cognitively normal (CN) older adults (n = 82) and adults with MCI (n = 91) based on consensus conference diagnosis. Participants completed baseline and up to six annual follow-up assessments that included standardized financial skills measurement (Financial Capacity Instrument; FCI; nine FCI domain and two global scores). We examined FCI change over time using mixed-model repeated measures analysis adjusted for baseline age and follow-up duration. At baseline, the CN group performed better than the MCI group across both global and seven domain scores. Group × Time interaction effects (all p's <.02) were found for all global and domain scores. The largest interaction effects were observed for complex domains of Financial Conceptual Knowledge, Checkbook Management, Bank Statement Management, and Bill Payment (all p's <.0001). Annualized decline in the MCI group's global scores, calculated in relation to CN group performance, was 10-17% over the initial 3-year time span and 22-24% at 6 years. Decline in FCI domain scores ranged from 6% (Knowledge of Assets/Estate) to 22% (Investment Decision-Making) at 3 year follow-up, and from 15% (Basic Monetary Skills) to 37% (Financial Judgment) at 6 year follow-up. Over a 6-year period, persons with MCI demonstrated significant declines in multiple financial skills and in particular financial judgment. The findings highlight the importance of ongoing oversight by family members and clinicians of financial skills and activities in persons with MCI.

Cluster decomposition of full configuration interaction wave functions: A tool for chemical interpretation of systems with strong correlation

NASA Astrophysics Data System (ADS)

Lehtola, Susi; Tubman, Norm M.; Whaley, K. Birgitta; Head-Gordon, Martin

2017-10-01

Approximate full configuration interaction (FCI) calculations have recently become tractable for systems of unforeseen size, thanks to stochastic and adaptive approximations to the exponentially scaling FCI problem. The result of an FCI calculation is a weighted set of electronic configurations, which can also be expressed in terms of excitations from a reference configuration. The excitation amplitudes contain information on the complexity of the electronic wave function, but this information is contaminated by contributions from disconnected excitations, i.e., those excitations that are just products of independent lower-level excitations. The unwanted contributions can be removed via a cluster decomposition procedure, making it possible to examine the importance of connected excitations in complicated multireference molecules which are outside the reach of conventional algorithms. We present an implementation of the cluster decomposition analysis and apply it to both true FCI wave functions, as well as wave functions generated from the adaptive sampling CI algorithm. The cluster decomposition is useful for interpreting calculations in chemical studies, as a diagnostic for the convergence of various excitation manifolds, as well as as a guidepost for polynomially scaling electronic structure models. Applications are presented for (i) the double dissociation of water, (ii) the carbon dimer, (iii) the π space of polyacenes, and (iv) the chromium dimer. While the cluster amplitudes exhibit rapid decay with an increasing rank for the first three systems, even connected octuple excitations still appear important in Cr2, suggesting that spin-restricted single-reference coupled-cluster approaches may not be tractable for some problems in transition metal chemistry.

Using the method of dominant incorrect answers with the FCI test to diagnose misconceptions held by first year college students

NASA Astrophysics Data System (ADS)

Bani-Salameh, Hisham N.

2017-01-01

We started this work with the goal of detecting misconceptions held by our students about force and motion. A total of 341 students participated in this study by taking the force concept inventory (FCI) test both before and after receiving instructions about force or motion. The data from this study were analysed using different statistical techniques with results from frequencies and the dominant incorrect answer reported in this paper. All misconceptions reported in the original paper of the designers of the FCI test (Hestenes et al 1992 Phys. Teach. 30 141-58) were examined and the results are reported. Only pre test results are reported in this paper leaving post data for future work. We used the modified version of the FCI containing 30 questions and therefore used the revised list of misconceptions. Problems with impetus and active force are among the most dominant ones found with the full list reported in this paper.

Using the Method of Dominant Incorrect Answers with the FCI Test to Diagnose Misconceptions Held by First Year College Students

ERIC Educational Resources Information Center

Bani-Salameh, Hisham N.

2017-01-01

We started this work with the goal of detecting misconceptions held by our students about force and motion. A total of 341 students participated in this study by taking the force concept inventory (FCI) test both before and after receiving instructions about force or motion. The data from this study were analysed using different statistical…

Gender fairness within the Force Concept Inventory

NASA Astrophysics Data System (ADS)

Traxler, Adrienne; Henderson, Rachel; Stewart, John; Stewart, Gay; Papak, Alexis; Lindell, Rebecca

2018-01-01

Research on the test structure of the Force Concept Inventory (FCI) has largely ignored gender, and research on FCI gender effects (often reported as "gender gaps") has seldom interrogated the structure of the test. These rarely crossed streams of research leave open the possibility that the FCI may not be structurally valid across genders, particularly since many reported results come from calculus-based courses where 75% or more of the students are men. We examine the FCI considering both psychometrics and gender disaggregation (while acknowledging this as a binary simplification), and find several problematic questions whose removal decreases the apparent gender gap. We analyze three samples (total Npre=5391 , Npost=5769 ) looking for gender asymmetries using classical test theory, item response theory, and differential item functioning. The combination of these methods highlights six items that appear substantially unfair to women and two items biased in favor of women. No single physical concept or prior experience unifies these questions, but they are broadly consistent with problematic items identified in previous research. Removing all significantly gender-unfair items halves the gender gap in the main sample in this study. We recommend that instructors using the FCI report the reduced-instrument score as well as the 30-item score, and that credit or other benefits to students not be assigned using the biased items.

Standardized Testing in Physics via the World Wide Web.

ERIC Educational Resources Information Center

MacIsaac, Dan; Cole, Rebecca Pollard; Cole, David M.; McCullough, Laura; Maxka, Jim

2002-01-01

Examines the differences in paper-based and web-based administrations of a commonly used assessment instrument, the Force Concept Inventory (FCI). Results demonstrated no appreciable difference on FCI scores or FCI items based on the type of administration. Concludes that the web-based administration of the FCI appears to be as efficacious as the…

Quantum computing applied to calculations of molecular energies: CH2 benchmark.

PubMed

Veis, Libor; Pittner, Jiří

2010-11-21

Quantum computers are appealing for their ability to solve some tasks much faster than their classical counterparts. It was shown in [Aspuru-Guzik et al., Science 309, 1704 (2005)] that they, if available, would be able to perform the full configuration interaction (FCI) energy calculations with a polynomial scaling. This is in contrast to conventional computers where FCI scales exponentially. We have developed a code for simulation of quantum computers and implemented our version of the quantum FCI algorithm. We provide a detailed description of this algorithm and the results of the assessment of its performance on the four lowest lying electronic states of CH(2) molecule. This molecule was chosen as a benchmark, since its two lowest lying (1)A(1) states exhibit a multireference character at the equilibrium geometry. It has been shown that with a suitably chosen initial state of the quantum register, one is able to achieve the probability amplification regime of the iterative phase estimation algorithm even in this case.

Examining gender differences on FCI performance in algebra and calculus based physics courses

NASA Astrophysics Data System (ADS)

Kreutzer, Kimberley; Boudreaux, Andrew

2009-05-01

The Force Concept Inventory (FCI) has been widely used to asses student understanding of Newtonian principles. Studies have shown a marked difference in the performance of men and women on both pre- and post-tests [1,2] and also indicate that experiential based instruction may lead to a reduction in this gender gap [1,3]. This poster presents FCI data collected at Western Washington University. Initial analysis of gender differences are consistent with those reported nationally. We also discuss factors that may contribute to the differences in performance and propose instructional strategies that are designed to address the gender gap. [4pt] [1] M. Lorenzo, et. al., ``Reducing the gender gap in the physics classroom,'' AJP 74(2), 118-122 (2006) [0pt] [2] J. Docktor and K. Heller, ``Gender Differences in Both Force Concept Inventory and Introductory Physics Performance,'' Proceedings at the 2008 PERC [0pt] [3] S. Pollack, et. al., ``Reducing the gender gap in the physics classroom: How sufficient is interactive engagement?'' PRST-PER 3 (2007)

78 FR 39772 - Huntingdon County Site, FCI USA, LLC, Americas Division, a Subsidiary of FCI SA, Including On...

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Iron chelated cyclic peptide, ferrichrysin, for oral treatment of iron deficiency: solution properties and efficacy in anemic rats.

PubMed

Suzuki, Sachiko; Fukuda, Katsuharu; Irie, Motoko; Hata, Yoji

2007-01-01

Ferrichrysin (Fcy), which is produced by Aspergillus oryzae and is present in foods used for human consumption, belongs to a group of hydroxamate siderophore ferric iron chelators. Fcy (100 mg/mL) dissolves completely at both pH 2.0 and 7.0, being very stable at a wide range of pH, high temperatures and pressures, with little reactivity to dietary iron absorption inhibitors, phytic acid, tannic acid, and catechin. We studied the effect of Fcy in male Sprague-Dawley rats with iron-deficiency anemia, which were separated into three different dietary groups (n=5) and supplementing diets as follows: (i) ferric citrate, (ii) heme iron concentrate, and (iii) Fcy (35 mg Fe/kg diet) for three weeks. Fcy exhibited the same beneficial effect in improving iron deficiency anemia as ferric citrate, being significantly greater than the effect of heme iron. The iron concentration of liver in the Fcy group was 35% greater than that in the ferric citrate group. These findings indicate that Fcy could be an efficient oral iron supplement to prevent or treat iron deficiency.

Using a psychometric lens to examine gender differences on the FCI

NASA Astrophysics Data System (ADS)

Lindell, Rebecca; Papak, Alexis; Stewart, John; Traxler, Adrienne

2017-01-01

Multiple research studies show that there appears to be an inherent difference between male and female students' performance on the Force Concept Inventory (FCI). Unlike these studies, we chose to create two different samples, one with only female students and the other with only male students, to reduce the effects of the gender-imbalance inherent in a single sample of all physics students. Using a psychometric lens, we evaluate the differences between the male and female students' performance on the FCI. We utilized classical test theory to flag 13 items on the FCI that were poorly functioning for female students. Notably, most of these items were not flagged when the dataset was aggregated across genders. In the next stage of the research, we utilized Item Response Theory (IRT) to discover if the remaining 17 items on the FCI are also poorly functioning for female students. By eliminating the poorly functioning items on the FCI, we further examined the gender difference of the Force Concept Inventory.

Dual-energy-X-ray imaging to measure phase volume fractions in a transient multiphase flow

NASA Astrophysics Data System (ADS)

Loewen, Eric Paul

1999-12-01

The objective of this research was to visualize the pre-mixing phase of a fuel-coolant interaction (FCI) by using combinations of high-speed cinematography and dual energy X-ray imaging to identify and quantify the spatial and temporal characteristics of the three FCI phases---metal (fuel), liquid (coolant water), and voids (generated steam). (1) The high-speed cinematography imaging subsystem and the low-energy X-ray imaging subsystem provided visual photographs and distinguished generated voids from water. (2) The high-energy X-Ray imaging subsystem provided additional discernment of metal from water and vapor. This is the first time that dynamic dual X-ray images have been provided with quantitative results. The data provide new information concerning the melt fractions, melt jet configuration, melt jet velocity, and qualitative spatial and temporal quantification of the pre-mixing event. This information provides new insight into the FCI phenomenon that could not have been deduced from visible-light imaging or other instrumentation such as thermocouples, void sensors, or pressure transmitters. Significant findings include: (1) the fuel column (molten Pb jet) penetrated deeply (<7 cm) into the coolant (water) while maintaining its columnar shape. (2) Energetic FCIs occurred (and were imaged) below the melt-coolant interface temperature equal to the homogenous nucleation temperature (310°C). (3) The molten jet breakup was observed to be caused by hydrodynamic forces. (4) The Pb/water thermal interaction zone was imaged over melt temperatures from 330°C to 640°C and coolant subcooling of 4°C to 80°C. (5) The interface regions between the molten Pb and coolant was observed to grow with decreasing coolant subcooling. This imaging process can be applied to further study of the FCI phenomena at other test facilities. It can also be applied for observation of other two- or three-phase flow phenomena previously opaque to conventional imaging systems.

Analyzing force concept inventory with item response theory

NASA Astrophysics Data System (ADS)

Wang, Jing; Bao, Lei

2010-10-01

Item response theory is a popular assessment method used in education. It rests on the assumption of a probability framework that relates students' innate ability and their performance on test questions. Item response theory transforms students' raw test scores into a scaled proficiency score, which can be used to compare results obtained with different test questions. The scaled score also addresses the issues of ceiling effects and guessing, which commonly exist in quantitative assessment. We used item response theory to analyze the force concept inventory (FCI). Our results show that item response theory can be useful for analyzing physics concept surveys such as the FCI and produces results about the individual questions and student performance that are beyond the capability of classical statistics. The theory yields detailed measurement parameters regarding the difficulty, discrimination features, and probability of correct guess for each of the FCI questions.

Force Concept Inventory-based multiple-choice test for investigating students' representational consistency

NASA Astrophysics Data System (ADS)

Nieminen, Pasi; Savinainen, Antti; Viiri, Jouni

2010-07-01

This study investigates students’ ability to interpret multiple representations consistently (i.e., representational consistency) in the context of the force concept. For this purpose we developed the Representational Variant of the Force Concept Inventory (R-FCI), which makes use of nine items from the 1995 version of the Force Concept Inventory (FCI). These original FCI items were redesigned using various representations (such as motion map, vectorial and graphical), yielding 27 multiple-choice items concerning four central concepts underpinning the force concept: Newton’s first, second, and third laws, and gravitation. We provide some evidence for the validity and reliability of the R-FCI; this analysis is limited to the student population of one Finnish high school. The students took the R-FCI at the beginning and at the end of their first high school physics course. We found that students’ (n=168) representational consistency (whether scientifically correct or not) varied considerably depending on the concept. On average, representational consistency and scientifically correct understanding increased during the instruction, although in the post-test only a few students performed consistently both in terms of representations and scientifically correct understanding. We also compared students’ (n=87) results of the R-FCI and the FCI, and found that they correlated quite well.

Gender Fairness within the Force Concept Inventory

ERIC Educational Resources Information Center

Traxler, Adrienne; Henderson, Rachel; Stewart, John; Stewart, Gay; Papak, Alexis; Lindell, Rebecca

2018-01-01

Research on the test structure of the Force Concept Inventory (FCI) has largely ignored gender, and research on FCI gender effects (often reported as "gender gaps") has seldom interrogated the structure of the test. These rarely crossed streams of research leave open the possibility that the FCI may not be structurally valid across…

A Comparison of Paper-Based and Web-Based Testing.

ERIC Educational Resources Information Center

Cole, Rebecca Pollard; MacIsaac, Dan; Cole, David M.

The purpose of this study (1,313 college student participants) was to examine the differences in paper-based and Web-based administrations of a commonly used assessment instrument, the Force Concept Inventory (FCI) (D. Hestenes, M. Wells, and G. Swackhamer, 1992). Results demonstrated no appreciable difference on FCI scores or FCI items based on…

Dirichlet boundary conditions for arbitrary-shaped boundaries in stellarator-like magnetic fields for the Flux-Coordinate Independent method

NASA Astrophysics Data System (ADS)

Hill, Peter; Shanahan, Brendan; Dudson, Ben

2017-04-01

We present a technique for handling Dirichlet boundary conditions with the Flux Coordinate Independent (FCI) parallel derivative operator with arbitrary-shaped material geometry in general 3D magnetic fields. The FCI method constructs a finite difference scheme for ∇∥ by following field lines between poloidal planes and interpolating within planes. Doing so removes the need for field-aligned coordinate systems that suffer from singularities in the metric tensor at null points in the magnetic field (or equivalently, when q → ∞). One cost of this method is that as the field lines are not on the mesh, they may leave the domain at any point between neighbouring planes, complicating the application of boundary conditions. The Leg Value Fill (LVF) boundary condition scheme presented here involves an extrapolation/interpolation of the boundary value onto the field line end point. The usual finite difference scheme can then be used unmodified. We implement the LVF scheme in BOUT++ and use the Method of Manufactured Solutions to verify the implementation in a rectangular domain, and show that it does not modify the error scaling of the finite difference scheme. The use of LVF for arbitrary wall geometry is outlined. We also demonstrate the feasibility of using the FCI approach in no n-axisymmetric configurations for a simple diffusion model in a "straight stellarator" magnetic field. A Gaussian blob diffuses along the field lines, tracing out flux surfaces. Dirichlet boundary conditions impose a last closed flux surface (LCFS) that confines the density. Including a poloidal limiter moves the LCFS to a smaller radius. The expected scaling of the numerical perpendicular diffusion, which is a consequence of the FCI method, in stellarator-like geometry is recovered. A novel technique for increasing the parallel resolution during post-processing, in order to reduce artefacts in visualisations, is described.

Pair 2-electron reduced density matrix theory using localized orbitals

NASA Astrophysics Data System (ADS)

Head-Marsden, Kade; Mazziotti, David A.

2017-08-01

Full configuration interaction (FCI) restricted to a pairing space yields size-extensive correlation energies but its cost scales exponentially with molecular size. Restricting the variational two-electron reduced-density-matrix (2-RDM) method to represent the same pairing space yields an accurate lower bound to the pair FCI energy at a mean-field-like computational scaling of O (r3) where r is the number of orbitals. In this paper, we show that localized molecular orbitals can be employed to generate an efficient, approximately size-extensive pair 2-RDM method. The use of localized orbitals eliminates the substantial cost of optimizing iteratively the orbitals defining the pairing space without compromising accuracy. In contrast to the localized orbitals, the use of canonical Hartree-Fock molecular orbitals is shown to be both inaccurate and non-size-extensive. The pair 2-RDM has the flexibility to describe the spectra of one-electron RDM occupation numbers from all quantum states that are invariant to time-reversal symmetry. Applications are made to hydrogen chains and their dissociation, n-acene from naphthalene through octacene, and cadmium telluride 2-, 3-, and 4-unit polymers. For the hydrogen chains, the pair 2-RDM method recovers the majority of the energy obtained from similar calculations that iteratively optimize the orbitals. The localized-orbital pair 2-RDM method with its mean-field-like computational scaling and its ability to describe multi-reference correlation has important applications to a range of strongly correlated phenomena in chemistry and physics.

78 FR 37790 - In the Matter of: Mario Salinas-Lucio, Inmate Number #61687-279, FCI La Tuna, Federal Corrections...

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... DEPARTMENT OF COMMERCE Bureau of Industry and Security In the Matter of: Mario Salinas-Lucio, Inmate Number 61687-279, FCI La Tuna, Federal Corrections Institution, Federal Satellite Low, P.O. Box... Salinas-Lucio, with a last known address at: Inmate Number 61687-279, FCI La Tuna, Federal Corrections...

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2013-12-19

... DEPARTMENT OF COMMERCE Bureau of Industry and Security Igor Bobel, Inmate -67253-066, FCI Loretto, Federal Correctional Institution, P.O. Box 1000, Loretto, PA 15940; Order Denying Export Privileges On May... a last known address at: Inmate -67253-066, FCI Loretto, Federal Correctional Institution, P.O. Box...

Patterns of Incorrect Responses on the FCI and Course Success

NASA Astrophysics Data System (ADS)

Wells, James; Mokaya, Fridah; Valente, Diego

The Force Concept Inventory (FCI) is often used to measure the effectiveness of instructional pedagogy in introductory physics courses both at the algebra- and calculus-based level. Scores on the FCI are correlated with the performance of students in a class, as measured by their final course grade. We have collected data from several semesters of first-semester introductory mechanics courses at a public 4-year university, taught in large-scale classrooms with pedagogy including elements of Just-in-Time Teaching pedagogy along with active learning course components. The data collected includes pre- and post-test FCI scores, midterm exam grades, and final course grades. We examine whether certain patterns of incorrect answers on the FCI post-test are predictive of course grades, indicating whether certain specific student preconceptions are more detrimental than others to the success of students in an introductory mechanics course. Funding from UConn - College of Liberal Arts and Sciences (CLAS).

FINANCIAL CAPACITY OF OLDER AFRICAN AMERICANS WITH AMNESTIC MILD COGNITIVE IMPAIRMENT

PubMed Central

Triebel, Kristen L.; Okonkwo, Ozioma C.; Martin, Roy; Griffith, H. Randall; Crowther, Martha; Marson, Daniel C.

2010-01-01

This study investigated financial abilities of 154 patients with mild cognitive impairment (MCI) (116 Caucasian, 38 African American) using the Financial Capacity Instrument (FCI). In a series of linear regression models, we examined the effect of race on FCI performance and identified preliminary predictor variables that mediated observed racial differences on the FCI. Prior/premorbid abilities were identified. Predictor variables examined in the models included race and other demographic factors (age, education, gender), performance on global cognitive measures (MMSE, DRS-2 Total Score), history of cardiovascular disease (hypertension, diabetes, hypercholesterolemia), and a measure of educational achievement (WRAT-3 Arithmetic). African American patients with MCI performed below Caucasian patients with MCI on six of the seven FCI domains examined and on the FCI total score. WRAT-3 Arithmetic emerged as a partial mediator of group differences on the FCI, accounting for 54% of variance. In contrast, performance on global cognitive measures and history of cardiovascular disease only accounted for 14% and 2%, respectively, of the variance. Racial disparities in financial capacity appear to exist among patients with amnestic MCI. Basic academic math skills related to educational opportunity and quality of education account for a substantial proportion of the group difference in financial performance. PMID:20625268

Financial capacity of older African Americans with amnestic mild cognitive impairment.

PubMed

Triebel, Kristen L; Okonkwo, Ozioma C; Martin, Roy; Griffith, Henry Randall; Crowther, Martha; Marson, Daniel C

2010-01-01

This study investigated financial abilities of 154 patients with mild cognitive impairment (MCI) (116 white, 38 African American) using the Financial Capacity Instrument (FCI). In a series of linear regression models, we examined the effect of race on FCI performance and identified preliminary predictor variables that mediated observed racial differences on the FCI. Prior/premorbid abilities were identified. Predictor variables examined in the models included race and other demographic factors (age, education, sex), performance on global cognitive measures (MMSE, DRS-2 Total Score), history of cardiovascular disease (hypertension, diabetes, hypercholesterolemia), and a measure of educational achievement (WRAT-3 Arithmetic). African American patients with MCI performed below white patients with MCI on 6 of the 7 FCI domains examined and on the FCI total score. WRAT-3 Arithmetic emerged as a partial mediator of group differences on the FCI, accounting for 54% of variance. In contrast, performance on global cognitive measures and history of cardiovascular disease only accounted for 14% and 2%, respectively, of the variance. Racial disparities in financial capacity seem to exist among patients with amnestic MCI. Basic academic math skills related to educational opportunity and quality of education account for a substantial proportion of the group difference in financial performance.

Cookbook Procedures in MBL Physics Exercises.

ERIC Educational Resources Information Center

Royuk, Brent; Brooks, David W.

2003-01-01

Presents results of a controlled experiment comparing the conceptual mechanics learning gains as measured by the Force Concept Inventory (FCI) between two laboratory groups. One group completed cookbook labs while the other completed Interactive-Engagement (IE) labs in RealTime Physics. Suggests that laboratory activities should engage students in…

Dividing the Force Concept Inventory into two equivalent half-length tests

NASA Astrophysics Data System (ADS)

Han, Jing; Bao, Lei; Chen, Li; Cai, Tianfang; Pi, Yuan; Zhou, Shaona; Tu, Yan; Koenig, Kathleen

2015-06-01

The Force Concept Inventory (FCI) is a 30-question multiple-choice assessment that has been a building block for much of the physics education research done today. In practice, there are often concerns regarding the length of the test and possible test-retest effects. Since many studies in the literature use the mean score of the FCI as the primary variable, it would be useful then to have different shorter tests that can produce FCI-equivalent scores while providing the benefits of being quicker to administer and overcoming the test-retest effects. In this study, we divide the 1995 version of the FCI into two half-length tests; each contains a different subset of the original FCI questions. The two new tests are shorter, still cover the same set of concepts, and produce mean scores equivalent to those of the FCI. Using a large quantitative data set collected at a large midwestern university, we statistically compare the assessment features of the two half-length tests and the full-length FCI. The results show that the mean error of equivalent scores between any two of the three tests is within 3%. Scores from all tests are well correlated. Based on the analysis, it appears that the two half-length tests can be a viable option for score based assessment that need to administer tests quickly or need to measure short-term gains where using identical pre- and post-test questions is a concern.

The effects of modeling instruction on high school physics academic achievement

NASA Astrophysics Data System (ADS)

Wright, Tiffanie L.

The purpose of this study was to explore whether Modeling Instruction, compared to traditional lecturing, is an effective instructional method to promote academic achievement in selected high school physics classes at a rural middle Tennessee high school. This study used an ex post facto , quasi-experimental research methodology. The independent variables in this study were the instructional methods of teaching. The treatment variable was Modeling Instruction and the control variable was traditional lecture instruction. The Treatment Group consisted of participants in Physical World Concepts who received Modeling Instruction. The Control Group consisted of participants in Physical Science who received traditional lecture instruction. The dependent variable was gains scores on the Force Concepts Inventory (FCI). The participants for this study were 133 students each in both the Treatment and Control Groups (n = 266), who attended a public, high school in rural middle Tennessee. The participants were administered the Force Concepts Inventory (FCI) prior to being taught the mechanics of physics. The FCI data were entered into the computer-based Statistical Package for the Social Science (SPSS). Two independent samples t-tests were conducted to answer the research questions. There was a statistically significant difference between the treatment and control groups concerning the instructional method. Modeling Instructional methods were found to be effective in increasing the academic achievement of students in high school physics. There was no statistically significant difference between FCI gains scores for gender. Gender was found to have no effect on the academic achievement of students in high school physics classes. However, even though there was not a statistically significant difference, female students' gains scores were higher than male students' gains scores when Modeling Instructional methods of teaching were used. Based on these findings, it is recommended that high school science teachers should use Modeling Instructional methods of teaching daily in their classrooms. A recommendation for further research is to expand the Modeling Instructional methods of teaching into different content areas, (i.e., reading and language arts) to explore academic achievement gains.

Detecting and Reducing Science Teacher Candidate’s (STC) Misconception About Motion and Force By Using Force Concept Inventory (FCI) and problem Based Learning (PBL)

NASA Astrophysics Data System (ADS)

Oktarisa, Y.; Utami, I. S.; Denny, Y. R.

2017-02-01

This study has been done to 34 science teacher candidates of Teachers’ Training and Education Faculty of Sultan Ageng Tirtayasa University at their first year of study during 2015-2016 school years. This research focused on student’s misconception about motion and force and how Problem Based Learning (PBL) reducing it. Diagnostic test of misconception about motion and force has been detected by using Force Concept Inventory (FCI). FCI had been used in pretest and posttest, and to find the reducing of students’ misconception N-Gain pretest and posttest of each student had been calculated. Quasi experiment one group pretest and posttest had been used as the research method, and Problem Based Learning (PBL) used as the treatment of manipulation. After two weeks learning motion and force with PBL approach, N-gain which obtained prove that misconception about motion and force had been reducing.

Investigating Arabic to Speakers of Other Languages (ASOL) Lecturers' Attitudes towards Utilizing Flipped Classroom Instruction (FCI): A Qualitative Study at Jordanian Public Universities

ERIC Educational Resources Information Center

Al rababah, Ibraheem Hasan; Rababah, Luqman

2017-01-01

Although Flipped Classroom Instruction (FCI) is not a new concept, the practice is relatively new in the Arab region, especially, in Jordan, where the face-to face approach is still widely used. This qualitative study examined the attitudes of Arabic language lecturers at three Jordanian public universities towards utilizing FCI in their…

77 FR 19610 - Marc Knapp, Inmate #-06450-015, FCI Safford, P.O. Box 9000, Safford, AZ 85548; Order Denying...

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... DEPARTMENT OF COMMERCE Bureau of Industry and Security Marc Knapp, Inmate --06450-015, FCI Safford, P.O. Box 9000, Safford, AZ 85548; Order Denying Export Privileges On September 13, 2011, in the U.S..., with the last known address at: Inmate --06450-015, FCI Safford, P.O. Box 9000, Safford, AZ 85548, and...

Functional recovery patterns in seriously injured automotive crash victims.

PubMed

McMurry, Timothy L; Poplin, Gerald S; Crandall, Jeff

2016-09-01

The functional capacity index (FCI) is designed to predict functional loss 12 months post-injury for each injury in the 2008 Abbreviated Injury Scale (AIS) manual on a scale from 0 (death) to 100 (full recovery), but FCI has never been validated. This study compared FCI predicted loss with patient-reported 12-month outcomes as measured through the Short Form 36 (SF-36) health assessment survey. Using follow-up data collected on 2,858 adult car crash occupants in the Crash Injury Research and Engineering Network (CIREN) database, we compared FCI predicted outcomes to occupants' Physical Component Summary (PCS) scores, which are weighted averages of the SF-36 items addressing physical function. Our analyses included descriptive statistics, plots of typical recovery patterns, and a mixed effects regression model that describes PCS as a function of FCI, demographics, comorbidities, and injury pattern while also adjusting for the occupants' pre-crash physical capabilities. We further examined injuries in patients who report a significant drop in PCS 12 months post-crash despite being predicted to fully recover. At baseline, the CIREN population exhibited PCS scores similar to the overall population (mean = 51.1, SD = 10.3). Twelve months post-crash, occupants with predicted impairment (FCI < 100) report a substantial decrease in physical function, and those who were predicted to fully recover still report some, albeit less, impairment. In the multivariate mixed-effects regression model, FCI is a strongly significant (P-value <.0001) predictor of PCS, with each 1-point drop in FCI predicting a 0.27-point drop in PCS. Maximum AIS severities in the head, spine, and lower extremity body regions were also significantly associated with PCS (P-values <.05). Among occupants who were expected to fully recover but who report a significant drop in PCS at 12 months, spinal fractures without cord involvement account for 5 of the 10 most common AIS 2+ injuries. FCI was associated with 12-month outcomes but may not adequately describe the recovery from some head, spine, and lower extremity injuries. Some occupants who were expected to recover still report functional loss 12 months post-injury.

Current food chain information provides insufficient information for modern meat inspection of pigs.

PubMed

Felin, Elina; Jukola, Elias; Raulo, Saara; Heinonen, Jaakko; Fredriksson-Ahomaa, Maria

2016-05-01

Meat inspection now incorporates a more risk-based approach for protecting human health against meat-borne biological hazards. Official post-mortem meat inspection of pigs has shifted to visual meat inspection. The official veterinarian decides on additional post-mortem inspection procedures, such as incisions and palpations. The decision is based on declarations in the food chain information (FCI), ante-mortem inspection and post-mortem inspection. However, a smooth slaughter and inspection process is essential. Therefore, one should be able to assess prior to slaughter which pigs are suitable for visual meat inspection only, and which need more profound inspection procedures. This study evaluates the usability of the FCI provided by pig producers and considered the possibility for risk ranking of incoming slaughter batches according to the previous meat inspection data and the current FCI. Eighty-five slaughter batches comprising 8954 fattening pigs were randomly selected at a slaughterhouse that receives animals from across Finland. The mortality rate, the FCI and the meat inspection results for each batch were obtained. The current FCI alone provided insufficient and inaccurate information for risk ranking purposes for meat inspection. The partial condemnation rate for a batch was best predicted by the partial condemnation rate calculated for all the pigs sent for slaughter from the same holding in the previous year (p<0.001) and by prior information on cough declared in the current FCI (p=0.02) statement. Training and information to producers are needed to make the FCI reporting procedures more accurate. Historical meat inspection data on pigs slaughtered from the same holdings and well-chosen symptoms/signs for reporting, should be included in the FCI to facilitate the allocation of pigs for visual inspection. The introduced simple scoring system can be easily used for additional information for directing batches to appropriate meat inspection procedures. To control the main biological public health hazards related to pork, serological surveillance should be done and the information obtained from analyses should be used as part of the FCI. Copyright © 2016 Elsevier B.V. All rights reserved.

On the Use of Two Versions of the Force Concept Inventory to Test Conceptual Understanding of Mechanics in Lao PDR

ERIC Educational Resources Information Center

Luangrath, Phimpho; Pettersson, Sune; Benckert, Sylvia

2011-01-01

In this study, we investigated why Laotian students had a low score, when they were tested by the Force Concept Inventory (FCI). About 400 first year university students answered the FCI or a Lao version of the FCI (LFCI) with the contexts of some questions changed. The students answered a questionnaire and 34 of the students were interviewed. The…

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

Lan, Keng-Hsueh; Shih, Yi-Sheng; Chang, Cheng Allen

Highlights: Black-Right-Pointing-Pointer EGFR-expressing epithelial cancers account for significant portion of cancer deaths. Black-Right-Pointing-Pointer EGF-EGFR signaling pathway is validated as an important anticancer drug target. Black-Right-Pointing-Pointer EGF and Fcy fusion protein (Fcy-hEGF) can bind to EGFR and convert 5-FC to 5-FU. Black-Right-Pointing-Pointer Fcy-hEGF combined with 5-FC preferentially inhibits EGFR-expressing cells viability. -- Abstract: Human epithelial cancers account for approximately 50% of all cancer deaths. This type of cancer is characterized by excessive activation and expression of the epidermal growth factor receptor (EGFR). The EGFR pathway is critical for cancer cell proliferation, survival, metastasis and angiogenesis. The EGF-EGFR signaling pathway has beenmore » validated as an important anticancer drug target. Increasing numbers of targeted therapies against this pathway have been either approved or are currently under development. Here, we adopted a prodrug system that uses 5-fluorocytosine (5-FC) and human EGF (hEGF) fused with yeast cytosine deaminase (Fcy) to target EGFR-overexpressing cancer cells and to convert 5-FC to a significantly more toxic chemotherapeutic, 5-fluorouracil (5-FU). We cloned and purified the Fcy-hEGF fusion protein from Pichia pastoris yeast. This fusion protein specifically binds to EGFR with a similar affinity as hEGF, approximately 10 nM. Fcy-hEGF binds tightly to A431 and MDA-MB-468 cells, which overexpress EGFR, but it binds with a lower affinity to MDA-MB-231 and MCF-7, which express lower levels of EGFR. Similarly, the viability of EGFR-expressing cells was suppressed by Fcy-hEGF in the presence of increasing concentrations of 5-FC, and the IC{sub 50} values for A431 and MDA-MB-468 were approximately 10-fold lower than those of MDA-MB-231 and MCF-7. This novel prodrug system, Fcy-hEGF/5-FC, might represent a promising addition to the available class of inhibitors that specifically target EGFR-expressing cancers.« less

Accounting for the exact degeneracy and quasidegeneracy in the automerization of cyclobutadiene via multireference coupled-cluster methods.

PubMed

Li, Xiangzhu; Paldus, Josef

2009-09-21

The automerization of cyclobutadiene (CBD) is employed to test the performance of the reduced multireference (RMR) coupled-cluster (CC) method with singles and doubles (RMR CCSD) that employs a modest-size MR CISD wave function as an external source for the most important (primary) triples and quadruples in order to account for the nondynamic correlation effects in the presence of quasidegeneracy, as well as of its perturbatively corrected version accounting for the remaining (secondary) triples [RMR CCSD(T)]. The experimental results are compared with those obtained by the standard CCSD and CCSD(T) methods, by the state universal (SU) MR CCSD and its state selective or state specific (SS) version as formulated by Mukherjee et al. (SS MRCC or MkMRCC) and, wherever available, by the Brillouin-Wigner MRCC [MR BWCCSD(T)] method. Both restricted Hartree-Fock (RHF) and multiconfigurational self-consistent field (MCSCF) molecular orbitals are employed. For a smaller STO-3G basis set we also make a comparison with the exact full configuration interaction (FCI) results. Both fundamental vibrational energies-as obtained via the integral averaging method (IAM) that can handle anomalous potentials and automatically accounts for anharmonicity- and the CBD automerization barrier for the interconversion of the two rectangular structures are considered. It is shown that the RMR CCSD(T) potential has the smallest nonparallelism error relative to the FCI potential and the corresponding fundamental vibrational frequencies compare reasonably well with the experimental ones and are very close to those recently obtained by other authors. The effect of anharmonicity is assessed using the second-order perturbation theory (MP2). Finally, the invariance of the RMR CC methods with respect to orbital rotations is also examined.

Uncovering the Hidden Meaning of Cross-Curriculum Comparison Results on the Force Concept Inventory

ERIC Educational Resources Information Center

Ding, Lin; Caballero, Marcos D.

2014-01-01

In a recent study, Caballero and colleagues conducted a large-scale evaluation using the Force Concept Inventory (FCI) to compare student learning outcomes between two introductory physics curricula: the Matter and Interactions (M&I) mechanics course and a pedagogically-reformed-traditional-content (PRTC) mechanics course. Using a conventional…

Magnetic resonance imaging volume of the angular gyri predicts financial skill deficits in people with amnestic mild cognitive impairment.

PubMed

Griffith, H Randall; Stewart, Christopher C; Stoeckel, Luke E; Okonkwo, Ozioma C; den Hollander, Jan A; Martin, Roy C; Belue, Katherine; Copeland, Jacquelynn N; Harrell, Lindy E; Brockington, John C; Clark, David G; Marson, Daniel C

2010-02-01

To better understand how brain atrophy in amnestic mild cognitive impairment (MCI) as measured using magnetic resonance imaging (MRI) volumetrics could affect instrumental activities of daily living (IADLs) such as financial abilities. Controlled, matched-sample, cross-sectional analysis regressing MRI volumetrics with financial performance measures. University medical and research center. Thirty-eight people with MCI and 28 older adult controls. MRI volumetric measurement of the hippocampi, angular gyri, precunei, and medial frontal lobes. Participants also completed neuropsychological tests and the Financial Capacity Instrument (FCI). Correlations were performed between FCI scores and MRI volumes in the group with MCI. People with MCI performed significantly below controls on the FCI and had significantly smaller hippocampi. Among people with MCI, performance on the FCI was moderately correlated with angular gyri and precunei volumes. Regression models demonstrated that angular gyrus volumes were predictive of FCI scores. Tests of mediation showed that measures of arithmetic and possibly attention partially mediated the relationship between angular gyrus volume and FCI score. Impaired financial abilities in amnestic MCI correspond with volume of the angular gyri as mediated by arithmetic knowledge. The findings suggest that early neuropathology within the lateral parietal region in MCI leads to a breakdown of cognitive abilities that affect everyday financial skills. The findings have implications for diagnosis and clinical care of people with MCI and AD.

Analyzing false positives of four questions in the Force Concept Inventory

NASA Astrophysics Data System (ADS)

Yasuda, Jun-ichiro; Mae, Naohiro; Hull, Michael M.; Taniguchi, Masa-aki

2018-06-01

In this study, we analyze the systematic error from false positives of the Force Concept Inventory (FCI). We compare the systematic errors of question 6 (Q.6), Q.7, and Q.16, for which clearly erroneous reasoning has been found, with Q.5, for which clearly erroneous reasoning has not been found. We determine whether or not a correct response to a given FCI question is a false positive using subquestions. In addition to the 30 original questions, subquestions were introduced for Q.5, Q.6, Q.7, and Q.16. This modified version of the FCI was administered to 1145 university students in Japan from 2015 to 2017. In this paper, we discuss our finding that the systematic errors of Q.6, Q.7, and Q.16 are much larger than that of Q.5 for students with mid-level FCI scores. Furthermore, we find that, averaged over the data sample, the sum of the false positives from Q.5, Q.6, Q.7, and Q.16 is about 10% of the FCI score of a midlevel student.

Examining student performance in an introductory Physics for engineering course: A quantitative case study.

NASA Astrophysics Data System (ADS)

Valente, Diego; Savkar, Amit; Mokaya, Fridah; Wells, James

The Force Concept Inventory (FCI) has been analyzed and studied in various ways with regards to students' understanding of basic physics concepts. We present normalized learning gains and effect size calculations of FCI scores, taken in the context of large-scale classes in a 4-year public university and course instruction that incorporates elements of Just-In-Time teaching and active learning components. In addition, we will present here a novel way of using FCI pre- and post-test as a predictor of students' performance on midterm and final exams. Utilizing a taxonomy table of physics concepts, we will look at student performance broken down by topic, while also examining possible correlations between FCI post-test scores and other course assessments. College of Liberal Arts and Sciences (CLAS), UConn.

Confirmatory factor analysis applied to the Force Concept Inventory

NASA Astrophysics Data System (ADS)

Eaton, Philip; Willoughby, Shannon D.

2018-06-01

In 1995, Huffman and Heller used exploratory factor analysis to draw into question the factors of the Force Concept Inventory (FCI). Since then several papers have been published examining the factors of the FCI on larger sets of student responses and understandable factors were extracted as a result. However, none of these proposed factor models have been verified to not be unique to their original sample through the use of independent sets of data. This paper seeks to confirm the factor models proposed by Scott et al. in 2012, and Hestenes et al. in 1992, as well as another expert model proposed within this study through the use of confirmatory factor analysis (CFA) and a sample of 20 822 postinstruction student responses to the FCI. Upon application of CFA using the full sample, all three models were found to fit the data with acceptable global fit statistics. However, when CFA was performed using these models on smaller sample sizes the models proposed by Scott et al. and Eaton and Willoughby were found to be far more stable than the model proposed by Hestenes et al. The goodness of fit of these models to the data suggests that the FCI can be scored on factors that are not unique to a single class. These scores could then be used to comment on how instruction methods effect the performance of students along a single factor and more in-depth analyses of curriculum changes may be possible as a result.

Rasch model based analysis of the Force Concept Inventory

NASA Astrophysics Data System (ADS)

Planinic, Maja; Ivanjek, Lana; Susac, Ana

2010-06-01

The Force Concept Inventory (FCI) is an important diagnostic instrument which is widely used in the field of physics education research. It is therefore very important to evaluate and monitor its functioning using different tools for statistical analysis. One of such tools is the stochastic Rasch model, which enables construction of linear measures for persons and items from raw test scores and which can provide important insight in the structure and functioning of the test (how item difficulties are distributed within the test, how well the items fit the model, and how well the items work together to define the underlying construct). The data for the Rasch analysis come from the large-scale research conducted in 2006-07, which investigated Croatian high school students’ conceptual understanding of mechanics on a representative sample of 1676 students (age 17-18 years). The instrument used in research was the FCI. The average FCI score for the whole sample was found to be (27.7±0.4)% , indicating that most of the students were still non-Newtonians at the end of high school, despite the fact that physics is a compulsory subject in Croatian schools. The large set of obtained data was analyzed with the Rasch measurement computer software WINSTEPS 3.66. Since the FCI is routinely used as pretest and post-test on two very different types of population (non-Newtonian and predominantly Newtonian), an additional predominantly Newtonian sample ( N=141 , average FCI score of 64.5%) of first year students enrolled in introductory physics course at University of Zagreb was also analyzed. The Rasch model based analysis suggests that the FCI has succeeded in defining a sufficiently unidimensional construct for each population. The analysis of fit of data to the model found no grossly misfitting items which would degrade measurement. Some items with larger misfit and items with significantly different difficulties in the two samples of students do require further examination. The analysis revealed some problems with item distribution in the FCI and suggested that the FCI may function differently in non-Newtonian and predominantly Newtonian population. Some possible improvements of the test are suggested.

Declining financial capacity in mild cognitive impairment: A 1-year longitudinal study.

PubMed

Triebel, K L; Martin, R; Griffith, H R; Marceaux, J; Okonkwo, O C; Harrell, L; Clark, D; Brockington, J; Bartolucci, A; Marson, Daniel C

2009-09-22

To investigate 1-year change in financial capacity in relation to conversion from amnestic mild cognitive impairment (MCI) to dementia. Seventy-six cognitively healthy older controls, 25 patients with amnestic MCI who converted to Alzheimer-type dementia during the study period (MCI converters), and 62 patients with MCI who did not convert to dementia (MCI nonconverters) were administered the Financial Capacity Instrument (FCI) at baseline and 1-year follow-up. Performance on the FCI domain and global scores was compared within and between groups using multivariate repeated-measures analyses. At baseline, controls performed better than MCI converters and nonconverters on almost all FCI domains and on both FCI total scores. MCI converters performed below nonconverters on domains of financial concepts, cash transactions, bank statement management, and bill payment and on both FCI total scores. At 1-year follow-up, MCI converters showed significantly greater decline than controls and MCI nonconverters for the domain of checkbook management and for both FCI total scores. The domain of bank statement management showed a strong trend. For both the checkbook and bank statement domains, MCI converters showed declines in procedural skills, such as calculating the correct balance in a checkbook register, but not in conceptual understanding of a checkbook or a bank statement. Declining financial skills are detectable in patients with mild cognitive impairment (MCI) in the year before their conversion to Alzheimer disease. Clinicians should proactively monitor patients with MCI for declining financial skills and advise patients and families about appropriate interventions.

A Study of Impairing Injuries in Real World Crashes Using the Injury Impairment Scale (IIS) and the Predicted Functional Capacity Index (PFCI-AIS)

PubMed Central

Barnes, Jo; Morris, Andrew

2009-01-01

The ability to predict impairment outcomes in large databases using a simplified technique allows researchers to focus attention on preventing costly impairing injuries. The dilemma that exists for researchers is to determine which method is the most reliable and valid. This study examines available methods to predict impairment and explores the differences between the IIS and pFCI applied to real world crash injury data. Occupant injury data from the UK Co-operative Crash Injury Study (CCIS) database have been coded using AIS 1990 and AIS 2005. The data have subsequently been recoded using the associated impairment scales namely the Injury Impairment Scale (IIS) and the predicted Functional Capacity Index (pFCI) to determine the predicted impairment levels of injuries at one year post crash. Comparisons between the levels of impairment were made and any differences further explored. Injury data for the period February 2006 to September 2008 from the CCIS database were used in the analysis which involved a dataset of 2,437 occcupants who sustained over 8000 injuries. This study found some differences between the impairment scales for injuries coded to the AIS 1990 and AIS 2005 coding dictionaries. The pFCI predicts 31.5% of injuries to be impairing in AIS 2005, less than the IIS (38.5%) using AIS 1990. Using CCIS data the pFCI predicted that only 6% of the occupants with a coded injury would have an impairing injury compared to 24% of occupants using the IIS. The main body regions identified as having the major differences between the two impairment scales for car occupants were the head and spine. Follow up data were then used for a small number of cases (n=31, lower extremity and whiplash injuries) to examine any differences in predicted impairment versus perceived impairment. These data were selected from a previous study conducted between 2003 and 2006 and identified the discrepancy between predicted impairment and actual perceived impairment as defined by the participant. Overall the work highlights the variaton between the pFCI and IIS and emphasises the importance and need for a single validated impairment scale that can be universally applied. This would allow emphasis to be directed towards preventing injuries that are associated with the most significant impairment outcomes. PMID:20184844

A study of impairing injuries in real world crashes using the Injury Impairment Scale (IIS) and the predicted Functional Capacity Index (PFCI-AIS).

PubMed

Barnes, Jo; Morris, Andrew

2009-10-01

The ability to predict impairment outcomes in large databases using a simplified technique allows researchers to focus attention on preventing costly impairing injuries. The dilemma that exists for researchers is to determine which method is the most reliable and valid. This study examines available methods to predict impairment and explores the differences between the IIS and pFCI applied to real world crash injury data. Occupant injury data from the UK Co-operative Crash Injury Study (CCIS) database have been coded using AIS 1990 and AIS 2005. The data have subsequently been recoded using the associated impairment scales namely the Injury Impairment Scale (IIS) and the predicted Functional Capacity Index (pFCI) to determine the predicted impairment levels of injuries at one year post crash. Comparisons between the levels of impairment were made and any differences further explored. Injury data for the period February 2006 to September 2008 from the CCIS database were used in the analysis which involved a dataset of 2,437 occcupants who sustained over 8000 injuries. This study found some differences between the impairment scales for injuries coded to the AIS 1990 and AIS 2005 coding dictionaries. The pFCI predicts 31.5% of injuries to be impairing in AIS 2005, less than the IIS (38.5%) using AIS 1990. Using CCIS data the pFCI predicted that only 6% of the occupants with a coded injury would have an impairing injury compared to 24% of occupants using the IIS. The main body regions identified as having the major differences between the two impairment scales for car occupants were the head and spine. Follow up data were then used for a small number of cases (n=31, lower extremity and whiplash injuries) to examine any differences in predicted impairment versus perceived impairment. These data were selected from a previous study conducted between 2003 and 2006 and identified the discrepancy between predicted impairment and actual perceived impairment as defined by the participant. Overall the work highlights the variation between the pFCI and IIS and emphasises the importance and need for a single validated impairment scale that can be universally applied. This would allow emphasis to be directed towards preventing injuries that are associated with the most significant impairment outcomes.

Neurocognitive predictors of financial capacity in traumatic brain injury.

PubMed

Martin, Roy C; Triebel, Kristen; Dreer, Laura E; Novack, Thomas A; Turner, Crystal; Marson, Daniel C

2012-01-01

To develop cognitive models of financial capacity (FC) in patients with traumatic brain injury (TBI). Longitudinal design. Inpatient brain injury rehabilitation unit. Twenty healthy controls, and 24 adults with moderate-to-severe TBI were assessed at baseline (30 days postinjury) and 6 months postinjury. The FC instrument (FCI) and a neuropsychological test battery. Univariate correlation and multiple regression procedures were employed to develop cognitive models of FCI performance in the TBI group, at baseline and 6-month time follow-up. Three cognitive predictor models of FC were developed. At baseline, measures of mental arithmetic/working memory and immediate verbal memory predicted baseline FCI performance (R = 0.72). At 6-month follow-up, measures of executive function and mental arithmetic/working memory predicted 6-month FCI performance (R = 0.79), and a third model found that these 2 measures at baseline predicted 6-month FCI performance (R = 0.71). Multiple cognitive functions are associated with initial impairment and partial recovery of FC in moderate-to-severe TBI patients. In particular, arithmetic, working memory, and executive function skills appear critical to recovery of FC in TBI. The study results represent an initial step toward developing a neurocognitive model of FC in patients with TBI.

National Historic Preservation Act (NHPA) Section 106 Process: Florence Copper, Inc. (FCI)

EPA Pesticide Factsheets

Collection of National Historic Preservation Act (NHPA) documents relating to Public Notice of Intent to Issue a Class III Underground Injection Control Area Permit for Florence Copper, Inc. (FCI) - Florence, AZ (closed)

Secondary implementation of interactive engagement teaching techniques: Choices and challenges in a Gulf Arab context

NASA Astrophysics Data System (ADS)

Hitt, G. W.; Isakovic, A. F.; Fawwaz, O.; Bawa'aneh, M. S.; El-Kork, N.; Makkiyil, S.; Qattan, I. A.

2014-12-01

We report on efforts to design the "Collaborative Workshop Physics" (CWP) instructional strategy to deliver the first interactive engagement (IE) physics course at Khalifa University of Science, Technology and Research (KU), United Arab Emirates (UAE). To our knowledge, this work reports the first calculus-based, introductory mechanics course on the Arabian Peninsula using physics education research (PER)-based instruction. A brief history and present context of general university and STEM teaching in the UAE is given. We present this secondary implementation (SI) as a case study of a novel context and use it to determine if PER-based instruction can be successfully implemented far from the cultural context of the primary developer and, if so, how might such SIs differ from SIs within the United States (U.S.) in terms of criteria for and risks to their success. With these questions in view, a prereform baseline comprised of Maryland Physics Expectations in Physics survey, Force Concept Inventory (FCI), course exam grades, and English language proficiency data are used to design a hybrid implementation of Cooperative Group Problem Solving. We find that for students with high English proficiency, normalized gain on FCI improves substantially, from ⟨g⟩=0.16±0.10 prereform to ⟨g⟩=0.47±0.08 in the CWP pilot (standard errors), indicating a successful SI. However, we also find evidence that normalized gains on FCI are strongly modulated by language proficiency and discuss likely causes. Regardless of language ability, problem-solving skill is also substantially improved and course drop-fail-withdrawal rates are cut from 50% to 24%. In particular, we find evidence in postreform student interviews that prior classroom experiences, and not broader cultural expectations about education, are the more significant cause of expectations that are at odds with the classroom norms of well-functioning PER-based instruction. We present this result as evidence that PER-based innovations can be implemented across great changes in cultural context, provided that the method is thoughtfully adapted in anticipation of context and culture-specific student expectations. This case study should be valuable for future reforms at KU, the broader Gulf region, and other institutions facing similar challenges involving SI of PER-based instruction outside the U.S.

Evaluating learning and teaching using the Force Concept Inventory

NASA Astrophysics Data System (ADS)

Zitzewitz, Paul

1997-04-01

Teaching methods used in the calculus-based mechanics course for engineers and scientists (P150) at the University of Michigan-Dearborn were markedly changed in September, 1996. Lectures emphasize active learning with Mazur's ConcepTests, Sokoloff's Interactive Demonstrations, and Van Heuvelen's ALPS Kit worksheets. Students solve context-rich problems using Van Heuvelen's multiple representation format in cooperative groups in discussion sections. Labs were changed to use MBL emphasizing concepts and Experiment Problems to learn lab-based problem solving. Pre- and post-testing of 400 students with the Force Concept Inventory has demonstrated considerable success. The average increase in score has been 35-45methods as defined by Hake. The methods and results will be discussed. Detailed analyses of the FCI results will look at success in teaching specific concepts and the effect of student preparation in mathematics and high school physics.

Seniority and orbital symmetry as tools for establishing a full configuration interaction hierarchy.

PubMed

Bytautas, Laimutis; Henderson, Thomas M; Jiménez-Hoyos, Carlos A; Ellis, Jason K; Scuseria, Gustavo E

2011-07-28

We explore the concept of seniority number (defined as the number of unpaired electrons in a determinant) when applied to the problem of electron correlation in atomic and molecular systems. Although seniority is a good quantum number only for certain model Hamiltonians (such as the pairing Hamiltonian), we show that it provides a useful partitioning of the electronic full configuration interaction (FCI) wave function into rapidly convergent Hilbert subspaces whose weight diminishes as its seniority number increases. The primary focus of this study is the adequate description of static correlation effects. The examples considered are the ground states of the helium, beryllium, and neon atoms, the symmetric dissociation of the N(2) and CO(2) molecules, as well as the symmetric dissociation of an H(8) hydrogen chain. It is found that the symmetry constraints that are normally placed on the spatial orbitals greatly affect the convergence rate of the FCI expansion. The energy relevance of the seniority zero sector (determinants with all paired electrons) increases dramatically if orbitals of broken spatial symmetry (as those commonly used for Hubbard Hamiltonian studies) are allowed in the wave function construction. © 2011 American Institute of Physics

Expanding the FCI to Eevaluate Conceptual Mastery of Energy, Momentum, and Rotational Dynamics

NASA Astrophysics Data System (ADS)

Chediak, Alex; Hay, Katrina

2010-03-01

Normalized gain on the Force Concept Inventory (FCI) has deservedly become a widely accepted assessment tool to evaluate conceptual mastery in a high school, college, or university-level mechanics course. Left out of this assessment, however, are important physics concepts typically presented in the same course. Conservation of energy and momentum as well as rotational motion receive scant (if any) coverage on the FCI (or, for that matter, the Mechanics Baseline Test). Yet these concepts are foundational for popular majors such as mechanical engineering, where high failure rates are often a concern. A revised assessment tool is presented, one that incorporates the strengths of the FCI (and preserves the straightforward multiple choice format), but assesses these other mechanics-related concepts. Ten additional questions are included, inspired in part by material from the Physics Education Group at the University of Washington and in part by the authors' own experiences with common student misperceptions. The questions are given as pre- and post tests at the authors' institutions, California Baptist University and Pacific Lutheran University, in both calculus-based and algebra-based mechanics courses, exploring breadth of applicability for our findings. We present normalized gain data for the traditional thirty FCI questions and for our ten additional questions.

78 FR 49469 - Stephen Glen Guerra, Inmate #98595-279, FCI Yazoo City Medium, Federal Correctional Institution...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-14

... DEPARTMENT OF COMMERCE Bureau of Industry and Security Stephen Glen Guerra, Inmate 98595-279, FCI... Export Privileges On February 6, 2012, in the U.S. District Court, Western District of Texas, Stephen... conviction. [[Page 49470

Improving student learning and views of physics in a large enrollment introductory physics class

NASA Astrophysics Data System (ADS)

Salehzadeh Einabad, Omid

Introductory physics courses often serve as gatekeepers for many scientific and engineering programs and, increasingly, colleges are relying on large, lecture formats for these courses. Many students, however, leave having learned very little physics and with poor views of the subject. In interactive engagement (IE), classroom activities encourage students to engage with each other and with physics concepts and to be actively involved in their own learning. These methods have been shown to be effective in introductory physics classes with small group recitations. This study examined student learning and views of physics in a large enrollment course that included IE methods with no separate, small-group recitations. In this study, a large, lecture-based course included activities that had students explaining their reasoning both verbally and in writing, revise their ideas about physics concepts, and apply their reasoning to various problems. The questions addressed were: (a) What do students learn about physics concepts and how does student learning in this course compare to that reported in the literature for students in a traditional course?, (b) Do students' views of physics change and how do students' views of physics compare to that reported in the literature for students in a traditional course?, and (c) Which of the instructional strategies contribute to student learning in this course? Data included: pre-post administration of the Force Concept Inventory (FCI), classroom exams during the term, pre-post administration of the Colorado Learning Attitudes About Science Survey (CLASS), and student work, interviews, and open-ended surveys. The average normalized gain (=0.32) on the FCI falls within the medium-gain range as reported in the physics education literature, even though the average pre-test score was very low (30%) and this was the instructor's first implementation of IE methods. Students' views of physics remained relatively unchanged by instruction. Findings also indicate that the interaction of the instructional strategies together contributed to student learning. Based on these results, IE methods should be adopted in introductory physics classes, particularly in classes where students have low pre-test scores. It is also important to provide support for instructors new to IE strategies.

Validating two questions in the Force Concept Inventory with subquestions

NASA Astrophysics Data System (ADS)

Yasuda, Jun-ichiro; Taniguchi, Masa-aki

2013-06-01

In this study, we evaluate the structural validity of Q.16 and Q.7 in the Force Concept Inventory (FCI). We address whether respondents who answer Q.16 and Q.7 correctly actually have an understanding of the concepts of physics tested in the questions. To examine respondents’ levels of understanding, we use subquestions that test them on concepts believed to be required to answer the actual FCI questions. Our sample size comprises 111 respondents; we derive false-positive ratios for prelearners and postlearners and then statistically test the difference between them. We find a difference at the 0.05 significance level for both Q.16 and Q.7, implying that it is possible for postlearners to answer both questions without an understanding of the concepts of physics tested in the questions; therefore, the structures of Q.16 and Q.7 are invalid. In this study, we only evaluate the validity of these two FCI questions; we do not assess the validity of previous studies that have compared total FCI scores.

Applying a Force and Motion Learning Progression over an Extended Time Span using the Force Concept Inventory

NASA Astrophysics Data System (ADS)

Fulmer, Gavin W.; Liang, Ling L.; Liu, Xiufeng

2014-11-01

This exploratory study applied a proposed force and motion learning progression (LP) to high-school and university students and to content involving both one- and two-dimensional force and motion situations. The Force Concept Inventory (FCI) was adapted, based on a previous content analysis and coding of the questions in the FCI in terms of the level descriptors of the LP. Using a Rasch measurement model and latent class analysis, students' responses were tested for fit with the proposed LP. Results indicated that the recoded FCI response options are generally consistent with a progression of difficulties as proposed in the LP, and that the students could be organized into different groups with progressively different levels of ability. However, reliability for the ability estimates was only moderate and response options at lower levels of the LP were not well differentiated. Implications for the assessments with LPs and revisions for both the FCI and the force and motion LP are also discussed.

Phase transitions and adiabatic preparation of a fractional Chern insulator in a boson cold-atom model

NASA Astrophysics Data System (ADS)

Motruk, Johannes; Pollmann, Frank

2017-10-01

We investigate the fate of hardcore bosons in a Harper-Hofstadter model which was experimentally realized by Aidelsburger et al. [Nat. Phys. 11, 162 (2015), 10.1038/nphys3171] at half-filling of the lowest band. We discuss the stability of an emergent fractional Chern insulator (FCI) state in a finite region of the phase diagram that is separated from a superfluid state by a first-order transition when tuning the band topology following the protocol used in the experiment. Since crossing a first-order transition is unfavorable for adiabatically preparing the FCI state, we extend the model to stabilize a featureless insulating state. The transition between this phase and the topological state proves to be continuous, providing a path in parameter space along which an FCI state could be adiabatically prepared. To further corroborate this statement, we perform time-dependent DMRG calculations which demonstrate that the FCI state may indeed be reached by adiabatically tuning a simple product state.

Personality types and student performance in an introductory physics course

NASA Astrophysics Data System (ADS)

Harlow, Jason J. B.; Harrison, David M.; Justason, Michael; Meyertholen, Andrew; Wilson, Brian

2017-12-01

We measured the personality type of the students in a large introductory physics course of mostly life science students using the True Colors instrument. We found large correlations of personality type with performance on the precourse Force Concept Inventory (FCI), both term tests, the postcourse FCI, and the final examination. We also saw correlations with the normalized gain on the FCI. The personality profile of the students in this course is very different from the profile of the physics faculty and graduate students, and also very different from the profile of students taking the introductory physics course intended for physics majors and specialists.

The Facilities Condition Index: A Useful Tool for Capital Asset Planning.

ERIC Educational Resources Information Center

Briselden, Don J.; Cain, David A.

2001-01-01

Describes the development and history of the Facilities Condition Index (FCI) and its use in rating a facility's condition and measuring the amount of deferred maintenance needed. Also discusses the FCI's position within the Strategic Assessment Model and its usefulness to facilities managers. (GR)

Fetal Intervention in Right Outflow Tract Obstructive Disease: Selection of Candidates and Results

PubMed Central

Gómez Montes, E.; Herraiz, I.; Mendoza, A.; Galindo, A.

2012-01-01

Objectives. To describe the process of selection of candidates for fetal cardiac intervention (FCI) in fetuses diagnosed with pulmonary atresia-critical stenosis with intact ventricular septum (PA/CS-IVS) and report our own experience with FCI for such disease. Methods. We searched our database for cases of PA/CS-IVS prenatally diagnosed in 2003–2012. Data of 38 fetuses were retrieved and analyzed. FCI were offered to 6 patients (2 refused). In the remaining it was not offered due to the presence of either favourable prognostic echocardiographic markers (n = 20) or poor prognostic indicators (n = 12). Results. The outcome of fetuses with PA/CS-IVS was accurately predicted with multiparametric scoring systems. Pulmonary valvuloplasty was technically successful in all 4 fetuses. The growth of the fetal right heart and hemodynamic parameters showed a Gaussian-like behaviour with an improvement in the first weeks and slow worsening as pregnancy advanced, probably indicating a restenosis. Conclusions. The most likely type of circulation after birth may be predicted in the second trimester of pregnancy by means of combining cardiac dimensions and functional parameters. Fetal pulmonary valvuloplasty in midgestation is technically feasible and in well-selected cases may improve right heart growth, fetal hemodynamics, and postnatal outcome. PMID:22928144

Seniority Number in Valence Bond Theory.

PubMed

Chen, Zhenhua; Zhou, Chen; Wu, Wei

2015-09-08

In this work, a hierarchy of valence bond (VB) methods based on the concept of seniority number, defined as the number of singly occupied orbitals in a determinant or an orbital configuration, is proposed and applied to the studies of the potential energy curves (PECs) of H8, N2, and C2 molecules. It is found that the seniority-based VB expansion converges more rapidly toward the full configuration interaction (FCI) or complete active space self-consistent field (CASSCF) limit and produces more accurate PECs with smaller nonparallelity errors than its molecular orbital (MO) theory-based analogue. Test results reveal that the nonorthogonal orbital-based VB theory provides a reverse but more efficient way to truncate the complete active Hilbert space by seniority numbers.

Bioliteracy and Teaching Efficacy: What Biologists Can Learn from Physicists

ERIC Educational Resources Information Center

Klymkowsky, Michael W.; Garvin-Doxas, Kathy; Zeilik, Michael

2003-01-01

The introduction of the Force Concept Inventory (FCI) by David Hestenes and colleagues in 1992 produced a remarkable impact within the community of physics teachers. An instrument to measure student comprehension of the Newtonian concept of force, the FCI demonstrates that active learning leads to far superior student conceptual learning than…

Personality Types and Student Performance in an Introductory Physics Course

ERIC Educational Resources Information Center

Harlow, Jason J. B.; Harrison, David M.; Justason, Michael; Meyertholen, Andrew; Wilson, Brian

2017-01-01

We measured the personality type of the students in a large introductory physics course of mostly life science students using the True Colors instrument. We found large correlations of personality type with performance on the precourse Force Concept Inventory (FCI), both term tests, the postcourse FCI, and the final examination. We also saw…

Vortex-dislodged cells from bone marrow trephine biopsy yield satisfactory results for flow cytometric immunophenotyping.

PubMed

Bommannan, K; Sachdeva, M U S; Gupta, M; Bose, P; Kumar, N; Sharma, P; Naseem, S; Ahluwalia, J; Das, R; Varma, N

2016-10-01

A good bone marrow (BM) sample is essential in evaluating many hematologic disorders. An unsuccessful BM aspiration (BMA) procedure precludes a successful flow cytometric immunophenotyping (FCI) in most hematologic malignancies. Apart from FCI, most ancillary diagnostic techniques in hematology are less informative. We describe the feasibility of FCI in vortex-dislodged cell preparation obtained from unfixed trephine biopsy (TB) specimens. In pancytopenic patients and dry tap cases, routine diagnostic BMA and TB samples were complemented by additional trephine biopsies. These supplementary cores were immediately transferred into sterile tubes filled with phosphate-buffered saline, vortexed, and centrifuged. The cell pellet obtained was used for flow cytometric immunophenotyping. Of 7955 BMAs performed in 42 months, 34 dry tap cases were eligible for the study. Vortexing rendered a cell pellet in 94% of the cases (32 of 34), and FCI rendered a rapid diagnosis in 100% of the cases (32 of 32) where cell pellets were available. We describe an efficient procedure which could be effectively utilized in resource-limited centers and reduce the frequency of repeat BMA procedures. © 2016 John Wiley & Sons Ltd.

GRILLIX: a 3D turbulence code based on the flux-coordinate independent approach

NASA Astrophysics Data System (ADS)

Stegmeir, Andreas; Coster, David; Ross, Alexander; Maj, Omar; Lackner, Karl; Poli, Emanuele

2018-03-01

The GRILLIX code is presented with which plasma turbulence/transport in various geometries can be simulated in 3D. The distinguishing feature of the code is that it is based on the flux-coordinate independent approach (FCI) (Hariri and Ottaviani 2013 Comput. Phys. Commun. 184 2419; Stegmeir et al 2016 Comput. Phys. Commun. 198 139). Cylindrical or Cartesian grids are used on which perpendicular operators are discretised via standard finite difference methods and parallel operators via a field line tracing and interpolation procedure (field line map). This offers a very high flexibility with respect to geometry, especially a separatrix with X-point(s) or a magnetic axis can be treated easily in contrast to approaches which are based on field aligned coordinates and suffer from coordinate singularities. Aiming finally for simulation of edge and scrape-off layer (SOL) turbulence, an isothermal electrostatic drift-reduced Braginskii model (Zeiler et al 1997 Phys. Plasmas 4 2134) has been implemented in GRILLIX. We present the numerical approach, which is based on a toroidally staggered formulation of the FCI, we show verification of the code with the method of manufactured solutions and show a benchmark based on a TORPEX blob experiment, previously performed by several edge/SOL codes (Riva et al 2016 Plasma Phys. Control. Fusion 58 044005). Examples for slab, circular, limiter and diverted geometry are presented. Finally, the results show that the FCI approach in general and GRILLIX in particular are viable approaches in order to tackle simulation of edge/SOL turbulence in diverted geometry.

Experimental Validation of the Half-Length Force Concept Inventory

ERIC Educational Resources Information Center

Han, Jing; Koenig, Kathleen; Cui, Lili; Fritchman, Joseph; Li, Dan; Sun, Wanyi; Fu, Zhao; Bao, Lei

2016-01-01

In a recent study, the 30-question Force Concept Inventory (FCI) was theoretically split into two 14-question "half-length" tests (HFCIs) covering the same set of concepts and producing mean scores that can be equated to those of the original FCI. The HFCIs require less administration time and reduce test-retest issues when different…

Examining Evolving Performance on the Force Concept Inventory Using Factor Analysis

ERIC Educational Resources Information Center

Semak, M. R.; Dietz, R. D.; Pearson, R. H.; Willis, C. W

2017-01-01

The application of factor analysis to the "Force Concept Inventory" (FCI) has proven to be problematic. Some studies have suggested that factor analysis of test results serves as a helpful tool in assessing the recognition of Newtonian concepts by students. Other work has produced at best ambiguous results. For the FCI administered as a…

Exploratory Factor Analysis of a Force Concept Inventory Data Set

ERIC Educational Resources Information Center

Scott, Terry F.; Schumayer, Daniel; Gray, Andrew R.

2012-01-01

We perform a factor analysis on a "Force Concept Inventory" (FCI) data set collected from 2109 respondents. We address two questions: the appearance of conceptual coherence in student responses to the FCI and some consequences of this factor analysis on the teaching of Newtonian mechanics. We will highlight the apparent conflation of Newton's…

Applying Quantum Monte Carlo to the Electronic Structure Problem

NASA Astrophysics Data System (ADS)

Powell, Andrew D.; Dawes, Richard

2016-06-01

Two distinct types of Quantum Monte Carlo (QMC) calculations are applied to electronic structure problems such as calculating potential energy curves and producing benchmark values for reaction barriers. First, Variational and Diffusion Monte Carlo (VMC and DMC) methods using a trial wavefunction subject to the fixed node approximation were tested using the CASINO code.[1] Next, Full Configuration Interaction Quantum Monte Carlo (FCIQMC), along with its initiator extension (i-FCIQMC) were tested using the NECI code.[2] FCIQMC seeks the FCI energy for a specific basis set. At a reduced cost, the efficient i-FCIQMC method can be applied to systems in which the standard FCIQMC approach proves to be too costly. Since all of these methods are statistical approaches, uncertainties (error-bars) are introduced for each calculated energy. This study tests the performance of the methods relative to traditional quantum chemistry for some benchmark systems. References: [1] R. J. Needs et al., J. Phys.: Condensed Matter 22, 023201 (2010). [2] G. H. Booth et al., J. Chem. Phys. 131, 054106 (2009).

Combination of a fusogenic glycoprotein, prodrug activation, and oncolytic herpes simplex virus for enhanced local tumor control.

PubMed

Simpson, Guy R; Han, Ziqun; Liu, Binlei; Wang, Yibing; Campbell, Gregor; Coffin, Robert S

2006-05-01

We have previously developed an oncolytic herpes simplex virus-1 based on a clinical virus isolate, which was deleted for ICP34.5 to provide tumor selected replication and ICP47 to increase antigen presentation as well as tumor selective virus replication. A phase I/II clinical trial using a version of this virus expressing granulocyte macrophage colony-stimulating factor has shown promising results. The work reported here aimed to develop a version of this virus in which local tumor control was further increased through the combined expression of a highly potent prodrug activating gene [yeast cytosine deaminase/uracil phospho-ribosyltransferase fusion (Fcy::Fur)] and the fusogenic glycoprotein from gibbon ape leukemia virus (GALV), which it was hoped would aid the spread of the activated prodrug through the tumor. Viruses expressing the two genes individually or in combination were constructed and tested, showing (a) GALV and/or Fcy::Fur expression did not affect virus growth; (b) GALV expression causes cell fusion and increases the tumor cell killing at least 30-fold in vitro and tumor shrinkage 5- to 10-fold in vivo; (c) additional expression of Fcy::Fur combined with 5-fluorocytosine administration improves tumor shrinkage further. These results indicate, therefore, that the combined expression of the GALV protein and Fcy::Fur provides a highly potent oncolytic virus with improved capabilities for local tumor control. It is intended to enter the GALV/Fcy::Fur expressing virus into clinical development for the treatment of tumor types, such as pancreatic or lung cancer, where local control would be anticipated to be clinically advantageous.

[Dental fluorosis prevalence in Mexican localities of 27 states and the D.F.: six years after the publication of the Salt Fluoridation Mexican Official Regulation].

PubMed

Betancourt-Lineares, Armandor; Irigoyen-Camacho, María Esther; Mejía-González, Adriana; Zepeda-Zapeda, Marco; Sánchez-Pérez, Leonor

2013-01-01

To identify the prevalence and severity of dental fluorosis in communities located in 28 states of Mexico. The National Dental Caries Survey 2001 (NDCS2001) data base was analyzed. The information of 26,893 students, ages 12 and 15 years old, of 27 states and the Federal District was examined. Dean's dental fluorosis index was applied by standardized examiners. The fluorosis prevalence and the Community Fluorosis Index (FCI) were calculated. The fluorosis prevalence was 27.9% (95% CI 24.4, 28.5). A statistical significance difference in the fluorosis prevalence was observed among the states studied (p < 0.0001). The lowest prevalence was detected in Morelos (3.2%) and the highest in Durango (88.8%). In 18 (64.3%) of the states included more than 90% of the participants showed very mild or lower levels of the dental fluorosis index. A low level of the FCI was found in the localities belonging to 19 (67.9%) of the states studied (FCI < 0.4). The lowest FCI was found in Colima, Yucatán and Morelos. The highest FCI were found in Durango, Zacatecas, Aguascalientes and San Luis Potosí (1 ≤ ICF). This information indicates that in these states dental fluorosis is a public health problem. Two-thirds of the states had localities with low prevalence of dental fluorosis; however, approximately, one-third of the states investigated the fluorosis levels showed the need of a reduction in fluoride exposure among the young population.

The effect of constraint on fuel-coolant interactions in a confined geometry

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

Park, H.; Corradini, M.L.

A Fuel-Coolant Interaction (FCI or vapor explosion) is the phenomena in which a hot liquid rapidly transfers its internal energy into a surrounding colder and more volatile liquid. The energetics of such a complex multi-phase and multi-component phenomenon is partially determined by the surrounding boundary conditions. As one of the boundary conditions, we studied the effect of constraint on FCIs. The WFCI-D series of experiments were performed specifically to observe this effect. The results from these and our previous WFCI tests as well as those of other investigators are compared.

Biochemical non-invasive assessment of liver fibrosis cannot replace biopsy in HIV-HCV coinfected patients.

PubMed

Kliemann, Dimas A; Wolff, Fernando H; Tovo, Cristiane V; Alencastro, Paulo R; Ikeda, Maria L R; Brandão, Ajácio B M; Barcellos, Nêmora; Fuchs, Sandra C

2016-01-01

The liver biopsy has been considered the gold standard for the diagnosis and quantification of fibrosis. However, this method presents limitations. In addition, the non-invasive evaluation of liver fibrosis is a challenge. The aim of this study was to validate the fibrosis cirrhosis index (FCI) index in a cohort of human immunodeficiency virus (HIV)/hepatitis C virus (HCV) coinfected patients, and compare to AST/ALT ratio (AAR), AST to platelet ratio index (APRI) and FIB-4 scores, as a tool for the assessment of liver fibrosis in coinfected patients. Retrospective cross sectional study including 92 HIV-HCV coinfected patients evaluated in two reference centers for HIV treatment in the Public Health System in Southern Brazil. Patients who underwent liver biopsy for any indication and had concomitant laboratory data in the 3 months prior to liver biopsy, to allow the calculation of studied noninvasive markers (AAR, APRI, FIB-4 and FCI) were included. APRI < 0.5 presents the higher specificity to detect no or minimal fibrosis, whereas APRI > 1.5 presents the best negative predictive value and FCI > 1.25 the best specificity to detect significant fibrosis. The values of noninvasive markers for each Metavir fibrosis stage showed statistically significant differences only for APRI. In conclusion, until better noninvasive markers for liver fibrosis are developed and validated for HIV-HCV coinfected patients, noninvasive serum markers should be used carefully in this population.

Teaching Assistants' Performance at Identifying Common Introductory Student Difficulties in Mechanics Revealed by the Force Concept Inventory

ERIC Educational Resources Information Center

Maries, Alexandru; Singh, Chandralekha

2016-01-01

The Force Concept Inventory (FCI) has been widely used to assess student understanding of introductory mechanics concepts by a variety of educators and physics education researchers. One reason for this extensive use is that many of the items on the FCI have strong distractor choices which correspond to students' alternate conceptions in…

78 FR 49470 - Adrian Jesus Reyna, Inmate Number #80629-280, FCI Bastrop, Federal Correctional Institution, P.O...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-14

... DEPARTMENT OF COMMERCE Bureau of Industry and Security Adrian Jesus Reyna, Inmate Number 80629-280... Privileges On January 27, 2012, in the U.S. District Court, Western District of Texas, Adrian Jesus Reyna.... Until January 27, 2022, Adrian Jesus Reyna, with a last known address at: Inmate Number 80629-280, FCI...

Dividing the Force Concept Inventory into Two Equivalent Half-Length Tests

ERIC Educational Resources Information Center

Han, Jing; Bao, Lei; Chen, Li; Cai, Tianfang; Pi, Yuan; Zhou, Shaona; Tu, Yan; Koenig, Kathleen

2015-01-01

The Force Concept Inventory (FCI) is a 30-question multiple-choice assessment that has been a building block for much of the physics education research done today. In practice, there are often concerns regarding the length of the test and possible test-retest effects. Since many studies in the literature use the mean score of the FCI as the…

Correlation of understanding of physics and psychological symptoms among high-school students in Greece

NASA Astrophysics Data System (ADS)

Aggeliki, Anagnostopoulou; Miltiades, Kyprianou; Antigoni-Elisavet, Rota; Evangelia, Pavlatou; Loizos, Zaphiris

2017-09-01

Depression may essentially influence cognitive function contributing to poor school performance. The present study undertakes to determine the existence and strength of correlation between depressive symptomatology and other mental conditions with the acquired level of understanding of Newtonian physics taught in schools. The current study recruited 490 students (262 girls, 228 boys) attending the first semester of the Greek Second Grade of General Lyceum School. Force Concept Inventory (FCI) tested the depth of the students’ understanding of Newtonian Physics. Symptom Checklist-90-R assessed general mental status. The tests took place in the classroom during a 1 h session. Low FCI scores significantly correlated with mental conditions, with depression ranking first. Girls had higher scores in all nine symptoms scales of SCL-90 and lower FCI scores. Stepwise regression models proved that the gender effect on FCI could be effectively explained through the significant effect of depression. An understanding of Newtonian physics among high school students may be restricted by common problematic mental conditions, with depression being the greatest among all. Further research, using a more systematic approach to measure depression among adolescents with poor understanding of physics, would help to elucidate the nature of the effect.

Eye-tracking of visual attention in web-based assessment using the Force Concept Inventory

NASA Astrophysics Data System (ADS)

Han, Jing; Chen, Li; Fu, Zhao; Fritchman, Joseph; Bao, Lei

2017-07-01

This study used eye-tracking technology to investigate students’ visual attention while taking the Force Concept Inventory (FCI) in a web-based interface. Eighty nine university students were randomly selected into a pre-test group and a post-test group. Students took the 30-question FCI on a computer equipped with an eye-tracker. There were seven weeks of instruction between the pre- and post-test data collection. Students’ performance on the FCI improved significantly from pre-test to post-test. Meanwhile, the eye-tracking results reveal that the time students spent on taking the FCI test was not affected by student performance and did not change from pre-test to post-test. Analysis of students’ attention to answer choices shows that on the pre-test students primarily focused on the naïve choices and ignored the expert choices. On the post-test, although students had shifted their primary attention to the expert choices, they still kept a high level of attention to the naïve choices, indicating significant conceptual mixing and competition during problem solving. Outcomes of this study provide new insights on students’ conceptual development in learning physics.

Role of fuel carbon intensity in achieving 2050 greenhouse gas reduction goals within the light-duty vehicle sector.

PubMed

Melaina, M; Webster, K

2011-05-01

Recent U.S. climate change policy developments include aggressive proposals to reduce greenhouse gas emissions, including cap-and-trade legislation with a goal of an 83% reduction below 2005 levels by 2050. This study examines behavioral and technological changes required to achieve this reduction within the light-duty vehicle (LDV) sector. Under this "fair share" sectoral assumption, aggressive near-term actions are necessary in three areas: vehicle miles traveled (VMT), vehicle fuel economy (FE), and fuel carbon intensity (FCI). Two generic scenarios demonstrate the important role of FCI in meeting the 2050 goal. The first scenario allows deep reductions in FCI to compensate for relatively modest FE improvements and VMT reductions. The second scenario assumes optimistic improvements in FE, relatively large reductions in VMT and less aggressive FCI reductions. Each generic scenario is expanded into three illustrative scenarios to explore the theoretical implications of meeting the 2050 goal by relying exclusively on biofuels and hybrid vehicles, biofuels and plug-in hybrid vehicles, or hydrogen fuel cell electric vehicles. These scenarios inform a discussion of resource limitations, technology development and deployment challenges, and policy goals required to meet the 2050 GHG goal for LDVs.

Applying a Force and Motion Learning Progression over an Extended Time Span Using the Force Concept Inventory

ERIC Educational Resources Information Center

Fulmer, Gavin W.; Liang, Ling L.; Liu, Xiufeng

2014-01-01

This exploratory study applied a proposed force and motion learning progression (LP) to high-school and university students and to content involving both one- and two-dimensional force and motion situations. The Force Concept Inventory (FCI) was adapted, based on a previous content analysis and coding of the questions in the FCI in terms of the…

The influence of restrained and external eating patterns on overeating.

PubMed

Burton, Pat; Smit, Hendrik J; Lightowler, Helen J

2007-07-01

Eating in response to an increasingly obesogenic environment has been strongly implicated as a salient aspect of eating behaviour, arguably influenced by learning and experience. Interindividual differences in susceptibility to weight gain may be due, in part, to variability in response to environmental triggers. The phenomenon of food craving may also be an important factor influencing appetite control. The present study tested a model, in which food craving was hypothesised to be an intervening causal variable, on a causal pathway between responsivity to environmental cues and the development of obesity. One hundred and twenty four participants (aged 21-71 years, 83 females and 41 males) completed the study. Participants completed the Dutch eating behaviour questionnaire (DEBQ), measuring external eating (externality), emotional eating (emotionality) and restrained eating behaviour (restraint), and an adapted form of the food craving inventory (FCI), assessing cravings for carbohydrate, fats, sweets and fast food fats, in addition to total food cravings. Initial analysis showed positive correlations between FCI-tot and body mass index (BMI), FCI-fats and BMI and FCI-fast food fats and BMI in both men and women, and between FCI-carbohydrates and BMI in men only. Multiple regression analyses showed externality as the principal predictor of food craving, which was greater in males compared to females, but differential for different food groups between genders. Restrained eating and cravings for fats and fast food fats were negatively associated in women only. As predicted, total cravings, and cravings for fats and fast food foods mediated the positive association between external eating and BMI. It is concluded that appetitive response to external cues as an important risk factor in appetite control is mediated through cravings for particular food groups and is gender-dependent.

The FCI on board MTG : optical design and performances

NASA Astrophysics Data System (ADS)

Ouaknine, J.; Viard, T.; Napierala, B.; Foerster, U.; Fray, S.; Hallibert, P.; Durand, Y.; Imperiali, S.; Pelouas, P.; Rodolfo, J.; Riguet, F.; Carel, J.-L.

2017-11-01

Meteosat Third Generation is the next ESA Program of Earth Observation dedicated to provide Europe with an operational satellite system able to support accurate prediction of meteorological phenomena until the late 2030s. The satellites will be operating from the Geostationary orbit using a 3 axes stabilized platform. The main instrument is called the Flexible Combined Imager (FCI), currently under development by Thales Alenia Space France. It will continue the successful operation of the Spinning Enhanced Visible and Infrared Imager (SEVIRI) on Meteosat Second Generation (MSG) with improved performance. This instrument will provide full images of the Earth every 10 minutes in 16 spectral channels between 0.44 and 13.3 μm. The ground resolution is ranging from 0.5 km to 2 km. The FCI is composed of a telescope developed by Kayser-Threde, which includes a Scan mirror for the full Earth coverage, and a calibration mechanism with an embedded black body dedicated to accurate in-flight IR radiometric calibration. The image produced by the telescope is split into several spectral groups by a spectral separation assembly (SSA) thanks to dichroïc beamsplitters. The output beams are collimated to ease the instrument integration before reaching the cryostat. Inside, the cold optics (CO-I) focalize the optical beams onto the IR detectors. The cold optics and IR detectors are accurately positioned inside a common cold plate to improve registration between spectral channels. Spectral filters are integrated on top of the detectors in order to achieve the required spectral selection. This article describes the FCI optical design and performances. We will focus on the image quality needs, the high line-of-sight stability required, the spectral transmittance performance, and the stray-light rejection. The FCI currently under development will exhibit a significant improvement of performances with respect to MSG.

Food cravings among Brazilian population.

PubMed

Queiroz de Medeiros, Anna Cecília; Pedrosa, Lucia de Fatima Campos; Yamamoto, Maria Emilia

2017-01-01

This study aimed to develop and validate a Brazilian version of the Food Craving Inventory (FCI-Br), adapted to the cultural-gastronomic context of Brazil, and to explore this behavior among adult Brazilians. The Study 1 population consisted of 453 adults from all regions of Brazil. Participants responded to a preliminary form of the instrument online. Exploratory factor analysis revealed an FCI-Br presenting 23 items and three factors: High Fat, Sweet Food and Traditional Meal. The FCI-Br overall reliability was considered adequate (α = 0.82), as were each of the sub-scales. The food items receiving higher average scores from the application of the instrument were chocolate (3.14 ± 1.28; women) and bread (2.94 ± 1.44, men). A significant association was observed between the specific-craving for Sweet Food and female respondents. Most participants reported experiencing more frequent episodes of food craving when alone (68.0%; n = 391) and during the afternoon (32.2%; n = 127) or evening (43.8%; n = 173) hours. Application of the FCI-Br in a population of 649 university students (Study 2) demonstrated a good adjustment of the model developed according to the Confirmatory factor analysis (χ 2 /gl = 2.82, CFI = 0.94; TLI = 0.93; RMSEA = 0.06). The current findings indicate that the FCI-Br has adequate psychometric properties to measure craving behavior with respect to specific food groups in the resident population of Brazil. The results of this study also shed light on the importance of considering the cultural diversity of a population when investigating eating behaviors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Spectroscopic and structural investigation for the ground and excited states of CaNa+ molecular ion

NASA Astrophysics Data System (ADS)

Jellali, Soulef; Habli, Héla; Mejrissi, Leila; Hamdi, Rafika; Oujia, Brahim; Xavier Gadéa, Florent

2018-04-01

In the current theoretical study, we investigated several electronic states correlated with the {Ca+Na+} and {Ca++Na} asymptotic limits of different symmetries (Σ+, Π, Δ). Our calculations were based on ab intio method using semi-empirical pseudo-potential theory of both cores Na+ and Ca2+ and Full Configuration Interaction (FCI). Hence, we computed the adiabatic potential energy curves (PECs) and vibrational levels of the ground state along with several higher states of (CaNa)+ molecular ion. From these curves, we extracted all related spectroscopic parameters (De, D0, Te, Re, Be, ωe and ωeχe). Dipolar properties of (CaNa)+ such as Permanent and Transition Dipole Moments (PDM, TDM) were determined and analyzed. Numerous Avoided Crossings (ACs) were detected in PECs and their reflections were clearly observed in PDM and TDM functions. The strong interactions could lead to significant charge or excitation transfer for atom-ion collisions in the diverse charge or excited states.

Identification of CD56 and CD57 by flow cytometry in Ewing's sarcoma or primitive neuroectodermal tumor.

PubMed

Gardner, L J; Polski, J M; Fallon, R; Dunphy, C H

1998-07-01

CD56 and CD57 are commonly considered as natural killer and neuroectodermal markers, but their expression has been identified in a wide spectrum of neoplasms including some cases of Ewing's sarcoma (ES) and primitive neuroectodermal tumor (PNET). We report two cases of small, round blue cell tumor (SRBCT), in which flow cytometry immunophenotyping (FCI) detected strong expression of CD56 and CD57 (one case). Immunohistochemical staining with Leu-19 and Leu-7 confirmed the FI results. Although CD56 and CD57 expression is consistent with ES/PNET, it can be potentially misleading if results of FCI are interpreted in the absence of other findings. These cases suggest the utility of FCI in undifferentiated SRBCT. The literature on CD56 and CD57 expression in ES/PNET is reviewed and discussed.

An item response curves analysis of the Force Concept Inventory

NASA Astrophysics Data System (ADS)

Morris, Gary A.; Harshman, Nathan; Branum-Martin, Lee; Mazur, Eric; Mzoughi, Taha; Baker, Stephen D.

2012-09-01

Several years ago, we introduced the idea of item response curves (IRC), a simplistic form of item response theory (IRT), to the physics education research community as a way to examine item performance on diagnostic instruments such as the Force Concept Inventory (FCI). We noted that a full-blown analysis using IRT would be a next logical step, which several authors have since taken. In this paper, we show that our simple approach not only yields similar conclusions in the analysis of the performance of items on the FCI to the more sophisticated and complex IRT analyses but also permits additional insights by characterizing both the correct and incorrect answer choices. Our IRC approach can be applied to a variety of multiple-choice assessments but, as applied to a carefully designed instrument such as the FCI, allows us to probe student understanding as a function of ability level through an examination of each answer choice. We imagine that physics teachers could use IRC analysis to identify prominent misconceptions and tailor their instruction to combat those misconceptions, fulfilling the FCI authors' original intentions for its use. Furthermore, the IRC analysis can assist test designers to improve their assessments by identifying nonfunctioning distractors that can be replaced with distractors attractive to students at various ability levels.

Interband excitations in the 1D limit of two-band fractional Chern insulators

NASA Astrophysics Data System (ADS)

Jaworowski, Błażej; Kaczmarkiewicz, Piotr; Potasz, Paweł; Wójs, Arkadiusz

2018-05-01

We investigate the stability of the one-dimensional limit of ν = 1 / 3 Laughlin-like fractional Chern insulator with respect to the interband interaction. We propose a construction for the excitations in the infinite-interaction case and show that the energy gap remains finite in the thermodynamic limit. Next, by means of exact diagonalization and Density Matrix Renormalization Group approaches, we consider deviations from ideal dimerization and show that they reduce the stability of the FCI-like states. Finally, to show that our approach is not restricted to one model, we identify the dimer structure behind the thin-torus limit of other system - the checkerboard lattice.

Acute promyelocytic leukemia, hypogranular variant, with uncharacteristic staining with chloroacetate esterase.

PubMed

Dunphy, C H; Polski, J M; Johns, G; Evans, H L; Gardner, L J

2001-06-01

A diagnosis of the hypogranular variant of acute promyelocytic leukemia (APLv) may be difficult to establish based on cytomorphology alone. However, the great majority of cases have a classical immunophenotype by flow cytometric immunophenotyping (FCI) (CD13+, CD33+, dim CD64+, HLA-DR-, and CD34-) and a classical enzyme cytochemical (EC) staining pattern. [intensely staining with myeloperoxidase, Sudan Black B, and chloroacetate esterase (CAE) and negative with alpha'-naphthyl acetate and butyrate esterases]. Although the immunophenotype of APLv by FCI has varied in the literature (HLA-DR +/- and CD34 +/-), the EC staining pattern has remained constant. We report a case of APLv with characteristic cytomorphology, compatible FCI data (CD13+, CD33+, dim CD64+, HLA-DR +/-, and CD34-), chromosomal detection of t(15; 17), and molecular detection of the PML/RAR alpha fusion gene; however, staining of the leukemic cells with CAE was quite uncharacteristic. We describe our findings.

Isometric Arm Strength and Subjective Rating of Upper Limb Fatigue in Two-Handed Carrying Tasks

PubMed Central

Li, Kai Way; Chiu, Wen-Sheng

2015-01-01

Sustained carrying could result in muscular fatigue of the upper limb. Ten male and ten female subjects were recruited for measurements of isometric arm strength before and during carrying a load for a period of 4 minutes. Two levels of load of carrying were tested for each of the male and female subjects. Exponential function based predictive equations for the isometric arm strength were established. The mean absolute deviations of these models in predicting the isometric arm strength were in the range of 3.24 to 17.34 N. Regression analyses between the subjective ratings of upper limb fatigue and force change index (FCI) for the carrying were also performed. The results indicated that the subjective rating of muscular fatigue may be estimated by multiplying the FCI with a constant. The FCI may, therefore, be adopted as an index to assess muscular fatigue for two-handed carrying tasks. PMID:25794159

Isometric arm strength and subjective rating of upper limb fatigue in two-handed carrying tasks.

PubMed

Li, Kai Way; Chiu, Wen-Sheng

2015-01-01

Sustained carrying could result in muscular fatigue of the upper limb. Ten male and ten female subjects were recruited for measurements of isometric arm strength before and during carrying a load for a period of 4 minutes. Two levels of load of carrying were tested for each of the male and female subjects. Exponential function based predictive equations for the isometric arm strength were established. The mean absolute deviations of these models in predicting the isometric arm strength were in the range of 3.24 to 17.34 N. Regression analyses between the subjective ratings of upper limb fatigue and force change index (FCI) for the carrying were also performed. The results indicated that the subjective rating of muscular fatigue may be estimated by multiplying the FCI with a constant. The FCI may, therefore, be adopted as an index to assess muscular fatigue for two-handed carrying tasks.

Description and performance of the OGSE for VNIR absolute spectroradiometric calibration of MTG-I satellites

NASA Astrophysics Data System (ADS)

Glastre, W.; Marque, J.; Compain, E.; Deep, A.; Durand, Y.; Aminou, D. M. A.

2017-09-01

The Meteosat Third Generation (MTG) Programme is being realised through the well-established and successful Cooperation between EUMETSAT and ESA. It will ensure the future continuity of MSG with the capabilities to enhance nowcasting, global and regional numerical weather prediction, climate and atmospheric chemistry monitoring data from Geostationary Orbit. This will be achieved through a series of 6 satellites named MTG-I and MTG-S to bring to the meteorological community continuous high spatial, spectral and temporal resolution observations and geophysical parameters of the Earth based on sensors from the geo-stationary orbit. In particular, the imagery mission MTG-I will bring an improved continuation of the MSG satellites series with the Flexible Combined Imager (FCI) a broad spectral range (from UV to LWIR) with better spatial and spectral resolutions. The FCI will be able to take high spatial resolution pictures of the Earth within 8 VNIR and 8 IR channels. As one of the mission of this instrument is to provide a quantitative analysis of atmosphere compounds, the absolute observed radiance needs to be known with a specified accuracy for VNIR as low as to 5% at k=3 over its full dynamic. While the FCI is regularly recalibrated every 6 month at equinoxes, it is however requiring initial ground calibration for the beginning of its mission. The Multi Optical Test Assembly (MOTA) is one of the Optical Ground Support Equipment (OGSE) dedicated to various missions necessary for the integration of the FCI . This equipment, provided by Bertin Technologies, will be delivered to TAS-F by the end of 2016. One of its mission, is the on-ground absolute calibration of VNIR channels. In order to handle this, the MOTA will be placed in front of the FCI under representative vacuum conditions and will be able to project a perfectly known, calibrated radiance level within the full dynamic of FCI instrument. The main difficulty is the very demanding calibration level with respect to primary standards down to 3% (k=3) coupled with constraining environment (vacuum), large dynamic (up to factor 100), high spectral resolution of 3 nm. Another main difficulty is to adapt the specific MOTA etendue (300 mm pupil, 9 mrad field) to available primary standards. Each of these constraints were addressed by specific tool design and production, a fine optimization of the calibration procedure with a large involvement of metrology laboratories. This paper introduces the missions of MTG satellites and particularly of the FCI instrument. The requirements regarding the absolute calibration over the different spectrometric channels and the global strategy to fulfill them are described. The MOTA architecture and calibration strategy are then discussed and final expected results are presented, showing state of the art performances.

Universal state-selective corrections to multireference coupled-cluster theories with single and double excitations

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

Brabec, Jiri; van Dam, Hubertus JJ; Pittner, Jiri

2012-03-28

The recently proposed Universal State-Selective (USS) corrections [K. Kowalski, J. Chem. Phys. 134, 194107 (2011)] to approximate Multi-Reference Coupled Cluster (MRCC) energies can be commonly applied to any type of MRCC theory based on the Jeziorski-Monkhorst [B. Jeziorski, H.J. Monkhorst, Phys. Rev. A 24, 1668 (1981)] exponential Ansatz. In this letter we report on the performance of a simple USS correction to the Brillouin-Wigner MRCC (BW-MRCC) formalism employing single and double excitations (BW-MRCCSD). It is shown that the resulting formalism (USS-BW-MRCCSD), which uses the manifold of single and double excitations to construct the correction, can be related to a posteriorimore » corrections utilized in routine BW-MRCCSD calculations. In several benchmark calculations we compare the results of the USS-BW-MRCCSD method with results of the BW-MRCCSD approach employing a posteriori corrections and with results obtained with the Full Configuration Interaction (FCI) method.« less

British Military freezing cold injuries: a 13-year review.

PubMed

Heil, Kieran M; Oakley, E H N; Wood, A M

2016-12-01

Cold injuries have been a recurrent feature of warfare for millennia and continue to present during British Military operations today. Those affecting the peripheries are divided into freezing cold injury (FCI) and non-FCI. FCI occurs when tissue fluids freeze at around -0.5°C and is commonly referred to as frostnip or frostbite. All FMED7 notes held at the Institute of Naval Medicine's Cold Weather Injury Clinic (CIC) from 2002 to 2014 were searched for the terms 'frostbite' and 'frostnip' and then analysed to identify common themes. In total 245 results were found and from these, 149 patients with a positive FCI diagnosis were identified and formed the cohort of this study. Royal Marines (RM) represented over 50% of patients and Arctic training in Norway accounted for over two thirds of the total cases. The extremities were almost always those areas which were affected by FCI. Further analysis of the RM cases showed the majority of those injured were of the most junior rank (Marine/Private or Lance Corporal). A lack of supporting climatic and activity data meant that it was difficult to draw additional conclusions from the data collected. In future, a greater emphasis should be placed on collection of climatic and additional data when FCIs are diagnosed. These data should be collated at the end of each deployment and published as was regularly done historically. It is hoped that these data could then be used as the starting point for an annual climatic study day, where issues related to FCIs could be discussed in a Tri-Service environment and lessons learned disseminated around all British Forces personnel. 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/.

Conceptual physics differences by pedagogy and gender: Questioning the deficit model

NASA Astrophysics Data System (ADS)

Majors, Twanelle Deann Walker

The differences in physics performance between males and females have been studied extensively (Blue & Heller, 2003; Coletta, 2015; Madsen, McKagan, & Sayre 2013; McCullough, 2002, 2004, 2011; Pollock, Finkelstein, & Kost, 2007; Zohar & Sela, 2003). The purpose of this study was to look at the ways teaching methods and assessment choices have fabricated a gender gap. Deficit ways of thinking have further marginalized women by renegotiating prior acts of power that initiated and perpetuated marginalization. Outside of the deficit model, the blame for the underperformance of females has been attributed to discourses of power as well as less-than-critical ways of evaluating learning and schooling. Students in introductory algebra-based physics courses from 2008-2014 at Tennessee Technological University were self-enrolled in PHYS2010 sections that were taught using either a traditional or constructivist, interactive-engagement Learner-centered Environment for Algebra-based Physics (LEAP) pedagogy. Propensity scoring on all feasible and relevant independent variables was used to adjust for the probability of students choosing either LEAP or traditional sections. The Force Concept Inventory (FCI) and Gender Force Concept Inventory (GFCI) were used as the measures to gauge students' performance on physics concepts. The results showed that there were no differences in the FCI or GFCI performance of males and females. Results also showed that when accounting for pretest performance and the likelihood of choosing a LEAP section, LEAP pedagogy accounted for roughly 30% of performance differences. Not only was this true on the average, it was true for both genders. This meant that the main effect of LEAP pedagogy was even stronger and more generalizable. Gender did not moderate pedagogy, indicating that a pedagogy gap focus was more appropriate for evaluating physics learners.

Validation of the rheumatic disease comorbidity index.

PubMed

England, Bryant R; Sayles, Harlan; Mikuls, Ted R; Johnson, Dannette S; Michaud, Kaleb

2015-05-01

There is no consensus on which comorbidity index is optimal for rheumatic health outcomes research. We compared a new Rheumatic Disease Comorbidity Index (RDCI) with the Charlson-Deyo Index (CDI), Functional Comorbidity Index (FCI), Elixhauser Total Score (ETS), Elixhauser Point System (EPS), and a simple comorbidity count (COUNT) using a US cohort of rheumatoid arthritis (RA) patients. Using administrative diagnostic codes and patient self-reporting, we tested predictive values of the RDCI, CDI, FCI, ETS, EPS, and COUNT for 2 outcomes: all-cause mortality and physical functioning. Indices were compared using 3 models: bare (consisting of age, sex, and race), administrative (bare plus visit frequency, body mass index, and treatments), and clinic (administrative plus erythrocyte sedimentation rate, nodules, rheumatoid factor positivity, and patient activity scale). The ETS and RDCI best predicted death, with FCI performing the worst. The FCI best predicted function, with ETS and RDCI performing nearly as well. CDI predicted function poorly. The order of indices remained relatively unchanged in the different models, though the magnitude of improvement in Akaike's information criterion decreased in the administrative and clinic models. The RDCI and ETS are excellent indices as a means of accounting for comorbid illness when the RA-related outcomes of death and physical functioning are studied using administrative data. The RDCI is a versatile index and appears to perform well with self-report data as well as administrative data. Further studies are warranted to compare these indices using other outcomes in diverse study populations. © 2015, American College of Rheumatology.

Financial capacity in dementia: a systematic review.

PubMed

Sudo, Felipe Kenji; Laks, Jerson

2017-07-01

Financial capacity (FC) refers to a set of cognitively mediated abilities related to one's competency to manage propriety and income. Identifying intact from impaired FC in older persons with dementia is a growing concern in geriatric practice, but the best methods to assess this function still need to be determined. This study aims to review data on FC in dementia and on instruments used to assess this domain of capacity. Database search was performed in Medline, ISI Web of Knowledge, LILACS and PsycINFO. Studies that objectively assessed FC in dementia of any etiology were included. Of a total of 125 articles, 10 were included. Mild Alzheimer's Disease (AD) was associated with impaired complex FC abilities, namely checkbook management, bank statement management and financial judgment, but simple FC skills were preserved. Moderate AD was associated with impairment in all domains of FC. The Financial Capacity Instrument (FCI) was applied in most of the selected studies and correlated with neuropsychological and neuroimaging variables. Early dementia is associated with partially preserved FC. More validation studies using objective and evidence-based FC assessment tools, such as the FCI, are still needed.

[Resistivity and hemodynamic reactions of essentially healthy pilots to the passive orthostatic test].

PubMed

Bondareva, S V; Vartbaronov, R A; Ponomarenko, K V; Bagaudinov, K G; Khomenko, M N

2009-01-01

The paper analyzes the data of expert tilt testing (-80 degrees, 20 min.) of 66 essentially healthy pilots. Hemodynamic reactions were characterized based on the standard concept of functional classes (FC). Good test tolerance was recorded in 86.4% of cases among which 36.4% were referred to FC-I and 50%--to FC-II. Adequate test tolerance (FC-II) was recorded in 10.6%; reduced and poor test tolerance (FC-IV and FC-V)--in 3%. According to ECG and computerized tachooscillography, the adaptive hemodynamic reactions were optimum in pilots of group FC-I as compared with group FC-II and all the more so when compared with FC-III. The last two groups showed some objective symptoms that had not been looked for in the past (a distinct lability of blood pressure, and incomplete hypertensive and hypotensive reactions) that differentiated these groups from FC-I. Results of the analysis made it possible to put forward additional clinical functional criteria to assess tilt tolerance of pilots with different levels of functional tolerance.

Active Learning in the Physics Classroom

NASA Astrophysics Data System (ADS)

Naron, Carol

Many students enter physics classes filled with misconceptions about physics concepts. Students tend to retain these misconceptions into their adult lives, even after physics instruction. Constructivist researchers have found that students gain understanding through their experiences. Researchers have also found that active learning practices increase conceptual understanding of introductory physics students. This project study sought to examine whether incorporating active learning practices in an advanced placement physics classroom increased conceptual understanding as measured by the force concept inventory (FCI). Physics students at the study site were given the FCI as both a pre- and posttest. Test data were analyzed using two different methods---a repeated-measures t test and the Hake gain method. The results of this research project showed that test score gains were statistically significant, as measured by the t test. The Hake gain results indicated a low (22.5%) gain for the class. The resulting project was a curriculum plan for teaching the mechanics portion of Advanced Placement (AP) physics B as well as several active learning classroom practices supported by the research. This project will allow AP physics teachers an opportunity to improve their curricular practices. Locally, the results of this project study showed that research participants gained understanding of physics concepts. Social change may occur as teachers implement active learning strategies, thus creating improved student understanding of physics concepts.

Age and education corrected older adult normative data for a short form version of the Financial Capacity Instrument.

PubMed

Gerstenecker, Adam; Eakin, Amanda; Triebel, Kristen; Martin, Roy; Swenson-Dravis, Dana; Petersen, Ronald C; Marson, Daniel

2016-06-01

Financial capacity is an instrumental activity of daily living (IADL) that comprises multiple abilities and is critical to independence and autonomy in older adults. Because of its cognitive complexity, financial capacity is often the first IADL to show decline in prodromal and clinical Alzheimer's disease and related disorders. Despite its importance, few standardized assessment measures of financial capacity exist and there is little, if any, normative data available to evaluate financial skills in the elderly. The Financial Capacity Instrument-Short Form (FCI-SF) is a brief measure of financial skills designed to evaluate financial skills in older adults with cognitive impairment. In the current study, we present age- and education-adjusted normative data for FCI-SF variables in a sample of 1344 cognitively normal, community-dwelling older adults participating in the Mayo Clinic Study of Aging (MCSA) in Olmsted County, Minnesota. Individual FCI-SF raw scores were first converted to age-corrected scaled scores based on position within a cumulative frequency distribution and then grouped within 4 empirically supported and overlapping age ranges. These age-corrected scaled scores were then converted to age- and education-corrected scaled scores using the same methodology. This study has the potential to substantially enhance financial capacity evaluations of older adults through the introduction of age- and education-corrected normative data for the FCI-SF by allowing clinicians to: (a) compare an individual's performance to that of a sample of similar age and education peers, (b) interpret various aspects of financial capacity relative to a normative sample, and (c) make comparisons between these aspects. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Talking and learning physics: Predicting future grades from network measures and Force Concept Inventory pretest scores

NASA Astrophysics Data System (ADS)

Bruun, Jesper; Brewe, Eric

2013-12-01

The role of student interactions in learning situations is a foundation of sociocultural learning theory, and social network analysis can be used to quantify student relations. We discuss how self-reported student interactions can be viewed as processes of meaning making and use this to understand how quantitative measures that describe the position in a network, called centrality measures, can be understood in terms of interactions that happen in the context of a university physics course. We apply this discussion to an empirical data set of self-reported student interactions. In a weekly administered survey, first year university students enrolled in an introductory physics course at a Danish university indicated with whom they remembered having communicated within different interaction categories. For three categories pertaining to (1) communication about how to solve physics problems in the course (called the PS category), (2) communications about the nature of physics concepts (called the CD category), and (3) social interactions that are not strictly related to the content of the physics classes (called the ICS category) in the introductory mechanics course, we use the survey data to create networks of student interaction. For each of these networks, we calculate centrality measures for each student and correlate these measures with grades from the introductory course, grades from two subsequent courses, and the pretest Force Concept Inventory (FCI) scores. We find highly significant correlations (p<0.001) between network centrality measures and grades in all networks. We find the highest correlations between network centrality measures and future grades. In the network composed of interactions regarding problem solving (the PS network), the centrality measures hide and PageRank show the highest correlations (r=-0.32 and r=0.33, respectively) with future grades. In the CD network, the network measure target entropy shows the highest correlation (r=0.45) with future grades. In the network composed solely of noncontent related social interactions, these patterns of correlation are maintained in the sense that these network measures show the highest correlations and maintain their internal ranking. Using hierarchical linear regression, we find that a linear model that adds the network measures hide and target entropy, calculated on the ICS network, significantly improves a base model that uses only the FCI pretest scores from the beginning of the semester. Though one should not infer causality from these results, they do point to how social interactions in class are intertwined with academic interactions. We interpret this as an integral part of learning, and suggest that physics is a robust example.

Towards nonaxisymmetry; initial results using the Flux Coordinate Independent method in BOUT++

NASA Astrophysics Data System (ADS)

Shanahan, B. W.; Hill, P.; Dudson, B. D.

2016-11-01

Fluid simulation of stellarator edge transport is difficult due to the complexities of mesh generation; the stochastic edge and strong nonaxisymmetry inhibit the use of field aligned coordinate systems. The recent implementation of the Flux Coordinate Independent method for calculating parallel derivatives in BOUT++ has allowed for more complex geometries. Here we present initial results of nonaxisymmetric diffusion modelling as a step towards stellarator turbulence modelling. We then present initial (non-turbulent) transport modelling using the FCI method and compare the results with analytical calculations. The prospects for future stellarator transport and turbulence modelling are discussed.

Ion beam generated modes in the lower hybrid frequency range in a laboratory magnetoplasma

NASA Astrophysics Data System (ADS)

Van Compernolle, B.; Tripathi, S.; Gekelman, W. N.; Colestock, P. L.; Pribyl, P.

2012-12-01

The generation of waves by ion ring distributions is of great importance in many instances in space plasmas. They occur naturally in the magnetosphere through the interaction with substorms, or they can be man-made in ionospheric experiments by photo-ionization of neutral atoms injected perpendicular to the earth's magnetic field. The interaction of a fast ion beam with a low β plasma has been studied in the laboratory. Experiments were performed at the LArge Plasma Device (LAPD) at UCLA. The experiments were done in a Helium plasma (n ≃ 1012 \\ cm-3, B0 = 1000 G - 1800 G, fpe}/f{ce ≃ 1 - 5, Te = 0.25\\ eV, vte ≤ vA). The ion beam \\cite{Tripathi_ionbeam} is a Helium beam with energies ranging from 5 keV to 18 keV. The fast ion velocity is on the order of the Alfvén velocity. The beam is injected from the end of the machine, and spirals down the linear device. Waves were observed below fci in the shear Alfvén wave regime, and in a broad spectrum above fci in the lower hybrid frequency range, the focus of this paper. The wave spectra have distinct peaks close to ion cyclotron harmonics, extending out to the 100th harmonic in some cases. The wave generation was studied for various magnetic fields and background plasma densities, as well as for different beam energies and pitch angles. The waves were measured with 3-axis electric and magnetic probes. Detailed measurements of the perpendicular mode structure will be shown. Langmuir probes were used to measure density and temperature evolution due to the beam-plasma interaction. Retarding field energy analyzers captured the ion beam profiles. The work was performed at the LArge Plasma Device at the Basic Plasma Science Facility (BaPSF) at UCLA, funded by DOE/NSF.

Information-theoretic metric as a tool to investigate nonclassical correlations

NASA Astrophysics Data System (ADS)

Rudolph, Alexander L.; Lamine, Brahim; Joyce, Michael; Vignolles, Hélène; Consiglio, David

2014-06-01

We report on a project to introduce interactive learning strategies (ILS) to physics classes at the Université Pierre et Marie Curie, one of the leading science universities in France. In Spring 2012, instructors in two large introductory classes, first-year, second-semester mechanics, and second-year introductory electricity and magnetism, enrolling approximately 500 and 250 students, respectively, introduced ILS into some, but not all, of the sections of each class. The specific ILS utilized were think-pair-share questions and Peer Instruction in the main lecture classrooms, and University of Washington Tutorials for Introductory Physics in recitation sections. Pre- and postinstruction assessments [Force Concept Inventory (FCI) and Conceptual Survey of Electricity and Magnetism (CSEM), respectively] were given, along with a series of demographic questions. Since not all lecture or recitation sections in these classes used ILS, we were able to compare the results of the FCI and CSEM between interactive and noninteractive classes taught simultaneously with the same curriculum. We also analyzed final exam results, as well as the results of student and instructor attitude surveys between classes. In our analysis, we argue that multiple linear regression modeling is superior to other common analysis tools, including normalized gain. Our results show that ILS are effective at improving student learning by all measures used: research-validated concept inventories and final exam scores, on both conceptual and traditional problem-solving questions. Multiple linear regression analysis reveals that interactivity in the classroom is a significant predictor of student learning, showing a similar or stronger relationship with student learning than such ascribed characteristics as parents’ education, and achieved characteristics such as grade point average and hours studied per week. Analysis of student and instructor attitudes shows that both groups believe that ILS improve student learning in the physics classroom and increase student engagement and motivation. All of the instructors who used ILS in this study plan to continue their use.

An algorithm for direct causal learning of influences on patient outcomes.

PubMed

Rathnam, Chandramouli; Lee, Sanghoon; Jiang, Xia

2017-01-01

This study aims at developing and introducing a new algorithm, called direct causal learner (DCL), for learning the direct causal influences of a single target. We applied it to both simulated and real clinical and genome wide association study (GWAS) datasets and compared its performance to classic causal learning algorithms. The DCL algorithm learns the causes of a single target from passive data using Bayesian-scoring, instead of using independence checks, and a novel deletion algorithm. We generate 14,400 simulated datasets and measure the number of datasets for which DCL correctly and partially predicts the direct causes. We then compare its performance with the constraint-based path consistency (PC) and conservative PC (CPC) algorithms, the Bayesian-score based fast greedy search (FGS) algorithm, and the partial ancestral graphs algorithm fast causal inference (FCI). In addition, we extend our comparison of all five algorithms to both a real GWAS dataset and real breast cancer datasets over various time-points in order to observe how effective they are at predicting the causal influences of Alzheimer's disease and breast cancer survival. DCL consistently outperforms FGS, PC, CPC, and FCI in discovering the parents of the target for the datasets simulated using a simple network. Overall, DCL predicts significantly more datasets correctly (McNemar's test significance: p<0.0001) than any of the other algorithms for these network types. For example, when assessing overall performance (simple and complex network results combined), DCL correctly predicts approximately 1400 more datasets than the top FGS method, 1600 more datasets than the top CPC method, 4500 more datasets than the top PC method, and 5600 more datasets than the top FCI method. Although FGS did correctly predict more datasets than DCL for the complex networks, and DCL correctly predicted only a few more datasets than CPC for these networks, there is no significant difference in performance between these three algorithms for this network type. However, when we use a more continuous measure of accuracy, we find that all the DCL methods are able to better partially predict more direct causes than FGS and CPC for the complex networks. In addition, DCL consistently had faster runtimes than the other algorithms. In the application to the real datasets, DCL identified rs6784615, located on the NISCH gene, and rs10824310, located on the PRKG1 gene, as direct causes of late onset Alzheimer's disease (LOAD) development. In addition, DCL identified ER category as a direct predictor of breast cancer mortality within 5 years, and HER2 status as a direct predictor of 10-year breast cancer mortality. These predictors have been identified in previous studies to have a direct causal relationship with their respective phenotypes, supporting the predictive power of DCL. When the other algorithms discovered predictors from the real datasets, these predictors were either also found by DCL or could not be supported by previous studies. Our results show that DCL outperforms FGS, PC, CPC, and FCI in almost every case, demonstrating its potential to advance causal learning. Furthermore, our DCL algorithm effectively identifies direct causes in the LOAD and Metabric GWAS datasets, which indicates its potential for clinical applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Can dual processing theory explain physics students' performance on the Force Concept Inventory?

NASA Astrophysics Data System (ADS)

Wood, Anna K.; Galloway, Ross K.; Hardy, Judy

2016-12-01

According to dual processing theory there are two types, or modes, of thinking: system 1, which involves intuitive and nonreflective thinking, and system 2, which is more deliberate and requires conscious effort and thought. The Cognitive Reflection Test (CRT) is a widely used and robust three item instrument that measures the tendency to override system 1 thinking and to engage in reflective, system 2 thinking. Each item on the CRT has an intuitive (but wrong) answer that must be rejected in order to answer the item correctly. We therefore hypothesized that performance on the CRT may give useful insights into the cognitive processes involved in learning physics, where success involves rejecting the common, intuitive ideas about the world (often called misconceptions) and instead carefully applying physical concepts. This paper presents initial results from an ongoing study examining the relationship between students' CRT scores and their performance on the Force Concept Inventory (FCI), which tests students' understanding of Newtonian mechanics. We find that a higher CRT score predicts a higher FCI score for both precourse and postcourse tests. However, we also find that the FCI normalized gain is independent of CRT score. The implications of these results are discussed.

The mechanistic basis of pH-dependent 5-flucytosine resistance in Aspergillus fumigatus.

PubMed

Gsaller, Fabio; Furukawa, Takanori; Carr, Paul D; Rash, Bharat; Jöchl, Christoph; Bertuzzi, Margherita; Bignell, Elaine M; Bromley, Michael J

2018-04-02

The antifungal drug 5-flucytosine (5FC), a derivative of the nucleobase cytosine, is licenced for treatment of fungal diseases however it is rarely used as a monotherapeutic to treat Aspergillus infection. Despite being potent against other fungal pathogens, 5FC has limited activity against A. fumigatus when standard in vitro assays are used to determine susceptibility. However, in modified in vitro assays where the pH is set to pH 5 the activity of 5FC increases significantly.Here we provide evidence that fcyB , a gene that encodes a purine-cytosine permease orthologous to known 5FC importers is downregulated at pH 7 and is the primary factor responsible for the low efficacy of 5FC at pH 7. We also uncover two transcriptional regulators that are responsible for repression of fcyB and consequently mediators of 5FC resistance, the CCAAT binding complex (CBC) and the pH regulatory protein PacC. We propose that the activity of 5FC might be enhanced by perturbation of factors that repress fcyB expression such as PacC or other components of the pH sensing machinery. Copyright © 2018 American Society for Microbiology.

Novel method for comparing coverage by future methods of ballistic facial protection.

PubMed

Breeze, J; Allanson-Bailey, L C; Hepper, A E; Lewis, E A

2015-01-01

The wearing of eye protection by United Kingdom soldiers in Afghanistan has reduced the morbidity caused by explosive fragments. However, the remaining face remains uncovered because there is a lack of evidence to substantiate the procurement of methods to protect it. Using a new computerised tool we entered details of the entry sites of surface wounds caused by explosive fragments in all UK soldiers who were injured in the face between 1 January 2010 and 31 December 2011. We compared clinical and predicted immediate and long term outcomes (as defined by the Abbreviated Injury Score (AIS) and the Functional Capacity Index (pFCI), respectively). We also used the tool to predict how additional protection in the form of a visor and mandible guard would affect outcomes. A soldier wearing eye protection was 9 times (1.03/0.12) less likely to sustain an eye injury than one without. However, 38% of soldiers in this series were not wearing eye protection at the time of injury. There was no significant difference between the AIS and pFCI scores predicted by the tool and those found clinically. There is limited evidence to support the use of a mandible guard; its greatest asset is better protection of the nose, but a visor would be expected to reduce long-term morbidity more than eye protection alone, and we recommend future trials to assess its acceptability to users. We think that use of this novel tool can help in the selection of future methods of ballistic facial protection. Copyright © 2014. Published by Elsevier Ltd.

Surgical Stabilization of Costoclavicular Injuries - A Combination of Flail Chest Injuries and a Clavicula Fracture.

PubMed

Langenbach, Andreas; Pinther, Melina; Krinner, Sebastian; Grupp, Sina; Ekkernkamp, Axel; Hennig, Friedrich F; Schulz-Drost, Stefan

2017-01-01

Background: Flail chest injuries (FCI) are associated with a high morbidity and mortality rate. As a concomitant clavicle fracture in FCI even worsens the outcome, the question is how can those costoclavicular injuries (CCI) be managed surgically. Methods: 11 patients with CCI were surgically treated by a locked plate osteosynthesis of the Clavicle and the underlying ribs through limited surgical approaches under general anesthesia. Patients were followed up after 2, 6, 12, 26 and 52 weeks. Results: All patients showed severe chest wall deformity due to severely displaced fractures of the ribs and the clavicle. They were suffering from pain and restriction of respiratory movements. The chest wall could be restored to normal shape in all cases with uneventful bone healing and a high patient convenience. Fractures of the clavicle and the second rib were managed through an innovative clavipectoral approach, the others through standard approaches to the anterolateral and the posterolateral chest wall. Two patients complained about numbness around the lateral approach and lasting periscapular pain. Conclusions: Surgical stabilization might be the appropriate therapy in CCI with dislocated fractures since they would cause severe deformity and loss of function of the chest wall and the shoulder. Celsius.

LETTERS AND COMMENTS: Comment on 'The effects of students' reasoning abilities on conceptual understanding and problem-solving skills in introductory mechanics'

NASA Astrophysics Data System (ADS)

Coletta, Vincent P.; Phillips, Jeffrey A.; Savinainen, Antti; Steinert, Jeffrey J.

2008-09-01

In a recent article, Ates and Cataloglu (2007 Eur. J. Phys. 28 1161-71), in analysing results for a course in introductory mechanics for prospective science teachers, found no statistically significant correlation between students' pre-instruction scores on the Lawson classroom test of scientific reasoning ability (CTSR) and post-instruction scores on the force concept inventory (FCI). As a possible explanation, the authors suggest that the FCI does not probe for skills required to determine reasoning abilities. Our previously published research directly contradicts the authors' finding. We summarize our research and present a likely explanation for their observation of no correlation.

Cognitive correlates of financial abilities in mild cognitive impairment.

PubMed

Okonkwo, Ozioma C; Wadley, Virginia G; Griffith, H Randall; Ball, Karlene; Marson, Daniel C

2006-11-01

To investigate the cognitive correlates of financial abilities in mild cognitive impairment (MCI). Controlled, matched-sample, cross-sectional analysis regressing five cognitive composites on financial performance measures. University medical and research centers. Forty-three persons with MCI and 43 normal controls. The Financial Capacity Instrument (FCI) and a comprehensive neurocognitive battery. Patients with MCI performed significantly worse than controls on cognitive domains of executive function, memory, and language and on FCI domains of financial conceptual knowledge, bank statement management, and bill payment. Patients with MCI also needed significantly more time to complete a multistep financial task and were significantly more likely than controls to make errors on this task. Stepwise regression models revealed that, within the MCI group, attention and executive function were significant correlates of FCI performance. Although impaired memory is the cardinal deficit in MCI, the neurocognitive basis of lower functional performance in MCI appears to be emergent declines in abilities to selectively attend, self-monitor, and temporally integrate information. Compromised performance on cognitive measures of attention and executive function may constitute clinical markers of lower financial abilities and should be evaluated for its relationship to functional ability in general. These cognitive domains may be appropriate targets of future intervention studies aimed at preservation of functional independence in people with MCI.

Deriving common comorbidity indices from the MedDRA classification and exploring their performance on key outcomes in patients with rheumatoid arthritis.

PubMed

Putrik, Polina; Ramiro, Sofia; Lie, Elisabeth; Michaud, Kaleb; Kvamme, Maria K; Keszei, Andras P; Kvien, Tore K; Uhlig, Till; Boonen, Annelies

2018-03-01

To develop algorithms for calculating the Rheumatic Diseases Comorbidity Index (RDCI), Charlson-Deyo Index (CDI) and Functional Comorbidity Index (FCI) from the Medical Dictionary for Regulatory Activities (MedDRA), and to assess how these MedDRA-derived indices predict clinical outcomes, utility and health resource utilization (HRU). Two independent researchers linked the preferred terms of the MedDRA classification into the conditions included in the RDCI, the CDI and the FCI. Next, using data from the Norwegian Register-DMARD study (a register of patients with inflammatory joint diseases treated with DMARDs), the explanatory value of these indices was studied in models adjusted for age, gender and DAS28. Model fit statistics were compared in generalized estimating equation (prediction of outcome over time) models using as outcomes: modified HAQ, HAQ, physical and mental component summary of SF-36, SF6D and non-RA related HRU. Among 4126 patients with RA [72% female, mean (s.d.) age 56 (14) years], median (interquartile range) of RDCI at baseline was 0.0 (1.0) [range 0-6], CDI 0.0 (0.0) [0-7] and FCI 0.0 (1.0) [0-6]. All the comorbidity indices were associated with each outcome, and differences in their performance were moderate. The RDCI and FCI performed better on clinical outcomes: modified HAQ and HAQ, hospitalization, physical and mental component summary, and SF6D. Any non-RA related HRU was best predicted by RDCI followed by CDI. An algorithm is now available to compute three commonly used comorbidity indices from MedDRA classification. Indices performed comparably well in predicting a variety of outcomes, with the CDI performing slightly worse when predicting outcomes reflecting functioning and health. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Latent information in fluency lists predicts functional decline in persons at risk for Alzheimer disease.

PubMed

Clark, D G; Kapur, P; Geldmacher, D S; Brockington, J C; Harrell, L; DeRamus, T P; Blanton, P D; Lokken, K; Nicholas, A P; Marson, D C

2014-06-01

We constructed random forest classifiers employing either the traditional method of scoring semantic fluency word lists or new methods. These classifiers were then compared in terms of their ability to diagnose Alzheimer disease (AD) or to prognosticate among individuals along the continuum from cognitively normal (CN) through mild cognitive impairment (MCI) to AD. Semantic fluency lists from 44 cognitively normal elderly individuals, 80 MCI patients, and 41 AD patients were transcribed into electronic text files and scored by four methods: traditional raw scores, clustering and switching scores, "generalized" versions of clustering and switching, and a method based on independent components analysis (ICA). Random forest classifiers based on raw scores were compared to "augmented" classifiers that incorporated newer scoring methods. Outcome variables included AD diagnosis at baseline, MCI conversion, increase in Clinical Dementia Rating-Sum of Boxes (CDR-SOB) score, or decrease in Financial Capacity Instrument (FCI) score. Receiver operating characteristic (ROC) curves were constructed for each classifier and the area under the curve (AUC) was calculated. We compared AUC between raw and augmented classifiers using Delong's test and assessed validity and reliability of the augmented classifier. Augmented classifiers outperformed classifiers based on raw scores for the outcome measures AD diagnosis (AUC .97 vs. .95), MCI conversion (AUC .91 vs. .77), CDR-SOB increase (AUC .90 vs. .79), and FCI decrease (AUC .89 vs. .72). Measures of validity and stability over time support the use of the method. Latent information in semantic fluency word lists is useful for predicting cognitive and functional decline among elderly individuals at increased risk for developing AD. Modern machine learning methods may incorporate latent information to enhance the diagnostic value of semantic fluency raw scores. These methods could yield information valuable for patient care and clinical trial design with a relatively small investment of time and money. Published by Elsevier Ltd.

The Use of Interactive Technologies to Improve Student Learning of Physics from Middle School to College

NASA Astrophysics Data System (ADS)

Sheldon, Peter; Wellington, Tracey

2003-03-01

The Physics Department at Randolph-Macon Woman's College, a liberal arts women's college of 720, has traditionally turned out approximately 0.6 majors/year. We have invigorated the program by adding community (e.g. SPS, physical space, organized activities), adding a significant technical component (e.g. web-assisted and computer interfaced labs and more technology in the classes [1]), and incorporating new learning techniques (JITT, Physlets, Peer Instruction [2], Interactive DVD's, and using the Personal Response System [3]). Students have responded well as evidenced by significant increases in enrollments as well as strong scores on the FCI. As an offshoot of this original project supported by the NSF, we have applied some of these teaching methods to teach younger children and teachers of younger children. In this presentation, we will discuss the implementation of the new curricular developments and the specific changes we have seen and hope to see in student learning. [1] This work is supported in part by the NSF CCLI Program under grant DUE-9980890. [2] See, for example, the project Galileo website http://galileo.harvard.edu for a description of all of these techniques. [3] The Personal Response System is a wireless response system made by Educue, www.educue.com.

Exciting Alfven Waves using Modulated Electron Heating by High Power Microwaves

NASA Astrophysics Data System (ADS)

Wang, Yuhou; Gekelman, Walter; Pribyl, Patrick; van Compernolle, Bart; Papadopoulos, Konstantinos

2014-10-01

Experiments exploring the physics of ionospheric modification with intense perpendicular propagating waves (k-> ⊥B->0) on the Large Plasma Device (LaPD) at UCLA have been upgraded with the addition of a high power rapidly pulsed microwave source. The plasma is irradiated with ten pulses (250 kW X-band) near the upper-hybrid frequency. The pulses are modulated at a frequency of a fraction (0.1-1.0) of fci (ion cyclotron frequency). Based on a previous single-pulse experiment, the modulated electron heating may drive a large amplitude shear Alfvén wave (f

Effect of inclusion or non-inclusion of short lactations and cow and/or dam genetic group on genetic evaluation of Girolando dairy cattle.

PubMed

Canaza-Cayo, A W; Silva, M V G B; Cobuci, J A; Martins, M F; Lopes, P S

2016-04-04

The objective of this study was to evaluate the effects of inclusion or non-inclusion of short lactations and cow (CGG) and/or dam (DGG) genetic group on the genetic evaluation of 305-day milk yield (MY305), age at first calving (AFC), and first calving interval (FCI) of Girolando cows. Covariance components were estimated by the restricted maximum likelihood method in an animal model of single trait analyses. The heritability estimates for MY305, AFC, and FCI ranged from 0.23 to 0.29, 0.40 to 0.44, and 0.13 to 0.14, respectively, when short lactations were not included, and from 0.23 to 0.28, 0.39 to 0.43, and 0.13 to 0.14, respectively, when short lactations were included. The inclusion of short lactations caused little variation in the variance components and heritability estimates of traits, but their non-inclusion resulted in the re-ranking of animals. Models with CGG or DGG fixed effects had higher heritability estimates for all traits compared with models that consider these two effects simultaneously. We recommend using the model with fixed effects of CGG and inclusion of short lactations for the genetic evaluation of Girolando cattle.

Implications of Functional Capacity Loss and Fatality for Vehicle Safety Prioritization.

PubMed

McMurry, Timothy L; Sherwood, Chris; Poplin, Gerald S; Seguí-Gómez, María; Crandall, Jeff

2015-01-01

We investigate the use of the Functional Capacity Index (FCI) as a tool for establishing vehicle safety priorities by comparing the life year burden of injuries to the burden of fatality in frontal and side automotive crashes. We demonstrate FCI's utility by investigating in detail the resulting disabling injuries and their life year costs. We selected occupants in the 2000-2013 NASS-CDS database involved in frontal and side crashes, merged their injuries with FCI, and then used the merged data to estimate each occupant's overall functional loss. Lifetime functional loss was assessed by combining this measure of impairment with the occupants' expected future life spans, estimated from the Social Security Administration's Actuarial Life Table. Frontal crashes produce a large number of disabling injuries, particularly to the lower extremities. In our population, these crashes are estimated to account for approximately 400,000 life years lost to disability in comparison with 500,000 life years lost to fatality. Victims of side crashes experienced a higher rate of fatality but a significantly lower rate of disabling injury (0.3 vs. 1.0%), resulting in approximately 370,000 life years lost to fatality versus 50,000 life years lost to disability. The burden of disabling injuries to car crash survivors should be considered when setting vehicle safety design priorities. In frontal crashes this burden in life years is similar to the burden attributable to fatality.

Stimulated Brillouin scatter in a magnetized ionospheric plasma.

PubMed

Bernhardt, P A; Selcher, C A; Lehmberg, R H; Rodriguez, S P; Thomason, J F; Groves, K M; McCarrick, M J; Frazer, G J

2010-04-23

High power electromagnetic waves transmitted from the HAARP facility in Alaska can excite low-frequency electrostatic waves by magnetized stimulated Brillouin scatter. Either an ion-acoustic wave with a frequency less than the ion cyclotron frequency (f(CI)) or an electrostatic ion cyclotron (EIC) wave just above f(CI) can be produced. The coupled equations describing the magnetized stimulated Brillouin scatter instability show that the production of both ion-acoustic and EIC waves is strongly influenced by the wave propagation relative to the background magnetic field. Experimental observations of stimulated electromagnetic emissions using the HAARP transmitter have confirmed that only ion-acoustic waves are excited for propagation along the magnetic zenith and that EIC waves can only be detected with oblique propagation angles. The ion composition can be obtained from the measured EIC frequency.

A Taxonomy of Introductory Physics Concepts.

NASA Astrophysics Data System (ADS)

Mokaya, Fridah; Savkar, Amit; Valente, Diego

We have designed and implemented a hierarchical taxonomic classification of physics concepts for our introductory physics for engineers course sequence taught at the University of Connecticut. This classification can be used to provide a mechanism to measure student progress in learning at the level of individual concepts or clusters of concepts, and also as part of a tool to measure effectiveness of teaching pedagogy. We examine our pre- and post-test FCI results broken down by topics using Hestenes et al.'s taxonomy classification for the FCI, and compare these results with those found using our own taxonomy classification. In addition, we expand this taxonomic classification to measure performance in our other course exams, investigating possible correlations in results achieved across different assessments at the individual topic level. UCONN CLAS(College of Liberal Arts and Science).

On the Foundations of the Two Measures Field Theory

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

Guendelman, E. I.; Kaganovich, A. B.

2006-11-03

Two Measures Field Theory (TMT) uses both the Riemannian volume element {radical}(-g)d{sup 4}x and a new one Fcy d4x where the new measure of integration Fcy can be build of four scalar fields. Arguments in favor of TMT, both from the point of view of first principles and from the TMT results are summarized. Possible origin of the TMT and symmetries that protect the structure of TMT are reviewed. It appears that four measure scalar fields treated as 'physical coordinates' allow to define local observables in quantum gravity. The resolution of the old cosmological constant problem as a possible directmore » consequence of the TMT structure is discussed. Other applications of TMT to cosmology and particle physics are also mentioned.« less

Floquet high Chern insulators in periodically driven chirally stacked multilayer graphene

NASA Astrophysics Data System (ADS)

Li, Si; Liu, Cheng-Cheng; Yao, Yugui

2018-03-01

Chirally stacked N-layer graphene is a semimetal with ±p N band-touching at two nonequivalent corners in its Brillioun zone. We predict that an off-resonant circularly polarized light (CPL) drives chirally stacked N-layer graphene into a Floquet Chern insulators (FCIs), aka quantum anomalous Hall insulators, with tunable high Chern number C F = ±N and large gaps. A topological phase transition between such a FCI and a valley Hall (VH) insulator with high valley Chern number C v = ±N induced by a voltage gate can be engineered by the parameters of the CPL and voltage gate. We propose a topological domain wall between the FCI and VH phases, along which perfectly valley-polarized N-channel edge states propagate unidirectionally without backscattering.

Toward equity through participation in Modeling Instruction in introductory university physics

NASA Astrophysics Data System (ADS)

Brewe, Eric; Sawtelle, Vashti; Kramer, Laird H.; O'Brien, George E.; Rodriguez, Idaykis; Pamelá, Priscilla

2010-06-01

We report the results of a five year evaluation of the reform of introductory calculus-based physics by implementation of Modeling Instruction (MI) at Florida International University (FIU), a Hispanic-serving institution. MI is described in the context of FIU’s overall effort to enhance student participation in physics and science broadly. Our analysis of MI from a “participationist” perspective on learning identifies aspects of MI including conceptually based instruction, culturally sensitive instruction, and cooperative group learning, which are consistent with research on supporting equitable learning and participation by students historically under-represented in physics (i.e., Black, Hispanic, women). This study uses markers of conceptual understanding as measured by the Force Concept Inventory (FCI) and odds of success as measured by the ratio of students completing introductory physics and earning a passing grade (i.e., C- or better) by students historically under-represented in physics to reflect equity and participation in introductory physics. FCI pre and post scores for students in MI are compared with lecture-format taught students. Modeling Instruction students outperform students taught in lecture-format classes on post instruction FCI (61.9% vs 47.9%, p<0.001 ), where these benefits are seen across both ethnic and gender comparisons. In addition, we report that the odds of success in MI are 6.73 times greater than in lecture instruction. Both odds of success and FCI scores within Modeling Instruction are further disaggregated by ethnicity and by gender to address the question of equity within the treatment. The results of this disaggregation indicate that although ethnically under-represented students enter with lower overall conceptual understanding scores, the gap is not widened during introductory physics but instead is maintained, and the odds of success for under-represented students is not different from majority students. Women, similarly enter with scores indicating lower conceptual understanding, and over the course of MI this understanding gap increases, yet we do not find differences in the odds of success between men and women. Contrasting these results with the participationist view on learning indicates a movement toward greater equity in introductory physics but also indicates that the instructional environment can be improved.

Frequency of DEA 1 antigen in 1037 mongrel and PUREBREED dogs in ITALY.

PubMed

Carli, E; Carminato, A; Ravagnan, S; Capello, K; Antognoni, M T; Miglio, A; Furlanello, T; Proverbio, D; Spada, E; Stefani, A; Mutinelli, F; Vascellari, M

2017-11-29

The prevalence of dog erythrocyte antigen (DEA 1) in canine population is approximately 40-60%. Often data are limited to a small number of breeds and/or dogs. The aims of this study were to evaluate frequency of DEA 1 in a large population of purebred and mongrel dogs including Italian native breeds and to recognize a possible association between DEA 1 and breed, sex, and genetic and phenotypical/functional classifications of breeds. Frequencies of DEA 1 blood group collected from screened/enrolled blood donors and from healthy and sick dogs were retrospectively evaluated. The breed and the sex were recorded when available. DEA 1 blood typing was assessed by immunocromatographic test on K3EDTA blood samples. The prevalence of DEA 1 antigen was statistically related to breed, gender, Fédération Cynologique Internationale (FCI) and genotypic grouping. Sixty-two per cent dogs resulted DEA 1+ and 38% DEA 1-. DEA 1- was statistically associated with Dogo Argentino, Dobermann, German Shepherd, Boxer, Corso dogs, the molossian dogs, the FCI group 1, 2 and 3 and the genetic groups "working dogs" and "mastiff". DEA 1+ was statistically associated with Rottweiler, Briquet Griffon Vendéen, Bernese mountain dog, Golden Retriever, the hunting breeds, the FCI group 4, 6, 7 and 8 and the genetic groups "scent hounds" and "retrievers". No gender association was observed. Data obtained by this work may be clinically useful to drive blood donor enrollment and selection among different breeds.

Assessing students' conceptual knowledge of electricity and magnetism

NASA Astrophysics Data System (ADS)

McColgan, Michele W.; Finn, Rose A.; Broder, Darren L.; Hassel, George E.

2017-12-01

We present the Electricity and Magnetism Conceptual Assessment (EMCA), a new assessment aligned with second-semester introductory physics courses. Topics covered include electrostatics, electric fields, circuits, magnetism, and induction. We have two motives for writing a new assessment. First, we find other assessments such as the Brief Electricity and Magnetism Assessment and the Conceptual Survey on Electricity and Magnetism not well aligned with the topics and content depth of our courses. We want to test introductory physics content at a level appropriate for our students. Second, we want the assessment to yield scores and gains comparable to the widely used Force Concept Inventory (FCI). After five testing and revision cycles, the assessment was finalized in early 2015 and is available online. We present performance results for a cohort of 225 students at Siena College who were enrolled in our algebra- and calculus-based physics courses during the spring 2015 and 2016 semesters. We provide pretest, post-test, and gain analyses, as well as individual question and whole test statistics to quantify difficulty and reliability. In addition, we compare EMCA and FCI scores and gains, and we find that students' FCI scores are strongly correlated with their performance on the EMCA. Finally, the assessment was piloted in an algebra-based physics course at George Washington University (GWU). We present performance results for a cohort of 130 GWU students and we find that their EMCA scores are comparable to the scores of students in our calculus-based physics course.

Treatment summaries, follow-up care instructions, and patient navigation: could they be combined to improve cancer survivor's receipt of follow-up care?

PubMed

Jabson, Jennifer M

2015-12-01

Cancer survivors require follow-up care to ensure early detection of recurrence, management of late/long term effects, preventive screening for early detection of second primary malignancies, as well as other forms of preventive care. But not all survivors receive necessary follow-up care. Combining survivorship care plans and patient navigation may be a successful strategy to improve survivor's receipt of necessary follow-up care. Using data from the 2010 LIVESTRONG online survey of cancer survivors (N = 3854), this study tested associations between receipt of follow-up care instructions (FCI) and treatment summaries (TS) paired with patient navigation (PN), and survivor's receipt of cancer surveillance, preventive cancer screening, and attendance at regular medical appointments. Survivors who received FCI, TS, and patient navigation were the most likely to report attendance at all medical appointments (aOR 4.17, 95% CI 2.30, 7.57, p ≤ .001) and receipt of preventive cancer screening (aOR 3.56, 95% CI 2.28, 5.55, p ≤ .001). Likelihood of receiving follow-up care was greatest when survivors received FCI, TS, and PN. This pairing appeared to be most beneficial for survivor's attendance at medical appointments and receipt of preventive cancer screening. By improving attendance at medical appointments and prevention cancer screening, pairing SCP and PN could benefit survivors through reduced recurrence, earlier recurrence detection, and prevention of second primaries.

Generation of Shear Alfvén Waves by Repetitive High Power Microwave Pulses Near the Electron Plasma Frequency - A laboratory study of a ``Virtual Antenna''

NASA Astrophysics Data System (ADS)

Wang, Yuhou; Gekelman, Walter; Pribyl, Patrick; van Compernolle, Bart; Papadopoulos, Konstantinos

2015-11-01

ELF / ULF waves are important in terrestrial radio communications but difficult to launch using ground-based structures due to their enormous wavelengths. In spite of this generation of such waves by field-aligned ionospheric heating modulation was first demonstrated using the HAARP facility. In the future heaters near the equator will be constructed and laboratory experiments on cross-field wave propagation could be key to the program's success. Here we report a detailed laboratory study conducted on the Large Plasma Device (LaPD) at UCLA. In this experiment, ten rapid pulses of high power microwaves (250 kW X-band) near the plasma frequency were launched transverse to the background field, and were modulated at a variable fraction (0.1-1.0) of fci. Along with bulk electron heating and density modification, the microwave pulses generated a population of fast electrons. The field-aligned current carried by the fast electrons acted as an antenna that radiated shear Alfvén waves. It was demonstrated that a controllable arbitrary frequency (f

Gender Differences in Both Force Concept Inventory and Introductory Physics Performance

NASA Astrophysics Data System (ADS)

Docktor, Jennifer; Heller, Kenneth

2008-10-01

We present data from a decade of introductory calculus-based physics courses for science and engineering students at the University of Minnesota taught using cooperative group problem solving. The data include 40 classes with more than 5500 students taught by 22 different professors. The average normalized gain for males is 0.4 for these large classes that emphasized problem solving. Female students made up approximately 20% of these classes. We present relationships between pre and post Force Concept Inventory (FCI) scores, course grades, and final exam scores for females and males. We compare our results with previous studies from Harvard [2] and the University of Colorado [3,4]. Our data show there is a significant gender gap in pre-test FCI scores that persists post-instruction although there is essentially no gender difference in course performance as determined by course grade.

First principles electron-correlated calculations of optical absorption in magnesium clusters★

NASA Astrophysics Data System (ADS)

Shinde, Ravindra; Shukla, Alok

2017-11-01

In this paper, we report large-scale configuration interaction (CI) calculations of linear optical absorption spectra of various isomers of magnesium clusters Mgn (n = 2-5), corresponding to valence transitions. Geometry optimization of several low-lying isomers of each cluster was carried out using coupled-cluster singles doubles (CCSD) approach, and these geometries were subsequently employed to perform ground and excited state calculations using either the full-CI (FCI) or the multi-reference singles-doubles configuration interaction (MRSDCI) approach, within the frozen-core approximation. Our calculated photoabsorption spectrum of magnesium dimer (Mg2) is in excellent agreement with the experiments both for peak positions, and intensities. Owing to the sufficiently inclusive electron-correlation effects, these results can serve as benchmarks against which future experiments, as well as calculations performed using other theoretical approaches, can be tested. Supplementary material in the form of one pdf fille available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-80356-6.

Financial Capacity Following Traumatic Brain Injury: A Six-Month Longitudinal Study

PubMed Central

Dreer, Laura E.; DeVivo, Michael J.; Novack, Thomas A.; Marson, Daniel C.

2015-01-01

Objective To longitudinally investigate financial capacity (FC) following traumatic brain injury (TBI). Design Longitudinal study comparing FC in cognitively healthy adults and persons with moderate to severe TBI at time of acute hospitalization (Time 1) and at six months post injury (Time 2). Setting Inpatient brain injury rehabilitation unit. Participants Twenty healthy adult controls and 24 adult persons with moderate to severe TBI. Main Outcome Measures Participants were administered the Financial Capacity Instrument (FCI-9), a standardized instrument that measures performance on eighteen financial tasks, nine domains, and two global scores. Between and within group differences were examined for each FCI-9 domain and global scores. Using control group referenced cut scores, participants with TBI were also assigned an impairment rating (intact, marginal, or impaired) on each domain and global score. Results At Time 1, participants with TBI performed significantly below controls on the majority of financial variables tested. At Time 2, participants with TBI demonstrated within group improvement on both simple and complex financial skills, but continued to perform below adult controls on complex financial skills and both global scores. Group by time interactions were significant for five domains and both global scores. At Time 1, high percentages of participants with TBI were assigned either ‘marginal’ or ‘impaired’ ratings on the domains and global scores, with significant percentage increases of ‘intact’ ratings at Time 2. Conclusions Immediately following acute injury, persons with moderate to severe TBI show global impairment of FC. Findings indicate improvement of both simple and complex financial skills over a six month period, but continued impairment on more complex financial skills. Future studies should examine loss and recovery of FC following TBI over longer time periods and a wider range of injury severity. PMID:22369113

Effect of Modeling Instruction on Concept Knowledge Among Ninth Grade Physics Students

NASA Astrophysics Data System (ADS)

Ditmore, Devin Alan

A basic knowledge of physics concepts is the gateway to success through high-paying careers in science, technology, engineering, and mathematics (STEM). Many students show little understanding of concepts following traditional physics instruction. As an alternative to current lecture-based approaches for high school physics instruction, Piaget's theory of cognitive development supports using real scientific experiences to lead learners from concrete to formal understanding of complex concepts. Modeling instruction (MI) is a pedagogy that guides learners through genuine scientific experiences. This project study analyzed the effects of MI on 9th grade physics students' gains on the test measuring mastery of physics concepts, Force Concept Inventory (FCI). A quasi-experimental design was used to compare the FCI scores of a traditional lecture-taught control group to a treatment group taught using MI. A t test t(-.201) = 180.26, p = .841 comparing the groups and an analysis of variance F(2,181) = 5.20 comparing female to male students indicated MI had no significant positive effect on students. A partial eta squared of the effect size showed that 5.4% of the variance in FCI gains was accounted for by gender, favoring female participants for both groups. The significant relationship between content and gender bears further inquiry. A lesson plan guide was designed to help teachers use computer simulation technology within the MI curriculum. The project promotes positive social change by exploring further ways to help adolescents experience success in physics at the beginning of high school, leading to future success in all STEM areas.

Students' proficiency scores within multitrait item response theory

NASA Astrophysics Data System (ADS)

Scott, Terry F.; Schumayer, Daniel

2015-12-01

In this paper we present a series of item response models of data collected using the Force Concept Inventory. The Force Concept Inventory (FCI) was designed to poll the Newtonian conception of force viewed as a multidimensional concept, that is, as a complex of distinguishable conceptual dimensions. Several previous studies have developed single-trait item response models of FCI data; however, we feel that multidimensional models are also appropriate given the explicitly multidimensional design of the inventory. The models employed in the research reported here vary in both the number of fitting parameters and the number of underlying latent traits assumed. We calculate several model information statistics to ensure adequate model fit and to determine which of the models provides the optimal balance of information and parsimony. Our analysis indicates that all item response models tested, from the single-trait Rasch model through to a model with ten latent traits, satisfy the standard requirements of fit. However, analysis of model information criteria indicates that the five-trait model is optimal. We note that an earlier factor analysis of the same FCI data also led to a five-factor model. Furthermore the factors in our previous study and the traits identified in the current work match each other well. The optimal five-trait model assigns proficiency scores to all respondents for each of the five traits. We construct a correlation matrix between the proficiencies in each of these traits. This correlation matrix shows strong correlations between some proficiencies, and strong anticorrelations between others. We present an interpretation of this correlation matrix.

78 FR 49468 - Arturo Guillermo Nino, Inmate Number #04908-379, FCI Beaumont Low, Federal Correctional Institute...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-14

... to Mexico a defense article, that is to wit: several AK-47 type rifles and magazines, without having..., or business organization related to Nino by affiliation, ownership, control or position of...

Very high stability systems: LMJ target alignment system and MTG imager test setup

NASA Astrophysics Data System (ADS)

Compain, Eric; Maquet, Philippe; Kunc, Thierry; Marque, Julien; Lauer-Solelhac, Maxime; Delage, Laurent; Lanternier, Catherine

2015-09-01

Most of space instruments and research facilities require test equipment with demanding opto-mechanical stability. In some specific cases, when the stability performance directly drives the final performance of the scientific mission and when feasibility is questionable, specific methods must be implemented for the associated technical risk management. In present paper, we will present our heritage in terms of methodology, design, test and the associated results for two specific systems : the SOPAC-POS and the MOTA, generating new references for future developments. From a performance point of view, we will emphasis on following key parameters : design symmetry, thermal load management, and material and structural choices. From a method point of view the difficulties arise first during design, from the strong coupling between the thermal, mechanical and optical performance models, and then during testing, from the difficulty of conceiving test setup having appropriate performance level. We will present how these limitations have been overcome. SOPAC-POS is the target alignment system of the LMJ, Laser Mega Joule, the French inertial confinement fusion research center. Its stability has been demonstrated by tests in 2014 after 10 years of research and development activities, achieving 1μm stability @ 6m during one hour periods. MOTA is an Optical Ground Support Equipment aiming at qualifying by tests the Flexible Combined Imager (FCI). FCI is an instrument for the meteorological satellite MTG-I, a program of and funded by the European Space Agency and under prime contractorship of Thales Alenia Space. Optimized design will allow to get better than 0.2 μrad stability for one hour periods, as required for MTF measurement.

Examining the impact of the Guided Constructivist teaching method on students' misconceptions about concepts of Newtonian physics

NASA Astrophysics Data System (ADS)

Ibrahim, Hyatt Abdelhaleem

The effect of Guided Constructivism (Interactivity-Based Learning Environment) and Traditional Expository instructional methods on students' misconceptions about concepts of Newtonian Physics was investigated. Four groups of 79 of University of Central Florida students enrolled in Physics 2048 participated in the study. A quasi-experimental design of nonrandomized, nonequivalent control and experimental groups was employed. The experimental group was exposed to the Guided Constructivist teaching method, while the control group was taught using the Traditional Expository teaching approach. The data collection instruments included the Force Concept Inventory Test (FCI), the Mechanics Baseline Test (MBT), and the Maryland Physics Expectation Survey (MPEX). The Guided Constructivist group had significantly higher means than the Traditional Expository group on the criterion variables of: (1) conceptions of Newtonian Physics, (2) achievement in Newtonian Physics, and (3) beliefs about the content of Physics knowledge, beliefs about the role of Mathematics in learning Physics, and overall beliefs about learning/teaching/appropriate roles of learners and teachers/nature of Physics. Further, significant relationships were found between (1) achievement, conceptual structures, beliefs about the content of Physics knowledge, and beliefs about the role of Mathematics in learning Physics; (2) changes in misconceptions about the physical phenomena, and changes in beliefs about the content of Physics knowledge. No statistically significant difference was found between the two teaching methods on achievement of males and females. These findings suggest that differences in conceptual learning due to the nature of the teaching method used exist. Furthermore, greater conceptual learning is fostered when teachers use interactivity-based teaching strategies to train students to link everyday experience in the real physical world to formal school concepts. The moderate effect size and power of the study suggest that the effect may not be subtle, but reliable. Physics teachers can use these results to inform their decisions about structuring learning environment when conceptual learning is important.

Flight Crew Integration (FCI) ISS Crew Comments Database & Products Summary

NASA Technical Reports Server (NTRS)

Schuh, Susan

2016-01-01

This Crew Debrief Data provides support for design and development of vehicles, hardware, requirements, procedures, processes, issue resolution, lessons learned, consolidation and trending for current Programs; and much of the data is also used to support development of future Programs.

Risk based meat hygiene--examples on food chain information and visual meat inspection.

PubMed

Ellerbroek, Lüppo

2007-08-01

The Regulation (EC) No. 854/2004 refers in particularly to a broad spectrum of official supervision of products of animal origin. The supervision should be based on the most current relevant information which is available. The proposal presented includes forms for implementation of Food Chain Information (FCI) as laid down in the Regulation (EC) No. 853/2004 as well as suggestions for the implementation of the visual inspection and criteria for a practical approach to assist the competent authority and the business operator. These suggestions are summarised in two forms including the FCI and practical information from the farm of origin as well as from the slaughterhouse needed for the competent authority to permit the visual meat inspection of fattening pigs. The requested information from the farm level include i.e. an animal loss rate during the fattening period and diagnostic findings of carcasses and respectively on organs of the animals during meat inspection procedure. The evaluation of findings in liver and pleura at the slaughterhouse level indicate a correlation to the general health status of the fattening conditions at farm level. The criteria developed are in principle suited for a "gold standard" of the health status of fattening pigs and the criteria may serve as practical implementation of the term Good Farming Practice in relation to consumer protection. Only for fattening pigs deriving from farms fulfilling this "gold standard" the visual meat inspection shall be permitted. It is proposed to integrate the two forms for FCI and additional information for authorisation of visual meat inspection for fattening pigs in the working document of the DG SANCO titled "Commission regulation of laying down specific rules on official controls for the inspection of meat" (SANCO/2696/2006).

Adrenocortical reserves in hyperthyroidism.

PubMed

Agbaht, Kemal; Gullu, Sevim

2014-02-01

Explicit data regarding the changes in adrenocortical reserves during hyperthyroidism do not exist. We aimed to document the capability (response) of adrenal gland to secrete cortisol and DHEA-S during hyperthyroidism compared to euthyroidism, and to describe factors associated with these responses. A standard-dose (0.25 mg/i.v.) ACTH stimulation test was performed to the same patients before hyperthyroidism treatment, and after attainment of euthyroidism. Baseline cortisol (Cor(0)), DHEA-S (DHEA-S(0)), cortisol binding globulin (CBG), ACTH, calculated free cortisol (by Coolen's equation = CFC), free cortisol index (FCI), 60-min cortisol (Cor(60)), and DHEA-S (DHEA-S(60)), delta cortisol (ΔCor), delta DHEA-S (ΔDHEA-S) responses were evaluated. Forty-one patients [22 females, 49.5 ± 15.2 years old, 32 Graves disease, nine toxic nodular goiter] had similar Cor(0), DHEA-S(0), CFC, FCI, and DHEA-S(60) in hyperthyroid and euthyroid states. Cor(60), ΔCor, and ΔDHEA-S were lower in hyperthyroidism. In four (10 %) patients the peak ACTH-stimulated cortisol values were lower than 18 μg/dL. When the test repeated after attainment of euthyroidism, all of the patients had normal cortisol response. Regression analysis demonstrated an independent association of Cor(60) with free T3 in hyperthyroidism. However, the predictors of CFC, FCI, and DHEA-S levels were serum creatinine levels in hyperthyroidism, and both creatinine and transaminase levels in euthyroidism. ACTH-stimulated peak cortisol, delta cortisol, and delta DHEA-S levels are decreased during hyperthyroidism, probably due to increased turnover. Since about 10 % of the subjects with hyperthyroidism are at risk for adrenal insufficiency, clinicians dealing with Graves' disease should be alert to the possibility of adrenal insufficiency during hyperthyroid stage.

Epidemiology of ocular disorders presumed to be inherited in three large Italian dog breeds in Italy.

PubMed

Guandalini, Adolfo; Di Girolamo, Nicola; Santillo, Daniele; Andreani, Valentina; Corvi, Roberta; Bandini, Marina; Peruccio, Claudio

2017-09-01

To describe the epidemiology and the types of eye disorders that are presumed to be inherited (PIED) in three large Italian dog breeds. Three large Italian dog breeds: Neapolitan Mastiff (FCI code: 197), Maremma Sheepdog (FCI code: 201), and Italian Corso dog (FCI code: 343). All dogs that underwent a complete ophthalmic examination between 1992 and 2012 were included in this prospective observational study. The prevalence of eye disorders with 95% confidence intervals was reported for presumed healthy dogs and for dogs referred to a veterinary center for an ophthalmic consultation. Univariate and multivariate logistic regression techniques were used to generate odds ratios. Of 605 dogs examined during the study period, 351 dogs were affected by at least one PIED (58%; 95% CI: 54-62%). The prevalence of PIED was significantly lower in dogs presented for ophthalmic examination (53.8%) as compared to presumed healthy dogs (62.2%)(OR: 1.4; 95% CI: 1.02-1.9; P = 0.037). Also after multivariate adjustment for the period of observation, the odds of Neapolitan Mastiff (92.1%; OR: 21.4; 95% CI: 11.1-41.4) and of Cane Corso (57.7%; OR: 2.5; 95% CI: 1.7-3.6) suffering a PIED were greater than the Maremma Sheepdog (35.4%). The most common PIED in each breed were entropion (24.3% of all the PIED) in the Neapolitan Mastiff, ectropion (36.6%) in the Corso dog, and cataract (27.9%) in the Maremma Sheepdog. Clinicians should be aware that three large Italian dog breeds frequently suffer PIED. Breed standards should be reconsidered, and breeding programs should be directed at limiting such disorders. © 2016 American College of Veterinary Ophthalmologists.

Benchmarking the FCI at Illinois State's Residential Life.

ERIC Educational Resources Information Center

Cain, David A.

1998-01-01

Describes how Office of Residential Life at one university met maintenance challenges facing its residential and food-service facilities. Discusses study conducted in 1992 to evaluate widespread management practices and addresses its findings, including six recommended practices. Examines development and implementation of facilities audit,…

The role of optical sensors in environmental applications

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

Coulter, S.L.; Klainer, S.M.; Saini, D.

1995-12-31

With the ever increasing regulations and public consciousness on pollution control there is an increasing demand for effective monitors for field use. The specifications for an effective field monitor are that it be an in situ sensor which presents real time data; that data are received without sampling or testing artifacts; and, that there is a low cost associated with running multiple tests. Fiber optic chemical sensors have been designed by FCI Environmental, Inc. which meet these specifications for the detection of hydrocarbons in air, water or soil. Recent developments at FCI Environmental in the field of optic chemical sensorsmore » include the development of a chip level waveguide sensor. With the improvements in the size and function of the sensor, which impacts the manufacturability and cost of the sensors, this new technology presents new opportunities in the fields of in situ monitoring. Current activities in the development of this technology and applications of specific solid-state immunoassay are discussed.« less

Evidence on the coherence-pieces debate from the force concept inventory

NASA Astrophysics Data System (ADS)

Badagnani, D.; Petrucci, D.; Cappannini, O.

2018-01-01

We use force concept inventory (FCI) data to probe the consistency of commonsense physics as a knowledge system. The source of this data is the administration of the FCI to first-year science university students. Data quality was checked using item response theory and studying answer distributions for each question. We find apparently paradoxical results: depending on how the data is analysed, answers seem highly systematic or almost random-like. These results are compatible with others found in the literature and can be construed as arising either from a coherent knowledge system or from knowledge in pieces. We hypothesise as a possible source of this apparent contradiction that predictions and explanations use different resources: the former would use reflex, low-cost cognitive resources while the latter would involve conceptualisations. We show that the articulation of both resources may be crucial for expert thinking productivity (the ability to apply a theory to novel situations). We sketch some consequences of the proposed structure of commonsense thinking for teaching and further research.

Electrostatic ion-cyclotron waves in a nonuniform magnetic field

NASA Technical Reports Server (NTRS)

Cartier, S. L.; Dangelo, N.; Merlino, R. L.

1985-01-01

The properties of electrostatic ion-cyclotron waves excited in a single-ended cesium Q machine with a nonuniform magnetic field are described. The electrostatic ion-cyclotron waves are generated in the usual manner by drawing an electron current to a small exciter disk immersed in the plasma column. The parallel and perpendicular (to B) wavelengths and phase velocities are determined by mapping out two-dimensional wave phase contours. The wave frequency f depends on the location of the exciter disk in the nonuniform magnetic field, and propagating waves are only observed in the region where f is approximately greater than fci, where fci is the local ion-cyclotron frequency. The parallel phase velocity is in the direction of the electron drift. From measurements of the plasma properties along the axis, it is inferred that the electron drift velocity is not uniform along the entire current channel. The evidence suggests that the waves begin being excited at that axial position where the critical drift velocity is first exceeded, consistent with a current-driven excitation mechanism.

Analysis of Newton's Third Law Questions on the Force Concepts Inventory at Georgia State University

NASA Astrophysics Data System (ADS)

Oakley, Christopher; Thoms, Brian

2012-03-01

A major emphasis of the Physics Education Research program at Georgia State University is an effort to assess and improve students' understanding of Newton's Laws concepts. As part of these efforts the Force Concepts Inventory (FCI) has been given to students in both the algebra-based and calculus-based introductory physics sequences. In addition, the algebra-based introductory physics sequence is taught in both a SCALE-UP and a traditional lecture format. The results of the FCI have been analyzed by individual question and also as categorized by content. The analysis indicates that students in both algebra and calculus-based courses are successful at overcoming Aristotelian misconceptions regarding Newton's Third Law (N3) in the context of a stationary system. However, students are less successful on N3 questions involving objects in constant motion or accelerating. Interference between understanding of Newton's Second and Third Laws as well as other possible explanations for lower student performance on N3 questions involving non-stationary objects will be discussed.

Condition of Florida Educational Facilities and Balancing Budgets

ERIC Educational Resources Information Center

Jones, Margaret Moore

2012-01-01

The purpose of this study was to examine if relationships existed between the condition of instructional facilities within Florida Coastal School District, as measured by the Facilities Condition Index (FCI), and enrollment percentages for special education students, African American students, Caucasian students, and students receiving free and…

Effects of increasing the allowable compressive stress at release on the shear strength of prestressed concrete girders.

DOT National Transportation Integrated Search

2008-09-01

In recent years, several research projects have been conducted to study the feasibility of increasing the allowable : compressive stress in concrete at prestress transfer, currently defined as 0.60f'ci in the AASHTO LRFD Bridge : Design Specification...

NPDES Permit for Federal Corrections Institution, Englewood Municipal Separate Storm Sewer System in Colorado

EPA Pesticide Factsheets

Under NPDES permit CO-R042005, the Federal Corrections Institution (FCI), Englewood is authorized to discharge from all MS4 outfalls to receiving waters which include Bear Creek, the South Platte River in the City of Lakewood, Jefferson County, Colo.

Tutorials in Introductory Physics: The Pain and the Gain

ERIC Educational Resources Information Center

Cruz, Emerson; O'Shea, Brian; Schaffenberger, Werner; Wolf, Steven; Kortemeyer, Gerd

2010-01-01

In an introductory physics sequence with a large enrollment of premedical students, traditional recitation sessions were replaced by "Tutorials in Introductory Physics," developed by the Physics Education Group at the University of Washington. Initially, summative test scores (as well as FCI scores) dramatically increased, but so did…

77 FR 3499 - FCI USA, LLC Corporate Administrative Division Including On-Site Leased Workers From JFC...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-24

... Administrative Division Including On-Site Leased Workers From JFC Including Teleworkers Located Throughout the United States Reporting to Etters, PA; Amended Certification Regarding Eligibility To Apply for Worker.... 2273, the Department of Labor issued a Certification of Eligibility To Apply for Worker Adjustment...

76 FR 56471 - Membership of the Senior Executive Service Standing Performance Review Boards

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-13

..., OK. LOCKETT, CHARLES L COMPLEX WARDEN-USP, FCC, TERRE HAUTE, IN. LONGLEY, ARCHELAUS WARDEN, FCI... ADMINISTRATIVE SERVICES STAFF. HOLTGREWE, KENT L DIRECTOR, IT POLICY AND PLANNING STAFF. JOHNSTON, JAMES W.... STEWART, MALCOLM L DEPUTY SOLICITOR GENERAL. Antitrust Division--ATR POZEN, SHARIS PRINCIPAL DEPUTY...

76 FR 11756 - Action Affecting Export Privileges; Ali Amirnazmi; Order Denying Export Privileges

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-03

... DEPARTMENT OF COMMERCE Bureau of Industry and Security Action Affecting Export Privileges; Ali Amirnazmi; Order Denying Export Privileges In the Matter of: Ali Amirnazmi, Register 63302-066, FCI... release and forfeit $81,277.37. Section 766.25 of the Export Administration Regulations (``EAR'' or...

Assessing Conceptual Knowledge for the Physics of Semiconductors

ERIC Educational Resources Information Center

Ene, Emanuela

2013-01-01

Following the trend in science and engineering education generated by the visible impact created by the Force Concept Inventory (FCI), the investigator developed a Physics of Semiconductors Concept Inventory (PSCI). PSCI fills the need of standardized concept tests for undergraduate education in photonics and electrical engineering. The structure…

New Methods for the Detection and Interception of Frequency-Hopped Waveforms

DTIC Science & Technology

1990-11-01

that £[p2 Q2 /O] = uF + 2 + o(cos 0 + 6 sin9)2 + 4n(acos0+/3sin)(7ycos0+6sinO)+o r(acos0+sinO)2 I + ( acosO +/3sinO) 2(Tcos9+ 6sin O)2 (3.134) i which...Jcins I lopk ins lI mvtrsi! t3 A pplied Physics Laborator Before1 NII After Figure 4.4: Deconvolut ion Applivod to Oi-fFci i r 100 The Johns 11opkins...Arlington, VA 20360 Library 2 Naval Postgraduate School Monterey, CA 92940 Library 2 Naval Research Laborator . Washington, DC 20375 Library 2 J. W

Rugby and elliptical-shaped hohlraums experiments on the OMEGA laser facility

NASA Astrophysics Data System (ADS)

Tassin, Veronique; Monteil, Marie-Christine; Depierreux, Sylvie; Masson-Laborde, Paul-Edouard; Philippe, Franck; Seytor, Patricia; Fremerye, Pascale; Villette, Bruno

2017-10-01

We are pursuing on the OMEGA laser facility indirect drive implosions experiments in gas-filled rugby-shaped hohlraums in preparation for implosion plateforms on LMJ. The question of the precise wall shape of rugby hohlraum has been addressed as part of future megajoule-scale ignition designs. Calculations show that elliptical-shaped holhraum is more efficient than spherical-shaped hohlraum. There is less wall hydrodynamics and less absorption for the inner cone, provided a better control of time-dependent symmetry swings. In this context, we have conducted a series of experiments on the OMEGA laser facility. The goal of these experiments was therefore to characterize energetics with a complete set of laser-plasma interaction measurements and capsule implosion in gas-filled elliptical-shaped hohlraum with comparison with spherical-shaped hohlraum. Experiments results are discussed and compared to FCI2 radiation hydrodynamics simulations.

Rasch Model Based Analysis of the Force Concept Inventory

ERIC Educational Resources Information Center

Planinic, Maja; Ivanjek, Lana; Susac, Ana

2010-01-01

The Force Concept Inventory (FCI) is an important diagnostic instrument which is widely used in the field of physics education research. It is therefore very important to evaluate and monitor its functioning using different tools for statistical analysis. One of such tools is the stochastic Rasch model, which enables construction of linear…

Force Concept Inventory-Based Multiple-Choice Test for Investigating Students' Representational Consistency

ERIC Educational Resources Information Center

Nieminen, Pasi; Savinainen, Antti; Viiri, Jouni

2010-01-01

This study investigates students' ability to interpret multiple representations consistently (i.e., representational consistency) in the context of the force concept. For this purpose we developed the Representational Variant of the Force Concept Inventory (R-FCI), which makes use of nine items from the 1995 version of the Force Concept Inventory…

Students' Proficiency Scores within Multitrait Item Response Theory

ERIC Educational Resources Information Center

Scott, Terry F.; Schumayer, Daniel

2015-01-01

In this paper we present a series of item response models of data collected using the Force Concept Inventory. The Force Concept Inventory (FCI) was designed to poll the Newtonian conception of force viewed as a multidimensional concept, that is, as a complex of distinguishable conceptual dimensions. Several previous studies have developed…

High performance equipped mirrors for MTG FCI-TA and IRS-FTO

NASA Astrophysics Data System (ADS)

Kazakov, T.; San Juan, J. L.; Serrano, J.; Moreno, J.; González, D.; Rodríguez, G.; López, D.; Vázquez, E.; Aivar, J.; Motos, A.; Rahmouni, Christophe; Imperiali, Stephan; Fappani, Denis

2017-09-01

The Meteosat Third Generation (MTG) Programme is being realised through the well established and successful Cooperation between EUMETSAT and ESA. It will ensure the future continuity of MSG with the capabilities to enhance nowcasting, global and regional numerical weather prediction, climate and atmospheric chemistry monitoring data from Geostationary Orbit.

Polarization of Physics on Global Courses

ERIC Educational Resources Information Center

Alinea, Allan L.; Naylor, Wade

2015-01-01

Since October 2010, the Chemistry-Biology Combined Major Program, an international course taught in English at Osaka University, has been teaching small classes (no more than 20 in size). We present data from the Force Concept Inventory (FCI) given to first-year classical mechanics students (N = 47 students over three years) pre and post score,…

NIF Rugby High Foot Campaign from the design side

NASA Astrophysics Data System (ADS)

Leidinger, J.-P.; Callahan, D. A.; Berzak-Hopkins, L. F.; Ralph, J. E.; Amendt, P.; Hinkel, D. E.; Michel, P.; Moody, J. D.; Ross, J. S.; Rygg, J. R.; Celliers, P.; Clouët, J.-F.; Dewald, E. L.; Kaiser, P.; Khan, S.; Kritcher, A. L.; Liberatore, S.; Marion, D.; Masson-Laborde, P.-E.; Milovich, J. L.; Morice, O.; Pak, A. E.; Poujade, O.; Strozzi, D.; Hurricane, O. A.

2016-05-01

The NIF Rugby High Foot campaign results, with 8 shots to date, are compared with the 2D FCI2 design simulations. A special emphasis is placed on the predictive features and on those areas where some work is still required to achieve the best possible modelling of these MJ-class experiments.

Finding Frequent Closed Itemsets in Sliding Window in Linear Time

NASA Astrophysics Data System (ADS)

Chen, Junbo; Zhou, Bo; Chen, Lu; Wang, Xinyu; Ding, Yiqun

One of the most well-studied problems in data mining is computing the collection of frequent itemsets in large transactional databases. Since the introduction of the famous Apriori algorithm [14], many others have been proposed to find the frequent itemsets. Among such algorithms, the approach of mining closed itemsets has raised much interest in data mining community. The algorithms taking this approach include TITANIC [8], CLOSET+[6], DCI-Closed [4], FCI-Stream [3], GC-Tree [15], TGC-Tree [16] etc. Among these algorithms, FCI-Stream, GC-Tree and TGC-Tree are online algorithms work under sliding window environments. By the performance evaluation in [16], GC-Tree [15] is the fastest one. In this paper, an improved algorithm based on GC-Tree is proposed, the computational complexity of which is proved to be a linear combination of the average transaction size and the average closed itemset size. The algorithm is based on the essential theorem presented in Sect. 4.2. Empirically, the new algorithm is several orders of magnitude faster than the state of art algorithm, GC-Tree.

Assessing the Impacts of a Hybrid ``Flipped'' Approach to University Physics.

NASA Astrophysics Data System (ADS)

Hughes, Chris; Paulson, Scott

2015-03-01

Over the course of several years, the physics faculty at James Madison University has been gradually reforming the introductory calculus-based physics sequence to a hybrid model using a ``flipped classroom'' approach. The content traditionally delivered during lecture was divided into approximately 150 short (5-10 minute) videos. For homework, students are assigned 3-5 videos to watch before each class session. These assignments are combined with in-class activities including gouger problem solving and the tutorials developed by the University of Washington group to provide the students with focused guidance on concepts and skills that students traditionally have left our classes not having mastered. For the fall semester course on mechanics, the Force Concept Inventory (FCI) was used to evaluate student outcomes. For the spring semester course on E&M and optics, the Conceptual Survey of Electricity and Magnetism (CSEM) was used. Student reaction to the course structure was generally positive though there were some complaints in the student evaluations at the end of each semester. However, a positive impact on student outcomes was observed based on the Hake gains on the FCI.

Moving toward change: Institutionalizing reform through implementation of the Learning Assistant model and Open Source Tutorials

NASA Astrophysics Data System (ADS)

Goertzen, Renee Michelle; Brewe, Eric; Kramer, Laird H.; Wells, Leanne; Jones, David

2011-12-01

Florida International University has undergone a reform in the introductory physics classes by focusing on the laboratory component of these classes. We present results from the secondary implementation of two research-based instructional strategies: the implementation of the Learning Assistant model as developed by the University of Colorado at Boulder and the Open Source Tutorial curriculum developed at the University of Maryland, College Park. We examine the results of the Force Concept Inventory (FCI) for introductory students over five years (n=872) and find that the mean raw gain of students in transformed lab sections was 0.243, while the mean raw gain of the traditional labs was 0.159, with a Cohen’s d effect size of 0.59. Average raw gains on the FCI were 0.243 for Hispanic students and 0.213 for women in the transformed labs, indicating that these reforms are not widening the gaps between underrepresented student groups and majority groups. Our results illustrate how research-based instructional strategies can be successfully implemented in a physics department with minimal department engagement and in a sustainable manner.

Image Reconstruction from Data Collected with an Imaging Interferometer

NASA Astrophysics Data System (ADS)

DeSantis, Z. J.; Thurman, S. T.; Hix, T. T.; Ogden, C. E.

The intensity distribution of an incoherent source and the spatial coherence function at some distance away are related by a Fourier transform, via the Van Cittert-Zernike theorem. Imaging interferometers measure the spatial coherence of light propagated from the incoherently illuminated object by combining light from spatially separated points to measure interference fringes. The contrast and phase of the fringe are the amplitude and phase of a Fourier component of the source’s intensity distribution. The Fiber-Coupled Interferometer (FCI) testbed is a visible light, lab-based imaging interferometer designed to test aspects of an envisioned ground-based interferometer for imaging geosynchronous satellites. The front half of the FCI testbed consists of the scene projection optics, which includes an incoherently backlit scene, located at the focus of a 1 m aperture f/100 telescope. The projected light was collected by the back half of the FCI testbed. The collection optics consisted of three 11 mm aperture fiber-coupled telescopes. Light in the fibers was combined pairwise and dispersed onto a sensor to measure the interference fringe as a function of wavelength, which produces a radial spoke of measurements in the Fourier domain. The visibility function was sampled throughout the Fourier domain by recording fringe data at many different scene rotations and collection telescope separations. Our image reconstruction algorithm successfully produced images for the three scenes we tested: asymmetric pair of pinholes, U.S. Air Force resolution bar target, and satellite scene. The bar target reconstruction shows detail and resolution near the predicted resolution limit. This research was developed with funding from the Defense Advanced Research Projects Agency (DARPA). The views, opinions and/or findings expressed are those of the author(s) and should not be interpreted as reflecting the official views or policies of the Department of Defense or the U.S. Government.

Quantum Algorithms for Scientific Computing and Approximate Optimization

NASA Astrophysics Data System (ADS)

Hadfield, Stuart Andrew

Diversity and inclusion has been a concern for the physics community for nearly 50 years. Despite significant efforts including the American Physical Society (APS) Conferences for Undergraduate Women in Physics (CUWiP) and the APS Bridge Program, women, African Americans, and Hispanics continue to be substantially underrepresented in the physics profession. Similar efforts within the field of engineering, whose students make up the majority of students in the introductory calculus-based physics courses, have also met with limited success. With the introduction of research-based instruments such as the Force Concept Inventory (FCI), the Force and Motion Conceptual Evaluation (FMCE), and the Conceptual Survey of Electricity and Magnetism (CSEM), differences in performance by gender began to be reported. Researchers have yet to come to an agreement as to why these "gender gaps" exist in the conceptual inventories that are widely used in physics education research and/or how to reduce the gaps. The "gender gap" has been extensively studied; on average, for the mechanics conceptual inventories, male students outperform female students by 13% on the pretest and by 12% post instruction. While much of the gender gap research has been geared toward the mechanics conceptual inventories, there have been few studies exploring the gender gap in the electricity and magnetism conceptual inventories. Overall, male students outperform female students by 3.7% on the pretest and 8.5% on the post-test; however, these studies have much more variation including one study showing female students outperforming male students on the CSEM. Many factors have been proposed that may influence the gender gap, from differences in background and preparation to various psychological and sociocultural effects. A parallel but largely disconnected set of research has identified gender biased questions within the FCI. This research has produced sporadic results and has only been performed on the FCI. The work performed in this manuscript will seek to synthesize these strands and use large datasets and deep demographic data to understand the persistent differences in male and female performance.

Learning physics concepts as a function of colloquial language usage

NASA Astrophysics Data System (ADS)

Maier, Steven J.

Data from two sections of college introductory, algebra-based physics courses (n1 = 139, n2 = 91) were collected using three separate instruments to investigate the relationships between reasoning ability, conceptual gain and colloquial language usage. To obtain a measure of reasoning ability, Lawson's Classroom Test of Scientific Reasoning Ability (TSR) was administered once near mid-term for each sample. The Force Concept Inventory (FCI) was administered at the beginning and at the end of the term for pre- and post-test measures. Pre- and post-test data from the Mechanics Language Usage instrument were also collected in conjunction with FCI data collection at the beginning and end of the term. The MLU was developed specifically for this study prior to data collection, and results of a pilot test to establish validity and reliability are reported. T-tests were performed on the data collected to compare the means from each sample. In addition, correlations among the measures were investigated between the samples separately and combined. Results from these investigations served as justification for combining the samples into a single sample of 230 for performing further statistical analyses. The primary objective of this study was to determine if scientific reasoning ability (a function of developmental stage) and conceptual gains in Newtonian mechanics predict students' usages of "force" as measured by the MLU. Regression analyses were performed to evaluate these mediated relationships among TSR and FCI performance as a predictor of MLU performance. Statistically significant correlations and relationships existed among several of the measures, which are discussed at length in the body of the narrative. The findings of this research are that although there exists a discernable relationship between reasoning ability and conceptual change, more work needs to be done to establish improved quantitative measures of the role language usage has in developing understandings of course content.

(Wh-)Indeterminates, Free Choice, and Expressive Content in Korean

ERIC Educational Resources Information Center

Park, Eun-Hae

2009-01-01

This dissertation investigates the semantics and pragmatics of two types of free choice items (FCIs) in Korean which employ a wh-indeterminate (i.e., wh-morphology. e.g., "nwukwu" "who/someone") and a non-deictic-indefinite (e.g., "amwu") respectively in combination with a suffixal particle--"na." Both wh-indeterminate-based FCI (wh-(N)-"na")…

Coping with Separation: An Analysis of Outcomes and Strategies Used by Working and Nonworking Wives during Routine Deployment. Part A

DTIC Science & Technology

1987-06-22

of approaching problems) and specfic coping efforts (behavioral or intra- psychic action taken in situations that are aimed at reducing stress... unemployed . Military Medicine, 1981, 146, 10. * I McCubbin, H.I., Boss, P., Wilson, L. & Dahl, B. Family Coping Inventory WI (FCI). In Family

Revitalizing the Physics Department: The Use of Interactive Technologies to Improve Student Learning

NASA Astrophysics Data System (ADS)

Sheldon, Peter; Groover, Holly

2002-04-01

The Physics Department at Randolph-Macon Woman's College, a liberal arts women's college of 720, has traditionally turned out approximately 0.6 majors/year. We have invigorated the program by adding community (e.g. SPS, physical space, organized activities), adding a significant technical component (e.g. web-assisted and computerized labs and more technology in the classes [1]), and incorporating new learning techniques (JITT, Physlets, Peer Instruction and Cooperative Learning [2]). Students have responded well as evidenced by significant increases in enrollments as well as strong scores on the FCI. We have seen mixed results in the lab, but increased performance in the class, which is attributed to the interactive learning techniques that are being implemented through new technologies. In this presentation, we will discuss the implementation of the new curricular developments and the specific changes we have seen in student learning. [1] This work is supported in part by the NSF CCLI Program under grant DUE-9980890. Additional support has been from the Virginia Foundation of Private Colleges and AT&T. [2] See, for example, the project Galileo website http://galileo.harvard.edu for a description of all of these techniques.

78 FR 19193 - Richard Phillips, Currently Incarcerated at: Inmate No. 81783-079, FCI Ray Brook Federal...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-29

...'') was convicted of violating the International Emergency Economic Powers Act (50 U.S.C. 1701, et seq..., license, or order issued under the International Emergency Economic Powers Act (50 U.S.C. 1701-1706); 18.... Obtain from the Denied Person in the United States any item subject to the Regulations with knowledge or...

Validating Two Questions in the Force Concept Inventory with Subquestions

ERIC Educational Resources Information Center

Yasuda, Jun-ichiro; Taniguchi, Masa-aki

2013-01-01

In this study, we evaluate the structural validity of Q.16 and Q.7 in the Force Concept Inventory (FCI). We address whether respondents who answer Q.16 and Q.7 correctly actually have an understanding of the concepts of physics tested in the questions. To examine respondents' levels of understanding, we use subquestions that test them on concepts…

78 FR 37788 - In the Matter of: Juan Ricardo Puente-Paez, Inmate Number #05086-379, FCI McDowell, Federal...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-24

... exported from the United States to Mexico four military spec Interceptor body armor vests, which were... owned, possessed or controlled by the Denied Person, or service any item, of whatever origin, that is... subject to the Regulations are the foreign-produced direct product of U.S.-origin technology. V. This...

The Presence of Gender Disparity on the Force Concept Inventory in a Sample of Canadian Undergraduate Students

ERIC Educational Resources Information Center

Normandeau, Magdalen; Iyengar, Seshu; Newling, Benedict

2017-01-01

Concept inventories (CI) are validated, research-based, multiple-choice tests, which are widely used to assess the effectiveness of pedagogical practices in bringing about conceptual change. In order to be a useful diagnostic tool, a CI must reflect only the student understanding of the conceptual material. The Force Concept Inventory (FCI) is…

NEW BEDFORD, ACUSHNET RIVER ESTUARY WETLANDS ASSESSMENT REPORT, 04-01-1988, SDMS#51719

EPA Pesticide Factsheets

2013-06-11

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Understanding the relationship between student attitudes and student learning

NASA Astrophysics Data System (ADS)

Cahill, Michael J.; McDaniel, Mark A.; Frey, Regina F.; Hynes, K. Mairin; Repice, Michelle; Zhao, Jiuqing; Trousil, Rebecca

2018-02-01

Student attitudes, defined as the extent to which one holds expertlike beliefs about and approaches to physics, are a major research topic in physics education research. An implicit but rarely tested assumption underlying much of this research is that student attitudes play a significant part in student learning and performance. The current study directly tested this attitude-learning link by measuring the association between incoming attitudes (Colorado Learning Attitudes about Science Survey) and student learning during the semester after statistically controlling for the effects of prior knowledge [early-semester Force Concept Inventory (FCI) or Brief Electricity and Magnetism Assessment (BEMA)]. This study spanned four different courses and included two complementary measures of student knowledge: late-semester concept inventory scores (FCI or BEMA) and exam averages. In three of the four courses, after controlling for prior knowledge, attitudes significantly predicted both late-semester concept inventory scores and exam averages, but in all cases these attitudes explained only a small amount of variance in concept-inventory and exam scores. Results indicate that after accounting for students' incoming knowledge, attitudes may uniquely but modestly relate to how much students learn and how well they perform in the course.

Laser plasma interaction on rugby hohlraum on the Omega Laser Facility: Comparisons between cylinder, rugby, and elliptical hohlraums

NASA Astrophysics Data System (ADS)

Masson-Laborde, P. E.; Monteil, M. C.; Tassin, V.; Philippe, F.; Gauthier, P.; Casner, A.; Depierreux, S.; Neuville, C.; Villette, B.; Laffite, S.; Seytor, P.; Fremerye, P.; Seka, W.; Teychenné, D.; Debayle, A.; Marion, D.; Loiseau, P.; Casanova, M.

2016-02-01

Gas-filled rugby-shaped hohlraums have demonstrated high performances compared to a classical similar diameter cylinder hohlraum with a nearly 40% increase of x-ray drive, 10% higher measured peak drive temperature, and an increase in neutron production. Experimental comparisons have been done between rugby, cylinder, and elliptical hohlraums. The impact of these geometry differences on the laser plasma instabilities is examined. Using comparisons with hydrodynamic simulations carried out with the code FCI2 and postprocessed by Piranah, we have been able to reproduce the stimulated Raman and Brillouin scattering spectrum of the different beams. Using a methodology based on a statistical analysis for the gain calculations, we show that the behavior of the laser plasma instabilities in rugby hohlraums can be reproduced. The efficiency of laser smoothing techniques to mitigate these instabilities are discussed, and we show that while rugby hohlraums exhibit more laser plasma instabilities than cylinder hohlraum, the latter can be mitigated in the case of an elliptical hohlraum.

Examining issues of underrepresented minority students in introductory physics

NASA Astrophysics Data System (ADS)

Watkins, Jessica Ellen

In this dissertation we examine several issues related to the retention of under-represented minority students in physics and science. In the first section, we show that in calculus-based introductory physics courses, the gender gap on the FCI is diminished through the use of interactive techniques, but in lower-level introductory courses, the gap persists, similar to reports published at other institutions. We find that under-represented racial minorities perform similar to their peers with comparable academic preparation on conceptual surveys, but their average exam grades and course grades are lower. We also examine student persistence in science majors; finding a significant relationship between pedagogy in an introductory physics course and persistence in science. In the second section, we look at student end-of-semester evaluations and find that female students rate interactive teaching methods a full point lower than their male peers. Looking more deeply at student interview data, we find that female students report more social issues related to the discussions in class and both male and female students cite feeling pressure to obtain the correct answer to clicker questions. Finally, we take a look an often-cited claim for gender differences in STEM participation: cognitive differences explain achievement differences in physics. We examine specifically the role of mental rotations in physics achievement and problem-solving, viewing mental rotations as a tool that students can use on physics problems. We first look at student survey results for lower-level introductory students, finding a low, but significant correlation between performance on a mental rotations test and performance in introductory physics courses. In contrast, we did not find a significant relationship for students in the upper-level introductory course. We also examine student problem-solving interviews to investigate the role of mental rotations on introductory problems.

Establishment of A431 cell membrane chromatography-RPLC method for screening target components from Radix Caulophylli.

PubMed

Hou, Xiaofang; Wang, Sicen; Hou, Jingjing; He, Langchong

2011-03-01

We describe here an analytical method of A431 cell membrane chromatography (A431/CMC) (CMC, cell membrane chromatography) combined with RPLC for recognition, separation, and identification of target components from traditional Chinese medicines (TCMs) Radix Caulophylli. The A431 cells with high expressed epidermal growth factor receptor (EGFR) were used to prepare the stationary phase in the CMC model. Retention fractions on the A431-CMC model were collected using an automated fraction collection and injection module (FC/I). Each fraction was analyzed by RPLC under the optimized conditions. Gefitinib and erlotinib were used as standard compounds to investigate the suitability and reliability of the A431 cell membrane chromatography-RPLC method prior to screening target component from Radix Caulophylli total alkaloids. The results indicated that caulophine and taspine were the target component acting on the epidermal growth factor receptor. This method could be an efficient way in drug discovery using natural medicinal herbs as a source of novel compounds. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analyzing False Positives of Four Questions in the Force Concept Inventory

ERIC Educational Resources Information Center

Yasuda, Jun-ichro; Mae, Naohiro; Hull, Michael M.; Taniguchi, Masa-aki

2018-01-01

In this study, we analyze the systematic error from false positives of the Force Concept Inventory (FCI). We compare the systematic errors of question 6 (Q.6), Q.7, and Q.16, for which clearly erroneous reasoning has been found, with Q.5, for which clearly erroneous reasoning has not been found. We determine whether or not a correct response to a…

Validating Proposed Learning Progressions on Force and Motion Using the Force Concept Inventory: Findings from Singapore Secondary Schools

ERIC Educational Resources Information Center

Fulmer, Gavin W.

2015-01-01

This study examines the validity of 2 proposed learning progressions on the force concept when tested using items from the Force Concept Inventory (FCI). This is the first study to compare students' performance with respect to learning progressions both for force and motion and for Newton's third law in parallel. It is also among the first studies…

The Development of Alternative Food Cost Indexes

DTIC Science & Technology

1974-11-01

Frozen frufts, vegetables , fruit juices , and cake mixes are added and the quantity of purchased bread increased in this FCI. Comment was made that some... Grain , Frozen Vegetables , Mixed, Frozen Beans, Green, Frozen Peaches, Canned Apples, Fresh Oranges, Fresh Strawberries, Frozen Juice , Pineapple...also falls to recognize such accepted food service practices as the use of frozen fruits , vegetables , and juices , or prepared cake mixes, Tj,e

FCI experiments in the corium/water system

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

Huhtiniemi, I.; Hohmann, H.; Magallon, D.

The KROTOS fuel coolant interaction (FCI) tests aim at providing benchmark data to examine the effect of fuel/coolant initial conditions and mixing on explosion energetics. Experiments, fundamental in nature, are performed in well-controlled geometries and are complementary to the FARO large scale tests. Recently, a new test series was started using 3 kg of prototypical core material (80 w/o UO{sub 2}, 20 w/o ZrO{sub 2}) which was poured into a water column of {le} 1.25 m in height (95 mm and 200 mm in diameter) under 0.1 MPa ambient pressure. Four tests have been performed in the test section ofmore » 95 mm in diameter (ID) with different subcooling levels (10-80K) and with and without an external trigger. Additionally, one test has been performed with a test section of 200 mm in diameter (ID) and with an external trigger. No spontaneous or triggered energetic FCIs (steam explosions) have been observed in these corium tests. This is in sharp contrast with the steam explosions observed in the previously reported Al{sub 2}O{sub 3} test series which had the same initial conditions of ambient pressure and subcooling. The post-test analysis of the corium experiments indicated that strong vaporisation at the melt/water contact led to a partial expulsion of the melt from the test section into the pressure vessel. In order to avoid this and to obtain a good penetration and premixing os the corium melt, an additional test has been performed with a larger diameter test section. In all the UO{sub 2}-ZrO{sub 2} tests an efficient quenching process (0.7-1.2 MW/kg-melt) with total fuel fragmentation (mass mean diameter 1.4-2.5 mm) was observed. Results from Al{sub 2}O{sub 3} tests under the same initial conditions are also presented for further confirmation of the observed differences in behaviour between Al{sub 2}O{sub 3} and UO{sub 2}-ZrO{sub 2} melts.« less

European Immunology Congress (7th), Jerusalem, Israel.

DTIC Science & Technology

1985-11-22

Zan-Bar, Israel. glycoprotein hormone which plays a key tivity, and the authors postulated that immunoregulatory role by inducing ac- IL-2 may have a...the expres- tion relationship of this important im- sion of 33B31 receptors, slows down the . munoregulatory hormone . turnover of these receptors once...Israel) have been studying the stimula- stimulation with monoclonal anti-idio- tion of growth by an FCy receptor ex- typic antibodies against

Examining the effects of testwiseness in conceptual physics evaluations

NASA Astrophysics Data System (ADS)

DeVore, Seth; Stewart, John; Stewart, Gay

2016-12-01

Testwiseness is defined as the set of cognitive strategies used by a student that is intended to improve his or her score on a test regardless of the test's subject matter. Questions with elements that may be affected by testwiseness are common in physics assessments, even in those which have been extensively validated and widely used as evaluation tools in physics education research. The potential effect of several elements of testwiseness were analyzed for questions in the Force Concept Inventory (FCI) and Conceptual Survey on Electricity and Magnetism that contain distractors that are predicted to be influenced by testwiseness. This analysis was performed using data sets collected between fall 2001 and spring 2014 at one midwestern U.S. university (including over 9500 students) and between Spring 2011 and Spring 2015 at a second eastern U.S. university (including over 2500 students). Student avoidance of "none of the above" or "zero" distractors was statistically significant. The effect of the position of a distractor on its likelihood to be selected was also significant. The effects of several potential positive and negative testwiseness effects on student scores were also examined by developing two modified versions of the FCI designed to include additional elements related to testwiseness; testwiseness produced little effect post-instruction in student performance on the modified instruments.

Innovative Training of In-service Teachers for Active Learning: A Short Teacher Development Course Based on Physics Education Research

NASA Astrophysics Data System (ADS)

Zavala, Genaro; Alarcón, Hugo; Benegas, Julio

2007-08-01

In this contribution we describe a short development course for in-service physics teachers. The course structure and materials are based on the results of educational research, and its main objective is to provide in-service teachers with a first contact with the active learning strategy “Tutorials in Introductory Physics,” developed by the Physics Education Research Group at the University of Washington. The course was organized in a constructivist, active learning environment, so that teachers have first to experience, as regular students, the whole Tutorial sequence of activities: Tutorial pre-test, Tutorial, and Tutorial Homework. After each Tutorial, teachers reflect on, and recognize their own students’ learning difficulties, discussing their teaching experiences with their colleagues in small collaborative groups first and the whole class later. Finally they read and discuss specific Physics Education Research literature, where these learning difficulties have been extensively studied by researchers. At the beginning and at the end of the course the participants were given the conceptual multiple-choice test Force Concept Inventory (FCI). The pre-/post-instruction FCI data were presented as a practical example of the use of a research-based test widely used in educational research and in formative assessment processes designed to improve instruction.

Neuroprotective effect of mesenchymal stem cell through complement component 3 downregulation after transient focal cerebral ischemia in mice.

PubMed

Jung, Hye-Seon; Jeong, Si-Yeon; Yang, Jiwon; Kim, So-Dam; Zhang, Baojin; Yoo, Hyun Seung; Song, Sun U; Jeon, Myung-Shin; Song, Yun Seon

2016-10-28

Bone marrow-derived mesenchymal stem cells (MSCs) are used in stroke treatment despite the poor understanding of its mode of action. The immune suppressive and anti-inflammatory properties of MSCs possibly play important roles in regulating neuroinflammation after stroke. We investigated whether MSCs reduce the inflammatory complement component 3 (C3) levels, thus, providing neuroprotection during stroke. Mice were subjected to transient focal cerebral ischemia (tFCI), after which MSCs were intravenously injected. The infarct volume of the brain was reduced in MSC-injected tFCI mice, and C3 expression was significantly reduced in both the brain and the blood. Additionally, the profiles of other inflammatory mediators demonstrated neuroprotective changes in the MSCs-treated group. In order to analyze the effect of MSCs on neurons during cerebral ischemia, primary cortical neurons were co-cultured with MSCs under oxygen-glucose deprivation (OGD). Primary neurons co-cultured with MSCs exhibited reduced levels of C3 expression and increased protection against OGD, indicating that treatment with MSCs reduces excessive C3 expression and rescues ischemia-induced neuronal damage. Our finding suggests that reduction of C3 expression by MSCs can help to ameliorate ischemic brain damage, offering a new neuroprotective strategy in stroke therapy. Copyright © 2016. Published by Elsevier Ireland Ltd.

Prevalence and co-occurrence of hip dysplasia and elbow dysplasia in Dutch pure-bred dogs.

PubMed

Lavrijsen, I C M; Heuven, H C M; Meij, B P; Theyse, L F H; Nap, R C; Leegwater, P A J; Hazewinkel, H A W

2014-05-01

Hip as well as elbow dysplasia (HD, ED) are developmental disorders leading to malformation of their respective joints. For a long time both disorders have been scored and targeted for improvement using selective breeding in several Dutch dog populations. In this paper all scores for both HD and ED, given to pure bred dogs in the Netherlands from 2002 to 2010, were analyzed. Heritabilities and correlations between HD and ED were calculated for the 4 most frequently scored breeds. Heritabilities ranged from 0.0 to 0.37 for HD related traits (FCI-score, osteoarthritis, congruity, shape and laxity (Norberg angle); FCI: Fédération Cynologique Internationale) and from 0.0 to 0.39 for ED related traits (IEWG score, osteoarthritis, sclerosis and indentation; IEWG: International Elbow Working Group). HD related traits showed high genetic and residual correlations among each other but were only to a minor extent correlated with ED related traits, which also showed high correlations among each other. Genetic correlations were higher than residual correlations. Phenotypic and genetic trends since 2001 for the four most scored breeds were slightly positive but decreasing over time, indicating that selection over the past decade has not been effective. Copyright © 2014. Published by Elsevier B.V.

Hydroxyapatite ocular implant and non-integrated implants in eviscerated patients

PubMed Central

Gradinaru, S; Popescu, V; Leasu, C; Pricopie, S; Yasin, S; Ciuluvica, R; Ungureanu, E

2015-01-01

Introduction: This study compares the outcomes and complications of hydroxyapatite ocular implant and non-integrated ocular implants following evisceration. Materials and Methods: This is a retrospective study of 90 patients who underwent evisceration for different ocular affections, in the Ophthalmology Department of the University Emergency Hospital Bucharest, between January 2009 and December 2013. The outcomes measured were conjunctival dehiscence, socket infection, implant exposure and extrusion rate. Results: Forty-three patients had the hydroxyapatite implant (coralline–Integrated Ocular Implants, USA or synthetic–FCI, France) and forty-seven received non-integrated ocular implants (24 acrylic and 23 silicone). Five cases of socket infection, thirteen cases of extrusion and two cases of conjunctival dehiscence were encountered. Conclusions: There was a higher rate of conjunctival dehiscence with hydroxyapatite ocular implant, but implant extrusion and socket infection were found in non-integrated ocular implants. PMID:25914747

An excerpt from an eye-tracking comparative study between Poland and Japan with the use of Force Concept Inventory

NASA Astrophysics Data System (ADS)

Rosiek, Roman; Sajka, Mirosława; Ohno, Eizo; Shimojo, Atsushi; Iwata, Michiru; Wcisło, Dariusz

2017-01-01

The paper presents the initial results of a comparative Polish-Japanese study. The research was conducted at the Department of Mathematics, Physics and Technical Science at the Pedagogical University of Cracow and at the University of Hokkaido. The participants of the study were university students of humanistic courses. The research concerns the comparison of the respondents' knowledge and understanding of the concept of force in mechanics and their ways of solving problems in the field of a basic mechanics course. A special theoretical tool was used. It was the standardized, international test diagnosing the understanding of the concept of force - the so-called "Force Concept Inventory" (FCI), in its official Polish and Japanese translations. The eye-tracking method was combined with structured interviews and discussions with all the respondents.

Characterization of a hybrid target multi-keV x-ray source by a multi-parameter statistical analysis of titanium K-shell emission

DOE PAGES

Primout, M.; Babonneau, D.; Jacquet, L.; ...

2015-11-10

We studied the titanium K-shell emission spectra from multi-keV x-ray source experiments with hybrid targets on the OMEGA laser facility. Using the collisional-radiative TRANSPEC code, dedicated to K-shell spectroscopy, we reproduced the main features of the detailed spectra measured with the time-resolved MSPEC spectrometer. We developed a general method to infer the N e, T e and T i characteristics of the target plasma from the spectral analysis (ratio of integrated Lyman-α to Helium-α in-band emission and the peak amplitude of individual line ratios) of the multi-keV x-ray emission. Finally, these thermodynamic conditions are compared to those calculated independently bymore » the radiation-hydrodynamics transport code FCI2.« less

Structure of FcRY, an avian immunoglobulin receptor related to mammalian mannose receptors, and its complex with IgY

PubMed Central

He, Yongning; Bjorkman, Pamela J.

2011-01-01

Fc receptors transport maternal antibodies across epithelial cell barriers to passively immunize newborns. FcRY, the functional counterpart of mammalian FcRn (a major histocompatibility complex homolog), transfers IgY across the avian yolk sac, and represents a new class of Fc receptor related to the mammalian mannose receptor family. FcRY and FcRn bind immunoglobulins at pH ≤6.5, but not pH ≥7, allowing receptor–ligand association inside intracellular vesicles and release at the pH of blood. We obtained structures of monomeric and dimeric FcRY and an FcRY–IgY complex and explored FcRY's pH-dependent binding mechanism using electron cryomicroscopy (cryoEM) and small-angle X-ray scattering. The cryoEM structure of FcRY at pH 6 revealed a compact double-ring “head,” in which the N-terminal cysteine-rich and fibronectin II domains were folded back to contact C-type lectin-like domains 1–6, and a “tail” comprising C-type lectin-like domains 7–8. Conformational changes at pH 8 created a more elongated structure that cannot bind IgY. CryoEM reconstruction of FcRY dimers at pH 6 and small-angle X-ray scattering analysis at both pH values confirmed both structures. The cryoEM structure of the FcRY–IgY revealed symmetric binding of two FcRY heads to the dimeric FcY, each head contacting the CH4 domain of one FcY chain. FcRY shares structural properties with mannose receptor family members, including a head and tail domain organization, multimerization that may regulate ligand binding, and pH-dependent conformational changes. Our results facilitate understanding of immune recognition by the structurally related mannose receptor family and comparison of diverse methods of Ig transport across evolution. PMID:21746914

Tackling sun intrusion: a challenge of close collaboration of thermal, mechanical, structural and optical engineers

NASA Astrophysics Data System (ADS)

Kroneberger, Monika; Calleri, Andrea; Ulfers, Hendrik; Klossek, Andreas; Goepel, Michael

2017-09-01

The Meteosat Third Generation (MTG) program will ensure the continuity and enhancement of meteorological data from geostationary orbit as currently provided by the Meteosat Second Generation (MSG) system. OHB-Munich, as part of the core team consortium of the industrial prime contractor for the space segment Thales Alenia Space (France), is responsible for the Flexible Combined Imager - Telescope Assembly (FCI-TA) as well as the Infrared Sounder (IRS).

Laser plasma interaction in rugby-shaped hohlraums

NASA Astrophysics Data System (ADS)

Masson-Laborde, P.-E.; Philippe, F.; Tassin, V.; Monteil, M.-C.; Gauthier, P.; Casner, A.; Depierreux, S.; Seytor, P.; Teychenne, D.; Loiseau, P.; Freymerie, P.

2014-10-01

Rugby shaped-hohlraum has proven to give high performance compared to a classical similar-diameter cylinder hohlraum. Due to this performance, this hohlraum has been chosen as baseline ignition target for the Laser MegaJoule (LMJ). Many experiments have therefore been performed during the last years on the Omega laser facility in order to study in details the rugby hohlraum. In this talk, we will discuss the interpretation of these experiments from the point of view of the laser plasma instability problem. Experimental comparisons have been done between rugby, cylinder and elliptical shape rugby hohlraums and we will discuss how the geometry differences will affect the evolution of laser plasma instabilities (LPI). The efficiency of laser smoothing techniques on these instabilities will also be discussed as well as gas filling effect. The experimental results will be compared with FCI2 hydroradiative calculations and linear postprocessing with Piranah. Experimental Raman and Brillouin spectrum, from which we can infer the location of the parametric instabilities, will be compared to simulated ones, and will give the possibility to compare LPI between the different hohlraum geometries.

Final report of fuel dynamics Test E7

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

Doerner, R.C.; Murphy, W.F.; Stanford, G.S.

1977-04-01

Test data from an in-pile failure experiment of high-power LMFBR-type fuel pins in a simulated $3/s transient-overpower (TOP) accident are reported and analyzed. Major conclusions are that (1) a series of cladding ruptures during the 100-ms period preceding fuel release injected small bursts of fission gas into the flow stream; (2) gas release influenced subsequent cladding melting and fuel release (there were no measurable FCI's (fuel-coolant interactions), and all fuel motion observed by the hodoscope was very slow); (3) the predominant postfailure fuel motion appears to be radial swelling that left a spongy fuel crust on the holder wall; (4)more » less than 4 to 6 percent of the fuel moved axially out of the original fuel zone, and most of this froze within a 10-cm region above the original top of the fuel zone to form the outlet blockage. An inlet blockage approximately 1 cm long was formed and consisted of large interconnected void regions. Both blockages began just beyond the ends of the fuel pellets.« less

Effect of the science teaching advancement through modeling physical science professional development workshop on teachers' attitudes, beliefs and content knowledge and students' content knowledge

NASA Astrophysics Data System (ADS)

Dietz, Laura

The Science Teaching Advancement through Modeling Physical Science (STAMPS) professional development workshop was evaluated for effectiveness in improving teachers' and students' content knowledge. Previous research has shown modeling to be an effective method of instruction for improving student and teacher content knowledge, evidenced by assessment scores. Data includes teacher scores on the Force Concept Inventory (FCI; Hestenes, Wells, & Swackhamer, 1992) and the Chemistry Concept Inventory (CCI; Jenkins, Birk, Bauer, Krause, & Pavelich, 2004), as well as student scores on a physics and chemistry assessment. Quantitative data is supported by teacher responses to a post workshop survey and classroom observations. Evaluation of the data shows that the STAMPS professional development workshop was successful in improving both student and teacher content knowledge. Conclusions and suggestions for future study are also included.

The H2 + + He proton transfer reaction: quantum reactive differential cross sections to be linked with future velocity mapping experiments

NASA Astrophysics Data System (ADS)

Hernández Vera, Mario; Wester, Roland; Gianturco, Francesco Antonio

2018-01-01

We construct the velocity map images of the proton transfer reaction between helium and molecular hydrogen ion {{{H}}}2+. We perform simulations of imaging experiments at one representative total collision energy taking into account the inherent aberrations of the velocity mapping in order to explore the feasibility of direct comparisons between theory and future experiments planned in our laboratory. The asymptotic angular distributions of the fragments in a 3D velocity space is determined from the quantum state-to-state differential reactive cross sections and reaction probabilities which are computed by using the time-independent coupled channel hyperspherical coordinate method. The calculations employ an earlier ab initio potential energy surface computed at the FCI/cc-pVQZ level of theory. The present simulations indicate that the planned experiments would be selective enough to differentiate between product distributions resulting from different initial internal states of the reactants.

Force Balance Allocation Model

DTIC Science & Technology

1982-11-19

1 53V jiAiA 2 400 , I,4 v 1 fCI A., 𔃺. " 3,. 54 QVA fA 8,1...Virginia 22209 19 November 1982 Technical Report CONTRACT No. DNA 001-82-C-0283 C’ APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED. N" . 1 ’ CI" THIS...JAN 1 2 1984 DEFENSE NUCLEAR AGENCY Washington, DC 20305 ’-’C *" ’ . . . • mw Destroy this report when it is no longer needed. Do not return to

On ancestors of dog breeds with focus on Weimaraner hunting dogs.

PubMed

Kropatsch, R; Streitberger, K; Schulte-Middelmann, T; Dekomien, G; Epplen, J T

2011-02-01

Paternally inherited Y chromosomal markers and maternally inherited mitochondrial (mt) DNA sequences were investigated in 27 dog breeds (Canis familiaris), of which the Weimaraner hunting dog was studied in greater detail. Altogether, nine potentially polymorphic markers of the Y chromosome were examined as well as parts of the canine mt genome (1947 base pairs) in 111 male dogs and four wolves for comparison. Twenty Y chromosomal and fifty-nine mitochondrial DNA (mtDNA) haplotypes were identified in the canine breeds and wolves. In 34 Weimaraners, four distinct Y chromosomal haplotypes were observed as well as three mtDNA types thus reflecting at least four male and three female ancestors for the current population in Germany. Tracing patri- and matrilineages, several entries in the Weimaraner stud book cannot be reconciled with the male-only, Y chromosomal neither the female-only, mt inheritance patterns, respectively. The investigated breeds represent 9 of 10 groups defined by the Fédération Cynologique Internationale (FCI). The level of Y chromosomal and especially mtDNA diversity was immense considering the relatively small number of individuals investigated per breed. Unique haplotypes were found only in a few breeds and the wolf. Other haplotypes were shared among several breeds, also across different FCI groups, suggesting that these canine breeds had common male and female ancestors. © 2010 Blackwell Verlag GmbH.

Natural and technical factors in faecal contamination incidents of drinking water in small distribution networks, France, 2003-2004: a geographical study.

PubMed

Beaudeau, Pascal; Valdes, Danièle; Mouly, Damien; Stempfelet, Morgane; Seux, René

2010-03-01

This geographical study aimed to show natural or water-processing-related factors of faecal contamination incidents (FCIs) of drinking water in continental France. We defined a FCI as the occurrence of at least 20 colony-forming Escherichia coli or enterococci among all the 100 mL samples collected for regulatory purpose within one day from a given drinking water supply zone (SZ). We explored correlations between the standardized number of FCIs per département (N_Pols) and various indicators related to weather, land cover, topography, geology and water management for three SZ size sub-classes. In 2003-2004, 2,739 FCIs occurred in SZs supplying fewer than 2,000 people, mainly with simply disinfected groundwater. N_Pols correlates with four covariates: (1) precipitation; (2) the extension of the karst outcrops; (3) the extent of disinfection; and (4) catchment protection. One hundred millimetres of yearly excess in precipitation increases the pollution risk by 28-37%, depending on the sub-class. A 10% extension of the karst areas, a 10% increase of unprotected resources, or of SZs with no disinfection, could entail a higher risk of FCI by about 10%. The correlations are reproducible over the three sub-classes and corroborate expert appraisals. These results encourage the ongoing effort to generalize disinfection and catchment protection.

The Mosquito and the Colossus: Operation Just Cause through the Eyes of General Manuel Antonio Noriega

DTIC Science & Technology

2008-05-22

power via a coup. 2. Historical role is the modernization of society. 3. The bourgeoisie trades its political rights and power in exchange for the...years at Miami’s Federal Correctional Institution (FCI).60 General Noriega is now to be sent to France where he was convicted for money laundering...2165809,00.html (accessed December 22, 2007). 61 Cristina Machin, interview by author, Leavenworth, KS., October 7, 2007. In 1987 France gave General

Communication Interface for a System of Distributed Processes.

DTIC Science & Technology

1981-03-03

Tnterprocess Communication Service Apnlied in a nistrihuted Data Rase System" (submitte to VCI, Miinchen 10/Rl) and "The Trans- port Service of an...1980 4) B6’-hme, K.: An Tnternrocess Communication Service Applied in a Distribut.1 Data Pase System. Submitted to FCI, tliinchen, Oct. 3091l 5) ribme...K(. The "ransport Service of an Tnterprocess Commiunication Systell. Snbmitte to 7th Data Cor’nunicatinrin rooi1 !’exico City, Oct. 1091 ’"’h~e oi1

Interactive Volume Rendering of Diffusion Tensor Data

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

Hlawitschka, Mario; Weber, Gunther; Anwander, Alfred

As 3D volumetric images of the human body become an increasingly crucial source of information for the diagnosis and treatment of a broad variety of medical conditions, advanced techniques that allow clinicians to efficiently and clearly visualize volumetric images become increasingly important. Interaction has proven to be a key concept in analysis of medical images because static images of 3D data are prone to artifacts and misunderstanding of depth. Furthermore, fading out clinically irrelevant aspects of the image while preserving contextual anatomical landmarks helps medical doctors to focus on important parts of the images without becoming disoriented. Our goal wasmore » to develop a tool that unifies interactive manipulation and context preserving visualization of medical images with a special focus on diffusion tensor imaging (DTI) data. At each image voxel, DTI provides a 3 x 3 tensor whose entries represent the 3D statistical properties of water diffusion locally. Water motion that is preferential to specific spatial directions suggests structural organization of the underlying biological tissue; in particular, in the human brain, the naturally occuring diffusion of water in the axon portion of neurons is predominantly anisotropic along the longitudinal direction of the elongated, fiber-like axons [MMM+02]. This property has made DTI an emerging source of information about the structural integrity of axons and axonal connectivity between brain regions, both of which are thought to be disrupted in a broad range of medical disorders including multiple sclerosis, cerebrovascular disease, and autism [Mos02, FCI+01, JLH+99, BGKM+04, BJB+03].« less

Understanding the International Space Station Crew Perspective following Long-Duration Missions through Data Analytics & Visualization of Crew Feedback

NASA Technical Reports Server (NTRS)

Bryant, Cody; Meza, David; Schoenstein, Nicole; Schuh, Susan

2017-01-01

The International Space Station (ISS) first became a home and research laboratory for NASA and International Partner crewmembers over 16 years ago. Each ISS mission lasts approximately 6 months and consists of three to six crewmembers. After returning to Earth, most crewmembers participate in an extensive series of 30+ debriefs intended to further understand life onboard ISS and allow crews to reflect on their experiences. Examples of debrief data collected include ISS crew feedback about sleep, dining, payload science, scheduling and time planning, health & safety, and maintenance. The Flight Crew Integration (FCI) Operational Habitability (OpsHab) team, based at Johnson Space Center (JSC), is a small group of Human Factors engineers and one stenographer that has worked collaboratively with the NASA Astronaut office and ISS Program to collect, maintain, disseminate and analyze this data. The database provides an exceptional and unique resource for understanding the "crew perspective" on long duration space missions. Data is formatted and categorized to allow for ease of search, reporting, and ultimately trending, in order to understand lessons learned, recurring issues and efficiencies gained over time. Recently, the FCI OpsHab team began collaborating with the NASA JSC Knowledge Management team to provide analytical analysis and visualization of these over 75,000 crew comments in order to better ascertain the crew's perspective on long duration spaceflight and gain insight on changes over time. In this initial phase of study, a text mining framework was used to cluster similar comments and develop measures of similarity useful for identifying relevant topics affecting crew health or performance, locating similar comments when a particular issue or item of operational interest is identified, and providing search capabilities to identify information pertinent to future spaceflight systems and processes for things like procedure development and training. In addition, the comments were scored for sentiment using a polarity scoring algorithm to identify both positive and negative comments for particular groups and clusters, allowing the team to make analytically informed decisions regarding future hardware and operating procedures. The use of polarity scoring with time series analysis was used to provide insight into how crew health and habitability is changing throughout various spaceflight increments or the station lifecycle as a whole. Finally, a visualization framework was developed to address the needs of the end users to search for and analyze comments by user, category or mission. This paper will discuss how the use of an analytical framework in conjunction with the current human interface, improved the understanding of crew perspective and shortened the time for analysis allowing for more informed decisions and rapid development of improvements. These methods are significantly optimizing the way that this valuable data can be assessed and applied to current and future spaceflight design and development. This collaboration allows the FCI OpsHab team to effectively analyze and share data in a more automated and timely fashion. Trends are no longer derived manually and can be illustrated effectively and accurately with these evolving techniques to an ever growing group of human spaceflight end users.

Examining evolving performance on the Force Concept Inventory using factor analysis

NASA Astrophysics Data System (ADS)

Semak, M. R.; Dietz, R. D.; Pearson, R. H.; Willis, C. W.

2017-06-01

The application of factor analysis to the Force Concept Inventory (FCI) has proven to be problematic. Some studies have suggested that factor analysis of test results serves as a helpful tool in assessing the recognition of Newtonian concepts by students. Other work has produced at best ambiguous results. For the FCI administered as a pre- and post-test, we see factor analysis as a tool by which the changes in conceptual associations made by our students may be gauged given the evolution of their response patterns. This analysis allows us to identify and track conceptual linkages, affording us insight as to how our students have matured due to instruction. We report on our analysis of 427 pre- and post-tests. The factor models for the pre- and post-tests are explored and compared along with the methodology by which these models were fit to the data. The post-test factor pattern is more aligned with an expert's interpretation of the questions' content, as it allows for a more readily identifiable relationship between factors and physical concepts. We discuss this evolution in the context of approaching the characteristics of an expert with force concepts. Also, we find that certain test items do not significantly contribute to the pre- or post-test factor models and attempt explanations as to why this is so. This may suggest that such questions may not be effective in probing the conceptual understanding of our students.

Bioliteracy and Teaching Efficacy: What Biologists Can Learn from Physicists

PubMed Central

Klymkowsky, Michael W.; Garvin-Doxas, Kathy; Zeilik, Michael

2003-01-01

The introduction of the Force Concept Inventory (FCI) by David Hestenes and colleagues in 1992 produced a remarkable impact within the community of physics teachers. An instrument to measure student comprehension of the Newtonian concept of force, the FCI demonstrates that active learning leads to far superior student conceptual learning than didactic lectures. Compared to a working knowledge of physics, biological literacy and illiteracy have an even more direct, dramatic, and personal impact. They shape public research and reproductive health policies, the acceptance or rejection of technological advances, such as vaccinations, genetically modified foods and gene therapies, and, on the personal front, the reasoned evaluation of product claims and lifestyle choices. While many students take biology courses at both the secondary and the college levels, there is little in the way of reliable and valid assessment of the effectiveness of biological education. This lack has important consequences in terms of general bioliteracy and, in turn, for our society. Here we describe the beginning of a community effort to define what a bioliterate person needs to know and to develop, validate, and disseminate a tiered series of instruments collectively known as the Biology Concept Inventory (BCI), which accurately measures student comprehension of concepts in introductory, genetic, molecular, cell, and developmental biology. The BCI should serve as a lever for moving our current educational system in a direction that delivers a deeper conceptual understanding of the fundamental ideas upon which biology and biomedical sciences are based. PMID:14506504

High Power HF Excitation of Low Frequency Stimulated Electrostatic Waves in the Ionospheric Plasma over HAARP

NASA Astrophysics Data System (ADS)

Bernhardt, Paul; Selcher, Craig A.

High Power electromagnetic (EM) waves transmitted from the HAARP facility in Alaska can excite low frequency electrostatic waves by several processes including (1) direct magnetized stimulated Brillouin scatter (MSBS) and (2) parametric decay of high frequency electrostatic waves into electron and ion Bernstein waves. Either an ion acoustic (IA) wave with a frequency less than the ion cyclotron frequency (fCI) or an electrostatic ion cyclotron (EIC) wave just above fCI can be produced by MSBS. The coupled equations describing the MSBS instabil-ity show that the production of both IA and EIC waves is strongly influenced by the wave propagation direction relative to the background magnetic field. Experimental observations of stimulated electromagnetic emissions (SEE) using the HAARP transmitter in Alaska have confirmed the theoretical predictions that only IA waves are excited for propagation along the magnetic zenith and that EIC waves can only be detected with oblique propagation angles. The electron temperature in the heated plasma is obtained from the IA spectrum offsets from the pump frequency. The ion composition can be determined from the measured EIC frequency. Near the second harmonic of the electron cyclotron frequency, the EM pump wave is converted into an electron Bernstein (EB) wave that decays into another EB wave and an ion Bernstein (IB) wave. Strong cyclotron resonance with the EB wave leads to acceleration of the electrons. Ground based SEE observations are related to the theory of low-frequency electrostatic wave generation.

Effect of Lorcaserin Alone and in Combination with Phentermine on Food Cravings After 12-Week Treatment: A Randomized Substudy.

PubMed

Rebello, Candida J; Nikonova, Elena V; Zhou, Sharon; Aronne, Louis J; Fujioka, Ken; Garvey, W Timothy; Smith, Steven R; Coulter, Ann A; Greenway, Frank L

2018-02-01

This study evaluated the effect of lorcaserin 10 mg twice daily (LOR BID), or with phentermine 15 mg once daily (LOR BID + PHEN QD) and 15 mg twice daily (LOR BID + PHEN BID), in conjunction with energy restriction on food cravings. Two hundred and thirty-five patients without diabetes but with obesity or overweight and ≥ 1 comorbidity received LOR BID, LOR BID + PHEN QD, or LOR BID + PHEN BID for 12 weeks in a randomized double-blind study. The Food Craving Inventory (FCI) and the Control of Eating Questionnaire (COEQ) were administered over 12 weeks. The FCI total score and the subscale scores reduced from baseline in all groups. The least squares means (95% confidence intervals) for the total scores were -0.65 (-0.75 to -0.55), -0.75 (-0.84 to -0.65), and -0.84 (-0.95 to -0.74) in the LOR BID, LOR BID + PHEN QD, and LOR BID + PHEN BID groups, respectively. Cravings assessed by COEQ reduced from baseline in all groups. In general, the combination treatments were more effective than lorcaserin alone. At week 12, except for fruit juice and dairy products, general and specific cravings reduced in LOR BID + PHEN BID compared with LOR BID (P < 0.05). Lorcaserin in combination with phentermine improves control of food cravings during short-term energy restriction. © 2018 The Obesity Society.

Examining the Association Between Comorbidity Indexes and Functional Status in Hospitalized Medicare Fee-for-Service Beneficiaries

PubMed Central

Graham, James E.; Resnik, Linda; Karmarkar, Amol M.; Deutsch, Anne; Tan, Alai; Al Snih, Soham; Ottenbacher, Kenneth J.

2016-01-01

Background Medicare data from acute hospitals do not contain information on functional status. This lack of information limits the ability to conduct rehabilitation-related health services research. Objective The purpose of this study was to examine the associations between 5 comorbidity indexes derived from acute care claims data and functional status assessed at admission to an inpatient rehabilitation facility (IRF). Comorbidity indexes included tier comorbidity, Functional Comorbidity Index (FCI), Charlson Comorbidity Index, Elixhauser Comorbidity Index, and Hierarchical Condition Category (HCC). Design This was a retrospective cohort study. Methods Medicare beneficiaries with stroke, lower extremity joint replacement, and lower extremity fracture discharged to an IRF in 2011 were studied (N=105,441). Data from the beneficiary summary file, Medicare Provider Analysis and Review (MedPAR) file, and Inpatient Rehabilitation Facility–Patient Assessment Instrument (IRF-PAI) file were linked. Inpatient rehabilitation facility admission functional status was used as a proxy for acute hospital discharge functional status. Separate linear regression models for each impairment group were developed to assess the relationships between the comorbidity indexes and functional status. Base models included age, sex, race/ethnicity, disability, dual eligibility, and length of stay. Subsequent models included individual comorbidity indexes. Values of variance explained (R2) with each comorbidity index were compared. Results Base models explained 7.7% of the variance in motor function ratings for stroke, 3.8% for joint replacement, and 7.3% for fracture. The R2 increased marginally when comorbidity indexes were added to base models for stroke, joint replacement, and fracture: Charlson Comorbidity Index (0.4%, 0.5%, 0.3%), tier comorbidity (0.2%, 0.6%, 0.5%), FCI (0.4%, 1.2%, 1.6%), Elixhauser Comorbidity Index (1.2%, 1.9%, 3.5%), and HCC (2.2%, 2.1%, 2.8%). Limitation Patients from 3 impairment categories were included in the sample. Conclusions The 5 comorbidity indexes contributed little to predicting functional status. The indexes examined were not useful as proxies for functional status in the acute settings studied. PMID:26564253

60-MW test using the 30-MW klystrons for the KEKB project

NASA Astrophysics Data System (ADS)

Fukuda, S.; Michizono, S.; Nakao, K.; Saito, Y.; Anami, S.

1995-07-01

The B-Factory is a future plan, requiring an energy upgrade of the KEK linac from 2.5 GeV to 8.0 GeV (KEKB Project). This paper describes the recent development of an S-band high-power pulse klystron to be used as the PF-linac rf-source of the B-Factory. This tube is a modified version of the existing 30-MW tube, which produces 51 MW at a 310 kV beam voltage by optimizing the focusing magnetic field. In order to increase the reliability, the cathode diameter, the gun housing, and the insulation ceramic-seal were enlarged. This tube was redesigned so as to have the same characteristics as the test results of 30-MW tubes at a higher applied voltage without changing the rf interaction region. Four prototype tubes have been manufactured; final test results showed that these new tubes produce an output power of more than 50 MW at 310 kV with an efficiency of 46%. Recently this tube has produced more than 60 MW at a 350 kV beam voltage for a demonstration test. A comparison between the FCI-code prediction and the test results is also given in this paper.

Advanced Electron Optics for Vibrational Spectroscopy.

DTIC Science & Technology

1987-10-02

observations of vibrational losses measured 0 2z b n t l o a i r u e h s i by inelastic elctron scattering from surfaces. The basic dif- ference...AFOSR-86-6291 UNCLASSIFIED F/Ci 26/14 U EhEilEEEEEBI / E /EEiEEElh E /EEEE~h R-~ ~ 3 -00 0 0 S *...S :04 *.: UNA A ASSIFIED 469 RT CLASSIFICATION OF THIS...Surfaces", J.L. Erskine, American Vacuum Society Lecture, Texas A&M Unversity, College Station, Texas, April 24,1984. e "Electron Energy Loss Studies of

Understanding Graduate Teaching Assistants as Tutorial Instructors

NASA Astrophysics Data System (ADS)

Scherr, Rachel E.; Elby, A.

2006-12-01

Physics graduate teaching assistants are essential to the implementation of many collaborative active-learning environments, including tutorials. However, many TAs have trouble teaching effectively in these formats. Anecdotal evidence suggests that the problems may include inappropriate models of physics students, unproductive theories of learning, lack of experience with modern pedagogical methods, and weaknesses in understanding basic physics topics. A new research project at the University of Maryland is investigating the specific nature of TAs' experience with reform instruction using in-depth studies of TAs in course preparation sessions, in the tutorial classroom, in a weekly teaching seminar, and in reflective interviews. We find that all TAs studied recognize the insufficiency of traditional instruction to at least some extent, citing as evidence their own learning experiences, prior teaching experiences, and exposure to FCI-type data. We also observe great variability in views of the nature of physics knowledge and learning (both professed and enacted). These results are informing the development of the professional development program for physics teaching assistants at the University of Maryland.

The total position-spread tensor: Spin partition

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

El Khatib, Muammar, E-mail: elkhatib@irsamc.ups-tlse.fr; Evangelisti, Stefano, E-mail: stefano@irsamc.ups-tlse.fr; Leininger, Thierry, E-mail: Thierry.Leininger@irsamc.ups-tlse.fr

2015-03-07

The Total Position Spread (TPS) tensor, defined as the second moment cumulant of the position operator, is a key quantity to describe the mobility of electrons in a molecule or an extended system. In the present investigation, the partition of the TPS tensor according to spin variables is derived and discussed. It is shown that, while the spin-summed TPS gives information on charge mobility, the spin-partitioned TPS tensor becomes a powerful tool that provides information about spin fluctuations. The case of the hydrogen molecule is treated, both analytically, by using a 1s Slater-type orbital, and numerically, at Full Configuration Interactionmore » (FCI) level with a V6Z basis set. It is found that, for very large inter-nuclear distances, the partitioned tensor growths quadratically with the distance in some of the low-lying electronic states. This fact is related to the presence of entanglement in the wave function. Non-dimerized open chains described by a model Hubbard Hamiltonian and linear hydrogen chains H{sub n} (n ≥ 2), composed of equally spaced atoms, are also studied at FCI level. The hydrogen systems show the presence of marked maxima for the spin-summed TPS (corresponding to a high charge mobility) when the inter-nuclear distance is about 2 bohrs. This fact can be associated to the presence of a Mott transition occurring in this region. The spin-partitioned TPS tensor, on the other hand, has a quadratical growth at long distances, a fact that corresponds to the high spin mobility in a magnetic system.« less

Displacement damage dose and implantation temperature effects on the trapping and release of deuterium implanted into SiC

NASA Astrophysics Data System (ADS)

Muñoz, P.; García-Cortés, I.; Sánchez, F. J.; Moroño, A.; Malo, M.; Hodgson, E. R.

2017-09-01

Radiation damage to flow channel insert (FCI) materials is an important issue for the concept of dual-coolant blanket development in future fusion devices. Silicon Carbide (SiC) is one of the most suitable materials for FCI. Because of the severe radiation environment and exposure to tritium during operation it is of fundamental importance to study hydrogen isotope trapping and release in these materials. Here the trapping, detrapping, and diffusion of deuterium implanted into SiC is studied in correlation with pre- and post-damage induced under different conditions. For this, SiC samples are pre-damaged with 50 keV Ne+ ions at different temperatures (20, 200, 450, 700 °C) to different damage doses (1, 3.6, 7 dpa). Next, deuterium is introduced into the samples at 450 °C by ion implantation at 7 keV. The implanted deuterium retained in the sample is analysed using secondary ion mass spectrometry (SIMS) and thermo-stimulated desorption (TSD) measurements. The results indicate that with increasing neon damage dose, the maximum deuterium desorption occurs at higher temperatures. In contrast, when increasing neon implantation temperature for a fixed dose, the maximum deuterium desorption release temperature decreases. It is interpreted that the neon bombardment produces thermally stable traps for hydrogen isotopes and the stability of this damage increases with neon pre-implantation dose. A decrease of the trapping of implanted deuterium is also observed to occur due to damage recovery by thermal annealing during pre-implantation at the higher temperatures. Finally, direct particle bombardment induced deuterium release is also observed.

Photoabsorption in sodium clusters: first principles configuration interaction calculations

NASA Astrophysics Data System (ADS)

Priya, Pradip Kumar; Rai, Deepak Kumar; Shukla, Alok

2017-05-01

We present systematic and comprehensive correlated-electron calculations of the linear photoabsorption spectra of small neutral closed- and open-shell sodium clusters (Nan, n = 2 - 6), as well as closed-shell cation clusters (Nan+, n = 3, 5). We have employed the configuration interaction (CI) methodology at the full CI (FCI) and quadruple CI (QCI) levels to compute the ground, and the low-lying excited states of the clusters. For most clusters, besides the minimum energy structures, we also consider their energetically close isomers. The photoabsorption spectra were computed under the electric-dipole approximation, employing the dipole-matrix elements connecting the ground state with the excited states of each isomer. Our calculations were tested rigorously for convergence with respect to the basis set, as well as with respect to the size of the active orbital space employed in the CI calculations. These calculations reveal that as far as electron-correlation effects are concerned, core excitations play an important role in determining the optimized ground state geometries of various clusters, thereby requiring all-electron correlated calculations. But, when it comes to low-lying optical excitations, only valence electron correlation effects play an important role, and excellent agreement with the experimental results is obtained within the frozen-core approximation. For the case of Na6, the largest cluster studied in this work, we also discuss the possibility of occurrence of plasmonic resonance in the optical absorption spectrum. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-70728-3

Validation of a stream and riparian habitat assessment protocol using stream salamanders in the southwest Virginia coalfields

USGS Publications Warehouse

Sweeten, Sara E.; Ford, W. Mark

2016-01-01

Within the central Appalachia Coalfields, the aquatic impacts of large-scale land uses, such as surface mining, are of particular ecological concern. Identification and quantification of land use impacts to aquatic ecosystems are a necessary first step to aid in mitigation of negative consequences to biota. However, quantifying physical environmental quality such as stream and riparian habitat often can be quite difficult, particularly when there is time or fiscal limitations. As such, standard protocols such as the U.S. EPA’s Stream Habitat Rapid Bioassessment Protocol have been established to be cost- and time-effective. This protocol estimates ten different stream and riparian conditions on a scale of 0 to 20. Unfortunately, using estimations can be problematic because of large potential variation in the scoring depending on differences in training, experience, and opinion of the personnel doing the estimations. In order to help negate these biases and provide a simplified process, the U.S. Army Corps of Engineers (USACE) developed a functional assessment for streams that measures 11 stream and riparian variables along with watershed land use to calculate three different scores, a hydrology score, biogeochemical score, and habitat score. In our study, we examined the correlation of stream salamander presence and abundance to the three USACE scores. In the summer of 2013, we visited 70 sites in the southwest Virginia Coalfields multiple times to collect salamanders and quantify stream and riparian microhabitat parameters. Using occupancy and abundance analyses, we found strong relationships among three Desmognathus spp. and the USACE Habitat FCI score. Accordingly, the Habitat FCI score provides a reasonable assessment of physical instream and riparian conditions that may serve as a surrogate for understanding the community composition and integrity of aquatic salamander in the region.

Application of Peterson's stray light model to complex optical instruments

NASA Astrophysics Data System (ADS)

Fray, S.; Goepel, M.; Kroneberger, M.

2016-07-01

Gary L. Peterson (Breault Research Organization) presented a simple analytical model for in- field stray light evaluation of axial optical systems. We exploited this idea for more complex optical instruments of the Meteosat Third Generation (MTG) mission. For the Flexible Combined Imager (FCI) we evaluated the in-field stray light of its three-mirroranastigmat telescope, while for the Infrared Sounder (IRS) we performed an end-to-end analysis including the front telescope, interferometer and back telescope assembly and the cold optics. A comparison to simulations will be presented. The authors acknowledge the support by ESA and Thales Alenia Space through the MTG satellites program.

Interpretation of symmetry experiments on Omega

NASA Astrophysics Data System (ADS)

Lours, Laurence; Bastian, Josiane; Monteil, Marie-Christine; Philippe, Franck; Jadaud, Jean-Paul

2006-10-01

The interpretation of the symmetry experiments performed on Omega in 2005 with 3 cone LMJ-like irradiation is presented here. The goal of this campaign was the characterization of the irradiation symmetry by X-ray imaging of the D2Ar capsule. Images of backlit implosion (as done in earlier campaigns with foam balls) and core emission were obtained on the same shot, and can be compared to FCI2 simulations. This set of shots comfirms former results with foam balls of a good symmetry control with 3 cones in empty hohlraums. The influence of the hohlraum shape on symmetry is also studied by comparison of cylindrical hohlraums vs rugby ones.

Texas Science Teacher Characteristics and Conceptual Understanding of Newton's Laws of Motion

NASA Astrophysics Data System (ADS)

Busby, Karin Burk

Misconceptions of Newtonian mechanics and other physical science concepts are well documented in primary and pre-service teacher populations (Burgoon, Heddle, & Duran, 2009; Allen & Coole, 2012; Kruger, Summers, & Palacio, 1990; Ginns & Watters, 1995; Trumper, 1999; Asikainen & Hirovonen, 2014). These misconceptions match the misconceptions held by students, leaving teachers ill-equipped to rectify these concepts in the classroom (Kind, 2014; Kruger et al., 1990; Cochran & Jones, 1998). Little research has been devoted to misconceptions held by in-service secondary teachers, the population responsible for teaching Newtonian mechanics. This study focuses on Texas in-service science teachers in middle school and high school science, specifically sixth grade science, seventh grade science, eighth grade science, integrated physics and chemistry, and physics teachers. This study utilizes two instruments to gauge conceptual understanding of Newton's laws of motion: the Force Concept Inventory [FCI] (Hestenes, Wells, & Swackhamer, 1992) and a custom instrument developed for the Texas Regional Collaboratives for Excellence in Science and Mathematics Teaching (Urquhart, M., e-mail, April 4, 2017). Use of each instrument had its strengths and limitations. In the initial work of this study, the FCI was given to middle and high school teacher volunteers in two urban school districts in the Dallas- Fort Worth area to assess current conceptual understanding of Newtonian mechanics. Along with the FCI, each participant was asked to complete a demographic survey. Demographic data collected included participant's sex, years of service in teaching position, current teaching position, degrees, certification type, and current certifications for science education. Correlations between variables and overall average on the FCI were determined by t-tests and ANOVA tests with a post-hoc Holm-Bonferroni correction test. Test questions pertaining to each of Newton's three laws of motion were extrapolated to determine any correlations. The sample size for this study was small (n=24), requiring a second study investigate potential correlations to teacher characteristics. The second study was conducted using the 2013-2014 school year participants in the Texas Regional Collaboratives for Excellence in Science and Mathematics Teaching [TRC] (Texas Regional Collaborative for Excellence in Science and Mathematics Teaching, 2013), a statewide program led by The University of Texas at Austin Center for STEM Education (Texas Regional Collaborative for Excellence in Science and Mathematics Teaching, 2013). Participants completed a demographic survey and took the TRC Physics Assessment instrument developed for the TRC to determine current conceptual understanding of Newtonian mechanics as defined by the Texas Essential Knowledge and Skills. The TRC also collected demographic data including Texas Educational Agency region, participant's sex, years of service in teaching, current teaching position, level of highest degree earned, whether or not the participant had a STEM degree, and certification type. Correlations were determined between overall average and conceptual force questions only. The sample size was substantial (n=368) but due to time constraints in its development, the TRC Physics Assessment was unable to undergo reliability or validity testing before implementation. Test question pertaining to each of Newton's three laws of motion were extrapolated to determine any correlations. A significance value of p= 0.05 was used for all tests. Both content assessments indicated that, on average, teacher-participants had a considerable misunderstanding of Newtonian mechanics with Newton's third law questions especially difficult for the populations. Teachers' current teaching assignment was statistically significant for most tests, suggesting that high school physics teachers have more conceptual understanding of Newtonian mechanics than middle school teachers but have not necessarily mastered Newtonian mechanics. STEM majors and participant's sex were significant only for the TRC Physics Assessment. One outcome of this study is a recommendation that the Texas teacher certification process for middle school science change to include a general science test that includes physical science. Also, in-service science teachers responsible for teaching Newton's laws of motion should participate in specific professional development from a physics content educational expert to address misconceptions. Additional recommendations include that physics teachers take a mentoring role to help other teachers in physical science concepts and that middle school curriculum provide assistance to teachers for addressing misconceptions of Newton's third law.

Opto-mechanical design of the MTG FCI spectral separation assembly

NASA Astrophysics Data System (ADS)

Riguet, François; Brousse, Emmanuel; Carel, Jean-Louis; Cottenye, Justine; Harmann, David; Joncour, Marc; Makhlouf, Houssine; Mouricaud, Daniel; Oussalah, Meihdi; Rodolfo, Jacques

2015-09-01

The Spectral Separation Assembly is a key component of the Flexible Combined Imager, an instrument that will be on-board Meteosat Third Generation. It splits the input beam coming from the telescope into five spectral groups, for a total of 16 channels, from 0.4 to 13.3 μm. It comprises a set of four dichroics separators followed by four collimating optics for the infrared spectral groups, which feed the cold imaging optics. The visible spectral group is directly imaged on a detector. This paper presents the optical design of the assembly, the mechanical mounting of the optical components, and the coatings developed for the dichroics, mirrors and lenses.

A Summary of Source Data in Military Psychiatric Epidemiology

DTIC Science & Technology

1975-12-01

AD-A02 1 265 A SUMMARY OF SOURCE DATA IN MILITARY PSYCHIATRIC EPIDEMIOLOGY Willia m E. Datel Walter Reed Army Institute of Research Washington...1 1.1 1 ’? • ~) 1 J•·" n .I.• I •.o .1 l’ , ..-.~ nt .# 1 a. 1 l... I - j_ l· ,,, ,, .. _ ... f f •d ’ M t H\\• ( rl’ . , ’ I ·~·· f N l U A’ f fC...i llnesn acror:s ;■ L L three f-erviccr- ::; u/ierofore attenuated. :•!. .!;(.’i.; i. ;;ere, -7- ■■■ -■ --■ - -■■■■.■■=—^-^^-i^* m .""- Bfcl m

Decoding the Assessment Alphabet Soup

NASA Astrophysics Data System (ADS)

Engelhardt, Paula

2010-10-01

The number of assessment instruments that help physics instructors evaluate the conceptual learning of their students has grown over the last twenty years. Today, the number of tests that are available begin to look like an alphabet soup, FCI, MBT, TUG-K, CSE, CSM, CSEM, DIRECT, BEMA, LOCE, FMCE, SEMCO, etc. What can these assessment tests do for you that is different from what you regularly do? How do these tests differ from the tests and other assessments you already give in class? What is meant by formative and summative assessment and why should you care? What are some of the issues associated with giving one of these assessment tests? These are the questions that will be addressed in this talk.

Scattering of magnetic mirror trapped electrons by an Alfven wave

NASA Astrophysics Data System (ADS)

Wang, Y.; Gekelman, W. N.; Pribyl, P.; Papadopoulos, K.; Karavaev, A. V.; Shao, X.; Sharma, A. S.

2010-12-01

Highly energetic particles from large solar flares or other events can be trapped in the Earth’s magnetic mirror field and pose a danger to intricate space satellites. Aiming for artificially de-trapping these particles, an experimental and theoretical study of the interactions of a shear Alfven wave with electrons trapped in a magnetic mirror was performed on the Large Plasma Device (LaPD) at UCLA, with critical parameter ratios matched in the lab plasma to those in space. The experiment was done in a quiescent afterglow plasma with ne≈5×1011cm-3, Te≈0.5eV, B0≈1000G, L=18m, and diameter=60cm. A magnetic mirror was established in LaPD (mirror ratio≈1.5, Lmirror≈3m). An electron population with large v⊥ (E⊥≈1keV) was introduced by microwave heating at upper-hybrid frequency with a 2.45GHz pulsed microwave source at up to 5kW. A shear Alfven wave with arbitrary polarization (fwave≈0.5fci , Bwave/B0≈0.5%) was launched by a Rotating Magnetic Field (RMF) antenna axially 2m away from the center of the mirror. It was observed that the Alfven wave effectively eliminated the trapped electrons. A diagnostic probe was developed for this experiment to measure electrons with large v⊥ in the background plasma. Plasma density and temperature perturbations from the Alfven wave were observed along with electron scattering. Computer simulations tracking single particle motion with wave field are ongoing. In these the Alfven wave’s effect on the electrons pitch angle distribution by a Monte-Carlo method is studied. Planned experiments include upgrading the microwave source for up to 100kW pulses to make electrons with higher transverse energy and longer mirror trapping time. This work is supported by The Office of Naval Research under a MURI award. Work was done at the Basic Plasma Science Facility which is supported by DOE and NSF.

Mobility and cognition are associated with wellbeing and health related quality of life among older adults: a cross-sectional analysis of the Vancouver Falls Prevention Cohort.

PubMed

Davis, Jennifer C; Bryan, Stirling; Li, Linda C; Best, John R; Hsu, Chun Liang; Gomez, Caitlin; Vertes, Kelly A; Liu-Ambrose, Teresa

2015-07-05

Ascertaining individuals' quality of life and wellbeing is essential in public health and clinical research. The impact of these two pressing geriatric syndromes--impaired mobility and cognitive function--on wellbeing and quality of life is not well examined. Hence, our objective was to identify key clinically relevant outcome measures of mobility and cognitive function that explain variation in wellbeing and health related quality of life (HRQoL) among community dwelling older adults. We conducted a cross-sectional analysis of 229 participants presenting to the Vancouver Falls Prevention Clinic from June 2010 through October 2013. The linear regression models included two dependent variables: the ICECAP-O assessing wellbeing and the EQ-5D-3L assessing HRQoL. Key independent variables included the Short Performance Physical Battery (SPPB) and the Montreal Cognitive Assessment (MoCA). Covariates included Functional Comorbidity Index (FCI), sex and age. In the two multiple linear regression models, age was statistically controlled. Other covariates (i.e., sex and FCI) were included based on statistical significance (i.e., p < 0.05). The SPPB was significantly associated with HRQoL and with wellbeing after adjusting for known covariates (p < 0.05, Unstandardized ß (Standard Error) 0.023 (0.006) for HRQoL and 0.016 (0.003) for wellbeing). The MoCA was significantly associated with wellbeing after adjusting for known covariates (p = 0.006), Unstandardized ß (Standard Error) 0.005 (0.002) but not with health related quality of life (p > 0.05). We found that a measure of mobility and balance was associated with HRQoL and wellbeing. However, cognitive function was associated with wellbeing only. This study highlights the potential importance of considering wellbeing as an outcome measure if interventions are intended to have a broader impact than health alone.

Measuring Conceptual Gains and Benefits of Student Problem Designs

NASA Astrophysics Data System (ADS)

Mandell, Eric; Snyder, Rachel; Oswald, Wayne

2011-10-01

Writing assignments can be an effective way of getting students to practice higher-order learning skills in physics. One example of such an assignment is that of problem design. One version of the problem design assignment asks the student to evaluate the material from a chapter, after all instruction and other activities are complete. The student is to decide what concepts and ideas are most central, or critical in the chapter, and construct a problem that he or she feels best encompasses the major themes. Here, we use two concept surveys (FCI and EMCS) to measure conceptual gains for students completing the problem design assignment and present the preliminary results, comparing across several categories including gender, age, degree program, and class standing.

Tri-Service Literacy and Readability: Workshop Proceedings.

DTIC Science & Technology

1980-03-01

LN zC t’ DC D -2l C CC U CC., r C CzC.C-.C, CC C ~ ., caCQ.. *’UC - -C CL UQC’CC Ci - CT 0 --. . C DJZDCU- CC C C. C C...8217 flCCD.- CC, CCC~4J o zC C-Ca C ,.-C,-.O ,-,- CC CC,.. -- r C C,- -z~~~~~~~~~~~~~~~ (U’~’ C- O’ ,.0 C CCC,.. D Ca D CCCO.C - 0.a l F--Ci E CC CC CDO C C...understanding in problem solving. In Catellan, N. J., Jr., Pisoni, D . B., & Potts G. R . (Eds.), Cognitive theory. Hillsdale, NJ: Lawrence Erlbaum

Electronic Structures of Anti-Ferromagnetic Tetraradicals: Ab Initio and Semi-Empirical Studies.

PubMed

Zhang, Dawei; Liu, Chungen

2016-04-12

The energy relationships and electronic structures of the lowest-lying spin states in several anti-ferromagnetic tetraradical model systems are studied with high-level ab initio and semi-empirical methods. The Full-CI method (FCI), the complete active space second-order perturbation theory (CASPT2), and the n-electron valence state perturbation theory (NEVPT2) are employed to obtain reference results. By comparing the energy relationships predicted from the Heisenberg and Hubbard models with ab initio benchmarks, the accuracy of the widely used Heisenberg model for anti-ferromagnetic spin-coupling in low-spin polyradicals is cautiously tested in this work. It is found that the strength of electron correlation (|U/t|) concerning anti-ferromagnetically coupled radical centers could range widely from strong to moderate correlation regimes and could become another degree of freedom besides the spin multiplicity. Accordingly, the Heisenberg-type model works well in the regime of strong correlation, which reproduces well the energy relationships along with the wave functions of all the spin states. In moderately spin-correlated tetraradicals, the results of the prototype Heisenberg model deviate severely from those of multi-reference electron correlation ab initio methods, while the extended Heisenberg model, containing four-body terms, can introduce reasonable corrections and maintains its accuracy in this condition. In the weak correlation regime, both the prototype Heisenberg model and its extended forms containing higher-order correction terms will encounter difficulties. Meanwhile, the Hubbard model shows balanced accuracy from strong to weak correlation cases and can reproduce qualitatively correct electronic structures, which makes it more suitable for the study of anti-ferromagnetic coupling in polyradical systems.

Assessing the development & implementation of a student-centered, "flipped" secondary physics curriculum in which IO-lab digital sensors are issued to students on a 1-to-1 basis

NASA Astrophysics Data System (ADS)

Cunnings, Christopher P.

This teacher-driven, action research dissertation study chronicles the development and implementation of a transformative, two-pronged, student-centered secondary physics education curriculum. From an instructional perspective, the curriculum was situated in the "flipped classroom" teaching approach, which minimizes in-class lecturing and instead predicates classroom learning on collaborative, hands-on, and activity-based lessons. Additionally, all students were issued IO-Lab digital sensors--learning tools developed by professors at the University of Illinois at Urbana-Champaign capable of collecting a vast array of real-time physical data-- on a 1-to-1, 24/7 basis for both in-class and at-home use. In-class, students participated in predominantly activity-based learning, with a sizeable portion of in-class activities incorporating IO-Labs for experimental data collection. Outside of class, students designed real-world research projects using their IO-Labs to study the physics underlying their everyday experiences, and all projects were video recorded, uploaded to YouTube, and then watched in-class to simulate a "mock science conference" in which students provided constructive feedback to each other on their experimental methods and results. The synergistic blending of a) flipped physics instruction, and b) perpetual access to state-of-the-art laboratory equipment, the two prongs forming the basis of this research study, inspired the curriculum title "Flipped IO-Lab," or "F-IO" curriculum. This dissertation study will provide a comprehensive assessment of the benefits and challenges that emerged while designing and implementing the F-IO curriculum from a practitioner's perspective. The assessment of the F-IO curriculum came about through a mixed-methods research methodology during kinematics and dynamics instruction. Specifically, this study includes "Force Concept Inventory" (FCI) pretest/posttest analysis to gauge changes in students' conceptual understanding of physics, as well as "Colorado Learning Attitudes about Science Survey" (CLASS) pre/post data to monitor students' shifts in scientific attitudes throughout the study. The aforementioned pre/post data will be triangulated with field notes and web-based "course opinion survey questions" to provide a comprehensive view of the F-IO curriculum. Significant analysis of the development of the course, as well as the relevant benefits, challenges, and considerations for "flipping" physics instruction, is also contained in this dissertation. The results of the research study include an FCI normalized gain of 0.74 (a "high gain" course), which indicates significant improvement in students' conceptual understanding of Newtonian Mechanics. Additionally, CLASS results indicate significant shifts in student attitudes from generally novice initial scientific perspectives to predominantly expert scientific perspectives by the conclusion of the research study. Of particular interest was students' acknowledgement and appreciation of the real-world implications of what they learned in physics class, as evidenced by CLASS survey data, real-world video challenge projects, and student comments before, during, and after class sessions. However, even despite all of the positive results that emerged throughout the study, a variety of challenges and concerns also materialized with regards to the utilization of F-IO curriculum principles, with the most pronounced being a subset of students whom remained unwilling to embrace web-based and/or flipped instructional teaching methods, preferring instead a more traditional instructional approach. The results and implications of this research study may not only be of interest to physics instructors, but also STEM educators, secondary curriculum designers, digital learning tool designers and researchers, and educational researchers.

Measurements and non-local thermodynamic equilibrium modeling of mid-Z plasma emission

NASA Astrophysics Data System (ADS)

Jacquet, L.; Primout, M.; Kaiser, P.; Clouët, J. F.; Girard, F.; Villette, B.; Reverdin, C.; Oudot, G.

2015-12-01

The x-ray yields from laser-irradiated thin foils of iron, copper, zinc, and germanium have been measured in the soft and multi-keV x-ray ranges at the OMEGA laser at the Laboratory for Laser Energetics. The incident laser power had a pre-pulse to enhance the x-ray emission of a 1 ns flat-top main pulse. The experimental results have been compared with post-shot simulations performed with the two-dimensional radiation-hydrodynamics code FCI2. A new non-local thermodynamic equilibrium model, NOO-RAD, have been incorporated into FCI2. In this approach, the plasma ionization state is in-line calculated by the atomic physics NOHEL package. In the soft x-ray bands, both simulations using RADIOM [M. Busquet, Phys. Fluids B 5, 4191 (1993)] and NOO-RAD clearly over-predict the powers and energies measured by a broad-band spectrometer. In one case (the iron foil), the discrepancy between the measured and simulated x-ray output is nevertheless significantly reduced when NOO-RAD is used in the simulations. In the multi-keV x-ray bands, the simulations display a strong sensitivity to the coupling between the electron thermal conductivity and the NLTE models, and for some particular combinations of these, provide a close match to the measured emission. The comparison between the measured and simulated H-like to He-like line-intensity ratios deduced from high-resolution spectra indicates higher experimental electron temperatures were achieved, compared to the simulated ones. Measurements of the plasma conditions have been achieved using the Thomson-scattering diagnostic. The electron temperatures are found to range from 3 to 5 keV at the end of the laser pulse and are greater than predicted by the simulations. The measured flow velocities are in reasonable agreement with the calculated ones. This last finding gives us confidence in our numerical predictions for the plasma parameters, which are over that time mainly determined by hydrodynamics, such as the mass densities and the ion temperatures.

Role of multiple representations in physics problem solving

NASA Astrophysics Data System (ADS)

Maries, Alexandru

This thesis explores the role of multiple representations in introductory physics students' problem solving performance through several investigations. Representations can help students focus on the conceptual aspects of physics and play a major role in effective problem solving. Diagrammatic representations can play a particularly important role in the initial stages of conceptual analysis and planning of the problem solution. Findings suggest that students who draw productive diagrams are more successful problem solvers even if their approach is primarily mathematical. Furthermore, students provided with a diagram of the physical situation presented in a problem sometimes exhibited deteriorated performance. Think-aloud interviews suggest that this deteriorated performance is in part due to reduced conceptual planning time which caused students to jump to the implementation stage without fully understanding the problem and planning problem solution. Another study investigated two interventions aimed at improving introductory students' representational consistency between mathematical and graphical representations and revealed that excessive scaffolding can have a detrimental effect. The detrimental effect was partly due to increased cognitive load brought on by the additional steps and instructions. Moreover, students who exhibited representational consistency also showed improved problem solving performance. The final investigation is centered on a problem solving task designed to provide information about the pedagogical content knowledge (PCK) of graduate student teaching assistants (TAs). In particular, the TAs identified what they considered to be the most common difficulties of introductory physics students related to graphical representations of kinematics concepts as they occur in the Test of Understanding Graphs in Kinematics (TUG-K). As an extension, the Force Concept Inventory (FCI) was also used to assess this aspect of PCK related to knowledge of student difficulties of both physics instructors and TAs. We find that teaching an independent course and recent teaching experience do not correlate with improved PCK. In addition, the performance of American TAs, Chinese TAs and other foreign TAs in identifying common student difficulties both in the context of the TUG-K and in the context of the FCI is similar. Moreover, there were many common difficulties of introductory physics students that were not identified by many instructors and TAs.

The derivative discontinuity of the exchange-correlation functional.

PubMed

Mori-Sánchez, Paula; Cohen, Aron J

2014-07-28

The derivative discontinuity is a key concept in electronic structure theory in general and density functional theory in particular. The electronic energy of a quantum system exhibits derivative discontinuities with respect to different degrees of freedom that are a consequence of the integer nature of electrons. The classical understanding refers to the derivative discontinuity of the total energy as a function of the total number of electrons (N), but it can also manifest at constant N. Examples are shown in models including several hydrogen systems with varying numbers of electrons or nuclear charge (Z), as well as the 1-dimensional Hubbard model (1DHM). Two sides of the problem are investigated: first, the failure of currently used approximate exchange-correlation functionals in DFT and, second, the importance of the derivative discontinuity in the exact electronic structure of molecules, as revealed by full configuration interaction (FCI). Currently, all approximate functionals, including hybrids, miss the derivative discontinuity, leading to basic errors that can be seen in many ways: from the complete failure to give the total energy of H2 and H2(+), to the missing gap in Mott insulators such as stretched H2 and the thermodynamic limit of the 1DHM, or a qualitatively incorrect density in the HZ molecule with two electrons and incorrect electron transfer processes. Description of the exact particle behaviour of electrons is emphasised, which is key to many important physical processes in real systems, especially those involving electron transfer, and offers a challenge for the development of new exchange-correlation functionals.

The Evaluation of Foam Performance and Flooding Efficiency

NASA Astrophysics Data System (ADS)

Keliang, Wang; Yuhao, Chen; Gang, Wang; Gen, Li

2017-12-01

ROSS-Miles and spinning drop interfacial tensionmeter are used to select suitable foam system through foam composite index (FCI) and interfacial tension (IT). The selected foam system are taken to conduct further test. The further tests are evaluating the foam system resistance to adsorption with multi-round core flooding dynamic adsorption test and evaluating the performance of foam system with four kinds of different transport distance, quantitatively analyzing the foam system effective distance after dynamic adsorption. The result shows that the foaming ability and the mobilizing ability of the foam system decrease with the increase of the round of dynamic adsorption. As the transport distance increases, the foaming ability and the mobilizing ability of the foam system decrease. This result further reveals the flooding characteristics of nitrogen foam flooding, which provides a reference for the implementation of nitrogen foam flooding technology.

Sixteen years of collaborative learning through active sense-making in physics (CLASP) at UC Davis

NASA Astrophysics Data System (ADS)

Potter, Wendell; Webb, David; Paul, Cassandra; West, Emily; Bowen, Mark; Weiss, Brenda; Coleman, Lawrence; De Leone, Charles

2014-02-01

This paper describes our large reformed introductory physics course at UC Davis, which bioscience students have been taking since 1996. The central feature of this course is a focus on sense-making by the students during the 5 h per week discussion/labs in which the students take part in activities emphasizing peer-peer discussions, argumentation, and presentations of ideas. The course differs in many fundamental ways from traditionally taught introductory physics courses. After discussing the unique features of CLASP and its implementation at UC Davis, various student outcome measures are presented that show increased performance by students who took the CLASP course compared to students who took a traditionally taught introductory physics course. Measures we use include upper-division GPAs, MCAT scores, FCI gains, and MPEX-II scores.

Summary of Synoptic Meteorological Observations (SSMO), Central American Coastal Marine Areas, West Coast. Volume 2. Area 6 - Manzanillo SE, Area 7 - Acapulco South, Area 8 - Gulf of Tehuantepec, Area 9 - Guatemala SW Coast, Area 10 - Nicaragua SW Coast, Area 11 - Punta Burica

DTIC Science & Technology

1981-02-01

8 . 3.9 88.1 9 . .5 8 . 19 . 8 . 8 . . 8 8 .. .88 8 10 , 38 0 28 81 803 38. .0 8 93 48 378 C. 8 88 1.0 .1 988008.3 .9 8.9 18 . 8 . 3 0. .. 8 * 8 ...915 "- 979 AREA 0011 PUNTA IU5I A 0908-5.5. 192-5979 TAIL[ 10 0oRN 93.U PERCENT FREQUECY o CEILING HEIGHTS tFCI0 )%/a AND0 0CCUROn PE OF 89 (1/ 8 a9...PERFORMING ORG. REPORT NUMBER 7. AUTHOR(a) 8 . CONTRACT OR GRANT NUMBER(&) .N./A 9. PERFORMING

Explicit reflection in an introductory physics course

NASA Astrophysics Data System (ADS)

Scott, Michael Lee

This dissertation details a classroom intervention that supplements assigned in-class problems in weekly problem sets with reflective activities that are aimed to assist in knowledge integration. Using the framework of cognitive load theory, this intervention should assist in schema acquisition leading to (1) students recognizing the use and appropriately applying physical concepts across different problem contexts, and (2) enhanced physics understanding of students resulting in improved class performance. The intervention was embedded in the discussion component of an introductory, university physics course, and spanned a 14-week period. Evaluation of the intervention was based on the relative performance between a control and treatment group. Instruments used in this study to assess performance included the Force Concept Inventory (FCI), a physics problem categorization test, and four class exams. A full discussion of this implementation and the accompanying measures will be given. Possible limitations to this study and lines of future research will be proposed.

H3+: superficies de energía potencial, estados y transiciones rovibracionales

NASA Astrophysics Data System (ADS)

Aguado, M. Paniagua Y. A.

Hemos calculado varias superficies globales de energía potencial para el estado fundamental y excitados del sistema H3+ en más de ocho mil geometrías diferentes usando una base (9s 3p 1d)/[4s 3p 1d] en cada átomo de Hidrógeno y mediante un método de cálculo de interacción de configuraciones completa (FCI). Hemos ajustado las superficies a formas analíticas del tipo Aguado y Paniagua con un error promedio menor de 50 cm-1 y menor en el pozo de potencial del estado fundamental. Finalmente hemos calculado y analizado los niveles vibracionales para los dos estados electrónicos más bajos, siendo la desviación respecto de los mejores valores publicados, tanto experimentales como teóricos, de unos pocos números de onda.

Asymetrically driven implosion experiment on the Laser MégaJoule

NASA Astrophysics Data System (ADS)

Philippe, Franck; Seytor, Patricia; Tassin, Veronique; Rosch, Rudolf; Villette, Bruno

2017-10-01

We report on the results of the first implosion experiments performed on the Laser MégaJoule (LMJ) facility. Their main purpose was to study implosion with large polar asymmetries of incident radiative flux on a capsule, while preserving azimuthal symmetry, in the context of ICF. In these experiments, one quad of LMJ is focused axially on a gold shield inside a hohlraum. The shield effectively divides the hohlraum in two compartments, and a capsule placed in the second compartment is indirectly driven by the x-ray flux generated in the first one. The subsequent asymmetric implosion is backlit by an x-ray source generated by another quad of LMJ and imaged with an x-ray microscope coupled to a framing camera. Time-gated x-ray radiographs of the imploding capsule and diode array measurements of the hohlraum x-ray emission are found to be in good agreement with FCI2 radiative hydrodynamics simulations.

Multi Jet Induced Forces and Moments on VTOL Aircraft Hovering in and Out of Ground Effect

DTIC Science & Technology

1977-06-19

It e01 L. h; Lilt’ IFe 1𔃺t MI 111)4t , tIpo Ia 1p ra’ue o r 11Iii (’t l I I ’ll I lit V 101 Of it I r, frinm. mit’ kd.own Fot) en us oeu t (I frOe-.1...protX 1111;1 L VIN, M( 0.25. Re fvrenru 5 de ITinus the ecl of ITle roa fcI Low rugilon andic tilL bg n 111lug Of t~he lXIsymmetnriC ca rgi a a11 I’oMtC...impIngement polnt. bC des .! gned as () Thtis dens:1ty Is used to determine NSI in Equation (31). lhe tLotti mass F-.ow il the madi a wo3. ~lcjet in an

Carbon, nitrogen and phosphorus dynamics in nine sub-systems of the Sylt-Rømø Bight ecosystem, German Wadden Sea

NASA Astrophysics Data System (ADS)

Baird, Dan; Asmus, Harald; Asmus, Ragnhild

2011-01-01

Flow networks of nine sub-systems consisting of 59 components each of the Sylt-Rømø Bight, German Wadden Sea, were constructed depicting the standing stocks and flows of material and energy within and between the sub-systems. Carbon, nitrogen and phosphorous were used as currencies for each sub-system, thus resulting in 27 network models, which were analyzed by ecological network analytical protocols. Results show substantial variability in the dynamics of these elements within and between the nine sub-systems, which differ in habitat structure, species diversity and in the standing stocks of their constituent living and non-living components. The relationship between the biodiversity and selected information indices and ratios, derived from ecological network analysis, of individual sub-systems is variable and differ substantially between them. Ecosystem properties such as the structure and magnitude of the recycling of these elements, number of cycles, and total sub-system activity were calculated and discussed, highlighting the differences between and complexity of the flow of C, N and P in a coastal marine ecosystem. The average number of cycles increase from 179 for C, to 16,923 and 20,580 for N and P respectively, while the average amount of recycled material, as measured by the Finn Cycling Index (FCI), increase from 17% for C, to 52% for P and to 61% for N. The number of cycles and the FCI vary considerably between the sub-systems for the different elements. The largest number of cycles of all three elements was observed in the muddy sand flat sub-system, but the highest FCIs were computed for both C (32%) and N (85%) in the Arenicola Flats, and in sparse Zostera noltii sea grass beds for P (67%). Indices reflecting on the growth, organization and resilience of the sub-systems also showed considerable variability between and within the inter-tidal ecosystems in the Bight. Indices such as, for example, the relative ascendency ratios increase on average from C to N to P, whereas others, such as the Average Mutual Information and Flow Diversity indices, were found to be higher in the N models than in the C or P ones.

Turbulent magnetic fluctuations in laboratory reconnection

NASA Astrophysics Data System (ADS)

Von Stechow, Adrian; Grulke, Olaf; Klinger, Thomas

2016-07-01

The role of fluctuations and turbulence is an important question in astrophysics. While direct observations in space are rare and difficult dedicated laboratory experiments provide a versatile environment for the investigation of magnetic reconnection due to their good diagnostic access and wide range of accessible plasma parameters. As such, they also provide an ideal chance for the validation of space plasma reconnection theories and numerical simulation results. In particular, we studied magnetic fluctuations within reconnecting current sheets for various reconnection parameters such as the reconnection rate, guide field, as well as plasma density and temperature. These fluctuations have been previously interpreted as signatures of current sheet plasma instabilities in space and laboratory systems. Especially in low collisionality plasmas these may provide a source of anomalous resistivity and thereby contribute a significant fraction of the reconnection rate. We present fluctuation measurements from two complementary reconnection experiments and compare them to numerical simulation results. VINETA.II (Greifswald, Germany) is a cylindrical, high guide field reconnection experiment with an open field line geometry. The reconnecting current sheet has a three-dimensional structure that is predominantly set by the magnetic pitch angle which results from the superposition of the guide field and the in-plane reconnecting field. Within this current sheet, high frequency magnetic fluctuations are observed that correlate well with the local current density and show a power law spectrum with a spectral break at the lower hybrid frequency. Their correlation lengths are found to be extremely short, but propagation is nonetheless observed with high phase velocities that match the Whistler dispersion. To date, the experiment has been run with an external driving field at frequencies higher than the ion cyclotron frequency f_{ci}, which implies that the EMHD framework applies. Recent machine upgrades allow the inclusion of ion dynamics by reducing the drive frequency below f_{ci}. Two numerical codes (EMHD and hybrid, respectively) have been developed at the Max Planck Institute for solar physics and are used to investigate instability mechanisms and scaling laws for the observed results. MRX (PPPL. Princeton) is a zero to medium guide field, toroidal reconnection experiment. Despite the differing plasma parameters, the qualitative magnetic fluctuation behavior (amplitude profiles, spectra and propagation properties) is comparable to VINETA.II. Results from a new measurement campaign at several different guide fields provides partial overlap with VINETA.II guide field ratios and thereby extends the accessible parameter space of our studies.

A state-specific approach to multireference coupled electron-pair approximation like methods: Development and applications

NASA Astrophysics Data System (ADS)

Chattopadhyay, Sudip; Pahari, Dola; Mukherjee, Debashis; Mahapatra, Uttam Sinha

2004-04-01

The traditional multireference (MR) coupled-cluster (CC) methods based on the effective Hamiltonian are often beset by the problem of intruder states, and are not suitable for studying potential energy surface (PES) involving real or avoided curve crossing. State-specific MR-based approaches obviate this limitation. The state-specific MRCC (SS-MRCC) method developed some years ago [Mahapatra et al., J. Chem. Phys. 110, 6171 (1999)] can handle quasidegeneracy of varying degrees over a wide range of PES, including regions of real or avoided curve-crossing. Motivated by its success, we have suggested and explored in this paper a suite of physically motivated coupled electron-pair approximations (SS-MRCEPA) like methods, which are designed to capture the essential strength of the parent SS-MRCC method without significant sacrificing its accuracy. These SS-MRCEPA theories, like their CC counterparts, are based on complete active space, treat all the reference functions on the same footing and provide a description of potentially uniform precision of PES of states with varying MR character. The combining coefficients of the reference functions are self-consistently determined along with the cluster amplitudes themselves. The newly developed SS-MRCEPA methods are size-extensive, and are also size-consistent with localized orbitals. Among the various versions, there are two which are invariant with respect to the restricted rotations among doubly occupied and active orbitals separately. Similarity of performance of this latter and the noninvariant versions at the crossing points of the degenerate orbitals imply that the all the methods presented are rather robust with respect to the rotations among degenerate orbitals. Illustrative numerical applications are presented for PES of the ground state of a number of difficult test cases such as the model H4, H8 problems, the insertion of Be into H2, and Li2, where intruders exist and for a state of a molecule such as CH2, with pronounced MR character. Results obtained with SS-MRCEPA methods are found to be comparable in accuracy to the parent SS-MRCC and FCI/large scale CI results throughout the PES, which indicates the efficacy of our SS-MRCEPA methods over a wide range of geometries, despite their neglect of a host of complicated nonlinear terms, even when the traditional MR-based methods based on effective Hamiltonians fail due to intruders.

Iterative universal state selective correction for the Brillouin-Wigner multireference coupled-cluster theory

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

Banik, Subrata; Ravichandran, Lalitha; Brabec, Jiri

2015-03-21

As a further development of the previously introduced a posteriori Universal State-Selective (USS) corrections [K. Kowalski, J. Chem. Phys. 134, 194107 (2011)] and [Brabec et al., J. Chem. Phys., 136, 124102 (2012)], we suggest an iterative form of the USS correction by means of correcting effective Hamiltonian matrix elements. We also formulate USS corrections via the left Bloch equations. The convergence of the USS corrections with excitation level towards the FCI limit is also investigated. Various forms of the USS and simplified diagonal USSD corrections at the SD and SD(T) levels are numerically assessed on several model systems and onmore » the ozone and tetramethyleneethane molecules. It is shown that the iterative USS correction can successfully replace the previously developed a posteriori BWCC size-extensivity correction, while it is not sensitive to intruder states and performs well also in other cases when the a posteriori one fails, like e.g. for the asymmetric vibration mode of ozone.« less

Changing classroom designs: Easy; Changing instructors' pedagogies: Not so easy...

NASA Astrophysics Data System (ADS)

Lasry, Nathaniel; Charles, Elizabeth; Whittaker, Chris; Dedic, Helena; Rosenfield, Steven

2013-01-01

Technology-rich student-centered classrooms such as SCALE-UP and TEAL are designed to actively engage students. We examine what happens when instructors adopt the classroom but not the pedagogy that goes with it. We measure the effect of using socio-technological spaces on students' conceptual change and compare learning gains made in groups using different pedagogies (active learning vs. conventional instruction). We also correlate instructors' self-reported instructional approach (teacher-centered, student-centered) with their classes' normalized FCI gains. We find that technology-rich spaces are only effective when implemented with student-centered active pedagogies. In their absence, the technology-rich classroom is not significantly different from conventional teacher-centered classrooms. We also find that instructors' self-reported perception of student-centeredness accounts for a large fraction of the variance (r2 = 0.83) in their class' average normalized gain. Adopting student-centered pedagogies appears to be a necessary condition for the effective use of technology-rich spaces. However, adopting a new pedagogy seems more difficult than adopting new technology.

Use of Family Care Indicators and Their Relationship with Child Development in Bangladesh

PubMed Central

Tofail, Fahmida; Hilaly, Afroza; Huda, Syed N.; Engle, Patrice; Grantham-McGregor, Sally M.

2010-01-01

Poor stimulation in the home is one of the main factors affecting the development of children living in poverty. The family care indicators (FCIs) were developed to measure home stimulation in large populations and were derived from the Home Observations for Measurement of the Environment (HOME). The FCIs were piloted with 801 rural Bangladeshi mothers of children aged 18 months. Five subscales were created: ‘play activities’ (PA), ‘varieties of play materials’ (VP), ‘sources of play materials’, ‘household books’, and ‘magazines and newspapers’ (MN). All subscales had acceptable short-term reliability. Mental and motor development of the children was assessed on the Bayley Scales of Infant Development and their language expression and comprehension by mothers’ report. After controlling for socioeconomic variables, VP and PA independently predicted four and three of the developmental outcomes respectively, and MN predicted both the Bayley scores. The FCI is promising as a survey-based indicator of the quality of children's home environment. PMID:20214083

Student Responses to a Flipped Introductory Physics Class with built-in Post-Video Feedback Quizzes

NASA Astrophysics Data System (ADS)

Ramos, Roberto

We present and analyze student responses to multiple Introductory physics classes in a university setting, taught in a ''flipped'' class format. The classes included algebra- and calculus-based introductory physics. Outside class, students viewed over 100 online video lectures on Classical Mechanics, Electricity and Magnetism, and Modern Physics prepared by this author and in some cases, by a third-party lecture package available over YouTube. Inside the class, students solved and discussed problems and conceptual issues in greater detail. A pre-class online quiz was deployed as an important source of feedback. I will report on the student reactions to the feedback mechanism, student responses using data based on anonymous surveys, as well as on learning gains from pre-/post- physics diagnostic tests. The results indicate a broad mixture of responses to different lecture video packages that depend on learning styles and perceptions. Students preferred the online quizzes as a mechanism to validate their understanding. The learning gains based on FCI and CSEM surveys were significant.

Investigation of the LMJ ignition target sensitivity to the laser pulse shape with 2D integrated calculations

NASA Astrophysics Data System (ADS)

Cherfils, Catherine; Malinie, Guy; Boniface, Claude; Gauthier, Pascal; Laffite, Stephane; Loiseau, Pascal

2010-11-01

The A943 cryogenic target in a Rugby hohlraum is our current nominal design for ignition with 160 beams on the Laser MegaJoule (Laffite et al 2007, 49th Annual Meeting of the Division of Plasma Physics, Loiseau et al 2010, 40th Annual Anomalous Absorption Conference). In this study we redesign the laser pulse of the target under the form of a sum of six supergaussians, which is more amenable to a sensitivity study : four supergaussians are used to launch the four main shocks in the capsule, and two additional supergaussians are used first to remove the LEH windows and then to control the acceleration of the first shock, respectively. We use our 2D FCI2 code to compare the radiation hydro of the capsule, obtained with this new pulse, to what was previously obtained. We investigate the sensitivity of the yield on some parameters, which are the maximum powers and respective timings of the different components of the laser pulse.

Convergent ablation measurements with gas-filled rugby hohlraum on OMEGA

NASA Astrophysics Data System (ADS)

Casner, A.; Jalinaud, T.; Galmiche, D.

2016-03-01

Convergent ablation experiments with gas-filled rugby hohlraum were performed for the first time on the OMEGA laser facility. A time resolved 1D streaked radiography of capsule implosion is acquired in the direction perpendicular to hohlraum axis, whereas a 2D gated radiography is acquired at the same time along the hohlraum axis on a x-ray framing camera. The implosion trajectory has been measured for various kinds of uniformly doped ablators, including germanium-doped and silicon-doped polymers (CH), at two different doping fraction (2% and 4% at.). Our experiments aimed also at measuring the implosion performance of laminated capsules. A laminated ablator is constituted by thin alternate layers of un-doped and doped CH. It has been previously shown in planar geometry that laminated ablators could mitigate Rayleigh Taylor growth at ablation front. Our results confirm that the implosion of a capsule constituted with a uniform or laminated ablator behaves similarly, in accordance with post-shot simulations performed with the CEA hydrocode FCI2.

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

Ho, I-Ting; Sessler, Jonathan L.; Gambhir, Sanjiv Sam

Chemical tools that can report radioactive isotopes would be of interest to the defense community. Here in this paper we report –250 nm polymeric nanoparticles containing porphyrinoid macrocycles with and without pre-complexed depleted uranium and demonstrate that the latter species may be detected easily and with high sensitivity via photoacoustic imaging. The porphyrinoid macrocycles used in the present study are non-aromatic in the absence of the uranyl cation, but aromatic after cation complexation. We solubilized both the freebase and metalated forms of the macrocycles in poly(lactic-co-glycolic acid) and found a peak in the photoacoustic spectrum at 910 nm excitation inmore » the case of the uranyl complex. The signal was stable for at least 15 minutes and allowed detection of uranium concentrations down to 6.2 ppb (5.7 nM) in vitro and 0.57 ppm (19 fCi; 0.52 μM) in vivo. Furthermore, to the best of our knowledge, this is the first report of a nanoparticle that detects an actinide cation via photoacoustic imaging.« less

Modifying ``Six Ideas that Shaped Physics'' for a Life-Science major audience at Hope College

NASA Astrophysics Data System (ADS)

Mader, Catherine

2005-04-01

The ``Six Ideas That Shaped Physics'' textbook has been adapted and used for use in the algebra-based introductory physics course for non-physics science majors at Hope College. The results of the first use will be presented. Comparison of FCI for pre and post test scores will be compared with results from 8 years of results from both the algebra-based course and the calculus-based course (when we first adopted ``Six Ideas that Shaped Physcs" for the Calculus-based course). In addition, comparison on quantitative tests and homework problems with prior student groups will also be made. Because a large fraction of the audience in the algebra-based course is life-science majors, a goal of this project is to make the material relevant for these students. Supplemental materials that emphasize the connection between the life sciences and the fundamental physics concepts are being be developed to accompany the new textbook. Samples of these materials and how they were used (and received) during class testing will be presented.

Parts per billion detection of uranium with a porphyrinoid-containing nanoparticle and in vivo photoacoustic imaging

DOE PAGES

Ho, I-Ting; Sessler, Jonathan L.; Gambhir, Sanjiv Sam; ...

2015-04-01

Chemical tools that can report radioactive isotopes would be of interest to the defense community. Here in this paper we report –250 nm polymeric nanoparticles containing porphyrinoid macrocycles with and without pre-complexed depleted uranium and demonstrate that the latter species may be detected easily and with high sensitivity via photoacoustic imaging. The porphyrinoid macrocycles used in the present study are non-aromatic in the absence of the uranyl cation, but aromatic after cation complexation. We solubilized both the freebase and metalated forms of the macrocycles in poly(lactic-co-glycolic acid) and found a peak in the photoacoustic spectrum at 910 nm excitation inmore » the case of the uranyl complex. The signal was stable for at least 15 minutes and allowed detection of uranium concentrations down to 6.2 ppb (5.7 nM) in vitro and 0.57 ppm (19 fCi; 0.52 μM) in vivo. Furthermore, to the best of our knowledge, this is the first report of a nanoparticle that detects an actinide cation via photoacoustic imaging.« less

Long pulse gas-filled halfraums on OMEGA for high growth-factor ablative Rayleigh-Taylor experiments

NASA Astrophysics Data System (ADS)

Casner, Alexis; Huser, G.; Villette, B.; Vandenboomgaerde, M.; Galmiche, D.; Liberatore, S.; Philippe, F.; Masse, L.

2007-11-01

Mitigation of Rayleigh-Taylor instabilities growth is crucial to enhance the performance of LMJ and NIF ignition targets. We recently develop on OMEGA a long-pulse platform in order to experimentally prove two mechanisms invoked for RTI stabilization, i.e the graded-doped ablator [1] and the new laminated ablator concept [2]. We used gas-filled halfraums (1 atm neopentane) and stack up to 20 drive beams along 3 cones to create a 7 ns long radiation drive. The new E-IDI-300 phase plates were associated with 1D SSD and halfraum energetics was validated along P5/P8 axis for backscattering measurements along 2 cones. We will also present the first face-on radiographies for modulated CH(Ge) samples and compare them with FCI2 hydrocodes simulations. Foil thickness optimization based on these simulations allows us to anticipate growth factors up to 500 in optical depth and the experimental emulator designs for [1,2] will be presented. [1] S.W. Haan et al., Phys. Plasmas 12, 056316 (2005). [2] L. Masse., Phys. Rev. Lett. 98, 245001 (2007). DPP07 invited talk.

Economic Assessment of Supercritical CO2 Extraction of Waxes as Part of a Maize Stover Biorefinery.

PubMed

Attard, Thomas M; McElroy, Con Robert; Hunt, Andrew J

2015-07-31

To date limited work has focused on assessing the economic viability of scCO2 extraction to obtain waxes as part of a biorefinery. This work estimates the economic costs for wax extraction from maize stover. The cost of manufacture (COM) for maize stover wax extraction was found to be € 88.89 per kg of wax, with the fixed capital investment (FCI) and utility costs (CUT) contributing significantly to the COM. However, this value is based solely on scCO2 extraction of waxes and does not take into account the downstream processing of the biomass following extraction. The cost of extracting wax from maize stover can be reduced by utilizing pelletized leaves and combusting the residual biomass to generate electricity. This would lead to an overall cost of € 10.87 per kg of wax (based on 27% combustion efficiency for electricity generation) and €4.56 per kg of wax (based on 43% combustion efficiency for electricity generation). A sensitivity analysis study showed that utility costs (cost of electricity) had the greatest effect on the COM.

Gas-filled Rugby hohlraum energetics and implosions experiments on OMEGA

NASA Astrophysics Data System (ADS)

Casner, Alexis; Philippe, F.; Tassin, V.; Seytor, P.; Monteil, M. C.; Villette, B.; Reverdin, C.

2010-11-01

Recent experiments [1,2] have validated the x-ray drive enhancement provided by rugby-shaped hohlraums over cylinders in the indirect drive (ID) approach to inertial confinement fusion (ICF). This class of hohlraum is the baseline design for the Laser Mégajoule program, is also applicable to the National Ignition Facility and could therefore benefit ID Inertial Fusion Energy studies. We have carried out a serie of energetics and implosions experiments with OMEGA ``scale 1'' rugby hohlraums [1,2]. For empty hohlraums these experiments provide complementary measurements of backscattered light along 42 cone, as well as detailed drive history. In the case of gas-filled rugby hohlraums we have also study implosion performance (symmetry, yield, bangtime, hotspot spectra...) using a high contrast shaped pulse leading to a different implosion regime and for a range of capsule convergence ratios. These results will be compared with FCI2 hydrocodes calculations and future experimental campaigns will be suggested. [4pt] [1] F. Philippe et al., Phys. Rev. Lett. 104, 035004 (2010). [0pt] [2] H. Robey et al., Phys. Plasnas 17, 056313 (2010).

Hohlraum design for the LMJ ignition target

NASA Astrophysics Data System (ADS)

Malinie, G.; Cherfils, C.; Gauthier, P.; Lambert, F.; Monteil, M. C.

2011-10-01

First experiments with the Laser MegaJoule (LMJ) are scheduled to be performed in 2014. The current nominal point design for ignition with 160 beams on the LMJ has been described in. It consists of an indirectly driven A943 capsule, with a plastic ablator doped with Germanium. This capsule is mounted in the center of a Rugby-shaped hohlraum, which is filled with a low density H/He gas, and has a gold-uranium cocktail wall lined with pure gold. We investigate the influence of two key parameters of the hohlraum design: the radius of the laser entrance holes (LEHs), and the thickness of the cocktail layer. Since the Rugby shape of the nominal point design is that of a half-ellipse going from the hohlraum waist to the LEH, any change in the LEH radius has a global effect on the hohlraum shape. Taking into account the current laser spot profiles of the LMJ and using 2D integrated calculations with our FCI2 radiation hydrodynamics code, we assess the flexiblility we have to reduce the LEH radius and/or the cocktail layer thickness.

Mode-coupling and 3D effects in Indirect-Drive Rayleigh-Taylor experiments on OMEGA

NASA Astrophysics Data System (ADS)

Casner, Alexis; Huser, G.; Jadaud, J.-P.; Liberatore, S.; Galmiche, D.; Vandenboomgaerde, M.

2006-10-01

Indirect-Drive Rayleigh-Taylor experiments have been performed on the OMEGA laser facility since 2002 with rugby-ball shaped hohlraums [1]. A set of consistent data has been acquired for different single mode wavelengths (λ = 35, 50 and 70 μm) machined on brominated and germanium-doped samples. Hohlraum energetics was characterized by Dante measurements through the LEH while complementary shock breakout measurements or side-on radiography allow us to assess the x-ray flux incident on the wall-mounted sample. We recently address the problem of mode-coupling by comparing the growth of 2-mode patterns (λ = 35 and 70 μm), either in phase or in opposite phase. Depending on phase one or the other wavelength becomes predominant. Comparison between the FCI2 code calculations and the experimental data will be shown. We will also compare the experimental growth of 3D pattern (70 μm * 70 μm) with the equivalent 2D (λ =50 μm) one. [1] A. Casner et al., Proceedings of the 4^thIFSA Conference, Biarritz (2005).

Coherence and incoherence collective behavior in financial market

NASA Astrophysics Data System (ADS)

Zhao, Shangmei; Xie, Qiuchao; Lu, Qing; Jiang, Xin; Chen, Wei

2015-10-01

Financial markets have been extensively studied as highly complex evolving systems. In this paper, we quantify financial price fluctuations through a coupled dynamical system composed of phase oscillators. We find that a Financial Coherence and Incoherence (FCI) coexistence collective behavior emerges as the system evolves into the stable state, in which the stocks split into two groups: one is represented by coherent, phase-locked oscillators, the other is composed of incoherent, drifting oscillators. It is demonstrated that the size of the coherent stock groups fluctuates during the economic periods according to real-world financial instabilities or shocks. Further, we introduce the coherent characteristic matrix to characterize the involvement dynamics of stocks in the coherent groups. Clustering results on the matrix provides a novel manifestation of the correlations among stocks in the economic periods. Our analysis for components of the groups is consistent with the Global Industry Classification Standard (GICS) classification and can also figure out features for newly developed industries. These results can provide potentially implications on characterizing the inner dynamical structure of financial markets and making optimal investment into tragedies.

``Physics with a Smile''-Explaining Phenomena with a Qualitative Problem-Solving Strategy

NASA Astrophysics Data System (ADS)

Mualem, Roni; Eylon, Bat-Sheva

2007-03-01

Various studies indicate that high school physics students and even college students majoring in physics have difficulties in qualitative understanding of basic concepts and principles of physics.1-5 For example, studies carried out with the Force Concept Inventory (FCI)1,6 illustrate that qualitative tasks are not easy to solve even at the college level. Consequently, "conceptual physics" courses have been designed to foster qualitative understanding, and advanced high school physics courses as well as introductory college-level courses strive to develop qualitative understanding. Many physics education researchers emphasize the importance of acquiring some qualitative understanding of basic concepts in physics as early as middle school or in the context of courses that offer "Physics First" in the ninth grade before biology or chemistry.7 This trend is consistent with the call to focus the science curriculum on a small number of basic concepts and ideas, and to instruct students in a more "meaningful way" leading to better understanding. Studies7-10 suggest that familiar everyday contexts (see Fig. 1) are useful in fostering qualitative understanding.

Enabling Large Focal Plane Arrays Through Mosaic Hybridization

NASA Technical Reports Server (NTRS)

Miller, Timothy M.; Jhabvala, Christine A.; Leong, Edward; Costen, Nick P.; Sharp, Elmer; Adachi, Tomoko; Benford, Dominic J.

2012-01-01

We have demonstrated advances in mosaic hybridization that will enable very large format far-infrared detectors. Specifically we have produced electrical detector models via mosaic hybridization yielding superconducting circuit patbs by hybridizing separately fabricated sub-units onto a single detector unit. The detector model was made on a 100mm diameter wafer while four model readout quadrant chips were made from a separate 100mm wafer. The individually fabric.ted parts were hybridized using a Suss FCI50 flip chip bonder to assemble the detector-readout stack. Once all of the hybridized readouts were in place, a single, large and thick silicon substrate was placed on the stack and attached with permanent epoxy to provide strength and a Coefficient of Thermal Expansion match to the silicon components underneath. Wirebond pads on the readout chips connect circuits to warm readout electronics; and were used to validate the successful superconducting electrical interconnection of the model mosaic-hybrid detector. This demonstration is directly scalable to 150 mm diameter wafers, enabling pixel areas over ten times the area currently available.

Economic Assessment of Supercritical CO2 Extraction of Waxes as Part of a Maize Stover Biorefinery

PubMed Central

Attard, Thomas M.; McElroy, Con Robert; Hunt, Andrew J.

2015-01-01

To date limited work has focused on assessing the economic viability of scCO2 extraction to obtain waxes as part of a biorefinery. This work estimates the economic costs for wax extraction from maize stover. The cost of manufacture (COM) for maize stover wax extraction was found to be €88.89 per kg of wax, with the fixed capital investment (FCI) and utility costs (CUT) contributing significantly to the COM. However, this value is based solely on scCO2 extraction of waxes and does not take into account the downstream processing of the biomass following extraction. The cost of extracting wax from maize stover can be reduced by utilizing pelletized leaves and combusting the residual biomass to generate electricity. This would lead to an overall cost of €10.87 per kg of wax (based on 27% combustion efficiency for electricity generation) and €4.56 per kg of wax (based on 43% combustion efficiency for electricity generation). A sensitivity analysis study showed that utility costs (cost of electricity) had the greatest effect on the COM. PMID:26263976

Determination of plutonium-239, thorium-232, and natural uranium isotopic concentrations in biological samples using photofission track analysis

NASA Astrophysics Data System (ADS)

Parry, James Roswell

Fission track analysis (FTA) has many uses in the scientific community including but not limited to geological dating, neutron flux mapping, and dose reconstruction. The common method of fission for FTA is through neutrons from a nuclear reactor. This dissertation investigates the use of bremsstrahlung radiation produced from an electron linear accelerator to induce fission in FTA samples. This provides a means of simultaneously measuring the amount of Pu-239, U-nat, and Th-232 in a single sample. The benefit of measuring the three isotopes simultaneously is the possible elimination of costly and time consuming chemical processing for dose reconstruction samples. Samples containing the three isotopes were irradiated in two different bremsstrahlung spectra and a neutron spectrum to determine the amount of Pu-239, U-nat, and Th-232 in the samples. The reaction rate from the calibration samples and the counted fission tracks on the samples were used in determining the concentration of each isotope in the samples. The results were accurate to within a factor of two or three, showing that the method can work to predict the concentrations of multiple isotopes in a sample. The limitations of current accelerators and detectors limits the application of this specific procedure to higher concentrations of isotopes. The method detection limits for Pu-239, U-nat, and Th-232 are 20 pCi, 1 fCi, and 0.4 flCI respectively. Analysis of extremely low concentrations of isotopes would require the use of different detectors such as quartz due to the embrittlement encountered in the Lexan at high exposures. Cracking of the Texan detectors started to appear at a fluence of about 2 x 1018 electrons from the accelerator. This may be partly due to the beam stop not being an adequate thickness. The procedure is likely limited to specialty applications for the near term. However, with the world concerns of exposure to depleted uranium, this procedure may find applications in this area since it would be simple to adapt the procedure to depleted uranium detection.

Whiteboarding: A Tool for Moving Classroom Discourse from Answer-Making to Sense-Making

NASA Astrophysics Data System (ADS)

Megowan-Romanowicz, Colleen

2016-02-01

In 1998 I had been teaching science for 13 years. I was a good teacher: I had the plaques and certificates to prove it. But often I felt like an impostor (which I have since learned is not unusual—70% of all people feel like a fake at one time or another). While my students could solve problems and ace tests, every June when I sat down to look at their Force Concept Inventory (FCI) results, I was confronted by how little they had actually learned in my physics classes. It was this annual reality check that drove me to pursue my first Modeling Workshop in summer of 1998. For four weeks I was a physics student again—every day, for six to eight hours a day. I (re)learned to think aloud, to "speak physics" and to listen to how I and others (students) spoke physics. That summer changed everything. When I returned to my high school physics classroom equipped with a new way of teaching in September of 1998, I was excited. I felt like I had the key to the perfect year—I wouldn't be an impostor anymore.

The Kelvin-Helmholtz instability in National Ignition Facility hohlraums as a source of gold-gas mixing

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

Vandenboomgaerde, M.; Bonnefille, M.; Gauthier, P.

Highly resolved radiation-hydrodynamics FCI2 simulations have been performed to model laser experiments on the National Ignition Facility. In these experiments, cylindrical gas-filled hohlraums with gold walls are driven by a 20 ns laser pulse. For the first time, simulations show the appearance of Kelvin-Helmholtz (KH) vortices at the interface between the expanding wall material and the gas fill. In this paper, we determine the mechanisms which generate this instability: the increase of the gas pressure around the expanding gold plasma leads to the aggregation of an over-dense gold layer simultaneously with shear flows. At the surface of this layer, all themore » conditions are met for a KH instability to grow. Later on, as the interface decelerates, the Rayleigh-Taylor instability also comes into play. A potential scenario for the generation of a mixing zone at the gold-gas interface due to the KH instability is presented. Our estimates of the Reynolds number and the plasma diffusion width at the interface support the possibility of such a mix. The key role of the first nanosecond of the laser pulse in the instability occurrence is also underlined.« less

Asian Influence Over the Western North Pacific during the Fall Season: Inferences from Lead 210, Soluble Ionic Species and Ozone

NASA Technical Reports Server (NTRS)

Dibb, J. E.; Talbot, R. W.; Klemm, K. I.; Gregory, G. L.; Singh, H. B.; Bradshaw, J. D.; Sandholm, S. T.

1996-01-01

Aerosol samples collected over the western Pacific during the NASA/Global Tropospheric Experiment Pacific Exploratory Mission (PEM-West A) expedition (September - October 1991) revealed mean Pb-210 concentrations in the free troposphere in the 5-10 fCi m(exp -3) STP range. Most soluble ionic aerosol-associated species were near detection limits [much less than 40 parts per trillion by volume (pptv)] in these same samples. The altitude distribution of O3 near Asia closely resembled that of Pb-210, while no relationship was found between the concentrations of O3 and Be-7. Free tropospheric air over the western Pacific was depleted in soluble aerosol-associated species but enriched in Pb-210 and O3, indicative of deep wet convection over the Asian continent. The influence of Asian air on the composition of the free troposphere over the western Pacific was evident on most of the PEM-West A flights. However, evidence of continental influence was largely restricted to those species that are relatively insoluble (or have insoluble precursors), hence escape scavenging during vertical transport from the boundary layer into the free troposphere by wet convective activity.

Experimental Study of RF Sheath Formation on a Fast Wave Antenna and Limiter in the LAPD

NASA Astrophysics Data System (ADS)

Martin, Michael; Gekelman, Walter; Pribyl, Patrick; van Compernolle, Bart; Carter, Troy

2015-11-01

Ion cyclotron resonance heating (ICRH) will be an essential component of heating power in ITER. During ICRH, radio frequency (RF) sheaths may form both at the exciting antenna and further away, e.g. in the divertor region, and may cause wall material sputtering and decreased RF power coupling to the plasma. It is important to do detailed laboratory experiments that fully diagnose the sheaths and wave fields. This is not possible in fusion devices. A new RF system has recently been constructed for performing such studies in the LAPD plasma column (ne ~1012 -1013cm-3 , Te ~ 1 - 10 eV ,B0 ~ 400 - 2000 G , diameter ~ 60cm , length ~ 18 m) . The RF system is capable of pulsing at the 1 Hz rep. rate of the LAPD plasma and operating between 2-6 MHz (1st - 9th harmonic of fci in H) with a power output of 200 kW. First results of this system driving a single-strap fast wave antenna will be presented. Emissive and Langmuir probe measurements in the vicinity of both the antenna and a remote limiter and wave coupling measured by magnetic pickup loops will be presented.

Computational studies of the helium-lithium hydride system

NASA Astrophysics Data System (ADS)

Taylor, Brian Keith

2000-12-01

We have computed an ab initio potential energy surface for the He-LiH system. We compute the He- LiH interaction energy at the CCSD(T) level using large correlation consistent atomic basis sets supplemented with bond functions. To capture the severe anisotropy of the He-LH potential, we interpolate our ab initio points in the angular direction with cubic splines, then expand the splines in terms of Legendre polynomials. We have constructed both a He-LiH rigid rotor potential and a complete He-LiH potential where the LiH bond length is allowed to change. The resulting potential surface has a unique shape. The He- LiH rigid rotor colinear geometry has a very attractive minimum of -176.7 cm-1, while the LiH-He colinear geometry has a local minimum of only -9.8 cm -1. Using our computed He-LiH potential energy surface, we investigate the collision dynamics of He-LiH. Using a totally quantum mechanical treatment of collisions dynamics, we compute both pure rotational and rovibrational state-to-state cross sections. We integrate our rovibrational cross sections over a Maxwell-Boltzmann distribution of energies to obtain temperature dependent vibrational excitation and relaxation rate constants. The vibrational excitation rate constants are very small for temperature below 400 K, but become significant at higher temperatures. These results suggests that He-LiH collisions probably were important in the very early Universe, especially in the larger primordial gas clouds. We also investigate the structure and dynamics of small HeN-LiH clusters using diffusion quantum Monte Carlo techniques. We find that three body effects are negligible, so we take the HeN-LiH potential to be a pairwise additive potential; we use the HFD-B3-FCI1 He-He potential of Aziz and Janzen [R. A. Aziz and A. R. Janzen, Phys. Rev. Lett. 74, 1586 (1995)] and our He-LiH potential. Because of the strong He-LiH attraction, one helium is always located in the attractive well at the lithium end of the LiH.

Similarities in food cravings and mood states between obese women and women who smoke tobacco.

PubMed

Pepino, M Yanina; Finkbeiner, Susana; Mennella, Julie A

2009-06-01

The present study assessed food cravings in a cohort of 229 women who differed in smoking history (i.e., never smoker, former smoker, and current smoker) and body weight (i.e., normal weight, overweight, and obese). Each subject completed the Food Craving Inventory (FCI), which measures cravings for sweets, high fats, carbohydrates/starches, and fast-food fats, and the Profile of Mood States (POMS), which measures psychological distress. Smoking and obesity were independently associated with specific food cravings and mood states. Current smokers craved high fats more frequently than former and never smokers. They also craved starches more frequently and felt more depressed and angry than never smokers, but not former smokers. Whereas cravings for starchy foods and some mood states may be characteristic of women who are likely to smoke, more frequent cravings for fat among smokers is related to smoking per se. Similarly, obese women craved high fats more frequently than nonobese women and depression symptoms were intensified with increasing body weights. We hypothesize that the overlapping neuroendocrine alterations associated with obesity and smoking and the remarkable similarities in food cravings and mood states between women who smoke and women who are obese suggest that common biological mechanisms modulate cravings for fat in these women.

Fast wave experiments in LAPD: RF sheaths, convective cells and density modifications

NASA Astrophysics Data System (ADS)

Carter, T. A.; van Compernolle, B.; Martin, M.; Gekelman, W.; Pribyl, P.; van Eester, D.; Crombe, K.; Perkins, R.; Lau, C.; Martin, E.; Caughman, J.; Tripathi, S. K. P.; Vincena, S.

2017-10-01

An overview is presented of recent work on ICRF physics at the Large Plasma Device (LAPD) at UCLA. The LAPD has typical plasma parameters ne 1012 -1013 cm-3, Te 1 - 10 eV and B 1000 G. A new high-power ( 150 kW) RF system and fast wave antenna have been developed for LAPD. The source runs at a frequency of 2.4 MHz, corresponding to 1 - 7fci , depending on plasma parameters. Evidence of rectified RF sheaths is seen in large increases ( 10Te) in the plasma potential on field lines connected to the antenna. The rectified potential scales linearly with antenna current. The rectified RF sheaths set up convective cells of local E × B flows, measured indirectly by potential measurements, and measured directly with Mach probes. At high antenna powers substantial modifications of the density profile were observed. The plasma density profile initially exhibits transient low frequency oscillations (10 kHz). The amplitude of the fast wave fields in the core plasma is modulated at the same low frequency, suggesting fast wave coupling is affected by the density rearrangement. Work performed at the Basic Plasma Science Facility, supported jointly by the National Science Foundation and the Department of Energy.

Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain–Domain Interactions Mediating Protein–Protein Interactions

PubMed Central

Jothi, Raja; Cherukuri, Praveen F.; Tasneem, Asba; Przytycka, Teresa M.

2006-01-01

Recent advances in functional genomics have helped generate large-scale high-throughput protein interaction data. Such networks, though extremely valuable towards molecular level understanding of cells, do not provide any direct information about the regions (domains) in the proteins that mediate the interaction. Here, we performed co-evolutionary analysis of domains in interacting proteins in order to understand the degree of co-evolution of interacting and non-interacting domains. Using a combination of sequence and structural analysis, we analyzed protein–protein interactions in F1-ATPase, Sec23p/Sec24p, DNA-directed RNA polymerase and nuclear pore complexes, and found that interacting domain pair(s) for a given interaction exhibits higher level of co-evolution than the noninteracting domain pairs. Motivated by this finding, we developed a computational method to test the generality of the observed trend, and to predict large-scale domain–domain interactions. Given a protein–protein interaction, the proposed method predicts the domain pair(s) that is most likely to mediate the protein interaction. We applied this method on the yeast interactome to predict domain–domain interactions, and used known domain–domain interactions found in PDB crystal structures to validate our predictions. Our results show that the prediction accuracy of the proposed method is statistically significant. Comparison of our prediction results with those from two other methods reveals that only a fraction of predictions are shared by all the three methods, indicating that the proposed method can detect known interactions missed by other methods. We believe that the proposed method can be used with other methods to help identify previously unrecognized domain–domain interactions on a genome scale, and could potentially help reduce the search space for identifying interaction sites. PMID:16949097

SELF-BLM: Prediction of drug-target interactions via self-training SVM.

PubMed

Keum, Jongsoo; Nam, Hojung

2017-01-01

Predicting drug-target interactions is important for the development of novel drugs and the repositioning of drugs. To predict such interactions, there are a number of methods based on drug and target protein similarity. Although these methods, such as the bipartite local model (BLM), show promise, they often categorize unknown interactions as negative interaction. Therefore, these methods are not ideal for finding potential drug-target interactions that have not yet been validated as positive interactions. Thus, here we propose a method that integrates machine learning techniques, such as self-training support vector machine (SVM) and BLM, to develop a self-training bipartite local model (SELF-BLM) that facilitates the identification of potential interactions. The method first categorizes unlabeled interactions and negative interactions among unknown interactions using a clustering method. Then, using the BLM method and self-training SVM, the unlabeled interactions are self-trained and final local classification models are constructed. When applied to four classes of proteins that include enzymes, G-protein coupled receptors (GPCRs), ion channels, and nuclear receptors, SELF-BLM showed the best performance for predicting not only known interactions but also potential interactions in three protein classes compare to other related studies. The implemented software and supporting data are available at https://github.com/GIST-CSBL/SELF-BLM.

Drug-target interaction prediction via class imbalance-aware ensemble learning.

PubMed

Ezzat, Ali; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

2016-12-22

Multiple computational methods for predicting drug-target interactions have been developed to facilitate the drug discovery process. These methods use available data on known drug-target interactions to train classifiers with the purpose of predicting new undiscovered interactions. However, a key challenge regarding this data that has not yet been addressed by these methods, namely class imbalance, is potentially degrading the prediction performance. Class imbalance can be divided into two sub-problems. Firstly, the number of known interacting drug-target pairs is much smaller than that of non-interacting drug-target pairs. This imbalance ratio between interacting and non-interacting drug-target pairs is referred to as the between-class imbalance. Between-class imbalance degrades prediction performance due to the bias in prediction results towards the majority class (i.e. the non-interacting pairs), leading to more prediction errors in the minority class (i.e. the interacting pairs). Secondly, there are multiple types of drug-target interactions in the data with some types having relatively fewer members (or are less represented) than others. This variation in representation of the different interaction types leads to another kind of imbalance referred to as the within-class imbalance. In within-class imbalance, prediction results are biased towards the better represented interaction types, leading to more prediction errors in the less represented interaction types. We propose an ensemble learning method that incorporates techniques to address the issues of between-class imbalance and within-class imbalance. Experiments show that the proposed method improves results over 4 state-of-the-art methods. In addition, we simulated cases for new drugs and targets to see how our method would perform in predicting their interactions. New drugs and targets are those for which no prior interactions are known. Our method displayed satisfactory prediction performance and was able to predict many of the interactions successfully. Our proposed method has improved the prediction performance over the existing work, thus proving the importance of addressing problems pertaining to class imbalance in the data.

[Prevalence of dental fluorosis and consumption of hidden fluoride in school children in the municipality of Nezahualcóyotl].

PubMed

Chacón, Luis Fernando Galicia; López, María Lilia Adriana Juárez; Frechero, Nelly Molina

2009-01-01

Dental fluorosis is a dental tissue disease, characterized by hypomineralization resulting from excess fluoride reaching the developing tooth. In Mexico in recent years, the prevalence of fluorosis has increased by the exposure to different fluoridated sources such as those found in soft drinks and beverages. Our objective was to determine the prevalence of dental fluorosis among school children living in Nezahualcoyotl, state of Mexico and identify associated risk factors. We conducted a cross-sectional study among 455 children aged 6-13 years who had been assessed by a previously standardized observer following WHO criteria. We administered The Community Fluorosis index (FCI) and a survey that analyzed the exposure to fluorides hidden in carbonated drinks, juices, bottled water, tea and the use of fluoride toothpastes. The prevalence of dental fluorosis was 73.4%. Very mild and mild fluorosis were the more common levels. The Community Fluorosis index (ICF) was 1.18 +/- 0.80. School children living at Nezahualcoyotl that answered they did drink hidden fluorides > 0.71 ppm thought bottled beverages were more of a risk to develop dental fluorosis (RM 1,554, 95% CI 1.016-2.378, p<0.05). Dental fluorosis results from fluoride intake by different sources, however our study, consumption of fluoride hidden in soft and bottled drinks showed a significant correlation with observed fluorosis.

Characterization of a purine permease family gene OsPUP7 involved in growth and development control in rice.

PubMed

Qi, Zhuyun; Xiong, Lizhong

2013-11-01

In this study, PUP-type cytokinin transporter genes were identified in rice (Oryza sativa L.). The Oryza sativa purine permease (OsPUP) family has 12 members that show similar predicted protein sequences with AtPUPs. To reveal the functions of OsPUP genes, we searched the T-DNA mutant library of rice and found one mutant for the member OsPUP7. The T-DNA insertion caused a new transcript that encodes a protein with 26 amino acids different from the native OsPUP7 at the C-terminus. The mutant showed multiple phenotypic changes including increased plant height, big seeds, and delayed flowering. The mutant also showed increased sensitivity to drought and salt stresses and treatments with kinetin and abscisic acid. OsPUP7 is expressed mainly in the vascular bundle, pistil, and stamens. The measurement of cytokinins (CKs) showed that CK content in the mutant spikelets accumulated higher than that in the wild type. Moreover, uptake experiment in the yeast fcy2 mutant suggested that OsPUP7 has the ability to transport caffeine, a CK derivative. Our results indicate that the PUP transport system also exists in rice, and OsPUP7 has an important role in the transport of CK, thus affecting developmental process and stress responses. © 2013 Institute of Botany, Chinese Academy of Sciences.

Progress on DCLL Blanket Concept

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

Wong, Clement; Abdou, M.; Katoh, Yutai

2013-09-01

Under the US Fusion Nuclear Science and Technology Development program, we have selected the Dual Coolant Lead Lithium concept (DCLL) as a reference blanket, which has the potential to be a high performance DEMO blanket design with a projected thermal efficiency of >40%. Reduced activation ferritic/martensitic (RAF/M) steel is used as the structural material. The self-cooled breeder PbLi is circulated for power conversion and for tritium breeding. A SiC-based flow channel insert (FCI) is used as a means for magnetohydrodynamic pressure drop reduction from the circulating liquid PbLi and as a thermal insulator to separate the high-temperature PbLi (~700°C) frommore » the helium-cooled RAF/M steel structure. We are making progress on related R&D needs to address critical Fusion Nuclear Science and Facility (FNSF) and DEMO blanket development issues. When performing the function as the Interface Coordinator for the DCLL blanket concept, we had been developing the mechanical design and performing neutronics, structural and thermal hydraulics analyses of the DCLL TBM module. We had estimated the necessary ancillary equipment that will be needed at the ITER site and a detailed safety impact report has been prepared. This provided additional understanding of the DCLL blanket concept in preparation for the FNSF and DEMO. This paper will be a summary report on the progress of the DCLL TBM design and R&Ds for the DCLL blanket concept.« less

Experimental Study of Convective Cells and RF Sheaths Excited by a Fast Wave Antenna in the LAPD

NASA Astrophysics Data System (ADS)

Martin, Michael; Gekelman, Walter; Pribyl, Patrick; van Compernolle, Bart; Carter, Troy; van Eester, Dirk; Crombé, Kristel

2016-10-01

Ion cyclotron resonance heating (ICRH) will be essential for ITER where it is planned to couple 20 MW to the plasma. During ICRH, radio frequency (RF) sheaths may form on the antenna or farther away, and convective cells are suspected to form adjacent to ICRH antennas, negatively affecting both machine and plasma performance. The LAPD (ne 10 12 - 13cm-3 , Te 1-10 eV, B0 0.4 to 2 kG, diameter 60 cm, length 17m) is an ideal device for performing detailed experiments to fully diagnose these phenomena. A 200 kW RF system capable of pulsing at the 1 Hz. rep. rate of the LAPD and operating from 2 to 2.5 MHz has been constructed to perform such studies. B0 can be adjusted so that this encompasses the 1st to 7th harmonic of fci in H plasmas. Emissive, Mach, Langmuir, and B-field probes measured plasma potential, bulk plasma flows, wave patterns, ne, and Te in 2D planes at various axial locations from the antenna. Plasma potential enhancements of up to 90 V along magnetic field lines connected to the antenna and induced ExB flows consistent in structure with convective cells were observed. Details of these observations along with power scaling of RF sheath voltage and convective cell flows will be presented.

Turbulence scaling study in an MHD wind tunnel on the Swarthmore Spheromak Experiment

NASA Astrophysics Data System (ADS)

Schaffner, D. A.; Wan, A.; Owusu-Boateng, J.; Brown, M. R.; Lukin, V. S.

2013-10-01

The turbulence of colliding spheromaks are explored in the MHD wind tunnel on the SSX. Fully ionized hydrogen plasma is produced by two plasma guns on opposite sides of a 1 m by 15 cm copper cylinder. Modification of B-field, Ti and β are made through stuffing flux variation of the plasma guns. Presented here are turbulent f-/ k-spectra and correlation times/lengths of B-field fluctuations as measured by a 16 channel B-dot radial probe array at the chamber midplane. Power-law fits to spectra show scaling that is robust to changes in stuffing flux; fits are on the order of f-3 and k - 2 . 1 for all flux variations. Dissipation range modification of the spectra is observed; changes to the f-spectra slopes occur around f =fci while changes in k-spectra slopes appear around ~ 5ρi . Dissipation range fits are made with an exponentially modified power-law model [Terry et al., PoP 2012]. Fluctuations in axial velocity are made using a Mach probe. Both B-field and velocity fluctuations persist on the same timescale in these experiments. Mach velocity f-spectra show power-laws similar to that for B-field. Comparison of spectra from MHD and Hall MHD simulations of SSX performed within the HiFi modeling framework are made to the experimental results.

Combining multiple positive training sets to generate confidence scores for protein-protein interactions.

PubMed

Yu, Jingkai; Finley, Russell L

2009-01-01

High-throughput experimental and computational methods are generating a wealth of protein-protein interaction data for a variety of organisms. However, data produced by current state-of-the-art methods include many false positives, which can hinder the analyses needed to derive biological insights. One way to address this problem is to assign confidence scores that reflect the reliability and biological significance of each interaction. Most previously described scoring methods use a set of likely true positives to train a model to score all interactions in a dataset. A single positive training set, however, may be biased and not representative of true interaction space. We demonstrate a method to score protein interactions by utilizing multiple independent sets of training positives to reduce the potential bias inherent in using a single training set. We used a set of benchmark yeast protein interactions to show that our approach outperforms other scoring methods. Our approach can also score interactions across data types, which makes it more widely applicable than many previously proposed methods. We applied the method to protein interaction data from both Drosophila melanogaster and Homo sapiens. Independent evaluations show that the resulting confidence scores accurately reflect the biological significance of the interactions.

Comparative analysis of methods for detecting interacting loci

PubMed Central

2011-01-01

Background Interactions among genetic loci are believed to play an important role in disease risk. While many methods have been proposed for detecting such interactions, their relative performance remains largely unclear, mainly because different data sources, detection performance criteria, and experimental protocols were used in the papers introducing these methods and in subsequent studies. Moreover, there have been very few studies strictly focused on comparison of existing methods. Given the importance of detecting gene-gene and gene-environment interactions, a rigorous, comprehensive comparison of performance and limitations of available interaction detection methods is warranted. Results We report a comparison of eight representative methods, of which seven were specifically designed to detect interactions among single nucleotide polymorphisms (SNPs), with the last a popular main-effect testing method used as a baseline for performance evaluation. The selected methods, multifactor dimensionality reduction (MDR), full interaction model (FIM), information gain (IG), Bayesian epistasis association mapping (BEAM), SNP harvester (SH), maximum entropy conditional probability modeling (MECPM), logistic regression with an interaction term (LRIT), and logistic regression (LR) were compared on a large number of simulated data sets, each, consistent with complex disease models, embedding multiple sets of interacting SNPs, under different interaction models. The assessment criteria included several relevant detection power measures, family-wise type I error rate, and computational complexity. There are several important results from this study. First, while some SNPs in interactions with strong effects are successfully detected, most of the methods miss many interacting SNPs at an acceptable rate of false positives. In this study, the best-performing method was MECPM. Second, the statistical significance assessment criteria, used by some of the methods to control the type I error rate, are quite conservative, thereby limiting their power and making it difficult to fairly compare them. Third, as expected, power varies for different models and as a function of penetrance, minor allele frequency, linkage disequilibrium and marginal effects. Fourth, the analytical relationships between power and these factors are derived, aiding in the interpretation of the study results. Fifth, for these methods the magnitude of the main effect influences the power of the tests. Sixth, most methods can detect some ground-truth SNPs but have modest power to detect the whole set of interacting SNPs. Conclusion This comparison study provides new insights into the strengths and limitations of current methods for detecting interacting loci. This study, along with freely available simulation tools we provide, should help support development of improved methods. The simulation tools are available at: http://code.google.com/p/simulation-tool-bmc-ms9169818735220977/downloads/list. PMID:21729295

Comparative analysis of methods for detecting interacting loci.

PubMed

Chen, Li; Yu, Guoqiang; Langefeld, Carl D; Miller, David J; Guy, Richard T; Raghuram, Jayaram; Yuan, Xiguo; Herrington, David M; Wang, Yue

2011-07-05

Interactions among genetic loci are believed to play an important role in disease risk. While many methods have been proposed for detecting such interactions, their relative performance remains largely unclear, mainly because different data sources, detection performance criteria, and experimental protocols were used in the papers introducing these methods and in subsequent studies. Moreover, there have been very few studies strictly focused on comparison of existing methods. Given the importance of detecting gene-gene and gene-environment interactions, a rigorous, comprehensive comparison of performance and limitations of available interaction detection methods is warranted. We report a comparison of eight representative methods, of which seven were specifically designed to detect interactions among single nucleotide polymorphisms (SNPs), with the last a popular main-effect testing method used as a baseline for performance evaluation. The selected methods, multifactor dimensionality reduction (MDR), full interaction model (FIM), information gain (IG), Bayesian epistasis association mapping (BEAM), SNP harvester (SH), maximum entropy conditional probability modeling (MECPM), logistic regression with an interaction term (LRIT), and logistic regression (LR) were compared on a large number of simulated data sets, each, consistent with complex disease models, embedding multiple sets of interacting SNPs, under different interaction models. The assessment criteria included several relevant detection power measures, family-wise type I error rate, and computational complexity. There are several important results from this study. First, while some SNPs in interactions with strong effects are successfully detected, most of the methods miss many interacting SNPs at an acceptable rate of false positives. In this study, the best-performing method was MECPM. Second, the statistical significance assessment criteria, used by some of the methods to control the type I error rate, are quite conservative, thereby limiting their power and making it difficult to fairly compare them. Third, as expected, power varies for different models and as a function of penetrance, minor allele frequency, linkage disequilibrium and marginal effects. Fourth, the analytical relationships between power and these factors are derived, aiding in the interpretation of the study results. Fifth, for these methods the magnitude of the main effect influences the power of the tests. Sixth, most methods can detect some ground-truth SNPs but have modest power to detect the whole set of interacting SNPs. This comparison study provides new insights into the strengths and limitations of current methods for detecting interacting loci. This study, along with freely available simulation tools we provide, should help support development of improved methods. The simulation tools are available at: http://code.google.com/p/simulation-tool-bmc-ms9169818735220977/downloads/list.

Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut

NASA Astrophysics Data System (ADS)

Leiserson, Mark D. M.; Tatar, Diana; Cowen, Lenore J.; Hescott, Benjamin J.

A new method based on a mathematically natural local search framework for max cut is developed to uncover functionally coherent module and BPM motifs in high-throughput genetic interaction data. Unlike previous methods which also consider physical protein-protein interaction data, our method utilizes genetic interaction data only; this becomes increasingly important as high-throughput genetic interaction data is becoming available in settings where less is known about physical interaction data. We compare modules and BPMs obtained to previous methods and across different datasets. Despite needing no physical interaction information, the BPMs produced by our method are competitive with previous methods. Biological findings include a suggested global role for the prefoldin complex and a SWR subcomplex in pathway buffering in the budding yeast interactome.

Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut.

PubMed

Leiserson, Mark D M; Tatar, Diana; Cowen, Lenore J; Hescott, Benjamin J

2011-11-01

A new method based on a mathematically natural local search framework for max cut is developed to uncover functionally coherent module and BPM motifs in high-throughput genetic interaction data. Unlike previous methods, which also consider physical protein-protein interaction data, our method utilizes genetic interaction data only; this becomes increasingly important as high-throughput genetic interaction data is becoming available in settings where less is known about physical interaction data. We compare modules and BPMs obtained to previous methods and across different datasets. Despite needing no physical interaction information, the BPMs produced by our method are competitive with previous methods. Biological findings include a suggested global role for the prefoldin complex and a SWR subcomplex in pathway buffering in the budding yeast interactome.

Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut

PubMed Central

Leiserson, Mark D.M.; Tatar, Diana; Cowen, Lenore J.

2011-01-01

Abstract A new method based on a mathematically natural local search framework for max cut is developed to uncover functionally coherent module and BPM motifs in high-throughput genetic interaction data. Unlike previous methods, which also consider physical protein-protein interaction data, our method utilizes genetic interaction data only; this becomes increasingly important as high-throughput genetic interaction data is becoming available in settings where less is known about physical interaction data. We compare modules and BPMs obtained to previous methods and across different datasets. Despite needing no physical interaction information, the BPMs produced by our method are competitive with previous methods. Biological findings include a suggested global role for the prefoldin complex and a SWR subcomplex in pathway buffering in the budding yeast interactome. PMID:21882903

Interpreting Assessments of Student Learning in the Introductory Physics Classroom and Laboratory

NASA Astrophysics Data System (ADS)

Dowd, Jason Edward

Assessment is the primary means of feedback between students and instructors. However, to effectively use assessment, the ability to interpret collected information is essential. We present insights into three unique, important avenues of assessment in the physics classroom and laboratory. First, we examine students' performance on conceptual surveys. The goal of this research project is to better utilize the information collected by instructors when they administer the Force Concept Inventory (FCI) to students as a pre-test and post-test of their conceptual understanding of Newtonian mechanics. We find that ambiguities in the use of the normalized gain, g, may influence comparisons among individual classes. Therefore, we propose using stratagrams, graphical summaries of the fraction of students who exhibit "Newtonian thinking," as a clearer, more informative method of both assessing a single class and comparing performance among classes. Next, we examine students' expressions of confusion when they initially encounter new material. The goal of this research project is to better understand what such confusion actually conveys to instructors about students' performance and engagement. We investigate the relationship between students' self-assessment of their confusion over material and their performance, confidence in reasoning, pre-course self-efficacy and several other measurable characteristics of engagement. We find that students' expressions of confusion are negatively related to initial performance, confidence and self-efficacy, but positively related to final performance when all factors are considered together. Finally, we examine students' exhibition of scientific reasoning abilities in the instructional laboratory. The goal of this research project is to explore two inquiry-based curricula, each of which proposes a different degree of scaffolding. Students engage in sequences of these laboratory activities during one semester of an introductory physics course. We find that students who participate in the less scaffolded activities exhibit marginally stronger scientific reasoning abilities in distinct exercises throughout the semester, but exhibit no differences in the final, common exercises. Overall, we find that, although students demonstrate some enhanced scientific reasoning skills, they fail to exhibit or retain even some of the most strongly emphasized skills.

Revealing protein functions based on relationships of interacting proteins and GO terms.

PubMed

Teng, Zhixia; Guo, Maozu; Liu, Xiaoyan; Tian, Zhen; Che, Kai

2017-09-20

In recent years, numerous computational methods predicted protein function based on the protein-protein interaction (PPI) network. These methods supposed that two proteins share the same function if they interact with each other. However, it is reported by recent studies that the functions of two interacting proteins may be just related. It will mislead the prediction of protein function. Therefore, there is a need for investigating the functional relationship between interacting proteins. In this paper, the functional relationship between interacting proteins is studied and a novel method, called as GoDIN, is advanced to annotate functions of interacting proteins in Gene Ontology (GO) context. It is assumed that the functional difference between interacting proteins can be expressed by semantic difference between GO term and its relatives. Thus, the method uses GO term and its relatives to annotate the interacting proteins separately according to their functional roles in the PPI network. The method is validated by a series of experiments and compared with the concerned method. The experimental results confirm the assumption and suggest that GoDIN is effective on predicting functions of protein. This study demonstrates that: (1) interacting proteins are not equal in the PPI network, and their function may be same or similar, or just related; (2) functional difference between interacting proteins can be measured by their degrees in the PPI network; (3) functional relationship between interacting proteins can be expressed by relationship between GO term and its relatives.

What Predicts Use of Learning-Centered, Interactive Engagement Methods?

ERIC Educational Resources Information Center

Madson, Laura; Trafimow, David; Gray, Tara; Gutowitz, Michael

2014-01-01

What makes some faculty members more likely to use interactive engagement methods than others? We use the theory of reasoned action to predict faculty members' use of interactive engagement methods. Results indicate that faculty members' beliefs about the personal positive consequences of using these methods (e.g., "Using interactive…

Developing and Evaluating a Technology Enhanced Interaction Framework and Method That Can Enhance the Accessibility of Mobile Learning

ERIC Educational Resources Information Center

Angkananon, Kewalin; Wald, Mike; Gilbert, Lester

2014-01-01

This paper focuses on the development and evaluation of a Technology Enhanced Interaction Framework and Method that can help with designing accessible mobile learning interactions involving disabled people. This new framework and method were developed to help design technological support for communication and interactions between people,…

Renyi entanglement entropy of interacting fermions calculated using the continuous-time quantum Monte Carlo method.

PubMed

Wang, Lei; Troyer, Matthias

2014-09-12

We present a new algorithm for calculating the Renyi entanglement entropy of interacting fermions using the continuous-time quantum Monte Carlo method. The algorithm only samples the interaction correction of the entanglement entropy, which by design ensures the efficient calculation of weakly interacting systems. Combined with Monte Carlo reweighting, the algorithm also performs well for systems with strong interactions. We demonstrate the potential of this method by studying the quantum entanglement signatures of the charge-density-wave transition of interacting fermions on a square lattice.

Three-dimensional, position-sensitive radiation detection

DOEpatents

He, Zhong; Zhang, Feng

2010-04-06

Disclosed herein is a method of determining a characteristic of radiation detected by a radiation detector via a multiple-pixel event having a plurality of radiation interactions. The method includes determining a cathode-to-anode signal ratio for a selected interaction of the plurality of radiation interactions based on electron drift time data for the selected interaction, and determining the radiation characteristic for the multiple-pixel event based on both the cathode-to-anode signal ratio and the electron drift time data. In some embodiments, the method further includes determining a correction factor for the radiation characteristic based on an interaction depth of the plurality of radiation interactions, a lateral distance between the selected interaction and a further interaction of the plurality of radiation interactions, and the lateral positioning of the plurality of radiation interactions.

A Generalized Weizsacker-Williams Method Applied to Pion Production in Proton-Proton Collisions

NASA Technical Reports Server (NTRS)

Ahern, Sean C.; Poyser, William J.; Norbury, John W.; Tripathi, R. K.

2002-01-01

A new "Generalized" Weizsacker-Williams method (GWWM) is used to calculate approximate cross sections for relativistic peripheral proton-proton collisions. Instead of a mass less photon mediator, the method allows for the mediator to have mass for short range interactions. This method generalizes the Weizsacker-Williams method (WWM) from Coulomb interactions to GWWM for strong interactions. An elastic proton-proton cross section is calculated using GWWM with experimental data for the elastic p+p interaction, where the mass p+ is now the mediator. The resulting calculated cross sections is compared to existing data for the elastic proton-proton interaction. A good approximate fit is found between the data and the calculation.

Enhanced identification of synergistic and antagonistic emergent interactions among three or more drugs

PubMed Central

White, Cynthia; Mao, Zhiyuan; Savage, Van M.

2016-01-01

Interactions among drugs play a critical role in the killing efficacy of multi-drug treatments. Recent advances in theory and experiment for three-drug interactions enable the search for emergent interactions—ones not predictable from pairwise interactions. Previous work has shown it is easier to detect synergies and antagonisms among pairwise interactions when a rescaling method is applied to the interaction metric. However, no study has carefully examined whether new types of normalization might be needed for emergence. Here, we propose several rescaling methods for enhancing the classification of the higher order drug interactions based on our conceptual framework. To choose the rescaling that best separates synergism, antagonism and additivity, we conducted bacterial growth experiments in the presence of single, pairwise and triple-drug combinations among 14 antibiotics. We found one of our rescaling methods is far better at distinguishing synergistic and antagonistic emergent interactions than any of the other methods. Using our new method, we find around 50% of emergent interactions are additive, much less than previous reports of greater than 90% additivity. We conclude that higher order emergent interactions are much more common than previously believed, and we argue these findings for drugs suggest that appropriate rescaling is crucial to infer higher order interactions. PMID:27278366

Full-Potential Modeling of Blade-Vortex Interactions. Degree awarded by George Washington Univ., Feb. 1987

NASA Technical Reports Server (NTRS)

Jones, Henry E.

1997-01-01

A study of the full-potential modeling of a blade-vortex interaction was made. A primary goal of this study was to investigate the effectiveness of the various methods of modeling the vortex. The model problem restricts the interaction to that of an infinite wing with an infinite line vortex moving parallel to its leading edge. This problem provides a convenient testing ground for the various methods of modeling the vortex while retaining the essential physics of the full three-dimensional interaction. A full-potential algorithm specifically tailored to solve the blade-vortex interaction (BVI) was developed to solve this problem. The basic algorithm was modified to include the effect of a vortex passing near the airfoil. Four different methods of modeling the vortex were used: (1) the angle-of-attack method, (2) the lifting-surface method, (3) the branch-cut method, and (4) the split-potential method. A side-by-side comparison of the four models was conducted. These comparisons included comparing generated velocity fields, a subcritical interaction, and a critical interaction. The subcritical and critical interactions are compared with experimentally generated results. The split-potential model was used to make a survey of some of the more critical parameters which affect the BVI.

Computational methods for identifying miRNA sponge interactions.

PubMed

Le, Thuc Duy; Zhang, Junpeng; Liu, Lin; Li, Jiuyong

2017-07-01

Recent findings show that coding genes are not the only targets that miRNAs interact with. In fact, there is a pool of different RNAs competing with each other to attract miRNAs for interactions, thus acting as competing endogenous RNAs (ceRNAs). The ceRNAs indirectly regulate each other via the titration mechanism, i.e. the increasing concentration of a ceRNA will decrease the number of miRNAs that are available for interacting with other targets. The cross-talks between ceRNAs, i.e. their interactions mediated by miRNAs, have been identified as the drivers in many disease conditions, including cancers. In recent years, some computational methods have emerged for identifying ceRNA-ceRNA interactions. However, there remain great challenges and opportunities for developing computational methods to provide new insights into ceRNA regulatory mechanisms.In this paper, we review the publically available databases of ceRNA-ceRNA interactions and the computational methods for identifying ceRNA-ceRNA interactions (also known as miRNA sponge interactions). We also conduct a comparison study of the methods with a breast cancer dataset. Our aim is to provide a current snapshot of the advances of the computational methods in identifying miRNA sponge interactions and to discuss the remaining challenges. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Interactive Video Usage on Autism Spectrum Disorder Training in Medical Education

ERIC Educational Resources Information Center

Taslibeyaz, Elif; Dursun, Onur Burak; Karaman, Selcuk

2017-01-01

This study aimed to compare the effects of interactive and non-interactive videos concerning the autism spectrum disorder on medical students' achievement. It also evaluated the relation between the interactive videos' interactivity and the students' decision-making process. It used multiple methods, including quantitative and qualitative methods.…

Implementation of Scientific Community Laboratories and Their Effect on Student Conceptual Learning, Attitudes, and Understanding of Uncertainty

NASA Astrophysics Data System (ADS)

Lark, Adam

Scientific Community Laboratories, developed by The University of Maryland, have shown initial promise as laboratories meant to emulate the practice of doing physics. These laboratories have been re-created by incorporating their design elements with the University of Toledo course structure and resources. The laboratories have been titled the Scientific Learning Community (SLC) Laboratories. A comparative study between these SLC laboratories and the University of Toledo physics department's traditional laboratories was executed during the fall 2012 semester on first semester calculus-based physics students. Three tests were executed as pre-test and post-tests to capture the change in students' concept knowledge, attitudes, and understanding of uncertainty. The Force Concept Inventory (FCI) was used to evaluate students' conceptual changes through the semester and average normalized gains were compared between both traditional and SLC laboratories. The Colorado Learning Attitudes about Science Survey for Experimental Physics (E-CLASS) was conducted to elucidate students' change in attitudes through the course of each laboratory. Finally, interviews regarding data analysis and uncertainty were transcribed and coded to track changes in the way students understand uncertainty and data analysis in experimental physics after their participation in both laboratory type. Students in the SLC laboratories showed a notable an increase conceptual knowledge and attitudes when compared to traditional laboratories. SLC students' understanding of uncertainty showed most improvement, diverging completely from students in the traditional laboratories, who declined throughout the semester.

Longitudinal analysis of head and somatic growth in fetuses with congenital heart defects.

PubMed

Turan, Sifa; Rosenbloom, Joshua I; Hussein, Mostafa; Berg, Christoph; Gembruch, Ulrich; Baschat, Ahmet A; Turan, Ozhan M

2017-02-01

Fetal head and somatic growth dynamics differs in fetuses with congenital heart defects (CHD). We longitudinally characterized fetal head and somatic growth in relation to the type of CHD. Four hundred eleven exams from isolated CHD were compared with 1,219 controls. Head and somatic growth was assessed using head circumference (HC), brain volume (BrV = 1/6 × π × (HC/π)3)/2), fetal cephalization index (FCI = BrV/[estimated fetal weight]), and growth percentile. Umbilical and middle cerebral artery Doppler indices were obtained. CHD were grouped as: (1) d-transposition of great arteries (n = 11); (2) left ventricular outflow tract obstruction with retrograde isthmic flow (n = 18); (3) left ventricular outflow tract obstruction with antegrade isthmic flow (n = 16); (4) pulmonary outflow tract obstructions (n = 22). The smallest head size was seen in group 1. Growth asymmetry was diagnosed in group 2. Brain sparing was seen in groups 2 and 4 (p < 0.0001). HC and BrV percentiles decreased with advancing gestational age (p < 0.001) in group 2, and a significant drop was observed around 28 weeks. d-Transposition of great arteries and left-sided CHD leading to isthmic blood flow reversal are associated with delayed head growth. Prenatal evaluation of central hemodynamics in CHD may be contributive for predicting neurodevelopmental risks in CHD and help directing prenatal interventions. © 2016 Wiley Periodicals, Inc. J Clin Ultrasound 45:96-104, 2017. © 2016 Wiley Periodicals, Inc.

Medical and surgical management for chronic thromboembolic pulmonary hypertension: a single center experience.

PubMed

Coronel, María Lorena; Chamorro, Núria; Blanco, Isabel; Amado, Verónica; Del Pozo, Roberto; Pomar, José Luis; Badia, Joan Ramón; Rovira, Irene; Matute, Purificación; Argemí, Gemma; Castellà, Manuel; Barberà, Joan Albert

2014-12-01

Pulmonary endarterectomy (PE) is the treatment of choice for chronic thromboembolic pulmonary hypertension (CTEPH). The aim of this study was to analyze our experience in the medical and surgical management of CTEPH. We included 80 patients diagnosed with CTEPH between January 2000 and July 2012. Thirty two patients underwent PE and 48 received medical treatment (MT). We analyzed functional class (FC), six-minute walking distance (6MWD) and pulmonary hemodynamics. Mortality in both groups and periods were analyzed. Patients who underwent PE were younger, mostly men, and had longer 6MWD. No differences were observed in pulmonary hemodynamics or FC at diagnosis. One year after treatment, all PE patients versus 41% in MT group were at FCI-II. At follow-up, the PE group showed greater increase in 6MWD, and greater reduction in mean pulmonary arterial pressure and pulmonary vascular resistance than the MT group (P<.05). Overall survival in the MT group at 1 and 5years was 83% and 69%, respectively. Conditional survival in patients alive 100days post-PE at 1 and 5years was 95% and 88%, respectively. Surgical mortality in operated patients in the first period (2000-2006) was 31,3%, and 6,3% in the second (2007-2012). PE provides good clinical results, and improves pulmonary hemodynamics in patients who successfully overcome the immediate postoperative period. After a learning period, the current operatory mortality in our center is similar to international standards. Copyright © 2013 SEPAR. Published by Elsevier Espana. All rights reserved.

Investigating High Frequency Magnetic Activity During Local Helicity Injection on the Pegasus Toroidal Experiment

NASA Astrophysics Data System (ADS)

Richner, N. J.; Bongard, M. W.; Fonck, R. J.; Pachicano, J. L.; Perry, J. M.; Reusch, J. A.

2017-10-01

Understanding the current drive mechanism(s) of Local Helicity Injection (LHI) is needed for confident scaling to next-step devices. 3D resistive MHD NIMROD simulations ascribe large-scale reconnection events of helical injector current streams as a current drive mechanism. The events generate n = 1 B fluctuations on outboard Mirnov coils, consistent with experiment. New results suggest additional mechanisms are also active during LHI. Reconnection-driven ion heating is better correlated with high frequency activity than the n = 1 bursts. Experiments with inboard injectors can exhibit an abrupt ( 250 μs) transition to a reduced MHD state on outboard Mirnovs where the n = 1 feature vanishes, while still maintaining current growth and/or sustainment. A new insertable magnetics probe was developed to investigate these phenomena. It measures TeXBz up to 3.5 MHz at 15 points over a 14 cm radial extent (ΔR 1 cm). Measurements with this probe are consistent with the outboard Mirnovs when positioned far from the plasma boundary. However, measurements near the plasma edge lack the reduction in broadband power (up to 2 MHz) following the transition. The probe shows power is concentrated at higher frequencies during LHI, with mostly flat B spectra up to 600-800 kHz ( fci) at which there is a resonance-like feature; at higher frequencies, the power decreases. These measurements suggest short-wavelength activity may play a significant role in LHI current drive. Work supported by US DOE Grant DE-FG02-96ER54375.

Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions.

PubMed

Takemoto, Kazuhiro; Aie, Kazuki

2017-05-25

Host-pathogen interactions are important in a wide range of research fields. Given the importance of metabolic crosstalk between hosts and pathogens, a metabolic network-based reverse ecology method was proposed to infer these interactions. However, the validity of this method remains unclear because of the various explanations presented and the influence of potentially confounding factors that have thus far been neglected. We re-evaluated the importance of the reverse ecology method for evaluating host-pathogen interactions while statistically controlling for confounding effects using oxygen requirement, genome, metabolic network, and phylogeny data. Our data analyses showed that host-pathogen interactions were more strongly influenced by genome size, primary network parameters (e.g., number of edges), oxygen requirement, and phylogeny than the reserve ecology-based measures. These results indicate the limitations of the reverse ecology method; however, they do not discount the importance of adopting reverse ecology approaches altogether. Rather, we highlight the need for developing more suitable methods for inferring host-pathogen interactions and conducting more careful examinations of the relationships between metabolic networks and host-pathogen interactions.

Solving Fluid Structure Interaction Problems with an Immersed Boundary Method

NASA Technical Reports Server (NTRS)

Barad, Michael F.; Brehm, Christoph; Kiris, Cetin C.

2016-01-01

An immersed boundary method for the compressible Navier-Stokes equations can be used for moving boundary problems as well as fully coupled fluid-structure interaction is presented. The underlying Cartesian immersed boundary method of the Launch Ascent and Vehicle Aerodynamics (LAVA) framework, based on the locally stabilized immersed boundary method previously presented by the authors, is extended to account for unsteady boundary motion and coupled to linear and geometrically nonlinear structural finite element solvers. The approach is validated for moving boundary problems with prescribed body motion and fully coupled fluid structure interaction problems. Keywords: Immersed Boundary Method, Higher-Order Finite Difference Method, Fluid Structure Interaction.

Research Techniques Made Simple: Emerging Methods to Elucidate Protein Interactions through Spatial Proximity.

PubMed

Che, Yonglu; Khavari, Paul A

2017-12-01

Interactions between proteins are essential for fundamental cellular processes, and the diversity of such interactions enables the vast variety of functions essential for life. A persistent goal in biological research is to develop assays that can faithfully capture different types of protein interactions to allow their study. A major step forward in this direction came with a family of methods that delineates spatial proximity of proteins as an indirect measure of protein-protein interaction. A variety of enzyme- and DNA ligation-based methods measure protein co-localization in space, capturing novel interactions that were previously too transient or low affinity to be identified. Here we review some of the methods that have been successfully used to measure spatially proximal protein-protein interactions. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Faculty Members' Attitudes Predict Adoption of Interactive Engagement Methods

ERIC Educational Resources Information Center

Madson, Laura; Trafimow, David; Gray, Tara

2017-01-01

Why do some faculty members use interactive engagement methods and others rely on lecture? Using a cross-disciplinary sample of U.S. faculty members (N = 442), the best predictor of faculty members' self-reported use of these methods was their attitudes about the positive consequences of using interactive engagement methods for students and for…

Method and apparatus for modeling interactions

DOEpatents

Xavier, Patrick G.

2002-01-01

The present invention provides a method and apparatus for modeling interactions that overcomes drawbacks. The method of the present invention comprises representing two bodies undergoing translations by two swept volume representations. Interactions such as nearest approach and collision can be modeled based on the swept body representations. The present invention is more robust and allows faster modeling than previous methods.

Modeling and Detecting Feature Interactions among Integrated Services of Home Network Systems

NASA Astrophysics Data System (ADS)

Igaki, Hiroshi; Nakamura, Masahide

This paper presents a framework for formalizing and detecting feature interactions (FIs) in the emerging smart home domain. We first establish a model of home network system (HNS), where every networked appliance (or the HNS environment) is characterized as an object consisting of properties and methods. Then, every HNS service is defined as a sequence of method invocations of the appliances. Within the model, we next formalize two kinds of FIs: (a) appliance interactions and (b) environment interactions. An appliance interaction occurs when two method invocations conflict on the same appliance, whereas an environment interaction arises when two method invocations conflict indirectly via the environment. Finally, we propose offline and online methods that detect FIs before service deployment and during execution, respectively. Through a case study with seven practical services, it is shown that the proposed framework is generic enough to capture feature interactions in HNS integrated services. We also discuss several FI resolution schemes within the proposed framework.

Video Elicitation Interviews: A Qualitative Research Method for Investigating Physician-Patient Interactions

PubMed Central

Henry, Stephen G.; Fetters, Michael D.

2012-01-01

We describe the concept and method of video elicitation interviews and provide practical guidance for primary care researchers who want to use this qualitative method to investigate physician-patient interactions. During video elicitation interviews, researchers interview patients or physicians about a recent clinical interaction using a video recording of that interaction as an elicitation tool. Video elicitation is useful because it allows researchers to integrate data about the content of physician-patient interactions gained from video recordings with data about participants’ associated thoughts, beliefs, and emotions gained from elicitation interviews. This method also facilitates investigation of specific events or moments during interactions. Video elicitation interviews are logistically demanding and time consuming, and they should be reserved for research questions that cannot be fully addressed using either standard interviews or video recordings in isolation. As many components of primary care fall into this category, high-quality video elicitation interviews can be an important method for understanding and improving physician-patient interactions in primary care. PMID:22412003

Video elicitation interviews: a qualitative research method for investigating physician-patient interactions.

PubMed

Henry, Stephen G; Fetters, Michael D

2012-01-01

We describe the concept and method of video elicitation interviews and provide practical guidance for primary care researchers who want to use this qualitative method to investigate physician-patient interactions. During video elicitation interviews, researchers interview patients or physicians about a recent clinical interaction using a video recording of that interaction as an elicitation tool. Video elicitation is useful because it allows researchers to integrate data about the content of physician-patient interactions gained from video recordings with data about participants' associated thoughts, beliefs, and emotions gained from elicitation interviews. This method also facilitates investigation of specific events or moments during interactions. Video elicitation interviews are logistically demanding and time consuming, and they should be reserved for research questions that cannot be fully addressed using either standard interviews or video recordings in isolation. As many components of primary care fall into this category, high-quality video elicitation interviews can be an important method for understanding and improving physician-patient interactions in primary care.

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

PubMed Central

Burger, Lukas; van Nimwegen, Erik

2008-01-01

Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381

New analysis of nuclear interaction observed by Mt. Kanbara emulsion chamber experiment

NASA Technical Reports Server (NTRS)

Nanjo, H.

1985-01-01

To date the analysis of the air cascade family has been performed using a full Monte Carlo simulation. It is difficult to draw a definite conclusion about the interaction mechanism by using only this kind of simulation. On the other hand, attempts to reproduce the original gamma ray at the interaction point, for example decascading, have also been made. This method makes it possible to observe the interaction directly and to analyze the data from various angles. All of these methods, however, assume a constant ER in the cascade shower, where E is energy and R is the distance from the center of the cascade shower. It is impossible to reproduce the exact interaction height and energy by these methods. A relative method in separating one cascade shower from others is adopted. This method makes it possible to estimate the interaction height and energy by using information about the lateral spread of the cascade shower.

A facile method to screen inhibitors of protein-protein interactions including MDM2-p53 displayed on T7 phage.

PubMed

Ishi, Kazutomo; Sugawara, Fumio

2008-05-01

Protein-protein interactions are essential in many biological processes including cell cycle and apoptosis. It is currently of great medical interest to inhibit specific protein-protein interactions in order to treat a variety of disease states. Here, we describe a facile multiwell plate assay method using T7 phage display to screen for candidate inhibitors of protein-protein interactions. Because T7 phage display is an effective method for detecting protein-protein interactions, we aimed to utilize this technique to screen for small-molecule inhibitors that disrupt these types of interaction. We used the well-characterized interaction between p53 and MDM2 and an inhibitor of this interaction, nutlin 3, as a model system to establish a new screening method. Phage particles displaying p53 interacted with GST-MDM2 immobilized on 96-well plates, and the interaction was inhibited by nutlin 3. Multiwell plate assay was then performed using a natural product library, which identified dehydroaltenusin as a candidate inhibitor of the p53-MDM2 interaction. We discuss the potential applications of this novel T7 phage display methodology, which we propose to call 'reverse phage display'.

A Multidimensional Analysis Tool for Visualizing Online Interactions

ERIC Educational Resources Information Center

Kim, Minjeong; Lee, Eunchul

2012-01-01

This study proposes and verifies the performance of an analysis tool for visualizing online interactions. A review of the most widely used methods for analyzing online interactions, including quantitative analysis, content analysis, and social network analysis methods, indicates these analysis methods have some limitations resulting from their…

Lattice Boltzmann Methods for Fluid Structure Interaction

DTIC Science & Technology

2012-09-01

MONTEREY, CALIFORNIA DISSERTATION LATTICE BOLTZMANN METHODS FOR FLUID STRUCTURE INTERACTION by Stuart R. Blair September 2012 Dissertation Supervisor...200 words) The use of lattice Boltzmann methods (LBM) for fluid flow and its coupling with finite element method (FEM) structural models for fluid... structure interaction (FSI) is investigated. A body of high performance LBM software that exploits graphic processing unit (GPU) and multiprocessor

Drug-Target Interactions: Prediction Methods and Applications.

PubMed

Anusuya, Shanmugam; Kesherwani, Manish; Priya, K Vishnu; Vimala, Antonydhason; Shanmugam, Gnanendra; Velmurugan, Devadasan; Gromiha, M Michael

2018-01-01

Identifying the interactions between drugs and target proteins is a key step in drug discovery. This not only aids to understand the disease mechanism, but also helps to identify unexpected therapeutic activity or adverse side effects of drugs. Hence, drug-target interaction prediction becomes an essential tool in the field of drug repurposing. The availability of heterogeneous biological data on known drug-target interactions enabled many researchers to develop various computational methods to decipher unknown drug-target interactions. This review provides an overview on these computational methods for predicting drug-target interactions along with available webservers and databases for drug-target interactions. Further, the applicability of drug-target interactions in various diseases for identifying lead compounds has been outlined. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Membrane fouling in a submerged membrane bioreactor: New method and its applications in interfacial interaction quantification.

PubMed

Hong, Huachang; Cai, Xiang; Shen, Liguo; Li, Renjie; Lin, Hongjun

2017-10-01

Quantification of interfacial interactions between two rough surfaces represents one of the most pressing requirements for membrane fouling prediction and control in membrane bioreactors (MBRs). This study firstly constructed regularly rough membrane and particle surfaces by using rigorous mathematical equations. Thereafter, a new method involving surface element integration (SEI) method, differential geometry and composite Simpson's rule was proposed to quantify the interfacial interactions between the two constructed rough surfaces. This new method were then applied to investigate interfacial interactions in a MBR with the data of surface properties of membrane and foulants experimentally measured. The feasibility of the new method was verified. It was found that asperity amplitude and period of the membrane surface exerted profound effects on the total interaction. The new method had broad potential application fields especially including guiding membrane surface design for membrane fouling mitigation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Viscous-inviscid interaction method including wake effects for three-dimensional wing-body configurations

NASA Technical Reports Server (NTRS)

Streett, C. L.

1981-01-01

A viscous-inviscid interaction method has been developed by using a three-dimensional integral boundary-layer method which produces results in good agreement with a finite-difference method in a fraction of the computer time. The integral method is stable and robust and incorporates a model for computation in a small region of streamwise separation. A locally two-dimensional wake model, accounting for thickness and curvature effects, is also included in the interaction procedure. Computation time spent in converging an interacted result is, many times, only slightly greater than that required to converge an inviscid calculation. Results are shown from the interaction method, run at experimental angle of attack, Reynolds number, and Mach number, on a wing-body test case for which viscous effects are large. Agreement with experiment is good; in particular, the present wake model improves prediction of the spanwise lift distribution and lower surface cove pressure.

Hotspot-Centric De Novo Design of Protein Binders

PubMed Central

Fleishman, Sarel J.; Corn, Jacob E.; Strauch, Eva-Maria; Whitehead, Timothy A.; Karanicolas, John; Baker, David

2014-01-01

Protein–protein interactions play critical roles in biology, and computational design of interactions could be useful in a range of applications. We describe in detail a general approach to de novo design of protein interactions based on computed, energetically optimized interaction hotspots, which was recently used to produce high-affinity binders of influenza hemagglutinin. We present several alternative approaches to identify and build the key hotspot interactions within both core secondary structural elements and variable loop regions and evaluate the method's performance in natural-interface recapitulation. We show that the method generates binding surfaces that are more conformationally restricted than previous design methods, reducing opportunities for off-target interactions. PMID:21945116

Split luciferase complementation assay to detect regulated protein-protein interactions in rice protoplasts in a large-scale format

PubMed Central

2014-01-01

Background The rice interactome, in which a network of protein-protein interactions has been elucidated in rice, is a useful resource to identify functional modules of rice signal transduction pathways. Protein-protein interactions occur in cells in two ways, constitutive and regulative. While a yeast-based high-throughput method has been widely used to identify the constitutive interactions, a method to detect the regulated interactions is rarely developed for a large-scale analysis. Results A split luciferase complementation assay was applied to detect the regulated interactions in rice. A transformation method of rice protoplasts in a 96-well plate was first established for a large-scale analysis. In addition, an antibody that specifically recognizes a carboxyl-terminal fragment of Renilla luciferase was newly developed. A pair of antibodies that recognize amino- and carboxyl- terminal fragments of Renilla luciferase, respectively, was then used to monitor quality and quantity of interacting recombinant-proteins accumulated in the cells. For a proof-of-concept, the method was applied to detect the gibberellin-dependent interaction between GIBBERELLIN INSENSITIVE DWARF1 and SLENDER RICE 1. Conclusions A method to detect regulated protein-protein interactions was developed towards establishment of the rice interactome. PMID:24987490

Interactions between butterfly-shaped pulses in the inhomogeneous media

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

Liu, Wen-Jun; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190; Huang, Long-Gang

2014-10-15

Pulse interactions affect pulse qualities during the propagation. Interactions between butterfly-shaped pulses are investigated to improve pulse qualities in the inhomogeneous media. In order to describe the interactions between butterfly-shaped pulses, analytic two-soliton solutions are derived. Based on those solutions, influences of corresponding parameters on pulse interactions are discussed. Methods to control the pulse interactions are suggested. - Highlights: • Interactions between butterfly-shaped pulses are investigated. • Methods to control the pulse interactions are suggested. • Analytic two-soliton solutions for butterfly-shaped pulses are derived.

An Assessment of Phylogenetic Tools for Analyzing the Interplay Between Interspecific Interactions and Phenotypic Evolution.

PubMed

Drury, J P; Grether, G F; Garland, T; Morlon, H

2018-05-01

Much ecological and evolutionary theory predicts that interspecific interactions often drive phenotypic diversification and that species phenotypes in turn influence species interactions. Several phylogenetic comparative methods have been developed to assess the importance of such processes in nature; however, the statistical properties of these methods have gone largely untested. Focusing mainly on scenarios of competition between closely-related species, we assess the performance of available comparative approaches for analyzing the interplay between interspecific interactions and species phenotypes. We find that many currently used statistical methods often fail to detect the impact of interspecific interactions on trait evolution, that sister-taxa analyses are particularly unreliable in general, and that recently developed process-based models have more satisfactory statistical properties. Methods for detecting predictors of species interactions are generally more reliable than methods for detecting character displacement. In weighing the strengths and weaknesses of different approaches, we hope to provide a clear guide for empiricists testing hypotheses about the reciprocal effect of interspecific interactions and species phenotypes and to inspire further development of process-based models.

Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction.

PubMed

Du, Tianchuan; Liao, Li; Wu, Cathy H

2016-12-01

Identifying the residues in a protein that are involved in protein-protein interaction and identifying the contact matrix for a pair of interacting proteins are two computational tasks at different levels of an in-depth analysis of protein-protein interaction. Various methods for solving these two problems have been reported in the literature. However, the interacting residue prediction and contact matrix prediction were handled by and large independently in those existing methods, though intuitively good prediction of interacting residues will help with predicting the contact matrix. In this work, we developed a novel protein interacting residue prediction system, contact matrix-interaction profile hidden Markov model (CM-ipHMM), with the integration of contact matrix prediction and the ipHMM interaction residue prediction. We propose to leverage what is learned from the contact matrix prediction and utilize the predicted contact matrix as "feedback" to enhance the interaction residue prediction. The CM-ipHMM model showed significant improvement over the previous method that uses the ipHMM for predicting interaction residues only. It indicates that the downstream contact matrix prediction could help the interaction site prediction.

Stand, Harvest, and Equipment Interactions in Simulated Harvesting Prescriptions

Treesearch

Jingxin Wang; W. Dale Greene; Bryce J. Stokes

1998-01-01

We evaluated potential interactions of stand type, harvesting method, and equipment in an experiment using interactive simulation. We examined three felling methods (chain saw, feller-buncher, harvester) and two extraction methods (grapple skidder and forwarder) performing clearcuts, sheltenvood cuts, and single-tree selection cuts in both an uneven-aged natural stand...

GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data.

PubMed

Mifsud, Borbala; Martincorena, Inigo; Darbo, Elodie; Sugar, Robert; Schoenfelder, Stefan; Fraser, Peter; Luscombe, Nicholas M

2017-01-01

Hi-C is one of the main methods for investigating spatial co-localisation of DNA in the nucleus. However, the raw sequencing data obtained from Hi-C experiments suffer from large biases and spurious contacts, making it difficult to identify true interactions. Existing methods use complex models to account for biases and do not provide a significance threshold for detecting interactions. Here we introduce a simple binomial probabilistic model that resolves complex biases and distinguishes between true and false interactions. The model corrects biases of known and unknown origin and yields a p-value for each interaction, providing a reliable threshold based on significance. We demonstrate this experimentally by testing the method against a random ligation dataset. Our method outperforms previous methods and provides a statistical framework for further data analysis, such as comparisons of Hi-C interactions between different conditions. GOTHiC is available as a BioConductor package (http://www.bioconductor.org/packages/release/bioc/html/GOTHiC.html).

Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding

PubMed Central

Tajima, Satohiro; Yanagawa, Toru; Fujii, Naotaka; Toyoizumi, Taro

2015-01-01

Brain-wide interactions generating complex neural dynamics are considered crucial for emergent cognitive functions. However, the irreducible nature of nonlinear and high-dimensional dynamical interactions challenges conventional reductionist approaches. We introduce a model-free method, based on embedding theorems in nonlinear state-space reconstruction, that permits a simultaneous characterization of complexity in local dynamics, directed interactions between brain areas, and how the complexity is produced by the interactions. We demonstrate this method in large-scale electrophysiological recordings from awake and anesthetized monkeys. The cross-embedding method captures structured interaction underlying cortex-wide dynamics that may be missed by conventional correlation-based analysis, demonstrating a critical role of time-series analysis in characterizing brain state. The method reveals a consciousness-related hierarchy of cortical areas, where dynamical complexity increases along with cross-area information flow. These findings demonstrate the advantages of the cross-embedding method in deciphering large-scale and heterogeneous neuronal systems, suggesting a crucial contribution by sensory-frontoparietal interactions to the emergence of complex brain dynamics during consciousness. PMID:26584045

[Detection of protein-protein interactions by FRET and BRET methods].

PubMed

Matoulková, E; Vojtěšek, B

2014-01-01

Nowadays, in vivo protein-protein interaction studies have become preferable detecting meth-ods that enable to show or specify (already known) protein interactions and discover their inhibitors. They also facilitate detection of protein conformational changes and discovery or specification of signaling pathways in living cells. One group of in vivo methods enabling these findings is based on fluorescent resonance energy transfer (FRET) and its bio-luminescent modification (BRET). They are based on visualization of protein-protein interactions via light or enzymatic excitation of fluorescent or bio-luminescent proteins. These methods allow not only protein localization within the cell or its organelles (or small animals) but they also allow us to quantify fluorescent signals and to discover weak or strong interaction partners. In this review, we explain the principles of FRET and BRET, their applications in the characterization of protein-protein interactions and we describe several findings using these two methods that clarify molecular and cellular mechanisms and signals related to cancer biology.

A simple and efficient method for predicting protein-protein interaction sites.

PubMed

Higa, R H; Tozzi, C L

2008-09-23

Computational methods for predicting protein-protein interaction sites based on structural data are characterized by an accuracy between 70 and 80%. Some experimental studies indicate that only a fraction of the residues, forming clusters in the center of the interaction site, are energetically important for binding. In addition, the analysis of amino acid composition has shown that residues located in the center of the interaction site can be better discriminated from the residues in other parts of the protein surface. In the present study, we implement a simple method to predict interaction site residues exploiting this fact and show that it achieves a very competitive performance compared to other methods using the same dataset and criteria for performance evaluation (success rate of 82.1%).

A strategy to apply quantitative epistasis analysis on developmental traits.

PubMed

Labocha, Marta K; Yuan, Wang; Aleman-Meza, Boanerges; Zhong, Weiwei

2017-05-15

Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement. Using two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions. We developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes.

A proximity-based graph clustering method for the identification and application of transcription factor clusters.

PubMed

Spadafore, Maxwell; Najarian, Kayvan; Boyle, Alan P

2017-11-29

Transcription factors (TFs) form a complex regulatory network within the cell that is crucial to cell functioning and human health. While methods to establish where a TF binds to DNA are well established, these methods provide no information describing how TFs interact with one another when they do bind. TFs tend to bind the genome in clusters, and current methods to identify these clusters are either limited in scope, unable to detect relationships beyond motif similarity, or not applied to TF-TF interactions. Here, we present a proximity-based graph clustering approach to identify TF clusters using either ChIP-seq or motif search data. We use TF co-occurrence to construct a filtered, normalized adjacency matrix and use the Markov Clustering Algorithm to partition the graph while maintaining TF-cluster and cluster-cluster interactions. We then apply our graph structure beyond clustering, using it to increase the accuracy of motif-based TFBS searching for an example TF. We show that our method produces small, manageable clusters that encapsulate many known, experimentally validated transcription factor interactions and that our method is capable of capturing interactions that motif similarity methods might miss. Our graph structure is able to significantly increase the accuracy of motif TFBS searching, demonstrating that the TF-TF connections within the graph correlate with biological TF-TF interactions. The interactions identified by our method correspond to biological reality and allow for fast exploration of TF clustering and regulatory dynamics.

Interaction and the Online Distance Classroom: Do Instructional Methods Effect the Quality of Interaction?

ERIC Educational Resources Information Center

Kanuka, Heather

2011-01-01

In this special issue, I bring together two studies to provide a comprehensive overview on diverse and interactive instructional methods aimed to facilitate higher levels of learning. One study explored the effects of group interaction using different instructional strategies focusing on the learning "process" using the Community of Inquiry…

A Spatial-frequency Method for Analyzing Antenna-to-Probe Interactions in Near-field Antenna Measurements.

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

Brock, Billy C.

The measurement of the radiation characteristics of an antenna on a near-field range requires that the antenna under test be located very close to the near-field probe. Although the direct coupling is utilized for characterizing the near field, this close proximity also presents the opportunity for significant undesired interactions (for example, reflections) to occur between the antenna and the near-field probe. When uncompensated, these additional interactions will introduce error into the measurement, increasing the uncertainty in the final gain pattern obtained through the near-field-to-far-field transformation. Quantifying this gain-uncertainty contribution requires quantifying the various additional interactions. A method incorporating spatial-frequency analysismore » is described which allows the dominant interaction contributions to be easily identified and quantified. In addition to identifying the additional antenna-to-probe interactions, the method also allows identification and quantification of interactions with other nearby objects within the measurement room. Because the method is a spatial-frequency method, wide-bandwidth data is not required, and it can be applied even when data is available at only a single temporal frequency. This feature ensures that the method can be applied to narrow-band antennas, where a similar time-domain analysis would not be possible. - 3 - - 4 -« less

Parallel Exploration of Interaction Space by BioID and Affinity Purification Coupled to Mass Spectrometry.

PubMed

Hesketh, Geoffrey G; Youn, Ji-Young; Samavarchi-Tehrani, Payman; Raught, Brian; Gingras, Anne-Claude

2017-01-01

Complete understanding of cellular function requires knowledge of the composition and dynamics of protein interaction networks, the importance of which spans all molecular cell biology fields. Mass spectrometry-based proteomics approaches are instrumental in this process, with affinity purification coupled to mass spectrometry (AP-MS) now widely used for defining interaction landscapes. Traditional AP-MS methods are well suited to providing information regarding the temporal aspects of soluble protein-protein interactions, but the requirement to maintain protein-protein interactions during cell lysis and AP means that both weak-affinity interactions and spatial information is lost. A more recently developed method called BioID employs the expression of bait proteins fused to a nonspecific biotin ligase, BirA*, that induces in vivo biotinylation of proximal proteins. Coupling this method to biotin affinity enrichment and mass spectrometry negates many of the solubility and interaction strength issues inherent in traditional AP-MS methods, and provides unparalleled spatial context for protein interactions. Here we describe the parallel implementation of both BioID and FLAG AP-MS allowing simultaneous exploration of both spatial and temporal aspects of protein interaction networks.

Methodical and technological aspects of creation of interactive computer learning systems

NASA Astrophysics Data System (ADS)

Vishtak, N. M.; Frolov, D. A.

2017-01-01

The article presents a methodology for the development of an interactive computer training system for training power plant. The methods used in the work are a generalization of the content of scientific and methodological sources on the use of computer-based training systems in vocational education, methods of system analysis, methods of structural and object-oriented modeling of information systems. The relevance of the development of the interactive computer training systems in the preparation of the personnel in the conditions of the educational and training centers is proved. Development stages of the computer training systems are allocated, factors of efficient use of the interactive computer training system are analysed. The algorithm of work performance at each development stage of the interactive computer training system that enables one to optimize time, financial and labor expenditure on the creation of the interactive computer training system is offered.

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

PubMed

Duan, Lili; Liu, Xiao; Zhang, John Z H

2016-05-04

Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

Multi-View Interaction Modelling of human collaboration processes: a business process study of head and neck cancer care in a Dutch academic hospital.

PubMed

Stuit, Marco; Wortmann, Hans; Szirbik, Nick; Roodenburg, Jan

2011-12-01

In the healthcare domain, human collaboration processes (HCPs), which consist of interactions between healthcare workers from different (para)medical disciplines and departments, are of growing importance as healthcare delivery becomes increasingly integrated. Existing workflow-based process modelling tools for healthcare process management, which are the most commonly applied, are not suited for healthcare HCPs mainly due to their focus on the definition of task sequences instead of the graphical description of human interactions. This paper uses a case study of a healthcare HCP at a Dutch academic hospital to evaluate a novel interaction-centric process modelling method. The HCP under study is the care pathway performed by the head and neck oncology team. The evaluation results show that the method brings innovative, effective, and useful features. First, it collects and formalizes the tacit domain knowledge of the interviewed healthcare workers in individual interaction diagrams. Second, the method automatically integrates these local diagrams into a single global interaction diagram that reflects the consolidated domain knowledge. Third, the case study illustrates how the method utilizes a graphical modelling language for effective tree-based description of interactions, their composition and routing relations, and their roles. A process analysis of the global interaction diagram is shown to identify HCP improvement opportunities. The proposed interaction-centric method has wider applicability since interactions are the core of most multidisciplinary patient-care processes. A discussion argues that, although (multidisciplinary) collaboration is in many cases not optimal in the healthcare domain, it is increasingly considered a necessity to improve integration, continuity, and quality of care. The proposed method is helpful to describe, analyze, and improve the functioning of healthcare collaboration. Copyright © 2011 Elsevier Inc. All rights reserved.

Quantum mechanics study of repulsive π-π interaction and flexibility of phenyl moiety in the iron azodioxide complex

NASA Astrophysics Data System (ADS)

Liu, Yuemin; Liu, Yucheng; Murru, Siva; Tzeng, Nianfeng; Srivastava, Radhey S.

2015-10-01

In this study, repulsive π-π interactions within iron azodioxide complex Fe[Ph(O)NN(O)Ph]3 were quantum mechanically characterized using DFT, MP2 and CCSD(T) methods. Flexibility of six phenyl moieties in this complex structure was also investigated by structural optimization approach using the DFT methods. Our MP2 and CCSD(T) calculations of the closest pair provided interaction energy of 6.62 and 8.29 kcal/mol respectively, which indicate a strongest repulsion among these intra-molecular π-π interactions. Interaction energy of the particular π-π pair calculated from 24 hybrid DFT methods ranges from 4.56 kcal/mol from BHandH method to 15.15 kcal/mol from O3LYP method. Cares should be exercised when interpreting interaction energy and geometry optimization from DFT simulation of systems containing π-π interaction. Comparison between the DFT results and the benchmark CCSD(T) results shows that the DFT calculations of π-π interaction are reasonable but still need to be interpreted with caution. Furthermore, MP2 interaction energy of -44.69 kcal/mol between two substituted π systems/phenyl rings Ph(O)N-moieties suggested that above energetically unfavorable π-π interaction can be compensated by the covalent bond N-N in a single ligand Ph(O)NN(O)Ph, which allows for a reasonable stability across the complex molecules. Optimizations of the entire complex molecule using B3LYP and M06HF methods produced a large variation of π-π distances and orientations, which implied that the complex molecule may perform catalysis at room temperature.

Complete active space configuration interaction from state-averaged configuration interaction singles natural orbitals: Analytic first derivatives and derivative coupling vectors

NASA Astrophysics Data System (ADS)

Fales, B. Scott; Shu, Yinan; Levine, Benjamin G.; Hohenstein, Edward G.

2017-09-01

A new complete active space configuration interaction (CASCI) method was recently introduced that uses state-averaged natural orbitals from the configuration interaction singles method (configuration interaction singles natural orbital CASCI, CISNO-CASCI). This method has been shown to perform as well or better than state-averaged complete active space self-consistent field for a variety of systems. However, further development and testing of this method have been limited by the lack of available analytic first derivatives of the CISNO-CASCI energy as well as the derivative coupling between electronic states. In the present work, we present a Lagrangian-based formulation of these derivatives as well as a highly efficient implementation of the resulting equations accelerated with graphical processing units. We demonstrate that the CISNO-CASCI method is practical for dynamical simulations of photochemical processes in molecular systems containing hundreds of atoms.

Complete active space configuration interaction from state-averaged configuration interaction singles natural orbitals: Analytic first derivatives and derivative coupling vectors.

PubMed

Fales, B Scott; Shu, Yinan; Levine, Benjamin G; Hohenstein, Edward G

2017-09-07

A new complete active space configuration interaction (CASCI) method was recently introduced that uses state-averaged natural orbitals from the configuration interaction singles method (configuration interaction singles natural orbital CASCI, CISNO-CASCI). This method has been shown to perform as well or better than state-averaged complete active space self-consistent field for a variety of systems. However, further development and testing of this method have been limited by the lack of available analytic first derivatives of the CISNO-CASCI energy as well as the derivative coupling between electronic states. In the present work, we present a Lagrangian-based formulation of these derivatives as well as a highly efficient implementation of the resulting equations accelerated with graphical processing units. We demonstrate that the CISNO-CASCI method is practical for dynamical simulations of photochemical processes in molecular systems containing hundreds of atoms.

PPI-IRO: a two-stage method for protein-protein interaction extraction based on interaction relation ontology.

PubMed

Li, Chuan-Xi; Chen, Peng; Wang, Ru-Jing; Wang, Xiu-Jie; Su, Ya-Ru; Li, Jinyan

2014-01-01

Mining Protein-Protein Interactions (PPIs) from the fast-growing biomedical literature resources has been proven as an effective approach for the identification of biological regulatory networks. This paper presents a novel method based on the idea of Interaction Relation Ontology (IRO), which specifies and organises words of various proteins interaction relationships. Our method is a two-stage PPI extraction method. At first, IRO is applied in a binary classifier to determine whether sentences contain a relation or not. Then, IRO is taken to guide PPI extraction by building sentence dependency parse tree. Comprehensive and quantitative evaluations and detailed analyses are used to demonstrate the significant performance of IRO on relation sentences classification and PPI extraction. Our PPI extraction method yielded a recall of around 80% and 90% and an F1 of around 54% and 66% on corpora of AIMed and BioInfer, respectively, which are superior to most existing extraction methods.

Drug-Target Interaction Prediction through Label Propagation with Linear Neighborhood Information.

PubMed

Zhang, Wen; Chen, Yanlin; Li, Dingfang

2017-11-25

Interactions between drugs and target proteins provide important information for the drug discovery. Currently, experiments identified only a small number of drug-target interactions. Therefore, the development of computational methods for drug-target interaction prediction is an urgent task of theoretical interest and practical significance. In this paper, we propose a label propagation method with linear neighborhood information (LPLNI) for predicting unobserved drug-target interactions. Firstly, we calculate drug-drug linear neighborhood similarity in the feature spaces, by considering how to reconstruct data points from neighbors. Then, we take similarities as the manifold of drugs, and assume the manifold unchanged in the interaction space. At last, we predict unobserved interactions between known drugs and targets by using drug-drug linear neighborhood similarity and known drug-target interactions. The experiments show that LPLNI can utilize only known drug-target interactions to make high-accuracy predictions on four benchmark datasets. Furthermore, we consider incorporating chemical structures into LPLNI models. Experimental results demonstrate that the model with integrated information (LPLNI-II) can produce improved performances, better than other state-of-the-art methods. The known drug-target interactions are an important information source for computational predictions. The usefulness of the proposed method is demonstrated by cross validation and the case study.

Estimating interaction on an additive scale between continuous determinants in a logistic regression model.

PubMed

Knol, Mirjam J; van der Tweel, Ingeborg; Grobbee, Diederick E; Numans, Mattijs E; Geerlings, Mirjam I

2007-10-01

To determine the presence of interaction in epidemiologic research, typically a product term is added to the regression model. In linear regression, the regression coefficient of the product term reflects interaction as departure from additivity. However, in logistic regression it refers to interaction as departure from multiplicativity. Rothman has argued that interaction estimated as departure from additivity better reflects biologic interaction. So far, literature on estimating interaction on an additive scale using logistic regression only focused on dichotomous determinants. The objective of the present study was to provide the methods to estimate interaction between continuous determinants and to illustrate these methods with a clinical example. and results From the existing literature we derived the formulas to quantify interaction as departure from additivity between one continuous and one dichotomous determinant and between two continuous determinants using logistic regression. Bootstrapping was used to calculate the corresponding confidence intervals. To illustrate the theory with an empirical example, data from the Utrecht Health Project were used, with age and body mass index as risk factors for elevated diastolic blood pressure. The methods and formulas presented in this article are intended to assist epidemiologists to calculate interaction on an additive scale between two variables on a certain outcome. The proposed methods are included in a spreadsheet which is freely available at: http://www.juliuscenter.nl/additive-interaction.xls.

PIPE: a protein–protein interaction passage extraction module for BioCreative challenge

PubMed Central

Chu, Chun-Han; Su, Yu-Chen; Chen, Chien Chin; Hsu, Wen-Lian

2016-01-01

Identifying the interactions between proteins mentioned in biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this article, we propose PIPE, an interaction pattern generation module used in the Collaborative Biocurator Assistant Task at BioCreative V (http://www.biocreative.org/) to capture frequent protein-protein interaction (PPI) patterns within text. We also present an interaction pattern tree (IPT) kernel method that integrates the PPI patterns with convolution tree kernel (CTK) to extract PPIs. Methods were evaluated on LLL, IEPA, HPRD50, AIMed and BioInfer corpora using cross-validation, cross-learning and cross-corpus evaluation. Empirical evaluations demonstrate that our method is effective and outperforms several well-known PPI extraction methods. Database URL: PMID:27524807

Estimating Temporal Causal Interaction between Spike Trains with Permutation and Transfer Entropy

PubMed Central

Li, Zhaohui; Li, Xiaoli

2013-01-01

Estimating the causal interaction between neurons is very important for better understanding the functional connectivity in neuronal networks. We propose a method called normalized permutation transfer entropy (NPTE) to evaluate the temporal causal interaction between spike trains, which quantifies the fraction of ordinal information in a neuron that has presented in another one. The performance of this method is evaluated with the spike trains generated by an Izhikevich’s neuronal model. Results show that the NPTE method can effectively estimate the causal interaction between two neurons without influence of data length. Considering both the precision of time delay estimated and the robustness of information flow estimated against neuronal firing rate, the NPTE method is superior to other information theoretic method including normalized transfer entropy, symbolic transfer entropy and permutation conditional mutual information. To test the performance of NPTE on analyzing simulated biophysically realistic synapses, an Izhikevich’s cortical network that based on the neuronal model is employed. It is found that the NPTE method is able to characterize mutual interactions and identify spurious causality in a network of three neurons exactly. We conclude that the proposed method can obtain more reliable comparison of interactions between different pairs of neurons and is a promising tool to uncover more details on the neural coding. PMID:23940662

A comparative study of multivariable robustness analysis methods as applied to integrated flight and propulsion control

NASA Technical Reports Server (NTRS)

Schierman, John D.; Lovell, T. A.; Schmidt, David K.

1993-01-01

Three multivariable robustness analysis methods are compared and contrasted. The focus of the analysis is on system stability and performance robustness to uncertainty in the coupling dynamics between two interacting subsystems. Of particular interest is interacting airframe and engine subsystems, and an example airframe/engine vehicle configuration is utilized in the demonstration of these approaches. The singular value (SV) and structured singular value (SSV) analysis methods are compared to a method especially well suited for analysis of robustness to uncertainties in subsystem interactions. This approach is referred to here as the interacting subsystem (IS) analysis method. This method has been used previously to analyze airframe/engine systems, emphasizing the study of stability robustness. However, performance robustness is also investigated here, and a new measure of allowable uncertainty for acceptable performance robustness is introduced. The IS methodology does not require plant uncertainty models to measure the robustness of the system, and is shown to yield valuable information regarding the effects of subsystem interactions. In contrast, the SV and SSV methods allow for the evaluation of the robustness of the system to particular models of uncertainty, and do not directly indicate how the airframe (engine) subsystem interacts with the engine (airframe) subsystem.

Detection of Protein Complexes Based on Penalized Matrix Decomposition in a Sparse Protein⁻Protein Interaction Network.

PubMed

Cao, Buwen; Deng, Shuguang; Qin, Hua; Ding, Pingjian; Chen, Shaopeng; Li, Guanghui

2018-06-15

High-throughput technology has generated large-scale protein interaction data, which is crucial in our understanding of biological organisms. Many complex identification algorithms have been developed to determine protein complexes. However, these methods are only suitable for dense protein interaction networks, because their capabilities decrease rapidly when applied to sparse protein⁻protein interaction (PPI) networks. In this study, based on penalized matrix decomposition ( PMD ), a novel method of penalized matrix decomposition for the identification of protein complexes (i.e., PMD pc ) was developed to detect protein complexes in the human protein interaction network. This method mainly consists of three steps. First, the adjacent matrix of the protein interaction network is normalized. Second, the normalized matrix is decomposed into three factor matrices. The PMD pc method can detect protein complexes in sparse PPI networks by imposing appropriate constraints on factor matrices. Finally, the results of our method are compared with those of other methods in human PPI network. Experimental results show that our method can not only outperform classical algorithms, such as CFinder, ClusterONE, RRW, HC-PIN, and PCE-FR, but can also achieve an ideal overall performance in terms of a composite score consisting of F-measure, accuracy (ACC), and the maximum matching ratio (MMR).

Comparative Analysis of Western and Domestic Practice of Interactive Method Application in Teaching Social and Political Disciplines at the Universities

ERIC Educational Resources Information Center

Hladka, Halyna

2014-01-01

The comparative analysis of western and domestic practice of introducing active and interactive methods of studies in the process of teaching social science disciplines has been carried out. Features, realities, prospects and limitations in application of interactive methods of teaching in the process of implementing social-political science…

Predicting Human Protein Subcellular Locations by the Ensemble of Multiple Predictors via Protein-Protein Interaction Network with Edge Clustering Coefficients

PubMed Central

Du, Pufeng; Wang, Lusheng

2014-01-01

One of the fundamental tasks in biology is to identify the functions of all proteins to reveal the primary machinery of a cell. Knowledge of the subcellular locations of proteins will provide key hints to reveal their functions and to understand the intricate pathways that regulate biological processes at the cellular level. Protein subcellular location prediction has been extensively studied in the past two decades. A lot of methods have been developed based on protein primary sequences as well as protein-protein interaction network. In this paper, we propose to use the protein-protein interaction network as an infrastructure to integrate existing sequence based predictors. When predicting the subcellular locations of a given protein, not only the protein itself, but also all its interacting partners were considered. Unlike existing methods, our method requires neither the comprehensive knowledge of the protein-protein interaction network nor the experimentally annotated subcellular locations of most proteins in the protein-protein interaction network. Besides, our method can be used as a framework to integrate multiple predictors. Our method achieved 56% on human proteome in absolute-true rate, which is higher than the state-of-the-art methods. PMID:24466278

Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks.

PubMed

Nariai, N; Kim, S; Imoto, S; Miyano, S

2004-01-01

We propose a statistical method to estimate gene networks from DNA microarray data and protein-protein interactions. Because physical interactions between proteins or multiprotein complexes are likely to regulate biological processes, using only mRNA expression data is not sufficient for estimating a gene network accurately. Our method adds knowledge about protein-protein interactions to the estimation method of gene networks under a Bayesian statistical framework. In the estimated gene network, a protein complex is modeled as a virtual node based on principal component analysis. We show the effectiveness of the proposed method through the analysis of Saccharomyces cerevisiae cell cycle data. The proposed method improves the accuracy of the estimated gene networks, and successfully identifies some biological facts.

Micromechanical Devices for Control of Cell-Cell Interaction, and Methods of Use Thereof

NASA Technical Reports Server (NTRS)

Bhatia, Sangeeta N. (Inventor); Hui, Elliot (Inventor)

2017-01-01

The development and function of living tissues depends largely on interactions between cells that can vary in both time and space; however, temporal control of cell-cell interaction is experimentally challenging. By employing a micromachined silicon substrate with moving parts, herein is disclosed the dynamic regulation of cell-cell interactions via direct manipulation of adherent cells with micron-scale precision. The inventive devices and methods allow mechanical control of both tissue composition and spatial organization. The inventive device and methods enable the investigation of dynamic cell-cell interaction in a multitude of applications, such as intercellular communication, spanning embryogenesis, homeostasis, and pathogenic processes.

A Huygens immersed-finite-element particle-in-cell method for modeling plasma-surface interactions with moving interface

NASA Astrophysics Data System (ADS)

Cao, Huijun; Cao, Yong; Chu, Yuchuan; He, Xiaoming; Lin, Tao

2018-06-01

Surface evolution is an unavoidable issue in engineering plasma applications. In this article an iterative method for modeling plasma-surface interactions with moving interface is proposed and validated. In this method, the plasma dynamics is simulated by an immersed finite element particle-in-cell (IFE-PIC) method, and the surface evolution is modeled by the Huygens wavelet method which is coupled with the iteration of the IFE-PIC method. Numerical experiments, including prototypical engineering applications, such as the erosion of Hall thruster channel wall, are presented to demonstrate features of this Huygens IFE-PIC method for simulating the dynamic plasma-surface interactions.

An Immersed Boundary Method for Solving the Compressible Navier-Stokes Equations with Fluid Structure Interaction

NASA Technical Reports Server (NTRS)

Brehm, Christoph; Barad, Michael F.; Kiris, Cetin C.

2016-01-01

An immersed boundary method for the compressible Navier-Stokes equation and the additional infrastructure that is needed to solve moving boundary problems and fully coupled fluid-structure interaction is described. All the methods described in this paper were implemented in NASA's LAVA solver framework. The underlying immersed boundary method is based on the locally stabilized immersed boundary method that was previously introduced by the authors. In the present paper this method is extended to account for all aspects that are involved for fluid structure interaction simulations, such as fast geometry queries and stencil computations, the treatment of freshly cleared cells, and the coupling of the computational fluid dynamics solver with a linear structural finite element method. The current approach is validated for moving boundary problems with prescribed body motion and fully coupled fluid structure interaction problems in 2D and 3D. As part of the validation procedure, results from the second AIAA aeroelastic prediction workshop are also presented. The current paper is regarded as a proof of concept study, while more advanced methods for fluid structure interaction are currently being investigated, such as geometric and material nonlinearities, and advanced coupling approaches.

Interactive prostate segmentation using atlas-guided semi-supervised learning and adaptive feature selection

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

Park, Sang Hyun; Gao, Yaozong, E-mail: yzgao@cs.unc.edu; Shi, Yinghuan, E-mail: syh@nju.edu.cn

Purpose: Accurate prostate segmentation is necessary for maximizing the effectiveness of radiation therapy of prostate cancer. However, manual segmentation from 3D CT images is very time-consuming and often causes large intra- and interobserver variations across clinicians. Many segmentation methods have been proposed to automate this labor-intensive process, but tedious manual editing is still required due to the limited performance. In this paper, the authors propose a new interactive segmentation method that can (1) flexibly generate the editing result with a few scribbles or dots provided by a clinician, (2) fast deliver intermediate results to the clinician, and (3) sequentially correctmore » the segmentations from any type of automatic or interactive segmentation methods. Methods: The authors formulate the editing problem as a semisupervised learning problem which can utilize a priori knowledge of training data and also the valuable information from user interactions. Specifically, from a region of interest near the given user interactions, the appropriate training labels, which are well matched with the user interactions, can be locally searched from a training set. With voting from the selected training labels, both confident prostate and background voxels, as well as unconfident voxels can be estimated. To reflect informative relationship between voxels, location-adaptive features are selected from the confident voxels by using regression forest and Fisher separation criterion. Then, the manifold configuration computed in the derived feature space is enforced into the semisupervised learning algorithm. The labels of unconfident voxels are then predicted by regularizing semisupervised learning algorithm. Results: The proposed interactive segmentation method was applied to correct automatic segmentation results of 30 challenging CT images. The correction was conducted three times with different user interactions performed at different time periods, in order to evaluate both the efficiency and the robustness. The automatic segmentation results with the original average Dice similarity coefficient of 0.78 were improved to 0.865–0.872 after conducting 55–59 interactions by using the proposed method, where each editing procedure took less than 3 s. In addition, the proposed method obtained the most consistent editing results with respect to different user interactions, compared to other methods. Conclusions: The proposed method obtains robust editing results with few interactions for various wrong segmentation cases, by selecting the location-adaptive features and further imposing the manifold regularization. The authors expect the proposed method to largely reduce the laborious burdens of manual editing, as well as both the intra- and interobserver variability across clinicians.« less

A postprocessing method in the HMC framework for predicting gene function based on biological instrumental data

NASA Astrophysics Data System (ADS)

Feng, Shou; Fu, Ping; Zheng, Wenbin

2018-03-01

Predicting gene function based on biological instrumental data is a complicated and challenging hierarchical multi-label classification (HMC) problem. When using local approach methods to solve this problem, a preliminary results processing method is usually needed. This paper proposed a novel preliminary results processing method called the nodes interaction method. The nodes interaction method revises the preliminary results and guarantees that the predictions are consistent with the hierarchy constraint. This method exploits the label dependency and considers the hierarchical interaction between nodes when making decisions based on the Bayesian network in its first phase. In the second phase, this method further adjusts the results according to the hierarchy constraint. Implementing the nodes interaction method in the HMC framework also enhances the HMC performance for solving the gene function prediction problem based on the Gene Ontology (GO), the hierarchy of which is a directed acyclic graph that is more difficult to tackle. The experimental results validate the promising performance of the proposed method compared to state-of-the-art methods on eight benchmark yeast data sets annotated by the GO.

Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks.

PubMed

Deeter, Anthony; Dalman, Mark; Haddad, Joseph; Duan, Zhong-Hui

2017-01-01

The PubMed database offers an extensive set of publication data that can be useful, yet inherently complex to use without automated computational techniques. Data repositories such as the Genomic Data Commons (GDC) and the Gene Expression Omnibus (GEO) offer experimental data storage and retrieval as well as curated gene expression profiles. Genetic interaction databases, including Reactome and Ingenuity Pathway Analysis, offer pathway and experiment data analysis using data curated from these publications and data repositories. We have created a method to generate and analyze consensus networks, inferring potential gene interactions, using large numbers of Bayesian networks generated by data mining publications in the PubMed database. Through the concept of network resolution, these consensus networks can be tailored to represent possible genetic interactions. We designed a set of experiments to confirm that our method is stable across variation in both sample and topological input sizes. Using gene product interactions from the KEGG pathway database and data mining PubMed publication abstracts, we verify that regardless of the network resolution or the inferred consensus network, our method is capable of inferring meaningful gene interactions through consensus Bayesian network generation with multiple, randomized topological orderings. Our method can not only confirm the existence of currently accepted interactions, but has the potential to hypothesize new ones as well. We show our method confirms the existence of known gene interactions such as JAK-STAT-PI3K-AKT-mTOR, infers novel gene interactions such as RAS- Bcl-2 and RAS-AKT, and found significant pathway-pathway interactions between the JAK-STAT signaling and Cardiac Muscle Contraction KEGG pathways.

Pedestrian Injuries By Source: Serious and Disabling Injuries in US and European Cases

PubMed Central

Mallory, Ann; Fredriksson, Rikard; Rosén, Erik; Donnelly, Bruce

2012-01-01

US and European pedestrian crash cases were analyzed to determine frequency of injury by body region and by the vehicle component identified as the injury source. US pedestrian data was drawn from the Pedestrian Crash Data Study (PCDS). European pedestrian data was drawn from the German In-Depth Accident Study (GIDAS). Results were analyzed in terms of both serious injury (AIS 3+) and disabling injury estimated with the Functional Capacity Index (FCI). The results are presented in parallel for a more complete international perspective on injuries and injury sources. Lower extremity injury from bumper impact and head&face injury from windshield impact were the most frequent combinations for both serious and disabling injuries. Serious lower extremity injuries from bumper contact occurred in 43% of seriously injured pedestrian cases in US PCDS data and 35% of European GIDAS cases. Lower-extremity bumper injuries also account for more than 20% of disability in both datasets. Serious head &face injuries from windshield contact occur in 27% of PCDS and 15% of GIDAS serious injury cases. While bumper impacts primarily result in lower extremity injury and windshield impacts are most often associated with head & face injuries, the hood and hood leading edge are responsible for serious and disabling injuries to a number of different body regions. Therefore, while it is appropriate to focus on lower extremity injury when studying bumper performance and on head injury risk when studying windshield impact, pedestrian performance of other components may require better understanding of injury risk for multiple body regions. PMID:23169112

Analysis of Biological Interactions by Affinity Chromatography: Clinical and Pharmaceutical Applications

PubMed Central

Hage, David S.

2017-01-01

BACKGROUND The interactions between biochemical and chemical agents in the body are important in many clinical processes. Affinity chromatography and high-performance affinity chromatography (HPAC), in which a column contains an immobilized biologically-related binding agent, are two methods that can be used to study these interactions. CONTENT This review looks at various approaches that can be used in affinity chromatography and HPAC to characterize the strength or rate of a biological interaction, the number and types of sites that are involved in this process, and the interactions between multiple solutes for the same binding agent. A number of applications for these methods are examined, with an emphasis on recent developments and high-performance affinity methods. These applications include the use of these techniques for fundamental studies of biological interactions, high-throughput screening of drugs, work with modified proteins, tools for personalized medicine, and studies of drug-drug competition for a common binding agent. SUMMARY The wide range of formats and detection methods that can be used with affinity chromatography and HPAC for examining biological interactions makes these tools attractive for various clinical and pharmaceutical applications. Future directions in the development of small-scale columns and the coupling of these methods with other techniques, such as mass spectrometry or other separation methods, should continue to increase the flexibility and ease with which these approaches can be used in work involving clinical or pharmaceutical samples. PMID:28396561

Prediction and Dissection of Protein-RNA Interactions by Molecular Descriptors.

PubMed

Liu, Zhi-Ping; Chen, Luonan

2016-01-01

Protein-RNA interactions play crucial roles in numerous biological processes. However, detecting the interactions and binding sites between protein and RNA by traditional experiments is still time consuming and labor costing. Thus, it is of importance to develop bioinformatics methods for predicting protein-RNA interactions and binding sites. Accurate prediction of protein-RNA interactions and recognitions will highly benefit to decipher the interaction mechanisms between protein and RNA, as well as to improve the RNA-related protein engineering and drug design. In this work, we summarize the current bioinformatics strategies of predicting protein-RNA interactions and dissecting protein-RNA interaction mechanisms from local structure binding motifs. In particular, we focus on the feature-based machine learning methods, in which the molecular descriptors of protein and RNA are extracted and integrated as feature vectors of representing the interaction events and recognition residues. In addition, the available methods are classified and compared comprehensively. The molecular descriptors are expected to elucidate the binding mechanisms of protein-RNA interaction and reveal the functional implications from structural complementary perspective.

Rapid measurement of protein osmotic second virial coefficients by self-interaction chromatography.

PubMed Central

Tessier, Peter M; Lenhoff, Abraham M; Sandler, Stanley I

2002-01-01

Weak protein interactions are often characterized in terms of the osmotic second virial coefficient (B(22)), which has been shown to correlate with protein phase behavior, such as crystallization. Traditional methods for measuring B(22), such as static light scattering, are too expensive in terms of both time and protein to allow extensive exploration of the effects of solution conditions on B(22). In this work we have measured protein interactions using self-interaction chromatography, in which protein is immobilized on chromatographic particles and the retention of the same protein is measured in isocratic elution. The relative retention of the protein reflects the average protein interactions, which we have related to the second virial coefficient via statistical mechanics. We obtain quantitative agreement between virial coefficients measured by self-interaction chromatography and traditional characterization methods for both lysozyme and chymotrypsinogen over a wide range of pH and ionic strengths, yet self-interaction chromatography requires at least an order of magnitude less time and protein than other methods. The method thus holds significant promise for the characterization of protein interactions requiring only commonly available laboratory equipment, little specialized expertise, and relatively small investments of both time and protein. PMID:11867474

COMPUTATIONAL METHODS FOR STUDYING THE INTERACTION BETWEEN POLYCYCLIC AROMATIC HYDROCARBONS AND BIOLOGICAL MACROMOLECULES

EPA Science Inventory

Computational Methods for Studying the Interaction between Polycyclic Aromatic Hydrocarbons and Biological Macromolecules .

The mechanisms for the processes that result in significant biological activity of PAHs depend on the interaction of these molecules or their metabol...

Some experiences with the viscous-inviscid interaction approach

NASA Technical Reports Server (NTRS)

Vandalsem, W. R.; Steger, J. L.; Rao, K. V.

1987-01-01

Methods for simulating compressible viscous flow using the viscid-inviscid interaction approach are described. The formulations presented range from the more familiar full-potential/boundary-layer interaction schemes to a method for coupling Euler/Navier-Stokes and boundary-layer algorithms. An effort is made to describe the advantages and disadvantages of each formulation. Sample results are presented which illustrate the applicability of the methods.

Batch mode grid generation: An endangered species

NASA Technical Reports Server (NTRS)

Schuster, David M.

1992-01-01

Non-interactive grid generation schemes should thrive as emphasis shifts from development of numerical analysis and design methods to application of these tools to real engineering problems. A strong case is presented for the continued development and application of non-interactive geometry modeling methods. Guidelines, strategies, and techniques for developing and implementing these tools are presented using current non-interactive grid generation methods as examples. These schemes play an important role in the development of multidisciplinary analysis methods and some of these applications are also discussed.

Quantitative analysis of small molecule-nucleic acid interactions with a biosensor surface and surface plasmon resonance detection.

PubMed

Liu, Yang; Wilson, W David

2010-01-01

Surface plasmon resonance (SPR) technology with biosensor surfaces has become a widely-used tool for the study of nucleic acid interactions without any labeling requirements. The method provides simultaneous kinetic and equilibrium characterization of the interactions of biomolecules as well as small molecule-biopolymer binding. SPR monitors molecular interactions in real time and provides significant advantages over optical or calorimetic methods for systems with strong binding coupled to small spectroscopic signals and/or reaction heats. A detailed and practical guide for nucleic acid interaction analysis using SPR-biosensor methods is presented. Details of the SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples, as well as extensive information on experimental design, quantitative and qualitative data analysis and presentation. A specific example of the interaction of a minor-groove-binding agent with DNA is evaluated by both kinetic and steady-state SPR methods to illustrate the technique. Since the molecules that bind cooperatively to specific DNA sequences are attractive for many applications, a cooperative small molecule-DNA interaction is also presented.

An ontology-based search engine for protein-protein interactions

PubMed Central

2010-01-01

Background Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. Results We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Conclusion Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology. PMID:20122195

An ontology-based search engine for protein-protein interactions.

PubMed

Park, Byungkyu; Han, Kyungsook

2010-01-18

Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology.

[Research on Three-dimensional Medical Image Reconstruction and Interaction Based on HTML5 and Visualization Toolkit].

PubMed

Gao, Peng; Liu, Peng; Su, Hongsen; Qiao, Liang

2015-04-01

Integrating visualization toolkit and the capability of interaction, bidirectional communication and graphics rendering which provided by HTML5, we explored and experimented on the feasibility of remote medical image reconstruction and interaction in pure Web. We prompted server-centric method which did not need to download the big medical data to local connections and avoided considering network transmission pressure and the three-dimensional (3D) rendering capability of client hardware. The method integrated remote medical image reconstruction and interaction into Web seamlessly, which was applicable to lower-end computers and mobile devices. Finally, we tested this method in the Internet and achieved real-time effects. This Web-based 3D reconstruction and interaction method, which crosses over internet terminals and performance limited devices, may be useful for remote medical assistant.

A critical evaluation of various methods for the analysis of flow-solid interaction in a nest of thin cylinders subjected to cross flows

NASA Technical Reports Server (NTRS)

Kim, Sang-Wook

1987-01-01

Various experimental, analytical, and numerical analysis methods for flow-solid interaction of a nest of cylinders subjected to cross flows are reviewed. A nest of cylinders subjected to cross flows can be found in numerous engineering applications including the Space Shuttle Maine Engine-Main Injector Assembly (SSME-MIA) and nuclear reactor heat exchangers. Despite its extreme importance in engineering applications, understanding of the flow-solid interaction process is quite limited and design of the tube banks are mostly dependent on experiments and/or experimental correlation equations. For future development of major numerical analysis methods for the flow-solid interaction of a nest of cylinders subjected to cross flow, various turbulence models, nonlinear structural dynamics, and existing laminar flow-solid interaction analysis methods are included.

Evaluation of DFT methods for computing the interaction energies of homomolecular and heteromolecular dimers of monosubstituted benzene

NASA Astrophysics Data System (ADS)

Godfrey-Kittle, Andrew; Cafiero, Mauricio

We present density functional theory (DFT) interaction energies for the sandwich and T-shaped conformers of substituted benzene dimers. The DFT functionals studied include TPSS, HCTH407, B3LYP, and X3LYP. We also include Hartree-Fock (HF) and second-order Møller-Plesset perturbation theory calculations (MP2), as well as calculations using a new functional, P3LYP, which includes PBE and HF exchange and LYP correlation. Although DFT methods do not explicitly account for the dispersion interactions important in the benzene-dimer interactions, we find that our new method, P3LYP, as well as HCTH407 and TPSS, match MP2 and CCSD(T) calculations much better than the hybrid methods B3LYP and X3LYP methods do.

The in Silico Insight into Carbon Nanotube and Nucleic Acid Bases Interaction.

PubMed

Karimi, Ali Asghar; Ghalandari, Behafarid; Tabatabaie, Seyed Saleh; Farhadi, Mohammad

2016-05-01

To explore practical applications of carbon nanotubes (CNTs) in biomedical fields the properties of their interaction with biomolecules must be revealed. Recent years, the interaction of CNTs with biomolecules is a subject of research interest for practical applications so that previous research explored that CNTs have complementary structure properties with single strand DNA (ssDNA). Hence, the quantum mechanics (QM) method based on ab initio was used for this purpose. Therefore values of binding energy, charge distribution, electronic energy and other physical properties of interaction were studied for interaction of nucleic acid bases and SCNT. In this study, the interaction between nucleic acid bases and a (4, 4) single-walled carbon nanotube (SCNT) were investigated through calculations within quantum mechanics (QM) method at theoretical level of Hartree-Fock (HF) method using 6-31G basis set. Hence, the physical properties such as electronic energy, total dipole moment, charge distributions and binding energy of nucleic acid bases interaction with SCNT were investigated based on HF method. It has been found that the guanine base adsorption is bound stronger to the outer surface of nanotube in comparison to the other bases, consistent with the recent theoretical studies. In the other words, the results explored that guanine interaction with SCNT has optimum level of electronic energy so that their interaction is stable. Also, the calculations illustrated that SCNT interact to nucleic acid bases by noncovalent interaction because of charge distribution an electrostatic area is created in place of interaction. Consequently, small diameter SCNT interaction with nucleic acid bases is noncovalent. Also, the results revealed that small diameter SCNT interaction especially SCNT (4, 4) with nucleic acid bases can be useful in practical application area of biomedical fields such detection and drug delivery.

Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures

PubMed Central

Nealon, John Oliver; Philomina, Limcy Seby

2017-01-01

The elucidation of protein–protein interactions is vital for determining the function and action of quaternary protein structures. Here, we discuss the difficulty and importance of establishing protein quaternary structure and review in vitro and in silico methods for doing so. Determining the interacting partner proteins of predicted protein structures is very time-consuming when using in vitro methods, this can be somewhat alleviated by use of predictive methods. However, developing reliably accurate predictive tools has proved to be difficult. We review the current state of the art in predictive protein interaction software and discuss the problem of scoring and therefore ranking predictions. Current community-based predictive exercises are discussed in relation to the growth of protein interaction prediction as an area within these exercises. We suggest a fusion of experimental and predictive methods that make use of sparse experimental data to determine higher resolution predicted protein interactions as being necessary to drive forward development. PMID:29206185

Looking towards label-free biomolecular interaction analysis in a high-throughput format: a review of new surface plasmon resonance technologies.

PubMed

Boozer, Christina; Kim, Gibum; Cong, Shuxin; Guan, Hannwen; Londergan, Timothy

2006-08-01

Surface plasmon resonance (SPR) biosensors have enabled a wide range of applications in which researchers can monitor biomolecular interactions in real time. Owing to the fact that SPR can provide affinity and kinetic data, unique features in applications ranging from protein-peptide interaction analysis to cellular ligation experiments have been demonstrated. Although SPR has historically been limited by its throughput, new methods are emerging that allow for the simultaneous analysis of many thousands of interactions. When coupled with new protein array technologies, high-throughput SPR methods give users new and improved methods to analyze pathways, screen drug candidates and monitor protein-protein interactions.

A deeper look at two concepts of measuring gene-gene interactions: logistic regression and interaction information revisited.

PubMed

Mielniczuk, Jan; Teisseyre, Paweł

2018-03-01

Detection of gene-gene interactions is one of the most important challenges in genome-wide case-control studies. Besides traditional logistic regression analysis, recently the entropy-based methods attracted a significant attention. Among entropy-based methods, interaction information is one of the most promising measures having many desirable properties. Although both logistic regression and interaction information have been used in several genome-wide association studies, the relationship between them has not been thoroughly investigated theoretically. The present paper attempts to fill this gap. We show that although certain connections between the two methods exist, in general they refer two different concepts of dependence and looking for interactions in those two senses leads to different approaches to interaction detection. We introduce ordering between interaction measures and specify conditions for independent and dependent genes under which interaction information is more discriminative measure than logistic regression. Moreover, we show that for so-called perfect distributions those measures are equivalent. The numerical experiments illustrate the theoretical findings indicating that interaction information and its modified version are more universal tools for detecting various types of interaction than logistic regression and linkage disequilibrium measures. © 2017 WILEY PERIODICALS, INC.

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

PubMed

Ochoa, David; García-Gutiérrez, Ponciano; Juan, David; Valencia, Alfonso; Pazos, Florencio

2013-01-27

A widespread family of methods for studying and predicting protein interactions using sequence information is based on co-evolution, quantified as similarity of phylogenetic trees. Part of the co-evolution observed between interacting proteins could be due to co-adaptation caused by inter-protein contacts. In this case, the co-evolution is expected to be more evident when evaluated on the surface of the proteins or the internal layers close to it. In this work we study the effect of incorporating information on predicted solvent accessibility to three methods for predicting protein interactions based on similarity of phylogenetic trees. We evaluate the performance of these methods in predicting different types of protein associations when trees based on positions with different characteristics of predicted accessibility are used as input. We found that predicted accessibility improves the results of two recent versions of the mirrortree methodology in predicting direct binary physical interactions, while it neither improves these methods, nor the original mirrortree method, in predicting other types of interactions. That improvement comes at no cost in terms of applicability since accessibility can be predicted for any sequence. We also found that predictions of protein-protein interactions are improved when multiple sequence alignments with a richer representation of sequences (including paralogs) are incorporated in the accessibility prediction.

Inference on the Strength of Balancing Selection for Epistatically Interacting Loci

PubMed Central

Buzbas, Erkan Ozge; Joyce, Paul; Rosenberg, Noah A.

2011-01-01

Existing inference methods for estimating the strength of balancing selection in multi-locus genotypes rely on the assumption that there are no epistatic interactions between loci. Complex systems in which balancing selection is prevalent, such as sets of human immune system genes, are known to contain components that interact epistatically. Therefore, current methods may not produce reliable inference on the strength of selection at these loci. In this paper, we address this problem by presenting statistical methods that can account for epistatic interactions in making inference about balancing selection. A theoretical result due to Fearnhead (2006) is used to build a multi-locus Wright-Fisher model of balancing selection, allowing for epistatic interactions among loci. Antagonistic and synergistic types of interactions are examined. The joint posterior distribution of the selection and mutation parameters is sampled by Markov chain Monte Carlo methods, and the plausibility of models is assessed via Bayes factors. As a component of the inference process, an algorithm to generate multi-locus allele frequencies under balancing selection models with epistasis is also presented. Recent evidence on interactions among a set of human immune system genes is introduced as a motivating biological system for the epistatic model, and data on these genes are used to demonstrate the methods. PMID:21277883

Quantification of protein interaction kinetics in a micro droplet

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

Yin, L. L.; College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044; Wang, S. P., E-mail: shaopeng.wang@asu.edu, E-mail: njtao@asu.edu

Characterization of protein interactions is essential to the discovery of disease biomarkers, the development of diagnostic assays, and the screening for therapeutic drugs. Conventional flow-through kinetic measurements need relative large amount of sample that is not feasible for precious protein samples. We report a novel method to measure protein interaction kinetics in a single droplet with sub microliter or less volume. A droplet in a humidity-controlled environmental chamber is replacing the microfluidic channels as the reactor for the protein interaction. The binding process is monitored by a surface plasmon resonance imaging (SPRi) system. Association curves are obtained from the averagemore » SPR image intensity in the center area of the droplet. The washing step required by conventional flow-through SPR method is eliminated in the droplet method. The association and dissociation rate constants and binding affinity of an antigen-antibody interaction are obtained by global fitting of association curves at different concentrations. The result obtained by this method is accurate as validated by conventional flow-through SPR system. This droplet-based method not only allows kinetic studies for proteins with limited supply but also opens the door for high-throughput protein interaction study in a droplet-based microarray format that enables measurement of many to many interactions on a single chip.« less

Quantification of protein interaction kinetics in a micro droplet

NASA Astrophysics Data System (ADS)

Yin, L. L.; Wang, S. P.; Shan, X. N.; Zhang, S. T.; Tao, N. J.

2015-11-01

Characterization of protein interactions is essential to the discovery of disease biomarkers, the development of diagnostic assays, and the screening for therapeutic drugs. Conventional flow-through kinetic measurements need relative large amount of sample that is not feasible for precious protein samples. We report a novel method to measure protein interaction kinetics in a single droplet with sub microliter or less volume. A droplet in a humidity-controlled environmental chamber is replacing the microfluidic channels as the reactor for the protein interaction. The binding process is monitored by a surface plasmon resonance imaging (SPRi) system. Association curves are obtained from the average SPR image intensity in the center area of the droplet. The washing step required by conventional flow-through SPR method is eliminated in the droplet method. The association and dissociation rate constants and binding affinity of an antigen-antibody interaction are obtained by global fitting of association curves at different concentrations. The result obtained by this method is accurate as validated by conventional flow-through SPR system. This droplet-based method not only allows kinetic studies for proteins with limited supply but also opens the door for high-throughput protein interaction study in a droplet-based microarray format that enables measurement of many to many interactions on a single chip.

Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions.

PubMed

Agarwal, Shashank; Liu, Feifan; Yu, Hong

2011-10-03

Protein-protein interaction (PPI) is an important biomedical phenomenon. Automatically detecting PPI-relevant articles and identifying methods that are used to study PPI are important text mining tasks. In this study, we have explored domain independent features to develop two open source machine learning frameworks. One performs binary classification to determine whether the given article is PPI relevant or not, named "Simple Classifier", and the other one maps the PPI relevant articles with corresponding interaction method nodes in a standardized PSI-MI (Proteomics Standards Initiative-Molecular Interactions) ontology, named "OntoNorm". We evaluated our system in the context of BioCreative challenge competition using the standardized data set. Our systems are amongst the top systems reported by the organizers, attaining 60.8% F1-score for identifying relevant documents, and 52.3% F1-score for mapping articles to interaction method ontology. Our results show that domain-independent machine learning frameworks can perform competitively well at the tasks of detecting PPI relevant articles and identifying the methods that were used to study the interaction in such articles. Simple Classifier is available at http://sourceforge.net/p/simpleclassify/home/ and OntoNorm at http://sourceforge.net/p/ontonorm/home/.

Detection of time delays and directional interactions based on time series from complex dynamical systems

NASA Astrophysics Data System (ADS)

Ma, Huanfei; Leng, Siyang; Tao, Chenyang; Ying, Xiong; Kurths, Jürgen; Lai, Ying-Cheng; Lin, Wei

2017-07-01

Data-based and model-free accurate identification of intrinsic time delays and directional interactions is an extremely challenging problem in complex dynamical systems and their networks reconstruction. A model-free method with new scores is proposed to be generally capable of detecting single, multiple, and distributed time delays. The method is applicable not only to mutually interacting dynamical variables but also to self-interacting variables in a time-delayed feedback loop. Validation of the method is carried out using physical, biological, and ecological models and real data sets. Especially, applying the method to air pollution data and hospital admission records of cardiovascular diseases in Hong Kong reveals the major air pollutants as a cause of the diseases and, more importantly, it uncovers a hidden time delay (about 30-40 days) in the causal influence that previous studies failed to detect. The proposed method is expected to be universally applicable to ascertaining and quantifying subtle interactions (e.g., causation) in complex systems arising from a broad range of disciplines.

Transition-density-fragment interaction combined with transfer integral approach for excitation-energy transfer via charge-transfer states

NASA Astrophysics Data System (ADS)

Fujimoto, Kazuhiro J.

2012-07-01

A transition-density-fragment interaction (TDFI) combined with a transfer integral (TI) method is proposed. The TDFI method was previously developed for describing electronic Coulomb interaction, which was applied to excitation-energy transfer (EET) [K. J. Fujimoto and S. Hayashi, J. Am. Chem. Soc. 131, 14152 (2009)] and exciton-coupled circular dichroism spectra [K. J. Fujimoto, J. Chem. Phys. 133, 124101 (2010)]. In the present study, the TDFI method is extended to the exchange interaction, and hence it is combined with the TI method for applying to the EET via charge-transfer (CT) states. In this scheme, the overlap correction is also taken into account. To check the TDFI-TI accuracy, several test calculations are performed to an ethylene dimer. As a result, the TDFI-TI method gives a much improved description of the electronic coupling, compared with the previous TDFI method. Based on the successful description of the electronic coupling, the decomposition analysis is also performed with the TDFI-TI method. The present analysis clearly shows a large contribution from the Coulomb interaction in most of the cases, and a significant influence of the CT states at the small separation. In addition, the exchange interaction is found to be small in this system. The present approach is useful for analyzing and understanding the mechanism of EET.

S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures

PubMed Central

2011-01-01

With numerous new quantum chemistry methods being developed in recent years and the promise of even more new methods to be developed in the near future, it is clearly critical that highly accurate, well-balanced, reference data for many different atomic and molecular properties be available for the parametrization and validation of these methods. One area of research that is of particular importance in many areas of chemistry, biology, and material science is the study of noncovalent interactions. Because these interactions are often strongly influenced by correlation effects, it is necessary to use computationally expensive high-order wave function methods to describe them accurately. Here, we present a large new database of interaction energies calculated using an accurate CCSD(T)/CBS scheme. Data are presented for 66 molecular complexes, at their reference equilibrium geometries and at 8 points systematically exploring their dissociation curves; in total, the database contains 594 points: 66 at equilibrium geometries, and 528 in dissociation curves. The data set is designed to cover the most common types of noncovalent interactions in biomolecules, while keeping a balanced representation of dispersion and electrostatic contributions. The data set is therefore well suited for testing and development of methods applicable to bioorganic systems. In addition to the benchmark CCSD(T) results, we also provide decompositions of the interaction energies by means of DFT-SAPT calculations. The data set was used to test several correlated QM methods, including those parametrized specifically for noncovalent interactions. Among these, the SCS-MI-CCSD method outperforms all other tested methods, with a root-mean-square error of 0.08 kcal/mol for the S66 data set. PMID:21836824

Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering.

PubMed

Guo, Xuan; Meng, Yu; Yu, Ning; Pan, Yi

2014-04-10

Taking the advantage of high-throughput single nucleotide polymorphism (SNP) genotyping technology, large genome-wide association studies (GWASs) have been considered to hold promise for unravelling complex relationships between genotype and phenotype. At present, traditional single-locus-based methods are insufficient to detect interactions consisting of multiple-locus, which are broadly existing in complex traits. In addition, statistic tests for high order epistatic interactions with more than 2 SNPs propose computational and analytical challenges because the computation increases exponentially as the cardinality of SNPs combinations gets larger. In this paper, we provide a simple, fast and powerful method using dynamic clustering and cloud computing to detect genome-wide multi-locus epistatic interactions. We have constructed systematic experiments to compare powers performance against some recently proposed algorithms, including TEAM, SNPRuler, EDCF and BOOST. Furthermore, we have applied our method on two real GWAS datasets, Age-related macular degeneration (AMD) and Rheumatoid arthritis (RA) datasets, where we find some novel potential disease-related genetic factors which are not shown up in detections of 2-loci epistatic interactions. Experimental results on simulated data demonstrate that our method is more powerful than some recently proposed methods on both two- and three-locus disease models. Our method has discovered many novel high-order associations that are significantly enriched in cases from two real GWAS datasets. Moreover, the running time of the cloud implementation for our method on AMD dataset and RA dataset are roughly 2 hours and 50 hours on a cluster with forty small virtual machines for detecting two-locus interactions, respectively. Therefore, we believe that our method is suitable and effective for the full-scale analysis of multiple-locus epistatic interactions in GWAS.

Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering

PubMed Central

2014-01-01

Backgroud Taking the advan tage of high-throughput single nucleotide polymorphism (SNP) genotyping technology, large genome-wide association studies (GWASs) have been considered to hold promise for unravelling complex relationships between genotype and phenotype. At present, traditional single-locus-based methods are insufficient to detect interactions consisting of multiple-locus, which are broadly existing in complex traits. In addition, statistic tests for high order epistatic interactions with more than 2 SNPs propose computational and analytical challenges because the computation increases exponentially as the cardinality of SNPs combinations gets larger. Results In this paper, we provide a simple, fast and powerful method using dynamic clustering and cloud computing to detect genome-wide multi-locus epistatic interactions. We have constructed systematic experiments to compare powers performance against some recently proposed algorithms, including TEAM, SNPRuler, EDCF and BOOST. Furthermore, we have applied our method on two real GWAS datasets, Age-related macular degeneration (AMD) and Rheumatoid arthritis (RA) datasets, where we find some novel potential disease-related genetic factors which are not shown up in detections of 2-loci epistatic interactions. Conclusions Experimental results on simulated data demonstrate that our method is more powerful than some recently proposed methods on both two- and three-locus disease models. Our method has discovered many novel high-order associations that are significantly enriched in cases from two real GWAS datasets. Moreover, the running time of the cloud implementation for our method on AMD dataset and RA dataset are roughly 2 hours and 50 hours on a cluster with forty small virtual machines for detecting two-locus interactions, respectively. Therefore, we believe that our method is suitable and effective for the full-scale analysis of multiple-locus epistatic interactions in GWAS. PMID:24717145

Construction of ontology augmented networks for protein complex prediction.

PubMed

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian

2013-01-01

Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational methods for protein complex prediction. Most existing methods focus mainly on the topological structure of protein-protein interaction networks, and largely ignore the gene ontology annotation information. In this article, we constructed ontology augmented networks with protein-protein interaction data and gene ontology, which effectively unified the topological structure of protein-protein interaction networks and the similarity of gene ontology annotations into unified distance measures. After constructing ontology augmented networks, a novel method (clustering based on ontology augmented networks) was proposed to predict protein complexes, which was capable of taking into account the topological structure of the protein-protein interaction network, as well as the similarity of gene ontology annotations. Our method was applied to two different yeast protein-protein interaction datasets and predicted many well-known complexes. The experimental results showed that (i) ontology augmented networks and the unified distance measure can effectively combine the structure closeness and gene ontology annotation similarity; (ii) our method is valuable in predicting protein complexes and has higher F1 and accuracy compared to other competing methods.

Participant Interaction in Asynchronous Learning Environments: Evaluating Interaction Analysis Methods

ERIC Educational Resources Information Center

Blanchette, Judith

2012-01-01

The purpose of this empirical study was to determine the extent to which three different objective analytical methods--sequence analysis, surface cohesion analysis, and lexical cohesion analysis--can most accurately identify specific characteristics of online interaction. Statistically significant differences were found in all points of…

Investigating Learning with an Interactive Tutorial: A Mixed-Methods Strategy

ERIC Educational Resources Information Center

de Villiers, M. R.; Becker, Daphne

2017-01-01

From the perspective of parallel mixed-methods research, this paper describes interactivity research that employed usability-testing technology to analyse cognitive learning processes; personal learning styles and times; and errors-and-recovery of learners using an interactive e-learning tutorial called "Relations." "Relations"…

User Interaction in Semi-Automatic Segmentation of Organs at Risk: a Case Study in Radiotherapy.

PubMed

Ramkumar, Anjana; Dolz, Jose; Kirisli, Hortense A; Adebahr, Sonja; Schimek-Jasch, Tanja; Nestle, Ursula; Massoptier, Laurent; Varga, Edit; Stappers, Pieter Jan; Niessen, Wiro J; Song, Yu

2016-04-01

Accurate segmentation of organs at risk is an important step in radiotherapy planning. Manual segmentation being a tedious procedure and prone to inter- and intra-observer variability, there is a growing interest in automated segmentation methods. However, automatic methods frequently fail to provide satisfactory result, and post-processing corrections are often needed. Semi-automatic segmentation methods are designed to overcome these problems by combining physicians' expertise and computers' potential. This study evaluates two semi-automatic segmentation methods with different types of user interactions, named the "strokes" and the "contour", to provide insights into the role and impact of human-computer interaction. Two physicians participated in the experiment. In total, 42 case studies were carried out on five different types of organs at risk. For each case study, both the human-computer interaction process and quality of the segmentation results were measured subjectively and objectively. Furthermore, different measures of the process and the results were correlated. A total of 36 quantifiable and ten non-quantifiable correlations were identified for each type of interaction. Among those pairs of measures, 20 of the contour method and 22 of the strokes method were strongly or moderately correlated, either directly or inversely. Based on those correlated measures, it is concluded that: (1) in the design of semi-automatic segmentation methods, user interactions need to be less cognitively challenging; (2) based on the observed workflows and preferences of physicians, there is a need for flexibility in the interface design; (3) the correlated measures provide insights that can be used in improving user interaction design.

Within-brain classification for brain tumor segmentation.

PubMed

Havaei, Mohammad; Larochelle, Hugo; Poulin, Philippe; Jodoin, Pierre-Marc

2016-05-01

In this paper, we investigate a framework for interactive brain tumor segmentation which, at its core, treats the problem of interactive brain tumor segmentation as a machine learning problem. This method has an advantage over typical machine learning methods for this task where generalization is made across brains. The problem with these methods is that they need to deal with intensity bias correction and other MRI-specific noise. In this paper, we avoid these issues by approaching the problem as one of within brain generalization. Specifically, we propose a semi-automatic method that segments a brain tumor by training and generalizing within that brain only, based on some minimum user interaction. We investigate how adding spatial feature coordinates (i.e., i, j, k) to the intensity features can significantly improve the performance of different classification methods such as SVM, kNN and random forests. This would only be possible within an interactive framework. We also investigate the use of a more appropriate kernel and the adaptation of hyper-parameters specifically for each brain. As a result of these experiments, we obtain an interactive method whose results reported on the MICCAI-BRATS 2013 dataset are the second most accurate compared to published methods, while using significantly less memory and processing power than most state-of-the-art methods.

Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks

PubMed Central

Dalman, Mark; Haddad, Joseph; Duan, Zhong-Hui

2017-01-01

The PubMed database offers an extensive set of publication data that can be useful, yet inherently complex to use without automated computational techniques. Data repositories such as the Genomic Data Commons (GDC) and the Gene Expression Omnibus (GEO) offer experimental data storage and retrieval as well as curated gene expression profiles. Genetic interaction databases, including Reactome and Ingenuity Pathway Analysis, offer pathway and experiment data analysis using data curated from these publications and data repositories. We have created a method to generate and analyze consensus networks, inferring potential gene interactions, using large numbers of Bayesian networks generated by data mining publications in the PubMed database. Through the concept of network resolution, these consensus networks can be tailored to represent possible genetic interactions. We designed a set of experiments to confirm that our method is stable across variation in both sample and topological input sizes. Using gene product interactions from the KEGG pathway database and data mining PubMed publication abstracts, we verify that regardless of the network resolution or the inferred consensus network, our method is capable of inferring meaningful gene interactions through consensus Bayesian network generation with multiple, randomized topological orderings. Our method can not only confirm the existence of currently accepted interactions, but has the potential to hypothesize new ones as well. We show our method confirms the existence of known gene interactions such as JAK-STAT-PI3K-AKT-mTOR, infers novel gene interactions such as RAS- Bcl-2 and RAS-AKT, and found significant pathway-pathway interactions between the JAK-STAT signaling and Cardiac Muscle Contraction KEGG pathways. PMID:29049295

Enhancing the prediction of protein pairings between interacting families using orthology information

PubMed Central

Izarzugaza, Jose MG; Juan, David; Pons, Carles; Pazos, Florencio; Valencia, Alfonso

2008-01-01

Background It has repeatedly been shown that interacting protein families tend to have similar phylogenetic trees. These similarities can be used to predicting the mapping between two families of interacting proteins (i.e. which proteins from one family interact with which members of the other). The correct mapping will be that which maximizes the similarity between the trees. The two families may eventually comprise orthologs and paralogs, if members of the two families are present in more than one organism. This fact can be exploited to restrict the possible mappings, simply by impeding links between proteins of different organisms. We present here an algorithm to predict the mapping between families of interacting proteins which is able to incorporate information regarding orthologues, or any other assignment of proteins to "classes" that may restrict possible mappings. Results For the first time in methods for predicting mappings, we have tested this new approach on a large number of interacting protein domains in order to statistically assess its performance. The method accurately predicts around 80% in the most favourable cases. We also analysed in detail the results of the method for a well defined case of interacting families, the sensor and kinase components of the Ntr-type two-component system, for which up to 98% of the pairings predicted by the method were correct. Conclusion Based on the well established relationship between tree similarity and interactions we developed a method for predicting the mapping between two interacting families using genomic information alone. The program is available through a web interface. PMID:18215279

Simulation of wave packet tunneling of interacting identical particles

NASA Astrophysics Data System (ADS)

Lozovik, Yu. E.; Filinov, A. V.; Arkhipov, A. S.

2003-02-01

We demonstrate a different method of simulation of nonstationary quantum processes, considering the tunneling of two interacting identical particles, represented by wave packets. The used method of quantum molecular dynamics (WMD) is based on the Wigner representation of quantum mechanics. In the context of this method ensembles of classical trajectories are used to solve quantum Wigner-Liouville equation. These classical trajectories obey Hamiltonian-like equations, where the effective potential consists of the usual classical term and the quantum term, which depends on the Wigner function and its derivatives. The quantum term is calculated using local distribution of trajectories in phase space, therefore, classical trajectories are not independent, contrary to classical molecular dynamics. The developed WMD method takes into account the influence of exchange and interaction between particles. The role of direct and exchange interactions in tunneling is analyzed. The tunneling times for interacting particles are calculated.

CTE method and interaction solutions for the Kadomtsev-Petviashvili equation

NASA Astrophysics Data System (ADS)

Ren, Bo

2017-02-01

The consistent tanh expansion method is applied to the Kadomtsev-Petviashvili equation. The interaction solutions among one soliton and other types of solitary waves, such as multiple resonant soliton solutions and cnoidal waves, are explicitly given. Some special concrete interaction solutions are discussed both in analytical and graphical ways.

Interactive Anatomical and Surgical Live Stream Lectures Improve Students' Academic Performance in Applied Clinical Anatomy

ERIC Educational Resources Information Center

Shiozawa, Thomas; Butz, Benjamin; Herlan, Stephan; Kramer, Andreas; Hirt, Bernhard

2017-01-01

Tuebingen's "Sectio Chirurgica" (TSC) is an innovative, interactive, multimedia, and transdisciplinary teaching method designed to complement dissection courses. The Tuebingen's "Sectio Chirurgica" (TSC) allows clinical anatomy to be taught via interactive live stream surgeries moderated by an anatomist. This method aims to…

Nucleon-nucleon interactions via Lattice QCD: Methodology. HAL QCD approach to extract hadronic interactions in lattice QCD

NASA Astrophysics Data System (ADS)

Aoki, Sinya

2013-07-01

We review the potential method in lattice QCD, which has recently been proposed to extract nucleon-nucleon interactions via numerical simulations. We focus on the methodology of this approach by emphasizing the strategy of the potential method, the theoretical foundation behind it, and special numerical techniques. We compare the potential method with the standard finite volume method in lattice QCD, in order to make pros and cons of the approach clear. We also present several numerical results for nucleon-nucleon potentials.

Predicting Drug-Target Interactions for New Drug Compounds Using a Weighted Nearest Neighbor Profile.

PubMed

van Laarhoven, Twan; Marchiori, Elena

2013-01-01

In silico discovery of interactions between drug compounds and target proteins is of core importance for improving the efficiency of the laborious and costly experimental determination of drug-target interaction. Drug-target interaction data are available for many classes of pharmaceutically useful target proteins including enzymes, ion channels, GPCRs and nuclear receptors. However, current drug-target interaction databases contain a small number of drug-target pairs which are experimentally validated interactions. In particular, for some drug compounds (or targets) there is no available interaction. This motivates the need for developing methods that predict interacting pairs with high accuracy also for these 'new' drug compounds (or targets). We show that a simple weighted nearest neighbor procedure is highly effective for this task. We integrate this procedure into a recent machine learning method for drug-target interaction we developed in previous work. Results of experiments indicate that the resulting method predicts true interactions with high accuracy also for new drug compounds and achieves results comparable or better than those of recent state-of-the-art algorithms. Software is publicly available at http://cs.ru.nl/~tvanlaarhoven/drugtarget2013/.

A combined database related and de novo MS-identification of yeast mannose-1-phosphate guanyltransferase PSA1 interaction partners at different phases of batch cultivation

NASA Astrophysics Data System (ADS)

Parviainen, Ville; Joenväärä, Sakari; Peltoniemi, Hannu; Mattila, Pirkko; Renkonen, Risto

2009-04-01

Mass spectrometry-based proteomic research has become one of the main methods in protein-protein interaction research. Several high throughput studies have established an interaction landscape of exponentially growing Baker's yeast culture. However, many of the protein-protein interactions are likely to change in different environmental conditions. In order to examine the dynamic nature of the protein interactions we isolated the protein complexes of mannose-1-phosphate guanyltransferase PSA1 from Saccharomyces cerevisiae at four different time points during batch cultivation. We used the tandem affinity purification (TAP)-method to purify the complexes and subjected the tryptic peptides to LC-MS/MS. The resulting peak lists were analyzed with two different methods: the database related protein identification program X!Tandem and the de novo sequencing program Lutefisk. We observed significant changes in the interactome of PSA1 during the batch cultivation and identified altogether 74 proteins interacting with PSA1 of which only six were found to interact during all time points. All the other proteins showed a more dynamic nature of binding activity. In this study we also demonstrate the benefit of using both database related and de novo methods in the protein interaction research to enhance both the quality and the quantity of observations.

Particle-Surface Interaction Model and Method of Determining Particle-Surface Interactions

NASA Technical Reports Server (NTRS)

Hughes, David W. (Inventor)

2012-01-01

A method and model of predicting particle-surface interactions with a surface, such as the surface of a spacecraft. The method includes the steps of: determining a trajectory path of a plurality of moving particles; predicting whether any of the moving particles will intersect a surface; predicting whether any of the particles will be captured by the surface and/or; predicting a reflected trajectory and velocity of particles reflected from the surface.

Gamma-ray tracking method for pet systems

DOEpatents

Mihailescu, Lucian; Vetter, Kai M.

2010-06-08

Gamma-ray tracking methods for use with granular, position sensitive detectors identify the sequence of the interactions taking place in the detector and, hence, the position of the first interaction. The improved position resolution in finding the first interaction in the detection system determines a better definition of the direction of the gamma-ray photon, and hence, a superior source image resolution. A PET system using such a method will have increased efficiency and position resolution.

An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

PubMed Central

Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

2012-01-01

We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

Quantitative Investigation of Protein-Nucleic Acid Interactions by Biosensor Surface Plasmon Resonance.

PubMed

Wang, Shuo; Poon, Gregory M K; Wilson, W David

2015-01-01

Biosensor-surface plasmon resonance (SPR) technology has emerged as a powerful label-free approach for the study of nucleic acid interactions in real time. The method provides simultaneous equilibrium and kinetic characterization for biomolecular interactions with low sample requirements and without the need for external probes. A detailed and practical guide for protein-DNA interaction analyses using biosensor-SPR methods is presented. Details of SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips and samples, experimental design, quantitative and qualitative data analyses and presentation. A specific example of the interaction of a transcription factor with DNA is provided with results evaluated by both kinetic and steady-state SPR methods.

Parallelized Stochastic Cutoff Method for Long-Range Interacting Systems

NASA Astrophysics Data System (ADS)

Endo, Eishin; Toga, Yuta; Sasaki, Munetaka

2015-07-01

We present a method of parallelizing the stochastic cutoff (SCO) method, which is a Monte-Carlo method for long-range interacting systems. After interactions are eliminated by the SCO method, we subdivide a lattice into noninteracting interpenetrating sublattices. This subdivision enables us to parallelize the Monte-Carlo calculation in the SCO method. Such subdivision is found by numerically solving the vertex coloring of a graph created by the SCO method. We use an algorithm proposed by Kuhn and Wattenhofer to solve the vertex coloring by parallel computation. This method was applied to a two-dimensional magnetic dipolar system on an L × L square lattice to examine its parallelization efficiency. The result showed that, in the case of L = 2304, the speed of computation increased about 102 times by parallel computation with 288 processors.

Drug-target interaction prediction using ensemble learning and dimensionality reduction.

PubMed

Ezzat, Ali; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

2017-10-01

Experimental prediction of drug-target interactions is expensive, time-consuming and tedious. Fortunately, computational methods help narrow down the search space for interaction candidates to be further examined via wet-lab techniques. Nowadays, the number of attributes/features for drugs and targets, as well as the amount of their interactions, are increasing, making these computational methods inefficient or occasionally prohibitive. This motivates us to derive a reduced feature set for prediction. In addition, since ensemble learning techniques are widely used to improve the classification performance, it is also worthwhile to design an ensemble learning framework to enhance the performance for drug-target interaction prediction. In this paper, we propose a framework for drug-target interaction prediction leveraging both feature dimensionality reduction and ensemble learning. First, we conducted feature subspacing to inject diversity into the classifier ensemble. Second, we applied three different dimensionality reduction methods to the subspaced features. Third, we trained homogeneous base learners with the reduced features and then aggregated their scores to derive the final predictions. For base learners, we selected two classifiers, namely Decision Tree and Kernel Ridge Regression, resulting in two variants of ensemble models, EnsemDT and EnsemKRR, respectively. In our experiments, we utilized AUC (Area under ROC Curve) as an evaluation metric. We compared our proposed methods with various state-of-the-art methods under 5-fold cross validation. Experimental results showed EnsemKRR achieving the highest AUC (94.3%) for predicting drug-target interactions. In addition, dimensionality reduction helped improve the performance of EnsemDT. In conclusion, our proposed methods produced significant improvements for drug-target interaction prediction. Copyright © 2017 Elsevier Inc. All rights reserved.

Active subnetwork recovery with a mechanism-dependent scoring function; with application to angiogenesis and organogenesis studies

PubMed Central

2013-01-01

Background The learning active subnetworks problem involves finding subnetworks of a bio-molecular network that are active in a particular condition. Many approaches integrate observation data (e.g., gene expression) with the network topology to find candidate subnetworks. Increasingly, pathway databases contain additional annotation information that can be mined to improve prediction accuracy, e.g., interaction mechanism (e.g., transcription, microRNA, cleavage) annotations. We introduce a mechanism-based approach to active subnetwork recovery which exploits such annotations. We suggest that neighboring interactions in a network tend to be co-activated in a way that depends on the “correlation” of their mechanism annotations. e.g., neighboring phosphorylation and de-phosphorylation interactions may be more likely to be co-activated than neighboring phosphorylation and covalent bonding interactions. Results Our method iteratively learns the mechanism correlations and finds the most likely active subnetwork. We use a probabilistic graphical model with a Markov Random Field component which creates dependencies between the states (active or non-active) of neighboring interactions, that incorporates a mechanism-based component to the function. We apply a heuristic-based EM-based algorithm suitable for the problem. We validated our method’s performance using simulated data in networks downloaded from GeneGO against the same approach without the mechanism-based component, and two other existing methods. We validated our methods performance in correctly recovering (1) the true interaction states, and (2) global network properties of the original network against these other methods. We applied our method to networks generated from time-course gene expression studies in angiogenesis and lung organogenesis and validated the findings from a biological perspective against current literature. Conclusions The advantage of our mechanism-based approach is best seen in networks composed of connected regions with a large number of interactions annotated with a subset of mechanisms, e.g., a regulatory region of transcription interactions, or a cleavage cascade region. When applied to real datasets, our method recovered novel and biologically meaningful putative interactions, e.g., interactions from an integrin signaling pathway using the angiogenesis dataset, and a group of regulatory microRNA interactions in an organogenesis network. PMID:23432934

Assessing the performance of dispersionless and dispersion-accounting methods: helium interaction with cluster models of the TiO2(110) surface.

PubMed

de Lara-Castells, María Pilar; Stoll, Hermann; Mitrushchenkov, Alexander O

2014-08-21

As a prototypical dispersion-dominated physisorption problem, we analyze here the performance of dispersionless and dispersion-accounting methodologies on the helium interaction with cluster models of the TiO2(110) surface. A special focus has been given to the dispersionless density functional dlDF and the dlDF+Das construction for the total interaction energy (K. Pernal, R. Podeswa, K. Patkowski, and K. Szalewicz, Phys. Rev. Lett. 2009, 109, 263201), where Das is an effective interatomic pairwise functional form for the dispersion. Likewise, the performance of symmetry-adapted perturbation theory (SAPT) method is evaluated, where the interacting monomers are described by density functional theory (DFT) with the dlDF, PBE, and PBE0 functionals. Our benchmarks include CCSD(T)-F12b calculations and comparative analysis on the nuclear bound states supported by the He-cluster potentials. Moreover, intra- and intermonomer correlation contributions to the physisorption interaction are analyzed through the method of increments (H. Stoll, J. Chem. Phys. 1992, 97, 8449) at the CCSD(T) level of theory. This method is further applied in conjunction with a partitioning of the Hartree-Fock interaction energy to estimate individual interaction energy components, comparing them with those obtained using the different SAPT(DFT) approaches. The cluster size evolution of dispersionless and dispersion-accounting energy components is then discussed, revealing the reduced role of the dispersionless interaction and intramonomer correlation when the extended nature of the surface is better accounted for. On the contrary, both post-Hartree-Fock and SAPT(DFT) results clearly demonstrate the high-transferability character of the effective pairwise dispersion interaction whatever the cluster model is. Our contribution also illustrates how the method of increments can be used as a valuable tool not only to achieve the accuracy of CCSD(T) calculations using large cluster models but also to evaluate the performance of SAPT(DFT) methods for the physically well-defined contributions to the total interaction energy. Overall, our work indicates the excellent performance of a dlDF+Das approach in which the parameters are optimized using the smallest cluster model of the target surface to treat van der Waals adsorbate-surface interactions.

Calculation of the Coulomb Fission Cross Sections for Pb-Pb and Bi-Pb Interactions at 158 A GeV

NASA Technical Reports Server (NTRS)

Poyser, William J.; Ahern, Sean C.; Norbury, John W.; Tripathi, R. K.

2002-01-01

The Weizsacker-Williams (WW) method of virtual quanta is used to make approximate cross section calculations for peripheral relativistic heavy-ion collisions. We calculated the Coulomb fission cross sections for projectile ions of Pb-208 and Bi-209 with energies of 158 A GeV interacting with a Pb-208 target. We also calculated the electromagnetic absorption cross section for Pb-208 ion interacting as described. For comparison we use both the full WW method and a standard approximate WW method. The approximate WW method in larger cross sections compared to the more accurate full WW method.

Quantitative analysis of protein-ligand interactions by NMR.

PubMed

Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

2016-08-01

Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used to analyze population-averaged NMR quantities. Essentially, to apply NMR successfully, both the type of experiment and equation to fit the data must be carefully and specifically chosen for the protein-ligand interaction under analysis. In this review, we first explain the exchange regimes and kinetic models of protein-ligand interactions, and then describe the NMR methods that quantitatively analyze these specific interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction.

PubMed

Muley, Vijaykumar Yogesh; Ranjan, Akash

2012-01-01

Recent progress in computational methods for predicting physical and functional protein-protein interactions has provided new insights into the complexity of biological processes. Most of these methods assume that functionally interacting proteins are likely to have a shared evolutionary history. This history can be traced out for the protein pairs of a query genome by correlating different evolutionary aspects of their homologs in multiple genomes known as the reference genomes. These methods include phylogenetic profiling, gene neighborhood and co-occurrence of the orthologous protein coding genes in the same cluster or operon. These are collectively known as genomic context methods. On the other hand a method called mirrortree is based on the similarity of phylogenetic trees between two interacting proteins. Comprehensive performance analyses of these methods have been frequently reported in literature. However, very few studies provide insight into the effect of reference genome selection on detection of meaningful protein interactions. We analyzed the performance of four methods and their variants to understand the effect of reference genome selection on prediction efficacy. We used six sets of reference genomes, sampled in accordance with phylogenetic diversity and relationship between organisms from 565 bacteria. We used Escherichia coli as a model organism and the gold standard datasets of interacting proteins reported in DIP, EcoCyc and KEGG databases to compare the performance of the prediction methods. Higher performance for predicting protein-protein interactions was achievable even with 100-150 bacterial genomes out of 565 genomes. Inclusion of archaeal genomes in the reference genome set improves performance. We find that in order to obtain a good performance, it is better to sample few genomes of related genera of prokaryotes from the large number of available genomes. Moreover, such a sampling allows for selecting 50-100 genomes for comparable accuracy of predictions when computational resources are limited.

Fluid-structure interaction simulation of floating structures interacting with complex, large-scale ocean waves and atmospheric turbulence with application to floating offshore wind turbines

NASA Astrophysics Data System (ADS)

Calderer, Antoni; Guo, Xin; Shen, Lian; Sotiropoulos, Fotis

2018-02-01

We develop a numerical method for simulating coupled interactions of complex floating structures with large-scale ocean waves and atmospheric turbulence. We employ an efficient large-scale model to develop offshore wind and wave environmental conditions, which are then incorporated into a high resolution two-phase flow solver with fluid-structure interaction (FSI). The large-scale wind-wave interaction model is based on a two-fluid dynamically-coupled approach that employs a high-order spectral method for simulating the water motion and a viscous solver with undulatory boundaries for the air motion. The two-phase flow FSI solver is based on the level set method and is capable of simulating the coupled dynamic interaction of arbitrarily complex bodies with airflow and waves. The large-scale wave field solver is coupled with the near-field FSI solver with a one-way coupling approach by feeding into the latter waves via a pressure-forcing method combined with the level set method. We validate the model for both simple wave trains and three-dimensional directional waves and compare the results with experimental and theoretical solutions. Finally, we demonstrate the capabilities of the new computational framework by carrying out large-eddy simulation of a floating offshore wind turbine interacting with realistic ocean wind and waves.

Machine Learning for Detecting Gene-Gene Interactions

PubMed Central

McKinney, Brett A.; Reif, David M.; Ritchie, Marylyn D.; Moore, Jason H.

2011-01-01

Complex interactions among genes and environmental factors are known to play a role in common human disease aetiology. There is a growing body of evidence to suggest that complex interactions are ‘the norm’ and, rather than amounting to a small perturbation to classical Mendelian genetics, interactions may be the predominant effect. Traditional statistical methods are not well suited for detecting such interactions, especially when the data are high dimensional (many attributes or independent variables) or when interactions occur between more than two polymorphisms. In this review, we discuss machine-learning models and algorithms for identifying and characterising susceptibility genes in common, complex, multifactorial human diseases. We focus on the following machine-learning methods that have been used to detect gene-gene interactions: neural networks, cellular automata, random forests, and multifactor dimensionality reduction. We conclude with some ideas about how these methods and others can be integrated into a comprehensive and flexible framework for data mining and knowledge discovery in human genetics. PMID:16722772

Prediction of virus-host protein-protein interactions mediated by short linear motifs.

PubMed

Becerra, Andrés; Bucheli, Victor A; Moreno, Pedro A

2017-03-09

Short linear motifs in host organisms proteins can be mimicked by viruses to create protein-protein interactions that disable or control metabolic pathways. Given that viral linear motif instances of host motif regular expressions can be found by chance, it is necessary to develop filtering methods of functional linear motifs. We conduct a systematic comparison of linear motifs filtering methods to develop a computational approach for predicting motif-mediated protein-protein interactions between human and the human immunodeficiency virus 1 (HIV-1). We implemented three filtering methods to obtain linear motif sets: 1) conserved in viral proteins (C), 2) located in disordered regions (D) and 3) rare or scarce in a set of randomized viral sequences (R). The sets C,D,R are united and intersected. The resulting sets are compared by the number of protein-protein interactions correctly inferred with them - with experimental validation. The comparison is done with HIV-1 sequences and interactions from the National Institute of Allergy and Infectious Diseases (NIAID). The number of correctly inferred interactions allows to rank the interactions by the sets used to deduce them: D∪R and C. The ordering of the sets is descending on the probability of capturing functional interactions. With respect to HIV-1, the sets C∪R, D∪R, C∪D∪R infer all known interactions between HIV1 and human proteins mediated by linear motifs. We found that the majority of conserved linear motifs in the virus are located in disordered regions. We have developed a method for predicting protein-protein interactions mediated by linear motifs between HIV-1 and human proteins. The method only use protein sequences as inputs. We can extend the software developed to any other eukaryotic virus and host in order to find and rank candidate interactions. In future works we will use it to explore possible viral attack mechanisms based on linear motif mimicry.

Improving Classification of Protein Interaction Articles Using Context Similarity-Based Feature Selection.

PubMed

Chen, Yifei; Sun, Yuxing; Han, Bing-Qing

2015-01-01

Protein interaction article classification is a text classification task in the biological domain to determine which articles describe protein-protein interactions. Since the feature space in text classification is high-dimensional, feature selection is widely used for reducing the dimensionality of features to speed up computation without sacrificing classification performance. Many existing feature selection methods are based on the statistical measure of document frequency and term frequency. One potential drawback of these methods is that they treat features separately. Hence, first we design a similarity measure between the context information to take word cooccurrences and phrase chunks around the features into account. Then we introduce the similarity of context information to the importance measure of the features to substitute the document and term frequency. Hence we propose new context similarity-based feature selection methods. Their performance is evaluated on two protein interaction article collections and compared against the frequency-based methods. The experimental results reveal that the context similarity-based methods perform better in terms of the F1 measure and the dimension reduction rate. Benefiting from the context information surrounding the features, the proposed methods can select distinctive features effectively for protein interaction article classification.

Numerical investigation of nonlinear fluid-structure interaction dynamic behaviors under a general Immersed Boundary-Lattice Boltzmann-Finite Element method

NASA Astrophysics Data System (ADS)

Gong, Chun-Lin; Fang, Zhe; Chen, Gang

A numerical approach based on the immersed boundary (IB), lattice Boltzmann and nonlinear finite element method (FEM) is proposed to simulate hydrodynamic interactions of very flexible objects. In the present simulation framework, the motion of fluid is obtained by solving the discrete lattice Boltzmann equations on Eulerian grid, the behaviors of flexible objects are calculated through nonlinear dynamic finite element method, and the interactive forces between them are implicitly obtained using velocity correction IB method which satisfies the no-slip conditions well at the boundary points. The efficiency and accuracy of the proposed Immersed Boundary-Lattice Boltzmann-Finite Element method is first validated by a fluid-structure interaction (F-SI) benchmark case, in which a flexible filament flaps behind a cylinder in channel flow, then the nonlinear vibration mechanism of the cylinder-filament system is investigated by altering the Reynolds number of flow and the material properties of filament. The interactions between two tandem and side-by-side identical objects in a uniform flow are also investigated, and the in-phase and out-of-phase flapping behaviors are captured by the proposed method.

Interactive Videodisc as a Component in a Multi-Method Approach to Anatomy and Physiology.

ERIC Educational Resources Information Center

Wheeler, Donald A.; Wheeler, Mary Jane

At Cuyahoga Community College (Ohio), computer-controlled interactive videodisc technology is being used as one of several instructional methods to teach anatomy and physiology. The system has the following features: audio-visual instruction, interaction with immediate feedback, self-pacing, fill-in-the-blank quizzes for testing total recall,…

Genetic Risk by Experience Interaction for Childhood Internalizing Problems: Converging Evidence across Multiple Methods

ERIC Educational Resources Information Center

Vendlinski, Matthew K.; Lemery-Chalfant, Kathryn; Essex, Marilyn J.; Goldsmith, H. Hill

2011-01-01

Background: Identifying how genetic risk interacts with experience to predict psychopathology is an important step toward understanding the etiology of mental health problems. Few studies have examined genetic risk by experience interaction (GxE) in the development of childhood psychopathology. Methods: We used both co-twin and parent mental…

Estimating and Interpreting Latent Variable Interactions: A Tutorial for Applying the Latent Moderated Structural Equations Method

ERIC Educational Resources Information Center

Maslowsky, Julie; Jager, Justin; Hemken, Douglas

2015-01-01

Latent variables are common in psychological research. Research questions involving the interaction of two variables are likewise quite common. Methods for estimating and interpreting interactions between latent variables within a structural equation modeling framework have recently become available. The latent moderated structural equations (LMS)…

Probabilistic biological network alignment.

PubMed

Todor, Andrei; Dobra, Alin; Kahveci, Tamer

2013-01-01

Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

Filtering Gene Ontology semantic similarity for identifying protein complexes in large protein interaction networks.

PubMed

Wang, Jian; Xie, Dong; Lin, Hongfei; Yang, Zhihao; Zhang, Yijia

2012-06-21

Many biological processes recognize in particular the importance of protein complexes, and various computational approaches have been developed to identify complexes from protein-protein interaction (PPI) networks. However, high false-positive rate of PPIs leads to challenging identification. A protein semantic similarity measure is proposed in this study, based on the ontology structure of Gene Ontology (GO) terms and GO annotations to estimate the reliability of interactions in PPI networks. Interaction pairs with low GO semantic similarity are removed from the network as unreliable interactions. Then, a cluster-expanding algorithm is used to detect complexes with core-attachment structure on filtered network. Our method is applied to three different yeast PPI networks. The effectiveness of our method is examined on two benchmark complex datasets. Experimental results show that our method performed better than other state-of-the-art approaches in most evaluation metrics. The method detects protein complexes from large scale PPI networks by filtering GO semantic similarity. Removing interactions with low GO similarity significantly improves the performance of complex identification. The expanding strategy is also effective to identify attachment proteins of complexes.

A Protein Preparation Method for the High-throughput Identification of Proteins Interacting with a Nuclear Cofactor Using LC-MS/MS Analysis.

PubMed

Tsuchiya, Megumi; Karim, M Rezaul; Matsumoto, Taro; Ogawa, Hidesato; Taniguchi, Hiroaki

2017-01-24

Transcriptional coregulators are vital to the efficient transcriptional regulation of nuclear chromatin structure. Coregulators play a variety of roles in regulating transcription. These include the direct interaction with transcription factors, the covalent modification of histones and other proteins, and the occasional chromatin conformation alteration. Accordingly, establishing relatively quick methods for identifying proteins that interact within this network is crucial to enhancing our understanding of the underlying regulatory mechanisms. LC-MS/MS-mediated protein binding partner identification is a validated technique used to analyze protein-protein interactions. By immunoprecipitating a previously-identified member of a protein complex with an antibody (occasionally with an antibody for a tagged protein), it is possible to identify its unknown protein interactions via mass spectrometry analysis. Here, we present a method of protein preparation for the LC-MS/MS-mediated high-throughput identification of protein interactions involving nuclear cofactors and their binding partners. This method allows for a better understanding of the transcriptional regulatory mechanisms of the targeted nuclear factors.

A proteomics method using immunoaffinity fluorogenic derivatization-liquid chromatography/tandem mass spectrometry (FD-LC-MS/MS) to identify a set of interacting proteins.

PubMed

Nakata, Katsunori; Saitoh, Ryoichi; Ishigai, Masaki; Imai, Kazuhiro

2018-02-01

Biological functions in organisms are usually controlled by a set of interacting proteins, and identifying the proteins that interact is useful for understanding the mechanism of the functions. Immunoprecipitation is a method that utilizes the affinity of an antibody to isolate and identify the proteins that have interacted in a biological sample. In this study, the FD-LC-MS/MS method, which involves fluorogenic derivatization followed by separation and quantification by HPLC and finally identification of proteins by HPLC-tandem mass spectrometry, was used to identify proteins in immunoprecipitated samples, using heat shock protein 90 (HSP90) as a model of an interacting protein in HepaRG cells. As a result, HSC70 protein, which was known to form a complex with HSP90, was isolated, together with three different types of HSP90-beta. The results demonstrated that the proposed immunoaffinity-FD-LC-MS/MS method could be useful for simultaneously detecting and identifying the proteins that interact with a certain protein. Copyright © 2017 John Wiley & Sons, Ltd.

GEOPHYSICS, ASTRONOMY AND ASTROPHYSICS: Numerical method of studying nonlinear interactions between long waves and multiple short waves

NASA Astrophysics Data System (ADS)

Xie, Tao; Kuang, Hai-Lan; William, Perrie; Zou, Guang-Hui; Nan, Cheng-Feng; He, Chao; Shen, Tao; Chen, Wei

2009-07-01

Although the nonlinear interactions between a single short gravity wave and a long wave can be solved analytically, the solution is less tractable in more general cases involving multiple short waves. In this work we present a numerical method of studying nonlinear interactions between a long wave and multiple short harmonic waves in infinitely deep water. Specifically, this method is applied to the calculation of the temporal and spatial evolutions of the surface elevations in which a given long wave interacts with several short harmonic waves. Another important application of our method is to quantitatively analyse the nonlinear interactions between an arbitrary short wave train and another short wave train. From simulation results, we obtain that the mechanism for the nonlinear interactions between one short wave train and another short wave train (expressed as wave train 2) leads to the energy focusing of the other short wave train (expressed as wave train 3). This mechanism occurs on wave components with a narrow frequency bandwidth, whose frequencies are near that of wave train 3.

An examination of the earthquake behaviour of a retaining wall considering soil-structure interaction

NASA Astrophysics Data System (ADS)

Köktan, Utku; Demir, Gökhan; Kerem Ertek, M.

2017-04-01

The earthquake behavior of retaining walls is commonly calculated with pseudo static approaches based on Mononobe-Okabe method. The seismic ground pressure acting on the retaining wall by the Mononobe-Okabe method does not give a definite idea of the distribution of the seismic ground pressure because it is obtained by balancing the forces acting on the active wedge behind the wall. With this method, wave propagation effects and soil-structure interaction are neglected. The purpose of this study is to examine the earthquake behavior of a retaining wall taking into account the soil-structure interaction. For this purpose, time history seismic analysis of the soil-structure interaction system using finite element method has been carried out considering 3 different soil conditions. Seismic analysis of the soil-structure model was performed according to the earthquake record of "1971, San Fernando Pacoima Dam, 196 degree" existing in the library of MIDAS GTS NX software. The results obtained from the analyses show that the soil-structure interaction is very important for the seismic design of a retaining wall. Keywords: Soil-structure interaction, Finite element model, Retaining wall

ROCS: a Reproducibility Index and Confidence Score for Interaction Proteomics Studies

PubMed Central

2012-01-01

Background Affinity-Purification Mass-Spectrometry (AP-MS) provides a powerful means of identifying protein complexes and interactions. Several important challenges exist in interpreting the results of AP-MS experiments. First, the reproducibility of AP-MS experimental replicates can be low, due both to technical variability and the dynamic nature of protein interactions in the cell. Second, the identification of true protein-protein interactions in AP-MS experiments is subject to inaccuracy due to high false negative and false positive rates. Several experimental approaches can be used to mitigate these drawbacks, including the use of replicated and control experiments and relative quantification to sensitively distinguish true interacting proteins from false ones. Methods To address the issues of reproducibility and accuracy of protein-protein interactions, we introduce a two-step method, called ROCS, which makes use of Indicator Prey Proteins to select reproducible AP-MS experiments, and of Confidence Scores to select specific protein-protein interactions. The Indicator Prey Proteins account for measures of protein identifiability as well as protein reproducibility, effectively allowing removal of outlier experiments that contribute noise and affect downstream inferences. The filtered set of experiments is then used in the Protein-Protein Interaction (PPI) scoring step. Prey protein scoring is done by computing a Confidence Score, which accounts for the probability of occurrence of prey proteins in the bait experiments relative to the control experiment, where the significance cutoff parameter is estimated by simultaneously controlling false positives and false negatives against metrics of false discovery rate and biological coherence respectively. In summary, the ROCS method relies on automatic objective criterions for parameter estimation and error-controlled procedures. Results We illustrate the performance of our method by applying it to five previously published AP-MS experiments, each containing well characterized protein interactions, allowing for systematic benchmarking of ROCS. We show that our method may be used on its own to make accurate identification of specific, biologically relevant protein-protein interactions, or in combination with other AP-MS scoring methods to significantly improve inferences. Conclusions Our method addresses important issues encountered in AP-MS datasets, making ROCS a very promising tool for this purpose, either on its own or in conjunction with other methods. We anticipate that our methodology may be used more generally in proteomics studies and databases, where experimental reproducibility issues arise. The method is implemented in the R language, and is available as an R package called “ROCS”, freely available from the CRAN repository http://cran.r-project.org/. PMID:22682516

Fusing literature and full network data improves disease similarity computation.

PubMed

Li, Ping; Nie, Yaling; Yu, Jingkai

2016-08-30

Identifying relatedness among diseases could help deepen understanding for the underlying pathogenic mechanisms of diseases, and facilitate drug repositioning projects. A number of methods for computing disease similarity had been developed; however, none of them were designed to utilize information of the entire protein interaction network, using instead only those interactions involving disease causing genes. Most of previously published methods required gene-disease association data, unfortunately, many diseases still have very few or no associated genes, which impeded broad adoption of those methods. In this study, we propose a new method (MedNetSim) for computing disease similarity by integrating medical literature and protein interaction network. MedNetSim consists of a network-based method (NetSim), which employs the entire protein interaction network, and a MEDLINE-based method (MedSim), which computes disease similarity by mining the biomedical literature. Among function-based methods, NetSim achieved the best performance. Its average AUC (area under the receiver operating characteristic curve) reached 95.2 %. MedSim, whose performance was even comparable to some function-based methods, acquired the highest average AUC in all semantic-based methods. Integration of MedSim and NetSim (MedNetSim) further improved the average AUC to 96.4 %. We further studied the effectiveness of different data sources. It was found that quality of protein interaction data was more important than its volume. On the contrary, higher volume of gene-disease association data was more beneficial, even with a lower reliability. Utilizing higher volume of disease-related gene data further improved the average AUC of MedNetSim and NetSim to 97.5 % and 96.7 %, respectively. Integrating biomedical literature and protein interaction network can be an effective way to compute disease similarity. Lacking sufficient disease-related gene data, literature-based methods such as MedSim can be a great addition to function-based algorithms. It may be beneficial to steer more resources torward studying gene-disease associations and improving the quality of protein interaction data. Disease similarities can be computed using the proposed methods at http:// www.digintelli.com:8000/ .

Observing real-time social interaction via telecommunication methods in budgerigars (Melopsittacus undulatus).

PubMed

Ikkatai, Yuko; Okanoya, Kazuo; Seki, Yoshimasa

2016-07-01

Humans communicate with one another not only face-to-face but also via modern telecommunication methods such as television and video conferencing. We readily detect the difference between people actively communicating with us and people merely acting via a broadcasting system. We developed an animal model of this novel communication method seen in humans to determine whether animals also make this distinction. We built a system for two animals to interact via audio-visual equipment in real-time, to compare behavioral differences between two conditions, an "interactive two-way condition" and a "non-interactive (one-way) condition." We measured birds' responses to stimuli which appeared in these two conditions. We used budgerigars, which are small, gregarious birds, and found that the frequency of vocal interaction with other individuals did not differ between the two conditions. However, body synchrony between the two birds was observed more often in the interactive condition, suggesting budgerigars recognized the difference between these interactive and non-interactive conditions on some level. Copyright © 2016 Elsevier B.V. All rights reserved.

Applied Graph-Mining Algorithms to Study Biomolecular Interaction Networks

PubMed Central

2014-01-01

Protein-protein interaction (PPI) networks carry vital information on the organization of molecular interactions in cellular systems. The identification of functionally relevant modules in PPI networks is one of the most important applications of biological network analysis. Computational analysis is becoming an indispensable tool to understand large-scale biomolecular interaction networks. Several types of computational methods have been developed and employed for the analysis of PPI networks. Of these computational methods, graph comparison and module detection are the two most commonly used strategies. This review summarizes current literature on graph kernel and graph alignment methods for graph comparison strategies, as well as module detection approaches including seed-and-extend, hierarchical clustering, optimization-based, probabilistic, and frequent subgraph methods. Herein, we provide a comprehensive review of the major algorithms employed under each theme, including our recently published frequent subgraph method, for detecting functional modules commonly shared across multiple cancer PPI networks. PMID:24800226

Numerical simulation of the solitary wave interacting with an elastic structure using MPS-FEM coupled method

NASA Astrophysics Data System (ADS)

Rao, Chengping; Zhang, Youlin; Wan, Decheng

2017-12-01

Fluid-Structure Interaction (FSI) caused by fluid impacting onto a flexible structure commonly occurs in naval architecture and ocean engineering. Research on the problem of wave-structure interaction is important to ensure the safety of offshore structures. This paper presents the Moving Particle Semi-implicit and Finite Element Coupled Method (MPS-FEM) to simulate FSI problems. The Moving Particle Semi-implicit (MPS) method is used to calculate the fluid domain, while the Finite Element Method (FEM) is used to address the structure domain. The scheme for the coupling of MPS and FEM is introduced first. Then, numerical validation and convergent study are performed to verify the accuracy of the solver for solitary wave generation and FSI problems. The interaction between the solitary wave and an elastic structure is investigated by using the MPS-FEM coupled method.

A Penalized Robust Method for Identifying Gene-Environment Interactions

PubMed Central

Shi, Xingjie; Liu, Jin; Huang, Jian; Zhou, Yong; Xie, Yang; Ma, Shuangge

2015-01-01

In high-throughput studies, an important objective is to identify gene-environment interactions associated with disease outcomes and phenotypes. Many commonly adopted methods assume specific parametric or semiparametric models, which may be subject to model mis-specification. In addition, they usually use significance level as the criterion for selecting important interactions. In this study, we adopt the rank-based estimation, which is much less sensitive to model specification than some of the existing methods and includes several commonly encountered data and models as special cases. Penalization is adopted for the identification of gene-environment interactions. It achieves simultaneous estimation and identification and does not rely on significance level. For computation feasibility, a smoothed rank estimation is further proposed. Simulation shows that under certain scenarios, for example with contaminated or heavy-tailed data, the proposed method can significantly outperform the existing alternatives with more accurate identification. We analyze a lung cancer prognosis study with gene expression measurements under the AFT (accelerated failure time) model. The proposed method identifies interactions different from those using the alternatives. Some of the identified genes have important implications. PMID:24616063

Vesselness propagation: a fast interactive vessel segmentation method

NASA Astrophysics Data System (ADS)

Cai, Wenli; Dachille, Frank; Harris, Gordon J.; Yoshida, Hiroyuki

2006-03-01

With the rapid development of multi-detector computed tomography (MDCT), resulting in increasing temporal and spatial resolution of data sets, clinical use of computed tomographic angiography (CTA) is rapidly increasing. Analysis of vascular structures is much needed in CTA images; however, the basis of the analysis, vessel segmentation, can still be a challenging problem. In this paper, we present a fast interactive method for CTA vessel segmentation, called vesselness propagation. This method is a two-step procedure, with a pre-processing step and an interactive step. During the pre-processing step, a vesselness volume is computed by application of a CTA transfer function followed by a multi-scale Hessian filtering. At the interactive stage, the propagation is controlled interactively in terms of the priority of the vesselness. This method was used successfully in many CTA applications such as the carotid artery, coronary artery, and peripheral arteries. It takes less than one minute for a user to segment the entire vascular structure. Thus, the proposed method provides an effective way of obtaining an overview of vascular structures.

Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

PubMed Central

2010-01-01

Background Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI) is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles. Results In this paper, we propose a computational method to predict DDI using support vector machines (SVMs), based on domains represented as interaction profile hidden Markov models (ipHMM) where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB). Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD). Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to InterPreTS (Interaction Prediction through Tertiary Structure), an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure. Conclusions We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on the web at http://liao.cis.udel.edu/pub/svdsvm. Implemented in Matlab and supported on Linux and MS Windows. PMID:21034480

High throughput detection of antibody self-interaction by bio-layer interferometry.

PubMed

Sun, Tingwan; Reid, Felicia; Liu, Yuqi; Cao, Yuan; Estep, Patricia; Nauman, Claire; Xu, Yingda

2013-01-01

Self-interaction of an antibody may lead to aggregation, low solubility or high viscosity. Rapid identification of highly developable leads remains challenging, even though progress has been made with the introduction of techniques such as self-interaction chromatography (SIC) and cross-interaction chromatography (CIC). Here, we report a high throughput method to detect antibody clone self-interaction (CSI) using bio-layer interferometry (BLI) technology. Antibodies with strong self-interaction responses in the CSI-BLI assay also show delayed retention times in SIC and CIC. This method allows hundreds of candidates to be screened in a matter of hours with minimal material consumption.

Interactive Social Neuroscience to Study Autism Spectrum Disorder

PubMed Central

Rolison, Max J.; Naples, Adam J.; McPartland, James C.

2015-01-01

Individuals with autism spectrum disorder (ASD) demonstrate difficulty with social interactions and relationships, but the neural mechanisms underlying these difficulties remain largely unknown. While social difficulties in ASD are most apparent in the context of interactions with other people, most neuroscience research investigating ASD have provided limited insight into the complex dynamics of these interactions. The development of novel, innovative “interactive social neuroscience” methods to study the brain in contexts with two interacting humans is a necessary advance for ASD research. Studies applying an interactive neuroscience approach to study two brains engaging with one another have revealed significant differences in neural processes during interaction compared to observation in brain regions that are implicated in the neuropathology of ASD. Interactive social neuroscience methods are crucial in clarifying the mechanisms underlying the social and communication deficits that characterize ASD. PMID:25745371

Interactive social neuroscience to study autism spectrum disorder.

PubMed

Rolison, Max J; Naples, Adam J; McPartland, James C

2015-03-01

Individuals with autism spectrum disorder (ASD) demonstrate difficulty with social interactions and relationships, but the neural mechanisms underlying these difficulties remain largely unknown. While social difficulties in ASD are most apparent in the context of interactions with other people, most neuroscience research investigating ASD have provided limited insight into the complex dynamics of these interactions. The development of novel, innovative "interactive social neuroscience" methods to study the brain in contexts with two interacting humans is a necessary advance for ASD research. Studies applying an interactive neuroscience approach to study two brains engaging with one another have revealed significant differences in neural processes during interaction compared to observation in brain regions that are implicated in the neuropathology of ASD. Interactive social neuroscience methods are crucial in clarifying the mechanisms underlying the social and communication deficits that characterize ASD.

Computational Determination of the Effects of Bacteriophage Bacteriophage Interactions in Human body.

PubMed

Mostafa, Marwa Mostafa; Nassef, Mohammad; Badr, Amr

2017-10-19

Chronic diseases are becoming more serious and widely spreading and this carries a heavy burden on doctors to deal with such patients. Although many of these diseases can be treated by bacteriophages, the situation is significantly dangerous in patients having concomitant more than one chronic disease, where conflicts between phages used in treating these diseases are very closer to happen. This research paper presents a method to detecting the Bacteriophage-Bacteriophage Interaction. This method is implemented based on Domain-Domain Interactions model and it was used to infer Domain-Domain Interactions between the bacteriophages injected in the human body at the same time. By testing the method over bacteriophages that are used to treat tuberculosis, salmonella and virulent E.coli, many interactions have been inferred and detected between these bacteriophages. Several effects were detected for the resulted interactions such as: playing a role in DNA repair such as non-homologous end joining, playing a role in DNA replication, playing a role in the interaction between the immune system and the tumor cells and playing a role in the stiff man syndrome. We revised all patents relating to bacteriophage bacteriophage interactions and phage therapy. The proposed method is developed to help doctors to realize the effect of simultaneously injecting different bacteriophages into the human body to treat different diseases. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Identifying functional cancer-specific miRNA-mRNA interactions in testicular germ cell tumor.

PubMed

Sedaghat, Nafiseh; Fathy, Mahmood; Modarressi, Mohammad Hossein; Shojaie, Ali

2016-09-07

Testicular cancer is the most common cancer in men aged between 15 and 35 and more than 90% of testicular neoplasms are originated at germ cells. Recent research has shown the impact of microRNAs (miRNAs) in different types of cancer, including testicular germ cell tumor (TGCT). MicroRNAs are small non-coding RNAs which affect the development and progression of cancer cells by binding to mRNAs and regulating their expressions. The identification of functional miRNA-mRNA interactions in cancers, i.e. those that alter the expression of genes in cancer cells, can help delineate post-regulatory mechanisms and may lead to new treatments to control the progression of cancer. A number of sequence-based methods have been developed to predict miRNA-mRNA interactions based on the complementarity of sequences. While necessary, sequence complementarity is, however, not sufficient for presence of functional interactions. Alternative methods have thus been developed to refine the sequence-based interactions using concurrent expression profiles of miRNAs and mRNAs. This study aims to find functional cancer-specific miRNA-mRNA interactions in TGCT. To this end, the sequence-based predicted interactions are first refined using an ensemble learning method, based on two well-known methods of learning miRNA-mRNA interactions, namely, TaLasso and GenMiR++. Additional functional analyses were then used to identify a subset of interactions to be most likely functional and specific to TGCT. The final list of 13 miRNA-mRNA interactions can be potential targets for identifying TGCT-specific interactions and future laboratory experiments to develop new therapies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improving Method-in-Use through Classroom Observation

ERIC Educational Resources Information Center

Nunn, Roger

2011-01-01

Method-in-use (Nunn, Describing classroom interaction in intercultural curricular research and development, University of Reading, 1996, International Review of Applied Linguistics in Language Teaching 37: 23-42, 1999) is a description of the method actually being enacted through classroom interaction in a particular context. The description is…

Energetics of protein-DNA interactions.

PubMed

Donald, Jason E; Chen, William W; Shakhnovich, Eugene I

2007-01-01

Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that theoretical models describe the macromolecular interaction energetics accurately. While several methods have been proposed, there has not been a careful comparison of how well the different methods are able to predict biologically important quantities such as the correct DNA binding sequence, total binding free energy and free energy changes caused by DNA mutation. In addition to carrying out the comparison, we present two important theoretical models developed initially in protein folding that have not yet been tried on protein-DNA interactions. In the process, we find that the results of these knowledge-based potentials show a strong dependence on the interaction distance and the derivation method. Finally, we present a knowledge-based potential that gives comparable or superior results to the best of the other methods, including the molecular mechanics force field AMBER99.

An unsupervised method for quantifying the behavior of paired animals

NASA Astrophysics Data System (ADS)

Klibaite, Ugne; Berman, Gordon J.; Cande, Jessica; Stern, David L.; Shaevitz, Joshua W.

2017-02-01

Behaviors involving the interaction of multiple individuals are complex and frequently crucial for an animal’s survival. These interactions, ranging across sensory modalities, length scales, and time scales, are often subtle and difficult to characterize. Contextual effects on the frequency of behaviors become even more difficult to quantify when physical interaction between animals interferes with conventional data analysis, e.g. due to visual occlusion. We introduce a method for quantifying behavior in fruit fly interaction that combines high-throughput video acquisition and tracking of individuals with recent unsupervised methods for capturing an animal’s entire behavioral repertoire. We find behavioral differences between solitary flies and those paired with an individual of the opposite sex, identifying specific behaviors that are affected by social and spatial context. Our pipeline allows for a comprehensive description of the interaction between two individuals using unsupervised machine learning methods, and will be used to answer questions about the depth of complexity and variance in fruit fly courtship.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process

PubMed Central

Chen, Yang; Zhang, Michael Q.

2018-01-01

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. PMID:29440282

Ab initio O(N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems

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

Orimoto, Yuuichi; Xie, Peng; Liu, Kai

2015-03-14

An Elongation-counterpoise (ELG-CP) method was developed for performing accurate and efficient interaction energy analysis and correcting the basis set superposition error (BSSE) in biosystems. The method was achieved by combining our developed ab initio O(N) elongation method with the conventional counterpoise method proposed for solving the BSSE problem. As a test, the ELG-CP method was applied to the analysis of the DNAs’ inter-strands interaction energies with respect to the alkylation-induced base pair mismatch phenomenon that causes a transition from G⋯C to A⋯T. It was found that the ELG-CP method showed high efficiency (nearly linear-scaling) and high accuracy with a negligiblymore » small energy error in the total energy calculations (in the order of 10{sup −7}–10{sup −8} hartree/atom) as compared with the conventional method during the counterpoise treatment. Furthermore, the magnitude of the BSSE was found to be ca. −290 kcal/mol for the calculation of a DNA model with 21 base pairs. This emphasizes the importance of BSSE correction when a limited size basis set is used to study the DNA models and compare small energy differences between them. In this work, we quantitatively estimated the inter-strands interaction energy for each possible step in the transition process from G⋯C to A⋯T by the ELG-CP method. It was found that the base pair replacement in the process only affects the interaction energy for a limited area around the mismatch position with a few adjacent base pairs. From the interaction energy point of view, our results showed that a base pair sliding mechanism possibly occurs after the alkylation of guanine to gain the maximum possible number of hydrogen bonds between the bases. In addition, the steps leading to the A⋯T replacement accompanied with replications were found to be unfavorable processes corresponding to ca. 10 kcal/mol loss in stabilization energy. The present study indicated that the ELG-CP method is promising for performing effective interaction energy analyses in biosystems.« less

Reconstituting protein interaction networks using parameter-dependent domain-domain interactions

PubMed Central

2013-01-01

Background We can describe protein-protein interactions (PPIs) as sets of distinct domain-domain interactions (DDIs) that mediate the physical interactions between proteins. Experimental data confirm that DDIs are more consistent than their corresponding PPIs, lending support to the notion that analyses of DDIs may improve our understanding of PPIs and lead to further insights into cellular function, disease, and evolution. However, currently available experimental DDI data cover only a small fraction of all existing PPIs and, in the absence of structural data, determining which particular DDI mediates any given PPI is a challenge. Results We present two contributions to the field of domain interaction analysis. First, we introduce a novel computational strategy to merge domain annotation data from multiple databases. We show that when we merged yeast domain annotations from six annotation databases we increased the average number of domains per protein from 1.05 to 2.44, bringing it closer to the estimated average value of 3. Second, we introduce a novel computational method, parameter-dependent DDI selection (PADDS), which, given a set of PPIs, extracts a small set of domain pairs that can reconstruct the original set of protein interactions, while attempting to minimize false positives. Based on a set of PPIs from multiple organisms, our method extracted 27% more experimentally detected DDIs than existing computational approaches. Conclusions We have provided a method to merge domain annotation data from multiple sources, ensuring large and consistent domain annotation for any given organism. Moreover, we provided a method to extract a small set of DDIs from the underlying set of PPIs and we showed that, in contrast to existing approaches, our method was not biased towards DDIs with low or high occurrence counts. Finally, we used these two methods to highlight the influence of the underlying annotation density on the characteristics of extracted DDIs. Although increased annotations greatly expanded the possible DDIs, the lack of knowledge of the true biological false positive interactions still prevents an unambiguous assignment of domain interactions responsible for all protein network interactions. Executable files and examples are given at: http://www.bhsai.org/downloads/padds/ PMID:23651452

Theoretical study on the polar hydrogen-π (Hp-π) interactions between protein side chains

PubMed Central

2013-01-01

Background In the study of biomolecular structures and interactions the polar hydrogen-π bonds (Hp-π) are an extensive molecular interaction type. In proteins 11 of 20 natural amino acids and in DNA (or RNA) all four nucleic acids are involved in this type interaction. Results The Hp-π in proteins are studied using high level QM method CCSD/6-311 + G(d,p) + H-Bq (ghost hydrogen basis functions) in vacuum and in solutions (water, acetonitrile, and cyclohexane). Three quantum chemical methods (B3LYP, CCSD, and CCSD(T)) and three basis sets (6-311 + G(d,p), TZVP, and cc-pVTZ) are compared. The Hp-π donors include R2NH, RNH2, ROH, and C6H5OH; and the acceptors are aromatic amino acids, peptide bond unit, and small conjugate π-groups. The Hp-π interaction energies of four amino acid pairs (Ser-Phe, Lys-Phe, His-Phe, and Tyr-Phe) are quantitatively calculated. Conclusions Five conclusion points are abstracted from the calculation results. (1) The common DFT method B3LYP fails in describing the Hp-π interactions. On the other hand, CCSD/6-311 + G(d,p) plus ghost atom H-Bq can yield better results, very close to the state-of-the-art method CCSD(T)/cc-pVTZ. (2) The Hp-π interactions are point to π-plane interactions, possessing much more interaction conformations and broader energy range than other interaction types, such as common hydrogen bond and electrostatic interactions. (3) In proteins the Hp-π interaction energies are in the range 10 to 30 kJ/mol, comparable or even larger than common hydrogen bond interactions. (4) The bond length of Hp-π interactions are in the region from 2.30 to 3.00 Å at the perpendicular direction to the π-plane, much longer than the common hydrogen bonds (~1.9 Å). (5) Like common hydrogen bond interactions, the Hp-π interactions are less affected by solvation effects. PMID:23705926

A Kernel Machine Method for Detecting Effects of Interaction Between Multidimensional Variable Sets: An Imaging Genetics Application

PubMed Central

Ge, Tian; Nichols, Thomas E.; Ghosh, Debashis; Mormino, Elizabeth C.

2015-01-01

Measurements derived from neuroimaging data can serve as markers of disease and/or healthy development, are largely heritable, and have been increasingly utilized as (intermediate) phenotypes in genetic association studies. To date, imaging genetic studies have mostly focused on discovering isolated genetic effects, typically ignoring potential interactions with non-genetic variables such as disease risk factors, environmental exposures, and epigenetic markers. However, identifying significant interaction effects is critical for revealing the true relationship between genetic and phenotypic variables, and shedding light on disease mechanisms. In this paper, we present a general kernel machine based method for detecting effects of interaction between multidimensional variable sets. This method can model the joint and epistatic effect of a collection of single nucleotide polymorphisms (SNPs), accommodate multiple factors that potentially moderate genetic influences, and test for nonlinear interactions between sets of variables in a flexible framework. As a demonstration of application, we applied the method to data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) to detect the effects of the interactions between candidate Alzheimer's disease (AD) risk genes and a collection of cardiovascular disease (CVD) risk factors, on hippocampal volume measurements derived from structural brain magnetic resonance imaging (MRI) scans. Our method identified that two genes, CR1 and EPHA1, demonstrate significant interactions with CVD risk factors on hippocampal volume, suggesting that CR1 and EPHA1 may play a role in influencing AD-related neurodegeneration in the presence of CVD risks. PMID:25600633

RFDT: A Rotation Forest-based Predictor for Predicting Drug-Target Interactions Using Drug Structure and Protein Sequence Information.

PubMed

Wang, Lei; You, Zhu-Hong; Chen, Xing; Yan, Xin; Liu, Gang; Zhang, Wei

2018-01-01

Identification of interaction between drugs and target proteins plays an important role in discovering new drug candidates. However, through the experimental method to identify the drug-target interactions remain to be extremely time-consuming, expensive and challenging even nowadays. Therefore, it is urgent to develop new computational methods to predict potential drugtarget interactions (DTI). In this article, a novel computational model is developed for predicting potential drug-target interactions under the theory that each drug-target interaction pair can be represented by the structural properties from drugs and evolutionary information derived from proteins. Specifically, the protein sequences are encoded as Position-Specific Scoring Matrix (PSSM) descriptor which contains information of biological evolutionary and the drug molecules are encoded as fingerprint feature vector which represents the existence of certain functional groups or fragments. Four benchmark datasets involving enzymes, ion channels, GPCRs and nuclear receptors, are independently used for establishing predictive models with Rotation Forest (RF) model. The proposed method achieved the prediction accuracy of 91.3%, 89.1%, 84.1% and 71.1% for four datasets respectively. In order to make our method more persuasive, we compared our classifier with the state-of-theart Support Vector Machine (SVM) classifier. We also compared the proposed method with other excellent methods. Experimental results demonstrate that the proposed method is effective in the prediction of DTI, and can provide assistance for new drug research and development. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Application of Innovative P&E Method at Technical Universities in Slovakia

ERIC Educational Resources Information Center

Nemec, Miroslav; Krišták, Luboš; Hockicko, Peter; Danihelová, Zuzana; Velmovská, Klára

2017-01-01

The paper deals with innovative teaching methods at universities. The result of this effort is the interactive P&E method, whose main idea is the interactive work with students while solving problem tasks. The main aim of the given method is to change the students' position, by means of experiment analyses and qualitative tasks, from a passive…

Analyzing Interactions by an IIS-Map-Based Method in Face-to-Face Collaborative Learning: An Empirical Study

ERIC Educational Resources Information Center

Zheng, Lanqin; Yang, Kaicheng; Huang, Ronghuai

2012-01-01

This study proposes a new method named the IIS-map-based method for analyzing interactions in face-to-face collaborative learning settings. This analysis method is conducted in three steps: firstly, drawing an initial IIS-map according to collaborative tasks; secondly, coding and segmenting information flows into information items of IIS; thirdly,…

Experimental Methods for Protein Interaction Identification and Characterization

NASA Astrophysics Data System (ADS)

Uetz, Peter; Titz, Björn; Cagney, Gerard

There are dozens of methods for the detection of protein-protein interactions but they fall into a few broad categories. Fragment complementation assays such as the yeast two-hybrid (Y2H) system are based on split proteins that are functionally reconstituted by fusions of interacting proteins. Biophysical methods include structure determination and mass spectrometric (MS) identification of proteins in complexes. Biochemical methods include methods such as far western blotting and peptide arrays. Only the Y2H and protein complex purification combined with MS have been used on a larger scale. Due to the lack of data it is still difficult to compare these methods with respect to their efficiency and error rates. Current data does not favor any particular method and thus multiple experimental approaches are necessary to maximally cover the interactome of any target cell or organism.

Michael Sprague | NREL

Science.gov Websites

student, he developed a parallel spectral finite element method for treating the interaction of large mechanics of fluids, structures, and their interaction|Spectral finite-element methods for time-dependent

Numerical solution for the interaction of shock wave with laminar boundary layer in two-dimensional flow on a flat plate. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Landau, U.

1984-01-01

The finite difference computation method was investigated for solving problems of interaction between a shock wave and a laminar boundary layer, through solution of the complete Navier-Stokes equations. This method provided excellent solutions, was simple to perform and needed a relatively short solution time. A large number of runs for various flow conditions could be carried out from which the interaction characteristics and principal factors that influence interaction could be studied.

A computational study on the interaction between a vortex and a shock wave

NASA Technical Reports Server (NTRS)

Meadows, Kristine R.; Kumar, Ajay; Hussaini, M. Y.

1989-01-01

A computational study of two-dimensional shock vortex interaction is discussed in this paper. A second order upwind finite volume method is used to solve the Euler equations in conservation form. In this method, the shock wave is captured rather than fitted so that the cases where shock vortex interaction may cause secondary shocks can also be investigated. The effects of vortex strength on the computed flow and acoustic field generated by the interaction are qualitatively evaluated.

Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes.

PubMed

Uchikoga, Nobuyuki; Hirokawa, Takatsugu

2010-05-11

Protein-protein docking for proteins with large conformational changes was analyzed by using interaction fingerprints, one of the scales for measuring similarities among complex structures, utilized especially for searching near-native protein-ligand or protein-protein complex structures. Here, we have proposed a combined method for analyzing protein-protein docking by taking large conformational changes into consideration. This combined method consists of ensemble soft docking with multiple protein structures, refinement of complexes, and cluster analysis using interaction fingerprints and energy profiles. To test for the applicability of this combined method, various CaM-ligand complexes were reconstructed from the NMR structures of unbound CaM. For the purpose of reconstruction, we used three known CaM-ligands, namely, the CaM-binding peptides of cyclic nucleotide gateway (CNG), CaM kinase kinase (CaMKK) and the plasma membrane Ca2+ ATPase pump (PMCA), and thirty-one structurally diverse CaM conformations. For each ligand, 62000 CaM-ligand complexes were generated in the docking step and the relationship between their energy profiles and structural similarities to the native complex were analyzed using interaction fingerprint and RMSD. Near-native clusters were obtained in the case of CNG and CaMKK. The interaction fingerprint method discriminated near-native structures better than the RMSD method in cluster analysis. We showed that a combined method that includes the interaction fingerprint is very useful for protein-protein docking analysis of certain cases.

Detection of protein-protein interactions by ribosome display and protein in situ immobilisation.

PubMed

He, Mingyue; Liu, Hong; Turner, Martin; Taussig, Michael J

2009-12-31

We describe a method for identification of protein-protein interactions by combining two cell-free protein technologies, namely ribosome display and protein in situ immobilisation. The method requires only PCR fragments as the starting material, the target proteins being made through cell-free protein synthesis, either associated with their encoding mRNA as ribosome complexes or immobilised on a solid surface. The use of ribosome complexes allows identification of interacting protein partners from their attached coding mRNA. To demonstrate the procedures, we have employed the lymphocyte signalling proteins Vav1 and Grb2 and confirmed the interaction between Grb2 and the N-terminal SH3 domain of Vav1. The method has promise for library screening of pairwise protein interactions, down to the analytical level of individual domain or motif mapping.

Probing fibronectin–antibody interactions using AFM force spectroscopy and lateral force microscopy

PubMed Central

Kulik, Andrzej J; Lee, Kyumin; Pyka-Fościak, Grazyna; Nowak, Wieslaw

2015-01-01

Summary The first experiment showing the effects of specific interaction forces using lateral force microscopy (LFM) was demonstrated for lectin–carbohydrate interactions some years ago. Such measurements are possible under the assumption that specific forces strongly dominate over the non-specific ones. However, obtaining quantitative results requires the complex and tedious calibration of a torsional force. Here, a new and relatively simple method for the calibration of the torsional force is presented. The proposed calibration method is validated through the measurement of the interaction forces between human fibronectin and its monoclonal antibody. The results obtained using LFM and AFM-based classical force spectroscopies showed similar unbinding forces recorded at similar loading rates. Our studies verify that the proposed lateral force calibration method can be applied to study single molecule interactions. PMID:26114080

Construction of Interaction Layer on Socio-Environmental Simulation

NASA Astrophysics Data System (ADS)

Torii, Daisuke; Ishida, Toru

In this study, we propose a method to construct a system based on a legacy socio-environmental simulator which enables to design more realistic interaction models in socio-environmetal simulations. First, to provide a computational model suitable for agent interactions, an interaction layer is constructed and connected from outside of a legacy socio-environmental simulator. Next, to configure the agents interacting ability, connection description for controlling the flow of information in the connection area is provided. As a concrete example, we realized an interaction layer by Q which is a scenario description language and connected it to CORMAS, a socio-envirionmental simulator. Finally, we discuss the capability of our method, using the system, in the Fire-Fighter domain.

Thick-target transmission method for excitation functions of interaction cross sections

NASA Astrophysics Data System (ADS)

Aikawa, M.; Ebata, S.; Imai, S.

2016-09-01

We propose a method, called as thick-target transmission (T3) method, to obtain an excitation function of interaction cross sections. In an ordinal experiment to measure the excitation function of interaction cross sections by the transmission method, we need to change the beam energy for each cross section. In the T3 method, the excitation function is derived from the beam attenuations measured at the targets of different thicknesses without changing the beam energy. The advantage of the T3 method is the simplicity and availability for radioactive beams. To confirm the availability, we perform a simulation for the 12C + 27Al system with the PHITS code instead of actual experiments. Our results have large uncertainties but well reproduce the tendency of the experimental data.

Analysis of random structure-acoustic interaction problems using coupled boundary element and finite element methods

NASA Technical Reports Server (NTRS)

Mei, Chuh; Pates, Carl S., III

1994-01-01

A coupled boundary element (BEM)-finite element (FEM) approach is presented to accurately model structure-acoustic interaction systems. The boundary element method is first applied to interior, two and three-dimensional acoustic domains with complex geometry configurations. Boundary element results are very accurate when compared with limited exact solutions. Structure-interaction problems are then analyzed with the coupled FEM-BEM method, where the finite element method models the structure and the boundary element method models the interior acoustic domain. The coupled analysis is compared with exact and experimental results for a simplistic model. Composite panels are analyzed and compared with isotropic results. The coupled method is then extended for random excitation. Random excitation results are compared with uncoupled results for isotropic and composite panels.

Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions

PubMed Central

Yip, Kevin Y.; Gerstein, Mark

2009-01-01

Motivation: An important problem in systems biology is reconstructing complete networks of interactions between biological objects by extrapolating from a few known interactions as examples. While there are many computational techniques proposed for this network reconstruction task, their accuracy is consistently limited by the small number of high-confidence examples, and the uneven distribution of these examples across the potential interaction space, with some objects having many known interactions and others few. Results: To address this issue, we propose two computational methods based on the concept of training set expansion. They work particularly effectively in conjunction with kernel approaches, which are a popular class of approaches for fusing together many disparate types of features. Both our methods are based on semi-supervised learning and involve augmenting the limited number of gold-standard training instances with carefully chosen and highly confident auxiliary examples. The first method, prediction propagation, propagates highly confident predictions of one local model to another as the auxiliary examples, thus learning from information-rich regions of the training network to help predict the information-poor regions. The second method, kernel initialization, takes the most similar and most dissimilar objects of each object in a global kernel as the auxiliary examples. Using several sets of experimentally verified protein–protein interactions from yeast, we show that training set expansion gives a measurable performance gain over a number of representative, state-of-the-art network reconstruction methods, and it can correctly identify some interactions that are ranked low by other methods due to the lack of training examples of the involved proteins. Contact: mark.gerstein@yale.edu Availability: The datasets and additional materials can be found at http://networks.gersteinlab.org/tse. PMID:19015141

Application of viscous-inviscid interaction methods to transonic turbulent flows

NASA Technical Reports Server (NTRS)

Lee, D.; Pletcher, R. H.

1986-01-01

Two different viscous-inviscid interaction schemes were developed for the analysis of steady, turbulent, transonic, separated flows over axisymmetric bodies. The viscous and inviscid solutions are coupled through the displacement concept using a transpiration velocity approach. In the semi-inverse interaction scheme, the viscous and inviscid equations are solved in an explicitly separate manner and the displacement thickness distribution is iteratively updated by a simple coupling algorithm. In the simultaneous interaction method, local solutions of viscous and inviscid equations are treated simultaneously, and the displacement thickness is treated as an unknown and is obtained as a part of the solution through a global iteration procedure. The inviscid flow region is described by a direct finite-difference solution of a velocity potential equation in conservative form. The potential equation is solved on a numerically generated mesh by an approximate factorization (AF2) scheme in the semi-inverse interaction method and by a successive line overrelaxation (SLOR) scheme in the simultaneous interaction method. The boundary-layer equations are used for the viscous flow region. The continuity and momentum equations are solved inversely in a coupled manner using a fully implicit finite-difference scheme.

Multiple Interacting Risk Factors: On Methods for Allocating Risk Factor Interactions.

PubMed

Price, Bertram; MacNicoll, Michael

2015-05-01

A persistent problem in health risk analysis where it is known that a disease may occur as a consequence of multiple risk factors with interactions is allocating the total risk of the disease among the individual risk factors. This problem, referred to here as risk apportionment, arises in various venues, including: (i) public health management, (ii) government programs for compensating injured individuals, and (iii) litigation. Two methods have been described in the risk analysis and epidemiology literature for allocating total risk among individual risk factors. One method uses weights to allocate interactions among the individual risk factors. The other method is based on risk accounting axioms and finding an optimal and unique allocation that satisfies the axioms using a procedure borrowed from game theory. Where relative risk or attributable risk is the risk measure, we find that the game-theory-determined allocation is the same as the allocation where risk factor interactions are apportioned to individual risk factors using equal weights. Therefore, the apportionment problem becomes one of selecting a meaningful set of weights for allocating interactions among the individual risk factors. Equal weights and weights proportional to the risks of the individual risk factors are discussed. © 2015 Society for Risk Analysis.

Mapping the Small Molecule Interactome by Mass Spectrometry.

PubMed

Flaxman, Hope A; Woo, Christina M

2018-01-16

Mapping small molecule interactions throughout the proteome provides the critical structural basis for functional analysis of their impact on biochemistry. However, translation of mass spectrometry-based proteomics methods to directly profile the interaction between a small molecule and the whole proteome is challenging because of the substoichiometric nature of many interactions, the diversity of covalent and noncovalent interactions involved, and the subsequent computational complexity associated with their spectral assignment. Recent advances in chemical proteomics have begun fill this gap to provide a structural basis for the breadth of small molecule-protein interactions in the whole proteome. Innovations enabling direct characterization of the small molecule interactome include faster, more sensitive instrumentation coupled to chemical conjugation, enrichment, and labeling methods that facilitate detection and assignment. These methods have started to measure molecular interaction hotspots due to inherent differences in local amino acid reactivity and binding affinity throughout the proteome. Measurement of the small molecule interactome is producing structural insights and methods for probing and engineering protein biochemistry. Direct structural characterization of the small molecule interactome is a rapidly emerging area pushing new frontiers in biochemistry at the interface of small molecules and the proteome.

The E-music box: an empirical method for exploring the universal capacity for musical production and for social interaction through music.

PubMed

Novembre, Giacomo; Varlet, Manuel; Muawiyath, Shujau; Stevens, Catherine J; Keller, Peter E

2015-11-01

Humans are assumed to have a natural-universal-predisposition for making music and for musical interaction. Research in this domain is, however, typically conducted with musically trained individuals, and therefore confounded with expertise. Here, we present a rediscovered and updated invention-the E-music box-that we establish as an empirical method to investigate musical production and interaction in everyone. The E-music box transforms rotatory cyclical movements into pre-programmable digital musical output, with tempo varying according to rotation speed. The user's movements are coded as continuous oscillatory data, which can be analysed using linear or nonlinear analytical tools. We conducted a proof-of-principle experiment to demonstrate that, using this method, pairs of non-musically trained individuals can interact according to conventional musical practices (leader/follower roles and lower-pitch dominance). The results suggest that the E-music box brings 'active' and 'interactive' musical capacities within everyone's reach. We discuss the potential of this method for exploring the universal predisposition for music making and interaction in developmental and cross-cultural contexts, and for neurologic musical therapy and rehabilitation.

Study and selection of in vivo protein interactions by coupling bimolecular fluorescence complementation and flow cytometry.

PubMed

Morell, Montse; Espargaro, Alba; Aviles, Francesc Xavier; Ventura, Salvador

2008-01-01

We present a high-throughput approach to study weak protein-protein interactions by coupling bimolecular fluorescent complementation (BiFC) to flow cytometry (FC). In BiFC, the interaction partners (bait and prey) are fused to two rationally designed fragments of a fluorescent protein, which recovers its function upon the binding of the interacting proteins. For weak protein-protein interactions, the detected fluorescence is proportional to the interaction strength, thereby allowing in vivo discrimination between closely related binders with different affinity for the bait protein. FC provides a method for high-speed multiparametric data acquisition and analysis; the assay is simple, thousands of cells can be analyzed in seconds and, if required, selected using fluorescence-activated cell sorting (FACS). The combination of both methods (BiFC-FC) provides a technically straightforward, fast and highly sensitive method to validate weak protein interactions and to screen and identify optimal ligands in biologically synthesized libraries. Once plasmids encoding the protein fusions have been obtained, the evaluation of a specific interaction, the generation of a library and selection of active partners using BiFC-FC can be accomplished in 5 weeks.

An accurate cost effective DFT approach to study the sensing behaviour of polypyrrole towards nitrate ions in gas and aqueous phases.

PubMed

Wasim, Fatima; Mahmood, Tariq; Ayub, Khurshid

2016-07-28

Density functional theory (DFT) calculations have been performed to study the response of polypyrrole towards nitrate ions in gas and aqueous phases. First, an accurate estimate of interaction energies is obtained by methods calibrated against the gold standard CCSD(T) method. Then, a number of low cost DFT methods are also evaluated for their ability to accurately estimate the binding energies of polymer-nitrate complexes. The low cost methods evaluated here include dispersion corrected potential (DCP), Grimme's D3 correction, counterpoise correction of the B3LYP method, and Minnesota functionals (M05-2X). The interaction energies calculated using the counterpoise (CP) correction and DCP methods at the B3LYP level are in better agreement with the interaction energies calculated using the calibrated methods. The interaction energies of an infinite polymer (polypyrrole) with nitrate ions are calculated by a variety of low cost methods in order to find the associated errors. The electronic and spectroscopic properties of polypyrrole oligomers nPy (where n = 1-9) and nPy-NO3(-) complexes are calculated, and then extrapolated for an infinite polymer through a second degree polynomial fit. Charge analysis, frontier molecular orbital (FMO) analysis and density of state studies also reveal the sensing ability of polypyrrole towards nitrate ions. Interaction energies, charge analysis and density of states analyses illustrate that the response of polypyrrole towards nitrate ions is considerably reduced in the aqueous medium (compared to the gas phase).

Human-computer interface

DOEpatents

Anderson, Thomas G.

2004-12-21

The present invention provides a method of human-computer interfacing. Force feedback allows intuitive navigation and control near a boundary between regions in a computer-represented space. For example, the method allows a user to interact with a virtual craft, then push through the windshield of the craft to interact with the virtual world surrounding the craft. As another example, the method allows a user to feel transitions between different control domains of a computer representation of a space. The method can provide for force feedback that increases as a user's locus of interaction moves near a boundary, then perceptibly changes (e.g., abruptly drops or changes direction) when the boundary is traversed.

An inviscid-viscous interaction approach to the calculation of dynamic stall initiation on airfoils

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

Cebeci, T.; Platzer, M.F.; Jang, H.M.

An interactive boundary-layer method is described for computing unsteady incompressible flow over airfoils, including the initiation of dynamic stall. The inviscid unsteady panel method developed by Platzer and Teng is extended to include viscous effects. The solutions of the boundary-layer equations are obtained with an inverse finite-difference method employing an interaction law based on the Hilbert integral, and the algebraic eddy-viscosity formulation of Cebeci and Smith. The method is applied to airfoils subject to periodic and ramp-type motions and its abilities are examined for a range of angles of attack, reduced frequency, and pitch rate.

LWIR and VLWIR detectors development at SOFRADIR for space applications

NASA Astrophysics Data System (ADS)

Terrier, Bertrand; Delannoy, Anne; Chorier, Philippe; Maillard, Magalie; Rubaldo, Laurent

2010-10-01

SOFRADIR is one of the leading companies involved in the development and manufacturing of infrared detectors. Its offer covers the infrared spectrum from visible range (0.4 μm) up to very long wavelength range (15 μm). The need in this last field is driven by space activities, especially by meteorological instruments using imagery or spectrometry. In the frame of Meteosat Third Generation mission, ESA has launched pre-development activities to address the critical equipments for risk reduction. VLWIR detectors for FCI and IRS have been considered as challenging ones and thus SOFRADIR has been involved for manufacturing and testing 2D arrays with long cut-off wavelength (14.9μm at 50K) in order to evaluate their compliance to MTG requirements as far as dark current behaviour, quantum efficiency, photoresponse uniformity, spatial response, operability and reliability are concerned. In parallel, trends of space and tactical applications call for dark current reduction technology in order to improve systems performances in terms of operating temperature and signal to noise ratio. In the frame of its common laboratory DEFIR with CEA-LETI, Sofradir has developed a new MCT p on n technology to answer this need. First demonstrations were made with success (640x512, pitch 15μm and cut-off 9.5μm) and Sofradir is now industrializing this technology in particular for tactical application. Thanks to the communality between space and tactical activity at Sofradir, these results will benefit advantageously also to space activity. In this paper, we present a review of latest Sofradir results concerning LWIR and VLWIR technology. In particular, latest data, concerning development and characterization of generic VLWIR technology up to 15 μm cut-off wavelength, are presented as well as data concerning the promising p on n LWIR technology.

Accurate ab initio calculations which demonstrate a 3 Pi u ground state for Al2

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.; Taylor, Peter R.; Walch, Stephen P.

1986-01-01

The spectroscopic parameters and separations between the three low-lying X 3 Pi u, A 3 Sigma g -, and a 1 Sigma g + states of Al2 are studied as a function of both the one-particle and n-particle basis set. Approximate correlation treatments are calibrated against full Cl calculations correlating the six valence electrons in a double-zeta plus two d-function basis set. Since the CASSCF/MRCI 3 Pi u to 3 Sigma g - separation is in excellent agreement wtih the FCI value, the MRCI calculations were carried out in an extended (20s13p6d4f)/(6s5p3d2f) gaussian basis. Including a small correction for relativistic effects, the best estimate is that 3 Sigma g - state lies 174/cm above the 3 Pi u ground state. The 1 Sigma g + state lies at least 2000/cm higher in energy. At the CPF level, inclusion of 2s and 2p correlation has little effect on D sub e, reduces T sub e by only 26/cm, and shortens the bond lengths by about 0.02 a sub o. Further strong support for a 3 Pi u ground state comes from the experimental absorption spectra, since both observed transitions can be convincingly assigned as 3 Pi u yields 3 Pi g. The (2) 3 Pi g state is observed to be sensitive to the level of correlation treatment, and to have its minimum shifted to shorter rho values, such that the strongest experimental absorption peak probably corresponds to the 0 yields 2 transition.

Prediction of Heterodimeric Protein Complexes from Weighted Protein-Protein Interaction Networks Using Novel Features and Kernel Functions

PubMed Central

Ruan, Peiying; Hayashida, Morihiro; Maruyama, Osamu; Akutsu, Tatsuya

2013-01-01

Since many proteins express their functional activity by interacting with other proteins and forming protein complexes, it is very useful to identify sets of proteins that form complexes. For that purpose, many prediction methods for protein complexes from protein-protein interactions have been developed such as MCL, MCODE, RNSC, PCP, RRW, and NWE. These methods have dealt with only complexes with size of more than three because the methods often are based on some density of subgraphs. However, heterodimeric protein complexes that consist of two distinct proteins occupy a large part according to several comprehensive databases of known complexes. In this paper, we propose several feature space mappings from protein-protein interaction data, in which each interaction is weighted based on reliability. Furthermore, we make use of prior knowledge on protein domains to develop feature space mappings, domain composition kernel and its combination kernel with our proposed features. We perform ten-fold cross-validation computational experiments. These results suggest that our proposed kernel considerably outperforms the naive Bayes-based method, which is the best existing method for predicting heterodimeric protein complexes. PMID:23776458

Gene-Based Testing of Interactions in Association Studies of Quantitative Traits

PubMed Central

Ma, Li; Clark, Andrew G.; Keinan, Alon

2013-01-01

Various methods have been developed for identifying gene–gene interactions in genome-wide association studies (GWAS). However, most methods focus on individual markers as the testing unit, and the large number of such tests drastically erodes statistical power. In this study, we propose novel interaction tests of quantitative traits that are gene-based and that confer advantage in both statistical power and biological interpretation. The framework of gene-based gene–gene interaction (GGG) tests combine marker-based interaction tests between all pairs of markers in two genes to produce a gene-level test for interaction between the two. The tests are based on an analytical formula we derive for the correlation between marker-based interaction tests due to linkage disequilibrium. We propose four GGG tests that extend the following P value combining methods: minimum P value, extended Simes procedure, truncated tail strength, and truncated P value product. Extensive simulations point to correct type I error rates of all tests and show that the two truncated tests are more powerful than the other tests in cases of markers involved in the underlying interaction not being directly genotyped and in cases of multiple underlying interactions. We applied our tests to pairs of genes that exhibit a protein–protein interaction to test for gene-level interactions underlying lipid levels using genotype data from the Atherosclerosis Risk in Communities study. We identified five novel interactions that are not evident from marker-based interaction testing and successfully replicated one of these interactions, between SMAD3 and NEDD9, in an independent sample from the Multi-Ethnic Study of Atherosclerosis. We conclude that our GGG tests show improved power to identify gene-level interactions in existing, as well as emerging, association studies. PMID:23468652

Simple F Test Reveals Gene-Gene Interactions in Case-Control Studies

PubMed Central

Chen, Guanjie; Yuan, Ao; Zhou, Jie; Bentley, Amy R.; Adeyemo, Adebowale; Rotimi, Charles N.

2012-01-01

Missing heritability is still a challenge for Genome Wide Association Studies (GWAS). Gene-gene interactions may partially explain this residual genetic influence and contribute broadly to complex disease. To analyze the gene-gene interactions in case-control studies of complex disease, we propose a simple, non-parametric method that utilizes the F-statistic. This approach consists of three steps. First, we examine the joint distribution of a pair of SNPs in cases and controls separately. Second, an F-test is used to evaluate the ratio of dependence in cases to that of controls. Finally, results are adjusted for multiple tests. This method was used to evaluate gene-gene interactions that are associated with risk of Type 2 Diabetes among African Americans in the Howard University Family Study. We identified 18 gene-gene interactions (P < 0.0001). Compared with the commonly-used logistical regression method, we demonstrate that the F-ratio test is an efficient approach to measuring gene-gene interactions, especially for studies with limited sample size. PMID:22837643

The Delphi Method Online: Medical Expert Consensus Via the Internet

PubMed Central

Cam, Kenneth M.; McKnight, Patrick E.; Doctor, Jason N.

2002-01-01

Delphi is an expert consensus method. The theory behind the Delphi method is that the interaction of experts may lead to a reduction in individual bias. We have developed software that carries out all aspects of the Delphi method via the Internet. The Delphi method online consists of three components: 1) authorship, 2) interactive polling, and 3) reporting/results. We hope that researchers use this tool in future medical expert systems.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.

PubMed

Djekidel, Mohamed Nadhir; Chen, Yang; Zhang, Michael Q

2018-02-12

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. © 2018 Djekidel et al.; Published by Cold Spring Harbor Laboratory Press.

Virtual standardized patients: an interactive method to examine variation in depression care among primary care physicians

PubMed Central

Hooper, Lisa M.; Weinfurt, Kevin P.; Cooper, Lisa A.; Mensh, Julie; Harless, William; Kuhajda, Melissa C.; Epstein, Steven A.

2009-01-01

Background Some primary care physicians provide less than optimal care for depression (Kessler et al., Journal of the American Medical Association 291, 2581–90, 2004). However, the literature is not unanimous on the best method to use in order to investigate this variation in care. To capture variations in physician behaviour and decision making in primary care settings, 32 interactive CD-ROM vignettes were constructed and tested. Aim and method The primary aim of this methods-focused paper was to review the extent to which our study method – an interactive CD-ROM patient vignette methodology – was effective in capturing variation in physician behaviour. Specifically, we examined the following questions: (a) Did the interactive CD-ROM technology work? (b) Did we create believable virtual patients? (c) Did the research protocol enable interviews (data collection) to be completed as planned? (d) To what extent was the targeted study sample size achieved? and (e) Did the study interview protocol generate valid and reliable quantitative data and rich, credible qualitative data? Findings Among a sample of 404 randomly selected primary care physicians, our voice-activated interactive methodology appeared to be effective. Specifically, our methodology – combining interactive virtual patient vignette technology, experimental design, and expansive open-ended interview protocol – generated valid explanations for variations in primary care physician practice patterns related to depression care. PMID:20463864

A Combinatorial Approach to Detecting Gene-Gene and Gene-Environment Interactions in Family Studies

PubMed Central

Lou, Xiang-Yang; Chen, Guo-Bo; Yan, Lei; Ma, Jennie Z.; Mangold, Jamie E.; Zhu, Jun; Elston, Robert C.; Li, Ming D.

2008-01-01

Widespread multifactor interactions present a significant challenge in determining risk factors of complex diseases. Several combinatorial approaches, such as the multifactor dimensionality reduction (MDR) method, have emerged as a promising tool for better detecting gene-gene (G × G) and gene-environment (G × E) interactions. We recently developed a general combinatorial approach, namely the generalized multifactor dimensionality reduction (GMDR) method, which can entertain both qualitative and quantitative phenotypes and allows for both discrete and continuous covariates to detect G × G and G × E interactions in a sample of unrelated individuals. In this article, we report the development of an algorithm that can be used to study G × G and G × E interactions for family-based designs, called pedigree-based GMDR (PGMDR). Compared to the available method, our proposed method has several major improvements, including allowing for covariate adjustments and being applicable to arbitrary phenotypes, arbitrary pedigree structures, and arbitrary patterns of missing marker genotypes. Our Monte Carlo simulations provide evidence that the PGMDR method is superior in performance to identify epistatic loci compared to the MDR-pedigree disequilibrium test (PDT). Finally, we applied our proposed approach to a genetic data set on tobacco dependence and found a significant interaction between two taste receptor genes (i.e., TAS2R16 and TAS2R38) in affecting nicotine dependence. PMID:18834969

Emerging methods to study bacteriophage infection at the single-cell level.

PubMed

Dang, Vinh T; Sullivan, Matthew B

2014-01-01

Bacteria and their viruses (phages) are abundant across diverse ecosystems and their interactions influence global biogeochemical cycles and incidence of disease. Problematically, both classical and metagenomic methods insufficiently assess the host specificity of phages and phage-host infection dynamics in nature. Here we review emerging methods to study phage-host interaction and infection dynamics with a focus on those that offer resolution at the single-cell level. These methods leverage ever-increasing sequence data to identify virus signals from single-cell amplified genome datasets or to produce primers/probes to target particular phage-bacteria pairs (digital PCR and phageFISH), even in complex communities. All three methods enable study of phage infection of uncultured bacteria from environmental samples, while the latter also discriminates between phage-host interaction outcomes (e.g., lytic, chronic, lysogenic) in model systems. Together these techniques enable quantitative, spatiotemporal studies of phage-bacteria interactions from environmental samples of any ecosystem, which will help elucidate and predict the ecological and evolutionary impacts of specific phage-host pairings in nature.

A method for fast energy estimation and visualization of protein-ligand interaction

NASA Astrophysics Data System (ADS)

Tomioka, Nobuo; Itai, Akiko; Iitaka, Yoichi

1987-10-01

A new computational and graphical method for facilitating ligand-protein docking studies is developed on a three-dimensional computer graphics display. Various physical and chemical properties inside the ligand binding pocket of a receptor protein, whose structure is elucidated by X-ray crystal analysis, are calculated on three-dimensional grid points and are stored in advance. By utilizing those tabulated data, it is possible to estimate the non-bonded and electrostatic interaction energy and the number of possible hydrogen bonds between protein and ligand molecules in real time during an interactive docking operation. The method also provides a comprehensive visualization of the local environment inside the binding pocket. With this method, it becomes easier to find a roughly stable geometry of ligand molecules, and one can therefore make a rapid survey of the binding capability of many drug candidates. The method will be useful for drug design as well as for the examination of protein-ligand interactions.

Comparing Balance and Inverse Methods on Learning Conceptual and Procedural Knowledge in Equation Solving: A Cognitive Load Perspective

ERIC Educational Resources Information Center

Ngu, Bing Hiong; Phan, Huy Phuong

2016-01-01

We examined the use of balance and inverse methods in equation solving. The main difference between the balance and inverse methods lies in the operational line (e.g. +2 on both sides vs -2 becomes +2). Differential element interactivity favours the inverse method because the interaction between elements occurs on both sides of the equation for…

Teaching Undergraduate Marketing Students Using "Hot Seating through Puppetry": An Exploratory Study

ERIC Educational Resources Information Center

Pearce, Glenn; Hardiman, Nigel

2012-01-01

Changes in preferred methods of learning among many students in recent years have challenged educators to introduce more interactive and experiential teaching methods. "Hot seating"--where a person, such as an invited subject expert is interviewed by an audience--is a well-established interactive method of learning, but is often limited…

Explaining the Effectiveness of the Contrast Culture Method for Managing Interpersonal Interactions across Cultures

ERIC Educational Resources Information Center

Hiratsuka, Hiroyoshi; Suzuki, Hanako; Pusina, Alexis

2016-01-01

One of the current challenges in the field of intercultural education comes from the limited availability of training efficacy studies. The present study focused on explaining the effectiveness of the Contrast Culture Method (CCM) as an intercultural education method for managing interpersonal interactions across cultures between graduate…

Interactive Methods of Teaching Physics at Technical Universities

ERIC Educational Resources Information Center

Krišták, L'uboš; Nemec, Miroslav; Danihelová, Zuzana

2014-01-01

The paper presents results of "non-traditional" teaching of the basic course of Physics in the first year of study at the Technical University in Zvolen, specifically teaching via interactive method enriched with problem tasks and experiments. This paper presents also research results of the use of the given method in conditions of…

The Keyword Method and Children's Vocabulary Learning: An Interaction with Vocabulary Knowledge.

ERIC Educational Resources Information Center

McGivern, Julie E.; Levin, Joel R.

A study explored a potential aptitude-by-treatment interaction associated with the keyword method of vocabulary acquisition. This method is a two-stage mnemonic process whereby an unfamiliar term is first transformed into a familiar concrete stimulus and then a thematic relationship is created between the transformed stimulus and the information…

Analysis of the Interaction of Student Characteristics with Method in Micro-Teaching.

ERIC Educational Resources Information Center

Chavers, Katherine; And Others

A study examined the comparative effects on microteaching performance of (1) eight different methods of teacher training and (2) the interaction of method with student characteristics. Subjects, 71 enrollees in an educational psychology course, were randomly assigned to eight treatment groups (including one control group). Treatments consisted of…

Development of Support Service for Prevention and Recovery from Dementia and Science of Lethe

NASA Astrophysics Data System (ADS)

Otake, Mihoko

Purpose of this study is to explore service design method through the development of support service for prevention and recovery from dementia towards science of lethe. We designed and implemented conversation support service via coimagination method based on multiscale service design method, both were proposed by the author. Multiscale service model consists of tool, event, human, network, style and rule. Service elements at different scales are developed according to the model. Interactive conversation supported by coimagination method activates cognitive functions so as to prevent progress of dementia. This paper proposes theoretical bases for science of lethe. Firstly, relationship among coimagination method and three cognitive functions including division of attention, planning, episodic memory which decline at mild cognitive imparement. Secondly, thought state transition model during conversation which describes cognitive enhancement via interactive communication. Thirdly, Set Theoretical Measure of Interaction is proposed for evaluating effectiveness of conversation to cognitive enhancement. Simulation result suggests that the ideas which cannot be explored by each speaker are explored during interactive conversation. Finally, coimagination method compared with reminiscence therapy and its possibility for collaboration is discussed.

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.

PubMed

Jiang, Tingting; Raviram, Ramya; Snetkova, Valentina; Rocha, Pedro P; Proudhon, Charlotte; Badri, Sana; Bonneau, Richard; Skok, Jane A; Kluger, Yuval

2016-10-14

Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act in isolation of other interacting partners that also influence their impact. Indeed, the influence of multi-loci interactions remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these. Here we present a method that uses standard 4C-seq data to identify multi-loci interactions from the same cell. We demonstrate the feasibility of our method using 4C-seq data sets that identify known pairwise and novel tri-loci interactions involving the Tcrb and Igk antigen receptor enhancers. We further show that the three Igk enhancers, MiEκ, 3'Eκ and Edκ, interact simultaneously in this super-enhancer cluster, which add to our previous findings showing that loss of one element decreases interactions between all three elements as well as reducing their transcriptional output. These findings underscore the functional importance of simultaneous interactions and provide new insight into the relationship between enhancer elements. Our method opens the door for studying multi-loci interactions and their impact on gene regulation in other biological settings. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions

PubMed Central

Jiang, Tingting; Raviram, Ramya; Snetkova, Valentina; Rocha, Pedro P.; Proudhon, Charlotte; Badri, Sana; Bonneau, Richard; Skok, Jane A.; Kluger, Yuval

2016-01-01

Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act in isolation of other interacting partners that also influence their impact. Indeed, the influence of multi-loci interactions remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these. Here we present a method that uses standard 4C-seq data to identify multi-loci interactions from the same cell. We demonstrate the feasibility of our method using 4C-seq data sets that identify known pairwise and novel tri-loci interactions involving the Tcrb and Igk antigen receptor enhancers. We further show that the three Igk enhancers, MiEκ, 3′Eκ and Edκ, interact simultaneously in this super-enhancer cluster, which add to our previous findings showing that loss of one element decreases interactions between all three elements as well as reducing their transcriptional output. These findings underscore the functional importance of simultaneous interactions and provide new insight into the relationship between enhancer elements. Our method opens the door for studying multi-loci interactions and their impact on gene regulation in other biological settings. PMID:27439714

New methods for the analysis of the protein-solvent interface

NASA Astrophysics Data System (ADS)

Goodfellow, Julia M.; Pitt, William R.; Smart, Oliver S.; Williams, Mark A.

1995-09-01

The protein-solvent interface is complex and may include solvent channels and cavities as well as the normal surface water molecules. We describe several algorithms for investigating the intra- and inter-molecular interactions of proteins in general but with the aim of developing methods to accurately and definitively characterise the interactions of water and other small ligands with proteins. Specifically, we present the methods which underlie three programs (AQUARIUS2, HOLE and PRO_ACT) which can be used to to look at different aspects of these interactions.

Interactive computer methods for generating mineral-resource maps

USGS Publications Warehouse

Calkins, James Alfred; Crosby, A.S.; Huffman, T.E.; Clark, A.L.; Mason, G.T.; Bascle, R.J.

1980-01-01

Inasmuch as maps are a basic tool of geologists, the U.S. Geological Survey's CRIB (Computerized Resources Information Bank) was constructed so that the data it contains can be used to generate mineral-resource maps. However, by the standard methods used-batch processing and off-line plotting-the production of a finished map commonly takes 2-3 weeks. To produce computer-generated maps more rapidly, cheaply, and easily, and also to provide an effective demonstration tool, we have devised two related methods for plotting maps as alternatives to conventional batch methods. These methods are: 1. Quick-Plot, an interactive program whose output appears on a CRT (cathode-ray-tube) device, and 2. The Interactive CAM (Cartographic Automatic Mapping system), which combines batch and interactive runs. The output of the Interactive CAM system is final compilation (not camera-ready) paper copy. Both methods are designed to use data from the CRIB file in conjunction with a map-plotting program. Quick-Plot retrieves a user-selected subset of data from the CRIB file, immediately produces an image of the desired area on a CRT device, and plots data points according to a limited set of user-selected symbols. This method is useful for immediate evaluation of the map and for demonstrating how trial maps can be made quickly. The Interactive CAM system links the output of an interactive CRIB retrieval to a modified version of the CAM program, which runs in the batch mode and stores plotting instructions on a disk, rather than on a tape. The disk can be accessed by a CRT, and, thus, the user can view and evaluate the map output on a CRT immediately after a batch run, without waiting 1-3 days for an off-line plot. The user can, therefore, do most of the layout and design work in a relatively short time by use of the CRT, before generating a plot tape and having the map plotted on an off-line plotter.

Method of assessing parent-child grocery store purchasing interactions using a micro-camcorder.

PubMed

Calloway, Eric E; Roberts-Gray, Cindy; Ranjit, Nalini; Sweitzer, Sara J; McInnis, Katie A; Romo-Palafox, Maria J; Briley, Margaret E

2014-12-01

The purpose of this study was to assess the validity of using participant worn micro-camcorders (PWMC) to collect data on parent-child food and beverage purchasing interactions in the grocery store. Parent-child dyads (n = 32) were met at their usual grocery store and shopping time. Parents were mostly Caucasian (n = 27, 84.4%), mothers (n = 30, 93.8%). Children were 2-6 years old with 15 girls and 17 boys. A micro-camcorder was affixed to a baseball style hat worn by the child. The dyad proceeded to shop while being shadowed by an in-person observer. Video/audio data were coded for behavioral and environmental variables. The PWMC method was compared to in-person observation to assess sensitivity and relative validity for measuring parent-child interactions, and compared to receipt data to assess criterion validity for evaluating purchasing decisions. Inter-rater reliability for coding video/audio data collected using the PWMC method was also assessed. The PWMC method proved to be more sensitive than in-person observation revealing on average 1.4 (p < 0.01) more parent-child food and beverage purchasing interactions per shopping trip. Inter-rater reliability for coding PWMC data showed moderate to almost perfect agreement (Cohen's kappa = 0.461-0.937). The PWMC method was significantly correlated with in-person observation for measuring occurrences of parent-child food purchasing interactions (rho = 0.911, p < 0.01) and characteristics of those interactions (rho = 0.345-0.850, p < 0.01). Additionally, there was substantial agreement between the PWMC method and receipt data for measuring purchasing decisions (Cohen's kappa = 0.787). The PWMC method proved to be well suited to assess parent-child food and beverage purchasing interactions in the grocery store. Copyright © 2014 Elsevier Ltd. All rights reserved.

A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis.

PubMed

Tucker, George; Loh, Po-Ru; Berger, Bonnie

2013-10-04

Comprehensive protein-protein interaction (PPI) maps are a powerful resource for uncovering the molecular basis of genetic interactions and providing mechanistic insights. Over the past decade, high-throughput experimental techniques have been developed to generate PPI maps at proteome scale, first using yeast two-hybrid approaches and more recently via affinity purification combined with mass spectrometry (AP-MS). Unfortunately, data from both protocols are prone to both high false positive and false negative rates. To address these issues, many methods have been developed to post-process raw PPI data. However, with few exceptions, these methods only analyze binary experimental data (in which each potential interaction tested is deemed either observed or unobserved), neglecting quantitative information available from AP-MS such as spectral counts. We propose a novel method for incorporating quantitative information from AP-MS data into existing PPI inference methods that analyze binary interaction data. Our approach introduces a probabilistic framework that models the statistical noise inherent in observations of co-purifications. Using a sampling-based approach, we model the uncertainty of interactions with low spectral counts by generating an ensemble of possible alternative experimental outcomes. We then apply the existing method of choice to each alternative outcome and aggregate results over the ensemble. We validate our approach on three recent AP-MS data sets and demonstrate performance comparable to or better than state-of-the-art methods. Additionally, we provide an in-depth discussion comparing the theoretical bases of existing approaches and identify common aspects that may be key to their performance. Our sampling framework extends the existing body of work on PPI analysis using binary interaction data to apply to the richer quantitative data now commonly available through AP-MS assays. This framework is quite general, and many enhancements are likely possible. Fruitful future directions may include investigating more sophisticated schemes for converting spectral counts to probabilities and applying the framework to direct protein complex prediction methods.

Impact of abbreviated lecture with interactive mini-cases vs traditional lecture on student performance in the large classroom.

PubMed

Marshall, Leisa L; Nykamp, Diane L; Momary, Kathryn M

2014-12-15

To compare the impact of 2 different teaching and learning methods on student mastery of learning objectives in a pharmacotherapy module in the large classroom setting. Two teaching and learning methods were implemented and compared in a required pharmacotherapy module for 2 years. The first year, multiple interactive mini-cases with inclass individual assessment and an abbreviated lecture were used to teach osteoarthritis; a traditional lecture with 1 inclass case discussion was used to teach gout. In the second year, the same topics were used but the methods were flipped. Student performance on pre/post individual readiness assessment tests (iRATs), case questions, and subsequent examinations were compared each year by the teaching and learning method and then between years by topic for each method. Students also voluntarily completed a 20-item evaluation of the teaching and learning methods. Postpresentation iRATs were significantly higher than prepresentation iRATs for each topic each year with the interactive mini-cases; there was no significant difference in iRATs before and after traditional lecture. For osteoarthritis, postpresentation iRATs after interactive mini-cases in year 1 were significantly higher than postpresentation iRATs after traditional lecture in year 2; the difference in iRATs for gout per learning method was not significant. The difference between examination performance for osteoarthritis and gout was not significant when the teaching and learning methods were compared. On the student evaluations, 2 items were significant both years when answers were compared by teaching and learning method. Each year, students ranked their class participation higher with interactive cases than with traditional lecture, but both years they reported enjoying the traditional lecture format more. Multiple interactive mini-cases with an abbreviated lecture improved immediate mastery of learning objectives compared to a traditional lecture format, regardless of therapeutic topic, but did not improve student performance on subsequent examinations.

A scalable method for computing quadruplet wave-wave interactions

NASA Astrophysics Data System (ADS)

Van Vledder, Gerbrant

2017-04-01

Non-linear four-wave interactions are a key physical process in the evolution of wind generated ocean waves. The present generation operational wave models use the Discrete Interaction Approximation (DIA), but it accuracy is poor. It is now generally acknowledged that the DIA should be replaced with a more accurate method to improve predicted spectral shapes and derived parameters. The search for such a method is challenging as one should find a balance between accuracy and computational requirements. Such a method is presented here in the form of a scalable and adaptive method that can mimic both the time consuming exact Snl4 approach and the fast but inaccurate DIA, and everything in between. The method provides an elegant approach to improve the DIA, not by including more arbitrarily shaped wave number configurations, but by a mathematically consistent reduction of an exact method, viz. the WRT method. The adaptiveness is to adapt the abscissa of the locus integrand in relation to the magnitude of the known terms. The adaptiveness is extended to the highest level of the WRT method to select interacting wavenumber configurations in a hierarchical way in relation to their importance. This adaptiveness results in a speed-up of one to three orders of magnitude depending on the measure of accuracy. This definition of accuracy should not be expressed in terms of the quality of the transfer integral for academic spectra but rather in terms of wave model performance in a dynamic run. This has consequences for the balance between the required accuracy and the computational workload for evaluating these interactions. The performance of the scalable method on different scales is illustrated with results from academic spectra, simple growth curves to more complicated field cases using a 3G-wave model.

Empirical Methods for Identifying Specific Peptide-protein Interactions for Smart Reagent Development

DTIC Science & Technology

2012-09-01

orientated immobilization of proteins,” Biotechnology Progress, 22(2), 401-405 ( 2006 ). [26] J. M. Kogot, D. A. Sarkes , I. Val-Addo et al...Empirical Methods for Identifying Specific Peptide-protein Interactions for Smart Reagent Development by Joshua M. Kogot, Deborah A. Sarkes ...Peptide-protein Interactions for Smart Reagent Development Joshua M. Kogot, Deborah A. Sarkes , Dimitra N. Stratis-Cullum, and Paul M

State-of-the-art methods for computing the electromagnetic interaction of lightning with aircraft

NASA Technical Reports Server (NTRS)

Eriksen, F. J.; Perala, R. A.; Corbin, J. C., Jr.

1980-01-01

Nuclear electromagnetic pulse (NEMP) coupling codes and methods are evaluated and summarized. The differences between NEMP and lightning interaction with aircraft are discussed and critical parameters peculiar to lightning are examined.

Interactive Computer Lessons for Introductory Economics: Guided Inquiry-From Supply and Demand to Women in the Economy.

ERIC Educational Resources Information Center

Miller, John; Weil, Gordon

1986-01-01

The interactive feature of computers is used to incorporate a guided inquiry method of learning introductory economics, extending the Computer Assisted Instruction (CAI) method beyond drills. (Author/JDH)