Complex Multi-Chamber Airbag Performance Simulation Final Report CRADA No. TSB-961-94

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

Kay, Gregory; Kithil, Philip

The purpose of this small business CRADA was to evaluate the performance of new airbag concepts which were developed by the Advanced Safety Concepts, Inc. (ASCI). These new airbag concepts, if successful, could have major potential savings to society in terms of fewer injuries, lost time and lives.

Denoising embolic Doppler ultrasound signals using Dual Tree Complex Discrete Wavelet Transform.

PubMed

Serbes, Gorkem; Aydin, Nizamettin

2010-01-01

Early and accurate detection of asymptomatic emboli is important for monitoring of preventive therapy in stroke-prone patients. One of the problems in detection of emboli is the identification of an embolic signal caused by very small emboli. The amplitude of the embolic signal may be so small that advanced processing methods are required to distinguish these signals from Doppler signals arising from red blood cells. In this study instead of conventional discrete wavelet transform, the Dual Tree Complex Discrete Wavelet Transform was used for denoising embolic signals. Performances of both approaches were compared. Unlike the conventional discrete wavelet transform discrete complex wavelet transform is a shift invariant transform with limited redundancy. Results demonstrate that the Dual Tree Complex Discrete Wavelet Transform based denoising outperforms conventional discrete wavelet denoising. Approximately 8 dB improvement is obtained by using the Dual Tree Complex Discrete Wavelet Transform compared to the improvement provided by the conventional Discrete Wavelet Transform (less than 5 dB).

Binding energies and spatial structures of small carrier complexes in monolayer transition-metal dichalcogenides via diffusion Monte Carlo

DOE PAGES

Mayers, Matthew Z.; Berkelbach, Timothy C.; Hybertsen, Mark S.; ...

2015-10-09

Ground-state diffusion Monte Carlo is used to investigate the binding energies and intercarrier radial probability distributions of excitons, trions, and biexcitons in a variety of two-dimensional transition-metal dichalcogenide materials. We compare these results to approximate variational calculations, as well as to analogous Monte Carlo calculations performed with simplified carrier interaction potentials. Our results highlight the successes and failures of approximate approaches as well as the physical features that determine the stability of small carrier complexes in monolayer transition-metal dichalcogenide materials. In conclusion, we discuss points of agreement and disagreement with recent experiments.

Addressing geographic access barriers to emergency care services: a national ecologic study of hospitals in Brazil.

PubMed

Rocha, Thiago Augusto Hernandes; da Silva, Núbia Cristina; Amaral, Pedro Vasconcelos; Barbosa, Allan Claudius Queiroz; Rocha, João Victor Muniz; Alvares, Viviane; de Almeida, Dante Grapiuna; Thumé, Elaine; Thomaz, Erika Bárbara Abreu Fonseca; de Sousa Queiroz, Rejane Christine; de Souza, Marta Rovery; Lein, Adriana; Lopes, Daniel Paulino; Staton, Catherine A; Vissoci, João Ricardo Nickenig; Facchini, Luiz Augusto

2017-08-22

Unequal distribution of emergency care services is a critical barrier to be overcome to assure access to emergency and surgical care. Considering this context it was objective of the present work analyze geographic access barriers to emergency care services in Brazil. A secondary aim of the study is to define possible roles to be assumed by small hospitals in the Brazilian healthcare network to overcome geographic access challenges. The present work can be classified as a cross-sectional ecological study. To carry out the present study, data of all 5843 Brazilian hospitals were categorized among high complexity centers and small hospitals. The geographical access barriers were identified through the use of two-step floating catchment area method. Once concluded the previous step an evaluation using the Getis-Ord-Gi method was performed to identify spatial clusters of municipalities with limited access to high complexity centers but well covered by well-equipped small hospitals. The analysis of accessibility index of high complexity centers highlighted large portions of the country with nearly zero hospital beds by inhabitant. In contrast, it was possible observe a group of 1595 municipalities with high accessibility to small hospitals, simultaneously with a low coverage of high complexity centers. Among the 1595 municipalities with good accessibility to small hospitals, 74% (1183) were covered by small hospitals with at least 60% of minimum emergency service requirements. The spatial clusters analysis aggregated 589 municipalities with high values related to minimum emergency service requirements. Small hospitals in these 589 cities could promote the equity in access to emergency services benefiting more than eight million people. There is a spatial disequilibrium within the country with prominent gaps in the health care network for emergency services. Taking this challenge into consideration, small hospitals could be a possible solution and foster equity in access to emergency and surgical care. However more investments in are necessary to improve small hospitals capabilities to fill this gap.

Fabrication of the tetrathiafulvalene–2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane charge transfer complex with high crystallinity by eutectic melting method

NASA Astrophysics Data System (ADS)

Kim, Jueun; Kang, Youngjong; Lee, Jaejong

2018-06-01

We show that high crystallinity and charge transporting gain can be obtained in a noble donor–acceptor system (CT complex) composed of organic complex: tetrathiafulvalene–2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (TTF–F4TCNQ). The complex is small-gap organic metallic or semiconductor (less than 1 eV), and we predict having a high conductivity. We perform an approach to fabricate organic CT complex with high crystallinity by eutectic melting method. Our process is simple and shows crystal growth with improved crystallinity when combined with soft-lithography.

Effects of age, tenure, training, and job complexity on technical performance.

PubMed

Sparrow, P R; Davies, D R

1988-09-01

Effects on performance of age, tenure, training level, and job complexity were investigated in a cross-sectional study using a sample of 1,308 service engineers employed by a multinational office equipment company. Two measures of job performance were derived from production record data, one relating to the quality of servicing and the other to the speed with which services were completed. Scores for each performance measure were analyzed by analysis of variance. For the quality of servicing measure, a significant main effect of age and a significant Age X Training interaction were obtained, and the relation between age and job performance took the form of an inverted U. For the speed of servicing measure, the main effects of age, tenure, training level, and job complexity were significant and there were no significant interactions. However, for both performance measures, age accounted for only a very small proportion of the variance. We discuss these results with reference to the existing literature on age and technical job performance, and conclude that training, especially if it is recent, may moderate adverse effects of age on job performance.

An in vivo multiplexed small molecule screening platform

PubMed Central

Yang, Dian; Ogasawara, Daisuke; Dix, Melissa M.; Rogers, Zoë N.; Chuang, Chen-Hua; McFarland, Christopher D.; Chiou, Shin-Heng; Brown, J. Mark; Cravatt, Benjamin F.; Bogyo, Matthew; Winslow, Monte M.

2016-01-01

Phenotype-based small molecule screening is a powerful method to identify regulators of cellular function. However, such screens are generally performed in vitro using conditions that do not necessarily model complex physiological conditions or disease states. Here, we use molecular cell barcoding to enable direct in vivo phenotypic screening of libraries of small molecules. The multiplexed nature of this approach allows rapid in vivo analysis of hundreds to thousands of compounds. Using this platform, we screened >700 covalent inhibitors directed towards hydrolases for their effect on pancreatic cancer metastatic seeding. We identified multiple hits and confirmed the relevant target of one compound as the lipase ABHD6. Pharmacological and genetic studies confirmed the role of this enzyme as a regulator of metastatic fitness. Our results highlight the applicability of this multiplexed screening platform for investigating complex processes in vivo. PMID:27617390

Essential Requirements for Robust Signaling in Hfq Dependent Small RNA Networks

PubMed Central

Adamson, David N.; Lim, Han N.

2011-01-01

Bacteria possess networks of small RNAs (sRNAs) that are important for modulating gene expression. At the center of many of these sRNA networks is the Hfq protein. Hfq's role is to quickly match cognate sRNAs and target mRNAs from among a large number of possible combinations and anneal them to form duplexes. Here we show using a kinetic model that Hfq can efficiently and robustly achieve this difficult task by minimizing the sequestration of sRNAs and target mRNAs in Hfq complexes. This sequestration can be reduced by two non-mutually exclusive kinetic mechanisms. The first mechanism involves heterotropic cooperativity (where sRNA and target mRNA binding to Hfq is influenced by other RNAs bound to Hfq); this cooperativity can selectively decrease singly-bound Hfq complexes and ternary complexes with non-cognate sRNA-target mRNA pairs while increasing cognate ternary complexes. The second mechanism relies on frequent RNA dissociation enabling the rapid cycling of sRNAs and target mRNAs among different Hfq complexes; this increases the probability the cognate ternary complex forms before the sRNAs and target mRNAs degrade. We further demonstrate that the performance of sRNAs in isolation is not predictive of their performance within a network. These findings highlight the importance of experimentally characterizing duplex formation in physiologically relevant contexts with multiple RNAs competing for Hfq. The model will provide a valuable framework for guiding and interpreting these experiments. PMID:21876666

Minimus: a fast, lightweight genome assembler.

PubMed

Sommer, Daniel D; Delcher, Arthur L; Salzberg, Steven L; Pop, Mihai

2007-02-26

Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run. We have developed the Minimus assembler to address these issues, and tested it on a range of assembly problems. We show that Minimus performs well on several small assembly tasks, including the assembly of viral genomes, individual genes, and BAC clones. In addition, we evaluate Minimus' performance in assembling bacterial genomes in order to assess its suitability as a component of a larger assembly pipeline. We show that, unlike other software currently used for these tasks, Minimus produces significantly fewer assembly errors, at the cost of generating a more fragmented assembly. We find that for small genomes and other small assembly tasks, Minimus is faster and far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly suited to be a component of complex assembly pipelines. Minimus is released as an open-source software project and the code is available as part of the AMOS project at Sourceforge.

Simpler Alternative to an Optimum FQPSK-B Viterbi Receiver

NASA Technical Reports Server (NTRS)

Lee, Dennis; Simon, Marvin; Yan, Tsun-Yee

2003-01-01

A reduced-complexity alternative to an optimum FQPSK-B Viterbi receiver has been invented. As described, the reduction in complexity is achieved at the cost of only a small reduction in power performance [performance expressed in terms of a bit-energy-to-noise-energy ratio (Eb/N0) for a given bit-error rate (BER)]. The term "FQPSK-B" denotes a baseband-filtered version of Feher quadrature-phase-shift keying, which is a patented, bandwidth-efficient phase-modulation scheme named after its inventor. Heretofore, commercial FQPSK-B receivers have performed symbol-by-symbol detection, in each case using a detection filter (either the proprietary FQPSK-B filter for better BER performance, or a simple integrate-and-dump filter with degraded performance) and a sample-and-hold circuit.

The Arctic Regional Communications Small SATellite (ARCSAT)

NASA Technical Reports Server (NTRS)

Casas, Joseph; Kress, Martin; Sims, William; Spehn, Stephen; Jaeger, Talbot; Sanders, Devon

2013-01-01

Traditional satellite missions are extremely complex and expensive to design, build, test, launch and operate. Consequently many complementary operational, exploration and research satellite missions are being formulated as a growing part of the future space community capabilities using formations of small, distributed, simple to launch and inexpensive highly capable small scale satellites. The Arctic Regional Communications small SATellite (ARCSAT) initiative would launch a Mini-Satellite "Mothership" into Polar or Sun Sync low-earth-orbit (LEO). Once on orbit, the Mothership would perform orbital insertion of four internally stored independently maneuverable nanosatellites, each containing electronically steerable antennas and reconfigurable software-defined radios. Unlike the traditional geostationary larger complex satellite communication systems, this LEO communications system will be comprised of initially a five small satellite formation that can be later incrementally increased in the total number of satellites for additional data coverage. ARCSAT will provide significant enabling capabilities in the Arctic for autonomous voice and data communications relay, Maritime Domain Awareness (MDA), data-extraction from unattended sensors, and terrestrial Search & Rescue (SAR) beacon detection missions throughout the "data starved desert" of the Arctic Region.

Fast H.264/AVC FRExt intra coding using belief propagation.

PubMed

Milani, Simone

2011-01-01

In the H.264/AVC FRExt coder, the coding performance of Intra coding significantly overcomes the previous still image coding standards, like JPEG2000, thanks to a massive use of spatial prediction. Unfortunately, the adoption of an extensive set of predictors induces a significant increase of the computational complexity required by the rate-distortion optimization routine. The paper presents a complexity reduction strategy that aims at reducing the computational load of the Intra coding with a small loss in the compression performance. The proposed algorithm relies on selecting a reduced set of prediction modes according to their probabilities, which are estimated adopting a belief-propagation procedure. Experimental results show that the proposed method permits saving up to 60 % of the coding time required by an exhaustive rate-distortion optimization method with a negligible loss in performance. Moreover, it permits an accurate control of the computational complexity unlike other methods where the computational complexity depends upon the coded sequence.

A Performance Analysis of Long-term Acute-Care Hospitals Owned by Large, Multistate Investor-Owned Companies.

PubMed

Nayar, Preethy; Liu, Xinliang; McCue, Michael J

2016-01-01

This study provides a descriptive assessment of the operating performance of for-profit long-term acute-care hospitals owned by multistate, investor-owned companies (large FP LTCHs) compared with FP LTCHs owned by smaller FP companies (small FP LTCHs) and nonprofit LTCHs (NP LTCHs). The study used the Centers for Medicare & Medicaid Services cost report data for 290 LTCHs from 2010 through 2012 to compare the financial performance of large and small FP LTCHs and NP LTCHs. The study found that the median operating profit margin for large FP LTCHs was 8.06%, which was twice as high as that of the small FP LTCHs and NP LTCHs (4.78% and 2.80%, respectively). Larger size, serving a greater proportion of private pay and more complex patients and incurring lower operating expenses, including salary expenses, may account for the higher operating margin of the large FP LTCHs.

Development of Temperature Sensitive Paints for the Detection of Small Temperature Differences

NASA Technical Reports Server (NTRS)

Oglesby, Donald M.; Upchurch, Billy T.; Sealey, Bradley S.; Leighty, Bradley D.; Burkett, Cecil G., Jr.; Jalali, Amir

1997-01-01

Temperature sensitive paints (TSP s) have recently been used to detect small temperature differences on aerodynamic model surfaces. These types of applications impose stringent performance requirements on a paint system. The TSP s must operate over a broad temperature range, must be physically robust (cannot chip or peel), must be polishable to at least the smoothness of the model surface, and must have sufficient sensitivity to detect small temperature differences. TSP coatings based on the use of metal complexes in polymer binders were developed at NASA Langley Research Center which meet most of the requirements for detection of small temperature differences under severe environmental conditions.

Federal Reserve Could Improve the Efficiency of Bank Holding Company Inspections.

DTIC Science & Technology

1981-08-18

examiners have the essential qualifications and experience needed to perform many such tasks, and it would seem to require little additional effort...activities and where the holding company and subsidiary bank management are essentially the same. (See p. 32.) AGENCY COMMENTS The Federal Reserve has...consider- ably more complex and thus moe difficult to evaluate. Most small companies are tax shells and operate essentially as banks. The risk in small

The q-dependent detrended cross-correlation analysis of stock market

NASA Astrophysics Data System (ADS)

Zhao, Longfeng; Li, Wei; Fenu, Andrea; Podobnik, Boris; Wang, Yougui; Stanley, H. Eugene

2018-02-01

Properties of the q-dependent cross-correlation matrices of the stock market have been analyzed by using random matrix theory and complex networks. The correlation structures of the fluctuations at different magnitudes have unique properties. The cross-correlations among small fluctuations are much stronger than those among large fluctuations. The large and small fluctuations are dominated by different groups of stocks. We use complex network representation to study these q-dependent matrices and discover some new identities. By utilizing those q-dependent correlation-based networks, we are able to construct some portfolios of those more independent stocks which consistently perform better. The optimal multifractal order for portfolio optimization is around q  =  2 under the mean-variance portfolio framework, and q\\in[2, 6] under the expected shortfall criterion. These results have deepened our understanding regarding the collective behavior of the complex financial system.

Neutron Polarization Analysis for Biphasic Solvent Extraction Systems

DOE PAGES

Motokawa, Ryuhei; Endo, Hitoshi; Nagao, Michihiro; ...

2016-06-16

Here we performed neutron polarization analysis (NPA) of extracted organic phases containing complexes, comprised of Zr(NO 3) 4 and tri-n-butyl phosphate, which enabled decomposition of the intensity distribution of small-angle neutron scattering (SANS) into the coherent and incoherent scattering components. The coherent scattering intensity, containing structural information, and the incoherent scattering compete over a wide range of magnitude of scattering vector, q, specifically when q is larger than q* ≈ 1/R g, where R g is the radius of gyration of scatterer. Therefore, it is important to determine the incoherent scattering intensity exactly to perform an accurate structural analysis frommore » SANS data when R g is small, such as the aforementioned extracted coordination species. Although NPA is the best method for evaluating the incoherent scattering component for accurately determining the coherent scattering in SANS, this method is not used frequently in SANS data analysis because it is technically challenging. In this study, we successfully demonstrated that experimental determination of the incoherent scattering using NPA is suitable for sample systems containing a small scatterer with a weak coherent scattering intensity, such as extracted complexes in biphasic solvent extraction systems.« less

Unravelling the shape and structural assembly of the photosynthetic GAPDH-CP12-PRK complex from Arabidopsis thaliana by small-angle X-ray scattering analysis.

PubMed

Del Giudice, Alessandra; Pavel, Nicolae Viorel; Galantini, Luciano; Falini, Giuseppe; Trost, Paolo; Fermani, Simona; Sparla, Francesca

2015-12-01

Oxygenic photosynthetic organisms produce sugars through the Calvin-Benson cycle, a metabolism that is tightly linked to the light reactions of photosynthesis and is regulated by different mechanisms, including the formation of protein complexes. Two enzymes of the cycle, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK), form a supramolecular complex with the regulatory protein CP12 with the formula (GAPDH-CP122-PRK)2, in which both enzyme activities are transiently inhibited during the night. Small-angle X-ray scattering analysis performed on both the GAPDH-CP12-PRK complex and its components, GAPDH-CP12 and PRK, from Arabidopsis thaliana showed that (i) PRK has an elongated, bent and screwed shape, (ii) the oxidized N-terminal region of CP12 that is not embedded in the GAPDH-CP12 complex prefers a compact conformation and (iii) the interaction of PRK with the N-terminal region of CP12 favours the approach of two GAPDH tetramers. The interaction between the GAPDH tetramers may contribute to the overall stabilization of the GAPDH-CP12-PRK complex, the structure of which is presented here for the first time.

Realizing actual feedback control of complex network

NASA Astrophysics Data System (ADS)

Tu, Chengyi; Cheng, Yuhua

2014-06-01

In this paper, we present the concept of feedbackability and how to identify the Minimum Feedbackability Set of an arbitrary complex directed network. Furthermore, we design an estimator and a feedback controller accessing one MFS to realize actual feedback control, i.e. control the system to our desired state according to the estimated system internal state from the output of estimator. Last but not least, we perform numerical simulations of a small linear time-invariant dynamics network and a real simple food network to verify the theoretical results. The framework presented here could make an arbitrary complex directed network realize actual feedback control and deepen our understanding of complex systems.

Efficiency of bowel preparation for capsule endoscopy examination: a meta-analysis.

PubMed

Niv, Yaron

2008-03-07

Good preparation before endoscopic procedures is essential for successful visualization. The small bowel is difficult to evaluate because of its length and complex configuration. A meta-analysis was conducted of studies comparing small bowel visualization by capsule endoscopy with and without preparation. Medical data bases were searched for all studies investigating the preparation for capsule endoscopy of the small bowel up to July 31, 2007. Studies that scored bowel cleanness and measured gastric and small bowel transit time and rate of cecum visualization were included. The primary endpoint was the quality of bowel visualization. The secondary endpoints were transit times and proportion of examinations that demonstrated the cecum, with and without preparation. Meta-analysis was performed with StatDirect Statistical software, version 2.6.1 (http://statsdirect.com). Eight studies met the inclusion criteria. Bowel visualization was scored as "good" in 78% of the examinations performed with preparation and 49% performed without (P<0.0001). There were no significant differences in transit times or in the proportion of examinations that demonstrated the cecum with and without preparation. Capsule endoscopy preparation improves the quality of small bowel visualization, but has no effect on transit times, or demonstration of the cecum.

Efficiency of bowel preparation for capsule endoscopy examination: A meta-analysis

PubMed Central

Niv, Yaron

2008-01-01

Good preparation before endoscopic procedures is essential for successful visualization. The small bowel is difficult to evaluate because of its length and complex configuration. A meta-analysis was conducted of studies comparing small bowel visualization by capsule endoscopy with and without preparation. Medical data bases were searched for all studies investigating the preparation for capsule endoscopy of the small bowel up to July 31, 2007. Studies that scored bowel cleanness and measured gastric and small bowel transit time and rate of cecum visualization were included. The primary endpoint was the quality of bowel visualization. The secondary endpoints were transit times and proportion of examinations that demonstrated the cecum, with and without preparation. Meta-analysis was performed with StatDirect Statistical software, version 2.6.1 (http://statsdirect.com). Eight studies met the inclusion criteria. Bowel visualization was scored as “good” in 78% of the examinations performed with preparation and 49% performed without (P < 0.0001). There were no significant differences in transit times or in the proportion of examinations that demonstrated the cecum with and without preparation. Capsule endoscopy preparation improves the quality of small bowel visualization, but has no effect on transit times, or demonstration of the cecum. PMID:18322940

Development and evaluation of a predictive algorithm for telerobotic task complexity

NASA Technical Reports Server (NTRS)

Gernhardt, M. L.; Hunter, R. C.; Hedgecock, J. C.; Stephenson, A. G.

1993-01-01

There is a wide range of complexity in the various telerobotic servicing tasks performed in subsea, space, and hazardous material handling environments. Experience with telerobotic servicing has evolved into a knowledge base used to design tasks to be 'telerobot friendly.' This knowledge base generally resides in a small group of people. Written documentation and requirements are limited in conveying this knowledge base to serviceable equipment designers and are subject to misinterpretation. A mathematical model of task complexity based on measurable task parameters and telerobot performance characteristics would be a valuable tool to designers and operational planners. Oceaneering Space Systems and TRW have performed an independent research and development project to develop such a tool for telerobotic orbital replacement unit (ORU) exchange. This algorithm was developed to predict an ORU exchange degree of difficulty rating (based on the Cooper-Harper rating used to assess piloted operations). It is based on measurable parameters of the ORU, attachment receptacle and quantifiable telerobotic performance characteristics (e.g., link length, joint ranges, positional accuracy, tool lengths, number of cameras, and locations). The resulting algorithm can be used to predict task complexity as the ORU parameters, receptacle parameters, and telerobotic characteristics are varied.

Right-side-stretched multifractal spectra indicate small-worldness in networks

NASA Astrophysics Data System (ADS)

Oświȩcimka, Paweł; Livi, Lorenzo; Drożdż, Stanisław

2018-04-01

Complex network formalism allows to explain the behavior of systems composed by interacting units. Several prototypical network models have been proposed thus far. The small-world model has been introduced to mimic two important features observed in real-world systems: i) local clustering and ii) the possibility to move across a network by means of long-range links that significantly reduce the characteristic path length. A natural question would be whether there exist several ;types; of small-world architectures, giving rise to a continuum of models with properties (partially) shared with other models belonging to different network families. Here, we take advantage of the interplay between network theory and time series analysis and propose to investigate small-world signatures in complex networks by analyzing multifractal characteristics of time series generated from such networks. In particular, we suggest that the degree of right-sided asymmetry of multifractal spectra is linked with the degree of small-worldness present in networks. This claim is supported by numerical simulations performed on several parametric models, including prototypical small-world networks, scale-free, fractal and also real-world networks describing protein molecules. Our results also indicate that right-sided asymmetry emerges with the presence of the following topological properties: low edge density, low average shortest path, and high clustering coefficient.

Design Considerations for a Computationally-Lightweight Authentication Mechanism for Passive RFID Tags

DTIC Science & Technology

2009-09-01

suffer the power and complexity requirements of a public key system. 28 In [18], a simulation of the SHA –1 algorithm is performed on a Xilinx FPGA ... 256 bits. Thus, the construction of a hash table would need 2512 independent comparisons. It is known that hash collisions of the SHA –1 algorithm... SHA –1 algorithm for small-core FPGA design. Small-core FPGA design is the process by which a circuit is adapted to use the minimal amount of logic

Complex network view of evolving manifolds

NASA Astrophysics Data System (ADS)

da Silva, Diamantino C.; Bianconi, Ginestra; da Costa, Rui A.; Dorogovtsev, Sergey N.; Mendes, José F. F.

2018-03-01

We study complex networks formed by triangulations and higher-dimensional simplicial complexes representing closed evolving manifolds. In particular, for triangulations, the set of possible transformations of these networks is restricted by the condition that at each step, all the faces must be triangles. Stochastic application of these operations leads to random networks with different architectures. We perform extensive numerical simulations and explore the geometries of growing and equilibrium complex networks generated by these transformations and their local structural properties. This characterization includes the Hausdorff and spectral dimensions of the resulting networks, their degree distributions, and various structural correlations. Our results reveal a rich zoo of architectures and geometries of these networks, some of which appear to be small worlds while others are finite dimensional with Hausdorff dimension equal or higher than the original dimensionality of their simplices. The range of spectral dimensions of the evolving triangulations turns out to be from about 1.4 to infinity. Our models include simplicial complexes representing manifolds with evolving topologies, for example, an h -holed torus with a progressively growing number of holes. This evolving graph demonstrates features of a small-world network and has a particularly heavy-tailed degree distribution.

Midbond basis functions for weakly bound complexes

NASA Astrophysics Data System (ADS)

Shaw, Robert A.; Hill, J. Grant

2018-06-01

Weakly bound systems present a difficult problem for conventional atom-centred basis sets due to large separations, necessitating the use of large, computationally expensive bases. This can be remedied by placing a small number of functions in the region between molecules in the complex. We present compact sets of optimised midbond functions for a range of complexes involving noble gases, alkali metals and small molecules for use in high accuracy coupled -cluster calculations, along with a more robust procedure for their optimisation. It is shown that excellent results are possible with double-zeta quality orbital basis sets when a few midbond functions are added, improving both the interaction energy and the equilibrium bond lengths of a series of noble gas dimers by 47% and 8%, respectively. When used in conjunction with explicitly correlated methods, near complete basis set limit accuracy is readily achievable at a fraction of the cost that using a large basis would entail. General purpose auxiliary sets are developed to allow explicitly correlated midbond function studies to be carried out, making it feasible to perform very high accuracy calculations on weakly bound complexes.

Validation of the DIFFAL, HPAC and HotSpot Dispersion Models Using the Full-Scale Radiological Dispersal Device (FSRDD) Field Trials Witness Plate Deposition Dataset.

PubMed

Purves, Murray; Parkes, David

2016-05-01

Three atmospheric dispersion models--DIFFAL, HPAC, and HotSpot--of differing complexities have been validated against the witness plate deposition dataset taken during the Full-Scale Radiological Dispersal Device (FSRDD) Field Trials. The small-scale nature of these trials in comparison to many other historical radiological dispersion trials provides a unique opportunity to evaluate the near-field performance of the models considered. This paper performs validation of these models using two graphical methods of comparison: deposition contour plots and hotline profile graphs. All of the models tested are assessed to perform well, especially considering that previous model developments and validations have been focused on larger-scale scenarios. Of the models, HPAC generally produced the most accurate results, especially at locations within ∼100 m of GZ. Features present within the observed data, such as hot spots, were not well modeled by any of the codes considered. Additionally, it was found that an increase in the complexity of the meteorological data input to the models did not necessarily lead to an improvement in model accuracy; this is potentially due to the small-scale nature of the trials.

Surgical treatment of complex small bowel Crohn disease.

PubMed

Michelassi, Fabrizio; Sultan, Samuel

2014-08-01

The clinical presentations of Crohn disease of the small bowel vary from low to high complexity. Understanding the complexity of Crohn disease of the small bowel is important for the surgeon and the gastroenterologist caring for the patient and may be relevant for clinical research as a way to compare outcomes. Here, we present a categorization of complex small bowel Crohn disease and review its surgical treatment as a potential initial step toward the establishment of a definition of complex disease. The complexity of small bowel Crohn disease can be sorted into several categories: technical challenges, namely, fistulae, abscesses, bowel or ureteral obstruction, hemorrhage, cancer and thickened mesentery; extensive disease; the presence of short gut; a history of prolonged use of medications, particularly steroids, immunomodulators, and biological agents; and a high risk of recurrence. Although the principles of modern surgical treatment of Crohn disease have evolved to bowel conservation such as strictureplasty techniques and limited resection margins, such practices by themselves are often not sufficient for the management of complex small bowel Crohn disease. This manuscript reviews each category of complex small bowel Crohn disease, with special emphasis on appropriate surgical strategy.

Fast optimization algorithms and the cosmological constant

NASA Astrophysics Data System (ADS)

Bao, Ning; Bousso, Raphael; Jordan, Stephen; Lackey, Brad

2017-11-01

Denef and Douglas have observed that in certain landscape models the problem of finding small values of the cosmological constant is a large instance of a problem that is hard for the complexity class NP (Nondeterministic Polynomial-time). The number of elementary operations (quantum gates) needed to solve this problem by brute force search exceeds the estimated computational capacity of the observable Universe. Here we describe a way out of this puzzling circumstance: despite being NP-hard, the problem of finding a small cosmological constant can be attacked by more sophisticated algorithms whose performance vastly exceeds brute force search. In fact, in some parameter regimes the average-case complexity is polynomial. We demonstrate this by explicitly finding a cosmological constant of order 10-120 in a randomly generated 1 09-dimensional Arkani-Hamed-Dimopoulos-Kachru landscape.

Tailored Codes for Small Quantum Memories

NASA Astrophysics Data System (ADS)

Robertson, Alan; Granade, Christopher; Bartlett, Stephen D.; Flammia, Steven T.

2017-12-01

We demonstrate that small quantum memories, realized via quantum error correction in multiqubit devices, can benefit substantially by choosing a quantum code that is tailored to the relevant error model of the system. For a biased noise model, with independent bit and phase flips occurring at different rates, we show that a single code greatly outperforms the well-studied Steane code across the full range of parameters of the noise model, including for unbiased noise. In fact, this tailored code performs almost optimally when compared with 10 000 randomly selected stabilizer codes of comparable experimental complexity. Tailored codes can even outperform the Steane code with realistic experimental noise, and without any increase in the experimental complexity, as we demonstrate by comparison in the observed error model in a recent seven-qubit trapped ion experiment.

Advancing Clinical Proteomics via Analysis Based on Biological Complexes: A Tale of Five Paradigms.

PubMed

Goh, Wilson Wen Bin; Wong, Limsoon

2016-09-02

Despite advances in proteomic technologies, idiosyncratic data issues, for example, incomplete coverage and inconsistency, resulting in large data holes, persist. Moreover, because of naïve reliance on statistical testing and its accompanying p values, differential protein signatures identified from such proteomics data have little diagnostic power. Thus, deploying conventional analytics on proteomics data is insufficient for identifying novel drug targets or precise yet sensitive biomarkers. Complex-based analysis is a new analytical approach that has potential to resolve these issues but requires formalization. We categorize complex-based analysis into five method classes or paradigms and propose an even-handed yet comprehensive evaluation rubric based on both simulated and real data. The first four paradigms are well represented in the literature. The fifth and newest paradigm, the network-paired (NP) paradigm, represented by a method called Extremely Small SubNET (ESSNET), dominates in precision-recall and reproducibility, maintains strong performance in small sample sizes, and sensitively detects low-abundance complexes. In contrast, the commonly used over-representation analysis (ORA) and direct-group (DG) test paradigms maintain good overall precision but have severe reproducibility issues. The other two paradigms considered here are the hit-rate and rank-based network analysis paradigms; both of these have good precision-recall and reproducibility, but they do not consider low-abundance complexes. Therefore, given its strong performance, NP/ESSNET may prove to be a useful approach for improving the analytical resolution of proteomics data. Additionally, given its stability, it may also be a powerful new approach toward functional enrichment tests, much like its ORA and DG counterparts.

Atmospheric dispersion modelling over complex terrain at small scale

NASA Astrophysics Data System (ADS)

Nosek, S.; Janour, Z.; Kukacka, L.; Jurcakova, K.; Kellnerova, R.; Gulikova, E.

2014-03-01

Previous study concerned of qualitative modelling neutrally stratified flow over open-cut coal mine and important surrounding topography at meso-scale (1:9000) revealed an important area for quantitative modelling of atmospheric dispersion at small-scale (1:3300). The selected area includes a necessary part of the coal mine topography with respect to its future expansion and surrounding populated areas. At this small-scale simultaneous measurement of velocity components and concentrations in specified points of vertical and horizontal planes were performed by two-dimensional Laser Doppler Anemometry (LDA) and Fast-Response Flame Ionization Detector (FFID), respectively. The impact of the complex terrain on passive pollutant dispersion with respect to the prevailing wind direction was observed and the prediction of the air quality at populated areas is discussed. The measured data will be used for comparison with another model taking into account the future coal mine transformation. Thus, the impact of coal mine transformation on pollutant dispersion can be observed.

Low-complexity nonlinear adaptive filter based on a pipelined bilinear recurrent neural network.

PubMed

Zhao, Haiquan; Zeng, Xiangping; He, Zhengyou

2011-09-01

To reduce the computational complexity of the bilinear recurrent neural network (BLRNN), a novel low-complexity nonlinear adaptive filter with a pipelined bilinear recurrent neural network (PBLRNN) is presented in this paper. The PBLRNN, inheriting the modular architectures of the pipelined RNN proposed by Haykin and Li, comprises a number of BLRNN modules that are cascaded in a chained form. Each module is implemented by a small-scale BLRNN with internal dynamics. Since those modules of the PBLRNN can be performed simultaneously in a pipelined parallelism fashion, it would result in a significant improvement of computational efficiency. Moreover, due to nesting module, the performance of the PBLRNN can be further improved. To suit for the modular architectures, a modified adaptive amplitude real-time recurrent learning algorithm is derived on the gradient descent approach. Extensive simulations are carried out to evaluate the performance of the PBLRNN on nonlinear system identification, nonlinear channel equalization, and chaotic time series prediction. Experimental results show that the PBLRNN provides considerably better performance compared to the single BLRNN and RNN models.

Touch Spray Mass Spectrometry for In Situ Analysis of Complex Samples

PubMed Central

Kerian, Kevin S.; Jarmusch, Alan K.; Cooks, R. Graham

2014-01-01

Touch spray, a spray-based ambient in-situ ionization method, uses a small probe, e.g. a teasing needle to pick up sample and the application of voltage and solvent to cause field-induced droplet emission. Compounds extracted from the microsample are incorporated into the sprayed micro droplets. Performance tests include disease state of tissue, microorganism identification, and therapeutic drug quantitation. Chemical derivatization is performed simultaneously with ionization. PMID:24756256

Simulation evaluation of two VTOL control/display systems in IMC approach and shipboard landing

NASA Technical Reports Server (NTRS)

Merrick, V. K.

1984-01-01

Two control/display systems, which differed in overall complexity but were both designed for VTOL flight operations to and from small ships in instrument meteorological conditions (IMC), were tested using the Ames Flight Simulator for Advanced Aircraft (FSAA). Both systems have attitude command in transition and horizontal-velocity command in hover; the more complex system also has longitudinal-acceleration and flightpath-angle command in transition, and vertical-velocity command in hover. The most important overall distinction between the two systems for the viewpoint of implementation is that in one - the more complex - engine power and nozzle position are operated indirectly through flight controllers, whereas in the other they are operated directly by the pilot. Simulated landings were made on a moving model of a DD 963 Spruance-class destroyer. Acceptable transitions can be performed in turbulence of 3 m/sec rms using either system. Acceptable landings up to sea state 6 can be performed using the more complex system, and up to sea state 5 using the other system.

Fuzzy feature selection based on interval type-2 fuzzy sets

NASA Astrophysics Data System (ADS)

Cherif, Sahar; Baklouti, Nesrine; Alimi, Adel; Snasel, Vaclav

2017-03-01

When dealing with real world data; noise, complexity, dimensionality, uncertainty and irrelevance can lead to low performance and insignificant judgment. Fuzzy logic is a powerful tool for controlling conflicting attributes which can have similar effects and close meanings. In this paper, an interval type-2 fuzzy feature selection is presented as a new approach for removing irrelevant features and reducing complexity. We demonstrate how can Feature Selection be joined with Interval Type-2 Fuzzy Logic for keeping significant features and hence reducing time complexity. The proposed method is compared with some other approaches. The results show that the number of attributes is proportionally small.

Effect of dose and size on defect engineering in carbon cluster implanted silicon wafers

NASA Astrophysics Data System (ADS)

Okuyama, Ryosuke; Masada, Ayumi; Shigematsu, Satoshi; Kadono, Takeshi; Hirose, Ryo; Koga, Yoshihiro; Okuda, Hidehiko; Kurita, Kazunari

2018-01-01

Carbon-cluster-ion-implanted defects were investigated by high-resolution cross-sectional transmission electron microscopy toward achieving high-performance CMOS image sensors. We revealed that implantation damage formation in the silicon wafer bulk significantly differs between carbon-cluster and monomer ions after implantation. After epitaxial growth, small and large defects were observed in the implanted region of carbon clusters. The electron diffraction pattern of both small and large defects exhibits that from bulk crystalline silicon in the implanted region. On the one hand, we assumed that the silicon carbide structure was not formed in the implanted region, and small defects formed because of the complex of carbon and interstitial silicon. On the other hand, large defects were hypothesized to originate from the recrystallization of the amorphous layer formed by high-dose carbon-cluster implantation. These defects are considered to contribute to the powerful gettering capability required for high-performance CMOS image sensors.

Comm for Small Sats: The Lunar Atmosphere and Dust Environment Explorer (LADEE) Communications Subsystem

NASA Technical Reports Server (NTRS)

Kuroda, Vanessa M.; Allard, Mark R.; Lewis, Brian; Lindsay, Michael

2014-01-01

September 6, 2013 through April 21, 2014 marked the mission lifecycle of the highly successful LADEE (Lunar Atmosphere and Dust Environment Explorer) mission that orbited the moon to gather detailed information about the thin lunar atmosphere. This paper will address the development, risks, and lessons learned regarding the specification, selection, and deployment of LADEE's unique Radio Frequency based communications subsystem and supporting tools. This includes the Electronic Ground Support Equipment (EGSE), test regimes, and RF dynamic link analysis environment developed to meet mission requirements for small, flexible, low cost, high performance, fast turnaround, and reusable spacecraft communication capabilities with easy and reliable application to future similar low cost small satellite missions over widely varying needs for communications and communications system complexity. LADEE communication subsystem key components, architecture, and mission performance will be reviewed toward applicability for future mission planning, design, and utilization.

Eddy covariance measurements in complex terrain with a new fast response, closed-path analyzer: spectral characteristics and cross-system comparisons

EPA Science Inventory

In recent years, a new class of enclosed, closed-path gas analyzers suitable for eddy covariance applications has come to market, designed to combine the advantages of traditional closed-path systems (small density corrections, good performance in poor weather) and open-path syst...

Complex network analysis of brain functional connectivity under a multi-step cognitive task

NASA Astrophysics Data System (ADS)

Cai, Shi-Min; Chen, Wei; Liu, Dong-Bai; Tang, Ming; Chen, Xun

2017-01-01

Functional brain network has been widely studied to understand the relationship between brain organization and behavior. In this paper, we aim to explore the functional connectivity of brain network under a multi-step cognitive task involving consecutive behaviors, and further understand the effect of behaviors on the brain organization. The functional brain networks are constructed based on a high spatial and temporal resolution fMRI dataset and analyzed via complex network based approach. We find that at voxel level the functional brain network shows robust small-worldness and scale-free characteristics, while its assortativity and rich-club organization are slightly restricted to the order of behaviors performed. More interestingly, the functional connectivity of brain network in activated ROIs strongly correlates with behaviors and is obviously restricted to the order of behaviors performed. These empirical results suggest that the brain organization has the generic properties of small-worldness and scale-free characteristics, and its diverse functional connectivity emerging from activated ROIs is strongly driven by these behavioral activities via the plasticity of brain.

One-step manufacturing of innovative flat-knitted 3D net-shape preforms for composite applications

NASA Astrophysics Data System (ADS)

Bollengier, Quentin; Wieczorek, Florian; Hellmann, Sven; Trümper, Wolfgang; Cherif, Chokri

2017-10-01

Mostly due to the cost-intensive manually performed processing operations, the production of complex-shaped fibre reinforced plastic composites (FRPC) is currently very expensive and therefore either restricted to sectors with high added value or for small batch applications (e.g. in the aerospace or automotive industry). Previous works suggest that the successful integration of conventional textile manufacturing processes in the FRPC-process chain is the key to a cost-efficient manufacturing of complex three-dimensional (3D) FRPC-components with stress-oriented fibre arrangement. Therefore, this work focuses on the development of the multilayer weft knitting technology for the one-step manufacturing of complex 3D net-shaped preforms for high performance FRPC applications. In order to highlight the advantages of net-shaped multilayer weft knitted fabrics for the production of complex FRPC parts, seamless preforms such as 3D skin-stringer structures and tubular fabrics with load oriented fibre arrangement are realised. In this paper, the development of the textile bindings and performed technical modifications on flat knitting machines are presented. The results show that the multilayer weft knitting technology meets perfectly the requirements for a fully automated and reproducible manufacturing of complex 3D textile preforms with stress-oriented fibre arrangement.

Automated mask and wafer defect classification using a novel method for generalized CD variation measurements

NASA Astrophysics Data System (ADS)

Verechagin, V.; Kris, R.; Schwarzband, I.; Milstein, A.; Cohen, B.; Shkalim, A.; Levy, S.; Price, D.; Bal, E.

2018-03-01

Over the years, mask and wafers defects dispositioning has become an increasingly challenging and time consuming task. With design rules getting smaller, OPC getting complex and scanner illumination taking on free-form shapes - the probability of a user to perform accurate and repeatable classification of defects detected by mask inspection tools into pass/fail bins is reducing. The critical challenging of mask defect metrology for small nodes ( < 30 nm) was reviewed in [1]. While Critical Dimension (CD) variation measurement is still the method of choice for determining a mask defect future impact on wafer, the high complexity of OPCs combined with high variability in pattern shapes poses a challenge for any automated CD variation measurement method. In this study, a novel approach for measurement generalization is presented. CD variation assessment performance is evaluated on multiple different complex shape patterns, and is benchmarked against an existing qualified measurement methodology.

Performance Assessment of Two Whole-Lake Acoustic Positional Telemetry Systems - Is Reality Mining of Free-Ranging Aquatic Animals Technologically Possible?

PubMed Central

Baktoft, Henrik; Zajicek, Petr; Klefoth, Thomas; Svendsen, Jon C.; Jacobsen, Lene; Pedersen, Martin Wæver; March Morla, David; Skov, Christian; Nakayama, Shinnosuke; Arlinghaus, Robert

2015-01-01

Acoustic positional telemetry systems (APTs) represent a novel approach to study the behaviour of free ranging aquatic animals in the wild at unprecedented detail. System manufactures promise remarkably high temporal and spatial resolution. However, the performance of APTs has rarely been rigorously tested at the level of entire ecosystems. Moreover, the effect of habitat structure on system performance has only been poorly documented. Two APTs were deployed to cover two small lakes and a series of standardized stationary tests were conducted to assess system performance. Furthermore, a number of tow tests were conducted to simulate moving fish. Based on these data, we quantified system performance in terms of data yield, accuracy and precision as a function of structural complexity in relation to vegetation. Mean data yield of the two systems was 40 % (Lake1) and 60 % (Lake2). Average system accuracy (acc) and precision (prec) were Lake1: acc = 3.1 m, prec = 1.1 m; Lake2: acc = 1.0 m, prec = 0.2 m. System performance was negatively affected by structural complexity, i.e., open water habitats yielded far better performance than structurally complex vegetated habitats. Post-processing greatly improved data quality, and sub-meter accuracy and precision were, on average, regularly achieved in Lake2 but remained the exception in the larger and structurally more complex Lake1. Moving transmitters were tracked well by both systems. Whereas overestimation of moved distance is inevitable for stationary transmitters due to accumulation of small tracking errors, moving transmitters can result in both over- and underestimation of distances depending on circumstances. Both deployed APTs were capable of providing high resolution positional data at the scale of entire lakes and are suitable systems to mine the reality of free ranging fish in their natural environment. This opens important opportunities to advance several fields of study such as movement ecology and animal social networks in the wild. It is recommended that thorough performance tests are conducted in any study utilizing APTs. The APTs tested here appear best suited for studies in structurally simple ecosystems or for studying pelagic species. In such situations, the data quality provided by the APTs is exceptionally high. PMID:26000459

Bold endeavors: behavioral lessons from polar and space exploration

NASA Technical Reports Server (NTRS)

Stuster, J. W.

2000-01-01

Anecdotal comparisons frequently are made between expeditions of the past and space missions of the future. Spacecraft are far more complex than sailing ships, but from a psychological perspective, the differences are few between confinement in a small wooden ship locked in the polar ice cap and confinement in a small high-technology ship hurtling through interplanetary space. This paper discusses some of the behavioral lessons that can be learned from previous expeditions and applied to facilitate human adjustment and performance during future space expeditions of long duration.

Measuring helium bubble diameter distributions in tungsten with grazing incidence small angle x-ray scattering (GISAXS)

NASA Astrophysics Data System (ADS)

Thompson, M.; Kluth, P.; Doerner, R. P.; Kirby, N.; Riley, D.; Corr, C. S.

2016-02-01

Grazing incidence small angle x-ray scattering was performed on tungsten samples exposed to helium plasma in the MAGPIE and Pisces-A linear plasma devices to measure the size distributions of resulting helium nano-bubbles. Nano-bubbles were fitted assuming spheroidal particles and an exponential diameter distribution. These particles had mean diameters between 0.36 and 0.62 nm. Pisces-A exposed samples showed more complex patterns, which may suggest the formation of faceted nano-bubbles or nano-scale surface structures.

Fuel Cycle Performance of Thermal Spectrum Small Modular Reactors

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

Worrall, Andrew; Todosow, Michael

2016-01-01

Small modular reactors may offer potential benefits, such as enhanced operational flexibility. However, it is vital to understand the holistic impact of small modular reactors on the nuclear fuel cycle and fuel cycle performance. The focus of this paper is on the fuel cycle impacts of light water small modular reactors in a once-through fuel cycle with low-enriched uranium fuel. A key objective of this paper is to describe preliminary reactor core physics and fuel cycle analyses conducted in support of the U.S. Department of Energy Office of Nuclear Energy Fuel Cycle Options Campaign. Challenges with small modular reactors include:more » increased neutron leakage, fewer assemblies in the core (and therefore fewer degrees of freedom in the core design), complex enrichment and burnable absorber loadings, full power operation with inserted control rods, the potential for frequent load-following operation, and shortened core height. Each of these will impact the achievable discharge burn-up in the reactor and the fuel cycle performance. This paper summarizes the results of an expert elicitation focused on developing a list of the factors relevant to small modular reactor fuel, core, and operation that will impact fuel cycle performance. Preliminary scoping analyses were performed using a regulatory-grade reactor core simulator. The hypothetical light water small modular reactor considered in these preliminary scoping studies is a cartridge type one-batch core with 4.9% enrichment. Some core parameters, such as the size of the reactor and general assembly layout, are similar to an example small modular reactor concept from industry. The high-level issues identified and preliminary scoping calculations in this paper are intended to inform on potential fuel cycle impacts of one-batch thermal spectrum SMRs. In particular, this paper highlights the impact of increased neutron leakage and reduced number of batches on the achievable burn-up of the reactor. Fuel cycle performance metrics for a small modular reactor are compared to a conventional three-batch light water reactor in the following areas: nuclear waste management, environmental impact, and resource utilization. Metrics performance for a small modular reactor are degraded for mass of spent nuclear fuel and high level waste disposed, mass of depleted uranium disposed, land use per energy generated, and carbon emission per energy generated« less

Novel immunoassay formats for integrated microfluidic circuits: diffusion immunoassays (DIA)

NASA Astrophysics Data System (ADS)

Weigl, Bernhard H.; Hatch, Anson; Kamholz, Andrew E.; Yager, Paul

2000-03-01

Novel designs of integrated fluidic microchips allow separations, chemical reactions, and calibration-free analytical measurements to be performed directly in very small quantities of complex samples such as whole blood and contaminated environmental samples. This technology lends itself to applications such as clinical diagnostics, including tumor marker screening, and environmental sensing in remote locations. Lab-on-a-Chip based systems offer many *advantages over traditional analytical devices: They consume extremely low volumes of both samples and reagents. Each chip is inexpensive and small. The sampling-to-result time is extremely short. They perform all analytical functions, including sampling, sample pretreatment, separation, dilution, and mixing steps, chemical reactions, and detection in an integrated microfluidic circuit. Lab-on-a-Chip systems enable the design of small, portable, rugged, low-cost, easy to use, yet extremely versatile and capable diagnostic instruments. In addition, fluids flowing in microchannels exhibit unique characteristics ('microfluidics'), which allow the design of analytical devices and assay formats that would not function on a macroscale. Existing Lab-on-a-chip technologies work very well for highly predictable and homogeneous samples common in genetic testing and drug discovery processes. One of the biggest challenges for current Labs-on-a-chip, however, is to perform analysis in the presence of the complexity and heterogeneity of actual samples such as whole blood or contaminated environmental samples. Micronics has developed a variety of Lab-on-a-Chip assays that can overcome those shortcomings. We will now present various types of novel Lab- on-a-Chip-based immunoassays, including the so-called Diffusion Immunoassays (DIA) that are based on the competitive laminar diffusion of analyte molecules and tracer molecules into a region of the chip containing antibodies that target the analyte molecules. Advantages of this technique are a reduction in reagents, higher sensitivity, minimal preparation of complex samples such as blood, real-time calibration, and extremely rapid analysis.

Ultralight Weight Optical Systems Using Nano-Layered Synthesized Materials

NASA Technical Reports Server (NTRS)

Clark, Natalie; Breckinridge, James

2014-01-01

Optical imaging is important for many NASA science missions. Even though complex optical systems have advanced, the optics, based on conventional glass and mirrors, require components that are thick, heavy and expensive. As the need for higher performance expands, glass and mirrors are fast approaching the point where they will be too large, heavy and costly for spacecraft, especially small satellite systems. NASA Langley Research Center is developing a wide range of novel nano-layered synthesized materials that enable the development and fabrication of ultralight weight optical device systems that enable many NASA missions to collect science data imagery using small satellites. In addition to significantly reducing weight, the nano-layered synthesized materials offer advantages in performance, size, and cost.

Enhanced electrical stability of nitrate ligand-based hexaaqua complexes solution-processed ultrathin a-IGZO transistors

NASA Astrophysics Data System (ADS)

Choi, C.; Baek, Y.; Lee, B. M.; Kim, K. H.; Rim, Y. S.

2017-12-01

We report solution-processed, amorphous indium-gallium-zinc-oxide-based (a-IGZO-based) thin-film transistors (TFTs). Our proposed solution-processed a-IGZO films, using a simple spin-coating method, were formed through nitrate ligand-based metal complexes, and they were annealed at low temperature (250 °C) to achieve high-quality oxide films and devices. We investigated solution-processed a-IGZO TFTs with various thicknesses, ranging from 4 to 16 nm. The 4 nm-thick TFT films had smooth morphology and high-density, and they exhibited excellent performance, i.e. a high saturation mobility of 7.73  ±  0.44 cm2 V-1 s-1, a sub-threshold swing of 0.27 V dec-1, an on/off ratio of ~108, and a low threshold voltage of 3.10  ±  0.30 V. However, the performance of the TFTs degraded as the film thickness was increased. We further performed positive and negative bias stress tests to examine their electrical stability, and it was noted that the operating behavior of the devices was highly stable. Despite a small number of free charges, the high performance of the ultrathin a-IGZO TFTs was attributed to the small effect of the thickness of the channel, low bulk resistance, the quality of the a-IGZO/SiO2 interface, and high film density.

Chirality sensing with stereodynamic biphenolate zinc complexes.

PubMed

Bentley, Keith W; de Los Santos, Zeus A; Weiss, Mary J; Wolf, Christian

2015-10-01

Two bidentate ligands consisting of a fluxional polyarylacetylene framework with terminal phenol groups were synthesized. Reaction with diethylzinc gives stereodynamic complexes that undergo distinct asymmetric transformation of the first kind upon binding of chiral amines and amino alcohols. The substrate-to-ligand chirality imprinting at the zinc coordination sphere results in characteristic circular dichroism signals that can be used for direct enantiomeric excess (ee) analysis. This chemosensing approach bears potential for high-throughput ee screening with small sample amounts and reduced solvent waste compared to traditional high-performance liquid chromatography methods. © 2015 Wiley Periodicals, Inc.

Drawing the PDB: Protein-Ligand Complexes in Two Dimensions.

PubMed

Stierand, Katrin; Rarey, Matthias

2010-12-09

The two-dimensional representation of molecules is a popular communication medium in chemistry and the associated scientific fields. Computational methods for drawing small molecules with and without manual investigation are well-established and widely spread in terms of numerous software tools. Concerning the planar depiction of molecular complexes, there is considerably less choice. We developed the software PoseView, which automatically generates two-dimensional diagrams of macromolecular complexes, showing the ligand, the interactions, and the interacting residues. All depicted molecules are drawn on an atomic level as structure diagrams; thus, the output plots are clearly structured and easily readable for the scientist. We tested the performance of PoseView in a large-scale application on nearly all druglike complexes of the PDB (approximately 200000 complexes); for more than 92% of the complexes considered for drawing, a layout could be computed. In the following, we will present the results of this application study.

Structural Behavioral Study on the General Aviation Network Based on Complex Network

NASA Astrophysics Data System (ADS)

Zhang, Liang; Lu, Na

2017-12-01

The general aviation system is an open and dissipative system with complex structures and behavioral features. This paper has established the system model and network model for general aviation. We have analyzed integral attributes and individual attributes by applying the complex network theory and concluded that the general aviation network has influential enterprise factors and node relations. We have checked whether the network has small world effect, scale-free property and network centrality property which a complex network should have by applying degree distribution of functions and proved that the general aviation network system is a complex network. Therefore, we propose to achieve the evolution process of the general aviation industrial chain to collaborative innovation cluster of advanced-form industries by strengthening network multiplication effect, stimulating innovation performance and spanning the structural hole path.

Experimental study on local scouring at pile-supported piers

NASA Astrophysics Data System (ADS)

Moreno, Mario; Birjukova, Olga; Grimaldi, Carmelo; Gaudio, Roberto; Cardoso, António H.

2017-06-01

In spite of the increasing importance of complex piers for bridges, the number of studies on these piers is comparatively small and the predictors of scour depth at complex piers are only a few, derived from limited experimental evidence. The main purpose of this paper is to share with the hydraulics community the results of 67 tests on scouring at pile-supported piers (including complex piers) aligned with the flow, under clear-water conditions close to the threshold of beginning of sediment motion, while contributing to shade some more light on the influence of the pile-cap thickness on the equilibrium scour depth, the reliability of the superposition approach, the contribution of each one of the complex pier components to the equilibrium scour depth of the ensemble, and the performance of existing predictors of local scour at complex piers.

Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling

PubMed Central

Wagner, Bridget K.; Clemons, Paul A.

2009-01-01

Discovering small-molecule modulators for thousands of gene products requires multiple stages of biological testing, specificity evaluation, and chemical optimization. Many cellular profiling methods, including cellular sensitivity, gene-expression, and cellular imaging, have emerged as methods to assess the functional consequences of biological perturbations. Cellular profiling methods applied to small-molecule science provide opportunities to use complex phenotypic information to prioritize and optimize small-molecule structures simultaneously against multiple biological endpoints. As throughput increases and cost decreases for such technologies, we see an emerging paradigm of using more information earlier in probe- and drug-discovery efforts. Moreover, increasing access to public datasets makes possible the construction of “virtual” profiles of small-molecule performance, even when multiplexed measurements were not performed or when multidimensional profiling was not the original intent. We review some key conceptual advances in small-molecule phenotypic profiling, emphasizing connections to other information, such as protein-binding measurements, genetic perturbations, and cell states. We argue that to maximally leverage these measurements in probe and drug discovery requires a fundamental connection to synthetic chemistry, allowing the consequences of synthetic decisions to be described in terms of changes in small-molecule profiles. Mining such data in the context of chemical structure and synthesis strategies can inform decisions about chemistry procurement and library development, leading to optimal small-molecule screening collections. PMID:19825513

Would the solvent effect be the main cause of band shift in the theoretical absorption spectrum of large lanthanide complexes?

NASA Astrophysics Data System (ADS)

Freire, Ricardo O.; Rodrigues, Nailton M.; Rocha, Gerd B.; Gimenez, Iara F.; da Costa Junior, Nivan B.

2011-06-01

As most reactions take place in solution, the study of solvent effects on relevant molecular properties - either by experimental or theoretical methods - is crucial for the design of new processes and prediction of technological properties. In spite of this, only few works focusing the influence of the solvent nature specifically on the spectroscopic properties of lanthanide complexes can be found in the literature. The present work describes a theoretical study of the solvent effect on the prediction of the absorption spectra for lanthanide complexes, but other possible relevant factors have been also considered such as the molecular geometry and the excitation window used for interaction configuration (CI) calculations. The [Eu(ETA) 2· nH 2O] +1 complex has been chosen as an ideal candidate for this type of study due to its small number of atoms (only 49) and also because the absorption spectrum exhibits a single band. Two Monte Carlo simulations were performed, the first one considering the [Eu(ETA) 2] +1 complex in 400 water molecules, evidencing that the complex presents four coordinated water molecules. The second simulation considered the [Eu(ETA) 2·4H 2O] +1 complex in 400 ethanol molecules, in order to evaluate the solvent effect on the shift of the maximum absorption in calculated spectra, compared to the experimental one. Quantum chemical studies were also performed in order to evaluate the effect of the accuracy of calculated ground state geometry on the prediction of absorption spectra. The influence of the excitation window used for CI calculations on the spectral shift was also evaluated. No significant solvent effect was found on the prediction of the absorption spectrum for [Eu(ETA) 2·4H 2O] +1 complex. A small but significant effect of the ground state geometry on the transition energy and oscillator strength was also observed. Finally it must be emphasized that the absorption spectra of lanthanide complexes can be predicted with great accuracy by the combined use of semiempirical Sparkle/AM1 and INDO/S-CIS as long as the largest possible excitation window is used in the configuration interaction calculation.

Research on Multi Hydrological Models Applicability and Modelling Data Uncertainty Analysis for Flash Flood Simulation in Hilly Area

NASA Astrophysics Data System (ADS)

Ye, L.; Wu, J.; Wang, L.; Song, T.; Ji, R.

2017-12-01

Flooding in small-scale watershed in hilly area is characterized by short time periods and rapid rise and recession due to the complex underlying surfaces, various climate type and strong effect of human activities. It is almost impossible for a single hydrological model to describe the variation of flooding in both time and space accurately for all the catchments in hilly area because the hydrological characteristics can vary significantly among different catchments. In this study, we compare the performance of 5 hydrological models with varying degrees of complexity for simulation of flash flood for 14 small-scale watershed in China in order to find the relationship between the applicability of the hydrological models and the catchments characteristics. Meanwhile, given the fact that the hydrological data is sparse in hilly area, the effect of precipitation data, DEM resolution and their interference on the uncertainty of flood simulation is also illustrated. In general, the results showed that the distributed hydrological model (HEC-HMS in this study) performed better than the lumped hydrological models. Xinajiang and API models had good simulation for the humid catchments when long-term and continuous rainfall data is provided. Dahuofang model can simulate the flood peak well while the runoff generation module is relatively poor. In addition, the effect of diverse modelling data on the simulations is not simply superposed, and there is a complex interaction effect among different modelling data. Overall, both the catchment hydrological characteristics and modelling data situation should be taken into consideration in order to choose the suitable hydrological model for flood simulation for small-scale catchment in hilly area.

An Interactive, Versatile, Three-Dimensional Display, Manipulation and Plotting System for Biomedical Research

ERIC Educational Resources Information Center

Feldmann, Richard J.; And Others

1972-01-01

Computer graphics provides a valuable tool for the representation and a better understanding of structures, both small and large. Accurate and rapid construction, manipulation, and plotting of structures, such as macromolecules as complex as hemoglobin, are performed by a collection of computer programs and a time-sharing computer. (21 references)…

Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing.

PubMed

Cotney, Justin L; Noonan, James P

2015-02-02

Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) is a powerful method used to identify genome-wide binding patterns of transcription factors and distribution of various histone modifications associated with different chromatin states. In most published studies, ChIP-Seq has been performed on cultured cells grown under controlled conditions, allowing generation of large amounts of material in a homogeneous biological state. Although such studies have provided great insight into the dynamic landscapes of animal genomes, they do not allow the examination of transcription factor binding and chromatin states in adult tissues, developing embryonic structures, or tumors. Such knowledge is critical to understanding the information required to create and maintain a complex biological tissue and to identify noncoding regions of the genome directly involved in tissues affected by complex diseases such as autism. Studying these tissue types with ChIP-Seq can be challenging due to the limited availability of tissues and the lack of complex biological states able to be achieved in culture. These inherent differences require alterations of standard cross-linking and chromatin extraction typically used in cell culture. Here we describe a general approach for using small amounts of animal tissue to perform ChIP-Seq directed at histone modifications and transcription factors. Tissue is homogenized before treatment with formaldehyde to ensure proper cross-linking, and a two-step nuclear isolation is performed to increase extraction of soluble chromatin. Small amounts of soluble chromatin are then used for immunoprecipitation (IP) and prepared for multiplexed high-throughput sequencing. © 2015 Cold Spring Harbor Laboratory Press.

A new parallel plate shear cell for in situ real-space measurements of complex fluids under shear flow.

PubMed

Wu, Yu Ling; Brand, Joost H J; van Gemert, Josephus L A; Verkerk, Jaap; Wisman, Hans; van Blaaderen, Alfons; Imhof, Arnout

2007-10-01

We developed and tested a parallel plate shear cell that can be mounted on top of an inverted microscope to perform confocal real-space measurements on complex fluids under shear. To follow structural changes in time, a plane of zero velocity is created by letting the plates move in opposite directions. The location of this plane is varied by changing the relative velocities of the plates. The gap width is variable between 20 and 200 microm with parallelism better than 1 microm. Such a small gap width enables us to examine the total sample thickness using high numerical aperture objective lenses. The achieved shear rates cover the range of 0.02-10(3) s(-1). This shear cell can apply an oscillatory shear with adjustable amplitude and frequency. The maximum travel of each plate equals 1 cm, so that strains up to 500 can be applied. For most complex fluids, an oscillatory shear with such a large amplitude can be regarded as a continuous shear. We measured the flow profile of a suspension of silica colloids in this shear cell. It was linear except for a small deviation caused by sedimentation. To demonstrate the excellent performance and capabilities of this new setup we examined shear induced crystallization and melting of concentrated suspensions of 1 microm diameter silica colloids.

Sports teams as complex adaptive systems: manipulating player numbers shapes behaviours during football small-sided games.

PubMed

Silva, Pedro; Vilar, Luís; Davids, Keith; Araújo, Duarte; Garganta, Júlio

2016-01-01

Small-sided and conditioned games (SSCGs) in sport have been modelled as complex adaptive systems. Research has shown that the relative space per player (RSP) formulated in SSCGs can impact on emergent tactical behaviours. In this study we adopted a systems orientation to analyse how different RSP values, obtained through manipulations of player numbers, influenced four measures of interpersonal coordination observed during performance in SSCGs. For this purpose we calculated positional data (GPS 15 Hz) from ten U-15 football players performing in three SSCGs varying in player numbers (3v3, 4v4 and 5v5). Key measures of SSCG system behaviours included values of (1) players' dispersion, (2) teams' separateness, (3) coupling strength and time delays between participants' emerging movements, respectively. Results showed that values of participants' dispersion increased, but the teams' separateness remained identical across treatments. Coupling strength and time delay also showed consistent values across SSCGs. These results exemplified how complex adaptive systems, like football teams, can harness inherent degeneracy to maintain similar team spatial-temporal relations with opponents through changes in inter-individual coordination modes (i.e., players' dispersion). The results imply that different team behaviours might emerge at different ratios of field dimension/player numbers. Therefore, sport pedagogists should carefully evaluate the effects of changing RSP in SSCGs as a way of promoting increased or decreased pressure on players.

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

PubMed Central

2016-01-01

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

Circadian Effects on Simple Components of Complex Task Performance

NASA Technical Reports Server (NTRS)

Clegg, Benjamin A.; Wickens, Christopher D.; Vieane, Alex Z.; Gutzwiller, Robert S.; Sebok, Angelia L.

2015-01-01

The goal of this study was to advance understanding and prediction of the impact of circadian rhythm on aspects of complex task performance during unexpected automation failures, and subsequent fault management. Participants trained on two tasks: a process control simulation, featuring automated support; and a multi-tasking platform. Participants then completed one task in a very early morning (circadian night) session, and the other during a late afternoon (circadian day) session. Small effects of time of day were seen on simple components of task performance, but impacts on more demanding components, such as those that occur following an automation failure, were muted relative to previous studies where circadian rhythm was compounded with sleep deprivation and fatigue. Circadian low participants engaged in compensatory strategies, rather than passively monitoring the automation. The findings and implications are discussed in the context of a model that includes the effects of sleep and fatigue factors.

Space shuttle main engine computed tomography applications

NASA Technical Reports Server (NTRS)

Sporny, Richard F.

1990-01-01

For the past two years the potential applications of computed tomography to the fabrication and overhaul of the Space Shuttle Main Engine were evaluated. Application tests were performed at various government and manufacturer facilities with equipment produced by four different manufacturers. The hardware scanned varied in size and complexity from a small temperature sensor and turbine blades to an assembled heat exchanger and main injector oxidizer inlet manifold. The evaluation of capabilities included the ability to identify and locate internal flaws, measure the depth of surface cracks, measure wall thickness, compare manifold design contours to actual part contours, perform automatic dimensional inspections, generate 3D computer models of actual parts, and image the relationship of the details in a complex assembly. The capabilities evaluated, with the exception of measuring the depth of surface flaws, demonstrated the existing and potential ability to perform many beneficial Space Shuttle Main Engine applications.

The Effect of Oyster Reef Morphology on Particulate Transfer in a North Carolina Tidal Creek

NASA Astrophysics Data System (ADS)

Lemon, M. G.; Posey, M.; Mallin, M.; Alphin, T.

2014-12-01

The eastern oyster (Crassostrea virginica) is a vital ecosystem engineer species, providing a number of ecosystem services that structure and maintain estuarine environments through the construction of large, hard-bottom reef complexes. Through suspension feeding, oysters clear the water column of particulates, leading to decreased suspended material and enhanced benthic pelagic coupling. Past field studies have indicated the potential importance of the physical reef structure in regulating the transfer of particulate material in the seston. In order to directly assess the existence of the physical reef effect, multiple field experiments were performed in a small tidal creek estuary along the south eastern coast of North Carolina. Comparison of clearance rates derived from two different in situ methods, one accounting for the physical structure of the oyster reef in addition to oyster filtration and one looking at oyster filtration alone, indicate that the reef structure may increase the amount of particulate removal performed by the reef by more than 4 times the removal performed by oyster filtration alone. A defaunation experiment was performed by eliminating the live component of the oyster reef and comparing particulate transfer of this defaunated transect to that of an adjacent faunated transect. The defaunated transect had reduced but not significantly lower material removal when compared to the faunated transect prior to defaunation. Results from short and long term sediment collection and flow velocity measurements indicate that the physical effect of oyster reefs is strong over short temporal scales (days) but is much smaller when evaluated over longer time periods (months). Generally, large silt and small sand sized material is permanently removed from the seston due to the interaction of oyster reef structure and tidal flows, however the transfer of small and medium sized silt grains is only slowed down by the presence of large reef complexes. This effect has important ecological implications for downstream water quality and must be accounted for when modeling water quality improvements performed by oysters.

The Big Role of Small RNAs in Anxiety and Stress-Related Disorders.

PubMed

Malan-Müller, S; Hemmings, S M J

2017-01-01

In the study of complex, heterogeneous disorders, such as anxiety and stress-related disorders, epigenetic factors provide an additional level of heritable complexity. MicroRNAs (miRNAs) are a class of small, noncoding RNAs that function as epigenetic modulators of gene expression by binding to target messenger RNAs (mRNAs) and subsequently blocking translation or accelerating their degradation. In light of their abundance in the central nervous system (CNS) and their involvement in synaptic plasticity and neuronal differentiation, miRNAs represent an exciting frontier to be explored in the etiology and treatment of anxiety and stress-related disorders. This chapter will present a thorough review of miRNAs, their functions, and mRNA targets in the CNS, focusing on their role in anxiety and stress-related disorders as described by studies performed in animals and human subjects. © 2017 Elsevier Inc. All rights reserved.

Infrared small target detection based on directional zero-crossing measure

NASA Astrophysics Data System (ADS)

Zhang, Xiangyue; Ding, Qinghai; Luo, Haibo; Hui, Bin; Chang, Zheng; Zhang, Junchao

2017-12-01

Infrared small target detection under complex background and low signal-to-clutter ratio (SCR) condition is of great significance to the development on precision guidance and infrared surveillance. In order to detect targets precisely and extract targets from intricate clutters effectively, a detection method based on zero-crossing saliency (ZCS) map is proposed. The original map is first decomposed into different first-order directional derivative (FODD) maps by using FODD filters. Then the ZCS map is obtained by fusing all directional zero-crossing points. At last, an adaptive threshold is adopted to segment targets from the ZCS map. Experimental results on a series of images show that our method is effective and robust for detection under complex backgrounds. Moreover, compared with other five state-of-the-art methods, our method achieves better performance in terms of detection rate, SCR gain and background suppression factor.

Flow measurements in a water tunnel using a holocinematographic velocimeter

NASA Technical Reports Server (NTRS)

Weinstein, Leonard M.; Beeler, George B.

1987-01-01

Dual-view holographic movies were used to examine complex flows with full three-space and time resolution. This approach, which tracks the movement of small tracer particles in water, is termed holocinematographic velocimetry (HCV). A small prototype of a new water tunnel was used to demonstrate proof-of-concept for the HCV. After utilizing a conventional flow visualization apparatus with a laser light sheet to illuminate tracer particles to evaluate flow quality of the prototype tunnel, a simplified version of the HCV was employed to demonstrate the capabilities of the approach. Results indicate that a full-scale version of the water tunnel and a high performance version of the HCV should be able to check theoretical and numerical modeling of complex flows and examine the mechanisms operative in turbulent and vortex flow control concepts, providing an entirely unique instrument capable, for the first time, of simultaneous three-space and time measurements in turbulent flow.

Spectro-Imaging Polarimetry of the Local Corona During Solar Eclipse

NASA Astrophysics Data System (ADS)

Qu, Z. Q.; Dun, G. T.; Chang, L.; Murray, G.; Cheng, X. M.; Zhang, X. Y.; Deng, L. H.

2017-02-01

Results are presented from spectro-imaging polarimetry of radiation from the local solar corona during the 2013 total solar eclipse in Gabon. This polarimetric observation was performed from 516.3 nm to 532.6 nm using a prototype Fiber Arrayed Solar Optical Telescope (FASOT). A polarimetric noise level on the order of 10^{-3} results from a reduced polarimetric optical switching demodulation (RPOSD) procedure for data reduction. It is revealed that the modality of fractional linear polarization profiles of the green coronal line shows a diversity, which may indicate complex mechanisms. The polarization degree can approach 3.2 % above the continuum polarization level on a scale of 1500 km, and the nonuniform spatial distribution in amplitude and polarization direction is found even within a small field of view of 7500 km. All of this implies that the coronal polarization is highly structured and complex even on a small scale.

Robotic lateral pancreaticojejunostomy (Puestow).

PubMed

Meehan, John J; Sawin, Robert

2011-06-01

A lateral pancreaticojejunostomy (LPJ), also known as the Puestow procedure, is a complex procedure performed for chronic pancreatitis when the pancreatic duct is dilated and unable to drain properly. Traditionally, these procedures are performed with open surgery. A minimally invasive approach to the LPJ using rigid handheld nonarticulating instruments is tedious and rarely performed. In fact, there are no prior laparoscopic case reports for LPJ in children and only a small handful of cases in the adult literature. This lack of laparoscopic information may be an indication of the difficulty in performing this complex operation with nonarticulating laparoscopic instruments. The advantages of robotic surgery may help overcome these difficulties. We present the first robotic LPJ ever reported in a 14-year-old child with idiopathic chronic pancreatitis. This case demonstrates the utility of this advanced surgical technology and may lead to a new minimally invasive option for both adults and children with chronic pancreatitis requiring surgical intervention. Copyright © 2011 Elsevier Inc. All rights reserved.

Modified Multivisceral Transplant After Acute Abdominal Trauma.

PubMed

Nikeghbalian, Saman; Alaa Eldin, Ahmed; Aliakbarian, Mohsen; Kazemi, Kourosh; Shamsaeefar, Alireza; Gholami, Siavash; Malekhosseini, Seyed Ali

2016-04-01

A 50-year-old man sustained blunt abdominal trauma in a motor vehicle accident. He underwent exploratory laparotomy on the day of trauma, and severe bleeding from the base of the small bowel mesentery was controlled by mass ligation and through-and-through suturing. After transfer to our center, repeat exploratory laparotomy showed ischemic small intestine, ischemic right colon, and severe pancreatic trauma. The severely injured organs were excised including the entire small bowel, pancreas, spleen, stomach, and right hemicolon. The next day, a modified multivisceral transplant was performed including stomach, pancreaticoduodenal complex, and small bowel transplant. Postoperative complications included an intra-abdominal collection that was drained percutaneously with ultrasonographic guidance and severe rejection that was treated with anti-thymocyte globulin. In summary, for select patients who have severe abdominal trauma may be treated with acute multivisceral transplant.

RTD fluxgate performance for application in magnetic label-based bioassay: preliminary results.

PubMed

Ando, B; Ascia, A; Baglio, S; Bulsara, A R; Trigona, C; In, V

2006-01-01

Magnetic bioassay is becoming of great interest in several application including magnetic separation, drug delivery, hyperthermia treatments, magnetic resonance imaging (MRI) and magnetic labelling. The latter can be used to localize bio-entities (e.g. cancer tissues) by using magnetic markers and high sensitive detectors. To this aim SQUIDs can be adopted, however this result in a quite sophisticated and complex method involving high cost and complex set-up. In this paper, the possibility to adopt RTD fluxgate magnetometers as alternative low cost solution to perform magnetic bio-sensing is investigated. Some experimental results are shown that encourage to pursue this approach in order to obtain simple devices that can detect a certain number of magnetic particles accumulated onto a small surface such to be useful for diagnosis purposes.

Distributed intelligent control and status networking

NASA Technical Reports Server (NTRS)

Fortin, Andre; Patel, Manoj

1993-01-01

Over the past two years, the Network Control Systems Branch (Code 532) has been investigating control and status networking technologies. These emerging technologies use distributed processing over a network to accomplish a particular custom task. These networks consist of small intelligent 'nodes' that perform simple tasks. Containing simple, inexpensive hardware and software, these nodes can be easily developed and maintained. Once networked, the nodes can perform a complex operation without a central host. This type of system provides an alternative to more complex control and status systems which require a central computer. This paper will provide some background and discuss some applications of this technology. It will also demonstrate the suitability of one particular technology for the Space Network (SN) and discuss the prototyping activities of Code 532 utilizing this technology.

Complex background suppression using global-local registration strategy for the detection of small-moving target on moving platform

NASA Astrophysics Data System (ADS)

Zou, Tianhao; Zuo, Zhengrong

2018-02-01

Target detection is a very important and basic problem of computer vision and image processing. The most often case we meet in real world is a detection task for a moving-small target on moving platform. The commonly used methods, such as Registration-based suppression, can hardly achieve a desired result. To crack this hard nut, we introduce a Global-local registration based suppression method. Differ from the traditional ones, the proposed Global-local Registration Strategy consider both the global consistency and the local diversity of the background, obtain a better performance than normal background suppression methods. In this paper, we first discussed the features about the small-moving target detection on unstable platform. Then we introduced a new strategy and conducted an experiment to confirm its noisy stability. In the end, we confirmed the background suppression method based on global-local registration strategy has a better perform in moving target detection on moving platform.

Feedforward object-vision models only tolerate small image variations compared to human

PubMed Central

Ghodrati, Masoud; Farzmahdi, Amirhossein; Rajaei, Karim; Ebrahimpour, Reza; Khaligh-Razavi, Seyed-Mahdi

2014-01-01

Invariant object recognition is a remarkable ability of primates' visual system that its underlying mechanism has constantly been under intense investigations. Computational modeling is a valuable tool toward understanding the processes involved in invariant object recognition. Although recent computational models have shown outstanding performances on challenging image databases, they fail to perform well in image categorization under more complex image variations. Studies have shown that making sparse representation of objects by extracting more informative visual features through a feedforward sweep can lead to higher recognition performances. Here, however, we show that when the complexity of image variations is high, even this approach results in poor performance compared to humans. To assess the performance of models and humans in invariant object recognition tasks, we built a parametrically controlled image database consisting of several object categories varied in different dimensions and levels, rendered from 3D planes. Comparing the performance of several object recognition models with human observers shows that only in low-level image variations the models perform similar to humans in categorization tasks. Furthermore, the results of our behavioral experiments demonstrate that, even under difficult experimental conditions (i.e., briefly presented masked stimuli with complex image variations), human observers performed outstandingly well, suggesting that the models are still far from resembling humans in invariant object recognition. Taken together, we suggest that learning sparse informative visual features, although desirable, is not a complete solution for future progresses in object-vision modeling. We show that this approach is not of significant help in solving the computational crux of object recognition (i.e., invariant object recognition) when the identity-preserving image variations become more complex. PMID:25100986

Combination of large and small basis sets in electronic structure calculations on large systems

NASA Astrophysics Data System (ADS)

Røeggen, Inge; Gao, Bin

2018-04-01

Two basis sets—a large and a small one—are associated with each nucleus of the system. Each atom has its own separate one-electron basis comprising the large basis set of the atom in question and the small basis sets for the partner atoms in the complex. The perturbed atoms in molecules and solids model is at core of the approach since it allows for the definition of perturbed atoms in a system. It is argued that this basis set approach should be particularly useful for periodic systems. Test calculations are performed on one-dimensional arrays of H and Li atoms. The ground-state energy per atom in the linear H array is determined versus bond length.

Recommendations for Quantitative Analysis of Small Molecules by Matrix-assisted laser desorption ionization mass spectrometry

PubMed Central

Wang, Poguang; Giese, Roger W.

2017-01-01

Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) has been used for quantitative analysis of small molecules for many years. It is usually preceded by an LC separation step when complex samples are tested. With the development several years ago of “modern MALDI” (automation, high repetition laser, high resolution peaks), the ease of use and performance of MALDI as a quantitative technique greatly increased. This review focuses on practical aspects of modern MALDI for quantitation of small molecules conducted in an ordinary way (no special reagents, devices or techniques for the spotting step of MALDI), and includes our ordinary, preferred Methods The review is organized as 18 recommendations with accompanying explanations, criticisms and exceptions. PMID:28118972

Optimizing Aspect-Oriented Mechanisms for Embedded Applications

NASA Astrophysics Data System (ADS)

Hundt, Christine; Stöhr, Daniel; Glesner, Sabine

As applications for small embedded mobile devices are getting larger and more complex, it becomes inevitable to adopt more advanced software engineering methods from the field of desktop application development. Aspect-oriented programming (AOP) is a promising approach due to its advanced modularization capabilities. However, existing AOP languages tend to add a substantial overhead in both execution time and code size which restricts their practicality for small devices with limited resources. In this paper, we present optimizations for aspect-oriented mechanisms at the level of the virtual machine. Our experiments show that these optimizations yield a considerable performance gain along with a reduction of the code size. Thus, our optimizations establish the base for using advanced aspect-oriented modularization techniques for developing Java applications on small embedded devices.

A Zonal Approach for the Solution of Coupled Euler and Potential Solutions of Flows with Complex Geometries.

DTIC Science & Technology

1987-06-01

obtained from: A simple numerical intergration scheme is employed to perform the integral in Equations (B2) and (86) along the dividing streamline. A 11 4...angle of attack was small, the dividing streamline remained almost horizontal in this case. Results of a higher angle of attack case, in which the mesh

Prediction of Work Efficiency in Early Adolescence under the Effects of Noise

ERIC Educational Resources Information Center

Fosnaric, Samo; Planinsec, Jurij

2008-01-01

This is a short summary of research on how different stress factors in the work environment (climate, light, noise) affect work performance of early adolescents. Due to the complexity of the measurements, the research consisted of a small sample of male adolescents (N = 20); average age 13.5 years (SD = 0.25). Tasks were used which demanded…

Work for Play: Careers in Video Game Development

ERIC Educational Resources Information Center

Liming, Drew; Vilorio, Dennis

2011-01-01

Video games are not only for play; they also provide work. Making video games is a serious--and big--business. Creating these games is complex and requires the collaboration of many developers, who perform a variety of tasks, from production to programming. They work for both small and large game studios to create games that can be played on many…

Integer cosine transform for image compression

NASA Technical Reports Server (NTRS)

Cheung, K.-M.; Pollara, F.; Shahshahani, M.

1991-01-01

This article describes a recently introduced transform algorithm called the integer cosine transform (ICT), which is used in transform-based data compression schemes. The ICT algorithm requires only integer operations on small integers and at the same time gives a rate-distortion performance comparable to that offered by the floating-point discrete cosine transform (DCT). The article addresses the issue of implementation complexity, which is of prime concern for source coding applications of interest in deep-space communications. Complexity reduction in the transform stage of the compression scheme is particularly relevant, since this stage accounts for most (typically over 80 percent) of the computational load.

Toolsets Maintain Health of Complex Systems

NASA Technical Reports Server (NTRS)

2010-01-01

First featured in Spinoff 2001, Qualtech Systems Inc. (QSI), of Wethersfield, Connecticut, adapted its Testability, Engineering, and Maintenance System (TEAMS) toolset under Small Business Innovation Research (SBIR) contracts from Ames Research Center to strengthen NASA's systems health management approach for its large, complex, and interconnected systems. Today, six NASA field centers utilize the TEAMS toolset, including TEAMS-Designer, TEAMS-RT, TEAMATE, and TEAMS-RDS. TEAMS is also being used on industrial systems that generate power, carry data, refine chemicals, perform medical functions, and produce semiconductor wafers. QSI finds TEAMS can lower costs by decreasing problems requiring service by 30 to 50 percent.

Complexity of parallel implementation of domain decomposition techniques for elliptic partial differential equations

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

Gropp, W.D.; Keyes, D.E.

1988-03-01

The authors discuss the parallel implementation of preconditioned conjugate gradient (PCG)-based domain decomposition techniques for self-adjoint elliptic partial differential equations in two dimensions on several architectures. The complexity of these methods is described on a variety of message-passing parallel computers as a function of the size of the problem, number of processors and relative communication speeds of the processors. They show that communication startups are very important, and that even the small amount of global communication in these methods can significantly reduce the performance of many message-passing architectures.

A Hierarchical Algorithm for Fast Debye Summation with Applications to Small Angle Scattering

PubMed Central

Gumerov, Nail A.; Berlin, Konstantin; Fushman, David; Duraiswami, Ramani

2012-01-01

Debye summation, which involves the summation of sinc functions of distances between all pair of atoms in three dimensional space, arises in computations performed in crystallography, small/wide angle X-ray scattering (SAXS/WAXS) and small angle neutron scattering (SANS). Direct evaluation of Debye summation has quadratic complexity, which results in computational bottleneck when determining crystal properties, or running structure refinement protocols that involve SAXS or SANS, even for moderately sized molecules. We present a fast approximation algorithm that efficiently computes the summation to any prescribed accuracy ε in linear time. The algorithm is similar to the fast multipole method (FMM), and is based on a hierarchical spatial decomposition of the molecule coupled with local harmonic expansions and translation of these expansions. An even more efficient implementation is possible when the scattering profile is all that is required, as in small angle scattering reconstruction (SAS) of macromolecules. We examine the relationship of the proposed algorithm to existing approximate methods for profile computations, and show that these methods may result in inaccurate profile computations, unless an error bound derived in this paper is used. Our theoretical and computational results show orders of magnitude improvement in computation complexity over existing methods, while maintaining prescribed accuracy. PMID:22707386

AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.

PubMed

Labbé, Céline M; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O; Pajeva, Ilza; Miteva, Maria A

2017-07-03

AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics

PubMed Central

Labbé, Céline M.; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O.; Pajeva, Ilza

2017-01-01

Abstract AMMOS2 is an interactive web server for efficient computational refinement of protein–small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein–ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein–ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein–ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein–ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein–ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. PMID:28486703

An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes.

PubMed

Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Masaki, Shunpei; Nakayama, Hiroshi; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

2009-11-01

We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a approximately 21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes.

Isoelectric focusing of small non-covalent metal species from plants.

PubMed

Köster, Jessica; Hayen, Heiko; von Wirén, Nicolaus; Weber, Günther

2011-03-01

IEF is known as a powerful electrophoretic separation technique for amphoteric molecules, in particular for proteins. The objective of the present work is to prove the suitability of IEF also for the separation of small, non-covalent metal species. Investigations are performed with copper-glutathione complexes, with the synthetic ligand ethylenediamine-N,N'-bis(o-hydroxyphenyl)acetic acid (EDDHA) and respective metal complexes (Fe, Ga, Al, Ni, Zn), and with the phytosiderophore 2'-deoxymugineic acid (DMA) and its ferric complex. It is shown that ethylenediamine-N,N'-bis(o-hydroxyphenyl)acetic acid and DMA species are stable during preparative scale IEF, whereas copper-glutathione dissociates considerably. It is also shown that preparative scale IEF can be applied successfully to isolate ferric DMA from real plant samples, and that multidimensional separations are possible by combining preparative scale IEF with subsequent HPLC-MS analysis. Focusing of free ligands and respective metal complexes with di- and trivalent metals results in different pIs, but CIEF is usually needed for a reliable estimation of pI values. Limitations of the proposed methods (preparative IEF and CIEF) and consequences of the results with respect to metal speciation in plants are discussed. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteoform-specific protein binding of small molecules in complex matrices

USDA-ARS?s Scientific Manuscript database

Characterizing the specific binding between protein targets and small molecules is critically important for drug discovery. Conventional assays require isolation and purification of small molecules from complex matrices through multistep chromatographic fractionation, which may alter their original ...

Ravens, New Caledonian crows and jackdaws parallel great apes in motor self-regulation despite smaller brains.

PubMed

Kabadayi, Can; Taylor, Lucy A; von Bayern, Auguste M P; Osvath, Mathias

2016-04-01

Overriding motor impulses instigated by salient perceptual stimuli represent a fundamental inhibitory skill. Such motor self-regulation facilitates more rational behaviour, as it brings economy into the bodily interaction with the physical and social world. It also underlies certain complex cognitive processes including decision making. Recently, MacLean et al. (MacLean et al. 2014 Proc. Natl Acad. Sci. USA 111, 2140-2148. (doi:10.1073/pnas.1323533111)) conducted a large-scale study involving 36 species, comparing motor self-regulation across taxa. They concluded that absolute brain size predicts level of performance. The great apes were most successful. Only a few of the species tested were birds. Given birds' small brain size-in absolute terms-yet flexible behaviour, their motor self-regulation calls for closer study. Corvids exhibit some of the largest relative avian brain sizes-although small in absolute measure-as well as the most flexible cognition in the animal kingdom. We therefore tested ravens, New Caledonian crows and jackdaws in the so-called cylinder task. We found performance indistinguishable from that of great apes despite the much smaller brains. We found both absolute and relative brain volume to be a reliable predictor of performance within Aves. The complex cognition of corvids is often likened to that of great apes; our results show further that they share similar fundamental cognitive mechanisms.

Size ratio performance in detecting cerebral aneurysm rupture status is insensitive to small vessel removal.

PubMed

Lauric, Alexandra; Baharoglu, Merih I; Malek, Adel M

2013-04-01

The variable definition of size ratio (SR) for sidewall (SW) vs bifurcation (BIF) aneurysms raises confusion for lesions harboring small branches, such as carotid ophthalmic or posterior communicating locations. These aneurysms are considered SW by many clinicians, but SR methodology classifies them as BIF. To evaluate the effect of ignoring small vessels and SW vs stringent BIF labeling on SR ruptured aneurysm detection performance in borderline aneurysms with small branches, and to reconcile SR-based labeling with clinical SW/BIF classification. Catheter rotational angiographic datasets of 134 consecutive aneurysms (60 ruptured) were automatically measured in 3-dimensional. Stringent BIF labeling was applied to clinically labeled aneurysms, with 21 aneurysms switching label from SW to BIF. Parent vessel size was evaluated both taking into account, and ignoring, small vessels. SR was defined accordingly as the ratio between aneurysm and parent vessel sizes. Univariate and multivariate statistics identified significant features. The square of the correlation coefficient (R(2)) was reported for bivariate analysis of alternative SR calculations. Regardless of SW/BIF labeling method, SR was equally significant in discriminating aneurysm ruptured status (P < .001). Bivariate analysis of alternative SR had a high correlation of R(2) = 0.94 on the whole dataset, and R = 0.98 on the 21 borderline aneurysms. Ignoring small branches from SR calculation maintains rupture status detection performance, while reducing postprocessing complexity and removing labeling ambiguity. Aneurysms adjacent to these vessels can be considered SW for morphometric analysis. It is reasonable to use the clinical SW/BIF labeling when using SR for rupture risk evaluation.

Advanced Stochastic Collocation Methods for Polynomial Chaos in RAVEN

NASA Astrophysics Data System (ADS)

Talbot, Paul W.

As experiment complexity in fields such as nuclear engineering continually increases, so does the demand for robust computational methods to simulate them. In many simulations, input design parameters and intrinsic experiment properties are sources of uncertainty. Often small perturbations in uncertain parameters have significant impact on the experiment outcome. For instance, in nuclear fuel performance, small changes in fuel thermal conductivity can greatly affect maximum stress on the surrounding cladding. The difficulty quantifying input uncertainty impact in such systems has grown with the complexity of numerical models. Traditionally, uncertainty quantification has been approached using random sampling methods like Monte Carlo. For some models, the input parametric space and corresponding response output space is sufficiently explored with few low-cost calculations. For other models, it is computationally costly to obtain good understanding of the output space. To combat the expense of random sampling, this research explores the possibilities of using advanced methods in Stochastic Collocation for generalized Polynomial Chaos (SCgPC) as an alternative to traditional uncertainty quantification techniques such as Monte Carlo (MC) and Latin Hypercube Sampling (LHS) methods for applications in nuclear engineering. We consider traditional SCgPC construction strategies as well as truncated polynomial spaces using Total Degree and Hyperbolic Cross constructions. We also consider applying anisotropy (unequal treatment of different dimensions) to the polynomial space, and offer methods whereby optimal levels of anisotropy can be approximated. We contribute development to existing adaptive polynomial construction strategies. Finally, we consider High-Dimensional Model Reduction (HDMR) expansions, using SCgPC representations for the subspace terms, and contribute new adaptive methods to construct them. We apply these methods on a series of models of increasing complexity. We use analytic models of various levels of complexity, then demonstrate performance on two engineering-scale problems: a single-physics nuclear reactor neutronics problem, and a multiphysics fuel cell problem coupling fuels performance and neutronics. Lastly, we demonstrate sensitivity analysis for a time-dependent fuels performance problem. We demonstrate the application of all the algorithms in RAVEN, a production-level uncertainty quantification framework.

Modeling the effects of fire severity and spatial complexity on Small Mammals in Yosemite National Park, California

USGS Publications Warehouse

Roberts, Susan L.; Van Wagtendonk, Jan W.; Miles, A. Keith; Kelt, Douglas A.; Lutz, James A.

2008-01-01

We evaluated the impact of fire severity and related spatial and vegetative parameters on small mammal populations in 2 yr- to 15 yr-old burns in Yosemite National Park, California, USA. We also developed habitat models that would predict small mammal responses to fires of differing severity. We hypothesized that fire severity would influence the abundances of small mammals through changes in vegetation composition, structure, and spatial habitat complexity. Deer mouse (Peromyscus maniculatus) abundance responded negatively to fire severity, and brush mouse (P. boylii) abundance increased with increasing oak tree (Quercus spp.) cover. Chipmunk (Neotamias spp.) abundance was best predicted through a combination of a negative response to oak tree cover and a positive response to spatial habitat complexity. California ground squirrel (Spermophilus beecheyi) abundance increased with increasing spatial habitat complexity. Our results suggest that fire severity, with subsequent changes in vegetation structure and habitat spatial complexity, can influence small mammal abundance patterns.

Strategic Performance Management: Organizing People and Their Work in the SEA of the Future

ERIC Educational Resources Information Center

Redding, Sam; Layland, Allison

2015-01-01

A State Education Agency (SEA), whether in a large state or small, is responsible for a complex education system, responsive to a host of stakeholders, and charged with advocating for a multitude of students of all ages attending schools of every description. Much of what an SEA is tasked with accomplishing is set by external entities, from the…

SNPing at the Epidermal Barrier.

PubMed

Kelsell, David P; Byrne, Carolyn

2011-08-01

Filaggrin variants are well-established risk factors for atopic eczema (AE). Recent studies suggest additional epidermal differentiation complex (EDC) gene associations with AE. In this issue, Marenholz and colleagues confirm this prediction and show that a small proline-rich protein 3 (SPRR3) variant confers susceptibility to AE. This finding suggests that further genetic and functional characterization of SPRR3 should be performed in patients with AE.

Cavity-enhanced measurements for determining dielectric-membrane thickness and complex index of refraction.

PubMed

Stambaugh, Corey; Durand, Mathieu; Kemiktarak, Utku; Lawall, John

2014-08-01

The material properties of silicon nitride (SiN) play an important role in the performance of SiN membranes used in optomechanical applications. An optimum design of a subwavelength high-contrast grating requires accurate knowledge of the membrane thickness and index of refraction, and its performance is ultimately limited by material absorption. Here we describe a cavity-enhanced method to measure the thickness and complex index of refraction of dielectric membranes with small, but nonzero, absorption coefficients. By determining Brewster's angle and an angle at which reflection is minimized by means of destructive interference, both the real part of the index of refraction and the sample thickness can be measured. A comparison of the losses in the empty cavity and the cavity containing the dielectric sample provides a measurement of the absorption.

Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes.

PubMed

Risthaus, Tobias; Grimme, Stefan

2013-03-12

A new test set (S12L) containing 12 supramolecular noncovalently bound complexes is presented and used to evaluate seven different methods to account for dispersion in DFT (DFT-D3, DFT-D2, DFT-NL, XDM, dDsC, TS-vdW, M06-L) at different basis set levels against experimental, back-corrected reference energies. This allows conclusions about the performance of each method in an explorative research setting on "real-life" problems. Most DFT methods show satisfactory performance but, due to the largeness of the complexes, almost always require an explicit correction for the nonadditive Axilrod-Teller-Muto three-body dispersion interaction to get accurate results. The necessity of using a method capable of accounting for dispersion is clearly demonstrated in that the two-body dispersion contributions are on the order of 20-150% of the total interaction energy. MP2 and some variants thereof are shown to be insufficient for this while a few tested D3-corrected semiempirical MO methods perform reasonably well. Overall, we suggest the use of this benchmark set as a "sanity check" against overfitting to too small molecular cases.

Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions.

PubMed

Peterson, Lenna X; Shin, Woong-Hee; Kim, Hyungrae; Kihara, Daisuke

2018-03-01

We report our group's performance for protein-protein complex structure prediction and scoring in Round 37 of the Critical Assessment of PRediction of Interactions (CAPRI), an objective assessment of protein-protein complex modeling. We demonstrated noticeable improvement in both prediction and scoring compared to previous rounds of CAPRI, with our human predictor group near the top of the rankings and our server scorer group at the top. This is the first time in CAPRI that a server has been the top scorer group. To predict protein-protein complex structures, we used both multi-chain template-based modeling (TBM) and our protein-protein docking program, LZerD. LZerD represents protein surfaces using 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. Because 3DZD are a soft representation of the protein surface, LZerD is tolerant to small conformational changes, making it well suited to docking unbound and TBM structures. The key to our improved performance in CAPRI Round 37 was to combine multi-chain TBM and docking. As opposed to our previous strategy of performing docking for all target complexes, we used TBM when multi-chain templates were available and docking otherwise. We also describe the combination of multiple scoring functions used by our server scorer group, which achieved the top rank for the scorer phase. © 2017 Wiley Periodicals, Inc.

On Convergence of Development Costs and Cost Models for Complex Spaceflight Instrument Electronics

NASA Technical Reports Server (NTRS)

Kizhner, Semion; Patel, Umeshkumar D.; Kasa, Robert L.; Hestnes, Phyllis; Brown, Tammy; Vootukuru, Madhavi

2008-01-01

Development costs of a few recent spaceflight instrument electrical and electronics subsystems have diverged from respective heritage cost model predictions. The cost models used are Grass Roots, Price-H and Parametric Model. These cost models originated in the military and industry around 1970 and were successfully adopted and patched by NASA on a mission-by-mission basis for years. However, the complexity of new instruments recently changed rapidly by orders of magnitude. This is most obvious in the complexity of representative spaceflight instrument electronics' data system. It is now required to perform intermediate processing of digitized data apart from conventional processing of science phenomenon signals from multiple detectors. This involves on-board instrument formatting of computational operands from row data for example, images), multi-million operations per second on large volumes of data in reconfigurable hardware (in addition to processing on a general purpose imbedded or standalone instrument flight computer), as well as making decisions for on-board system adaptation and resource reconfiguration. The instrument data system is now tasked to perform more functions, such as forming packets and instrument-level data compression of more than one data stream, which are traditionally performed by the spacecraft command and data handling system. It is furthermore required that the electronics box for new complex instruments is developed for one-digit watt power consumption, small size and that it is light-weight, and delivers super-computing capabilities. The conflict between the actual development cost of newer complex instruments and its electronics components' heritage cost model predictions seems to be irreconcilable. This conflict and an approach to its resolution are addressed in this paper by determining the complexity parameters, complexity index, and their use in enhanced cost model.

N-heterocyclic carbene gold(I) and silver(I) complexes bearing functional groups for bio-conjugation

PubMed Central

Garner, Mary E.; Niu, Weijia; Chen, Xigao; Ghiviriga, Ion; Tan, Weihong; Veige, Adam S.

2015-01-01

This work describes several synthetic approaches to append organic functional groups to gold and silver N-heterocyclic carbene (NHC) complexes suitable for applications in biomolecule conjugation. Carboxylate appended NHC ligands (3) lead to unstable AuI complexes that convert into bis-NHC species (4). A benzyl protected carboxylate NHC-AuI complex 2 was synthesized but deprotection to produce the carboxylic acid functionality could not be achieved. A small library of new alkyne functionalized NHC proligands were synthesized and used for subsequent silver and gold metalation reactions. The alkyne appended NHC gold complex 13 readily react with benzyl azide in a copper catalyzed azide-alkyne cycloaddition reaction to form the triazole appended NHC gold complex 14. Cell cytotoxicity studies were performed on DLD-1 (colorectal adenocarcinoma), Hep-G2 (hepatocellular carcinoma), MCF-7 (breast adenocarcinoma), CCRF-CEM (human T-Cell leukemia), and HEK (human embryonic kidney). Complete spectroscopic characterization of the ligands and complexes was achieved using 1H and 13C NMR, gHMBC, ESI-MS, and combustion analysis. PMID:25490699

Pancreatic cancer planning: Complex conformal vs modulated therapies.

PubMed

Chapman, Katherine L; Witek, Matthew E; Chen, Hongyu; Showalter, Timothy N; Bar-Ad, Voichita; Harrison, Amy S

2016-01-01

To compare the roles of intensity-modulated radiation therapy (IMRT) and volumetric- modulated arc therapy (VMAT) therapy as compared to simple and complex 3-dimensional chemoradiotherpy (3DCRT) planning for resectable and borderline resectable pancreatic cancer. In all, 12 patients who received postoperative radiotherapy (8) or neoadjuvant concurrent chemoradiotherapy (4) were evaluated retrospectively. Radiotherapy planning was performed for 4 treatment techniques: simple 4-field box, complex 5-field 3DCRT, 5 to 6-field IMRT, and single-arc VMAT. All volumes were approved by a single observer in accordance with Radiation Therapy Oncology Group (RTOG) Pancreas Contouring Atlas. Plans included tumor/tumor bed and regional lymph nodes to 45Gy; with tumor/tumor bed boosted to 50.4Gy, at least 95% of planning target volume (PTV) received the prescription dose. Dose-volume histograms (DVH) for multiple end points, treatment planning, and delivery time were assessed. Complex 3DCRT, IMRT, and VMAT plans significantly (p < 0.05) decreased mean kidney dose, mean liver dose, liver (V30, V35), stomach (D10%), stomach (V45), mean right kidney dose, and right kidney (V15) as compared with the simple 4-field plans that are most commonly reported in the literature. IMRT plans resulted in decreased mean liver dose, liver (V35), and left kidney (V15, V18, V20). VMAT plans decreased small bowel (D10%, D15%), small bowel (V35, V45), stomach (D10%, D15%), stomach (V35, V45), mean liver dose, liver (V35), left kidney (V15, V18, V20), and right kidney (V18, V20). VMAT plans significantly decreased small bowel (D10%, D15%), left kidney (V20), and stomach (V45) as compared with IMRT plans. Treatment planning and delivery times were most efficient for simple 4-field box and VMAT. Excluding patient setup and imaging, average treatment delivery was within 10minutes for simple and complex 3DCRT, IMRT, and VMAT treatments. This article shows significant improvements in 3D plan performance with complex planning over the more frequently compared 3- or 4-field simple 3D planning techniques. VMAT plans continue to demonstrate potential for the most organ sparing. However, further studies are required to identify if dosimetric benefits associated with inverse optimized planning can be translated into clinical benefits and if these treatment techniques are value-added therapies for this group of patients with cancer. Published by Elsevier Inc.

Resolution-independent surface rendering using programmable graphics hardware

DOEpatents

Loop, Charles T.; Blinn, James Frederick

2008-12-16

Surfaces defined by a Bezier tetrahedron, and in particular quadric surfaces, are rendered on programmable graphics hardware. Pixels are rendered through triangular sides of the tetrahedra and locations on the shapes, as well as surface normals for lighting evaluations, are computed using pixel shader computations. Additionally, vertex shaders are used to aid interpolation over a small number of values as input to the pixel shaders. Through this, rendering of the surfaces is performed independently of viewing resolution, allowing for advanced level-of-detail management. By individually rendering tetrahedrally-defined surfaces which together form complex shapes, the complex shapes can be rendered in their entirety.

A Global Approach to the Optimal Trajectory Based on an Improved Ant Colony Algorithm for Cold Spray

NASA Astrophysics Data System (ADS)

Cai, Zhenhua; Chen, Tingyang; Zeng, Chunnian; Guo, Xueping; Lian, Huijuan; Zheng, You; Wei, Xiaoxu

2016-12-01

This paper is concerned with finding a global approach to obtain the shortest complete coverage trajectory on complex surfaces for cold spray applications. A slicing algorithm is employed to decompose the free-form complex surface into several small pieces of simple topological type. The problem of finding the optimal arrangement of the pieces is translated into a generalized traveling salesman problem (GTSP). Owing to its high searching capability and convergence performance, an improved ant colony algorithm is then used to solve the GTSP. Through off-line simulation, a robot trajectory is generated based on the optimized result. The approach is applied to coat real components with a complex surface by using the cold spray system with copper as the spraying material.

Clinical features and treatment outcome of non-small cell lung cancer (NSCLC) patients with uncommon or complex epidermal growth factor receptor (EGFR) mutations

PubMed Central

Fassan, Matteo; Indraccolo, Stefano; Calabrese, Fiorella; Favaretto, Adolfo; Bonanno, Laura; Polo, Valentina; Zago, Giulia; Lunardi, Francesca; Attili, Ilaria; Pavan, Alberto; Rugge, Massimo; Guarneri, Valentina; Conte, PierFranco; Pasello, Giulia

2017-01-01

Introduction Tyrosine-kinase inhibitors (TKIs) represent the best treatment for advanced non-small cell lung cancer (NSCLC) with common exon 19 deletion or exon 21 epidermal growth factor receptor mutation (EGFRm). This is an observational study investigating epidemiology, clinical features and treatment outcome of NSCLC cases harbouring rare/complex EGFRm. Results Among 764 non-squamous NSCLC cases with known EGFRm status, 26(3.4%) harboured rare/complex EGFRm. Patients receiving first-line TKIs (N = 17) achieved median Progression Free Survival (PFS) and Overall Survival (OS) of 53 (IC 95%, 2–105) and 84 (CI 95%, 27–141) weeks respectively, without significant covariate impact. Response Rate and Disease Control Rate (DCR) were 47% and 65%, respectively. Uncommon exon 19 mutations achieved longer OS and PFS and higher DCR compared with exon 18 and 20 mutations. No additional gene mutation was discovered by MassARRAY analysis. TKIs were globally well tolerated. Materials and methods A retrospective review of advanced non-squamous NSCLC harbouring rare/complex EGFRm referred to our Center between 2010 and 2015 was performed. Additional molecular pathways disregulation was explored in selected cases, through MassARRAY analysis. Conclusions Peculiar clinical features and lower TKIs sensitivity of uncommon/complex compared with common EGFRm were shown. Exon 19 EGFRm achieved the best TKIs treatment outcome, while the optimal treatment of exon 18 and 20 mutations should be further clarified. PMID:28427238

Synthetic vision display evaluation studies

NASA Technical Reports Server (NTRS)

Regal, David M.; Whittington, David H.

1994-01-01

The goal of this research was to help us understand the display requirements for a synthetic vision system for the High Speed Civil Transport (HSCT). Four experiments were conducted to examine the effects of different levels of perceptual cue complexity in displays used by pilots in a flare and landing task. Increased levels of texture mapping of terrain and runway produced mixed results, including harder but shorter landings and a lower flare initiation altitude. Under higher workload conditions, increased texture resulted in an improvement in performance. An increase in familiar size cues did not result in improved performance. Only a small difference was found between displays using two patterns of high resolution texture mapping. The effects of increased perceptual cue complexity on performance was not as strong as would be predicted from the pilot's subjective reports or from related literature. A description of the role of a synthetic vision system in the High Speed Civil Transport is provide along with a literature review covering applied research related to perceptual cue usage in aircraft displays.

NetMHCstab – predicting stability of peptide–MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery

PubMed Central

Jørgensen, Kasper W; Rasmussen, Michael; Buus, Søren; Nielsen, Morten

2014-01-01

Major histocompatibility complex class I (MHC-I) molecules play an essential role in the cellular immune response, presenting peptides to cytotoxic T lymphocytes (CTLs) allowing the immune system to scrutinize ongoing intracellular production of proteins. In the early 1990s, immunogenicity and stability of the peptide–MHC-I (pMHC-I) complex were shown to be correlated. At that time, measuring stability was cumbersome and time consuming and only small data sets were analysed. Here, we investigate this fairly unexplored area on a large scale compared with earlier studies. A recent small-scale study demonstrated that pMHC-I complex stability was a better correlate of CTL immunogenicity than peptide–MHC-I affinity. We here extended this study and analysed a total of 5509 distinct peptide stability measurements covering 10 different HLA class I molecules. Artificial neural networks were used to construct stability predictors capable of predicting the half-life of the pMHC-I complex. These predictors were shown to predict T-cell epitopes and MHC ligands from SYFPEITHI and IEDB to form significantly more stable MHC-I complexes compared with affinity-matched non-epitopes. Combining the stability predictions with a state-of-the-art affinity predictions NetMHCcons significantly improved the performance for identification of T-cell epitopes and ligands. For the HLA alleles included in the study, we could identify distinct sub-motifs that differentiate between stable and unstable peptide binders and demonstrate that anchor positions in the N-terminal of the binding motif (primarily P2 and P3) play a critical role for the formation of stable pMHC-I complexes. A webserver implementing the method is available at http://www.cbs.dtu.dk/services/NetMHCstab. PMID:23927693

From metamorphosis to maturity in complex life cycles: equal performance of different juvenile life history pathways.

PubMed

Schmidt, Benedikt R; Hödl, Walter; Schaub, Michael

2012-03-01

Performance in one stage of a complex life cycle may affect performance in the subsequent stage. Animals that start a new stage at a smaller size than conspecifics may either always remain smaller or they may be able to "catch up" through plasticity, usually elevated growth rates. We study how size at and date of metamorphosis affected subsequent performance in the terrestrial juvenile stage and lifetime fitness of spadefoot toads (Pelobates fuscus). We analyzed capture-recapture data of > 3000 individuals sampled during nine years with mark-recapture models to estimate first-year juvenile survival probabilities and age-specific first-time breeding probabilities of toads, followed by model selection to assess whether these probabilities were correlated with size at and date of metamorphosis. Males attained maturity after two years, whereas females reached maturity 2-4 years after metamorphosis. Age at maturity was weakly correlated with metamorphic traits. In both sexes, first-year juvenile survival depended positively on date of metamorphosis and, in males, also negatively on size at metamorphosis. In males, toads that metamorphosed early at a small size had the highest probability to reach maturity. However, because very few toadlets metamorphosed early, the vast majority of male metamorphs had a very similar probability to reach maturity. A matrix projection model constructed for females showed that different juvenile life history pathways resulted in similar lifetime fitness. We found that the effects of date of and size at metamorphosis on different juvenile traits cancelled each other out such that toads that were small or large at metamorphosis had equal performance. Because the costs and benefits of juvenile life history pathways may also depend on population fluctuations, ample phenotypic variation in life history traits may be maintained.

FlexAID: Revisiting Docking on Non-Native-Complex Structures.

PubMed

Gaudreault, Francis; Najmanovich, Rafael J

2015-07-27

Small-molecule protein docking is an essential tool in drug design and to understand molecular recognition. In the present work we introduce FlexAID, a small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specific geometric criteria, based on surface complementarity. The pairwise energy parameters were derived from a large dataset of true positive poses and negative decoys from the PDBbind database through an iterative process using Monte Carlo simulations. The prediction of binding poses is tested using the widely used Astex dataset as well as the HAP2 dataset, while performance in virtual screening is evaluated using a subset of the DUD dataset. We compare FlexAID to AutoDock Vina, FlexX, and rDock in an extensive number of scenarios to understand the strengths and limitations of the different programs as well as to reported results for Glide, GOLD, and DOCK6 where applicable. The most relevant among these scenarios is that of docking on flexible non-native-complex structures where as is the case in reality, the target conformation in the bound form is not known a priori. We demonstrate that FlexAID, unlike other programs, is robust against increasing structural variability. FlexAID obtains equivalent sampling success as GOLD and performs better than AutoDock Vina or FlexX in all scenarios against non-native-complex structures. FlexAID is better than rDock when there is at least one critical side-chain movement required upon ligand binding. In virtual screening, FlexAID results are lower on average than those of AutoDock Vina and rDock. The higher accuracy in flexible targets where critical movements are required, intuitive PyMOL-integrated graphical user interface and free source code as well as precompiled executables for Windows, Linux, and Mac OS make FlexAID a welcome addition to the arsenal of existing small-molecule protein docking methods.

Small molecular glasses based on multiposition encapsulated phenyl benzimidazole iridium(III) complexes: toward efficient solution-processable host-free electrophosphorescent diodes.

PubMed

Xu, Hui; Yu, Dong-Hui; Liu, Le-Le; Yan, Peng-Fei; Jia, Li-Wei; Li, Guang-Ming; Yue, Zheng-Yu

2010-01-14

Three electrophosphorescent small molecular Ir(3+) complexes, Ir(HexPhBI)(3) 1 (HexPhBI = 1-Hexyl-2-phenyl-1H-benzo[d]imidazole), Ir(CzPhBI)(3) 2 (CzPhBI = 9-(6-(2-phenyl-1H-benzo[d]imidazol-1-yl)hexyl)-9H-carbazole), and Ir(Cz(2)PhBI)(3) 3 (Cz(2)PhBI = 9-(6-(4-(1-(6-(9H-carbazol-9-yl)hexyl)-1H-benzo[d]imidazol-2-yl)phenoxy)hexyl)-9H-carbazole), were synthesized in which 3 was designed with the structure of multiposition encapsulation. Compared to the hexyl-substituted 1, 2 and 3 end-capped with the conjugated carbazole moieties have improved thermal stability. X-ray diffraction analysis proved the amorphous state of 2 and 3. High-photoluminescent efficiencies of 3 are achieved as 72% in solution and 61% in solid. It indicates that the peripheral carbazoles not only facilitate the separation of triplet-emission cores and reduce the intermolecular aggregation but also supply a routine for the intermolecular energy transfer. Electrochemical analysis showed the more oxidation states of 3, which might be anticipated to make it superior to 1 and 2 in hole injection and transporting. The important role of the peripheral carbazole moieties in carrier injection/transporting and the optical properties of the complexes were further investigated by Gaussian simulation. A dramatic electroluminescent (EL) performance, including external quantum efficiency of nearly 6%, low turn-on voltage of 2.5 V, and high brightness over 6000 cd m(-2), from the host-free spin-coated device of 3 was achieved. The superiority of multiencapsulation in EL was proved by comparing the EL performance of 2 and 3. By making comparison between the host-free and phosphor-doping devices, it indicated that the combined modification of the aliphatic chains and functional groups in multipositions is a feasible approach to realize the high-efficiency small molecular phosphorescent materials.

Short temporal asynchrony disrupts visual object recognition

PubMed Central

Singer, Jedediah M.; Kreiman, Gabriel

2014-01-01

Humans can recognize objects and scenes in a small fraction of a second. The cascade of signals underlying rapid recognition might be disrupted by temporally jittering different parts of complex objects. Here we investigated the time course over which shape information can be integrated to allow for recognition of complex objects. We presented fragments of object images in an asynchronous fashion and behaviorally evaluated categorization performance. We observed that visual recognition was significantly disrupted by asynchronies of approximately 30 ms, suggesting that spatiotemporal integration begins to break down with even small deviations from simultaneity. However, moderate temporal asynchrony did not completely obliterate recognition; in fact, integration of visual shape information persisted even with an asynchrony of 100 ms. We describe the data with a concise model based on the dynamic reduction of uncertainty about what image was presented. These results emphasize the importance of timing in visual processing and provide strong constraints for the development of dynamical models of visual shape recognition. PMID:24819738

Assessment of wastewater treatment alternatives for small communities: An analytic network process approach.

PubMed

Molinos-Senante, María; Gómez, Trinidad; Caballero, Rafael; Hernández-Sancho, Francesc; Sala-Garrido, Ramón

2015-11-01

The selection of the most appropriate wastewater treatment (WWT) technology is a complex problem since many alternatives are available and many criteria are involved in the decision-making process. To deal with this challenge, the analytic network process (ANP) is applied for the first time to rank a set of seven WWT technology set-ups for secondary treatment in small communities. A major advantage of ANP is that it incorporates interdependent relationships between elements. Results illustrated that extensive technologies, constructed wetlands and pond systems are the most preferred alternatives by WWT experts. The sensitivity analysis performed verified that the ranking of WWT alternatives is very stable since constructed wetlands are almost always placed in the first position. This paper showed that ANP analysis is suitable to deal with complex decision-making problems, such as the selection of the most appropriate WWT system contributing to better understand the multiple interdependences among elements involved in the assessment. Copyright © 2015 Elsevier B.V. All rights reserved.

Comprehensive proteomic analysis of the human spliceosome

NASA Astrophysics Data System (ADS)

Zhou, Zhaolan; Licklider, Lawrence J.; Gygi, Steven P.; Reed, Robin

2002-09-01

The precise excision of introns from pre-messenger RNA is performed by the spliceosome, a macromolecular machine containing five small nuclear RNAs and numerous proteins. Much has been learned about the protein components of the spliceosome from analysis of individual purified small nuclear ribonucleoproteins and salt-stable spliceosome `core' particles. However, the complete set of proteins that constitutes intact functional spliceosomes has yet to be identified. Here we use maltose-binding protein affinity chromatography to isolate spliceosomes in highly purified and functional form. Using nanoscale microcapillary liquid chromatography tandem mass spectrometry, we identify ~145 distinct spliceosomal proteins, making the spliceosome the most complex cellular machine so far characterized. Our spliceosomes comprise all previously known splicing factors and 58 newly identified components. The spliceosome contains at least 30 proteins with known or putative roles in gene expression steps other than splicing. This complexity may be required not only for splicing multi-intronic metazoan pre-messenger RNAs, but also for mediating the extensive coupling between splicing and other steps in gene expression.

Reaction factoring and bipartite update graphs accelerate the Gillespie Algorithm for large-scale biochemical systems.

PubMed

Indurkhya, Sagar; Beal, Jacob

2010-01-06

ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for large systems due to computational complexity. We observe, however, that when modeling complex biological systems: (1) a small number of reactions tend to occur a disproportionately large percentage of the time, and (2) a small number of species tend to participate in a disproportionately large percentage of reactions. We exploit these properties in LOLCAT Method, a new implementation of the Gillespie Algorithm. First, factoring reaction propensities allows many propensities dependent on a single species to be updated in a single operation. Second, representing dependencies between reactions with a bipartite graph of reactions and species requires only storage for reactions, rather than the required for a graph that includes only reactions. Together, these improvements allow our implementation of LOLCAT Method to execute orders of magnitude faster than currently existing Gillespie Algorithm variants when simulating several yeast MAPK cascade models.

Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems

PubMed Central

Indurkhya, Sagar; Beal, Jacob

2010-01-01

ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for large systems due to computational complexity. We observe, however, that when modeling complex biological systems: (1) a small number of reactions tend to occur a disproportionately large percentage of the time, and (2) a small number of species tend to participate in a disproportionately large percentage of reactions. We exploit these properties in LOLCAT Method, a new implementation of the Gillespie Algorithm. First, factoring reaction propensities allows many propensities dependent on a single species to be updated in a single operation. Second, representing dependencies between reactions with a bipartite graph of reactions and species requires only storage for reactions, rather than the required for a graph that includes only reactions. Together, these improvements allow our implementation of LOLCAT Method to execute orders of magnitude faster than currently existing Gillespie Algorithm variants when simulating several yeast MAPK cascade models. PMID:20066048

Single-molecule fluorescence measurements reveal the reaction mechanisms of the core RISC, composed of human Argonaute 2 and a guide RNA.

PubMed

Jo, Myung Hyun; Song, Ji-Joon; Hohng, Sungchul

2015-12-01

In eukaryotes, small RNAs play important roles in both gene regulation and resistance to viral infection. Argonaute proteins have been identified as a key component of the effector complexes of various RNA-silencing pathways, but the mechanistic roles of Argonaute proteins in these pathways are not clearly understood. To address this question, we performed single-molecule fluorescence experiments using an RNA-induced silencing complex (core-RISC) composed of a small RNA and human Argonaute 2. We found that target binding of core-RISC starts at the seed region of the guide RNA. After target binding, four distinct reactions followed: target cleavage, transient binding, stable binding, and Argonaute unloading. Target cleavage required extensive sequence complementarity and accelerated core-RISC dissociation for recycling. In contrast, the stable binding of core-RISC to target RNAs required seed-match only, suggesting a potential explanation for the seed-match rule of microRNA (miRNA) target selection.

Application of ultrasonic signature analysis for fatigue detection in complex structures

NASA Technical Reports Server (NTRS)

Zuckerwar, A. J.

1974-01-01

Ultrasonic signature analysis shows promise of being a singularly well-suited method for detecting fatigue in structures as complex as aircraft. The method employs instrumentation centered about a Fourier analyzer system, which features analog-to-digital conversion, digital data processing, and digital display of cross-correlation functions and cross-spectra. These features are essential to the analysis of ultrasonic signatures according to the procedure described here. In order to establish the feasibility of the method, the initial experiments were confined to simple plates with simulated and fatigue-induced defects respectively. In the first test the signature proved sensitive to the size of a small hole drilled into the plate. In the second test, performed on a series of fatigue-loaded plates, the signature proved capable of indicating both the initial appearance and subsequent growth of a fatigue crack. In view of these encouraging results it is concluded that the method has reached a sufficiently advanced stage of development to warrant application to small-scale structures or even actual aircraft.

Fornix and medial temporal lobe lesions lead to comparable deficits in complex visual perception.

PubMed

Lech, Robert K; Koch, Benno; Schwarz, Michael; Suchan, Boris

2016-05-04

Recent research dealing with the structures of the medial temporal lobe (MTL) has shifted away from exclusively investigating memory-related processes and has repeatedly incorporated the investigation of complex visual perception. Several studies have demonstrated that higher level visual tasks can recruit structures like the hippocampus and perirhinal cortex in order to successfully perform complex visual discriminations, leading to a perceptual-mnemonic or representational view of the medial temporal lobe. The current study employed a complex visual discrimination paradigm in two patients suffering from brain lesions with differing locations and origin. Both patients, one with extensive medial temporal lobe lesions (VG) and one with a small lesion of the anterior fornix (HJK), were impaired in complex discriminations while showing otherwise mostly intact cognitive functions. The current data confirmed previous results while also extending the perceptual-mnemonic theory of the MTL to the main output structure of the hippocampus, the fornix. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes.

PubMed

Srihari, Sriganesh; Yong, Chern Han; Patil, Ashwini; Wong, Limsoon

2015-09-14

Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand the functional organisation of cells. In this review, we discuss the key contributions of computational methods developed till date (approximately between 2003 and 2015) for identifying complexes from the network of interacting proteins (PPI network). We evaluate in depth the performance of these methods on PPI datasets from yeast, and highlight their limitations and challenges, in particular at detecting sparse and small or sub-complexes and discerning overlapping complexes. We describe methods for integrating diverse information including expression profiles and 3D structures of proteins with PPI networks to understand the dynamics of complex formation, for instance, of time-based assembly of complex subunits and formation of fuzzy complexes from intrinsically disordered proteins. Finally, we discuss methods for identifying dysfunctional complexes in human diseases, an application that is proving invaluable to understand disease mechanisms and to discover novel therapeutic targets. We hope this review aptly commemorates a decade of research on computational prediction of complexes and constitutes a valuable reference for further advancements in this exciting area. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Complex life cycles and offspring provisioning in marine invertebrates.

PubMed

Marshall, Dustin J; Keough, Michael J

2006-10-01

Offspring size can have pervasive effects throughout an organism's life history. Mothers can make either a few large or many small offspring, and the balance between these extremes is determined by the relationship between offspring size and performance. This relationship in turn is thought to be determined by the offspring's environment. Recently, it has become clear that events in one life-history stage can strongly affect performance in another. Given these strong carryover effects, we asked whether events in the larval phase can change the relationship between offspring size and performance in the adult phase. We manipulated the length of the larval period in the bryozoan Bugula neritina and then examined the relationship between offspring size and various parameters of adult performance under field conditions. We found that despite the adult stage being outplanted into identical conditions, different offspring sizes were predicted to be optimal, depending on the experience of those adults as larvae. This work highlights the fact that the strong phenotypic links between life-history stages may result in optimal offspring size being highly unpredictable for organisms with complex life cycles.

2013 R&D 100 Award: ‘Miniapps’ Bolster High Performance Computing

ScienceCinema

Belak, Jim; Richards, David

2018-06-12

Two Livermore computer scientists served on a Sandia National Laboratories-led team that developed Mantevo Suite 1.0, the first integrated suite of small software programs, also called "miniapps," to be made available to the high performance computing (HPC) community. These miniapps facilitate the development of new HPC systems and the applications that run on them. Miniapps (miniature applications) serve as stripped down surrogates for complex, full-scale applications that can require a great deal of time and effort to port to a new HPC system because they often consist of hundreds of thousands of lines of code. The miniapps are a prototype that contains some or all of the essentials of the real application but with many fewer lines of code, making the miniapp more versatile for experimentation. This allows researchers to more rapidly explore options and optimize system design, greatly improving the chances the full-scale application will perform successfully. These miniapps have become essential tools for exploring complex design spaces because they can reliably predict the performance of full applications.

Sleep Consolidates Motor Learning of Complex Movement Sequences in Mice.

PubMed

Nagai, Hirotaka; de Vivo, Luisa; Bellesi, Michele; Ghilardi, Maria Felice; Tononi, Giulio; Cirelli, Chiara

2017-02-01

Sleep-dependent consolidation of motor learning has been extensively studied in humans, but it remains unclear why some, but not all, learned skills benefit from sleep. Here, we compared 2 different motor tasks, both requiring the mice to run on an accelerating device. In the rotarod task, mice learn to maintain balance while running on a small rod, while in the complex wheel task, mice run on an accelerating wheel with an irregular rung pattern. In the rotarod task, performance improved to the same extent after sleep or after sleep deprivation (SD). Overall, using 7 different experimental protocols (41 sleep deprived mice, 26 sleeping controls), we found large interindividual differences in the learning and consolidation of the rotarod task, but sleep before/after training did not account for this variability. By contrast, using the complex wheel, we found that sleep after training, relative to SD, led to better performance from the beginning of the retest session, and longer sleep was correlated with greater subsequent performance. As in humans, the effects of sleep showed large interindividual variability and varied between fast and slow learners, with sleep favoring the preservation of learned skills in fast learners and leading to a net offline gain in the performance in slow learners. Using Fos expression as a proxy for neuronal activation, we also found that complex wheel training engaged motor cortex and hippocampus more than the rotarod training. Sleep specifically consolidates a motor skill that requires complex movement sequences and strongly engages both motor cortex and hippocampus. © Sleep Research Society 2016. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

Airborne Human Odorants: Detection, Dispersion and Characterization

DTIC Science & Technology

2012-03-01

begin this research. To allow the quantification of various human odorants we first calibrated the gas chromatography -mass spectrometry system that...odorants we have chosen for study are emitted from the body in axillary sweat which is a complex mixture of water, protein, lipids and other small...will be employed to quantify odorants collected from various headspaces . Experiment 1: a.) Calibration of GC-MS system was performed by injecting

Model-based inference for small area estimation with sampling weights

PubMed Central

Vandendijck, Y.; Faes, C.; Kirby, R.S.; Lawson, A.; Hens, N.

2017-01-01

Obtaining reliable estimates about health outcomes for areas or domains where only few to no samples are available is the goal of small area estimation (SAE). Often, we rely on health surveys to obtain information about health outcomes. Such surveys are often characterised by a complex design, stratification, and unequal sampling weights as common features. Hierarchical Bayesian models are well recognised in SAE as a spatial smoothing method, but often ignore the sampling weights that reflect the complex sampling design. In this paper, we focus on data obtained from a health survey where the sampling weights of the sampled individuals are the only information available about the design. We develop a predictive model-based approach to estimate the prevalence of a binary outcome for both the sampled and non-sampled individuals, using hierarchical Bayesian models that take into account the sampling weights. A simulation study is carried out to compare the performance of our proposed method with other established methods. The results indicate that our proposed method achieves great reductions in mean squared error when compared with standard approaches. It performs equally well or better when compared with more elaborate methods when there is a relationship between the responses and the sampling weights. The proposed method is applied to estimate asthma prevalence across districts. PMID:28989860

Integrated chemiresistor array for small sensor platforms

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

HUGHES,ROBERT C.; CASALNUOVO,STEPHEN A.; WESSENDORF,KURT O.

2000-04-13

Chemiresistors are fabricated from materials that change their electrical resistance when exposed to certain chemical species. Composites of soluble polymers with metallic particles have shown remarkable sensitivity to many volatile organic chemicals, depending on the ability of the analyte molecules to swell the polymer matrix. These sensors can be made extremely small (< 100 square microns), operate at ambient temperatures, and require almost no power to read-out. However, the chemiresistor itself is only a part of a more complex sensor system that delivers chemical information to a user who can act on the information. The authors present the design, fabricationmore » and performance of a chemiresistor array chip with four different chemiresistor materials, heaters and a temperature sensor. They also show the design and fabrication of an integrated chemiresistor array, where the electronics to read-out the chemiresistors is on the same chip with the electrodes for the chemiresistors. The circuit was designed to perform several functions to make the sensor data more useful. This low-power, integrated chemiresistor array is small enough to be deployed on a Sandia-developed microrobot platform.« less

Preparation and structural characterization of corn starch-aroma compound inclusion complexes.

PubMed

Zhang, Shu; Zhou, Yibin; Jin, Shanshan; Meng, Xin; Yang, Liping; Wang, Haisong

2017-01-01

Six corn starch inclusion complexes were synthesized using small nonpolar or weak polar aroma compounds (heptanolide, carvone and menthone) and small polar aroma compounds (linalool, heptanol and menthol). The objectives of this study were to (a) investigate the ability of corn starch to form inclusion complexes with these aroma compounds and (b) characterize the structure of the corn starch inclusion complexes. The resulting inclusion ratios were 75.6, 36.9, 43.8, 91.9, 67.2 and 54.7% for heptanolide, carvone, menthone, linalool, heptanol and menthol respectively. The inclusion complexes had laminated structures with a certain amount of holes or blocky constructions. Compared with gelatinized corn starch, the transition temperatures, peak temperatures and enthalpies of the inclusion complexes were significantly different. The major peak of CO at 1771 cm -1 and significant peak shifts revealed the formation of inclusion complexes. X-ray diffractometry (XRD) analyses revealed that the crystallinity of corn starch-polar aroma compound inclusion complexes increased. Based on cross-polarization magic angle spinning 13 C nuclear magnetic resonance (CP-MAS 13 C NMR) results, novel peaks and chemical shifts were attributed to the presence of small aroma compounds, thereby confirming the formation of corn starch inclusion complexes. Small nonpolar and polar aroma compounds can be complexed to corn starch. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Self-Healing Networks: Redundancy and Structure

PubMed Central

Quattrociocchi, Walter; Caldarelli, Guido; Scala, Antonio

2014-01-01

We introduce the concept of self-healing in the field of complex networks modelling; in particular, self-healing capabilities are implemented through distributed communication protocols that exploit redundant links to recover the connectivity of the system. We then analyze the effect of the level of redundancy on the resilience to multiple failures; in particular, we measure the fraction of nodes still served for increasing levels of network damages. Finally, we study the effects of redundancy under different connectivity patterns—from planar grids, to small-world, up to scale-free networks—on healing performances. Small-world topologies show that introducing some long-range connections in planar grids greatly enhances the resilience to multiple failures with performances comparable to the case of the most resilient (and least realistic) scale-free structures. Obvious applications of self-healing are in the important field of infrastructural networks like gas, power, water, oil distribution systems. PMID:24533065

Cationic liquid crystalline nanoparticles for the delivery of synthetic RNAi-based therapeutics.

PubMed

Gentile, Emanuela; Oba, Taro; Lin, Jing; Shao, Ruping; Meng, Feng; Cao, Xiaobo; Lin, Heather Y; Mourad, Majidi; Pataer, Apar; Baladandayuthapani, Veerabhadran; Cai, Dong; Roth, Jack A; Ji, Lin

2017-07-18

RNA interference (RNAi)-based therapeutics have been used to silence the expression of targeted pathological genes. Small interfering RNA (siRNAs) and microRNA (miRNAs) inhibitor have performed this function. However, short half-life, poor cellular uptake, and nonspecific distribution of small RNAs call for the development of novel delivery systems to facilitate the use of RNAi. We developed a novel cationic liquid crystalline nanoparticle (CLCN) to efficiently deliver synthetic siRNAs and miRNAs. CLCNs were prepared by using high-speed homogenization and assembled with synthetic siRNA or miRNA molecules in nuclease-free water to create CLCN/siRNA or miRNA complexes. The homogeneous and stable CLCNs and CLCN-siRNA complexes were about 100 nm in diameter, with positively charged surfaces. CLCNs are nontoxic and are taken up by human cells though endocytosis. Significant inhibition of gene expression was detected in transiently transfected lung cancer H1299 cells treated with CLCNs/anti-GFP complexes 24 hours after transfection. Biodistribution analysis showed that the CLCNs and CLCNs-RNAi complexes were successfully delivered to various organs and into the subcutaneous human lung cancer H1299 tumor xenografts in mice 24 hours after systemic administration. These results suggest that CLCNs are a unique and advanced delivery system capable of protecting RNAi from degradation and of efficiently delivering RNAi in vitro and in vivo.

Cationic liquid crystalline nanoparticles for the delivery of synthetic RNAi-based therapeutics

PubMed Central

Gentile, Emanuela; Oba, Taro; Lin, Jing; Shao, Ruping; Meng, Feng; Cao, Xiaobo; Lin, Heather Y.; Mourad, Majidi; Pataer, Apar; Baladandayuthapani, Veerabhadran; Cai, Dong; Roth, Jack A.; Ji, Lin

2017-01-01

RNA interference (RNAi)-based therapeutics have been used to silence the expression of targeted pathological genes. Small interfering RNA (siRNAs) and microRNA (miRNAs) inhibitor have performed this function. However, short half-life, poor cellular uptake, and nonspecific distribution of small RNAs call for the development of novel delivery systems to facilitate the use of RNAi. We developed a novel cationic liquid crystalline nanoparticle (CLCN) to efficiently deliver synthetic siRNAs and miRNAs. CLCNs were prepared by using high-speed homogenization and assembled with synthetic siRNA or miRNA molecules in nuclease-free water to create CLCN/siRNA or miRNA complexes. The homogeneous and stable CLCNs and CLCN-siRNA complexes were about 100 nm in diameter, with positively charged surfaces. CLCNs are nontoxic and are taken up by human cells though endocytosis. Significant inhibition of gene expression was detected in transiently transfected lung cancer H1299 cells treated with CLCNs/anti-GFP complexes 24 hours after transfection. Biodistribution analysis showed that the CLCNs and CLCNs-RNAi complexes were successfully delivered to various organs and into the subcutaneous human lung cancer H1299 tumor xenografts in mice 24 hours after systemic administration. These results suggest that CLCNs are a unique and advanced delivery system capable of protecting RNAi from degradation and of efficiently delivering RNAi in vitro and in vivo. PMID:28637023

Multi-class computational evolution: development, benchmark evaluation and application to RNA-Seq biomarker discovery.

PubMed

Crabtree, Nathaniel M; Moore, Jason H; Bowyer, John F; George, Nysia I

2017-01-01

A computational evolution system (CES) is a knowledge discovery engine that can identify subtle, synergistic relationships in large datasets. Pareto optimization allows CESs to balance accuracy with model complexity when evolving classifiers. Using Pareto optimization, a CES is able to identify a very small number of features while maintaining high classification accuracy. A CES can be designed for various types of data, and the user can exploit expert knowledge about the classification problem in order to improve discrimination between classes. These characteristics give CES an advantage over other classification and feature selection algorithms, particularly when the goal is to identify a small number of highly relevant, non-redundant biomarkers. Previously, CESs have been developed only for binary class datasets. In this study, we developed a multi-class CES. The multi-class CES was compared to three common feature selection and classification algorithms: support vector machine (SVM), random k-nearest neighbor (RKNN), and random forest (RF). The algorithms were evaluated on three distinct multi-class RNA sequencing datasets. The comparison criteria were run-time, classification accuracy, number of selected features, and stability of selected feature set (as measured by the Tanimoto distance). The performance of each algorithm was data-dependent. CES performed best on the dataset with the smallest sample size, indicating that CES has a unique advantage since the accuracy of most classification methods suffer when sample size is small. The multi-class extension of CES increases the appeal of its application to complex, multi-class datasets in order to identify important biomarkers and features.

The Est3 protein associates with yeast telomerase through an OB-fold domain

PubMed Central

Lee, Jaesung S.; Mandell, Edward K.; Tucey, Timothy M.; Morris, Danna K.; Victoria, Lundblad

2009-01-01

The Est3 protein is a small regulatory subunit of yeast telomerase which is dispensable for enzyme catalysis but essential for telomere replication in vivo. Using structure prediction combined with in vivo characterization, we show here that Est3 consists of a predicted OB (oligo-saccharide/oligo-nucleotide binding) fold. Mutagenesis of predicted surface residues was used to generate a functional map of one surface of Est3, which identified a site that mediates association with the telomerase complex. Surprisingly, the predicted OB-fold of Est3 is structurally similar to the OB-fold of the mammalian TPP1 protein, despite the fact that Est3 and TPP1, as components of telomerase and a telomere capping complex, respectively, perform functionally distinct tasks at chromosome ends. The analysis performed on Est3 may be instructive in generating comparable missense mutations on the surface of the OB-fold domain of TPP1. PMID:19172754

Variable learning performance: the levels of behaviour organization.

PubMed

Csányi, V; Altbäcker, V

1990-01-01

Our experiments were focused on some special aspects of learning in the paradise fish. Passive avoidance conditioning method was used with different success depending on the complexity of the learning tasks. In the case of simple behavioural elements various "constrains" on avoidance learning were found. In a small, covered place the fish were ready to perform freezing reaction and mild punishment increased the frequency and duration of the freezing bouts very substantially. However, it was very difficult to enhance the frequency of freezing by punishment in a tank with transparent walls, where the main response to punishment was escape. The most easily learned tasks were the complex ones which had several different solutions. The fish learned to avoid either side of an aquarium very easily because they could use various behavioural elements to solve the problem. These findings could be interpreted within the framework of different organizational levels of behaviour.

Rapid identifying high-influence nodes in complex networks

NASA Astrophysics Data System (ADS)

Song, Bo; Jiang, Guo-Ping; Song, Yu-Rong; Xia, Ling-Ling

2015-10-01

A tiny fraction of influential individuals play a critical role in the dynamics on complex systems. Identifying the influential nodes in complex networks has theoretical and practical significance. Considering the uncertainties of network scale and topology, and the timeliness of dynamic behaviors in real networks, we propose a rapid identifying method (RIM) to find the fraction of high-influential nodes. Instead of ranking all nodes, our method only aims at ranking a small number of nodes in network. We set the high-influential nodes as initial spreaders, and evaluate the performance of RIM by the susceptible-infected-recovered (SIR) model. The simulations show that in different networks, RIM performs well on rapid identifying high-influential nodes, which is verified by typical ranking methods, such as degree, closeness, betweenness, and eigenvector centrality methods. Project supported by the National Natural Science Foundation of China (Grant Nos. 61374180 and 61373136), the Ministry of Education Research in the Humanities and Social Sciences Planning Fund Project, China (Grant No. 12YJAZH120), and the Six Projects Sponsoring Talent Summits of Jiangsu Province, China (Grant No. RLD201212).

Designed Proteins Induce the Formation of Nanocage-containing Extracellular Vesicles

PubMed Central

Votteler, Jörg; Ogohara, Cassandra; Yi, Sue; Hsia, Yang; Nattermann, Una; Belnap, David M.; King, Neil P.; Sundquist, Wesley I.

2017-01-01

Complex biological processes are often performed by self-organizing nanostructures comprising multiple classes of macromolecules, such as ribosomes (proteins and RNA) or enveloped viruses (proteins, nucleic acids, and lipids). Approaches have been developed for designing self-assembling structures consisting of either nucleic acids1,2 or proteins3–5, but strategies for engineering hybrid biological materials are only beginning to emerge6,7. Here, we describe the design of self-assembling protein nanocages that direct their own release from human cells inside small vesicles in a manner that resembles some viruses. We refer to these hybrid biomaterials as Enveloped Protein Nanocages (EPNs). Robust EPN biogenesis required protein sequence elements that encode three distinct functions: membrane binding, self-assembly, and recruitment of the Endosomal Sorting Complexes Required for Transport (ESCRT) machinery8. A variety of synthetic proteins with these functional elements induced EPN biogenesis, highlighting the modularity and generality of the design strategy. Biochemical and electron cryomicroscopic (cryo-EM) analyses revealed that one design, EPN-01, comprised small (~100 nm) vesicles containing multiple protein nanocages that closely matched the structure of the designed 60-subunit self-assembling scaffold9. EPNs that incorporated the vesicular stomatitis viral glycoprotein (VSV-G) could fuse with target cells and deliver their contents, thereby transferring cargoes from one cell to another. These studies show how proteins can be programmed to direct the formation of hybrid biological materials that perform complex tasks, and establish EPNs as a novel class of designed, modular, genetically-encoded nanomaterials that can transfer molecules between cells. PMID:27919066

Self-templated formation of uniform NiCo2O4 hollow spheres with complex interior structures for lithium-ion batteries and supercapacitors.

PubMed

Shen, Laifa; Yu, Le; Yu, Xin-Yao; Zhang, Xiaogang; Lou, Xiong Wen David

2015-02-02

Despite the significant advancement in preparing metal oxide hollow structures, most approaches rely on template-based multistep procedures for tailoring the interior structure. In this work, we develop a new generally applicable strategy toward the synthesis of mixed-metal-oxide complex hollow spheres. Starting with metal glycerate solid spheres, we show that subsequent thermal annealing in air leads to the formation of complex hollow spheres of the resulting metal oxide. We demonstrate the concept by synthesizing highly uniform NiCo2O4 hollow spheres with a complex interior structure. With the small primary building nanoparticles, high structural integrity, complex interior architectures, and enlarged surface area, these unique NiCo2O4 hollow spheres exhibit superior electrochemical performances as advanced electrode materials for both lithium-ion batteries and supercapacitors. This approach can be an efficient self-templated strategy for the preparation of mixed-metal-oxide hollow spheres with complex interior structures and functionalities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An evaluation of MPI message rate on hybrid-core processors

DOE PAGES

Barrett, Brian W.; Brightwell, Ron; Grant, Ryan; ...

2014-11-01

Power and energy concerns are motivating chip manufacturers to consider future hybrid-core processor designs that may combine a small number of traditional cores optimized for single-thread performance with a large number of simpler cores optimized for throughput performance. This trend is likely to impact the way in which compute resources for network protocol processing functions are allocated and managed. In particular, the performance of MPI match processing is critical to achieving high message throughput. In this paper, we analyze the ability of simple and more complex cores to perform MPI matching operations for various scenarios in order to gain insightmore » into how MPI implementations for future hybrid-core processors should be designed.« less

vvtools v. 1.0

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

Drake, Richard R.

Vvtools is a suite of testing tools, with a focus on reproducible verification and validation. They are written in pure Python, and contain a test harness and an automated process management tool. Users of vvtools can develop suites of verification and validation tests and run them on small to large high performance computing resources in an automated and reproducible way. The test harness enables complex processes to be performed in each test and even supports a one-level parent/child dependency between tests. It includes a built in capability to manage workloads requiring multiple processors and platforms that use batch queueing systems.

Inverse halftoning via robust nonlinear filtering

NASA Astrophysics Data System (ADS)

Shen, Mei-Yin; Kuo, C.-C. Jay

1999-10-01

A new blind inverse halftoning algorithm based on a nonlinear filtering technique of low computational complexity and low memory requirement is proposed in this research. It is called blind since we do not require the knowledge of the halftone kernel. The proposed scheme performs nonlinear filtering in conjunction with edge enhancement to improve the quality of an inverse halftoned image. Distinct features of the proposed approach include: efficiently smoothing halftone patterns in large homogeneous areas, additional edge enhancement capability to recover the edge quality and an excellent PSNR performance with only local integer operations and a small memory buffer.

The effects of instructional sets on reactions to and performance on an intelligent tutoring system

NASA Technical Reports Server (NTRS)

Johnson, Debra Steele

1993-01-01

The effects of a contextual factor, i.e., task instructions, on performance on and reactions to an Intellegent Tutoring System (ITS) training Remote Manipulator System (RMS) tasks were examined. The results supported the first prediction that task instructions could be used to successfully induce a mastery versus an achievement orientation. Previous research suggests that a mastery orientation can result in beneficial effects on learning and performance of complex tasks. Furthermore, the results supported the second prediction that a mastery orientation would have beneficial effects on learning and performance as well as affective and cognitive reactions to the ITS tasks. Moreover, the results indicated that a mastery orientation was especially beneficial for the more complex ITS tasks and later in task practice, i.e., when a task was performed for the second time. A mastery orientation is posited to have its beneficial effects by focusing more effort and attention on task performance. Conclusions are drawn with some caution due to the small number of subjects, although the results for these subjects were consistent across multiple trials and multiple measures of performance. ITS designers are urged to consider contextual factors such as task instructions and feedback in terms of their potential to induce a mastery versus an achievement orientation.

High-performance mussel-inspired adhesives of reduced complexity.

PubMed

Ahn, B Kollbe; Das, Saurabh; Linstadt, Roscoe; Kaufman, Yair; Martinez-Rodriguez, Nadine R; Mirshafian, Razieh; Kesselman, Ellina; Talmon, Yeshayahu; Lipshutz, Bruce H; Israelachvili, Jacob N; Waite, J Herbert

2015-10-19

Despite the recent progress in and demand for wet adhesives, practical underwater adhesion remains limited or non-existent for diverse applications. Translation of mussel-inspired wet adhesion typically entails catechol functionalization of polymers and/or polyelectrolytes, and solution processing of many complex components and steps that require optimization and stabilization. Here we reduced the complexity of a wet adhesive primer to synthetic low-molecular-weight catecholic zwitterionic surfactants that show very strong adhesion (∼50 mJ m(-2)) and retain the ability to coacervate. This catecholic zwitterion adheres to diverse surfaces and self-assembles into a molecularly smooth, thin (<4 nm) and strong glue layer. The catecholic zwitterion holds particular promise as an adhesive for nanofabrication. This study significantly simplifies bio-inspired themes for wet adhesion by combining catechol with hydrophobic and electrostatic functional groups in a small molecule.

Using wood creep data to discuss the contribution of cell-wall reinforcing material.

PubMed

Gril, Joseph; Hunt, David; Thibaut, Bernard

2004-01-01

Longitudinal four-point creep bending tests were performed on small clear-wood spruce specimens having various microfibrillar angles. Cell-wall compliance was deduced from macroscopic data by accounting for porosity. Time-dependent compliance was converted into complex compliance and rigidity using the value and the slope of the compliance versus logarithm of time. Complex rigidity plots of all specimens, for the time range 10(3)-10(6) s, could be superimposed by a horizontal shift depending on the microfibrillar angle. The shape of complex trajectories allowed a decomposition of the cell-wall relaxation modulus as the sum of an elastic contribution function of the microfibrillar angle and a time-dependent term unrelated to it, and suggested a discussion on the contribution of the various cell-wall layers to the observed relaxation process.

Experimental and theoretical studies of light-to-heat conversion and collective heating effects in metal nanoparticle solutions.

PubMed

Richardson, Hugh H; Carlson, Michael T; Tandler, Peter J; Hernandez, Pedro; Govorov, Alexander O

2009-03-01

We perform a set of experiments on photoheating in a water droplet containing gold nanoparticles (NPs). Using photocalorimetric methods, we determine efficiency of light-to-heat conversion (eta) which turns out to be remarkably close to 1, (0.97 < eta < 1.03). Detailed studies reveal a complex character of heat transfer in an optically stimulated droplet. The main mechanism of equilibration is due to convectional flow. Theoretical modeling is performed to describe thermal effects at both nano- and millimeter scales. Theory shows that the collective photoheating is the main mechanism. For a large concentration of NPs and small laser intensity, an averaged temperature increase (at the millimeter scale) is significant (approximately 7 degrees C), whereas on the nanometer scale the temperature increase at the surface of a single NP is small (approximately 0.02 degrees C). In the opposite regime, that is, a small NP concentration and intense laser irradiation, we find an opposite picture: a temperature increase at the millimeter scale is small (0.1 degrees C) but a local, nanoscale temperature has strong local spikes at the surfaces of NPs (approximately 3 degrees C). These studies are crucial for the understanding of photothermal effects in NPs and for their potential and current applications in nano- and biotechnologies.

A relative navigation sensor for CubeSats based on LED fiducial markers

NASA Astrophysics Data System (ADS)

Sansone, Francesco; Branz, Francesco; Francesconi, Alessandro

2018-05-01

Small satellite platforms are becoming very appealing both for scientific and commercial applications, thanks to their low cost, short development times and availability of standard components and subsystems. The main disadvantage with such vehicles is the limitation of available resources to perform mission tasks. To overcome this drawback, mission concepts are under study that foresee cooperation between autonomous small satellites to accomplish complex tasks; among these, on-orbit servicing and on-orbit assembly of large structures are of particular interest and the global scientific community is putting a significant effort in the miniaturization of critical technologies that are required for such innovative mission scenarios. In this work, the development and the laboratory testing of an accurate relative navigation package for nanosatellites compliant to the CubeSat standard is presented. The system features a small camera and two sets of LED fiducial markers, and is conceived as a standard package that allows small spacecraft to perform mutual tracking during rendezvous and docking maneuvers. The hardware is based on off-the-shelf components assembled in a compact configuration that is compatible with the CubeSat standard. The image processing and pose estimation software was custom developed. The experimental evaluation of the system allowed to determine both the static and dynamic performances. The system is capable to determine the close range relative position and attitude faster than 10 S/s, with errors always below 10 mm and 2 deg.

Science, Technical Innovation and Applications in Bioacoustics: Summary of a Workshop

DTIC Science & Technology

2004-07-01

binaural processing have been neglected. From a signal-processing standpoint, we should avoid complex computational methods and instead use massively...design and/or build transducers or arrays with anywhere near the performance and, most importantly, environmental adaptability of animal binaural ...shell Small animal imaging Cardiac Imaging in Mice The Challenge Mouse heart • 7mm diameter • 8 beats /sec Mouse Heart L16-28MHzL5-10MHz Laptop

NASA/DOD Aerospace Knowledge Diffusion Research Project. Paper 69: Writing for the Aerospace Industry. Chapter 3; The Practice of Technical and Scientific Communication: Writing in Professional Contexts

NASA Technical Reports Server (NTRS)

Barclay, Rebecca O.; Pinelli, Thomas E.

1997-01-01

The large and complex aerospace industry, which employed approximately 850,000 people in 1994 (Aerospace Facts, 1994-95, p. 11), plays a vital role in the nation's economy. Although only a small percentage of those employed in aerospace are technical communicators, they perform a wide variety of communication duties in government and the private sector.

Localization of diffusion sources in complex networks with sparse observations

NASA Astrophysics Data System (ADS)

Hu, Zhao-Long; Shen, Zhesi; Tang, Chang-Bing; Xie, Bin-Bin; Lu, Jian-Feng

2018-04-01

Locating sources in a large network is of paramount importance to reduce the spreading of disruptive behavior. Based on the backward diffusion-based method and integer programming, we propose an efficient approach to locate sources in complex networks with limited observers. The results on model networks and empirical networks demonstrate that, for a certain fraction of observers, the accuracy of our method for source localization will improve as the increase of network size. Besides, compared with the previous method (the maximum-minimum method), the performance of our method is much better with a small fraction of observers, especially in heterogeneous networks. Furthermore, our method is more robust against noise environments and strategies of choosing observers.

Asynchronous oscillations of rigid rods drive viscous fluid to swirl

NASA Astrophysics Data System (ADS)

Hayashi, Rintaro; Takagi, Daisuke

2017-12-01

We present a minimal system for generating flow at low Reynolds number by oscillating a pair of rigid rods in silicone oil. Experiments show that oscillating them in phase produces no net flow, but a phase difference alone can generate rich flow fields. Tracer particles follow complex trajectory patterns consisting of small orbital movements every cycle and then drifting or swirling in larger regions after many cycles. Observations are consistent with simulations performed using the method of regularized Stokeslets, which reveal complex three-dimensional flow structures emerging from simple oscillatory actuation. Our findings reveal the basic underlying flow structure around oscillatory protrusions such as hairs and legs as commonly featured on living and nonliving bodies.

Limited-path-length entanglement percolation in quantum complex networks

NASA Astrophysics Data System (ADS)

Cuquet, Martí; Calsamiglia, John

2011-03-01

We study entanglement distribution in quantum complex networks where nodes are connected by bipartite entangled states. These networks are characterized by a complex structure, which dramatically affects how information is transmitted through them. For pure quantum state links, quantum networks exhibit a remarkable feature absent in classical networks: it is possible to effectively rewire the network by performing local operations on the nodes. We propose a family of such quantum operations that decrease the entanglement percolation threshold of the network and increase the size of the giant connected component. We provide analytic results for complex networks with an arbitrary (uncorrelated) degree distribution. These results are in good agreement with numerical simulations, which also show enhancement in correlated and real-world networks. The proposed quantum preprocessing strategies are not robust in the presence of noise. However, even when the links consist of (noisy) mixed-state links, one can send quantum information through a connecting path with a fidelity that decreases with the path length. In this noisy scenario, complex networks offer a clear advantage over regular lattices, namely, the fact that two arbitrary nodes can be connected through a relatively small number of steps, known as the small-world effect. We calculate the probability that two arbitrary nodes in the network can successfully communicate with a fidelity above a given threshold. This amounts to working out the classical problem of percolation with a limited path length. We find that this probability can be significant even for paths limited to few connections and that the results for standard (unlimited) percolation are soon recovered if the path length exceeds by a finite amount the average path length, which in complex networks generally scales logarithmically with the size of the network.

Enhancing the resiliency of small hydropower projects: environmental function, modularity, and stakeholder elicitation as design priorities

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

Witt, Adam M; Smith, Brennan T

Small hydropower plants supply reliable renewable energy to the grid, though few new plants have been developed in the Unites States over the past few decades due to complex environmental challenges and poor project economics. This paper describes the current landscape of small hydropower development, and introduces a new approach to facility design that co-optimizes the extraction of hydroelectric power from a stream with other important environmental functions such as fish, sediment, and recreational passage. The approach considers hydropower facilities as an integrated system of standardized interlocking modules, designed to sustain stream functions, generate power, and interface with the streambed.more » It is hypothesized that this modular eco-design approach, when guided by input from the broader small hydropower stakeholder community, can lead to cost savings across the facility, reduced licensing and approval timelines, and ultimately, to enhanced resiliency through improved environmental performance over the lifetime of the project.« less

An Approach to Experimental Design for the Computer Analysis of Complex Phenomenon

NASA Technical Reports Server (NTRS)

Rutherford, Brian

2000-01-01

The ability to make credible system assessments, predictions and design decisions related to engineered systems and other complex phenomenon is key to a successful program for many large-scale investigations in government and industry. Recently, many of these large-scale analyses have turned to computational simulation to provide much of the required information. Addressing specific goals in the computer analysis of these complex phenomenon is often accomplished through the use of performance measures that are based on system response models. The response models are constructed using computer-generated responses together with physical test results where possible. They are often based on probabilistically defined inputs and generally require estimation of a set of response modeling parameters. As a consequence, the performance measures are themselves distributed quantities reflecting these variabilities and uncertainties. Uncertainty in the values of the performance measures leads to uncertainties in predicted performance and can cloud the decisions required of the analysis. A specific goal of this research has been to develop methodology that will reduce this uncertainty in an analysis environment where limited resources and system complexity together restrict the number of simulations that can be performed. An approach has been developed that is based on evaluation of the potential information provided for each "intelligently selected" candidate set of computer runs. Each candidate is evaluated by partitioning the performance measure uncertainty into two components - one component that could be explained through the additional computational simulation runs and a second that would remain uncertain. The portion explained is estimated using a probabilistic evaluation of likely results for the additional computational analyses based on what is currently known about the system. The set of runs indicating the largest potential reduction in uncertainty is then selected and the computational simulations are performed. Examples are provided to demonstrate this approach on small scale problems. These examples give encouraging results. Directions for further research are indicated.

Structural correction of paleomagnetic vectors dispersed about two fold axes and application to the Duke Island (Alaska) ultramafic complex

NASA Astrophysics Data System (ADS)

Bogue, Scott W.; Grommé, C. Sherman

2004-11-01

A new analysis of paleomagnetic data from the mid-Cretaceous (˜110 Ma) ultramafic complex at Duke Island (southeast Alaska) supports large poleward transport of the Insular superterrane relative to North America consistent with the Baja British Columbia hypothesis. Previous paleomagnetic work has shown that the characteristic remanence of the ultramafic complex predates kilometer-scale deformation of the very well developed cumulate layering but that the layering was not horizontal everywhere before the folding. It is possible, however, to estimate paleohorizontal for the Duke Island ultramafic complex because the postremanence deformation of the intrusion occurred about two well-defined and spatially separate fold axes. In such a case the tectonically rotated paleomagnetic directions should be distributed along small circles centered on each of the two fold axes. The ancient field direction will lie on both small circles and therefore will be identifiable as one of their two intersection points. Interpreted this way, the tectonically rotated remanence of the Duke Island ultramafic complex defines a mid-Cretaceous (i.e., ancient) field direction that is within 2° of the paleomagnetic direction found by assuming the cumulate layering was initially horizontal (despite the paleomagnetic evidence to the contrary) and performing the standard structure correction. The inferred mid-Cretaceous paleolatitude of Duke Island is 21.2° (2350 km) anomalous with respect to cratonic North America. This result is concordant with southerly paleolatitudes determined by many other workers from bedded rocks of terranes farther inboard in the Insular and Intermontane superterranes.

Tryptophan oxidation catabolite, N-formylkynurenine, in photo degraded cell culture medium results in reduced cell culture performance.

PubMed

McElearney, Kyle; Ali, Amr; Gilbert, Alan; Kshirsagar, Rashmi; Zang, Li

2016-01-01

Chemically defined media have been widely used in the biopharmaceutical industry to enhance cell culture productivities and ensure process robustness. These media, which are quite complex, often contain a mixture of many components such as vitamins, amino acids, metals and other chemicals. Some of these components are known to be sensitive to various stress factors including photodegradation. Previous work has shown that small changes in impurity concentrations induced by these potential stresses can have a large impact on the cell culture process including growth and product quality attributes. Furthermore, it has been shown to be difficult to detect these modifications analytically due to the complexity of the cell culture media and the trace level of the degradant products. Here, we describe work performed to identify the specific chemical(s) in photodegraded medium that affect cell culture performance. First, we developed a model system capable of detecting changes in cell culture performance. Second, we used these data and applied an LC-MS analytical technique to characterize the cell culture media and identify degradant products which affect cell culture performance. Riboflavin limitation and N-formylkynurenine (NFK), a tryptophan oxidation catabolite, were identified as chemicals which results in a reduction in cell culture performance. © 2015 American Institute of Chemical Engineers.

Continuous Production of Discrete Plasmid DNA-Polycation Nanoparticles Using Flash Nanocomplexation.

PubMed

Santos, Jose Luis; Ren, Yong; Vandermark, John; Archang, Maani M; Williford, John-Michael; Liu, Heng-Wen; Lee, Jason; Wang, Tza-Huei; Mao, Hai-Quan

2016-12-01

Despite successful demonstration of linear polyethyleneimine (lPEI) as an effective carrier for a wide range of gene medicine, including DNA plasmids, small interfering RNAs, mRNAs, etc., and continuous improvement of the physical properties and biological performance of the polyelectrolyte complex nanoparticles prepared from lPEI and nucleic acids, there still exist major challenges to produce these nanocomplexes in a scalable manner, particularly for lPEI/DNA nanoparticles. This has significantly hindered the progress toward clinical translation of these nanoparticle-based gene medicine. Here the authors report a flash nanocomplexation (FNC) method that achieves continuous production of lPEI/plasmid DNA nanoparticles with narrow size distribution using a confined impinging jet device. The method involves the complex coacervation of negatively charged DNA plasmid and positive charged lPEI under rapid, highly dynamic, and homogeneous mixing conditions, producing polyelectrolyte complex nanoparticles with narrow distribution of particle size and shape. The average number of plasmid DNA packaged per nanoparticles and its distribution are similar between the FNC method and the small-scale batch mixing method. In addition, the nanoparticles prepared by these two methods exhibit similar cell transfection efficiency. These results confirm that FNC is an effective and scalable method that can produce well-controlled lPEI/plasmid DNA nanoparticles. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Continuous Production of Discrete Plasmid DNA-Polycation Nanoparticles Using Flash Nanocomplexation

PubMed Central

Santos, Jose Luis; Ren, Yong; Vandermark, John; Archang, Maani M.; Williford, John-Michael; Liu, Heng-wen; Lee, Jason; Wang, Tza-Huei; Mao, Hai-Quan

2016-01-01

Despite successful demonstration of linear polyethyleneimine (lPEI) as an effective carrier for a wide range of gene medicine, including DNA plasmids, small interfering RNAs, mRNAs, etc., and continuous improvement of the physical properties and biological performance of the polyelectrolyte complex nanoparticles prepared from lPEI and nucleic acids, there still exist major challenges to produce these nanocomplexes in a scalable manner, particularly for lPEI/DNA nanoparticles. This has significantly hindered the progress towards clinical translation of these nanoparticle-based gene medicine. Here we report a flash nanocomplexation (FNC) method that achieves continuous production of lPEI/plasmid DNA nanoparticles with narrow size distribution using a confined impinging jet device. The method involves the complex coacervation of negatively charged DNA plasmid and positive charged lPEI under rapid, highly dynamic, and homogeneous mixing conditions, producing polyelectrolyte complex nanoparticles with narrow distribution of particle size and shape. The average number of plasmid DNA packaged per nanoparticles and its distribution are similar between the FNC method and the small-scale batch mixing method. In addition, the nanoparticles prepared by these two methods exhibit similar cell transfection efficiency. These results confirm that FNC is an effective and scalable method that can produce well-controlled lPEI/plasmid DNA nanoparticles. PMID:27717227

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

PubMed Central

Mu, Lin

2018-01-01

This work introduces a number of algebraic topology approaches, including multi-component persistent homology, multi-level persistent homology, and electrostatic persistence for the representation, characterization, and description of small molecules and biomolecular complexes. In contrast to the conventional persistent homology, multi-component persistent homology retains critical chemical and biological information during the topological simplification of biomolecular geometric complexity. Multi-level persistent homology enables a tailored topological description of inter- and/or intra-molecular interactions of interest. Electrostatic persistence incorporates partial charge information into topological invariants. These topological methods are paired with Wasserstein distance to characterize similarities between molecules and are further integrated with a variety of machine learning algorithms, including k-nearest neighbors, ensemble of trees, and deep convolutional neural networks, to manifest their descriptive and predictive powers for protein-ligand binding analysis and virtual screening of small molecules. Extensive numerical experiments involving 4,414 protein-ligand complexes from the PDBBind database and 128,374 ligand-target and decoy-target pairs in the DUD database are performed to test respectively the scoring power and the discriminatory power of the proposed topological learning strategies. It is demonstrated that the present topological learning outperforms other existing methods in protein-ligand binding affinity prediction and ligand-decoy discrimination. PMID:29309403

The Study of Learners' Preference for Visual Complexity on Small Screens of Mobile Computers Using Neural Networks

ERIC Educational Resources Information Center

Wang, Lan-Ting; Lee, Kun-Chou

2014-01-01

The vision plays an important role in educational technologies because it can produce and communicate quite important functions in teaching and learning. In this paper, learners' preference for the visual complexity on small screens of mobile computers is studied by neural networks. The visual complexity in this study is divided into five…

Large Variability in the Diversity of Physiologically Complex Surgical Procedures Exists Nationwide Among All Hospitals Including Among Large Teaching Hospitals.

PubMed

Dexter, Franklin; Epstein, Richard H; Thenuwara, Kokila; Lubarsky, David A

2017-11-22

Multiple previous studies have shown that having a large diversity of procedures has a substantial impact on quality management of hospital surgical suites. At hospitals with substantial diversity, unless sophisticated statistical methods suitable for rare events are used, anesthesiologists working in surgical suites will have inaccurate predictions of surgical blood usage, case durations, cost accounting and price transparency, times remaining in late running cases, and use of intraoperative equipment. What is unknown is whether large diversity is a feature of only a few very unique set of hospitals nationwide (eg, the largest hospitals in each state or province). The 2013 United States Nationwide Readmissions Database was used to study heterogeneity among 1981 hospitals in their diversities of physiologically complex surgical procedures (ie, the procedure codes). The diversity of surgical procedures performed at each hospital was quantified using a summary measure, the number of different physiologically complex surgical procedures commonly performed at the hospital (ie, 1/Herfindahl). A total of 53.9% of all hospitals commonly performed <10 physiologically complex procedures (lower 99% confidence limit [CL], 51.3%). A total of 14.2% (lower 99% CL, 12.4%) of hospitals had >3-fold larger diversity (ie, >30 commonly performed physiologically complex procedures). Larger hospitals had greater diversity than the small- and medium-sized hospitals (P < .0001). Teaching hospitals had greater diversity than did the rural and urban nonteaching hospitals (P < .0001). A total of 80.0% of the 170 large teaching hospitals commonly performed >30 procedures (lower 99% CL, 71.9% of hospitals). However, there was considerable variability among the large teaching hospitals in their diversity (interquartile range of the numbers of commonly performed physiologically complex procedures = 19.3; lower 99% CL, 12.8 procedures). The diversity of procedures represents a substantive differentiator among hospitals. Thus, the usefulness of statistical methods for operating room management should be expected to be heterogeneous among hospitals. Our results also show that "large teaching hospital" alone is an insufficient description for accurate prediction of the extent to which a hospital sustains the operational and financial consequences of performing a wide diversity of surgical procedures. Future research can evaluate the extent to which hospitals with very large diversity are indispensable in their catchment area.

Identification of Novel Targets for Lung Cancer Therapy Using an Induced Pluripotent Stem Cell Model.

PubMed

Shukla, Vivek; Rao, Mahadev; Zhang, Hongen; Beers, Jeanette; Wangsa, Darawalee; Wangsa, Danny; Buishand, Floryne O; Wang, Yonghong; Yu, Zhiya; Stevenson, Holly; Reardon, Emily; McLoughlin, Kaitlin C; Kaufman, Andrew; Payabyab, Eden; Hong, Julie A; Zhang, Mary; Davis, Sean R; Edelman, Daniel C; Chen, Guokai; Miettinen, Markku; Restifo, Nicholas; Ried, Thomas; Meltzer, Paul S; Schrump, David S

2018-04-01

Despite extensive studies, the genetic and epigenetic mechanisms that mediate initiation and progression of lung cancers have not been fully elucidated. Previously, we have demonstrated that via complementary mechanisms, including DNA methylation, polycomb repressive complexes, and noncoding RNAs, cigarette smoke induces stem-like phenotypes that coincide with progression to malignancy in normal respiratory epithelia as well as enhanced growth and metastatic potential of lung cancer cells. To further investigate epigenetic mechanisms contributing to stemness/pluripotency in lung cancers and potentially identify novel therapeutic targets in these malignancies, induced pluripotent stem cells were generated from normal human small airway epithelial cells. Lung induced pluripotent stem cells were generated by lentiviral transduction of small airway epithelial cells of OSKM (Yamanaka) factors (octamer-binding transcription factor 4 [Oct4], sex-determining region Y box 2 [SOX2], Kruppel-like factor 4 [KLF4], and MYC proto-oncogene, bHLH transcription factor [MYC]). Western blot, real-time polymerase chain reaction, and chromatin immunoprecipitation sequencing analysis were performed. The lung induced pluripotent stem cells exhibited hallmarks of pluripotency, including morphology, surface antigen and stem cell gene expression, in vitro proliferation, and teratoma formation. In addition, lung induced pluripotent stem cells exhibited no chromosomal aberrations, complete silencing of reprogramming transgenes, genomic hypermethylation, upregulation of genes encoding components of polycomb repressive complex 2, hypermethylation of stem cell polycomb targets, and modulation of more than 15,000 other genes relative to parental small airway epithelial cells. Additional sex combs like-3 (ASXL3), encoding a polycomb repressive complex 2-associated protein not previously described in reprogrammed cells, was markedly upregulated in lung induced pluripotent stem cell as well as human small cell lung cancer lines and specimens. Overexpression of the additional sex combs like-3 gene correlated with increased genomic copy number in small cell lung cancer lines. Knock-down of the additional sex combs like-3 gene inhibited proliferation, clonogenicity, and teratoma formation by lung induced pluripotent stem cells and significantly diminished in vitro clonogenicity and growth of small cell lung cancer cells in vivo. Collectively, these studies highlight the potential utility of this lung induced pluripotent stem cell model for elucidating epigenetic mechanisms contributing to pulmonary carcinogenesis and suggest that additional sex combs like-3 is a novel target for small cell lung cancer therapy.

Online Low-Rank Representation Learning for Joint Multi-subspace Recovery and Clustering.

PubMed

Li, Bo; Liu, Risheng; Cao, Junjie; Zhang, Jie; Lai, Yu-Kun; Liua, Xiuping

2017-10-06

Benefiting from global rank constraints, the lowrank representation (LRR) method has been shown to be an effective solution to subspace learning. However, the global mechanism also means that the LRR model is not suitable for handling large-scale data or dynamic data. For large-scale data, the LRR method suffers from high time complexity, and for dynamic data, it has to recompute a complex rank minimization for the entire data set whenever new samples are dynamically added, making it prohibitively expensive. Existing attempts to online LRR either take a stochastic approach or build the representation purely based on a small sample set and treat new input as out-of-sample data. The former often requires multiple runs for good performance and thus takes longer time to run, and the latter formulates online LRR as an out-ofsample classification problem and is less robust to noise. In this paper, a novel online low-rank representation subspace learning method is proposed for both large-scale and dynamic data. The proposed algorithm is composed of two stages: static learning and dynamic updating. In the first stage, the subspace structure is learned from a small number of data samples. In the second stage, the intrinsic principal components of the entire data set are computed incrementally by utilizing the learned subspace structure, and the low-rank representation matrix can also be incrementally solved by an efficient online singular value decomposition (SVD) algorithm. The time complexity is reduced dramatically for large-scale data, and repeated computation is avoided for dynamic problems. We further perform theoretical analysis comparing the proposed online algorithm with the batch LRR method. Finally, experimental results on typical tasks of subspace recovery and subspace clustering show that the proposed algorithm performs comparably or better than batch methods including the batch LRR, and significantly outperforms state-of-the-art online methods.

Divergent Small Tim Homologues Are Associated with TbTim17 and Critical for the Biogenesis of TbTim17 Protein Complexes in Trypanosoma brucei

PubMed Central

Smith, Joseph T.; Singha, Ujjal K.; Misra, Smita

2018-01-01

ABSTRACT The small Tim proteins belong to a group of mitochondrial intermembrane space chaperones that aid in the import of mitochondrial inner membrane proteins with internal targeting signals. Trypanosoma brucei, the protozoan parasite that causes African trypanosomiasis, possesses multiple small Tim proteins that include homologues of T. brucei Tim9 (TbTim9) and Tim10 (TbTim10) and a unique small Tim that shares homology with both Tim8 and Tim13 (TbTim8/13). Here, we found that these three small TbTims are expressed as soluble mitochondrial intermembrane space proteins. Coimmunoprecipitation and mass spectrometry analysis showed that the small TbTims stably associated with each other and with TbTim17, the major component of the mitochondrial inner membrane translocase in T. brucei. Yeast two-hybrid analysis indicated direct interactions among the small TbTims; however, their interaction patterns appeared to be different from those of their counterparts in yeast and humans. Knockdown of the small TbTims reduced cell growth and decreased the steady-state level of TbTim17 and T. brucei ADP/ATP carrier (TbAAC), two polytopic mitochondrial inner membrane proteins. Knockdown of small TbTims also reduced the matured complexes of TbTim17 in mitochondria. Depletion of any of the small TbTims reduced TbTim17 import moderately but greatly hampered the stability of the TbTim17 complexes in T. brucei. Altogether, our results revealed that TbTim9, TbTim10, and TbTim8/13 interact with each other, associate with TbTim17, and play a crucial role in the integrity and maintenance of the levels of TbTim17 complexes. IMPORTANCE Trypanosoma brucei is the causative agent of African sleeping sickness. The parasite’s mitochondrion represents a useful source for potential chemotherapeutic targets. Similarly to yeast and humans, mitochondrial functions depend on the import of proteins that are encoded in the nucleus and made in the cytosol. Even though the machinery involved in this mitochondrial protein import process is becoming clearer in T. brucei, a comprehensive picture of protein complex composition and function is still lacking. In this study, we characterized three T. brucei small Tim proteins, TbTim9, TbTim10, and TbTim8/13. Although the parasite does not have the classical TIM22 complex that imports mitochondrial inner membrane proteins containing internal targeting signals in yeast or humans, we found that these small TbTims associate with TbTim17, the major subunit of the TbTIM complex in T. brucei, and play an essential role in the stability of the TbTim17 complexes. Therefore, these divergent proteins are critical for mitochondrial protein biogenesis in T. brucei. PMID:29925672

Divergent Small Tim Homologues Are Associated with TbTim17 and Critical for the Biogenesis of TbTim17 Protein Complexes in Trypanosoma brucei.

PubMed

Smith, Joseph T; Singha, Ujjal K; Misra, Smita; Chaudhuri, Minu

2018-06-27

The small Tim proteins belong to a group of mitochondrial intermembrane space chaperones that aid in the import of mitochondrial inner membrane proteins with internal targeting signals. Trypanosoma brucei , the protozoan parasite that causes African trypanosomiasis, possesses multiple small Tim proteins that include homologues of T. brucei Tim9 (TbTim9) and Tim10 (TbTim10) and a unique small Tim that shares homology with both Tim8 and Tim13 (TbTim8/13). Here, we found that these three small TbTims are expressed as soluble mitochondrial intermembrane space proteins. Coimmunoprecipitation and mass spectrometry analysis showed that the small TbTims stably associated with each other and with TbTim17, the major component of the mitochondrial inner membrane translocase in T. brucei Yeast two-hybrid analysis indicated direct interactions among the small TbTims; however, their interaction patterns appeared to be different from those of their counterparts in yeast and humans. Knockdown of the small TbTims reduced cell growth and decreased the steady-state level of TbTim17 and T. brucei ADP/ATP carrier (TbAAC), two polytopic mitochondrial inner membrane proteins. Knockdown of small TbTims also reduced the matured complexes of TbTim17 in mitochondria. Depletion of any of the small TbTims reduced TbTim17 import moderately but greatly hampered the stability of the TbTim17 complexes in T. brucei Altogether, our results revealed that TbTim9, TbTim10, and TbTim8/13 interact with each other, associate with TbTim17, and play a crucial role in the integrity and maintenance of the levels of TbTim17 complexes. IMPORTANCE Trypanosoma brucei is the causative agent of African sleeping sickness. The parasite's mitochondrion represents a useful source for potential chemotherapeutic targets. Similarly to yeast and humans, mitochondrial functions depend on the import of proteins that are encoded in the nucleus and made in the cytosol. Even though the machinery involved in this mitochondrial protein import process is becoming clearer in T. brucei , a comprehensive picture of protein complex composition and function is still lacking. In this study, we characterized three T. brucei small Tim proteins, TbTim9, TbTim10, and TbTim8/13. Although the parasite does not have the classical TIM22 complex that imports mitochondrial inner membrane proteins containing internal targeting signals in yeast or humans, we found that these small TbTims associate with TbTim17, the major subunit of the TbTIM complex in T. brucei , and play an essential role in the stability of the TbTim17 complexes. Therefore, these divergent proteins are critical for mitochondrial protein biogenesis in T. brucei . Copyright © 2018 Smith et al.

Infrared dim small target segmentation method based on ALI-PCNN model

NASA Astrophysics Data System (ADS)

Zhao, Shangnan; Song, Yong; Zhao, Yufei; Li, Yun; Li, Xu; Jiang, Yurong; Li, Lin

2017-10-01

Pulse Coupled Neural Network (PCNN) is improved by Adaptive Lateral Inhibition (ALI), while a method of infrared (IR) dim small target segmentation based on ALI-PCNN model is proposed in this paper. Firstly, the feeding input signal is modulated by lateral inhibition network to suppress background. Then, the linking input is modulated by ALI, and linking weight matrix is generated adaptively by calculating ALI coefficient of each pixel. Finally, the binary image is generated through the nonlinear modulation and the pulse generator in PCNN. The experimental results show that the segmentation effect as well as the values of contrast across region and uniformity across region of the proposed method are better than the OTSU method, maximum entropy method, the methods based on conventional PCNN and visual attention, and the proposed method has excellent performance in extracting IR dim small target from complex background.

Automatic detection of small surface targets with electro-optical sensors in a harbor environment

NASA Astrophysics Data System (ADS)

Bouma, Henri; de Lange, Dirk-Jan J.; van den Broek, Sebastiaan P.; Kemp, Rob A. W.; Schwering, Piet B. W.

2008-10-01

In modern warfare scenarios naval ships must operate in coastal environments. These complex environments, in bays and narrow straits, with cluttered littoral backgrounds and many civilian ships may contain asymmetric threats of fast targets, such as rhibs, cabin boats and jet-skis. Optical sensors, in combination with image enhancement and automatic detection, assist an operator to reduce the response time, which is crucial for the protection of the naval and land-based supporting forces. In this paper, we present our work on automatic detection of small surface targets which includes multi-scale horizon detection and robust estimation of the background intensity. To evaluate the performance of our detection technology, data was recorded with both infrared and visual-light cameras in a coastal zone and in a harbor environment. During these trials multiple small targets were used. Results of this evaluation are shown in this paper.

Pancreatic cancer planning: Complex conformal vs modulated therapies

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

Chapman, Katherine L.; Witek, Matthew E.; Chen, Hongyu

To compare the roles of intensity-modulated radiation therapy (IMRT) and volumetric- modulated arc therapy (VMAT) therapy as compared to simple and complex 3-dimensional chemoradiotherpy (3DCRT) planning for resectable and borderline resectable pancreatic cancer. In all, 12 patients who received postoperative radiotherapy (8) or neoadjuvant concurrent chemoradiotherapy (4) were evaluated retrospectively. Radiotherapy planning was performed for 4 treatment techniques: simple 4-field box, complex 5-field 3DCRT, 5 to 6-field IMRT, and single-arc VMAT. All volumes were approved by a single observer in accordance with Radiation Therapy Oncology Group (RTOG) Pancreas Contouring Atlas. Plans included tumor/tumor bed and regional lymph nodes to 45more » Gy; with tumor/tumor bed boosted to 50.4 Gy, at least 95% of planning target volume (PTV) received the prescription dose. Dose-volume histograms (DVH) for multiple end points, treatment planning, and delivery time were assessed. Complex 3DCRT, IMRT, and VMAT plans significantly (p < 0.05) decreased mean kidney dose, mean liver dose, liver (V{sub 30}, V{sub 35}), stomach (D{sub 10}%), stomach (V{sub 45}), mean right kidney dose, and right kidney (V{sub 15}) as compared with the simple 4-field plans that are most commonly reported in the literature. IMRT plans resulted in decreased mean liver dose, liver (V{sub 35}), and left kidney (V{sub 15}, V{sub 18}, V{sub 20}). VMAT plans decreased small bowel (D{sub 10}%, D{sub 15}%), small bowel (V{sub 35}, V{sub 45}), stomach (D{sub 10}%, D{sub 15}%), stomach (V{sub 35}, V{sub 45}), mean liver dose, liver (V{sub 35}), left kidney (V{sub 15}, V{sub 18}, V{sub 20}), and right kidney (V{sub 18}, V{sub 20}). VMAT plans significantly decreased small bowel (D{sub 10}%, D{sub 15}%), left kidney (V{sub 20}), and stomach (V{sub 45}) as compared with IMRT plans. Treatment planning and delivery times were most efficient for simple 4-field box and VMAT. Excluding patient setup and imaging, average treatment delivery was within 10 minutes for simple and complex 3DCRT, IMRT, and VMAT treatments. This article shows significant improvements in 3D plan performance with complex planning over the more frequently compared 3- or 4-field simple 3D planning techniques. VMAT plans continue to demonstrate potential for the most organ sparing. However, further studies are required to identify if dosimetric benefits associated with inverse optimized planning can be translated into clinical benefits and if these treatment techniques are value-added therapies for this group of patients with cancer.« less

Standard Free Droplet Digital Polymerase Chain Reaction as a New Tool for the Quality Control of High-Capacity Adenoviral Vectors in Small-Scale Preparations

PubMed Central

Boehme, Philip; Stellberger, Thorsten; Solanki, Manish; Zhang, Wenli; Schulz, Eric; Bergmann, Thorsten; Liu, Jing; Doerner, Johannes; Baiker, Armin E.

2015-01-01

Abstract High-capacity adenoviral vectors (HCAdVs) are promising tools for gene therapy as well as for genetic engineering. However, one limitation of the HCAdV vector system is the complex, time-consuming, and labor-intensive production process and the following quality control procedure. Since HCAdVs are deleted for all viral coding sequences, a helper virus (HV) is needed in the production process to provide the sequences for all viral proteins in trans. For the purification procedure of HCAdV, cesium chloride density gradient centrifugation is usually performed followed by buffer exchange using dialysis or comparable methods. However, performing these steps is technically difficult, potentially error-prone, and not scalable. Here, we establish a new protocol for small-scale production of HCAdV based on commercially available adenovirus purification systems and a standard method for the quality control of final HCAdV preparations. For titration of final vector preparations, we established a droplet digital polymerase chain reaction (ddPCR) that uses a standard free-end-point PCR in small droplets of defined volume. By using different probes, this method is capable of detecting and quantifying HCAdV and HV in one reaction independent of reference material, rendering this method attractive for accurately comparing viral titers between different laboratories. In summary, we demonstrate that it is possible to produce HCAdV in a small scale of sufficient quality and quantity to perform experiments in cell culture, and we established a reliable protocol for vector titration based on ddPCR. Our method significantly reduces time and required equipment to perform HCAdV production. In the future the ddPCR technology could be advantageous for titration of other viral vectors commonly used in gene therapy. PMID:25640117

microRNA profiling in the zoonotic parasite Echinococcus canadensis using a high-throughput approach.

PubMed

Macchiaroli, Natalia; Cucher, Marcela; Zarowiecki, Magdalena; Maldonado, Lucas; Kamenetzky, Laura; Rosenzvit, Mara Cecilia

2015-02-06

microRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. The particular developmental and metabolic characteristics of cestode parasites highlight the importance of studying miRNA gene regulation in these organisms. Here, we perform a comprehensive analysis of miRNAs in the parasitic cestode Echinococcus canadensis G7, one of the causative agents of the neglected zoonotic disease cystic echinococcosis. Small RNA libraries from protoscoleces and cyst walls of E. canadensis G7 and protoscoleces of E. granulosus sensu stricto G1 were sequenced using Illumina technology. For miRNA prediction, miRDeep2 core algorithm was used. The output list of candidate precursors was manually curated to generate a high confidence set of miRNAs. Differential expression analysis of miRNAs between stages or species was estimated with DESeq. Expression levels of selected miRNAs were validated using poly-A RT-qPCR. In this study we used a high-throughput approach and found transcriptional evidence of 37 miRNAs thus expanding the miRNA repertoire of E. canadensis G7. Differential expression analysis showed highly regulated miRNAs between life cycle stages, suggesting a role in maintaining the features of each developmental stage or in the regulation of developmental timing. In this work we characterize conserved and novel Echinococcus miRNAs which represent 30 unique miRNA families. Here we confirmed the remarkable loss of conserved miRNA families in E. canadensis, reflecting their low morphological complexity and high adaptation to parasitism. We performed the first in-depth study profiling of small RNAs in the zoonotic parasite E. canadensis G7. We found that miRNAs are the preponderant small RNA silencing molecules, suggesting that these small RNAs could be an essential mechanism of gene regulation in this species. We also identified both parasite specific and divergent miRNAs which are potential biomarkers of infection. This study will provide valuable information for better understanding of the complex biology of this parasite and could help to find new potential targets for therapy and/or diagnosis.

Short-term adaptations following Complex Training in team-sports: A meta-analysis

PubMed Central

Martinez-Rodriguez, Alejandro; Calleja-González, Julio; Alcaraz, Pedro E.

2017-01-01

Objective The purpose of this meta-analysis was to study the short-term adaptations on sprint and vertical jump (VJ) performance following Complex Training (CT) in team-sports. CT is a resistance training method aimed at developing both strength and power, which has a direct effect on sprint and VJ. It consists on alternating heavy resistance training exercises with plyometric/power ones, set for set, on the same workout. Methods A search of electronic databases up to July 2016 (PubMed-MEDLINE, SPORTDiscus, Web of Knowledge) was conducted. Inclusion criteria: 1) at least one CT intervention group; 2) training protocols ≥4-wks; 3) sample of team-sport players; 4) sprint or VJ as an outcome variable. Effect sizes (ES) of each intervention were calculated and subgroup analyses were performed. Results A total of 9 studies (13 CT groups) met the inclusion criteria. Medium effect sizes (ES) (ES = 0.73) were obtained for pre-post improvements in sprint, and small (ES = 0.41) in VJ, following CT. Experimental-groups presented better post-intervention sprint (ES = 1.01) and VJ (ES = 0.63) performance than control-groups. Sprint large ESs were exhibited in younger athletes (<20 years old; ES = 1.13); longer CT interventions (≥6 weeks; ES = 0.95); conditioning activities with intensities ≤85% 1RM (ES = 0.96) and protocols with frequencies of <3 sessions/week (ES = 0.84). Medium ESs were obtained in Division I players (ES = 0.76); training programs >12 total sessions (ES = 0.74). VJ Large ESs in programs with >12 total sessions (ES = 0.81). Medium ESs obtained for under-Division I individuals (ES = 0.56); protocols with intracomplex rest intervals ≥2 min (ES = 0.55); conditioning activities with intensities ≤85% 1RM (ES = 0.64); basketball/volleyball players (ES = 0.55). Small ESs were found for younger athletes (ES = 0.42); interventions ≥6 weeks (ES = 0.45). Conclusions CT interventions have positive medium effects on sprint performance and small effects on VJ in team-sport athletes. This training method is a suitable option to include in the season planning. PMID:28662108

Serendipitous Offline Learning in a Neuromorphic Robot.

PubMed

Stewart, Terrence C; Kleinhans, Ashley; Mundy, Andrew; Conradt, Jörg

2016-01-01

We demonstrate a hybrid neuromorphic learning paradigm that learns complex sensorimotor mappings based on a small set of hard-coded reflex behaviors. A mobile robot is first controlled by a basic set of reflexive hand-designed behaviors. All sensor data is provided via a spike-based silicon retina camera (eDVS), and all control is implemented via spiking neurons simulated on neuromorphic hardware (SpiNNaker). Given this control system, the robot is capable of simple obstacle avoidance and random exploration. To train the robot to perform more complex tasks, we observe the robot and find instances where the robot accidentally performs the desired action. Data recorded from the robot during these times is then used to update the neural control system, increasing the likelihood of the robot performing that task in the future, given a similar sensor state. As an example application of this general-purpose method of training, we demonstrate the robot learning to respond to novel sensory stimuli (a mirror) by turning right if it is present at an intersection, and otherwise turning left. In general, this system can learn arbitrary relations between sensory input and motor behavior.

Competitive pressures affect sexual signal complexity in Kurixalus odontotarsus: insights into the evolution of compound calls

PubMed Central

2017-01-01

ABSTRACT Male-male vocal competition in anuran species is critical for mating success; however, it is also energetically demanding and highly time-consuming. Thus, we hypothesized that males may change signal elaboration in response to competition in real time. Male serrate-legged small treefrogs (Kurixalus odontotarsus) produce compound calls that contain two kinds of notes, harmonic sounds called ‘A notes’ and short broadband sounds called ‘B notes’. Using male evoked vocal response experiments, we found that competition influences the temporal structure and complexity of vocal signals produced by males. Males produce calls with a higher ratio of notes:call, and more compound calls including more A notes but fewer B notes with contest escalation. In doing so, males minimize the energy costs and maximize the benefits of competition when the level of competition is high. This means that the evolution of sexual signal complexity in frogs may be susceptible to selection for plasticity related to adjusting performance to the pressures of competition, and supports the idea that more complex social contexts can lead to greater vocal complexity. PMID:29175862

A trypanosomal orthologue of an intermembrane space chaperone has a non-canonical function in biogenesis of the single mitochondrial inner membrane protein translocase.

PubMed

Wenger, Christoph; Oeljeklaus, Silke; Warscheid, Bettina; Schneider, André; Harsman, Anke

2017-08-01

Mitochondrial protein import is essential for Trypanosoma brucei across its life cycle and mediated by membrane-embedded heterooligomeric protein complexes, which mainly consist of trypanosomatid-specific subunits. However, trypanosomes contain orthologues of small Tim chaperones that escort hydrophobic proteins across the intermembrane space. Here we have experimentally analyzed three novel trypanosomal small Tim proteins, one of which contains only an incomplete Cx3C motif. RNAi-mediated ablation of TbERV1 shows that their import, as in other organisms, depends on the MIA pathway. Submitochondrial fractionation combined with immunoprecipitation and BN-PAGE reveals two pools of small Tim proteins: a soluble fraction forming 70 kDa complexes, consistent with hexamers and a second fraction that is tightly associated with the single trypanosomal TIM complex. RNAi-mediated ablation of the three proteins leads to a growth arrest and inhibits the formation of the TIM complex. In line with these findings, the changes in the mitochondrial proteome induced by ablation of one small Tim phenocopy the effects observed after ablation of TbTim17. Thus, the trypanosomal small Tims play an unexpected and essential role in the biogenesis of the single TIM complex, which for one of them is not linked to import of TbTim17.

Preliminary Analysis of Helicopter Options to Support Tunisian Counterterrorism Operations

DTIC Science & Technology

2016-04-27

locations along roads and tracks in border areas, and small settlements in complex terrain (Figure 1, right; examples shown in Figure 2). Analysis For...political implications. In this preliminary analysis , we focus on the question of cost-effectiveness in the UH-60M’s primary role: Which alternative...platforms could perform the assault mission, and at what cost? The core of our analysis is detailed modeling of key “mission tasks” on a sortie-by-sortie

Numerical calculation of thermo-mechanical problems at large strains based on complex step derivative approximation of tangent stiffness matrices

NASA Astrophysics Data System (ADS)

Balzani, Daniel; Gandhi, Ashutosh; Tanaka, Masato; Schröder, Jörg

2015-05-01

In this paper a robust approximation scheme for the numerical calculation of tangent stiffness matrices is presented in the context of nonlinear thermo-mechanical finite element problems and its performance is analyzed. The scheme extends the approach proposed in Kim et al. (Comput Methods Appl Mech Eng 200:403-413, 2011) and Tanaka et al. (Comput Methods Appl Mech Eng 269:454-470, 2014 and bases on applying the complex-step-derivative approximation to the linearizations of the weak forms of the balance of linear momentum and the balance of energy. By incorporating consistent perturbations along the imaginary axis to the displacement as well as thermal degrees of freedom, we demonstrate that numerical tangent stiffness matrices can be obtained with accuracy up to computer precision leading to quadratically converging schemes. The main advantage of this approach is that contrary to the classical forward difference scheme no round-off errors due to floating-point arithmetics exist within the calculation of the tangent stiffness. This enables arbitrarily small perturbation values and therefore leads to robust schemes even when choosing small values. An efficient algorithmic treatment is presented which enables a straightforward implementation of the method in any standard finite-element program. By means of thermo-elastic and thermo-elastoplastic boundary value problems at finite strains the performance of the proposed approach is analyzed.

A novel nonlinear adaptive filter using a pipelined second-order Volterra recurrent neural network.

PubMed

Zhao, Haiquan; Zhang, Jiashu

2009-12-01

To enhance the performance and overcome the heavy computational complexity of recurrent neural networks (RNN), a novel nonlinear adaptive filter based on a pipelined second-order Volterra recurrent neural network (PSOVRNN) is proposed in this paper. A modified real-time recurrent learning (RTRL) algorithm of the proposed filter is derived in much more detail. The PSOVRNN comprises of a number of simple small-scale second-order Volterra recurrent neural network (SOVRNN) modules. In contrast to the standard RNN, these modules of a PSOVRNN can be performed simultaneously in a pipelined parallelism fashion, which can lead to a significant improvement in its total computational efficiency. Moreover, since each module of the PSOVRNN is a SOVRNN in which nonlinearity is introduced by the recursive second-order Volterra (RSOV) expansion, its performance can be further improved. Computer simulations have demonstrated that the PSOVRNN performs better than the pipelined recurrent neural network (PRNN) and RNN for nonlinear colored signals prediction and nonlinear channel equalization. However, the superiority of the PSOVRNN over the PRNN is at the cost of increasing computational complexity due to the introduced nonlinear expansion of each module.

Gas pressure assisted microliquid-liquid extraction coupled online to direct infusion mass spectrometry: a new automated screening platform for bioanalysis.

PubMed

Raterink, Robert-Jan; Witkam, Yoeri; Vreeken, Rob J; Ramautar, Rawi; Hankemeier, Thomas

2014-10-21

In the field of bioanalysis, there is an increasing demand for miniaturized, automated, robust sample pretreatment procedures that can be easily connected to direct-infusion mass spectrometry (DI-MS) in order to allow the high-throughput screening of drugs and/or their metabolites in complex body fluids like plasma. Liquid-Liquid extraction (LLE) is a common sample pretreatment technique often used for complex aqueous samples in bioanalysis. Despite significant developments that have been made in automated and miniaturized LLE procedures, fully automated LLE techniques allowing high-throughput bioanalytical studies on small-volume samples using direct infusion mass spectrometry, have not been matured yet. Here, we introduce a new fully automated micro-LLE technique based on gas-pressure assisted mixing followed by passive phase separation, coupled online to nanoelectrospray-DI-MS. Our method was characterized by varying the gas flow and its duration through the solvent mixture. For evaluation of the analytical performance, four drugs were spiked to human plasma, resulting in highly acceptable precision (RSD down to 9%) and linearity (R(2) ranging from 0.990 to 0.998). We demonstrate that our new method does not only allow the reliable extraction of analytes from small sample volumes of a few microliters in an automated and high-throughput manner, but also performs comparable or better than conventional offline LLE, in which the handling of small volumes remains challenging. Finally, we demonstrate the applicability of our method for drug screening on dried blood spots showing excellent linearity (R(2) of 0.998) and precision (RSD of 9%). In conclusion, we present the proof of principe of a new high-throughput screening platform for bioanalysis based on a new automated microLLE method, coupled online to a commercially available nano-ESI-DI-MS.

Speech Discrimination Difficulties in High-Functioning Autism Spectrum Disorder Are Likely Independent of Auditory Hypersensitivity

PubMed Central

Dunlop, William A.; Enticott, Peter G.; Rajan, Ramesh

2016-01-01

Autism Spectrum Disorder (ASD), characterized by impaired communication skills and repetitive behaviors, can also result in differences in sensory perception. Individuals with ASD often perform normally in simple auditory tasks but poorly compared to typically developed (TD) individuals on complex auditory tasks like discriminating speech from complex background noise. A common trait of individuals with ASD is hypersensitivity to auditory stimulation. No studies to our knowledge consider whether hypersensitivity to sounds is related to differences in speech-in-noise discrimination. We provide novel evidence that individuals with high-functioning ASD show poor performance compared to TD individuals in a speech-in-noise discrimination task with an attentionally demanding background noise, but not in a purely energetic noise. Further, we demonstrate in our small sample that speech-hypersensitivity does not appear to predict performance in the speech-in-noise task. The findings support the argument that an attentional deficit, rather than a perceptual deficit, affects the ability of individuals with ASD to discriminate speech from background noise. Finally, we piloted a novel questionnaire that measures difficulty hearing in noisy environments, and sensitivity to non-verbal and verbal sounds. Psychometric analysis using 128 TD participants provided novel evidence for a difference in sensitivity to non-verbal and verbal sounds, and these findings were reinforced by participants with ASD who also completed the questionnaire. The study was limited by a small and high-functioning sample of participants with ASD. Future work could test larger sample sizes and include lower-functioning ASD participants. PMID:27555814

Self-controlled video feedback on tactical skills for soccer teams results in more active involvement of players.

PubMed

van Maarseveen, Mariëtte J J; Oudejans, Raôul R D; Savelsbergh, Geert J P

2018-02-01

Many studies have shown that self-controlled feedback is beneficial for learning motor tasks, and that learners prefer to receive feedback after supposedly good trials. However, to date all studies conducted on self-controlled learning have used individual tasks and mainly relatively simple skills. Therefore, the aim of this study was to examine self-controlled feedback on tactical skills in small-sided soccer games. Highly talented youth soccer players were assigned to a self-control or yoked group and received video feedback on their offensive performance in 3 vs. 2 small-sided games. The results showed that the self-control group requested feedback mostly after good trials, that is, after they scored a goal. In addition, the perceived performance of the self-control group was higher on feedback than on no-feedback trials. Analyses of the conversations around the video feedback revealed that the players and coach discussed good and poor elements of performance and how to improve it. Although the coach had a major role in these conversations, the players of the self-control group spoke more and showed more initiative compared to the yoked group. The results revealed no significant beneficial effect of self-controlled feedback on performance as judged by the coach. Overall, the findings suggest that in such a complex situation as small-sided soccer games, self-controlled feedback is used both to confirm correct performance elements and to determine and correct errors, and that self-controlled learning stimulates the involvement of the learner in the learning process. Copyright © 2017 Elsevier B.V. All rights reserved.

Animals In Synchrotrons: Overcoming Challenges For High-Resolution, Live, Small-Animal Imaging

NASA Astrophysics Data System (ADS)

Donnelley, Martin; Parsons, David; Morgan, Kaye; Siu, Karen

2010-07-01

Physiological studies in small animals can be complicated, but the complexity is increased dramatically when performing live-animal synchrotron X-ray imaging studies. Our group has extensive experience in high-resolution live-animal imaging at the Japanese SPring-8 synchrotron, primarily examining airways in two-dimensions. These experiments normally image an area of 1.8 mm×1.2 mm at a pixel resolution of 0.45 μm and are performed with live, intact, anaesthetized mice. There are unique challenges in this experimental setting. Importantly, experiments must be performed in an isolated imaging hutch not specifically designed for small-animal imaging. This requires equipment adapted to remotely monitor animals, maintain their anesthesia, and deliver test substances while collecting images. The horizontal synchrotron X-ray beam has a fixed location and orientation that limits experimental flexibility. The extremely high resolution makes locating anatomical regions-of-interest slow and can result in a high radiation dose, and at this level of magnification small animal movements produce motion-artifacts that can render acquired images unusable. Here we describe our experimental techniques and how we have overcome several challenges involved in performing live mouse synchrotron imaging. Experiments have tested different mouse strains, with hairless strains minimizing overlying skin and hair artifacts. Different anesthetics have also be trialed due to the limited choices available at SPring-8. Tracheal-intubation methods have been refined and controlled-ventilation is now possible using a specialized small-animal ventilator. With appropriate animal restraint and respiratory-gating, motion-artifacts have been minimized. The animal orientation (supine vs. head-high) also appears to affect animal physiology, and can alter image quality. Our techniques and image quality at SPring-8 have dramatically improved and in the near future we plan to translate this experience to the Imaging and Medical Beamline at the Australian Synchrotron. Overcoming these challenges has permitted increasingly sophisticated imaging of animals with synchrotron X-rays, and we expect a bright future for these techniques.

Animals In Synchrotrons: Overcoming Challenges For High-Resolution, Live, Small-Animal Imaging

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

Donnelley, Martin; Parsons, David; Women's and Children's Health Research Institute, Adelaide, South Australia

Physiological studies in small animals can be complicated, but the complexity is increased dramatically when performing live-animal synchrotron X-ray imaging studies. Our group has extensive experience in high-resolution live-animal imaging at the Japanese SPring-8 synchrotron, primarily examining airways in two-dimensions. These experiments normally image an area of 1.8 mmx1.2 mm at a pixel resolution of 0.45 {mu}m and are performed with live, intact, anaesthetized mice.There are unique challenges in this experimental setting. Importantly, experiments must be performed in an isolated imaging hutch not specifically designed for small-animal imaging. This requires equipment adapted to remotely monitor animals, maintain their anesthesia, andmore » deliver test substances while collecting images. The horizontal synchrotron X-ray beam has a fixed location and orientation that limits experimental flexibility. The extremely high resolution makes locating anatomical regions-of-interest slow and can result in a high radiation dose, and at this level of magnification small animal movements produce motion-artifacts that can render acquired images unusable. Here we describe our experimental techniques and how we have overcome several challenges involved in performing live mouse synchrotron imaging.Experiments have tested different mouse strains, with hairless strains minimizing overlying skin and hair artifacts. Different anesthetics have also be trialed due to the limited choices available at SPring-8. Tracheal-intubation methods have been refined and controlled-ventilation is now possible using a specialized small-animal ventilator. With appropriate animal restraint and respiratory-gating, motion-artifacts have been minimized. The animal orientation (supine vs. head-high) also appears to affect animal physiology, and can alter image quality. Our techniques and image quality at SPring-8 have dramatically improved and in the near future we plan to translate this experience to the Imaging and Medical Beamline at the Australian Synchrotron.Overcoming these challenges has permitted increasingly sophisticated imaging of animals with synchrotron X-rays, and we expect a bright future for these techniques.« less

Screening of Small Molecule Interactor Library by Using In-Cell NMR Spectroscopy (SMILI-NMR)

PubMed Central

Xie, Jingjing; Thapa, Rajiv; Reverdatto, Sergey; Burz, David S.; Shekhtman, Alexander

2011-01-01

We developed an in-cell NMR assay for screening small molecule interactor libraries (SMILI-NMR) for compounds capable of disrupting or enhancing specific interactions between two or more components of a biomolecular complex. The method relies on the formation of a well-defined biocomplex and utilizes in-cell NMR spectroscopy to identify the molecular surfaces involved in the interaction at atomic scale resolution. Changes in the interaction surface caused by a small molecule interfering with complex formation are used as a read-out of the assay. The in-cell nature of the experimental protocol insures that the small molecule is capable of penetrating the cell membrane and specifically engaging the target molecule(s). Utility of the method was demonstrated by screening a small dipeptide library against the FKBP–FRB protein complex involved in cell cycle arrest. The dipeptide identified by SMILI-NMR showed biological activity in a functional assay in yeast. PMID:19422228

Glide back booster wind tunnel model testing

NASA Astrophysics Data System (ADS)

Pricop, M. V.; Cojocaru, M. G.; Stoica, C. I.; Niculescu, M. L.; Neculaescu, A. M.; Persinaru, A. G.; Boscoianu, M.

2017-07-01

Affordable space access requires partial or ideally full launch vehicle reuse, which is in line with clean environment requirement. Although the idea is old, the practical use is difficult, requiring very large technology investment for qualification. Rocket gliders like Space Shuttle have been successfullyoperated but the price and correspondingly the energy footprint were found not sustainable. For medium launchers, finally there is a very promising platform as Falcon 9. For very small launchers the situation is more complex, because the performance index (payload to start mass) is already small, versus medium and heavy launchers. For partial reusable micro launchers this index is even smaller. However the challenge has to be taken because it is likely that in a multiyear effort, technology is going to enable the performance recovery to make such a system economically and environmentally feasible. The current paper is devoted to a small unitary glide back booster which is foreseen to be assembled in a number of possible configurations. Although the level of analysis is not deep, the solution is analyzed from the aerodynamic point of view. A wind tunnel model is designed, with an active canard, to enablea more efficient wind tunnel campaign, as a national level premiere.

Structure of Dimeric and Tetrameric Complexes of the BAR Domain Protein PICK1 Determined by Small-Angle X-Ray Scattering.

PubMed

Karlsen, Morten L; Thorsen, Thor S; Johner, Niklaus; Ammendrup-Johnsen, Ina; Erlendsson, Simon; Tian, Xinsheng; Simonsen, Jens B; Høiberg-Nielsen, Rasmus; Christensen, Nikolaj M; Khelashvili, George; Streicher, Werner; Teilum, Kaare; Vestergaard, Bente; Weinstein, Harel; Gether, Ulrik; Arleth, Lise; Madsen, Kenneth L

2015-07-07

PICK1 is a neuronal scaffolding protein containing a PDZ domain and an auto-inhibited BAR domain. BAR domains are membrane-sculpting protein modules generating membrane curvature and promoting membrane fission. Previous data suggest that BAR domains are organized in lattice-like arrangements when stabilizing membranes but little is known about structural organization of BAR domains in solution. Through a small-angle X-ray scattering (SAXS) analysis, we determine the structure of dimeric and tetrameric complexes of PICK1 in solution. SAXS and biochemical data reveal a strong propensity of PICK1 to form higher-order structures, and SAXS analysis suggests an offset, parallel mode of BAR-BAR oligomerization. Furthermore, unlike accessory domains in other BAR domain proteins, the positioning of the PDZ domains is flexible, enabling PICK1 to perform long-range, dynamic scaffolding of membrane-associated proteins. Together with functional data, these structural findings are compatible with a model in which oligomerization governs auto-inhibition of BAR domain function. Copyright © 2015 Elsevier Ltd. All rights reserved.

@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes.

PubMed

Pons, Jean-Luc; Labesse, Gilles

2009-07-01

@TOME 2.0 is new web pipeline dedicated to protein structure modeling and small ligand docking based on comparative analyses. @TOME 2.0 allows fold recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation. These tasks are routinely used in sequence analyses for structure prediction. In our pipeline the necessary software is efficiently interconnected in an original manner to accelerate all the processes. Furthermore, we have also connected comparative docking of small ligands that is performed using protein-protein superposition. The input is a simple protein sequence in one-letter code with no comment. The resulting 3D model, protein-ligand complexes and structural alignments can be visualized through dedicated Web interfaces or can be downloaded for further studies. These original features will aid in the functional annotation of proteins and the selection of templates for molecular modeling and virtual screening. Several examples are described to highlight some of the new functionalities provided by this pipeline. The server and its documentation are freely available at http://abcis.cbs.cnrs.fr/AT2/

@TOME-2: a new pipeline for comparative modeling of protein–ligand complexes

PubMed Central

Pons, Jean-Luc; Labesse, Gilles

2009-01-01

@TOME 2.0 is new web pipeline dedicated to protein structure modeling and small ligand docking based on comparative analyses. @TOME 2.0 allows fold recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation. These tasks are routinely used in sequence analyses for structure prediction. In our pipeline the necessary software is efficiently interconnected in an original manner to accelerate all the processes. Furthermore, we have also connected comparative docking of small ligands that is performed using protein–protein superposition. The input is a simple protein sequence in one-letter code with no comment. The resulting 3D model, protein–ligand complexes and structural alignments can be visualized through dedicated Web interfaces or can be downloaded for further studies. These original features will aid in the functional annotation of proteins and the selection of templates for molecular modeling and virtual screening. Several examples are described to highlight some of the new functionalities provided by this pipeline. The server and its documentation are freely available at http://abcis.cbs.cnrs.fr/AT2/ PMID:19443448

Free-Energy Landscape of Reverse tRNA Translocation through the Ribosome Analyzed by Electron Microscopy Density Maps and Molecular Dynamics Simulations

PubMed Central

Ishida, Hisashi; Matsumoto, Atsushi

2014-01-01

To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA. PMID:24999999

Free-energy landscape of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations.

PubMed

Ishida, Hisashi; Matsumoto, Atsushi

2014-01-01

To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA.

A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems.

PubMed

Yin, Weiwei; Garimalla, Swetha; Moreno, Alberto; Galinski, Mary R; Styczynski, Mark P

2015-08-28

There are increasing efforts to bring high-throughput systems biology techniques to bear on complex animal model systems, often with a goal of learning about underlying regulatory network structures (e.g., gene regulatory networks). However, complex animal model systems typically have significant limitations on cohort sizes, number of samples, and the ability to perform follow-up and validation experiments. These constraints are particularly problematic for many current network learning approaches, which require large numbers of samples and may predict many more regulatory relationships than actually exist. Here, we test the idea that by leveraging the accuracy and efficiency of classifiers, we can construct high-quality networks that capture important interactions between variables in datasets with few samples. We start from a previously-developed tree-like Bayesian classifier and generalize its network learning approach to allow for arbitrary depth and complexity of tree-like networks. Using four diverse sample networks, we demonstrate that this approach performs consistently better at low sample sizes than the Sparse Candidate Algorithm, a representative approach for comparison because it is known to generate Bayesian networks with high positive predictive value. We develop and demonstrate a resampling-based approach to enable the identification of a viable root for the learned tree-like network, important for cases where the root of a network is not known a priori. We also develop and demonstrate an integrated resampling-based approach to the reduction of variable space for the learning of the network. Finally, we demonstrate the utility of this approach via the analysis of a transcriptional dataset of a malaria challenge in a non-human primate model system, Macaca mulatta, suggesting the potential to capture indicators of the earliest stages of cellular differentiation during leukopoiesis. We demonstrate that by starting from effective and efficient approaches for creating classifiers, we can identify interesting tree-like network structures with significant ability to capture the relationships in the training data. This approach represents a promising strategy for inferring networks with high positive predictive value under the constraint of small numbers of samples, meeting a need that will only continue to grow as more high-throughput studies are applied to complex model systems.

Robust and stretchable indium gallium zinc oxide-based electronic textiles formed by cilia-assisted transfer printing

PubMed Central

Yoon, Jongwon; Jeong, Yunkyung; Kim, Heeje; Yoo, Seonggwang; Jung, Hoon Sun; Kim, Yonghun; Hwang, Youngkyu; Hyun, Yujun; Hong, Woong-Ki; Lee, Byoung Hun; Choa, Sung-Hoon; Ko, Heung Cho

2016-01-01

Electronic textile (e-textile) allows for high-end wearable electronic devices that provide easy access for carrying, handling and using. However, the related technology does not seem to be mature because the woven fabric hampers not only the device fabrication process directly on the complex surface but also the transfer printing of ultrathin planar electronic devices. Here we report an indirect method that enables conformal wrapping of surface with arbitrary yet complex shapes. Artificial cilia are introduced in the periphery of electronic devices as adhesive elements. The cilia also play an important role in confining a small amount of glue and damping mechanical stress to maintain robust electronic performance under mechanical deformation. The example of electronic applications depicts the feasibility of cilia for ‘stick-&-play' systems, which provide electronic functions by transfer printing on unconventional complex surfaces. PMID:27248982

High-performance mussel-inspired adhesives of reduced complexity

PubMed Central

Ahn, B. Kollbe; Das, Saurabh; Linstadt, Roscoe; Kaufman, Yair; Martinez-Rodriguez, Nadine R.; Mirshafian, Razieh; Kesselman, Ellina; Talmon, Yeshayahu; Lipshutz, Bruce H.; Israelachvili, Jacob N.; Waite, J. Herbert

2015-01-01

Despite the recent progress in and demand for wet adhesives, practical underwater adhesion remains limited or non-existent for diverse applications. Translation of mussel-inspired wet adhesion typically entails catechol functionalization of polymers and/or polyelectrolytes, and solution processing of many complex components and steps that require optimization and stabilization. Here we reduced the complexity of a wet adhesive primer to synthetic low-molecular-weight catecholic zwitterionic surfactants that show very strong adhesion (∼50 mJ m−2) and retain the ability to coacervate. This catecholic zwitterion adheres to diverse surfaces and self-assembles into a molecularly smooth, thin (<4 nm) and strong glue layer. The catecholic zwitterion holds particular promise as an adhesive for nanofabrication. This study significantly simplifies bio-inspired themes for wet adhesion by combining catechol with hydrophobic and electrostatic functional groups in a small molecule. PMID:26478273

Significance tests for functional data with complex dependence structure.

PubMed

Staicu, Ana-Maria; Lahiri, Soumen N; Carroll, Raymond J

2015-01-01

We propose an L 2 -norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

An optimal control model approach to the design of compensators for simulator delay

NASA Technical Reports Server (NTRS)

Baron, S.; Lancraft, R.; Caglayan, A.

1982-01-01

The effects of display delay on pilot performance and workload and of the design of the filters to ameliorate these effects were investigated. The optimal control model for pilot/vehicle analysis was used both to determine the potential delay effects and to design the compensators. The model was applied to a simple roll tracking task and to a complex hover task. The results confirm that even small delays can degrade performance and impose a workload penalty. A time-domain compensator designed by using the optimal control model directly appears capable of providing extensive compensation for these effects even in multi-input, multi-output problems.

Discrete Cu(i) complexes for azide-alkyne annulations of small molecules inside mammalian cells.

PubMed

Miguel-Ávila, Joan; Tomás-Gamasa, María; Olmos, Andrea; Pérez, Pedro J; Mascareñas, José L

2018-02-21

The archetype reaction of "click" chemistry, namely, the copper-promoted azide-alkyne cycloaddition (CuAAC), has found an impressive number of applications in biological chemistry. However, methods for promoting intermolecular annulations of exogenous, small azides and alkynes in the complex interior of mammalian cells, are essentially unknown. Herein we demonstrate that isolated, well-defined copper(i)-tris(triazolyl) complexes featuring designed ligands can readily enter mammalian cells and promote intracellular CuAAC annulations of small, freely diffusible molecules. In addition to simplifying protocols and avoiding the addition of "non-innocent" reductants, the use of these premade copper complexes leads to more efficient processes than with the alternative, in situ made copper species prepared from Cu(ii) sources, tris(triazole) ligands and sodium ascorbate. Under the reaction conditions, the well-defined copper complexes exhibit very good cell penetration properties, and do not present significant toxicities.

C3 generic workstation: Performance metrics and applications

NASA Technical Reports Server (NTRS)

Eddy, Douglas R.

1988-01-01

The large number of integrated dependent measures available on a command, control, and communications (C3) generic workstation under development are described. In this system, embedded communications tasks will manipulate workload to assess the effects of performance-enhancing drugs (sleep aids and decongestants), work/rest cycles, biocybernetics, and decision support systems on performance. Task performance accuracy and latency will be event coded for correlation with other measures of voice stress and physiological functioning. Sessions will be videotaped to score non-verbal communications. Physiological recordings include spectral analysis of EEG, ECG, vagal tone, and EOG. Subjective measurements include SWAT, fatigue, POMS and specialized self-report scales. The system will be used primarily to evaluate the effects on performance of drugs, work/rest cycles, and biocybernetic concepts. Performance assessment algorithms will also be developed, including those used with small teams. This system provides a tool for integrating and synchronizing behavioral and psychophysiological measures in a complex decision-making environment.

The Spot 42 RNA: A regulatory small RNA with roles in the central metabolism.

PubMed

Bækkedal, Cecilie; Haugen, Peik

2015-01-01

The Spot 42 RNA is a 109 nucleotide long (in Escherichia coli) noncoding small regulatory RNA (sRNA) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the majority of experimental work on Spot 42 RNA has been performed using E. coli, and recently Aliivibrio salmonicida. In the cell Spot 42 RNA plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP complex. Here we summarize the current knowledge on Spot 42, and present the natural distribution of spf, show family-specific secondary structural features of Spot 42, and link highly conserved structural regions to mRNA target binding.

Blind predictions of protein interfaces by docking calculations in CAPRI.

PubMed

Lensink, Marc F; Wodak, Shoshana J

2010-11-15

Reliable prediction of the amino acid residues involved in protein-protein interfaces can provide valuable insight into protein function, and inform mutagenesis studies, and drug design applications. A fast-growing number of methods are being proposed for predicting protein interfaces, using structural information, energetic criteria, or sequence conservation or by integrating multiple criteria and approaches. Overall however, their performance remains limited, especially when applied to nonobligate protein complexes, where the individual components are also stable on their own. Here, we evaluate interface predictions derived from protein-protein docking calculations. To this end we measure the overlap between the interfaces in models of protein complexes submitted by 76 participants in CAPRI (Critical Assessment of Predicted Interactions) and those of 46 observed interfaces in 20 CAPRI targets corresponding to nonobligate complexes. Our evaluation considers multiple models for each target interface, submitted by different participants, using a variety of docking methods. Although this results in a substantial variability in the prediction performance across participants and targets, clear trends emerge. Docking methods that perform best in our evaluation predict interfaces with average recall and precision levels of about 60%, for a small majority (60%) of the analyzed interfaces. These levels are significantly higher than those obtained for nonobligate complexes by most extant interface prediction methods. We find furthermore that a sizable fraction (24%) of the interfaces in models ranked as incorrect in the CAPRI assessment are actually correctly predicted (recall and precision ≥50%), and that these models contribute to 70% of the correct docking-based interface predictions overall. Our analysis proves that docking methods are much more successful in identifying interfaces than in predicting complexes, and suggests that these methods have an excellent potential of addressing the interface prediction challenge. © 2010 Wiley-Liss, Inc.

Natural Product Screening Reveals Naphthoquinone Complex I Bypass Factors

PubMed Central

Mevers, Emily; Higgins, Kathleen W.; Fomina, Yevgenia; Zhang, Jianming; Mandinova, Anna; Newman, David; Shaw, Stanley Y.; Clardy, Jon; Mootha, Vamsi K.

2016-01-01

Deficiency of mitochondrial complex I is encountered in both rare and common diseases, but we have limited therapeutic options to treat this lesion to the oxidative phosphorylation system (OXPHOS). Idebenone and menadione are redox-active molecules capable of rescuing OXPHOS activity by engaging complex I-independent pathways of entry, often referred to as “complex I bypass.” In the present study, we created a cellular model of complex I deficiency by using CRISPR genome editing to knock out Ndufa9 in mouse myoblasts, and utilized this cell line to develop a high-throughput screening platform for novel complex I bypass factors. We screened a library of ~40,000 natural product extracts and performed bioassay-guided fractionation on a subset of the top scoring hits. We isolated four plant-derived 1,4-naphthoquinone complex I bypass factors with structural similarity to menadione: chimaphilin and 3-chloro-chimaphilin from Chimaphila umbellata and dehydro-α-lapachone and dehydroiso-α-lapachone from Stereospermum euphoroides. We also tested a small number of structurally related naphthoquinones from commercial sources and identified two additional compounds with complex I bypass activity: 2-methoxy-1,4-naphthoquinone and 2-methoxy-3-methyl-1,4,-naphthoquinone. The six novel complex I bypass factors reported here expand this class of molecules and will be useful as tool compounds for investigating complex I disease biology. PMID:27622560

Surgical volume-to-outcome relationship and monitoring of technical performance in pediatric cardiac surgery.

PubMed

Kalfa, David; Chai, Paul; Bacha, Emile

2014-08-01

A significant inverse relationship of surgical institutional and surgeon volumes to outcome has been demonstrated in many high-stakes surgical specialties. By and large, the same results were found in pediatric cardiac surgery, for which a more thorough analysis has shown that this relationship depends on case complexity and type of surgical procedures. Lower-volume programs tend to underperform larger-volume programs as case complexity increases. High-volume pediatric cardiac surgeons also tend to have better results than low-volume surgeons, especially at the more complex end of the surgery spectrum (e.g., the Norwood procedure). Nevertheless, this trend for lower mortality rates at larger centers is not universal. All larger programs do not perform better than all smaller programs. Moreover, surgical volume seems to account for only a small proportion of the overall between-center variation in outcome. Intraoperative technical performance is one of the most important parts, if not the most important part, of the therapeutic process and a critical component of postoperative outcome. Thus, the use of center-specific, risk-adjusted outcome as a tool for quality assessment together with monitoring of technical performance using a specific score may be more reliable than relying on volume alone. However, the relationship between surgical volume and outcome in pediatric cardiac surgery is strong enough that it ought to support adapted and well-balanced health care strategies that take advantage of the positive influence that higher center and surgeon volumes have on outcome.

The Effects of Supplementation with a Vitamin and Mineral Complex with Guaraná Prior to Fasted Exercise on Affect, Exertion, Cognitive Performance, and Substrate Metabolism: A Randomized Controlled Trial.

PubMed

Veasey, Rachel C; Haskell-Ramsay, Crystal F; Kennedy, David O; Wishart, Karl; Maggini, Silvia; Fuchs, Caspar J; Stevenson, Emma J

2015-07-27

Exercise undertaken in a fasted state can lead to higher post-exercise mental fatigue. The administration of a vitamin and mineral complex with guaraná (MVM + G) has been shown to attenuate mental fatigue and improve performance during cognitively demanding tasks. This placebo-controlled, double-blind, randomized, balanced cross-over study examined the effect of MVM + G consumed prior to morning exercise on cognitive performance, affect, exertion, and substrate metabolism. Forty active males (age 21.4 ± 3.0 year; body mass index (BMI) 24.0 ± 2.4 kg/m2; maximal oxygen consumption (V̇O2max) 57.6 ± 7.3 mL/min/kg) completed two main trials, consuming either MVM + G or placebo prior to a 30-min run at 60% V̇O2max. Supplementation prior to exercise led to a small but significant reduction in Rating of Perceived Exertion (RPE) during exercise compared to the placebo. The MVM + G combination also led to significantly increased accuracy of numeric working memory and increased speed of picture recognition, compared to the placebo. There were no significant effects of supplementation on any other cognitive or mood measures or on substrate metabolism during exercise. These findings demonstrate that consuming a vitamin and mineral complex containing guaraná, prior to exercise, can positively impact subsequent memory performance and reduce perceived exertion during a moderate-intensity run in active males.

The Effects of Supplementation with a Vitamin and Mineral Complex with Guaraná Prior to Fasted Exercise on Affect, Exertion, Cognitive Performance, and Substrate Metabolism: A Randomized Controlled Trial

PubMed Central

Veasey, Rachel C.; Haskell-Ramsay, Crystal F.; Kennedy, David O.; Wishart, Karl; Maggini, Silvia; Fuchs, Caspar J.; Stevenson, Emma J.

2015-01-01

Exercise undertaken in a fasted state can lead to higher post-exercise mental fatigue. The administration of a vitamin and mineral complex with guaraná (MVM + G) has been shown to attenuate mental fatigue and improve performance during cognitively demanding tasks. This placebo-controlled, double-blind, randomized, balanced cross-over study examined the effect of MVM + G consumed prior to morning exercise on cognitive performance, affect, exertion, and substrate metabolism. Forty active males (age 21.4 ± 3.0 year; body mass index (BMI) 24.0 ± 2.4 kg/m2; maximal oxygen consumption (V̇O2max) 57.6 ± 7.3 mL/min/kg) completed two main trials, consuming either MVM + G or placebo prior to a 30-min run at 60% V̇O2max. Supplementation prior to exercise led to a small but significant reduction in Rating of Perceived Exertion (RPE) during exercise compared to the placebo. The MVM + G combination also led to significantly increased accuracy of numeric working memory and increased speed of picture recognition, compared to the placebo. There were no significant effects of supplementation on any other cognitive or mood measures or on substrate metabolism during exercise. These findings demonstrate that consuming a vitamin and mineral complex containing guaraná, prior to exercise, can positively impact subsequent memory performance and reduce perceived exertion during a moderate-intensity run in active males. PMID:26225993

Botulinum neurotoxin A complex recognizes host carbohydrates through its hemagglutinin component.

PubMed

Yao, Guorui; Lee, Kwangkook; Gu, Shenyan; Lam, Kwok-Ho; Jin, Rongsheng

2014-02-12

Botulinum neurotoxins (BoNTs) are potent bacterial toxins. The high oral toxicity of BoNTs is largely attributed to the progenitor toxin complex (PTC), which is assembled from BoNT and nontoxic neurotoxin-associated proteins (NAPs) that are produced together with BoNT in bacteria. Here, we performed ex vivo studies to examine binding of the highly homogeneous recombinant NAPs to mouse small intestine. We also carried out the first comprehensive glycan array screening with the hemagglutinin (HA) component of NAPs. Our data confirmed that intestinal binding of the PTC is partly mediated by the HA moiety through multivalent interactions between HA and host carbohydrates. The specific HA-carbohydrate recognition could be inhibited by receptor-mimicking saccharides.

The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): insights from genetic, morphological and acoustic data

PubMed Central

Sun, Keping; Kimball, Rebecca T.; Liu, Tong; Wei, Xuewen; Jin, Longru; Jiang, Tinglei; Lin, Aiqing; Feng, Jiang

2016-01-01

Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry. However, their evolutionary history has received little attention. Here, we used extensive sampling, morphological and acoustic data, as well as different genetic markers to investigate their evolutionary history. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial data identified three reciprocally monophyletic lineages: one representing all small forms from Southwest China, and the other two containing all large forms from Central and Southeast China, respectively. The large form showed paraphyly with respect to the small form. However, clustering analyses of microsatellite and Chd1 gene sequences support two divergent clusters separating the large form and the small form. Moreover, morphological and acoustic analyses were consistent with nuclear data. This unusual pattern in the R. macrotis complex might be accounted for by palaeoclimatic oscillations, shared ancestral polymorphism and/or interspecific hybridization. PMID:27748429

Molecular pathways in the transformation of model discoidal lipoprotein complexes induced by lecithin:cholesterol acyltransferase.

PubMed

Nichols, A V; Blanche, P J; Gong, E L; Shore, V G; Forte, T M

1985-05-17

Incubation (24 h, 37 degrees C) of discoidal complexes of phosphatidylcholine and apolipoprotein A-I (molar ratio 95 +/- 10 egg yolk phosphatidylcholine-apolipoprotein A-I; 10.5 X 4.0 nm, long X short dimension; designated, class 3 complexes) with the ultracentrifugal d greater than 1.21 g/ml fraction transformed the discoidal complexes to a small product with apparent mean hydrated and nonhydrated diameter of 7.8 and 6.6 nm, respectively. Formation of the small product was associated with marked reduction in phosphatidylcholine-apolipoprotein AI molar ratio of the complexes (on average from 95:1 to 45:1). Phospholipase A2 activity of lecithin:cholesterol acyltransferase participated in the depletion process, as evidenced by production of unesterified fatty acids. In the presence of the d greater than 1.21 g/ml fraction or partially purified lecithin:cholesterol acyltransferase and a source of unesterified cholesterol, the small product could be transformed to a core-containing (cholesteryl ester) round product with a hydrated and nonhydrated diameter of 8.6 and 7.5 nm, respectively. By means of cross-linking with dimethylsuberimidate, the protein moiety of the small product was shown to contain primarily two apolipoprotein A-I molecules per particle, while the large product contained three apolipoprotein A-I molecules per particle. The increase in number of apolipoprotein A-I molecules per particle during transformation of the small to the large product appeared to result from fusion of the small particles during core build-up and release of excess apolipoprotein A-I from the fusion product. The results obtained with the model complexes were consistent for the most part with recent observations (Chen, C., Applegate, K., King, W.C., Glomset, J.A., Norum, K.R. and Gjone, E. (1984) J. Lipid Res. 25, 269-282) on the transformation, by lecithin:cholesterol acyltransferase, of the small spherical high-density lipoproteins of patients with familial lecithin:cholesterol acyltransferase deficiency.

Single fiber model of particle retention in an acoustically driven porous mesh.

PubMed

Grossner, Michael T; Penrod, Alan E; Belovich, Joanne M; Feke, Donald L

2003-03-01

A method for the capture of small particles (tens of microns in diameter) from a continuously flowing suspension has recently been reported. This technique relies on a standing acoustic wave resonating in a rectangular chamber filled with a high-porosity mesh. Particles are retained in this chamber via a complex interaction between the acoustic field and the porous mesh. Although the mesh has a pore size two orders of magnitude larger than the particle diameter, collection efficiencies of 90% have been measured. A mathematical model has been developed to understand the experimentally observed phenomena and to be able to predict filtration performance. By examining a small region (a single fiber) of the porous mesh, the model has duplicated several experimental events such as the focusing of particles near an element of the mesh and the levitation of particles within pores. The single-fiber analysis forms the basis of modeling the overall performance of the particle filtration system. Copyright 2002 Elsevier Science B.V.

Ab initio folding of proteins using all-atom discrete molecular dynamics

PubMed Central

Ding, Feng; Tsao, Douglas; Nie, Huifen; Dokholyan, Nikolay V.

2008-01-01

Summary Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes, and applied to protein engineering and design of protein-protein interactions. PMID:18611374

Identification and verification of potential piRNAs from domesticated yak testis.

PubMed

Gong, Jishang; Zhang, Quanwei; Wang, Qi; Ma, Youji; Du, Jiaxiang; Zhang, Yong; Zhao, Xingxu

2018-02-01

PIWI-interacting RNAs (piRNA) are small non-coding RNA molecules expressed in animal germ cells that interact with PIWI family proteins to form RNA-protein complexes involved in epigenetic and post-transcriptional gene silencing of retrotransposons and other genetic elements in germ line cells, including reproductive stem cell self-sustainment, differentiation, meiosis and spermatogenesis. In the present study, we performed high-throughput sequencing of piRNAs in testis samples from yaks in different stages of sexual maturity. Deep sequencing of the small RNAs (18-40 nt in length) yielded 4,900,538 unique reads from a total of 53,035,635 reads. We identified yak small RNAs (18-30 nt) and performed functional characterization. Yak small RNAs showed a bimodal length distribution, with two peaks at 22 nt and >28 nt. More than 80% of the 3,106,033 putative piRNAs were mapped to 4637 piRNA-producing genomic clusters using RPKM. 6388 candidate piRNAs were identified from clean reads and the annotations were compared with the yak reference genome repeat region. Integrated network analysis suggested that some differentially expressed genes were involved in spermatogenesis through ECM-receptor interaction and PI3K-Akt signaling pathways. Our data provide novel insights into the molecular expression and regulation similarities and diversities in spermatogenesis and testicular development in yaks at different stages of sexual maturity. © 2018 The authors.

Identification and verification of potential piRNAs from domesticated yak testis

PubMed Central

Gong, Jishang; Zhang, Quanwei; Wang, Qi; Ma, Youji; Du, Jiaxiang; Zhang, Yong

2018-01-01

PIWI-interacting RNAs (piRNA) are small non-coding RNA molecules expressed in animal germ cells that interact with PIWI family proteins to form RNA–protein complexes involved in epigenetic and post-transcriptional gene silencing of retrotransposons and other genetic elements in germ line cells, including reproductive stem cell self-sustainment, differentiation, meiosis and spermatogenesis. In the present study, we performed high-throughput sequencing of piRNAs in testis samples from yaks in different stages of sexual maturity. Deep sequencing of the small RNAs (18–40 nt in length) yielded 4,900,538 unique reads from a total of 53,035,635 reads. We identified yak small RNAs (18–30 nt) and performed functional characterization. Yak small RNAs showed a bimodal length distribution, with two peaks at 22 nt and >28 nt. More than 80% of the 3,106,033 putative piRNAs were mapped to 4637 piRNA-producing genomic clusters using RPKM. 6388 candidate piRNAs were identified from clean reads and the annotations were compared with the yak reference genome repeat region. Integrated network analysis suggested that some differentially expressed genes were involved in spermatogenesis through ECM–receptor interaction and PI3K-Akt signaling pathways. Our data provide novel insights into the molecular expression and regulation similarities and diversities in spermatogenesis and testicular development in yaks at different stages of sexual maturity. PMID:29101267

Common Variants within Oxidative Phosphorylation Genes Influence Risk of Ischemic Stroke and Intracerebral Hemorrhage

PubMed Central

Anderson, Christopher D.; Biffi, Alessandro; Nalls, Michael A.; Devan, William J.; Schwab, Kristin; Ayres, Alison M.; Valant, Valerie; Ross, Owen A.; Rost, Natalia S.; Saxena, Richa; Viswanathan, Anand; Worrall, Bradford B.; Brott, Thomas G.; Goldstein, Joshua N.; Brown, Devin; Broderick, Joseph P.; Norrving, Bo; Greenberg, Steven M.; Silliman, Scott L.; Hansen, Björn M.; Tirschwell, David L.; Lindgren, Arne; Slowik, Agnieszka; Schmidt, Reinhold; Selim, Magdy; Roquer, Jaume; Montaner, Joan; Singleton, Andrew B.; Kidwell, Chelsea S.; Woo, Daniel; Furie, Karen L.; Meschia, James F.; Rosand, Jonathan

2013-01-01

Background and Purpose Prior studies demonstrated association between mitochondrial DNA variants and ischemic stroke (IS). We investigated whether variants within a larger set of oxidative phosphorylation (OXPHOS) genes encoded by both autosomal and mitochondrial DNA were associated with risk of IS and, based on our results, extended our investigation to intracerebral hemorrhage (ICH). Methods This association study employed a discovery cohort of 1643 individuals, a validation cohort of 2432 individuals for IS, and an extension cohort of 1476 individuals for ICH. Gene-set enrichment analysis (GSEA) was performed on all structural OXPHOS genes, as well as genes contributing to individual respiratory complexes. Gene-sets passing GSEA were tested by constructing genetic scores using common variants residing within each gene. Associations between each variant and IS that emerged in the discovery cohort were examined in validation and extension cohorts. Results IS was associated with genetic risk scores in OXPHOS as a whole (odds ratio (OR)=1.17, p=0.008) and Complex I (OR=1.06, p=0.050). Among IS subtypes, small vessel (SV) stroke showed association with OXPHOS (OR=1.16, p=0.007), Complex I (OR=1.13, p=0.027) and Complex IV (OR 1.14, p=0.018). To further explore this SV association, we extended our analysis to ICH, revealing association between deep hemispheric ICH and Complex IV (OR=1.08, p=0.008). Conclusions This pathway analysis demonstrates association between common genetic variants within OXPHOS genes and stroke. The associations for SV stroke and deep ICH suggest that genetic variation in OXPHOS influences small vessel pathobiology. Further studies are needed to identify culprit genetic variants and assess their functional consequences. PMID:23362085

Simian Virus 40 Large T Antigen Interacts with Human TFIIB-Related Factor and Small Nuclear RNA-Activating Protein Complex for Transcriptional Activation of TATA-Containing Polymerase III Promoters

PubMed Central

Damania, Blossom; Mital, Renu; Alwine, James C.

1998-01-01

The TATA-binding protein (TBP) is common to the basal transcription factors of all three RNA polymerases, being associated with polymerase-specific TBP-associated factors (TAFs). Simian virus 40 large T antigen has previously been shown to interact with the TBP-TAFII complexes, TFIID (B. Damania and J. C. Alwine, Genes Dev. 10:1369–1381, 1996), and the TBP-TAFI complex, SL1 (W. Zhai, J. Tuan, and L. Comai, Genes Dev. 11:1605–1617, 1997), and in both cases these interactions are critical for transcriptional activation. We show a similar mechanism for activation of the class 3 polymerase III (pol III) promoter for the U6 RNA gene. Large T antigen can activate this promoter, which contains a TATA box and an upstream proximal sequence element but cannot activate the TATA-less, intragenic VAI promoter (a class 2, pol III promoter). Mutants of large T antigen that cannot activate pol II promoters also fail to activate the U6 promoter. We provide evidence that large T antigen can interact with the TBP-containing pol III transcription factor human TFIIB-related factor (hBRF), as well as with at least two of the three TAFs in the pol III-specific small nuclear RNA-activating protein complex (SNAPc). In addition, we demonstrate that large T antigen can cofractionate and coimmunoprecipitate with the hBRF-containing complex TFIIIB derived from HeLa cells infected with a recombinant adenovirus which expresses large T antigen. Hence, similar to its function with pol I and pol II promoters, large T antigen interacts with TBP-containing, basal pol III transcription factors and appears to perform a TAF-like function. PMID:9488448

Towards Cost-Effective Operational Monitoring Systems for Complex Waters: Analyzing Small-Scale Coastal Processes with Optical Transmissometry

PubMed Central

Gonçalves-Araujo, Rafael; Wiegmann, Sonja; Torrecilla, Elena; Bardaji, Raul; Röttgers, Rüdiger; Bracher, Astrid; Piera, Jaume

2017-01-01

The detection and prediction of changes in coastal ecosystems require a better understanding of the complex physical, chemical and biological interactions, which involves that observations should be performed continuously. For this reason, there is an increasing demand for small, simple and cost-effective in situ sensors to analyze complex coastal waters at a broad range of scales. In this context, this study seeks to explore the potential of beam attenuation spectra, c(λ), measured in situ with an advanced-technology optical transmissometer, for assessing temporal and spatial patterns in the complex estuarine waters of Alfacs Bay (NW Mediterranean) as a test site. In particular, the information contained in the spectral beam attenuation coefficient was assessed and linked with different biogeochemical variables. The attenuation at λ = 710 nm was used as a proxy for particle concentration, TSM, whereas a novel parameter was adopted as an optical indicator for chlorophyll a (Chl-a) concentration, based on the local maximum of c(λ) observed at the long-wavelength side of the red band Chl-a absorption peak. In addition, since coloured dissolved organic matter (CDOM) has an important influence on the beam attenuation spectral shape and complementary measurements of particle size distribution were available, the beam attenuation spectral slope was used to analyze the CDOM content. Results were successfully compared with optical and biogeochemical variables from laboratory analysis of collocated water samples, and statistically significant correlations were found between the attenuation proxies and the biogeochemical variables TSM, Chl-a and CDOM. This outcome depicted the potential of high-frequency beam attenuation measurements as a simple, continuous and cost-effective approach for rapid detection of changes and patterns in biogeochemical properties in complex coastal environments. PMID:28107539

DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites

PubMed Central

Gowthaman, Ragul; Lyskov, Sergey; Karanicolas, John

2015-01-01

Over the past decade, protein-protein interactions have emerged as attractive but challenging targets for therapeutic intervention using small molecules. Due to the relatively flat surfaces that typify protein interaction sites, modern virtual screening tools developed for optimal performance against “traditional” protein targets perform less well when applied instead at protein interaction sites. Previously, we described a docking method specifically catered to the shallow binding modes characteristic of small-molecule inhibitors of protein interaction sites. This method, called DARC (Docking Approach using Ray Casting), operates by comparing the topography of the protein surface when “viewed” from a vantage point inside the protein against the topography of a bound ligand when “viewed” from the same vantage point. Here, we present five key enhancements to DARC. First, we use multiple vantage points to more accurately determine protein-ligand surface complementarity. Second, we describe a new scheme for rapidly determining optimal weights in the DARC scoring function. Third, we incorporate sampling of ligand conformers “on-the-fly” during docking. Fourth, we move beyond simple shape complementarity and introduce a term in the scoring function to capture electrostatic complementarity. Finally, we adjust the control flow in our GPU implementation of DARC to achieve greater speedup of these calculations. At each step of this study, we evaluate the performance of DARC in a “pose recapitulation” experiment: predicting the binding mode of 25 inhibitors each solved in complex with its distinct target protein (a protein interaction site). Whereas the previous version of DARC docked only one of these inhibitors to within 2 Å RMSD of its position in the crystal structure, the newer version achieves this level of accuracy for 12 of the 25 complexes, corresponding to a statistically significant performance improvement (p < 0.001). Collectively then, we find that the five enhancements described here – which together make up DARC 2.0 – lead to dramatically improved speed and performance relative to the original DARC method. PMID:26181386

EMU Suit Performance Simulation

NASA Technical Reports Server (NTRS)

Cowley, Matthew S.; Benson, Elizabeth; Harvill, Lauren; Rajulu, Sudhakar

2014-01-01

Introduction: Designing a planetary suit is very complex and often requires difficult trade-offs between performance, cost, mass, and system complexity. To verify that new suit designs meet requirements, full prototypes must be built and tested with human subjects. However, numerous design iterations will occur before the hardware meets those requirements. Traditional draw-prototype-test paradigms for research and development are prohibitively expensive with today's shrinking Government budgets. Personnel at NASA are developing modern simulation techniques that focus on a human-centric design paradigm. These new techniques make use of virtual prototype simulations and fully adjustable physical prototypes of suit hardware. This is extremely advantageous and enables comprehensive design down-selections to be made early in the design process. Objectives: The primary objective was to test modern simulation techniques for evaluating the human performance component of two EMU suit concepts, pivoted and planar style hard upper torso (HUT). Methods: This project simulated variations in EVA suit shoulder joint design and subject anthropometry and then measured the differences in shoulder mobility caused by the modifications. These estimations were compared to human-in-the-loop test data gathered during past suited testing using four subjects (two large males, two small females). Results: Results demonstrated that EVA suit modeling and simulation are feasible design tools for evaluating and optimizing suit design based on simulated performance. The suit simulation model was found to be advantageous in its ability to visually represent complex motions and volumetric reach zones in three dimensions, giving designers a faster and deeper comprehension of suit component performance vs. human performance. Suit models were able to discern differing movement capabilities between EMU HUT configurations, generic suit fit concerns, and specific suit fit concerns for crewmembers based on individual anthropometry

Rigorous theoretical framework for particle sizing in turbid colloids using light refraction.

PubMed

García-Valenzuela, Augusto; Barrera, Rubén G; Gutierrez-Reyes, Edahí

2008-11-24

Using a non-local effective-medium approach, we analyze the refraction of light in a colloidal medium. We discuss the theoretical grounds and all the necessary precautions to design and perform experiments to measure the effective refractive index in dilute colloids. As an application, we show that it is possible to retrieve the size of small dielectric particles in a colloid by measuring the complex effective refractive index and the volume fraction occupied by the particles.

Methods and new approaches to the calculation of physiological parameters by videodensitometry

NASA Technical Reports Server (NTRS)

Kedem, D.; Londstrom, D. P.; Rhea, T. C., Jr.; Nelson, J. H.; Price, R. R.; Smith, C. W.; Graham, T. P., Jr.; Brill, A. B.; Kedem, D.

1976-01-01

A complex system featuring a video-camera connected to a video disk, cine (medical motion picture) camera and PDP-9 computer with various input/output facilities has been developed. This system enables the performance of quantitative analysis of various functions recorded in clinical studies. Several studies are described, such as heart chamber volume calculations, left ventricle ejection fraction, blood flow through the lungs and also the possibility of obtaining information about blood flow and constrictions in small cross-section vessels

Towards a DNA Nanoprocessor: Reusable Tile-Integrated DNA Circuits.

PubMed

Gerasimova, Yulia V; Kolpashchikov, Dmitry M

2016-08-22

Modern electronic microprocessors use semiconductor logic gates organized on a silicon chip to enable efficient inter-gate communication. Here, arrays of communicating DNA logic gates integrated on a single DNA tile were designed and used to process nucleic acid inputs in a reusable format. Our results lay the foundation for the development of a DNA nanoprocessor, a small and biocompatible device capable of performing complex analyses of DNA and RNA inputs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Action detection by double hierarchical multi-structure space-time statistical matching model

NASA Astrophysics Data System (ADS)

Han, Jing; Zhu, Junwei; Cui, Yiyin; Bai, Lianfa; Yue, Jiang

2018-03-01

Aimed at the complex information in videos and low detection efficiency, an actions detection model based on neighboring Gaussian structure and 3D LARK features is put forward. We exploit a double hierarchical multi-structure space-time statistical matching model (DMSM) in temporal action localization. First, a neighboring Gaussian structure is presented to describe the multi-scale structural relationship. Then, a space-time statistical matching method is proposed to achieve two similarity matrices on both large and small scales, which combines double hierarchical structural constraints in model by both the neighboring Gaussian structure and the 3D LARK local structure. Finally, the double hierarchical similarity is fused and analyzed to detect actions. Besides, the multi-scale composite template extends the model application into multi-view. Experimental results of DMSM on the complex visual tracker benchmark data sets and THUMOS 2014 data sets show the promising performance. Compared with other state-of-the-art algorithm, DMSM achieves superior performances.

The inhibitory spillover effect: Controlling the bladder makes better liars *

PubMed Central

Fenn, Elise; Blandón-Gitlin, Iris; Coons, Jennifer; Pineda, Catherine; Echon, Reinalyn

2015-01-01

The Inhibitory-Spillover-Effect (ISE) on a deception task was investigated. The ISE occurs when performance in one self-control task facilitates performance in another (simultaneously conducted) self-control task. Deceiving requires increased access to inhibitory control. We hypothesized that inducing liars to control urination urgency (physical inhibition) would facilitate control during deceptive interviews (cognitive inhibition). Participants drank small (low-control) or large (high-control) amounts of water. Next, they lied or told the truth to an interviewer. Third-party observers assessed the presence of behavioral cues and made true/lie judgments. In the high-control, but not the low-control condition, liars displayed significantly fewer behavioral cues to deception, more behavioral cues signaling truth, and provided longer and more complex accounts than truth-tellers. Accuracy detecting liars in the high-control condition was significantly impaired; observers revealed bias toward perceiving liars as truth-tellers. The ISE can operate in complex behaviors. Acts of deception can be facilitated by covert manipulations of self-control. PMID:26366466

MS-CASPT2 study of hole transfer in guanine-indole complexes using the generalized Mulliken-Hush method: effective two-state treatment.

PubMed

Butchosa, C; Simon, S; Blancafort, L; Voityuk, A

2012-07-12

Because hole transfer from nucleobases to amino acid residues in DNA-protein complexes can prevent oxidative damage of DNA in living cells, computational modeling of the process is of high interest. We performed MS-CASPT2 calculations of several model structures of π-stacked guanine and indole and derived electron-transfer (ET) parameters for these systems using the generalized Mulliken-Hush (GMH) method. We show that the two-state model commonly applied to treat thermal ET between adjacent donor and acceptor is of limited use for the considered systems because of the small gap between the ground and first excited states in the indole radical cation. The ET parameters obtained within the two-state GMH scheme can deviate significantly from the corresponding matrix elements of the two-state effective Hamiltonian based on the GMH treatment of three adiabatic states. The computed values of diabatic energies and electronic couplings provide benchmarks to assess the performance of less sophisticated computational methods.

Efficient Lookup Table-Based Adaptive Baseband Predistortion Architecture for Memoryless Nonlinearity

NASA Astrophysics Data System (ADS)

Ba, Seydou N.; Waheed, Khurram; Zhou, G. Tong

2010-12-01

Digital predistortion is an effective means to compensate for the nonlinear effects of a memoryless system. In case of a cellular transmitter, a digital baseband predistorter can mitigate the undesirable nonlinear effects along the signal chain, particularly the nonlinear impairments in the radiofrequency (RF) amplifiers. To be practically feasible, the implementation complexity of the predistorter must be minimized so that it becomes a cost-effective solution for the resource-limited wireless handset. This paper proposes optimizations that facilitate the design of a low-cost high-performance adaptive digital baseband predistorter for memoryless systems. A comparative performance analysis of the amplitude and power lookup table (LUT) indexing schemes is presented. An optimized low-complexity amplitude approximation and its hardware synthesis results are also studied. An efficient LUT predistorter training algorithm that combines the fast convergence speed of the normalized least mean squares (NLMSs) with a small hardware footprint is proposed. Results of fixed-point simulations based on the measured nonlinear characteristics of an RF amplifier are presented.

Use of a New Portable Instrumented Impactor on the NASA Composite Crew Module Damage Tolerance Program

NASA Technical Reports Server (NTRS)

Jackson, Wade C.; Polis, Daniel L.

2014-01-01

Damage tolerance performance is critical to composite structures because surface impacts at relatively low energies may result in a significant strength loss. For certification, damage tolerance criteria require aerospace vehicles to meet design loads while containing damage at critical locations. Data from standard small coupon testing are difficult to apply to larger more complex structures. Due to the complexity of predicting both the impact damage and the residual properties, damage tolerance is demonstrated primarily by testing. A portable, spring-propelled, impact device was developed which allows the impact damage response to be investigated on large specimens, full-scale components, or entire vehicles. During impact, both the force history and projectile velocity are captured. The device was successfully used to demonstrate the damage tolerance performance of the NASA Composite Crew Module. The impactor was used to impact 18 different design features at impact energies up to 35 J. Detailed examples of these results are presented, showing impact force histories, damage inspection results, and response to loading.

Action detection by double hierarchical multi-structure space–time statistical matching model

NASA Astrophysics Data System (ADS)

Han, Jing; Zhu, Junwei; Cui, Yiyin; Bai, Lianfa; Yue, Jiang

2018-06-01

Aimed at the complex information in videos and low detection efficiency, an actions detection model based on neighboring Gaussian structure and 3D LARK features is put forward. We exploit a double hierarchical multi-structure space-time statistical matching model (DMSM) in temporal action localization. First, a neighboring Gaussian structure is presented to describe the multi-scale structural relationship. Then, a space-time statistical matching method is proposed to achieve two similarity matrices on both large and small scales, which combines double hierarchical structural constraints in model by both the neighboring Gaussian structure and the 3D LARK local structure. Finally, the double hierarchical similarity is fused and analyzed to detect actions. Besides, the multi-scale composite template extends the model application into multi-view. Experimental results of DMSM on the complex visual tracker benchmark data sets and THUMOS 2014 data sets show the promising performance. Compared with other state-of-the-art algorithm, DMSM achieves superior performances.

Managing Scientific Software Complexity with Bocca and CCA

DOE PAGES

Allan, Benjamin A.; Norris, Boyana; Elwasif, Wael R.; ...

2008-01-01

In high-performance scientific software development, the emphasis is often on short time to first solution. Even when the development of new components mostly reuses existing components or libraries and only small amounts of new code must be created, dealing with the component glue code and software build processes to obtain complete applications is still tedious and error-prone. Component-based software meant to reduce complexity at the application level increases complexity to the extent that the user must learn and remember the interfaces and conventions of the component model itself. To address these needs, we introduce Bocca, the first tool to enablemore » application developers to perform rapid component prototyping while maintaining robust software-engineering practices suitable to HPC environments. Bocca provides project management and a comprehensive build environment for creating and managing applications composed of Common Component Architecture components. Of critical importance for high-performance computing (HPC) applications, Bocca is designed to operate in a language-agnostic way, simultaneously handling components written in any of the languages commonly used in scientific applications: C, C++, Fortran, Python and Java. Bocca automates the tasks related to the component glue code, freeing the user to focus on the scientific aspects of the application. Bocca embraces the philosophy pioneered by Ruby on Rails for web applications: start with something that works, and evolve it to the user's purpose.« less

An evaluation of the accuracy and performance of lightweight GPS collars in a suburban environment.

PubMed

Adams, Amy L; Dickinson, Katharine J M; Robertson, Bruce C; van Heezik, Yolanda

2013-01-01

The recent development of lightweight GPS collars has enabled medium-to-small sized animals to be tracked via GPS telemetry. Evaluation of the performance and accuracy of GPS collars is largely confined to devices designed for large animals for deployment in natural environments. This study aimed to assess the performance of lightweight GPS collars within a suburban environment, which may be different from natural environments in a way that is relevant to satellite signal acquisition. We assessed the effects of vegetation complexity, sky availability (percentage of clear sky not obstructed by natural or artificial features of the environment), proximity to buildings, and satellite geometry on fix success rate (FSR) and location error (LE) for lightweight GPS collars within a suburban environment. Sky availability had the largest affect on FSR, while LE was influenced by sky availability, vegetation complexity, and HDOP (Horizontal Dilution of Precision). Despite the complexity and modified nature of suburban areas, values for FSR (mean= 90.6%) and LE (mean = 30.1 m) obtained within the suburban environment are comparable to those from previous evaluations of GPS collars designed for larger animals and within less built-up environments. Due to fine-scale patchiness of habitat within urban environments, it is recommended that resource selection methods that are not reliant on buffer sizes be utilised for selection studies.

NOTES: a review of the technical problems encountered and their solutions.

PubMed

Mintz, Yoav; Horgan, Santiago; Cullen, John; Stuart, David; Falor, Eric; Talamini, Mark A

2008-08-01

Natural orifice translumenal endoscopic surgery (NOTES) is currently investigated and developed worldwide. In the past few years, multiple groups have confronted this challenge. Many technical problems are encountered in this technique due to the currently available tools for this approach. Some of the unique technical problems in NOTES include: blindly performed primary incisions; uncontrolled pneumoperitoneal pressure; no support for the endoscope in the abdominal cavity; inadequate vision; insufficient illumination; limited retraction and exposure; and the complexity of suturing and performing a safe anastomosis. In this paper, we review the problems encountered in NOTES and provide possible temporary solutions. Acute and survival studies were performed on 15 farm pigs. The hybrid technique approach (i.e., endoscopic surgery with the aid of laparoscopic vision) was performed in all cases. Procedures performed included liver biopsies, bilateral tubal ligation, oophprectomy, cholecystectomy, splenectomy and small bowel resection, and anastomosis. All attempted procedures were successfully performed. New methods and techniques were developed to overcome the technical problems. Closure of the gastrotomy was achieved by T-bar sutures and by stapler closure of the stomach incision. Small bowel anastomosis was achieved by the dual-lumen NOTES technique. The hybrid technique serves as a temporary approach to aid in developing the NOTES technique. A rectal or vaginal port of entry enables and facilitates gastrointestinal NOTES by using available laparoscopic instruments. The common operations performed today in the laparoscopic fashion could be probably performed in the NOTES approach. The safety of these procedures, however, is yet to be determined.

Can small hydrophobic gold nanoparticles inhibit β2-microglobulin fibrillation?

NASA Astrophysics Data System (ADS)

Brancolini, Giorgia; Toroz, Dimitrios; Corni, Stefano

2014-06-01

Inorganic nanoparticles stabilized by a shell of organic ligands can enhance or suppress the natural propensity of proteins to form fibrils. Functionalization facilitates targeted delivery of the nanoparticles to various cell types, bioimaging, drug delivery and other therapeutic and diagnostic applications. In this study, we provide a computational model of the effect of a prototypical thiol-protected gold nanoparticle, Au25L18- (L = S(CH2)2Ph) on the β2-microglobulin natural fibrillation propensity. To reveal the molecular basis of the protein-nanoparticle association process, we performed various simulations at multiple levels (Classical Molecular Dynamics and Brownian Dynamics) that cover multiple length- and timescales. The results provide a model of the ensemble of structures constituting the protein-gold nanoparticle complexes, and insights into the driving forces for the binding of β2-microglobulin to hydrophobic small size gold nanoparticles. We have found that the small nanoparticles can bind the protein to form persistent complexes. This binding of nanoparticles is able to block the active sites of domains from binding to another protein, thus leading to potential inhibition of the fibrillation activity. A comparison with the binding patches identified for the interaction of the protein with a known inhibitor of fibrillation, supports our conclusion.Inorganic nanoparticles stabilized by a shell of organic ligands can enhance or suppress the natural propensity of proteins to form fibrils. Functionalization facilitates targeted delivery of the nanoparticles to various cell types, bioimaging, drug delivery and other therapeutic and diagnostic applications. In this study, we provide a computational model of the effect of a prototypical thiol-protected gold nanoparticle, Au25L18- (L = S(CH2)2Ph) on the β2-microglobulin natural fibrillation propensity. To reveal the molecular basis of the protein-nanoparticle association process, we performed various simulations at multiple levels (Classical Molecular Dynamics and Brownian Dynamics) that cover multiple length- and timescales. The results provide a model of the ensemble of structures constituting the protein-gold nanoparticle complexes, and insights into the driving forces for the binding of β2-microglobulin to hydrophobic small size gold nanoparticles. We have found that the small nanoparticles can bind the protein to form persistent complexes. This binding of nanoparticles is able to block the active sites of domains from binding to another protein, thus leading to potential inhibition of the fibrillation activity. A comparison with the binding patches identified for the interaction of the protein with a known inhibitor of fibrillation, supports our conclusion. Electronic supplementary information (ESI) available: Details on the molecular dynamics simulation results. Table S1 reports results of the MD trajectories with a single NP at different initial velocities (d1, d2, d3, and d4) (three-dimensional structures and contact residues). Table S2 reports results of the MD trajectories with a couple of NPs at different initial velocities (initial orientations, three-dimensional structures, contact residues and root-mean-square deviations). Table S3 reports root-mean-square fluctuations and divergence of the protein structure with respect to the NMR model. Table S4 describes the average energy of the final complexes. See DOI: 10.1039/c4nr01514b

Complex task performance in Cyberspace. Surgical procedures in a telepresence environment.

PubMed

Bowersox, J C; LaPorta, A J; Cordts, P R; Bhoyrul, S; Shah, A

1996-01-01

To assess the capabilities of our fully functional, prototype telepresence surgery system, experienced surgeons performed complete operative procedures on live, anesthetized pigs. Cholecystectomy, the prototypical procedure for evaluating the integration of surgical skills, was successfully performed in six animals. There were no aborted attempts or complications. Other procedures completed included gastrotomy and enterotomy closures, anastomosis of the small intestine, and nephrectomy. No specific training was required for using the telepresence surgery system, and the "feel" of the system was described as intuitive. Operative times were longer than required in conventional, open surgery, most likely the result of the four degrees of freedom available in the manipulators of the current-generation system. Force feedback and high-resolution, stereoscopic video input facilitated performance. Surgeons operating through a first-generation telepresence system can achieve technical results equivalent to those obtained in conventional surgery.

An Investigation of Unified Memory Access Performance in CUDA

PubMed Central

Landaverde, Raphael; Zhang, Tiansheng; Coskun, Ayse K.; Herbordt, Martin

2015-01-01

Managing memory between the CPU and GPU is a major challenge in GPU computing. A programming model, Unified Memory Access (UMA), has been recently introduced by Nvidia to simplify the complexities of memory management while claiming good overall performance. In this paper, we investigate this programming model and evaluate its performance and programming model simplifications based on our experimental results. We find that beyond on-demand data transfers to the CPU, the GPU is also able to request subsets of data it requires on demand. This feature allows UMA to outperform full data transfer methods for certain parallel applications and small data sizes. We also find, however, that for the majority of applications and memory access patterns, the performance overheads associated with UMA are significant, while the simplifications to the programming model restrict flexibility for adding future optimizations. PMID:26594668

Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas.

PubMed

Łukasik, Piotr; Nazario, Katherine; Van Leuven, James T; Campbell, Matthew A; Meyer, Mariah; Michalik, Anna; Pessacq, Pablo; Simon, Chris; Veloso, Claudio; McCutcheon, John P

2018-01-09

Bacterial endosymbionts that provide nutrients to hosts often have genomes that are extremely stable in structure and gene content. In contrast, the genome of the endosymbiont Hodgkinia cicadicola has fractured into multiple distinct lineages in some species of the cicada genus Tettigades To better understand the frequency, timing, and outcomes of Hodgkinia lineage splitting throughout this cicada genus, we sampled cicadas over three field seasons in Chile and performed genomics and microscopy on representative samples. We found that a single ancestral Hodgkinia lineage has split at least six independent times in Tettigades over the last 4 million years, resulting in complexes of between two and six distinct Hodgkinia lineages per host. Individual genomes in these symbiotic complexes differ dramatically in relative abundance, genome size, organization, and gene content. Each Hodgkinia lineage retains a small set of core genes involved in genetic information processing, but the high level of gene loss experienced by all genomes suggests that extensive sharing of gene products among symbiont cells must occur. In total, Hodgkinia complexes that consist of multiple lineages encode nearly complete sets of genes present on the ancestral single lineage and presumably perform the same functions as symbionts that have not undergone splitting. However, differences in the timing of the splits, along with dissimilar gene loss patterns on the resulting genomes, have led to very different outcomes of lineage splitting in extant cicadas.

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

PubMed

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

2018-01-01

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

RNA-induced silencing complex-bound small interfering RNA is a determinant of RNA interference-mediated gene silencing in mice.

PubMed

Wei, Jie; Jones, Jeffrey; Kang, Jing; Card, Ananda; Krimm, Michael; Hancock, Paula; Pei, Yi; Ason, Brandon; Payson, Elmer; Dubinina, Natalya; Cancilla, Mark; Stroh, Mark; Burchard, Julja; Sachs, Alan B; Hochman, Jerome H; Flanagan, W Michael; Kuklin, Nelly A

2011-06-01

Deeper knowledge of pharmacokinetic and pharmacodynamic (PK/PD) concepts for RNA therapeutics is important to streamline the drug development process and for rigorous selection of best performing drug candidates. Here we characterized the PK/PD relationship for small interfering RNAs (siRNAs) targeting luciferase by examining siRNA concentration in plasma and liver, the temporal RNA-induced silencing complex binding profiles, mRNA reduction, and protein inhibition measured by noninvasive bioluminescent imaging. A dose-dependent and time-related decrease in bioluminescence was detected over 25 days after a single treatment of a lipid nanoparticle-formulated siRNA targeting luciferase messenger RNA. A direct relationship was observed between the degree of in vivo mRNA and protein reduction and the Argonaute2 (Ago2)-bound siRNA fraction but not with the total amount of siRNA found in the liver, suggesting that the Ago2-siRNA complex is the key determinant of target inhibition. These observations were confirmed for an additional siRNA that targets endogenously expressed Sjögren syndrome antigen B (Ssb) mRNA, indicating that our observations are not limited to a transgenic mouse system. Our data provide detailed information of the temporal regulation of siRNA liver delivery, Ago2 loading, mRNA reduction, and protein inhibition that are essential for the rapid and cost-effective clinical development of siRNAs therapeutics.

Fluoxetine induces autophagic cell death via eEF2K-AMPK-mTOR-ULK complex axis in triple negative breast cancer.

PubMed

Sun, Dejuan; Zhu, Lingjuan; Zhao, Yuqian; Jiang, Yingnan; Chen, Lixia; Yu, Yang; Ouyang, Liang

2018-04-01

Triple negative breast cancer (TNBC) is a complex and intrinsically aggressive tumour with poor prognosis, and the discovery of targeted small-molecule drugs for TNBC treatment still remains in its infancy. In this study, we aimed to discover a small-molecule agent for TNBC treatment and illuminate its potential mechanisms. Cell viability was detected by using methylthiazoltetrazolium (MTT) assay. Electron microscopy, GFP-LC3 transfection, monodansylcadaverine staining and apoptosis assay were performed to determine Fluoxetine-induced autophagy and apoptosis. Western blotting and siRNA transfection were carried out to investigate the mechanisms of Fluoxetine-induced autophagy. iTRAQ-based proteomics analysis was used to explore the underlying mechanisms. We have demonstrated that Fluoxetine had remarkable anti-proliferative activities and induced autophagic cell death in MDA-MB-231 and MDA-MB-436 cells. The mechanism for Fluoxetine-induced autophagic cell death was associated with inhibition of eEF2K and activation of AMPK-mTOR-ULK complex axis. Further iTRAQ-based proteomics and network analyses revealed that Fluoxetine-induced mechanism was involved in BIRC6, BNIP1, SNAP29 and Bif-1. These results demonstrate that Fluoxetine induces apoptosis and autophagic cell death in TNBC, which will hold a promise for the future TNBC therapy. © 2017 John Wiley & Sons Ltd.

Identification of small molecule compounds targeting the interaction of HIV-1 Vif and human APOBEC3G by virtual screening and biological evaluation.

PubMed

Ma, Ling; Zhang, Zhixin; Liu, Zhenlong; Pan, Qinghua; Wang, Jing; Li, Xiaoyu; Guo, Fei; Liang, Chen; Hu, Laixing; Zhou, Jinming; Cen, Shan

2018-05-23

Human APOBEC3G (hA3G) is a restriction factor that inhibits human immunodeficiency 1 virus (HIV-1) replication. The virally encoded protein Vif binds to hA3G and induces its degradation, thereby counteracting the antiviral activity of hA3G. Vif-mediated hA3G degradation clearly represents a potential target for anti-HIV drug development. Herein, we have performed virtual screening to discover small molecule inhibitors that target the binding interface of the Vif/hA3G complex. Subsequent biochemical studies have led to the identification of a small molecule inhibitor, IMB-301 that binds to hA3G, interrupts the hA3G-Vif interaction and inhibits Vif-mediated degradation of hA3G. As a result, IMB-301 strongly inhibits HIV-1 replication in a hA3G-dependent manner. Our study further demonstrates the feasibility of inhibiting HIV replication by abrogating the Vif-hA3G interaction with small molecules.

Autonomy and interdependence: beliefs of Brazilian mothers from state capitals and small towns.

PubMed

Vieira, Mauro Luis; Seidl-de-Moura, Maria Lucia; Macarini, Samira Mafioletti; Martins, Gabriela Dal Forno; Lordelo, Eulina da Rocha; Tokumaru, Rosana Suemi; Oliva, Angela Donate

2010-11-01

This study aimed to investigate characteristics of Brazilian mothers' beliefs system, in the dimensions of autonomy and interdependence. A group of 600 women, half from state capitals and half from small towns, participated in the study. They were individually interviewed with Scales of Allocentrism, Beliefs about Parental Practices and Socialization Goals. Paired and Independent samples t tests and Multivariate GLM were performed. The results indicate that although mothers from both contexts value autonomy, mothers inhabiting small towns considered the relational dimension as the most important; whereas mothers inhabiting capitals valued equally both dimensions, either in their beliefs about practices or in the socialization goals for their children. Mothers from small towns have a higher mean score for allocentrism than mothers living in capitals. Thus, place of residence proved to be a relevant variable in the modulation of maternal beliefs. Educational level was not a significant factor in the variables considered and with this group of mothers. The study results are discussed in terms of their contribution to the understanding of the complex relationship between dimensions of autonomy and interdependence in mothers' beliefs system.

A Plasmonic Mass Spectrometry Approach for Detection of Small Nutrients and Toxins

NASA Astrophysics Data System (ADS)

Wu, Shu; Qian, Linxi; Huang, Lin; Sun, Xuming; Su, Haiyang; Gurav, Deepanjali D.; Jiang, Mawei; Cai, Wei; Qian, Kun

2018-07-01

Nutriology relies on advanced analytical tools to study the molecular compositions of food and provide key information on sample quality/safety. Small nutrients detection is challenging due to the high diversity and broad dynamic range of molecules in food samples, and a further issue is to track low abundance toxins. Herein, we developed a novel plasmonic matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) approach to detect small nutrients and toxins in complex biological emulsion samples. Silver nanoshells (SiO2@Ag) with optimized structures were used as matrices and achieved direct analysis of 6 nL of human breast milk without any enrichment or separation. We performed identification and quantitation of small nutrients and toxins with limit-of-detection down to 0.4 pmol (for melamine) and reaction time shortened to minutes, which is superior to the conventional biochemical method currently in use. The developed approach contributes to the near-future application of MALDI MS in a broad field and personalized design of plasmonic materials for real-case bio-analysis.[Figure not available: see fulltext.

RISC assembly: Coordination between small RNAs and Argonaute proteins.

PubMed

Kobayashi, Hotaka; Tomari, Yukihide

2016-01-01

Non-coding RNAs generally form ribonucleoprotein (RNP) complexes with their partner proteins to exert their functions. Small RNAs, including microRNAs, small interfering RNAs, and PIWI-interacting RNAs, assemble with Argonaute (Ago) family proteins into the effector complex called RNA-induced silencing complex (RISC), which mediates sequence-specific target gene silencing. RISC assembly is not a simple binding between a small RNA and Ago; rather, it follows an ordered multi-step pathway that requires specific accessory factors. Some steps of RISC assembly and RISC-mediated gene silencing are dependent on or facilitated by particular intracellular platforms, suggesting their spatial regulation. In this review, we summarize the currently known mechanisms for RISC assembly of each small RNA class and propose a revised model for the role of the chaperone machinery in the duplex-initiated RISC assembly pathway. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparative Analysis of Argonaute-dependent Small RNA Pathways in Drosophila

PubMed Central

Zhou, Rui; Hotta, Ikuko; Denli, Ahmet M.; Hong, Pengyu; Perrimon, Norbert; Hannon, Gregory J.

2008-01-01

Summary The specificity of RNAi pathways is determined by several classes of small RNAs, which include siRNAs, piRNAs, endo-siRNAs, and microRNAs (miRNAs). These small RNAs are invariably incorporated into large Argonaute (Ago)-containing effector complexes known as RNA-induced silencing complexes (RISCs), which they guide to silencing targets. Both genetic and biochemical strategies have yielded conserved molecular components of small RNA biogenesis and effector machineries. However, given the complexity of these pathways, there are likely to be additional components and regulators that remain to be uncovered. We have undertaken a comparative and comprehensive RNAi screen to identify genes that impact three major Ago-dependent small RNA pathways that operate in Drosophila S2 cells. We identify subsets of candidates that act positively or negatively in siRNA, endo-siRNA and miRNA pathways. Our studies indicate that many components are shared among all three Argonaute-dependent silencing pathways, though each is also impacted by discrete sets of genes. PMID:19026789

Motility of the oesophagus and small bowel in adults treated for Hirschsprung's disease during early childhood.

PubMed

Medhus, A W; Bjørnland, K; Emblem, R; Husebye, E

2010-02-01

Dysmotility of the upper gastrointestinal (GI) tract has been reported in children with Hirschsprung's disease (HD). In the present study, motility of the oesophagus and the small bowel was studied in adults treated for HD during early childhood to elucidate whether there are alterations in motility of the upper GI tract in this patient group. [Correction added after online publication 15 Sep: The preceding sentence has been rephrased for better clarity.] Ambulatory small bowel manometry with recording sites in duodenum/jejunum was performed in 16 adult patients with surgically treated HD and 17 healthy controls. In addition, oesophageal manometry was performed with station pull-through technique. The essential patterns of small bowel motility were recognized in all patients and controls. During fasting, phase III of the migrating motor complex (MMC) was more prominent in patients with HD than in controls when accounting for duration and propagation velocity (P = 0.006). Phase I of the MMC was of shorter duration (P = 0.008), and phase II tended to be of longer duration (P = 0.05) in the patients. During daytime fasting, propagated clustered contractions (PCCs) were more frequent in the patients (P = 0.01). Postprandially, the patients demonstrated a higher contractile frequency (P = 0.02), a shorter duration of contractions (P = 0.008) and more frequent PCCs (P < 0.001). The patients had normal oesophageal motility. This study demonstrates that adult patients with HD have preserved essential patterns of oesophageal and small bowel motility. However, abnormalities mainly characterized by increased contractile activity of the small bowel during fasting and postprandially are evident. These findings indicate alterations in neuronal control of motility and persistent involvement of the upper GI tract in this disease.

Use of Ice-Nucleating Proteins To Improve the Performance of Freeze-Thaw Valves in Microfluidic Devices.

PubMed

Gaiteri, Joseph C; Henley, W Hampton; Siegfried, Nathan A; Linz, Thomas H; Ramsey, J Michael

2017-06-06

Currently, reliable valving on integrated microfluidic devices fabricated from rigid materials is confined to expensive and complex methods. Freeze-thaw valves (FTVs) can provide a low cost, low complexity valving mechanism, but reliable implementation of them has been greatly hindered by the lack of ice nucleation sites within the valve body's small volume. Work to date has required very low temperatures (on the order of -40 °C or colder) to induce freezing without nucleation sites, making FTVs impractical due to instrument engineering challenges. Here, we report the use of ice-nucleating proteins (INPs) to induce ice formation at relatively warm temperatures in microfluidic devices. Microfluidic channels were filled with buffers containing femtomolar INP concentrations from Pseudomonas syringae. The channels were cooled externally with simple, small-footprint Peltier thermoelectric coolers (TECs), and the times required for channel freezing (valve closure) and thawing (valve opening) were measured. Under optimized conditions in plastic chips, INPs made sub-10 s actuations possible at TEC temperatures as warm as -13 °C. Additionally, INPs were found to have no discernible inhibitory effects in model enzyme-linked immunosorbent assays or polymerase chain reactions, indicating their compatibility with microfluidic systems that incorporate these widely used bioassays. FTVs with INPs provide a much needed reliable valving scheme for rigid plastic devices with low complexity, low cost, and no moving parts on the device or instrument. The reduction in freeze time, accessible actuation temperatures, chemical compatibility, and low complexity make the implementation of compact INP-based FTV arrays practical and attractive for the control of integrated biochemical assays.

Discrete Cu(i) complexes for azide–alkyne annulations of small molecules inside mammalian cells† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04643j

PubMed Central

Miguel-Ávila, Joan; Tomás-Gamasa, María; Olmos, Andrea

2018-01-01

The archetype reaction of “click” chemistry, namely, the copper-promoted azide–alkyne cycloaddition (CuAAC), has found an impressive number of applications in biological chemistry. However, methods for promoting intermolecular annulations of exogenous, small azides and alkynes in the complex interior of mammalian cells, are essentially unknown. Herein we demonstrate that isolated, well-defined copper(i)–tris(triazolyl) complexes featuring designed ligands can readily enter mammalian cells and promote intracellular CuAAC annulations of small, freely diffusible molecules. In addition to simplifying protocols and avoiding the addition of “non-innocent” reductants, the use of these premade copper complexes leads to more efficient processes than with the alternative, in situ made copper species prepared from Cu(ii) sources, tris(triazole) ligands and sodium ascorbate. Under the reaction conditions, the well-defined copper complexes exhibit very good cell penetration properties, and do not present significant toxicities. PMID:29675241

Making RISC.

PubMed

Kawamata, Tomoko; Tomari, Yukihide

2010-07-01

It is well established that 20- to 30-nt small RNAs, including small interfering RNAs, microRNAs and Piwi-interacting RNAs, play crucial roles in regulating gene expression and control a surprisingly diverse array of biological processes. These small RNAs cannot work alone: they must form effector ribonucleoprotein complexes - RNA-induced silencing complexes (RISCs) - to exert their function. Thus, RISC assembly is a key process in small RNA-mediated silencing. Recent biochemical analyses of RISC assembly, together with new structural studies of Argonaute, the core protein component of RISC, suggest a revised view of how mature RISC, which contains single-stranded guide RNA, is built from small RNAs that are born double-stranded. Copyright 2010 Elsevier Ltd. All rights reserved.

Initial Low-Reynolds Number Iced Aerodynamic Performance for CRM Wing

NASA Technical Reports Server (NTRS)

Woodard, Brian; Diebold, Jeff; Broeren, Andy; Potapczuk, Mark; Lee, Sam; Bragg, Michael

2015-01-01

NASA, FAA, ONERA, and other partner organizations have embarked on a significant, collaborative research effort to address the technical challenges associated with icing on large scale, three-dimensional swept wings. These are extremely complex phenomena important to the design, certification and safe operation of small and large transport aircraft. There is increasing demand to balance trade-offs in aircraft efficiency, cost and noise that tend to compete directly with allowable performance degradations over an increasing range of icing conditions. Computational fluid dynamics codes have reached a level of maturity that they are being proposed by manufacturers for use in certification of aircraft for flight in icing. However, sufficient high-quality data to evaluate their performance on iced swept wings are not currently available in the public domain and significant knowledge gaps remain.

Computational Aerodynamic Modeling of Small Quadcopter Vehicles

NASA Technical Reports Server (NTRS)

Yoon, Seokkwan; Ventura Diaz, Patricia; Boyd, D. Douglas; Chan, William M.; Theodore, Colin R.

2017-01-01

High-fidelity computational simulations have been performed which focus on rotor-fuselage and rotor-rotor aerodynamic interactions of small quad-rotor vehicle systems. The three-dimensional unsteady Navier-Stokes equations are solved on overset grids using high-order accurate schemes, dual-time stepping, low Mach number preconditioning, and hybrid turbulence modeling. Computational results for isolated rotors are shown to compare well with available experimental data. Computational results in hover reveal the differences between a conventional configuration where the rotors are mounted above the fuselage and an unconventional configuration where the rotors are mounted below the fuselage. Complex flow physics in forward flight is investigated. The goal of this work is to demonstrate that understanding of interactional aerodynamics can be an important factor in design decisions regarding rotor and fuselage placement for next-generation multi-rotor drones.

The Spot 42 RNA: A regulatory small RNA with roles in the central metabolism

PubMed Central

Bækkedal, Cecilie; Haugen, Peik

2015-01-01

The Spot 42 RNA is a 109 nucleotide long (in Escherichia coli) noncoding small regulatory RNA (sRNA) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the majority of experimental work on Spot 42 RNA has been performed using E. coli, and recently Aliivibrio salmonicida. In the cell Spot 42 RNA plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP complex. Here we summarize the current knowledge on Spot 42, and present the natural distribution of spf, show family-specific secondary structural features of Spot 42, and link highly conserved structural regions to mRNA target binding. PMID:26327359

New High-Performance Droplet Freezing Assay (HP-DFA) for the Analysis of Ice Nuclei with Complex Composition

NASA Astrophysics Data System (ADS)

Kunert, Anna Theresa; Scheel, Jan Frederik; Helleis, Frank; Klimach, Thomas; Pöschl, Ulrich; Fröhlich-Nowoisky, Janine

2016-04-01

Freezing of water above homogeneous freezing is catalyzed by ice nucleation active (INA) particles called ice nuclei (IN), which can be of various inorganic or biological origin. The freezing temperatures reach up to -1 °C for some biological samples and are dependent on the chemical composition of the IN. The standard method to analyze IN in solution is the droplet freezing assay (DFA) established by Gabor Vali in 1970. Several modifications and improvements were already made within the last decades, but they are still limited by either small droplet numbers, large droplet volumes or inadequate separation of the single droplets resulting in mutual interferences and therefore improper measurements. The probability that miscellaneous IN are concentrated together in one droplet increases with the volume of the droplet, which can be described by the Poisson distribution. At a given concentration, the partition of a droplet into several smaller droplets leads to finely dispersed IN resulting in better statistics and therefore in a better resolution of the nucleation spectrum. We designed a new customized high-performance droplet freezing assay (HP-DFA), which represents an upgrade of the previously existing DFAs in terms of temperature range and statistics. The necessity of observing freezing events at temperatures lower than homogeneous freezing due to freezing point depression, requires high-performance thermostats combined with an optimal insulation. Furthermore, we developed a cooling setup, which allows both huge and tiny temperature changes within a very short period of time. Besides that, the new DFA provides the analysis of more than 750 droplets per run with a small droplet volume of 5 μL. This enables a fast and more precise analysis of biological samples with complex IN composition as well as better statistics for every sample at the same time.

Amplifying human ability through autonomics and machine learning in IMPACT

NASA Astrophysics Data System (ADS)

Dzieciuch, Iryna; Reeder, John; Gutzwiller, Robert; Gustafson, Eric; Coronado, Braulio; Martinez, Luis; Croft, Bryan; Lange, Douglas S.

2017-05-01

Amplifying human ability for controlling complex environments featuring autonomous units can be aided by learned models of human and system performance. In developing a command and control system that allows a small number of people to control a large number of autonomous teams, we employ an autonomics framework to manage the networks that represent mission plans and the networks that are composed of human controllers and their autonomous assistants. Machine learning allows us to build models of human and system performance useful for monitoring plans and managing human attention and task loads. Machine learning also aids in the development of tactics that human supervisors can successfully monitor through the command and control system.

Speciation of cadmium and zinc with application to soil solutions

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

Holm, P.E.; Christensen, T.H.; Tjell, J.C.

1995-01-01

A two-part method has been developed for determination of Cd and Zn species in 50-mL soil solution samples containing low concentrations of Cd and Zn (1-10 {mu}g Cd L{sup -1} and 50-1000 {mu}g Zn L{sup -1}). The method uses two cation exchange resins (Amberlite CG 120 and Chelex 100) in a batch-column-batch procedure and relies on analytical determinations of Cd and Zn by graphite furnace atomic absorption spectrophotometry. The first part (batch) of the method allows determination of free divalent Cd{sup 2+} and Zn{sup 2+}. This part is experimentally sensitive to cation concentrations and ionic strength and these parameters shouldmore » be controlled during the experimental procedures. However, it is shown that Cd and Zn concentrations and pH do not influence the method. Speciations performed on samples containing chloride and sulfate were in accordance with theoretical calculations. The second part (column-batch) of the method operationally separates the complexed fraction into labile complexes, slowly labile complexes, and stable complexes. Chloro complexes were identified as labile complexes, while EDTA complexes were identified as stable complexes. The method works well with relatively small volumes of sample solutions and at low metal concentrations and may be useful in characterization of Cd and Zn in soil solutions. 12 refs., 6 figs., 3 tabs.« less

Performances and impedance spectroscopy of Small-molecule bulk heterojunction solar cells based on PtOEP: PCBM

NASA Astrophysics Data System (ADS)

Abuelwafa, A. A.; Dongol, M.; El-Nahass, M. M.; Soga, T.

2018-03-01

Small-molecule bulk heterojunction (SBHJ) solar cells based on platinum octaethylporphyrin (PtOEP) as donor material and phenyl-C61-butyric acid methyl ester (PCBM) as the acceptor were fabricated using spin coating techniques with weight ratios from 1:0.1 to 1:9. The formation of charge transfer complex CTC in the PtOEP: PCBM blend was specified from the redshift of the PtOEP absorption peak after blending with PCBM. The photovoltaic performance for PtOEP: PCBM blends were investigated using the external quantum efficiency (EQE) besides the current density-voltage (J-V) characteristics under illumination100 mW/cm2 (AM1.5G). The BHJ solar cell with PtOEP: PCBM ratio of 1:9 exhibited the best performance. The impedance spectroscopy (IS) was examined in the frequency range from 25 Hz to 1 MHz. The equivalent circuit model was evaluated in details to evaluate the impedance spectroscopy parameters. Dielectric constant {ɛ ^' }, dielectric loss {ɛ ^' ' }} and dielectric modulus were included and discussed in terms of dielectric polarization processes. Dielectric modulus displays the non-Debye relaxation in PtOEP: PCBM BHJ solar cells.

Hybrid video-assisted thoracic surgery with segmental-main bronchial sleeve resection for non-small cell lung cancer.

PubMed

Li, Shuben; Chai, Huiping; Huang, Jun; Zeng, Guangqiao; Shao, Wenlong; He, Jianxing

2014-04-01

The purpose of the current study is to present the clinical and surgical results in patients who underwent hybrid video-assisted thoracic surgery with segmental-main bronchial sleeve resection. Thirty-one patients, 27 men and 4 women, underwent segmental-main bronchial sleeve anastomoses for non-small cell lung cancer between May 2004 and May 2011. Twenty-six (83.9%) patients had squamous cell carcinoma, and 5 patients had adenocarcinoma. Six patients were at stage IIB, 24 patients at stage IIIA, and 1 patient at stage IIIB. Secondary sleeve anastomosis was performed in 18 patients, and Y-shaped multiple sleeve anastomosis was performed in 8 patients. Single segmental bronchiole anastomosis was performed in 5 cases. The average time for chest tube removal was 5.6 days. The average length of hospital stay was 11.8 days. No anastomosis fistula developed in any of the patients. The 1-, 2-, and 3-year survival rates were 83.9%, 71.0%, and 41.9%, respectively. Hybrid video-assisted thoracic surgery with segmental-main bronchial sleeve resection is a complex technique that requires training and experience, but it is an effective and safe operation for selected patients.

FPGA-Based Front-End Electronics for Positron Emission Tomography

PubMed Central

Haselman, Michael; DeWitt, Don; McDougald, Wendy; Lewellen, Thomas K.; Miyaoka, Robert; Hauck, Scott

2010-01-01

Modern Field Programmable Gate Arrays (FPGAs) are capable of performing complex discrete signal processing algorithms with clock rates above 100MHz. This combined with FPGA’s low expense, ease of use, and selected dedicated hardware make them an ideal technology for a data acquisition system for positron emission tomography (PET) scanners. Our laboratory is producing a high-resolution, small-animal PET scanner that utilizes FPGAs as the core of the front-end electronics. For this next generation scanner, functions that are typically performed in dedicated circuits, or offline, are being migrated to the FPGA. This will not only simplify the electronics, but the features of modern FPGAs can be utilizes to add significant signal processing power to produce higher resolution images. In this paper two such processes, sub-clock rate pulse timing and event localization, will be discussed in detail. We show that timing performed in the FPGA can achieve a resolution that is suitable for small-animal scanners, and will outperform the analog version given a low enough sampling period for the ADC. We will also show that the position of events in the scanner can be determined in real time using a statistical positioning based algorithm. PMID:21961085

Using recurrent neural networks for adaptive communication channel equalization.

PubMed

Kechriotis, G; Zervas, E; Manolakos, E S

1994-01-01

Nonlinear adaptive filters based on a variety of neural network models have been used successfully for system identification and noise-cancellation in a wide class of applications. An important problem in data communications is that of channel equalization, i.e., the removal of interferences introduced by linear or nonlinear message corrupting mechanisms, so that the originally transmitted symbols can be recovered correctly at the receiver. In this paper we introduce an adaptive recurrent neural network (RNN) based equalizer whose small size and high performance makes it suitable for high-speed channel equalization. We propose RNN based structures for both trained adaptation and blind equalization, and we evaluate their performance via extensive simulations for a variety of signal modulations and communication channel models. It is shown that the RNN equalizers have comparable performance with traditional linear filter based equalizers when the channel interferences are relatively mild, and that they outperform them by several orders of magnitude when either the channel's transfer function has spectral nulls or severe nonlinear distortion is present. In addition, the small-size RNN equalizers, being essentially generalized IIR filters, are shown to outperform multilayer perceptron equalizers of larger computational complexity in linear and nonlinear channel equalization cases.

An Exploratory Framework for Handling the Complexity of Mathematical Problem Posing in Small Groups

ERIC Educational Resources Information Center

Kontorovich, Igor; Koichu, Boris; Leikin, Roza; Berman, Avi

2012-01-01

The paper introduces an exploratory framework for handling the complexity of students' mathematical problem posing in small groups. The framework integrates four facets known from past research: task organization, students' knowledge base, problem-posing heuristics and schemes, and group dynamics and interactions. In addition, it contains a new…

Context Counts: Viewing Small School Leadership from the Inside out

ERIC Educational Resources Information Center

Clarke, Simon; Wildy, Helen

2004-01-01

This paper proceeds from the basis that leadership can only be understood in context and by viewing it from the inside. In particular, it argues that the contextual complexity of small school leadership warrants attention from researchers, policy makers and system administrators and describes the nature of this complexity as depicted in the…

FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects.

PubMed

Lagorce, David; Sperandio, Olivier; Galons, Hervé; Miteva, Maria A; Villoutreix, Bruno O

2008-09-24

Drug discovery and chemical biology are exceedingly complex and demanding enterprises. In recent years there are been increasing awareness about the importance of predicting/optimizing the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of small chemical compounds along the search process rather than at the final stages. Fast methods for evaluating ADMET properties of small molecules often involve applying a set of simple empirical rules (educated guesses) and as such, compound collections' property profiling can be performed in silico. Clearly, these rules cannot assess the full complexity of the human body but can provide valuable information and assist decision-making. This paper presents FAF-Drugs2, a free adaptable tool for ADMET filtering of electronic compound collections. FAF-Drugs2 is a command line utility program (e.g., written in Python) based on the open source chemistry toolkit OpenBabel, which performs various physicochemical calculations, identifies key functional groups, some toxic and unstable molecules/functional groups. In addition to filtered collections, FAF-Drugs2 can provide, via Gnuplot, several distribution diagrams of major physicochemical properties of the screened compound libraries. We have developed FAF-Drugs2 to facilitate compound collection preparation, prior to (or after) experimental screening or virtual screening computations. Users can select to apply various filtering thresholds and add rules as needed for a given project. As it stands, FAF-Drugs2 implements numerous filtering rules (23 physicochemical rules and 204 substructure searching rules) that can be easily tuned.

Cognitive Performance in Operational Environments

NASA Technical Reports Server (NTRS)

Russo, Michael; McGhee, James; Friedler, Edna; Thomas, Maria

2005-01-01

Optimal cognition during complex and sustained operations is a critical component for success in current and future military operations. "Cognitive Performance, Judgment, and Decision-making" (CPJD) is a newly organized U.S. Army Medical Research and Materiel Command research program focused on sustaining operational effectiveness of Future Force Warriors by developing paradigms through which militarily-relevant, higher-order cognitive performance, judgment, and decision-making can be assessed and sustained in individuals, small teams, and leaders of network-centric fighting units. CPJD evaluates the impact of stressors intrinsic to military operational environments (e.g., sleep deprivation, workload, fatigue, temperature extremes, altitude, environmental/physiological disruption) on military performance, evaluates noninvasive automated methods for monitoring and predicting cognitive performance, and investigates pharmaceutical strategies (e.g., stimulant countermeasures, hypnotics) to mitigate performance decrements. This manuscript describes the CPJD program, discusses the metrics utilized to relate militarily applied research findings to academic research, and discusses how the simulated combat capabilities of a synthetic battle laboratory may facilitate future cognitive performance research.

The operative management of children with complex perianal Crohn's disease.

PubMed

Seemann, Natashia M; King, Sebastian K; Elkadri, Abdul; Walters, Thomas; Fish, Joel; Langer, Jacob C

2016-12-01

Perianal Crohn's disease (PCD) can affect both quality of life and psychological wellbeing. A subset of pediatric patients with complex PCD require surgical intervention, although appropriate timing and treatment regimens remain unclear. This study aimed to describe a large pediatric cohort in a tertiary center to determine the range of surgical management in children with complex PCD. A retrospective review of children requiring operative intervention for PCD over 13 years (2002-2014) was performed. PCD was divided into simple and complex based on the type of surgical procedure, and the two groups were compared. The 57 children were divided into two groups: the simple group (N=43) underwent abscess drainage ± seton insertion alone, and the complex group (N=14) underwent loop ileostomy ± more extensive surgery. In the complex group, females were more predominant (57% of complex vs 30% of simple), and the average age at diagnosis was lower. Anti-TNF therapy was utilized in 79.1% of simple and 100% of complex PCD. All 14 complex patients underwent a defunctioning ileostomy, with 7 requiring further operations (subtotal colectomy=4, proctocolectomy ± anal sparing=5, plastic surgery reconstruction with perineal flap/graft=4). Complex PCD represents a small but challenging subset of patients in which major surgical intervention may be necessary to alleviate the symptoms of this debilitating condition. retrospective case study with no control group - level IV. Copyright © 2016 Elsevier Inc. All rights reserved.

Nanoscale supramolecular ordering in gel-surfactant complexes: Sodium alkyl sulfates in poly(diallyldimethylammonium chloride)

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

Sokolov, E.L.; Yeh, F.; Khokhlov, A.

1996-12-25

Studies of slightly cross-linked polycationic gels interacting with anionic surfactants have been performed by using random copolymers of poly(diallyldimethylammonium chloride) (PDADMACl) and polyacrylamide (PAAm) with varying content of PDADMACl and degree of cross-linking. Gel samples which had been fully swollen in water were placed in aqueous solutions of sodium alkyl sulfates (octyl(SOS), decyl-(SDCS), dodecyl (SDS), tetradecyl (STS), and hexyl (SHS) sulfates). The degree of the sample volume contraction depends on the PDADMACl content. The collapsed gel-surfactant complexes were studied using synchrotron small-angle X-ray scattering. All studied samples containing PDADMACl exhibited pronounced supramolecular nanostructures. The gel-SDCS complex exhibited a cubic structuremore » with a periodicity (7.75 nm) of approximately 4 times the surfactant molecular length, while the gel-SDS, gel-STS, and gel-SHS complexes showed hexagonal supramolecular ordering with a periodicity of approximately 2 times the surfactant molecular length. The d spacing of the longest periodicity in the complexes was dependent on the PDADMACl content and the surfactant. The d spacing generally increased with decreasing PDADMACl (charge) content and increasing number of carbon atoms in the surfactant alkyl chain. 20 refs., 11 figs., 5 tabs.« less

Copper(II) complex with 6-methylpyridine-2-carboxyclic acid: Experimental and computational study on the XRD, FT-IR and UV-Vis spectra, refractive index, band gap and NLO parameters

NASA Astrophysics Data System (ADS)

Altürk, Sümeyye; Avcı, Davut; Başoğlu, Adil; Tamer, Ömer; Atalay, Yusuf; Dege, Necmi

2018-02-01

Crystal structure of the synthesized copper(II) complex with 6-methylpyridine-2-carboxylic acid, [Cu(6-Mepic)2·H2O]·H2O, was determined by XRD, FT-IR and UV-Vis spectroscopic techniques. Furthermore, the geometry optimization, harmonic vibration frequencies for the Cu(II) complex were carried out by using Density Functional Theory calculations with HSEh1PBE/6-311G(d,p)/LanL2DZ level. Electronic absorption wavelengths were obtained by using TD-DFT/HSEh1PBE/6-311G(d,p)/LanL2DZ level with CPCM model and major contributions were determined via Swizard/Chemissian program. Additionally, the refractive index, linear optical (LO) and non-nonlinear optical (NLO) parameters of the Cu(II) complex were calculated at HSEh1PBE/6-311G(d,p) level. The experimental and computed small energy gap shows the charge transfer in the Cu(II) complex. Finally, the hyperconjugative interactions and intramolecular charge transfer (ICT) were studied by performing of natural bond orbital (NBO) analysis.

Copper(II) complex with 6-methylpyridine-2-carboxyclic acid: Experimental and computational study on the XRD, FT-IR and UV-Vis spectra, refractive index, band gap and NLO parameters.

PubMed

Altürk, Sümeyye; Avcı, Davut; Başoğlu, Adil; Tamer, Ömer; Atalay, Yusuf; Dege, Necmi

2018-02-05

Crystal structure of the synthesized copper(II) complex with 6-methylpyridine-2-carboxylic acid, [Cu(6-Mepic) 2 ·H 2 O]·H 2 O, was determined by XRD, FT-IR and UV-Vis spectroscopic techniques. Furthermore, the geometry optimization, harmonic vibration frequencies for the Cu(II) complex were carried out by using Density Functional Theory calculations with HSEh1PBE/6-311G(d,p)/LanL2DZ level. Electronic absorption wavelengths were obtained by using TD-DFT/HSEh1PBE/6-311G(d,p)/LanL2DZ level with CPCM model and major contributions were determined via Swizard/Chemissian program. Additionally, the refractive index, linear optical (LO) and non-nonlinear optical (NLO) parameters of the Cu(II) complex were calculated at HSEh1PBE/6-311G(d,p) level. The experimental and computed small energy gap shows the charge transfer in the Cu(II) complex. Finally, the hyperconjugative interactions and intramolecular charge transfer (ICT) were studied by performing of natural bond orbital (NBO) analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Spectral, thermal and kinetic studies of charge-transfer complexes formed between the highly effective antibiotic drug metronidazole and two types of acceptors: σ- and π-acceptors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Saad, Hosam A.; Adam, Abdel Majid A.

2015-04-01

Understanding the interaction between drugs and small inorganic or organic molecules is critical in being able to interpret the drug-receptor interactions and acting mechanism of these drugs. A combined solution and solid state study was performed to describe the complexation chemistry of drug metronidazole (MZ) which has a broad-spectrum antibacterial activity with two types of acceptors. The acceptors include, σ-acceptor (i.e., iodine) and π-acceptors (i.e., dichlorodicyanobenzoquinone (DDQ), chloranil (CHL) and picric acid (PA)). The molecular structure, spectroscopic characteristics, the binding modes as well as the thermal stability were deduced from IR, UV-vis, 1H NMR and thermal studies. The binding ratio of complexation (MZ: acceptor) was determined to be 1:2 for the iodine acceptor and 1:1 for the DDQ, CHL or PA acceptor, according to the CHN elemental analyses and spectrophotometric titrations. It has been found that the complexation with CHL and PA acceptors increases the values of enthalpy and entropy, while the complexation with DDQ and iodine acceptors decreases the values of these parameters compared with the free MZ donor.

Uncertainty of High Intensity Therapeutic Ultrasound (HITU) Field Characterization with Hydrophones: Effects of Nonlinearity, Spatial Averaging, and Complex Sensitivity

PubMed Central

Liu, Yunbo; Wear, Keith A.; Harris, Gerald R.

2017-01-01

Reliable acoustic characterization is fundamental for patient safety and clinical efficacy during high intensity therapeutic ultrasound (HITU) treatment. Technical challenges, such as measurement uncertainty and signal analysis still exist for HITU exposimetry using ultrasound hydrophones. In this work, four hydrophones were compared for pressure measurement: a robust needle hydrophone, a small PVDF capsule hydrophone and two different fiber-optic hydrophones. The focal waveform and beam distribution of a single element HITU transducer (1.05 MHz and 3.3 MHz) were evaluated. Complex deconvolution between the hydrophone voltage signal and frequency-dependent complex sensitivity was performed to obtain pressure waveform. Compressional pressure, rarefactional pressure, and focal beam distribution were compared up to 10.6/−6.0 MPa (p+ and p−) (1.05 MHz) and 20.65/−7.20 MPa (3.3 MHz). In particular, the effects of spatial averaging, local nonlinear distortion, complex deconvolution and hydrophone damage thresholds were investigated. This study showed an uncertainty of no better than 10–15% on hydrophone-based HITU pressure characterization. PMID:28735734

Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles

PubMed Central

Schneidman-Duhovny, Dina; Hammel, Michal

2018-01-01

Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure. Here, we describe protocols for modeling atomic structures based on SAXS profiles. The first protocol is for comparing solution and crystal structures including modeling of missing regions and determination of the oligomeric state. The second protocol performs multi-state modeling by finding a set of conformations and their weights that fit the SAXS profile starting from a single-input structure. The third protocol is for protein-protein docking based on the SAXS profile of the complex. We describe the underlying software, followed by demonstrating their application on interleukin 33 (IL33) with its primary receptor ST2 and DNA ligase IV-XRCC4 complex. PMID:29605933

Quantum Calculations of Electron Tunneling in Respiratory Complex III.

PubMed

Hagras, Muhammad A; Hayashi, Tomoyuki; Stuchebrukhov, Alexei A

2015-11-19

The most detailed and comprehensive to date study of electron transfer reactions in the respiratory complex III of aerobic cells, also known as bc1 complex, is reported. In the framework of the tunneling current theory, electron tunneling rates and atomistic tunneling pathways between different redox centers were investigated for all electron transfer reactions comprising different stages of the proton-motive Q-cycle. The calculations reveal that complex III is a smart nanomachine, which under certain conditions undergoes conformational changes gating electron transfer, or channeling electrons to specific pathways. One-electron tunneling approximation was adopted in the tunneling calculations, which were performed using hybrid Broken-Symmetry (BS) unrestricted DFT/ZINDO levels of theory. The tunneling orbitals were determined using an exact biorthogonalization scheme that uniquely separates pairs of tunneling orbitals with small overlaps out of the remaining Franck-Condon orbitals with significant overlap. Electron transfer rates in different redox pairs show exponential distance dependence, in agreement with the reported experimental data; some reactions involve coupled proton transfer. Proper treatment of a concerted two-electron bifurcated tunneling reaction at the Q(o) site is given.

An uracil-linked hydroxyflavone probe for the recognition of ATP

PubMed Central

Bojtár, Márton; Janzsó-Berend, Péter Zoltán; Mester, Dávid; Hessz, Dóra; Kállay, Mihály; Kubinyi, Miklós

2018-01-01

Background: Nucleotides are essential molecules in living systems due to their paramount importance in various physiological processes. In the past years, numerous attempts were made to selectively recognize and detect these analytes, especially ATP using small-molecule fluorescent chemosensors. Despite the various solutions, the selective detection of ATP is still challenging due to the structural similarity of various nucleotides. In this paper, we report the conjugation of a uracil nucleobase to the known 4’-dimethylamino-hydroxyflavone fluorophore. Results: The complexation of this scaffold with ATP is already known. The complex is held together by stacking and electrostatic interactions. To achieve multi-point recognition, we designed the uracil-appended version of this probe to include complementary base-pairing interactions. The theoretical calculations revealed the availability of multiple complex structures. The synthesis was performed using click chemistry and the nucleotide recognition properties of the probe were evaluated using fluorescence spectroscopy. Conclusions: The first, uracil-containing fluorescent ATP probe based on a hydroxyflavone fluorophore was synthesized and evaluated. A selective complexation with ATP was observed and a ratiometric response in the excitation spectrum. PMID:29719572

Variation of High-Intensity Therapeutic Ultrasound (HITU) Pressure Field Characterization: Effects of Hydrophone Choice, Nonlinearity, Spatial Averaging and Complex Deconvolution.

PubMed

Liu, Yunbo; Wear, Keith A; Harris, Gerald R

2017-10-01

Reliable acoustic characterization is fundamental for patient safety and clinical efficacy during high-intensity therapeutic ultrasound (HITU) treatment. Technical challenges, such as measurement variation and signal analysis, still exist for HITU exposimetry using ultrasound hydrophones. In this work, four hydrophones were compared for pressure measurement: a robust needle hydrophone, a small polyvinylidene fluoride capsule hydrophone and two fiberoptic hydrophones. The focal waveform and beam distribution of a single-element HITU transducer (1.05 MHz and 3.3 MHz) were evaluated. Complex deconvolution between the hydrophone voltage signal and frequency-dependent complex sensitivity was performed to obtain pressure waveforms. Compressional pressure (p + ), rarefactional pressure (p - ) and focal beam distribution were compared up to 10.6/-6.0 MPa (p + /p - ) (1.05 MHz) and 20.65/-7.20 MPa (3.3 MHz). The effects of spatial averaging, local non-linear distortion, complex deconvolution and hydrophone damage thresholds were investigated. This study showed a variation of no better than 10%-15% among hydrophones during HITU pressure characterization. Published by Elsevier Inc.

Cationic star-shaped polymer as an siRNA carrier for reducing MMP-9 expression in skin fibroblast cells and promoting wound healing in diabetic rats.

PubMed

Li, Na; Luo, Heng-Cong; Yang, Chuan; Deng, Jun-Jie; Ren, Meng; Xie, Xiao-Ying; Lin, Diao-Zhu; Yan, Li; Zhang, Li-Ming

2014-01-01

Excessive expression of matrix metalloproteinase-9 (MMP-9) is deleterious to the cutaneous wound-healing process in the context of diabetes. The aim of the present study was to explore whether a cationic star-shaped polymer consisting of β-cyclodextrin (β-CD) core and poly(amidoamine) dendron arms (β-CD-[D₃]₇) could be used as the gene carrier of small interfering RNA (siRNA) to reduce MMP-9 expression for enhanced diabetic wound healing. The cytotoxicity of β-CD-(D₃)₇ was investigated by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay (MMT) method in the rat CRL1213 skin fibroblast cell line. The transfection efficiency of β-CD-(D₃)₇/MMP-9-small interfering RNA (siRNA) complexes was determined by confocal microscopy and flow cytometry. Quantitative real time (RT) polymerase chain reaction was performed to measure the gene expression of MMP-9 after the transfection by β-CD-(D₃)₇/MMP-9-siRNA complexes. The β-CD-(D₃)₇/MMP-9-siRNA complexes were injected on the wounds of streptozocin-induced diabetic rats. Wound closure was measured on days 4 and 7 post-wounding. β-CD-(D₃)₇ exhibited low cytotoxicity in fibroblast cells, and easily formed the complexes with MMP-9-siRNA. The β-CD-(D₃)₇/MMP-9-siRNA complexes were readily taken up by fibroblast cells, resulting in the downregulation of MMP-9 gene expression (P<0.01). Animal experiments revealed that the treatment by β-CD-(D₃)₇/MMP-9-siRNA complexes enhanced wound closure in diabetic rats on day 7 post-wounding (P<0.05). β-CD-(D₃)₇ may be used as an efficient carrier for the delivery of MMP-9-siRNA to reduce MMP-9 expression in skin fibroblast cells and promote wound healing in diabetic rats.

Bidirectional selection between two classes in complex social networks.

PubMed

Zhou, Bin; He, Zhe; Jiang, Luo-Luo; Wang, Nian-Xin; Wang, Bing-Hong

2014-12-19

The bidirectional selection between two classes widely emerges in various social lives, such as commercial trading and mate choosing. Until now, the discussions on bidirectional selection in structured human society are quite limited. We demonstrated theoretically that the rate of successfully matching is affected greatly by individuals' neighborhoods in social networks, regardless of the type of networks. Furthermore, it is found that the high average degree of networks contributes to increasing rates of successful matches. The matching performance in different types of networks has been quantitatively investigated, revealing that the small-world networks reinforces the matching rate more than scale-free networks at given average degree. In addition, our analysis is consistent with the modeling result, which provides the theoretical understanding of underlying mechanisms of matching in complex networks.

[Occupational and non-occupational factors influencing health state of small and medium business workers].

PubMed

Fasikov, R M; Khuzhakhmetova, I B; Stepanov, E G

2010-01-01

Complex study of work conditions and health parameters of workers engaged into small and medium business proved that preserved and better health of these workers, prevention of occupational and occupationally mediated diseases necessitate federal and regional complex system of measures including legal basis, database on work conditions and their influence on small and medium business workers' health, occupational medicine training for employers and employees, more active involvement of medical institutioins into screening for occupational diseases.

Saccade and cognitive impairment associated with kava intoxication.

PubMed

Cairney, Sheree; Maruff, Paul; Clough, Alan R; Collie, Alex; Currie, Jon; Currie, Bart J

2003-10-01

Kava is an extract from the Piper methysticum Forst. f. plant that has social and spiritual importance in Pacific islands societies. Herbal remedies that contain kava are used for the psychiatric treatment of anxiety and insomnia. Laboratory studies have found only subtle, if any, changes on cognitive or motor functions from the acute effects of consuming small clinical doses of kava products. Intoxication from recreational doses of kava has not been studied. The performance of individuals intoxicated from drinking kava (n=11) was compared with a control group (n=17) using saccade and cognitive tests. On average, intoxicated individuals had consumed 205 g of kava powder each (approximately 150 times clinical doses) in a group session that went for 14.4 h and ended 8 h prior to testing. Intoxicated kava drinkers showed ataxia, tremors, sedation, blepharospasm and elevated liver enzymes (GGT and ALP), together with saccadic dysmetria, saccadic slowing and reduced accuracy performing a visual search task that only became evident as the task complexity increased. Kava intoxication is characterized by specific abnormalities of movement coordination and visual attention but normal performance of complex cognitive functions. Saccade abnormalities suggest disruption of cerebellar and GABAergic functions. Copyright 2003 John Wiley & Sons, Ltd.

Structural interaction fingerprints: a new approach to organizing, mining, analyzing, and designing protein-small molecule complexes.

PubMed

Singh, Juswinder; Deng, Zhan; Narale, Gaurav; Chuaqui, Claudio

2006-01-01

The combination of advances in structure-based drug design efforts in the pharmaceutical industry in parallel with structural genomics initiatives in the public domain has led to an explosion in the number of structures of protein-small molecule complexes structures. This information has critical importance to both the understanding of the structural basis for molecular recognition in biological systems and the design of better drugs. A significant challenge exists in managing this vast amount of data and fully leveraging it. Here, we review our work to develop a simple, fast way to store, organize, mine, and analyze large numbers of protein-small molecule complexes. We illustrate the utility of the approach to the management of inhibitor complexes from the protein kinase family. Finally, we describe our recent efforts in applying this method to the design of target-focused chemical libraries.

Optimized small molecule antibody labeling efficiency through continuous flow centrifugal diafiltration.

PubMed

Cappione, Amedeo; Mabuchi, Masaharu; Briggs, David; Nadler, Timothy

2015-04-01

Protein immuno-detection encompasses a broad range of analytical methodologies, including western blotting, flow cytometry, and microscope-based applications. These assays which detect, quantify, and/or localize expression for one or more proteins in complex biological samples, are reliant upon fluorescent or enzyme-tagged target-specific antibodies. While small molecule labeling kits are available with a range of detection moieties, the workflow is hampered by a requirement for multiple dialysis-based buffer exchange steps that are both time-consuming and subject to sample loss. In a previous study, we briefly described an alternative method for small-scale protein labeling with small molecule dyes whereby all phases of the conjugation workflow could be performed in a single centrifugal diafiltration device. Here, we expand on this foundational work addressing functionality of the device at each step in the workflow (sample cleanup, labeling, unbound dye removal, and buffer exchange/concentration) and the implications for optimizing labeling efficiency. When compared to other common buffer exchange methodologies, centrifugal diafiltration offered superior performance as measured by four key parameters (process time, desalting capacity, protein recovery, retain functional integrity). Originally designed for resin-based affinity purification, the device also provides a platform for up-front antibody purification or albumin carrier removal. Most significantly, by exploiting the rapid kinetics of NHS-based labeling reactions, the process of continuous diafiltration minimizes reaction time and long exposure to excess dye, guaranteeing maximal target labeling while limiting the risks associated with over-labeling. Overall, the device offers a simplified workflow with reduced processing time and hands-on requirements, without sacrificing labeling efficiency, final yield, or conjugate performance. Copyright © 2015 Elsevier B.V. All rights reserved.

Practical comparison of LC columns packed with different superficially porous particles for the separation of small molecules and medium size natural products.

PubMed

Yang, Peilin; McCabe, Terry; Pursch, Matthias

2011-11-01

Commercial C(18) columns packed with superficially porous particles of different sizes and shell thicknesses (Ascentis Express, Kinetex, and Poroshell 120) or sub-2-μm totally porous particles (Acquity BEH) were systematically compared using a small molecule mixture and a complex natural product mixture as text probes. Significant efficiency loss was observed on 2.1-mm id columns even with a low dispersion ultra-high pressure liquid chromatography system. The Kinetex 4.6-mm id column packed with 2.6-μm particles exhibited the best overall efficiency for small molecule separations and the Poroshell 120 column showed better performance for mid-size natural product analytes. The Kinetex 2.1-mm id column packed with 1.7-μm particles did not deliver the expected performance and the possible reasons besides extra column effect have been proved to be frictional heating effect and poor column packing quality. Different column retentivities and selectivities have been observed on the four C(18) columns of different brands for the natural product separation. Column batch-to-batch variability that has been previously observed on the Ascentis Express column was also observed on the Kinetex and Poroshell 120 column. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Compact Microwave Microfluidic Sensor Using a Re-Entrant Cavity.

PubMed

Hamzah, Hayder; Abduljabar, Ali; Lees, Jonathan; Porch, Adrian

2018-03-19

A miniaturized 2.4 GHz re-entrant cavity has been designed, manufactured and tested as a sensor for microfluidic compositional analysis. It has been fully evaluated experimentally with water and common solvents, namely methanol, ethanol, and chloroform, with excellent agreement with the expected behaviour predicted by the Debye model. The sensor's performance has also been assessed for analysis of segmented flow using water and oil. The samples' interaction with the electric field in the gap region has been maximized by aligning the sample tube parallel to the electric field in this region, and the small width of the gap (typically 1 mm) result in a highly localised complex permittivity measurement. The re-entrant cavity has simple mechanical geometry, small size, high quality factor, and due to the high concentration of electric field in the gap region, a very small mode volume. These factors combine to result in a highly sensitive, compact sensor for both pure liquids and liquid mixtures in capillary or microfluidic environments.

Simultaneous identification of the low-field-induced tiny variation of complex refractive index for anisotropic and opaque magnetic-fluid thin film by a stable heterodyne Mach-Zehnder interferometer.

PubMed

Hong, Chin-Yih; Chieh, Jen-Jie; Yang, Shieh-Yueh; Yang, Hong-Chang; Horng, Herng-Er

2009-10-10

We use a heterodyne Mach-Zehnder interferometer to simultaneously and simply measure the complex refractive index by only normal incidence on the specimen, instead of using a complicated measurement procedure or instrument that only measures the real or imaginary part of the complex refractive index. To study the tiny variation of the complex refractive index, the small complex refractive-index variation of a rare-concentration magnetic-fluid thin film, due to a weak field of less than 200 Oe, was processed by this interferometer. We also present the wavelength trend of the complex refractive index of magnetic fluids to verify the appearance of the slight change in a small wavelength range.

Are our dynamic water quality models too complex? A comparison of a new parsimonious phosphorus model, SimplyP, and INCA-P

NASA Astrophysics Data System (ADS)

Jackson-Blake, L. A.; Sample, J. E.; Wade, A. J.; Helliwell, R. C.; Skeffington, R. A.

2017-07-01

Catchment-scale water quality models are increasingly popular tools for exploring the potential effects of land management, land use change and climate change on water quality. However, the dynamic, catchment-scale nutrient models in common usage are complex, with many uncertain parameters requiring calibration, limiting their usability and robustness. A key question is whether this complexity is justified. To explore this, we developed a parsimonious phosphorus model, SimplyP, incorporating a rainfall-runoff model and a biogeochemical model able to simulate daily streamflow, suspended sediment, and particulate and dissolved phosphorus dynamics. The model's complexity was compared to one popular nutrient model, INCA-P, and the performance of the two models was compared in a small rural catchment in northeast Scotland. For three land use classes, less than six SimplyP parameters must be determined through calibration, the rest may be based on measurements, while INCA-P has around 40 unmeasurable parameters. Despite substantially simpler process-representation, SimplyP performed comparably to INCA-P in both calibration and validation and produced similar long-term projections in response to changes in land management. Results support the hypothesis that INCA-P is overly complex for the study catchment. We hope our findings will help prompt wider model comparison exercises, as well as debate among the water quality modeling community as to whether today's models are fit for purpose. Simpler models such as SimplyP have the potential to be useful management and research tools, building blocks for future model development (prototype code is freely available), or benchmarks against which more complex models could be evaluated.

Small- and Large-Effect Quantitative Trait Locus Interactions Underlie Variation in Yeast Sporulation Efficiency

PubMed Central

Lorenz, Kim; Cohen, Barak A.

2012-01-01

Quantitative trait loci (QTL) with small effects on phenotypic variation can be difficult to detect and analyze. Because of this a large fraction of the genetic architecture of many complex traits is not well understood. Here we use sporulation efficiency in Saccharomyces cerevisiae as a model complex trait to identify and study small-effect QTL. In crosses where the large-effect quantitative trait nucleotides (QTN) have been genetically fixed we identify small-effect QTL that explain approximately half of the remaining variation not explained by the major effects. We find that small-effect QTL are often physically linked to large-effect QTL and that there are extensive genetic interactions between small- and large-effect QTL. A more complete understanding of quantitative traits will require a better understanding of the numbers, effect sizes, and genetic interactions of small-effect QTL. PMID:22942125

An agile frequency synthesizer/RF generator for the SCAMP terminal

NASA Astrophysics Data System (ADS)

Wolfson, Harry M.

1992-09-01

This report describes a combination agile synthesizer and reference frequency generator called the RF Generator, which was developed for use in the Advanced SCAMP (ASCAMP) program. The ASCAMP is a hand-carried, battery-powered, man-portable ground terminal that is being developed for EHF satellite communications. In order to successfully achieve a truly portable terminal, all of the subsystems and components in ASCAMP were designed with the following critical goals: low power, lightweight, and small size. The RF Generator is based on a hybrid design approach of direct digital and direct analog synthesis techniques that was optimized for small size, low power consumption, fast tuning, low spurious, and low phase noise. The RF Generator was conceived with the philosophy that simplicity of design would lead to a synthesizer that differentiates itself from those used in the past by its ease of fabrication and tuning. By avoiding more complex design approaches, namely, indirect analog (phase lock loops), a more easily produceable design could be achieved. An effort was made to minimize the amount of circuitry in the RF Generator, thereby making trade-offs in performance versus complexity and parts count when it was appropriate.

Direct mass spectrometric peptide profiling and sequencing of nervous tissues to identify peptides involved in male copulatory behavior in Lymnaea stagnalis

NASA Astrophysics Data System (ADS)

Dreisewerd, Klaus; Kingston, Robert; Geraerts, Wijnand P. M.; Li, Ka Wan

1997-12-01

Matrix-assisted laser desorption mass spectrometry (MALDI-MS) was performed directly on a small piece of single penis nerve of the pond snail, Lymnaea stagnalis, and reveals the presence of complex peptide profiles, including many hitherto undescribed peptides. Two of the peptides have molecular weights corresponding exactly to the previously described Lymnaea small cardioactive peptides (SCP) A and B. We confirmed their identities by structural characterization of the two peptides directly from a single penis nerve by matrix-assisted laser desorption ionization high-energy collision tandem MS analysis. MALDI-MS of nervous tissues also demonstrates that a cluster of central neurons, which send their axons to the penis nerve, contain the two peptides. As the penis nerve is the nerve that innervates the penis complex, we propose that the peptides are involved in the modulation of male copulatory processes. A bioassay indeed showed that the peptides increase the contraction frequency of the vas deference in a dose-dependent manner. The results demonstrate the potential of direct MALDI-MS analysis of nervous tissue to complement or substitute conventional biochemical techniques for the identification and localization of neuropeptides.

High Fidelity Modeling of Turbulent Mixing and Chemical Kinetics Interactions in a Post-Detonation Flow Field

NASA Astrophysics Data System (ADS)

Sinha, Neeraj; Zambon, Andrea; Ott, James; Demagistris, Michael

2015-06-01

Driven by the continuing rapid advances in high-performance computing, multi-dimensional high-fidelity modeling is an increasingly reliable predictive tool capable of providing valuable physical insight into complex post-detonation reacting flow fields. Utilizing a series of test cases featuring blast waves interacting with combustible dispersed clouds in a small-scale test setup under well-controlled conditions, the predictive capabilities of a state-of-the-art code are demonstrated and validated. Leveraging physics-based, first principle models and solving large system of equations on highly-resolved grids, the combined effects of finite-rate/multi-phase chemical processes (including thermal ignition), turbulent mixing and shock interactions are captured across the spectrum of relevant time-scales and length scales. Since many scales of motion are generated in a post-detonation environment, even if the initial ambient conditions are quiescent, turbulent mixing plays a major role in the fireball afterburning as well as in dispersion, mixing, ignition and burn-out of combustible clouds in its vicinity. Validating these capabilities at the small scale is critical to establish a reliable predictive tool applicable to more complex and large-scale geometries of practical interest.

Modulation of cardiac contractility by the phospholamban/SERCA2a regulatome.

PubMed

Kranias, Evangelia G; Hajjar, Roger J

2012-06-08

Heart disease remains the leading cause of death and disability in the Western world. Current therapies aim at treating the symptoms rather than the subcellular mechanisms, underlying the etiology and pathological remodeling in heart failure. A universal characteristic, contributing to the decreased contractile performance in human and experimental failing hearts, is impaired calcium sequestration into the sarcoplasmic reticulum (SR). SR calcium uptake is mediated by a Ca(2+)-ATPase (SERCA2), whose activity is reversibly regulated by phospholamban (PLN). Dephosphorylated PLN is an inhibitor of SERCA and phosphorylation of PLN relieves this inhibition. However, the initial simple view of a PLN/SERCA regulatory complex has been modified by our recent identification of SUMO, S100 and the histidine-rich Ca-binding protein as regulators of SERCA activity. In addition, PLN activity is regulated by 2 phosphoproteins, the inhibitor-1 of protein phosphatase 1 and the small heat shock protein 20, which affect the overall SERCA-mediated Ca-transport. This review will highlight the regulatory mechanisms of cardiac contractility by the multimeric SERCA/PLN-ensemble and the potential for new therapeutic avenues targeting this complex by using small molecules and gene transfer methods.

Toward cost-efficient sampling methods

NASA Astrophysics Data System (ADS)

Luo, Peng; Li, Yongli; Wu, Chong; Zhang, Guijie

2015-09-01

The sampling method has been paid much attention in the field of complex network in general and statistical physics in particular. This paper proposes two new sampling methods based on the idea that a small part of vertices with high node degree could possess the most structure information of a complex network. The two proposed sampling methods are efficient in sampling high degree nodes so that they would be useful even if the sampling rate is low, which means cost-efficient. The first new sampling method is developed on the basis of the widely used stratified random sampling (SRS) method and the second one improves the famous snowball sampling (SBS) method. In order to demonstrate the validity and accuracy of two new sampling methods, we compare them with the existing sampling methods in three commonly used simulation networks that are scale-free network, random network, small-world network, and also in two real networks. The experimental results illustrate that the two proposed sampling methods perform much better than the existing sampling methods in terms of achieving the true network structure characteristics reflected by clustering coefficient, Bonacich centrality and average path length, especially when the sampling rate is low.

Fabrication methods for mesoscopic flying vehicle

NASA Astrophysics Data System (ADS)

Cheng, Yih-Lin

2001-10-01

Small-scale flying vehicles are attractive tools for atmospheric science research. A centimeter-size mesoscopic electric helicopter, the mesicopter, has been developed at Stanford University for these applications. The mesoscopic scale implies a design with critical features between tens of microns and several millimeters. Three major parts in the mesicopter are challenging to manufacture. Rotors require smooth 3D surfaces and a blade thickness of less than 100 mum. Components in the DC micro-motor must be made of engineering materials, which is difficult on the mesoscopic scale. Airframe fabrication has to integrate complex 3D geometry into one single structure at this scale. In this research, material selection and manufacturing approaches have been investigated and implemented. In rotor fabrication, high-strength polymers manufactured by the Shape Deposition Manufacturing (SDM) technique were the top choice. Aluminum alloys were only considered as the second choice because the fabrication process is more involved. Lift tests showed that the 4-blade polymer and aluminum rotors could deliver about 90% of the expected lift (4g). To explain the rotor performance, structural analyses of spinning rotors were performed and the fabricated geometry was investigated. The bending deflections and the torsional twists were found to be too small to degrade aerodynamic performance. The rotor geometry was verified by laser scanning and by cross-section observations. Commercially available motors are used in the prototypes but a smaller DC micro-motor was designed for future use. Components of the DC micro-motors were fabricated by the Mesoscopic Additive/Subtractive Material Processing technique, which is capable of shaping engineering materials on the mesoscopic scale. The approaches are described in this thesis. The airframe was manufactured using the SDM process, which is capable of building complex parts without assembly. Castable polymers were chosen and mixed with glass microspheres to reduce their density. The finished airframe (65.5 mm x 65.5 mm) weighed only 1.5g. Two mesicopter prototypes, weighing 3g and 17g, have illustrated that powered flight at this scale is feasible. This research provides solutions to manufacture the challenging parts for the mesicopter. The manufacturing approaches discussed here are applicable to other small flying vehicles in similar and even smaller size regimes.

High resolution modeling of a small urban catchment

NASA Astrophysics Data System (ADS)

Skouri-Plakali, Ilektra; Ichiba, Abdellah; Gires, Auguste; Tchiguirinskaia, Ioulia; Schertzer, Daniel

2016-04-01

Flooding is one of the most complex issues that urban environments have to deal with. In France, flooding remains the first natural risk with 72% of decrees state of natural disaster issued between October 1982 and mid-November 2014. Flooding is a result of meteorological extremes that are usually aggravated by the hydrological behavior of urban catchments and human factors. The continuing urbanization process is indeed changing the whole urban water cycle by limiting the infiltration and promoting runoff. Urban environments are very complex systems due to their extreme variability, the interference between human activities and natural processes but also the effect of the ongoing urbanization process that changes the landscape and hardly influences their hydrologic behavior. Moreover, many recent works highlight the need to simulate all urban water processes at their specific temporal and spatial scales. However, considering urban catchments heterogeneity still challenging for urban hydrology, even after advances noticed in term of high-resolution data collection and computational resources. This issue is more to be related to the architecture of urban models being used and how far these models are ready to take into account the extreme variability of urban catchments. In this work, high spatio-temporal resolution modeling is performed for a small and well-equipped urban catchment. The aim of this work is to identify urban modeling needs in terms of spatial and temporal resolution especially for a very small urban area (3.7 ha urban catchment located in the Perreux-sur-Marne city at the southeast of Paris) MultiHydro model was selected to carry out this work, it is a physical based and fully distributed model that interacts four existing modules each of them representing a portion of the water cycle in urban environments. MultiHydro was implemented at 10m, 5m and 2m resolution. Simulations were performed at different spatio-temporal resolutions and analyzed with respect to real flow measurements. First Results coming out show improvements obtained in terms of the model performance at high spatio-temporal resolution.

Trade-offs between robustness and small-world effect in complex networks

PubMed Central

Peng, Guan-Sheng; Tan, Suo-Yi; Wu, Jun; Holme, Petter

2016-01-01

Robustness and small-world effect are two crucial structural features of complex networks and have attracted increasing attention. However, little is known about the relation between them. Here we demonstrate that, there is a conflicting relation between robustness and small-world effect for a given degree sequence. We suggest that the robustness-oriented optimization will weaken the small-world effect and vice versa. Then, we propose a multi-objective trade-off optimization model and develop a heuristic algorithm to obtain the optimal trade-off topology for robustness and small-world effect. We show that the optimal network topology exhibits a pronounced core-periphery structure and investigate the structural properties of the optimized networks in detail. PMID:27853301

On the large eddy simulation of turbulent flows in complex geometry

NASA Technical Reports Server (NTRS)

Ghosal, Sandip

1993-01-01

Application of the method of Large Eddy Simulation (LES) to a turbulent flow consists of three separate steps. First, a filtering operation is performed on the Navier-Stokes equations to remove the small spatial scales. The resulting equations that describe the space time evolution of the 'large eddies' contain the subgrid-scale (sgs) stress tensor that describes the effect of the unresolved small scales on the resolved scales. The second step is the replacement of the sgs stress tensor by some expression involving the large scales - this is the problem of 'subgrid-scale modeling'. The final step is the numerical simulation of the resulting 'closed' equations for the large scale fields on a grid small enough to resolve the smallest of the large eddies, but still much larger than the fine scale structures at the Kolmogorov length. In dividing a turbulent flow field into 'large' and 'small' eddies, one presumes that a cut-off length delta can be sensibly chosen such that all fluctuations on a scale larger than delta are 'large eddies' and the remainder constitute the 'small scale' fluctuations. Typically, delta would be a length scale characterizing the smallest structures of interest in the flow. In an inhomogeneous flow, the 'sensible choice' for delta may vary significantly over the flow domain. For example, in a wall bounded turbulent flow, most statistical averages of interest vary much more rapidly with position near the wall than far away from it. Further, there are dynamically important organized structures near the wall on a scale much smaller than the boundary layer thickness. Therefore, the minimum size of eddies that need to be resolved is smaller near the wall. In general, for the LES of inhomogeneous flows, the width of the filtering kernel delta must be considered to be a function of position. If a filtering operation with a nonuniform filter width is performed on the Navier-Stokes equations, one does not in general get the standard large eddy equations. The complication is caused by the fact that a filtering operation with a nonuniform filter width in general does not commute with the operation of differentiation. This is one of the issues that we have looked at in detail as it is basic to any attempt at applying LES to complex geometry flows. Our principal findings are summarized.

Design and Evaluation of 10-Gbps Inter-satellite Optical Wireless Communication Link for Improved Performance

NASA Astrophysics Data System (ADS)

Gupta, Amit; Nagpal, Shaina

2017-05-01

Inter-satellite optical wireless communication (IsOWC) systems can be chosen over existing microwave satellite systems for deploying in space in the future due to their high bandwidth, small size, light weight, low power and low cost. However, the IsOWC system suffers from various attenuations due to weather conditions, turbulence or scintillations which limit its performance and decreases its availability. So, in order to improve the performance, IsOWC system using directly modulated laser source is proposed in this work. The system is designed and evaluated to be suitable for high data rate transmissions up to 10 Gbps. The performance of the system is investigated in order to reduce the cost and complexity of link and improving the quality of information signal. Further the proposed IsOWC system is analysed using BER analyser, power meter and oscilloscope Visualizer.

Small-Group Problem-Based Learning as a Complex Adaptive System

ERIC Educational Resources Information Center

Mennin, Stewart

2007-01-01

Small-group problem-based learning (PBL) is widely embraced as a method of study in health professions schools and at many different levels of education. Complexity science provides a different lens with which to view and understand the application of this method. It presents new concepts and vocabulary that may be unfamiliar to practitioners of…

The architecture of dynamic reservoir in the echo state network

NASA Astrophysics Data System (ADS)

Cui, Hongyan; Liu, Xiang; Li, Lixiang

2012-09-01

Echo state network (ESN) has recently attracted increasing interests because of its superior capability in modeling nonlinear dynamic systems. In the conventional echo state network model, its dynamic reservoir (DR) has a random and sparse topology, which is far from the real biological neural networks from both structural and functional perspectives. We hereby propose three novel types of echo state networks with new dynamic reservoir topologies based on complex network theory, i.e., with a small-world topology, a scale-free topology, and a mixture of small-world and scale-free topologies, respectively. We then analyze the relationship between the dynamic reservoir structure and its prediction capability. We utilize two commonly used time series to evaluate the prediction performance of the three proposed echo state networks and compare them to the conventional model. We also use independent and identically distributed time series to analyze the short-term memory and prediction precision of these echo state networks. Furthermore, we study the ratio of scale-free topology and the small-world topology in the mixed-topology network, and examine its influence on the performance of the echo state networks. Our simulation results show that the proposed echo state network models have better prediction capabilities, a wider spectral radius, but retain almost the same short-term memory capacity as compared to the conventional echo state network model. We also find that the smaller the ratio of the scale-free topology over the small-world topology, the better the memory capacities.

On the structure and spin states of Fe(III)-EDDHA complexes.

PubMed

Gómez-Gallego, Mar; Fernández, Israel; Pellico, Daniel; Gutiérrez, Angel; Sierra, Miguel A; Lucena, Juan J

2006-07-10

DFT methods are suitable for predicting both the geometries and spin states of EDDHA-Fe(III) complexes. Thus, extensive DFT computational studies have shown that the racemic-Fe(III) EDDHA complex is more stable than the meso isomer, regardless of the spin state of the central iron atom. A comparison of the energy values obtained for the complexes under study has also shown that high-spin (S = 5/2) complexes are more stable than low-spin (S = 1/2) ones. These computational results matched the experimental results of the magnetic susceptibility values of both isomers. In both cases, their behavior has been fitted as being due to isolated high-spin Fe(III) in a distorted octahedral environment. The study of the correlation diagram also confirms the high-spin iron in complex 2b. The geometry optimization of these complexes performed with the standard 3-21G* basis set for hydrogen, carbon, oxygen, and nitrogen and the Hay-Wadt small-core effective core potential (ECP) including a double-xi valence basis set for iron, followed by single-point energy refinement with the 6-31G* basis set, is suitable for predicting both the geometries and the spin-states of EDDHA-Fe(III) complexes. The presence of a high-spin iron in Fe(III)-EDDHA complexes could be the key to understanding their lack of reactivity in electron-transfer processes, either chemically or electrochemically induced, and their resistance to photodegradation.

SQL is Dead; Long-live SQL: Relational Database Technology in Science Contexts

NASA Astrophysics Data System (ADS)

Howe, B.; Halperin, D.

2014-12-01

Relational databases are often perceived as a poor fit in science contexts: Rigid schemas, poor support for complex analytics, unpredictable performance, significant maintenance and tuning requirements --- these idiosyncrasies often make databases unattractive in science contexts characterized by heterogeneous data sources, complex analysis tasks, rapidly changing requirements, and limited IT budgets. In this talk, I'll argue that although the value proposition of typical relational database systems are weak in science, the core ideas that power relational databases have become incredibly prolific in open source science software, and are emerging as a universal abstraction for both big data and small data. In addition, I'll talk about two open source systems we are building to "jailbreak" the core technology of relational databases and adapt them for use in science. The first is SQLShare, a Database-as-a-Service system supporting collaborative data analysis and exchange by reducing database use to an Upload-Query-Share workflow with no installation, schema design, or configuration required. The second is Myria, a service that supports much larger scale data, complex analytics, and supports multiple back end systems. Finally, I'll describe some of the ways our collaborators in oceanography, astronomy, biology, fisheries science, and more are using these systems to replace script-based workflows for reasons of performance, flexibility, and convenience.

An Experimental Study of Team Size and Performance on a Complex Task.

PubMed

Mao, Andrew; Mason, Winter; Suri, Siddharth; Watts, Duncan J

2016-01-01

The relationship between team size and productivity is a question of broad relevance across economics, psychology, and management science. For complex tasks, however, where both the potential benefits and costs of coordinated work increase with the number of workers, neither theoretical arguments nor empirical evidence consistently favor larger vs. smaller teams. Experimental findings, meanwhile, have relied on small groups and highly stylized tasks, hence are hard to generalize to realistic settings. Here we narrow the gap between real-world task complexity and experimental control, reporting results from an online experiment in which 47 teams of size ranging from n = 1 to 32 collaborated on a realistic crisis mapping task. We find that individuals in teams exerted lower overall effort than independent workers, in part by allocating their effort to less demanding (and less productive) sub-tasks; however, we also find that individuals in teams collaborated more with increasing team size. Directly comparing these competing effects, we find that the largest teams outperformed an equivalent number of independent workers, suggesting that gains to collaboration dominated losses to effort. Importantly, these teams also performed comparably to a field deployment of crisis mappers, suggesting that experiments of the type described here can help solve practical problems as well as advancing the science of collective intelligence.

An Experimental Study of Team Size and Performance on a Complex Task

PubMed Central

Mao, Andrew; Mason, Winter; Suri, Siddharth; Watts, Duncan J.

2016-01-01

The relationship between team size and productivity is a question of broad relevance across economics, psychology, and management science. For complex tasks, however, where both the potential benefits and costs of coordinated work increase with the number of workers, neither theoretical arguments nor empirical evidence consistently favor larger vs. smaller teams. Experimental findings, meanwhile, have relied on small groups and highly stylized tasks, hence are hard to generalize to realistic settings. Here we narrow the gap between real-world task complexity and experimental control, reporting results from an online experiment in which 47 teams of size ranging from n = 1 to 32 collaborated on a realistic crisis mapping task. We find that individuals in teams exerted lower overall effort than independent workers, in part by allocating their effort to less demanding (and less productive) sub-tasks; however, we also find that individuals in teams collaborated more with increasing team size. Directly comparing these competing effects, we find that the largest teams outperformed an equivalent number of independent workers, suggesting that gains to collaboration dominated losses to effort. Importantly, these teams also performed comparably to a field deployment of crisis mappers, suggesting that experiments of the type described here can help solve practical problems as well as advancing the science of collective intelligence. PMID:27082239

SPR imaging based electronic tongue via landscape images for complex mixture analysis.

PubMed

Genua, Maria; Garçon, Laurie-Amandine; Mounier, Violette; Wehry, Hillary; Buhot, Arnaud; Billon, Martial; Calemczuk, Roberto; Bonnaffé, David; Hou, Yanxia; Livache, Thierry

2014-12-01

Electronic noses/tongues (eN/eT) have emerged as promising alternatives for analysis of complex mixtures in the domain of food and beverage quality control. We have recently developed an electronic tongue by combining surface plasmon resonance imaging (SPRi) with an array of non-specific and cross-reactive receptors prepared by simply mixing two small molecules in varying and controlled proportions and allowing the mixtures to self-assemble on the SPRi prism surface. The obtained eT generated novel and unique 2D continuous evolution profiles (CEPs) and 3D continuous evolution landscapes (CELs) based on which the differentiation of complex mixtures such as red wine, beer and milk were successful. The preliminary experiments performed for monitoring the deterioration of UHT milk demonstrated its potential for quality control applications. Furthermore, the eT exhibited good repeatability and stability, capable of operating after a minimum storage period of 5 months. Copyright © 2014 Elsevier B.V. All rights reserved.

A cut-cell immersed boundary technique for fire dynamics simulation

NASA Astrophysics Data System (ADS)

Vanella, Marcos; McDermott, Randall; Forney, Glenn

2015-11-01

Fire simulation around complex geometry is gaining increasing attention in performance based design of fire protection systems, fire-structure interaction and pollutant transport in complex terrains, among others. This presentation will focus on our present effort in improving the capability of FDS (Fire Dynamics Simulator, developed at the Fire Research Division, NIST. https://github.com/firemodels/fds-smv) to represent fire scenarios around complex bodies. Velocities in the vicinity of the bodies are reconstructed using a classical immersed boundary scheme (Fadlun and co-workers, J. Comput. Phys., 161:35-60, 2000). Also, a conservative treatment of scalar transport equations (i.e. for chemical species) will be presented. In our method, discrete conservation and no penetration of species across solid boundaries are enforced using a cut-cell finite volume scheme. The small cell problem inherent to the method is tackled using explicit-implicit domain decomposition for scalar, within the FDS time integration scheme. Some details on the derivation, implementation and numerical tests of this numerical scheme will be discussed.

Large-Area High-Performance Flexible Pressure Sensor with Carbon Nanotube Active Matrix for Electronic Skin.

PubMed

Nela, Luca; Tang, Jianshi; Cao, Qing; Tulevski, George; Han, Shu-Jen

2018-03-14

Artificial "electronic skin" is of great interest for mimicking the functionality of human skin, such as tactile pressure sensing. Several important performance metrics include mechanical flexibility, operation voltage, sensitivity, and accuracy, as well as response speed. In this Letter, we demonstrate a large-area high-performance flexible pressure sensor built on an active matrix of 16 × 16 carbon nanotube thin-film transistors (CNT TFTs). Made from highly purified solution tubes, the active matrix exhibits superior flexible TFT performance with high mobility and large current density, along with a high device yield of nearly 99% over 4 inch sample area. The fully integrated flexible pressure sensor operates within a small voltage range of 3 V and shows superb performance featuring high spatial resolution of 4 mm, faster response than human skin (<30 ms), and excellent accuracy in sensing complex objects on both flat and curved surfaces. This work may pave the road for future integration of high-performance electronic skin in smart robotics and prosthetic solutions.

Graph theoretical analysis of complex networks in the brain

PubMed Central

Stam, Cornelis J; Reijneveld, Jaap C

2007-01-01

Since the discovery of small-world and scale-free networks the study of complex systems from a network perspective has taken an enormous flight. In recent years many important properties of complex networks have been delineated. In particular, significant progress has been made in understanding the relationship between the structural properties of networks and the nature of dynamics taking place on these networks. For instance, the 'synchronizability' of complex networks of coupled oscillators can be determined by graph spectral analysis. These developments in the theory of complex networks have inspired new applications in the field of neuroscience. Graph analysis has been used in the study of models of neural networks, anatomical connectivity, and functional connectivity based upon fMRI, EEG and MEG. These studies suggest that the human brain can be modelled as a complex network, and may have a small-world structure both at the level of anatomical as well as functional connectivity. This small-world structure is hypothesized to reflect an optimal situation associated with rapid synchronization and information transfer, minimal wiring costs, as well as a balance between local processing and global integration. The topological structure of functional networks is probably restrained by genetic and anatomical factors, but can be modified during tasks. There is also increasing evidence that various types of brain disease such as Alzheimer's disease, schizophrenia, brain tumours and epilepsy may be associated with deviations of the functional network topology from the optimal small-world pattern. PMID:17908336

Dephosphorylation of survival motor neurons (SMN) by PPM1G/PP2Cγ governs Cajal body localization and stability of the SMN complex

PubMed Central

Petri, Sebastian; Grimmler, Matthias; Over, Sabine; Fischer, Utz; Gruss, Oliver J.

2007-01-01

The survival motor neuron (SMN) complex functions in maturation of uridine-rich small nuclear ribonucleoprotein (RNP) particles. SMN mediates the cytoplasmic assembly of Sm proteins onto uridine-rich small RNAs, and then participates in targeting RNPs to nuclear Cajal bodies (CBs). Recent studies have suggested that phosphorylation might control localization and function of the SMN complex. Here, we show that the nuclear phosphatase PPM1G/PP2Cγ interacts with and dephosphorylates the SMN complex. Small interfering RNA knockdown of PPM1G leads to an altered phosphorylation pattern of SMN and Gemin3, loss of SMN from CBs, and reduced stability of SMN. Accumulation in CBs is restored upon overexpression of catalytically active, but not that of inactive, PPM1G. This demonstrates that PPM1G's phosphatase activity is necessary to maintain SMN subcellular distribution. Concomitant knockdown of unr interacting protein (unrip), a component implicated in cytoplasmic retention of the SMN complex, also rescues the localization defects. Our data suggest that an interplay between PPM1G and unrip determine compartment-specific phosphorylation patterns, localization, and function of the SMN complex. PMID:17984321

Landslide model performance in a high resolution small-scale landscape

NASA Astrophysics Data System (ADS)

De Sy, V.; Schoorl, J. M.; Keesstra, S. D.; Jones, K. E.; Claessens, L.

2013-05-01

The frequency and severity of shallow landslides in New Zealand threatens life and property, both on- and off-site. The physically-based shallow landslide model LAPSUS-LS is tested for its performance in simulating shallow landslide locations induced by a high intensity rain event in a small-scale landscape. Furthermore, the effect of high resolution digital elevation models on the performance was tested. The performance of the model was optimised by calibrating different parameter values. A satisfactory result was achieved with a high resolution (1 m) DEM. Landslides, however, were generally predicted lower on the slope than mapped erosion scars. This discrepancy could be due to i) inaccuracies in the DEM or in other model input data such as soil strength properties; ii) relevant processes for this environmental context that are not included in the model; or iii) the limited validity of the infinite length assumption in the infinite slope stability model embedded in the LAPSUS-LS. The trade-off between a correct prediction of landslides versus stable cells becomes increasingly worse with coarser resolutions; and model performance decreases mainly due to altering slope characteristics. The optimal parameter combinations differ per resolution. In this environmental context the 1 m resolution topography resembles actual topography most closely and landslide locations are better distinguished from stable areas than for coarser resolutions. More gain in model performance could be achieved by adding landslide process complexities and parameter heterogeneity of the catchment.

Preoperative Portal Vein Embolization Tailored to Prepare the Liver for Complex Resections: Initial Experience

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

Baere, T. de, E-mail: debaere@igr.fr; Robinson, J. M.; Deschamps, F.

The purpose of this study was to evaluate the safety and efficacy of preoperative portal vein embolization (PVE) tailored to prepare the liver for complex and extended resections. During the past 5 years, 12 PVEs were performed in noncirrhotic patients with liver metastases from colon cancer (n = 10), choroidal melanoma (n = 1), and leiomyosarcoma (n = 1) to prepare complex anatomical liver resections in patients with small future remnant livers. These liver resections planned to preserve only segment IV in four patients, segments IV, V, and VIII in four patients, segments II, III, VI, and VII in threemore » patients, and segments V and VI in one patient. PVE was performed under general anesthesia with a flow-guided injection of a mixture of cyanoacrylate and Lipiodol using a 5-Fr catheter. All portal branches feeding the liver segments to be resected were successfully embolized with cyanoacrylate except one, which was occluded with coils due to the risk of reflux with cyanoacrylate. After a mean of 32 days, CT volumetry revealed a mean hypertrophy of the unembolized liver of 47 {+-} 25% (range, 21-88%). Liver resections could be performed in 10 patients but were canceled in 2, due to the occurrence of a new hepatic tumor in one and an insufficiently increased volume in the other. Among the 10 patients who underwent the liver resection, 1 died of postoperative sepsis, 3 died 3 to 32 months after surgery, including 1 death unrelated to cancer, and 6 were alive after 6 to 36 months after surgery. In conclusion, in this preliminary report, PVE appears to be feasible and able to induce hypertrophy of the future remnant liver before a complex and extended hepatectomy. Further evaluation is needed in a larger cohort.« less

Application of miniaturized near-infrared spectroscopy for quality control of extemporaneous orodispersible films.

PubMed

Foo, Wen Chin; Widjaja, Effendi; Khong, Yuet Mei; Gokhale, Rajeev; Chan, Sui Yung

2018-02-20

Extemporaneous oral preparations are routinely compounded in the pharmacy due to a lack of suitable formulations for special populations. Such small-scale pharmacy preparations also present an avenue for individualized pharmacotherapy. Orodispersible films (ODF) have increasingly been evaluated as a suitable dosage form for extemporaneous oral preparations. Nevertheless, as with all other extemporaneous preparations, safety and quality remain a concern. Although the United States Pharmacopeia (USP) recommends analytical testing of compounded preparations for quality assurance, pharmaceutical assays are typically not routinely performed for such non-sterile pharmacy preparations, due to the complexity and high cost of conventional assay methods such as high performance liquid chromatography (HPLC). Spectroscopic methods including Raman, infrared and near-infrared spectroscopy have been successfully applied as quality control tools in the industry. The state-of-art benchtop spectrometers used in those studies have the advantage of superior resolution and performance, but are not suitable for use in a small-scale pharmacy setting. In this study, we investigated the application of a miniaturized near infrared (NIR) spectrometer as a quality control tool for identification and quantification of drug content in extemporaneous ODFs. Miniaturized near infrared (NIR) spectroscopy is suitable for small-scale pharmacy applications in view of its small size, portability, simple user interface, rapid measurement and real-time prediction results. Nevertheless, the challenge with miniaturized NIR spectroscopy is its lower resolution compared to state-of-art benchtop equipment. We have successfully developed NIR spectroscopy calibration models for identification of ODFs containing five different drugs, and quantification of drug content in ODFs containing 2-10mg ondansetron (OND). The qualitative model for drug identification produced 100% prediction accuracy. The quantitative model to predict OND drug content in ODFs was divided into two calibrations for improved accuracy: Calibration I and II covered the 2-4mg and 4-10mg ranges respectively. Validation was performed for method accuracy, linearity and precision. In conclusion, this study demonstrates the feasibility of miniaturized NIR spectroscopy as a quality control tool for small-scale, pharmacy preparations. Due to its non-destructive nature, every dosage unit can be tested thus affording positive impact on patient safety. Copyright © 2017 Elsevier B.V. All rights reserved.

Lessons from isolable nickel(I) precursor complexes for small molecule activation.

PubMed

Yao, Shenglai; Driess, Matthias

2012-02-21

Small-molecule activation by transition metals is essential to numerous organic transformations, both biological and industrial. Creating useful metal-mediated activation systems often depends on stabilizing the metal with uncommon low oxidation states and low coordination numbers. This provides a redox-active metal center with vacant coordination sites well suited for interacting with small molecules. Monovalent nickel species, with their d(9) electronic configuration, are moderately strong one-electron reducing agents that are synthetically attractive if they can be isolated. They represent suitable reagents for closing the knowledge gap in nickel-mediated activation of small molecules. Recently, the first strikingly stable dinuclear β-diketiminate nickel(I) precursor complexes were synthesized, proving to be suitable promoters for small-molecule binding and activation. They have led to many unprecedented nickel complexes bearing activated small molecules in different reduction stages. In this Account, we describe selected achievements in the activation of nitrous oxide (N(2)O), O(2), the heavier chalcogens (S, Se, and Te), and white phosphorus (P(4)) through this β-diketiminatonickel(I) precursor species. We emphasize the reductive activation of O(2), owing to its promise in oxidation processes. The one-electron-reduced O(2) activation product, that is, the corresponding β-diketiminato-supported Ni-O(2) complex, is a genuine superoxonickel(II) complex, representing an important intermediate in the early stages of O(2) activation. It selectively acts as an oxygen-atom transfer agent, hydrogen-atom scavenger, or both towards exogenous organic substrates to yield oxidation products. The one-electron reduction of the superoxonickel(II) moiety was examined by using elemental potassium, β-diketiminatozinc(II) chloride, and β-diketiminatoiron(I) complexes, affording the first heterobimetallic complexes featuring a [NiO(2)M] subunit (M is K, Zn, or Fe). Through density functional theory (DFT) calculations, the geometric and electronic structures of these complexes were established and their distinctive reactivity, including the unprecedented monooxygenase-like activity of a bis(μ-oxo)nickel-iron complex, was studied. The studies have further led to other heterobimetallic complexes containing a [NiO(2)M] core, which are useful for understanding the influence of the heterometal on structure-reactivity relationships. The activation of N(2)O led directly to the hydrogen-atom abstraction product bis(μ-hydroxo)nickel(II) species and prevented isolation of any intermediate. In contrast, the activation of elemental S, Se, and Te with the same nickel(I) reagent furnished activation products with superchalcogenido E(2)(-) (E is S, Se, or Te) and dichalcogenido E(2)(2-) ligand in different activation stages. The isolable supersulfidonickel(II) subunit may serve as a versatile building block for the synthesis of heterobimetallic disulfidonickel(II) complexes with a [NiS(2)M] core. In the case of white phosphorus, the P(4) molecule has been coordinated to the nickel(I) center of dinuclear β-diketiminatonickel(I) precursor complexes; however, the whole P(4) subunit is a weaker electron acceptor than the dichalcogen ligands E(2), thus remaining unreduced. This P(4) binding mode is rare and could open new doors for subsequent functionalization of P(4). Our advances in understanding how these small molecules are bound to a nickel(I) center and are activated for further transformation offer promise for designing new catalysts. These nickel-containing complexes offer exceptional potential for nickel-mediated transformations of organic molecules and as model compounds for mimicking active sites of nickel-containing metalloenzymes.

Probing the Topological Properties of Complex Networks Modeling Short Written Texts

PubMed Central

Amancio, Diego R.

2015-01-01

In recent years, graph theory has been widely employed to probe several language properties. More specifically, the so-called word adjacency model has been proven useful for tackling several practical problems, especially those relying on textual stylistic analysis. The most common approach to treat texts as networks has simply considered either large pieces of texts or entire books. This approach has certainly worked well—many informative discoveries have been made this way—but it raises an uncomfortable question: could there be important topological patterns in small pieces of texts? To address this problem, the topological properties of subtexts sampled from entire books was probed. Statistical analyses performed on a dataset comprising 50 novels revealed that most of the traditional topological measurements are stable for short subtexts. When the performance of the authorship recognition task was analyzed, it was found that a proper sampling yields a discriminability similar to the one found with full texts. Surprisingly, the support vector machine classification based on the characterization of short texts outperformed the one performed with entire books. These findings suggest that a local topological analysis of large documents might improve its global characterization. Most importantly, it was verified, as a proof of principle, that short texts can be analyzed with the methods and concepts of complex networks. As a consequence, the techniques described here can be extended in a straightforward fashion to analyze texts as time-varying complex networks. PMID:25719799

Camelina sativa, an oilseed at the nexus between model system and commercial crop.

PubMed

Malik, Meghna R; Tang, Jihong; Sharma, Nirmala; Burkitt, Claire; Ji, Yuanyuan; Mykytyshyn, Marie; Bohmert-Tatarev, Karen; Peoples, Oliver; Snell, Kristi D

2018-06-07

The rapid assessment of metabolic engineering strategies in plants is aided by crops that provide simple, high throughput transformation systems, a sequenced genome, and the ability to evaluate the resulting plants in field trials. Camelina sativa provides all of these attributes in a robust oilseed platform. The ability to perform field evaluation of Camelina is a useful, and in some studies essential benefit that allows researchers to evaluate how traits perform outside the strictly controlled conditions of a greenhouse. In the field the plants are subjected to higher light intensities, seasonal diurnal variations in temperature and light, competition for nutrients, and watering regimes dictated by natural weather patterns, all which may affect trait performance. There are difficulties associated with the use of Camelina. The current genetic resources available for Camelina pale in comparison to those developed for the model plant Arabidopsis thaliana; however, the sequence similarity of the Arabidopsis and Camelina genomes often allows the use of Arabidopsis as a reference when additional information is needed. Camelina's genome, an allohexaploid, is more complex than other model crops, but the diploid inheritance of its three subgenomes is straightforward. The need to navigate three copies of each gene in genome editing or mutagenesis experiments adds some complexity but also provides advantages for gene dosage experiments. The ability to quickly engineer Camelina with novel traits, advance generations, and bulk up homozygous lines for small-scale field tests in less than a year, in our opinion, far outweighs the complexities associated with the crop.

Structural studies of a crystalline insulin analog complex with protamine by atomic force microscopy.

PubMed Central

Yip, C M; Brader, M L; Frank, B H; DeFelippis, M R; Ward, M D

2000-01-01

Crystallographic studies of insulin-protamine complexes, such as neutral protamine Hagedorn (NPH) insulin, have been hampered by high crystal solvent content, small crystal dimensions, and extensive disorder in the protamine molecules. We report herein in situ tapping mode atomic force microscopy (TMAFM) studies of crystalline neutral protamine Lys(B28)Pro(B29) (NPL), a complex of Lys(B28)Pro(B29) insulin, in which the C-terminal prolyl and lysyl residues of human insulin are inverted, and protamine that is used as an intermediate time-action therapy for treating insulin-dependent diabetes. Tapping mode AFM performed at 6 degrees C on bipyramidally tipped tetragonal rod-shaped NPL crystals revealed large micron-sized islands separated by 44-A tall steps. Lattice images obtained by in situ TMAFM phase and height imaging on these islands were consistent with the arrangement of individual insulin-protamine complexes on the P4(1)2(1)2 (110) crystal plane of NPH, based on a low-resolution x-ray diffraction structure of NPH, arguing that the NPH and NPL insulins are isostructural. Superposition of the height and phase images indicated that tip-sample adhesion was larger in the interstices between NPL complexes in the (110) crystal plane than over the individual complexes. These results demonstrate the utility of low-temperature TMAFM height and phase imaging for the structural characterization of biomolecular complexes. PMID:10620310

Arterial supply of the upper cranial nerves: a comprehensive review.

PubMed

Hendrix, Philipp; Griessenauer, Christoph J; Foreman, Paul; Shoja, Mohammadali M; Loukas, Marios; Tubbs, R Shane

2014-11-01

The arterial supply to the upper cranial nerves is derived from a complex network of branches derived from the anterior and posterior cerebral circulations. We performed a comprehensive literature review of the arterial supply of the upper cranial nerves with an emphasis on clinical considerations. Arteries coursing in close proximity to the cranial nerves regularly give rise to small vessels that supply the nerve. Knowledge of the arteries supplying the cranial nerves is of particular importance during surgical approaches to the skull base. © 2014 Wiley Periodicals, Inc.

9-Fluorenylmethyloxycarbonyl/ tbutyl-based convergent protein synthesis.

PubMed

Barlos, K; Gatos, D

1999-01-01

Besides linear solid phase peptide synthesis, segment condensation in solution and chemical ligation, convergent peptide synthesis (CPS) was developed in order to enable the efficient preparation of complex peptides and small proteins. According to this synthetic strategy, solid phase synthesized and suitably protected peptide fragments corresponding to the entire peptide/protein-sequence are condensed on a solid support or in solution, to the target protein. This review summarizes CPS performed utilizing the mild 9-fluorenylmethyloxycarbonyl/tbutyloxycarbonyl-based protecting scheme for the amino acids. Copyright 1999 John Wiley & Sons, Inc.

Exploring Complex Systems Aspects of Blackout Risk and Mitigation

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

Newman, David E; Carreras, Benjamin A; Lynch, Vickie E

2011-01-01

Electric power transmission systems are a key infrastructure, and blackouts of these systems have major consequences for the economy and national security. Analyses of blackout data suggest that blackout size distributions have a power law form over much of their range. This result is an indication that blackouts behave as a complex dynamical system. We use a simulation of an upgrading power transmission system to investigate how these complex system dynamics impact the assessment and mitigation of blackout risk. The mitigation of failures in complex systems needs to be approached with care. The mitigation efforts can move the system tomore » a new dynamic equilibrium while remaining near criticality and preserving the power law region. Thus, while the absolute frequency of blackouts of all sizes may be reduced, the underlying forces can still cause the relative frequency of large blackouts to small blackouts to remain the same. Moreover, in some cases, efforts to mitigate small blackouts can even increase the frequency of large blackouts. This result occurs because the large and small blackouts are not mutually independent, but are strongly coupled by the complex dynamics.« less

12 CFR 563e.26 - Small savings association performance standards.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Small savings association performance standards... COMMUNITY REINVESTMENT Standards for Assessing Performance § 563e.26 Small savings association performance standards. (a) Performance criteria—(1) Small savings associations that are not intermediate small savings...

12 CFR 228.26 - Small bank performance standards.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 12 Banks and Banking 3 2011-01-01 2011-01-01 false Small bank performance standards. 228.26... RESERVE SYSTEM COMMUNITY REINVESTMENT (REGULATION BB) Standards for Assessing Performance § 228.26 Small bank performance standards. (a) Performance criteria—(1) Small banks that are not intermediate small...

12 CFR 563e.26 - Small savings association performance standards.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Small savings association performance standards... COMMUNITY REINVESTMENT Standards for Assessing Performance § 563e.26 Small savings association performance standards. (a) Performance criteria—(1) Small savings associations that are not intermediate small savings...

12 CFR 345.26 - Small bank performance standards.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 12 Banks and Banking 4 2011-01-01 2011-01-01 false Small bank performance standards. 345.26... GENERAL POLICY COMMUNITY REINVESTMENT Standards for Assessing Performance § 345.26 Small bank performance standards. (a) Performance criteria—(1) Small banks that are not intermediate small banks. The FDIC...

12 CFR 345.26 - Small bank performance standards.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Small bank performance standards. 345.26... GENERAL POLICY COMMUNITY REINVESTMENT Standards for Assessing Performance § 345.26 Small bank performance standards. (a) Performance criteria—(1) Small banks that are not intermediate small banks. The FDIC...

12 CFR 228.26 - Small bank performance standards.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Small bank performance standards. 228.26... RESERVE SYSTEM COMMUNITY REINVESTMENT (REGULATION BB) Standards for Assessing Performance § 228.26 Small bank performance standards. (a) Performance criteria—(1) Small banks that are not intermediate small...

Marginal Contribution-Based Distributed Subchannel Allocation in Small Cell Networks.

PubMed

Shah, Shashi; Kittipiyakul, Somsak; Lim, Yuto; Tan, Yasuo

2018-05-10

The paper presents a game theoretic solution for distributed subchannel allocation problem in small cell networks (SCNs) analyzed under the physical interference model. The objective is to find a distributed solution that maximizes the welfare of the SCNs, defined as the total system capacity. Although the problem can be addressed through best-response (BR) dynamics, the existence of a steady-state solution, i.e., a pure strategy Nash equilibrium (NE), cannot be guaranteed. Potential games (PGs) ensure convergence to a pure strategy NE when players rationally play according to some specified learning rules. However, such a performance guarantee comes at the expense of complete knowledge of the SCNs. To overcome such requirements, properties of PGs are exploited for scalable implementations, where we utilize the concept of marginal contribution (MC) as a tool to design learning rules of players’ utility and propose the marginal contribution-based best-response (MCBR) algorithm of low computational complexity for the distributed subchannel allocation problem. Finally, we validate and evaluate the proposed scheme through simulations for various performance metrics.

Steroid Profiling by Gas Chromatography–Mass Spectrometry and High Performance Liquid Chromatography–Mass Spectrometry for Adrenal Diseases

PubMed Central

McDonald, Jeffrey G.; Matthew, Susan

2012-01-01

The ability to measure steroid hormone concentrations in blood and urine specimens is central to the diagnosis and proper treatment of adrenal diseases. The traditional approach has been to assay each steroid hormone, precursor, or metabolite using individual aliquots of serum, each with a separate immunoassay. For complex diseases, such as congenital adrenal hyperplasia and adrenocortical cancer, in which the assay of several steroids is essential for management, this approach is time consuming and costly, in addition to using large amounts of serum. Gas chromatography/mass spectrometry profiling of steroid metabolites in urine has been employed for many years but only in a small number of specialized laboratories and suffers from slow throughput. The advent of commercial high-performance liquid chromatography instruments coupled to tandem mass spectrometers offers the potential for medium- to high-throughput profiling of serum steroids using small quantities of sample. Here, we review the physical principles of mass spectrometry, the instrumentation used for these techniques, the terminology used in this field and applications to steroid analysis. PMID:22170384

FEATURE 1, SMALL GUN POSITION, VIEW FACING NORTH. Naval ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

FEATURE 1, SMALL GUN POSITION, VIEW FACING NORTH. - Naval Air Station Barbers Point, Anti-Aircraft Battery Complex-Small Gun Position, East of Coral Sea Road, northwest of Hamilton Road, Ewa, Honolulu County, HI

Development of a rapid and sensitive method for the determination of aluminum by reverse-phase high-performance liquid chromatography using a fluorescence detector.

PubMed

Heena; Kumar, Rajesh; Rani, Susheela; Malik, Ashok Kumar

2015-01-01

This study represents a new analytical high-performance liquid chromatography-fluorescence detector method for the determination of Al(III) as Al(III) complex with 8-hydroxyquinoline-5-sulfonic acid in a tap water sample and a coke sample. A micellar liquid chromatographic method is proposed for the determination of aluminum metal in the presence of cetyltrimethylammonium bromide, a cationic surfactant (0.05 M) used for the solubilization of the aluminum complex. The influence of pH and ligand concentration on the formation of the complex was studied by adding a small amount of 0.1 M sodium hydroxide. The metal chelate was detected at λEx 410 nm and λEm 510 nm. This method eliminates the need for addition of reagent or organic modifier to the mobile phase. The complex was analyzed using an Ascentis Express C18 column and a mobile phase consisting of acetonitrile, methanol and water (55 : 30 : 15). Under the optimized conditions, the linear range was 1-200 µg L(-1) and the limit of detection was 0.05 µg L(-1). The method showed a good detector response over the range of interest and was successfully applied for the determination of trace Al(III) in canned coke and water samples containing excess of Mg(II), Ca(II) and other matrices. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Riparian and upland small mammals on the east slope of the Cascade Range, Washington

Treesearch

John F. Lehmkuhl; Roger D. Peffer; Margaret A. O' Connell

2008-01-01

Differences in small mammal diversity and abundance between riparian and upland areas have not been consistently shown in the Pacific Northwest, and the issue is expected to be complex along the east slope of the Cascade Range with its complex biogeography and forest landscape structure. The information is important for evaluating buffer zone management and the...

Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants.

PubMed

Iki, Taichiro; Yoshikawa, Manabu; Meshi, Tetsuo; Ishikawa, Masayuki

2012-01-18

Posttranscriptional gene silencing is mediated by RNA-induced silencing complexes (RISCs) that contain AGO proteins and single-stranded small RNAs. The assembly of plant AGO1-containing RISCs depends on the molecular chaperone HSP90. Here, we demonstrate that cyclophilin 40 (CYP40), protein phosphatase 5 (PP5), and several other proteins with the tetratricopeptide repeat (TPR) domain associates with AGO1 in an HSP90-dependent manner in extracts of evacuolated tobacco protoplasts (BYL). Intriguingly, CYP40, but not the other TPR proteins, could form a complex with small RNA duplex-bound AGO1. Moreover, CYP40 that was synthesized by in-vitro translation using BYL uniquely facilitated binding of small RNA duplexes to AGO1, and as a result, increased the amount of mature RISCs that could cleave target RNAs. CYP40 was not contained in mature RISCs, indicating that the association is transient. Addition of PP5 or cyclophilin-binding drug cyclosporine A prevented the association of endogenous CYP40 with HSP90-AGO1 complex and inhibited RISC assembly. These results suggest that a complex of AGO1, HSP90, CYP40, and a small RNA duplex is a key intermediate of RISC assembly in plants.

Landscape approach to the formation of the ecological frame of Moscow

NASA Astrophysics Data System (ADS)

Nizovtsev, Vyacheslav; Natalia, Erman

2015-04-01

The territory of Moscow, in particular in its former borders, is distinct for its strong transformation of the natural properties of virtually all types of landscape complexes. The modern landscape structure is characterized by fragmentation of natural land cover. Natural and quasinatural (natural and anthropogenic) landscape complexes with preserved natural structure are represented by isolated areas and occupy small areas. During recent years landscape diversity in general and biodiversity in particular have been rapidly declining, and many of the natural landscape complexes are under ever-increasing degradation. Ecological balance is broken, and preserved natural landscapes are not able to maintain it. Effective territorial organization of Moscow and the rational use of its territory are impossible without taking into account the natural component of the city as well as the properties and potential of the landscape complexes that integrate all natural features in specific areas. The formation of the ecological framework of the city is particularly important. It should be a single system of interrelated and complementary components that make up a single environmental space: habitat-forming cores (junctions), ecological corridors and elements of environmental infrastructure. Systemic unity of the environmental framework can support the territorial ecological compensation where a break of the ecological functions of one part of the system is compensated by maintaining or restoring them in another part and contribute to the polarization of incompatible types of land use. Habitat-forming cores should include as mandatory parts all the specifically protected natural areas (SPNAs), particularly valuable landscape complexes, as well as preserved adjacent forest areas. Their most important function should be to maintain resources and area reproducing abilities of landscapes, landscape diversity and biodiversity. Ecological corridors which perform environmental and operating transit functions should include unified landscape systems of river valleys, their hollow-beam upstreams and drained lows. The most important elements of environmental infrastructure include the most valuable forest and wetland complexes, springs and other landscape and aquatic complexes, cultural and historical landscape complexes, landscape complexes with high concentration of cultural heritage sites, sites of natural and green areas with great potential of natural and recreational resources, natural and recreational parks, natural monuments. They can serve as centers of landscape and biological diversity and perform partial transit (migration) and buffer functions. The territory of the ecological framework can be used for strictly regulated or limited recreation (tourism, short leisure). The adjacent natural and green spaces and natural parks may play a buffer role for the SPNAs and valuable landscape complexes. The spatial pattern of the landscape complexes of Moscow allows to create a single ecological framework based on the landscape, distinct for its interrelated and complementary components. Its basis may be consisted of uniform landscape complexes of valley outwash plains and river valleys, their hollow-beam upstreams and drained lows which perform system forming, environmental and transit functions. In the plan river valleys and small erosional forms are as if enclosed in the gullies and constitute single paradynamic systems unified by lateral flows. Therefore not only the edges of river valleys, but also the rear seams of the valley outwash plains should become important natural boundaries, limiting urban development of the area. Their most important functional feature is that they serve as local collectors and surface water runoff channels. These landscape complexes are distinct for most dynamic natural processes and thus negative exogenous processes. The authors have drawn indigenous (conditionally restored) and modern landscapes of Moscow on a scale of 1: 50,000 and on their basis an ecological framework map of Moscow. These maps are an important natural basis for the analysis of conditions and identification of limiting factors of the urban development of the big city.

3D radar wavefield tomography of comet interiors

NASA Astrophysics Data System (ADS)

Sava, Paul; Asphaug, Erik

2018-04-01

Answering fundamental questions about the origin and evolution of small planetary bodies hinges on our ability to image their surface and interior structure in detail and at high resolution. The interior structure is not easily accessible without systematic imaging using, e.g., radar transmission and reflection data from multiple viewpoints, as in medical tomography. Radar tomography can be performed using methodology adapted from terrestrial exploration seismology. Our feasibility study primarily focuses on full wavefield methods that facilitate high quality imaging of small body interiors. We consider the case of a monostatic system (co-located transmitters and receivers) operated in various frequency bands between 5 and 15 MHz, from a spacecraft in slow polar orbit around a spinning comet nucleus. Using realistic numerical experiments, we demonstrate that wavefield techniques can generate high resolution tomograms of comets nuclei with arbitrary shape and complex interior properties.

Use of small stand-alone Internet nodes as a distributed control system

NASA Astrophysics Data System (ADS)

Goodwin, Robert W.; Kucera, Michael J.; Shea, Michael F.

1994-12-01

For several years, the standard model for accelerator control systems has been workstation consoles connected to VME local stations by a Local Area Network with analog and digital data being accessed via a field bus to custom I/O interface electronics. Commercially available hardware has now made it possible to implement a small stand-alone data acquisition station that combines the LAN connection, the computer, and the analog and digital I/O interface on a single board. This eliminates the complexity of a field bus and the associated proprietary I/O hardware. A minimum control system is one data acquisition station and a Macintosh or workstation console, both connected to the network; larger systems have more consoles and nodes. An implementation of this architecture is described along with performance and operational experience.

High-beta steady-state research with integrated modeling in the JT-60 Upgrade

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

Ozeki, T.

2007-05-15

Improvement of high-beta performance and its long sustainment was obtained with ferritic steel tiles in the JT-60 Upgrade (JT-60U) [T. Fujita et al., Phys. Plasmas 50, 104 (2005)], which were installed inside the vacuum vessel to reduce fast ion loss by decreasing the toroidal field ripple. When a separation between the plasma surface and the wall was small, high-beta plasmas reached the ideal wall stability limit, i.e., the ideal magnetohydrodynamics stability limit with the wall stabilization. A small rotation velocity of 0.3% of the Alfven velocity was found to be effective for suppressing the resistive wall mode. Sustainment of themore » high normalized beta value of {beta}{sub N}=2.3 has been extended to 28.6 s ({approx}15 times the current diffusion time) by improvement of the confinement and increase in the net heating power. Based on the research in JT-60U experiments and first-principle simulations, integrated models of core, edge-pedestal, and scrape-off-layer (SOL) divertors were developed, and they clarified complex features of reactor-relevant plasmas. The integrated core plasma model indicated that the small amount of electron cyclotron (EC) current density of about half the bootstrap current density could effectively stabilize the neoclassical tearing mode by the localized EC current accurately aligned to the magnetic island center. The integrated edge-pedestal model clarified that the collisionality dependence of energy loss due to the edge-localized mode was caused by the change in the width of the unstable mode and the SOL transport. The integrated SOL-divertor model clarified the effect of the exhaust slot on the pumping efficiency and the cause of enhanced radiation near the X-point multifaceted asymmetric radiation from edge. Success in these consistent analyses using the integrated code indicates that it is an effective means to investigate complex plasmas and to control the integrated performance.« less

Renal cyst formation in patients treated with crizotinib for non-small cell lung cancer-Incidence, radiological features and clinical characteristics.

PubMed

Halpenny, Darragh F; McEvoy, Sinead; Li, Angela; Hayan, Sumar; Capanu, Marinela; Zheng, Junting; Riely, Gregory; Ginsberg, Michelle S

2017-04-01

Treatment with the ALK inhibitor crizotinib has been associated with complex renal cyst formation in patients with non-small cell lung cancer (NSCLC). Using patients treated with crizotinib, we aimed to evaluate the incidence of renal cyst formation, to identify risk factors for cyst formation and to provide a radiological description of cyst characteristics. Patients with ALK-positive NSCLC treated with crizotinib were retrospectively identified from an institutional database. Computed tomography (CT) imaging performed prior to and during crizotinib treatment was retrospectively reviewed to assess the size and complexity of pre-existing cysts, new cysts, and enlarging cysts. Demographic data including age, sex, ethnicity, smoking history and length of treatment were also recorded. Data from 60 patients with NSCLC treated with crizotinib at our institution between 6/5/2009 and 7/1/2015 were collected. 57 had CT imaging before and during treatment. Mean length of imaging follow-up was 18 months. 9 (16%) patients had cysts which enlarged or developed de novo during treatment. 2 (4%) patients developed complex renal cysts (1 of these patients also developed complex hepatic cysts). Female gender (p=0.008) and the presence of renal cysts on baseline scans (p=0.044) were significantly associated with cyst formation or growth. Renal cyst formation or growth occurred in 16% of crizotinib-treated patients. Women and those with pre-existing cysts were at greatest risk. Although the potential causal relationship between crizotinib use and renal cyst formation has yet to be fully defined, it is important for radiologists and clinicians to be aware of this finding. Copyright © 2017. Published by Elsevier B.V.

The Strata-1 experiment on small body regolith segregation

NASA Astrophysics Data System (ADS)

Fries, Marc; Abell, Paul; Brisset, Julie; Britt, Daniel; Colwell, Joshua; Dove, Adrienne; Durda, Dan; Graham, Lee; Hartzell, Christine; Hrovat, Kenneth; John, Kristen; Karrer, Dakotah; Leonard, Matthew; Love, Stanley; Morgan, Joseph; Poppin, Jayme; Rodriguez, Vincent; Sánchez-Lana, Paul; Scheeres, Dan; Whizin, Akbar

2018-01-01

The Strata-1 experiment studies the mixing and segregation dynamics of regolith on small bodies by exposing a suite of regolith simulants to the microgravity environment aboard the International Space Station (ISS) for one year. This will improve our understanding of regolith dynamics and properties on small asteroids, and may assist in interpreting analyses of samples from missions to small bodies such as OSIRIS-REx, Hayabusa-1 and -2, and future missions to small bodies. The Strata-1 experiment consists of four evacuated tubes partially filled with regolith simulants. The simulants are chosen to represent models of regolith covering a range of complexity and tailored to inform and improve computational studies. The four tubes are regularly imaged while moving in response to the ambient vibrational environment using dedicated cameras. The imagery is then downlinked to the Strata-1 science team about every two months. Analyses performed on the imagery includes evaluating the extent of the segregation of Strata-1 samples and comparing the observations to computational models. After Strata-1's return to Earth, x-ray tomography and optical microscopy will be used to study the post-flight simulant distribution. Strata-1 is also a pathfinder for the new "1E" ISS payload class, which is intended to simplify and accelerate emplacement of experiments on board ISS.

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: The Fractal Dimensions of Complex Networks

NASA Astrophysics Data System (ADS)

Guo, Long; Cai, XU

2009-08-01

It is shown that many real complex networks share distinctive features, such as the small-world effect and the heterogeneous property of connectivity of vertices, which are different from random networks and regular lattices. Although these features capture the important characteristics of complex networks, their applicability depends on the style of networks. To unravel the universal characteristics many complex networks have in common, we study the fractal dimensions of complex networks using the method introduced by Shanker. We find that the average 'density' (ρ(r)) of complex networks follows a better power-law function as a function of distance r with the exponent df, which is defined as the fractal dimension, in some real complex networks. Furthermore, we study the relation between df and the shortcuts Nadd in small-world networks and the size N in regular lattices. Our present work provides a new perspective to understand the dependence of the fractal dimension df on the complex network structure.

Multi-stage decoding for multi-level block modulation codes

NASA Technical Reports Server (NTRS)

Lin, Shu; Kasami, Tadao

1991-01-01

Various types of multistage decoding for multilevel block modulation codes, in which the decoding of a component code at each stage can be either soft decision or hard decision, maximum likelihood or bounded distance are discussed. Error performance for codes is analyzed for a memoryless additive channel based on various types of multi-stage decoding, and upper bounds on the probability of an incorrect decoding are derived. It was found that, if component codes of a multi-level modulation code and types of decoding at various stages are chosen properly, high spectral efficiency and large coding gain can be achieved with reduced decoding complexity. It was found that the difference in performance between the suboptimum multi-stage soft decision maximum likelihood decoding of a modulation code and the single stage optimum decoding of the overall code is very small, only a fraction of dB loss in SNR at the probability of an incorrect decoding for a block of 10(exp -6). Multi-stage decoding of multi-level modulation codes really offers a way to achieve the best of three worlds, bandwidth efficiency, coding gain, and decoding complexity.

Manifold regularized multitask learning for semi-supervised multilabel image classification.

PubMed

Luo, Yong; Tao, Dacheng; Geng, Bo; Xu, Chao; Maybank, Stephen J

2013-02-01

It is a significant challenge to classify images with multiple labels by using only a small number of labeled samples. One option is to learn a binary classifier for each label and use manifold regularization to improve the classification performance by exploring the underlying geometric structure of the data distribution. However, such an approach does not perform well in practice when images from multiple concepts are represented by high-dimensional visual features. Thus, manifold regularization is insufficient to control the model complexity. In this paper, we propose a manifold regularized multitask learning (MRMTL) algorithm. MRMTL learns a discriminative subspace shared by multiple classification tasks by exploiting the common structure of these tasks. It effectively controls the model complexity because different tasks limit one another's search volume, and the manifold regularization ensures that the functions in the shared hypothesis space are smooth along the data manifold. We conduct extensive experiments, on the PASCAL VOC'07 dataset with 20 classes and the MIR dataset with 38 classes, by comparing MRMTL with popular image classification algorithms. The results suggest that MRMTL is effective for image classification.

Research and Process-Optimization on Mixed Crystal Caused Uneven-Performance of High-strength Structural Car Steel QStE500TM

NASA Astrophysics Data System (ADS)

Jian-wen, Li; Hong-yan, Liu

Handan Iron and Steel production of high-strength structural car steel QStE500TM thin gauge products using Nb + Ti composite strengthening, with a small amount of Cr element to improve its hardenability, the process parameter control is inappropriate with Nb + Ti complex steel, it is easy to produce in the mixed crystal phenomenon, resulting in decreasing the toughness and uneven performance. In this paper, Gleeble 3500 thermal simulation testing machine for high-strength structural steel car QStE500TM product deformation austenite recrystallization behavior research, determined completely recrystallized, partial recrystallization and non-recrystallization region, provide theoretical basis and necessary data for reasonable controlled rolling process for production.

Fluorescent quantification of melanin.

PubMed

Fernandes, Bruno; Matamá, Teresa; Guimarães, Diana; Gomes, Andreia; Cavaco-Paulo, Artur

2016-11-01

Melanin quantification is reportedly performed by absorption spectroscopy, commonly at 405 nm. Here, we propose the implementation of fluorescence spectroscopy for melanin assessment. In a typical in vitro assay to assess melanin production in response to an external stimulus, absorption spectroscopy clearly overvalues melanin content. This method is also incapable of distinguishing non-melanotic/amelanotic control cells from those that are actually capable of performing melanogenesis. Therefore, fluorescence spectroscopy is the best method for melanin quantification as it proved to be highly specific and accurate, detecting even small variations in the synthesis of melanin. This method can also be applied to the quantification of melanin in more complex biological matrices like zebrafish embryos and human hair. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The performance of disk arrays in shared-memory database machines

NASA Technical Reports Server (NTRS)

Katz, Randy H.; Hong, Wei

1993-01-01

In this paper, we examine how disk arrays and shared memory multiprocessors lead to an effective method for constructing database machines for general-purpose complex query processing. We show that disk arrays can lead to cost-effective storage systems if they are configured from suitably small formfactor disk drives. We introduce the storage system metric data temperature as a way to evaluate how well a disk configuration can sustain its workload, and we show that disk arrays can sustain the same data temperature as a more expensive mirrored-disk configuration. We use the metric to evaluate the performance of disk arrays in XPRS, an operational shared-memory multiprocessor database system being developed at the University of California, Berkeley.

Structural changes of homodimers in the PDB.

PubMed

Koike, Ryotaro; Amemiya, Takayuki; Horii, Tatsuya; Ota, Motonori

2018-04-01

Protein complexes are involved in various biological phenomena. These complexes are intrinsically flexible, and structural changes are essential to their functions. To perform a large-scale automated analysis of the structural changes of complexes, we combined two original methods. An application, SCPC, compares two structures of protein complexes and decides the match of binding mode. Another application, Motion Tree, identifies rigid-body motions in various sizes and magnitude from the two structural complexes with the same binding mode. This approach was applied to all available homodimers in the Protein Data Bank (PDB). We defined two complex-specific motions: interface motion and subunit-spanning motion. In the former, each subunit of a complex constitutes a rigid body, and the relative movement between subunits occurs at the interface. In the latter, structural parts from distinct subunits constitute a rigid body, providing the relative movement spanning subunits. All structural changes were classified and examined. It was revealed that the complex-specific motions were common in the homodimers, detected in around 40% of families. The dimeric interfaces were likely to be small and flat for interface motion, while large and rugged for subunit-spanning motion. Interface motion was accompanied by a drastic change in contacts at the interface, while the change in the subunit-spanning motion was moderate. These results indicate that the interface properties of homodimers correlated with the type of complex-specific motion. The study demonstrates that the pipeline of SCPC and Motion Tree is useful for the massive analysis of structural change of protein complexes. Copyright © 2017 Elsevier Inc. All rights reserved.

Strategies for the structural analysis of multi-protein complexes: lessons from the 3D-Repertoire project.

PubMed

Collinet, B; Friberg, A; Brooks, M A; van den Elzen, T; Henriot, V; Dziembowski, A; Graille, M; Durand, D; Leulliot, N; Saint André, C; Lazar, N; Sattler, M; Séraphin, B; van Tilbeurgh, H

2011-08-01

Structural studies of multi-protein complexes, whether by X-ray diffraction, scattering, NMR spectroscopy or electron microscopy, require stringent quality control of the component samples. The inability to produce 'keystone' subunits in a soluble and correctly folded form is a serious impediment to the reconstitution of the complexes. Co-expression of the components offers a valuable alternative to the expression of single proteins as a route to obtain sufficient amounts of the sample of interest. Even in cases where milligram-scale quantities of purified complex of interest become available, there is still no guarantee that good quality crystals can be obtained. At this step, protein engineering of one or more components of the complex is frequently required to improve solubility, yield or the ability to crystallize the sample. Subsequent characterization of these constructs may be performed by solution techniques such as Small Angle X-ray Scattering and Nuclear Magnetic Resonance to identify 'well behaved' complexes. Herein, we recount our experiences gained at protein production and complex assembly during the European 3D Repertoire project (3DR). The goal of this consortium was to obtain structural information on multi-protein complexes from yeast by combining crystallography, electron microscopy, NMR and in silico modeling methods. We present here representative set case studies of complexes that were produced and analyzed within the 3DR project. Our experience provides useful insight into strategies that are more generally applicable for structural analysis of protein complexes. Copyright © 2011 Elsevier Inc. All rights reserved.

Identification of fracture zones and its application in automatic bone fracture reduction.

PubMed

Paulano-Godino, Félix; Jiménez-Delgado, Juan J

2017-04-01

The preoperative planning of bone fractures using information from CT scans increases the probability of obtaining satisfactory results, since specialists are provided with additional information before surgery. The reduction of complex bone fractures requires solving a 3D puzzle in order to place each fragment into its correct position. Computer-assisted solutions may aid in this process by identifying the number of fragments and their location, by calculating the fracture zones or even by computing the correct position of each fragment. The main goal of this paper is the development of an automatic method to calculate contact zones between fragments and thus to ease the computation of bone fracture reduction. In this paper, an automatic method to calculate the contact zone between two bone fragments is presented. In a previous step, bone fragments are segmented and labelled from CT images and a point cloud is generated for each bone fragment. The calculated contact zones enable the automatic reduction of complex fractures. To that end, an automatic method to match bone fragments in complex fractures is also presented. The proposed method has been successfully applied in the calculation of the contact zone of 4 different bones from the ankle area. The calculated fracture zones enabled the reduction of all the tested cases using the presented matching algorithm. The performed tests show that the reduction of these fractures using the proposed methods leaded to a small overlapping between fragments. The presented method makes the application of puzzle-solving strategies easier, since it does not obtain the entire fracture zone but the contact area between each pair of fragments. Therefore, it is not necessary to find correspondences between fracture zones and fragments may be aligned two by two. The developed algorithms have been successfully applied in different fracture cases in the ankle area. The small overlapping error obtained in the performed tests demonstrates the absence of visual overlapping in the figures. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Modal interactions between a large-wavelength inclined interface and small-wavelength multimode perturbations in a Richtmyer-Meshkov instability

NASA Astrophysics Data System (ADS)

McFarland, Jacob A.; Reilly, David; Black, Wolfgang; Greenough, Jeffrey A.; Ranjan, Devesh

2015-07-01

The interaction of a small-wavelength multimodal perturbation with a large-wavelength inclined interface perturbation is investigated for the reshocked Richtmyer-Meshkov instability using three-dimensional simulations. The ares code, developed at Lawrence Livermore National Laboratory, was used for these simulations and a detailed comparison of simulation results and experiments performed at the Georgia Tech Shock Tube facility is presented first for code validation. Simulation results are presented for four cases that vary in large-wavelength perturbation amplitude and the presence of secondary small-wavelength multimode perturbations. Previously developed measures of mixing and turbulence quantities are presented that highlight the large variation in perturbation length scales created by the inclined interface and the multimode complex perturbation. Measures are developed for entrainment, and turbulence anisotropy that help to identify the effects of and competition between each perturbations type. It is shown through multiple measures that before reshock the flow processes a distinct memory of the initial conditions that is present in both large-scale-driven entrainment measures and small-scale-driven mixing measures. After reshock the flow develops to a turbulentlike state that retains a memory of high-amplitude but not low-amplitude large-wavelength perturbations. It is also shown that the high-amplitude large-wavelength perturbation is capable of producing small-scale mixing and turbulent features similar to the small-wavelength multimode perturbations.

Enabling Technologies for Entrepreneurial Opportunities in 3D printing of SmallSats

NASA Technical Reports Server (NTRS)

Kwas, Andrew; MacDonald, Eric; Muse, Dan; Wicker, Ryan; Kief, Craig; Aarestad, Jim; Zemba, Mike; Marshall, Bill; Tolbert, Carol; Connor, Brett

2014-01-01

A consortium of innovative experts in additive manufacturing (AM) comprising Northrup Grumman Technical Services, University of Texas at El Paso (UTEP), Configurable Space Microsystems Innovations & Applications Center (COSMIAC), NASA Glenn Research Center (GRC), and Youngstown State University, have made significant breakthroughs in the goal of creating the first complete 3D printed small satellite. Since AM machines are relatively inexpensive, this should lead to many entrepreneurial opportunities for the small satellite community. Our technology advancements are focused on the challenges of embedding key components within the structure of the article. We have demonstrated, using advanced fused deposition modeling techniques, complex geometric shapes which optimize the spacecraft design. The UTEP Keck Center has developed a method that interrupts the printing process to insert components into specific cavities, resulting in a spacecraft that has minimal internal space allocated for what traditionally were functional purposes. This allows us to increase experiment and instrument capability by provided added volume in a confined small satellite space. Leveraging initial progress made on a NASA contract, the team investigated the potential of new materials that exploit the AM process, producing candidate compositions that exceed the capabilities of traditional materials. These "new materials" being produced and tested include some that have improved radiation shielding, increased permeability, enhanced thermal properties, better conductive properties, and increased structural performance. The team also investigated materials that were previously not possible to be made. Our testing included standard mechanical tests such as vibration, tensile, thermal cycling, and impact resistance as well as radiation and electromagnetic tests. The initial results of these products and their performance will be presented and compared with standard properties. The new materials with the highest probability to disrupt the future of small satellite systems by driving down costs will be highlighted, in conjunction with the electronic embedding process.

Novel Zn(II) complexes of 1,3-diphenyl-4-(arylazo)pyrazol-5-one derivatives: Synthesis, spectroscopic properties, DFT calculations and first order nonlinear optical properties

NASA Astrophysics Data System (ADS)

Abdel-Latif, Samir A.; Mohamed, Adel A.

2018-03-01

Eight novel Zn(II) complexes with substituted 1,3-diphenyl-4-(arylazo)pyrazol-5-one (L1-L4) derivatives have been synthesized and elucidated using various physicochemical techniques. Quantum mechanical calculations of energies, geometries were done by DFT using B3LYP/GEN functional combined with 6.311G (d,p) and LAN2DZ basis sets. The analyses of HOMO and LUMO have been used to explain the charge transfer within the ligands and complexes. The calculated small energy gap between HOMO and LUMO energies shows that the charge transfer occurs within Zn(II) complexes. Geometrical parameters, molecular electrostatic potential maps (MEP) and total electron densities analyses of the ligands and their Zn complexes have been carried out. Molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength has been investigated by the applying of natural bond orbital (NBO) analysis. Total static dipole moment (μ), the mean polarizability (<α>), the anisotropy of the polarizability (Δα), the mean first-order hyperpolarizability (<β>) have been also performed. The obtained values show that Zn(II) complexes is brilliant candidate to NLO materials. The analyses of the 1:1 complexes indicate that the Zn(II) ion is five-coordinated with water molecules at axial position in case of L1, L2 and L4 whereas, six-coordinated with L3 and non-electrolytic behaviour of complexes indicates the absence of counter ion.

Oligoanilines as a suppressor of polysulfide shuttling in lithium–sulfur batteries

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

Chang, Chi-Hao; Chung, Sheng-Heng; Han, Pauline

The migration of small polysulfide (LiPS) chains through the porous polymeric separators seriously jeopardizes the cycle life and energy density of lithium–sulfur (Li–S) batteries. Herein, we present a new concept in which an organic oligoaniline, amine-capped aniline trimer (ACAT), serves as an effective suppressor of the LiPS migration in Li–S cells. The strong interaction between LiPS and ACAT facilitates the formation of bulky ACAT–LiPS complexes (organoLiPS complexes), which are then size-selectively sieved by the porous polymeric separators employed in Li–S cells. Thus, the addition of ACAT significantly ameliorates the electrochemical performances of Li–S batteries due to suppressed LiPS migration. Thismore » new concept offers a viable strategy to achieve practically viable Li–S batteries.« less

Use of Multiple GPUs to Speedup the Execution of a Three-Dimensional Computational Model of the Innate Immune System

NASA Astrophysics Data System (ADS)

Xavier, M. P.; do Nascimento, T. M.; dos Santos, R. W.; Lobosco, M.

2014-03-01

The development of computational systems that mimics the physiological response of organs or even the entire body is a complex task. One of the issues that makes this task extremely complex is the huge computational resources needed to execute the simulations. For this reason, the use of parallel computing is mandatory. In this work, we focus on the simulation of temporal and spatial behaviour of some human innate immune system cells and molecules in a small three-dimensional section of a tissue. To perform this simulation, we use multiple Graphics Processing Units (GPUs) in a shared-memory environment. Despite of high initialization and communication costs imposed by the use of GPUs, the techniques used to implement the HIS simulator have shown to be very effective to achieve this purpose.

Development of procedures for calculating stiffness and damping properties of elastomers in engineering applications. Part 2: Elastomer characteristics at constant temperature

NASA Technical Reports Server (NTRS)

Gupta, P. K.; Tessarzik, J. M.; Cziglenyi, L.

1974-01-01

Dynamic properties of a commerical polybutadiene compound were determined at a constant temperature of 32 C by a forced-vibration resonant mass type of apparatus. The constant thermal state of the elastomer was ensured by keeping the ambient temperature constant and by limiting the power dissipation in the specimen. Experiments were performed with both compression and shear specimens at several preloads (nominal strain varying from 0 to 5 percent), and the results are reported in terms of a complex stiffness as a function of frequency. Very weak frequency dependence is observed and a simple power law type of correlation is shown to represent the data well. Variations in the complex stiffness as a function of preload are also found to be small for both compression and shear specimens.

Complex pattern of colon cancer recurrence including a kidney metastasis: A case report

PubMed Central

Waleczek, Helfried; Wente, Moritz N; Kozianka, Jürgen

2005-01-01

We report a case of a 77-year-old female with a local recurrence of cancer after right hemicolectomy which infiltrated the pancreatic head affording pancrea-toduodenectomy, who developed 3 years later recurrent tumor masses localized in the mesentery of the jejunum and in the lower pole of the left kidney. Partial nephrectomy and a segment resection of the small bowel were performed. Histological examination of both specimens revealed a necrotic metastasis of the primary carcinoma of the colon. Although intraluminal implantation of colon cancer cells in the renal pelvic mucosa from ureteric metastasis has been described, metastasis of a colorectal cancer in the kidney parenchyma is extremely rare and can be treated in an organ preserving manner. A complex pattern of colon cancer recurrence with unusual and rare sites of metastasis is reported. PMID:16222759

Oligoanilines as a suppressor of polysulfide shuttling in lithium–sulfur batteries

DOE PAGES

Chang, Chi-Hao; Chung, Sheng-Heng; Han, Pauline; ...

2017-07-25

The migration of small polysulfide (LiPS) chains through the porous polymeric separators seriously jeopardizes the cycle life and energy density of lithium–sulfur (Li–S) batteries. Herein, we present a new concept in which an organic oligoaniline, amine-capped aniline trimer (ACAT), serves as an effective suppressor of the LiPS migration in Li–S cells. The strong interaction between LiPS and ACAT facilitates the formation of bulky ACAT–LiPS complexes (organoLiPS complexes), which are then size-selectively sieved by the porous polymeric separators employed in Li–S cells. Thus, the addition of ACAT significantly ameliorates the electrochemical performances of Li–S batteries due to suppressed LiPS migration. Thismore » new concept offers a viable strategy to achieve practically viable Li–S batteries.« less

Force field inside the void in complex plasmas under microgravity conditions

NASA Astrophysics Data System (ADS)

Kretschmer, M.; Khrapak, S. A.; Zhdanov, S. K.; Thomas, H. M.; Morfill, G. E.; Fortov, V. E.; Lipaev, A. M.; Molotkov, V. I.; Ivanov, A. I.; Turin, M. V.

2005-05-01

Observations of complex plasmas under microgravity conditions onboard the International Space Station performed with the Plasma-Kristall experiment-Nefedov facility are reported. A weak instability of the boundary between the central void (region free of microparticles) and the microparticle cloud is observed at low gas pressures. The instability leads to periodic injections of a relatively small number of particles into the void region (by analogy this effect is called the “trampoline effect”). The trajectories of injected particles are analyzed providing information on the force field inside the void. The experimental results are compared with theory which assumes that the most important forces inside the void are the electric and the ion drag forces. Good agreement is found clearly indicating that under conditions investigated the void formation is caused by the ion drag force.

Dynamic system simulation of small satellite projects

NASA Astrophysics Data System (ADS)

Raif, Matthias; Walter, Ulrich; Bouwmeester, Jasper

2010-11-01

A prerequisite to accomplish a system simulation is to have a system model holding all necessary project information in a centralized repository that can be accessed and edited by all parties involved. At the Institute of Astronautics of the Technische Universitaet Muenchen a modular approach for modeling and dynamic simulation of satellite systems has been developed called dynamic system simulation (DySyS). DySyS is based on the platform independent description language SysML to model a small satellite project with respect to the system composition and dynamic behavior. A library of specific building blocks and possible relations between these blocks have been developed. From this library a system model of the satellite of interest can be created. A mapping into a C++ simulation allows the creation of an executable system model with which simulations are performed to observe the dynamic behavior of the satellite. In this paper DySyS is used to model and simulate the dynamic behavior of small satellites, because small satellite projects can act as a precursor to demonstrate the feasibility of a system model since they are less complex compared to a large scale satellite project.

Complex networks generated by the Penna bit-string model: Emergence of small-world and assortative mixing

NASA Astrophysics Data System (ADS)

Li, Chunguang; Maini, Philip K.

2005-10-01

The Penna bit-string model successfully encompasses many phenomena of population evolution, including inheritance, mutation, evolution, and aging. If we consider social interactions among individuals in the Penna model, the population will form a complex network. In this paper, we first modify the Verhulst factor to control only the birth rate, and introduce activity-based preferential reproduction of offspring in the Penna model. The social interactions among individuals are generated by both inheritance and activity-based preferential increase. Then we study the properties of the complex network generated by the modified Penna model. We find that the resulting complex network has a small-world effect and the assortative mixing property.

Responses of buried corrugated metal pipes to earthquakes

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

Davis, C.A.; Bardet, J.P.

2000-01-01

This study describes the results of field investigations and analyses carried out on 61 corrugated metal pipes (CMP) that were shaken by the 1994 Northridge earthquake. These CMPs, which include 29 small-diameter (below 107 cm) CMPs and 32 large-diameter (above 107 cm) CMPs, are located within a 10 km{sup 2} area encompassing the Van Normal Complex in the Northern San Fernando Valley, in Los Angeles, California. During the Northridge earthquake, ground movements were extensively recorded within the study area. Twenty-eight of the small-diameter CMPs performed well while the 32 large-diameter CMPs underwent performances ranging from no damage to complete collapse.more » The main cause of damage to the large-diameter CMPs was found to be the large ground strains. Based on this unprecedented data set, the factors controlling the seismic performance of the 32 large-diameter CMPs were identified and framed into a pseudostatic analysis method for evaluating the response of large diameter flexible underground pipes subjected to ground strain. The proposed analysis, which is applicable to transient and permanent strains, is capable of describing the observed performance of large-diameter CMPs during the 1994 Northridge earthquake. It indicates that peak ground velocity is a more reliable parameter for analyzing pipe damage than is peak ground acceleration. Results of this field investigation and analysis are useful for the seismic design and strengthening of flexible buried conduits.« less

Create the Plan, Work the Plan: A Look at Why the Independent Business Owner Has Trouble Calling a Franchisee a True Entrepreneur

ERIC Educational Resources Information Center

Buzza, John; Mosca, Joseph B.

2009-01-01

Our complex and intricate economic system is comprised of many different types and sizes of businesses, ranging from big corporations to small individually owned entities. The genre of business is and can be profoundly complex. Independence can vary from small single person mom and pops to consortiums of multiple partners, silent partners and…

Evaluation Report: Year 2 Implementation of the Small High Schools Initiative Manual Complex, Denver, Colorado

ERIC Educational Resources Information Center

Goldfeder, Elizabeth; Ross, Steven M.

2003-01-01

This report presents the findings of a study conducted by the Center for Research in Educational Policy (CREP) on the second year of implementation of the Small Schools Initiative at the Manual High School Complex. The major goal of this research was to evaluate perceived progress and outcomes at all three high schools. The design and methodology…

FEATURE 1, SMALL GUN POSITION, VIEW FACING NORTH, (with scale ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

FEATURE 1, SMALL GUN POSITION, VIEW FACING NORTH, (with scale stick). - Naval Air Station Barbers Point, Anti-Aircraft Battery Complex-Small Gun Position, East of Coral Sea Road, northwest of Hamilton Road, Ewa, Honolulu County, HI

A Three-Hybrid System to Probe In Vivo Protein-Protein Interactions: Application to the Essential Proteins of the RD1 Complex of M. tuberculosis

PubMed Central

Bhalla, Kuhulika; Ghosh, Anamika; Kumar, Krishan; Kumar, Sushil; Ranganathan, Anand

2011-01-01

Background Protein-protein interactions play a crucial role in enabling a pathogen to survive within a host. In many cases the interactions involve a complex of proteins rather than just two given proteins. This is especially true for pathogens like M. tuberculosis that are able to successfully survive the inhospitable environment of the macrophage. Studying such interactions in detail may help in developing small molecules that either disrupt or augment the interactions. Here, we describe the development of an E. coli based bacterial three-hybrid system that can be used effectively to study ternary protein complexes. Methodology/Principal Findings The protein-protein interactions involved in M. tuberculosis pathogenesis have been used as a model for the validation of the three-hybrid system. Using the M. tuberculosis RD1 encoded proteins CFP10, ESAT6 and Rv3871 for our proof-of-concept studies, we show that the interaction between the proteins CFP10 and Rv3871 is strengthened and stabilized in the presence of ESAT6, the known heterodimeric partner of CFP10. Isolating peptide candidates that can disrupt crucial protein-protein interactions is another application that the system offers. We demonstrate this by using CFP10 protein as a disruptor of a previously established interaction between ESAT6 and a small peptide HCL1; at the same time we also show that CFP10 is not able to disrupt the strong interaction between ESAT6 and another peptide SL3. Conclusions/Significance The validation of the three-hybrid system paves the way for finding new peptides that are stronger binders of ESAT6 compared even to its natural partner CFP10. Additionally, we believe that the system offers an opportunity to study tri-protein complexes and also perform a screening of protein/peptide binders to known interacting proteins so as to elucidate novel tri-protein complexes. PMID:22087330

Cheques and challenges: business performance in New Zealand general practice.

PubMed

Greatbanks, Richard; Doolan-Noble, Fiona; McKenna, Alex

2017-09-01

INTRODUCTION New Zealand general practice mainly functions as small businesses, usually owned by a single or small group of doctors. Consequently, owners often have to balance the provision of patient care with varying funding priorities, changing patient needs and the pressures of running a sustainable business. Such balancing inevitably leads to tensions developing between these factors. AIM To explore and understand these tensions and responses to them, by examining the business performance measurements used by general practice. METHODS For this study, the unit of analysis and focus were individual practices, but qualitative semi-structured interviews with general practitioners (GPs) and practice managers were used to gather the data. RESULTS All participating practices had some form of governance or board review, where high-level aggregated business performance data were presented. More sophisticated business performance measures were evident in the larger, more developed practices and in practices functioning as community trusts. Examples of such measures included doctor utilisation and efficiency, appraisal of risk, patient satisfaction with services and responses to changes in patient demand. DISCUSSION As the number of general practices based on the traditional model decrease, a corresponding increase is likely in the establishment and development of 'super practices' based on a corporatized, multi-service, single-location model. Consequently, service delivery will become increasingly complex and will drive a need for increased sophistication in how general practice measures its business performance, thus ensuring a balance between high-quality, safe patient care and the maintenance of a sustainable business.

Testing for independence in J×K contingency tables with complex sample survey data.

PubMed

Lipsitz, Stuart R; Fitzmaurice, Garrett M; Sinha, Debajyoti; Hevelone, Nathanael; Giovannucci, Edward; Hu, Jim C

2015-09-01

The test of independence of row and column variables in a (J×K) contingency table is a widely used statistical test in many areas of application. For complex survey samples, use of the standard Pearson chi-squared test is inappropriate due to correlation among units within the same cluster. Rao and Scott (1981, Journal of the American Statistical Association 76, 221-230) proposed an approach in which the standard Pearson chi-squared statistic is multiplied by a design effect to adjust for the complex survey design. Unfortunately, this test fails to exist when one of the observed cell counts equals zero. Even with the large samples typical of many complex surveys, zero cell counts can occur for rare events, small domains, or contingency tables with a large number of cells. Here, we propose Wald and score test statistics for independence based on weighted least squares estimating equations. In contrast to the Rao-Scott test statistic, the proposed Wald and score test statistics always exist. In simulations, the score test is found to perform best with respect to type I error. The proposed method is motivated by, and applied to, post surgical complications data from the United States' Nationwide Inpatient Sample (NIS) complex survey of hospitals in 2008. © 2015, The International Biometric Society.

Continuous monitoring of enzymatic activity within native electrophoresis gels: Application to mitochondrial oxidative phosphorylation complexes

PubMed Central

Covian, Raul; Chess, David; Balaban, Robert S.

2012-01-01

Native gel electrophoresis allows the separation of very small amounts of protein complexes while retaining aspects of their activity. In-gel enzymatic assays are usually performed by using reaction-dependent deposition of chromophores or light scattering precipitates quantified at fixed time points after gel removal and fixation, limiting the ability to analyze enzyme reaction kinetics. Herein, we describe a custom reaction chamber with reaction media recirculation and filtering and an imaging system that permits the continuous monitoring of in-gel enzymatic activity even in the presence of turbidity. Images were continuously collected using time-lapse high resolution digital imaging, and processing routines were developed to obtain kinetic traces of the in-gel activities and analyze reaction time courses. This system also permitted the evaluation of enzymatic activity topology within the protein bands of the gel. This approach was used to analyze the reaction kinetics of two mitochondrial complexes in native gels. Complex IV kinetics showed a short initial linear phase where catalytic rates could be calculated, whereas Complex V activity revealed a significant lag phase followed by two linear phases. The utility of monitoring the entire kinetic behavior of these reactions in native gels, as well as the general application of this approach, is discussed. PMID:22975200

Continuous monitoring of enzymatic activity within native electrophoresis gels: application to mitochondrial oxidative phosphorylation complexes.

PubMed

Covian, Raul; Chess, David; Balaban, Robert S

2012-12-01

Native gel electrophoresis allows the separation of very small amounts of protein complexes while retaining aspects of their activity. In-gel enzymatic assays are usually performed by using reaction-dependent deposition of chromophores or light-scattering precipitates quantified at fixed time points after gel removal and fixation, limiting the ability to analyze the enzyme reaction kinetics. Herein, we describe a custom reaction chamber with reaction medium recirculation and filtering and an imaging system that permits the continuous monitoring of in-gel enzymatic activity even in the presence of turbidity. Images were continuously collected using time-lapse high-resolution digital imaging, and processing routines were developed to obtain kinetic traces of the in-gel activities and analyze reaction time courses. This system also permitted the evaluation of enzymatic activity topology within the protein bands of the gel. This approach was used to analyze the reaction kinetics of two mitochondrial complexes in native gels. Complex IV kinetics showed a short initial linear phase in which catalytic rates could be calculated, whereas Complex V activity revealed a significant lag phase followed by two linear phases. The utility of monitoring the entire kinetic behavior of these reactions in native gels, as well as the general application of this approach, is discussed. Published by Elsevier Inc.

Linear quadratic Gaussian and feedforward controllers for the DSS-13 antenna

NASA Technical Reports Server (NTRS)

Gawronski, W. K.; Racho, C. S.; Mellstrom, J. A.

1994-01-01

The controller development and the tracking performance evaluation for the DSS-13 antenna are presented. A trajectory preprocessor, linear quadratic Gaussian (LQG) controller, feedforward controller, and their combination were designed, built, analyzed, and tested. The antenna exhibits nonlinear behavior when the input to the antenna and/or the derivative of this input exceeds the imposed limits; for slewing and acquisition commands, these limits are typically violated. A trajectory preprocessor was designed to ensure that the antenna behaves linearly, just to prevent nonlinear limit cycling. The estimator model for the LQG controller was identified from the data obtained from the field test. Based on an LQG balanced representation, a reduced-order LQG controller was obtained. The feedforward controller and the combination of the LQG and feedforward controller were also investigated. The performance of the controllers was evaluated with the tracking errors (due to following a trajectory) and the disturbance errors (due to the disturbances acting on the antenna). The LQG controller has good disturbance rejection properties and satisfactory tracking errors. The feedforward controller has small tracking errors but poor disturbance rejection properties. The combined LQG and feedforward controller exhibits small tracking errors as well as good disturbance rejection properties. However, the cost for this performance is the complexity of the controller.

Adaptive matched filter spatial detection performance on standard imagery from a wideband VHF/UHF SAR

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

Allen, M.R.; Phillips, S.A.; Sofianos, D.J.

1994-12-31

The adaptive matched filter was implemented as a spatial detector for amplitude-only or complex images, and applied to an image formed by standard narrow band means from a wide angle, wideband radar. Direct performance comparisons were made between different implementations and various matched and mismatched cases by using a novel approach to generate ROC curves parametrically. For perfectly matched cases, performance using imaged targets was found to be significantly lower than potential performance of artificial targets whose features differed from the background. Incremental gain due to whitening the background was also found to be small, indicating little background spatial correlation.more » It is conjectured that the relatively featureless behavior in both targets and background is due to the image formation process, since this technique averages together all wide angle, wideband information. For mismatched cases where the signature was unknown, the amplitude detector losses were approximately equal to whatever gain over noncoherent integration that matching provided. However, the complex detector was generally very sensitive to unknown information, especially phase, and produced much larger losses. Whitening under these mismatched conditions produced further losses. Detector choice thus depends primarily on how reproducible target signatures are, especially if phase is used, and the subsequent number of stored signatures necessary to account for various imaging aspect angles.« less

Effect of 18β-glycyrrhetinic acid and hydroxypropyl γcyclodextrin complex on indomethacin-induced small intestinal injury in mice.

PubMed

Ishida, Tsukasa; Miki, Ikuya; Tanahashi, Toshihito; Yagi, Saori; Kondo, Yasuyuki; Inoue, Jun; Kawauchi, Shoji; Nishiumi, Sin; Yoshida, Masaru; Maeda, Hideko; Tode, Chisato; Takeuchi, Atsuko; Nakayama, Hirokazu; Azuma, Takeshi; Mizuno, Shigeto

2013-08-15

Non-steroidal anti-inflammatory drugs (NSAIDs)-induced small intestinal injury is a serious clinical event with recent advances of diagnostic technologies, but a successful therapeutic method to treat such injuries is still lacking. Licorice, a traditional herbal medicine, and its derivatives have been widely used for the treatment of a variety of diseases due to their extensive biological actions. However, it is unknown whether these derivatives have an effect on NSAIDs-induced small intestinal damage. Previously, the anti-inflammatory effects of three compounds extracted from the licorice root, glycyrrhizin, 18β-glycyrrhetinic acid, and dipotassium glycyrrhizinate, were compared in vitro cell culture. The most prominent inhibitory effect on the tumor necrosis factor-α (TNF-α) production was observed with the administration of 18β-glycyrrhetinic acid as an active metabolite of glycyrrhizin. In this study, a complex compound of 18β-glycyrrhetinic acid and hydroxypropyl γcyclodextrin was examined to improve the oral bioavailability. After administration of this complex to indomethacin treated mice, a significantly high plasma concentration of 18β-glycyrrhetinic acid was detected using the tandem mass spectrometry coupled with the HPLC. Furthermore, the complex form of 18β-glycyrrhetinic acid and hydroxypropyl γcyclodextrin reduced mRNA expressions of TNF-α, interleukin (IL)-1β, and IL-6, which was histologically confirmed in the improvement of indomethacin-induced small intestinal damage. These results suggest that the complex of 18β-glycyrrhetinic acid and hydroxypropyl γcyclodextrin has the potential therapeutic value for preventing the adverse effects of indomethacin-induced small intestinal injury. Copyright © 2013 Elsevier B.V. All rights reserved.

First-principles study of stability of helium-vacancy complexes below tungsten surfaces

NASA Astrophysics Data System (ADS)

Yang, L.; Bergstrom, Z. J.; Wirth, B. D.

2018-05-01

Density function theory calculations have been performed to study the stability of small helium-vacancy (He-V) complexes near tungsten (W) surfaces of different orientations. The results show that the stability of vacancies and He-V complexes near W surfaces depends on surface orientation. However, as the depth below the surface increased beyond about 0.65-0.8 nm, the stability of He-V complexes is similar to the bulk. The formation energies of single vacancies and di-vacancies at depths less than 0.2 nm below the W(110) surface are higher than for W(100) or W(111) surfaces, but have lower energies at depths between 0.2 and 0.65 nm. The formation energies of He-V complexes below W surfaces are sensitive to the geometric orientation of the He and vacancy, especially below the W(111) surface. Within about 0.2 nm of the top layer of the three W surfaces, neither a vacancy nor a di-vacancy can trap He. Because of the lower formation energy of He-V complexes and higher He binding energy to vacancies below the W(110) surface, the He desorption from the W(110) surface is less likely to occur than from the W(100) and W(111) surfaces. Our results provide fundamental insight into the differences in surface morphology changes observed in single W crystals with different surface orientations under He plasma exposure.

Construction of a fuzzy and Boolean logic gates based on DNA.

PubMed

Zadegan, Reza M; Jepsen, Mette D E; Hildebrandt, Lasse L; Birkedal, Victoria; Kjems, Jørgen

2015-04-17

Logic gates are devices that can perform logical operations by transforming a set of inputs into a predictable single detectable output. The hybridization properties, structure, and function of nucleic acids can be used to make DNA-based logic gates. These devices are important modules in molecular computing and biosensing. The ideal logic gate system should provide a wide selection of logical operations, and be integrable in multiple copies into more complex structures. Here we show the successful construction of a small DNA-based logic gate complex that produces fluorescent outputs corresponding to the operation of the six Boolean logic gates AND, NAND, OR, NOR, XOR, and XNOR. The logic gate complex is shown to work also when implemented in a three-dimensional DNA origami box structure, where it controlled the position of the lid in a closed or open position. Implementation of multiple microRNA sensitive DNA locks on one DNA origami box structure enabled fuzzy logical operation that allows biosensing of complex molecular signals. Integrating logic gates with DNA origami systems opens a vast avenue to applications in the fields of nanomedicine for diagnostics and therapeutics. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a combined Docking and QM/MM MD Study.

NASA Astrophysics Data System (ADS)

Hitzenberger, Manuel; Schuster, Daniela; Hofer, Thomas S.

2017-10-01

Erroneous activation of the Hedgehog pathway has been linked to a great amount of cancerous diseases and therefore a large number of studies aiming at its inhibition have been carried out. One leverage point for novel therapeutic strategies targeting the proteins involved, is the prevention of complex formation between the extracellular signaling protein Sonic Hedgehog and the transmembrane protein Patched 1. In 2009 robotnikinin, a small molecule capable of binding to and inhibiting the activity of Sonic Hedgehog has been identified, however in the absence of X-ray structures of the Sonic Hedgehog-robotnikinin complex, the binding mode of this inhibitor remains unknown. In order to aid with the identification of novel Sonic Hedgehog inhibitors, the presented investigation elucidates the binding mode of robotnikinin by performing an extensive docking study, including subsequent molecular mechanical as well as quantum mechanical/molecular mechanical molecular dynamics simulations. The attained configurations enabled the identification of a number of key protein-ligand interactions, aiding complex formation and providing stabilizing contributions to the binding of the ligand. The predicted structure of the Sonic Hedgehog-robotnikinin complex is provided via a PDB file as supplementary material and can be used for further reference.

Solid State Pathways towards Molecular Complexity in Space

NASA Astrophysics Data System (ADS)

Linnartz, Harold; Bossa, Jean-Baptiste; Bouwman, Jordy; Cuppen, Herma M.; Cuylle, Steven H.; van Dishoeck, Ewine F.; Fayolle, Edith C.; Fedoseev, Gleb; Fuchs, Guido W.; Ioppolo, Sergio; Isokoski, Karoliina; Lamberts, Thanja; Öberg, Karin I.; Romanzin, Claire; Tenenbaum, Emily; Zhen, Junfeng

2011-12-01

It has been a long standing problem in astrochemistry to explain how molecules can form in a highly dilute environment such as the interstellar medium. In the last decennium more and more evidence has been found that the observed mix of small and complex, stable and highly transient species in space is the cumulative result of gas phase and solid state reactions as well as gas-grain interactions. Solid state reactions on icy dust grains are specifically found to play an important role in the formation of the more complex ``organic'' compounds. In order to investigate the underlying physical and chemical processes detailed laboratory based experiments are needed that simulate surface reactions triggered by processes as different as thermal heating, photon (UV) irradiation and particle (atom, cosmic ray, electron) bombardment of interstellar ice analogues. Here, some of the latest research performed in the Sackler Laboratory for Astrophysics in Leiden, the Netherlands is reviewed. The focus is on hydrogenation, i.e., H-atom addition reactions and vacuum ultraviolet irradiation of interstellar ice analogues at astronomically relevant temperatures. It is shown that solid state processes are crucial in the chemical evolution of the interstellar medium, providing pathways towards molecular complexity in space.

Protoenzymes: the case of hyperbranched polyesters

NASA Astrophysics Data System (ADS)

Mamajanov, Irena; Cody, George D.

2017-11-01

Enzymes are biopolymeric complexes that catalyse biochemical reactions and shape metabolic pathways. Enzymes usually work with small molecule cofactors that actively participate in reaction mechanisms and complex, usually globular, polymeric structures capable of specific substrate binding, encapsulation and orientation. Moreover, the globular structures of enzymes possess cavities with modulated microenvironments, facilitating the progression of reaction(s). The globular structure is ensured by long folded protein or RNA strands. Synthesis of such elaborate complexes has proven difficult under prebiotically plausible conditions. We explore here that catalysis may have been performed by alternative polymeric structures, namely hyperbranched polymers. Hyperbranched polymers are relatively complex structures that can be synthesized under prebiotically plausible conditions; their globular structure is ensured by virtue of their architecture rather than folding. In this study, we probe the ability of tertiary amine-bearing hyperbranched polyesters to form hydrophobic pockets as a reaction-promoting medium for the Kemp elimination reaction. Our results show that polyesters formed upon reaction between glycerol, triethanolamine and organic acid containing hydrophobic groups, i.e. adipic and methylsuccinic acid, are capable of increasing the rate of Kemp elimination by a factor of up to 3 over monomeric triethanolamine. This article is part of the themed issue 'Reconceptualizing the origins of life'.

EBLAST: an efficient high-compression image transformation 3. application to Internet image and video transmission

NASA Astrophysics Data System (ADS)

Schmalz, Mark S.; Ritter, Gerhard X.; Caimi, Frank M.

2001-12-01

A wide variety of digital image compression transforms developed for still imaging and broadcast video transmission are unsuitable for Internet video applications due to insufficient compression ratio, poor reconstruction fidelity, or excessive computational requirements. Examples include hierarchical transforms that require all, or large portion of, a source image to reside in memory at one time, transforms that induce significant locking effect at operationally salient compression ratios, and algorithms that require large amounts of floating-point computation. The latter constraint holds especially for video compression by small mobile imaging devices for transmission to, and compression on, platforms such as palmtop computers or personal digital assistants (PDAs). As Internet video requirements for frame rate and resolution increase to produce more detailed, less discontinuous motion sequences, a new class of compression transforms will be needed, especially for small memory models and displays such as those found on PDAs. In this, the third series of papers, we discuss the EBLAST compression transform and its application to Internet communication. Leading transforms for compression of Internet video and still imagery are reviewed and analyzed, including GIF, JPEG, AWIC (wavelet-based), wavelet packets, and SPIHT, whose performance is compared with EBLAST. Performance analysis criteria include time and space complexity and quality of the decompressed image. The latter is determined by rate-distortion data obtained from a database of realistic test images. Discussion also includes issues such as robustness of the compressed format to channel noise. EBLAST has been shown to perform superiorly to JPEG and, unlike current wavelet compression transforms, supports fast implementation on embedded processors with small memory models.

Photovoltaic performance models - A report card

NASA Technical Reports Server (NTRS)

Smith, J. H.; Reiter, L. R.

1985-01-01

Models for the analysis of photovoltaic (PV) systems' designs, implementation policies, and economic performance, have proliferated while keeping pace with rapid changes in basic PV technology and extensive empirical data compiled for such systems' performance. Attention is presently given to the results of a comparative assessment of ten well documented and widely used models, which range in complexity from first-order approximations of PV system performance to in-depth, circuit-level characterizations. The comparisons were made on the basis of the performance of their subsystem, as well as system, elements. The models fall into three categories in light of their degree of aggregation into subsystems: (1) simplified models for first-order calculation of system performance, with easily met input requirements but limited capability to address more than a small variety of design considerations; (2) models simulating PV systems in greater detail, encompassing types primarily intended for either concentrator-incorporating or flat plate collector PV systems; and (3) models not specifically designed for PV system performance modeling, but applicable to aspects of electrical system design. Models ignoring subsystem failure or degradation are noted to exclude operating and maintenance characteristics as well.

Chemodynamics of aquatic metal complexes: from small ligands to colloids.

PubMed

Van Leeuwen, Herman P; Buffle, Jacques

2009-10-01

Recent progress in understanding the formation/dissociation kinetics of aquatic metal complexes with complexants in different size ranges is evaluated and put in perspective, with suggestions for further studies. The elementary steps in the Eigen mechanism, i.e., diffusion and dehydration of the metal ion, are reviewed and further developed. The (de)protonation of both the ligand and the coordinating metal ion is reconsidered in terms of the consequences for dehydration rates and stabilities of the various outer-sphere complexes. In the nanoparticulate size range, special attention is given to the case of fulvic ligands, for which the impact of electrostatic interactions is especially large. In complexation with colloidal ligands (hard, soft, and combination thereof) the diffusive transport of metal ions is generally a slower step than in the case of complexation with small ligands in a homogeneous solution. The ensuing consequences for the chemodynamics of colloidal complexes are discussed in detail and placed in a generic framework, encompassing the complete range of ligand sizes.

Small Schools in the Big City: Neoliberalism, Bureaucracy and the Sustainability of Small by Design Schools in Chicago

ERIC Educational Resources Information Center

Pitluck, Corrin

2010-01-01

Assuming the strength of small by design schools for poor urban students of color to be a settled question, this project attempts to analyze the sustainability of small by design schools in a large, complex urban district. Asking what causes small schools to converge toward or diverge from the small by design model, I analyze three sets of design…

In-vitro simulation of luminal conditions for evaluation of performance of oral drug products: Choosing the appropriate test media.

PubMed

Markopoulos, Constantinos; Andreas, Cord J; Vertzoni, Maria; Dressman, Jennifer; Reppas, Christos

2015-06-01

Biorelevant media for evaluation of dosage form performance in the gastrointestinal lumen were first introduced in the late 1990s. Since then, a variety of additional media have been proposed, making it now possible to simulate most regions in the gastrointestinal tract in both prandial states. However, recent work suggests that the complexity and degree of biorelevance required to predict in-vivo release varies with the drug, dosage form and dosing conditions. The aim of this commentary was to establish which levels of biorelevant media are appropriate to various combinations of active pharmaceutical ingredient(s), dosage form and dosing conditions. With regard to their application, a decision tree for the selection of the appropriate biorelevant medium/media is proposed and illustrative case scenarios are provided. Additionally, media to represent the distal small intestine in both prandial states are presented. The newly proposed levels of biorelevance and accompanying decision tree may serve as a useful tool during formulation development in order to ensure high quality, predictive performance results without unnecessary complexity of media. In future work, further specific case examples will be evolved, which will additionally address the need to take gastrointestinal passage times and type and intensity of agitation into consideration. Copyright © 2015 Elsevier B.V. All rights reserved.

Acquisition of dental skills in preclinical technique courses: influence of spatial and manual abilities.

PubMed

Schwibbe, Anja; Kothe, Christian; Hampe, Wolfgang; Konradt, Udo

2016-10-01

Sixty years of research have not added up to a concordant evaluation of the influence of spatial and manual abilities on dental skill acquisition. We used Ackerman's theory of ability determinants of skill acquisition to explain the influence of spatial visualization and manual dexterity on the task performance of dental students in two consecutive preclinical technique courses. We measured spatial and manual abilities of applicants to Hamburg Dental School by means of a multiple choice test on Technical Aptitude and a wire-bending test, respectively. Preclinical dental technique tasks were categorized as consistent-simple and inconsistent-complex based on their contents. For analysis, we used robust regression to circumvent typical limitations in dental studies like small sample size and non-normal residual distributions. We found that manual, but not spatial ability exhibited a moderate influence on the performance in consistent-simple tasks during dental skill acquisition in preclinical dentistry. Both abilities revealed a moderate relation with the performance in inconsistent-complex tasks. These findings support the hypotheses which we had postulated on the basis of Ackerman's work. Therefore, spatial as well as manual ability are required for the acquisition of dental skills in preclinical technique courses. These results support the view that both abilities should be addressed in dental admission procedures in addition to cognitive measures.

Scaling Up Graph-Based Semisupervised Learning via Prototype Vector Machines

PubMed Central

Zhang, Kai; Lan, Liang; Kwok, James T.; Vucetic, Slobodan; Parvin, Bahram

2014-01-01

When the amount of labeled data are limited, semi-supervised learning can improve the learner's performance by also using the often easily available unlabeled data. In particular, a popular approach requires the learned function to be smooth on the underlying data manifold. By approximating this manifold as a weighted graph, such graph-based techniques can often achieve state-of-the-art performance. However, their high time and space complexities make them less attractive on large data sets. In this paper, we propose to scale up graph-based semisupervised learning using a set of sparse prototypes derived from the data. These prototypes serve as a small set of data representatives, which can be used to approximate the graph-based regularizer and to control model complexity. Consequently, both training and testing become much more efficient. Moreover, when the Gaussian kernel is used to define the graph affinity, a simple and principled method to select the prototypes can be obtained. Experiments on a number of real-world data sets demonstrate encouraging performance and scaling properties of the proposed approach. It also compares favorably with models learned via ℓ1-regularization at the same level of model sparsity. These results demonstrate the efficacy of the proposed approach in producing highly parsimonious and accurate models for semisupervised learning. PMID:25720002

Isolation and characterization of the stage-specific cytochrome b small subunit (CybS) of Ascaris suum complex II from the aerobic respiratory chain of larval mitochondria.

PubMed

Amino, Hisako; Osanai, Arihiro; Miyadera, Hiroko; Shinjyo, Noriko; Tomitsuka, Eriko; Taka, Hikari; Mineki, Reiko; Murayama, Kimie; Takamiya, Shinzaburo; Aoki, Takashi; Miyoshi, Hideto; Sakamoto, Kimitoshi; Kojima, Somei; Kita, Kiyoshi

2003-05-01

We recently reported that Ascaris suum mitochondria express stage-specific isoforms of complex II: the flavoprotein subunit and the small subunit of cytochrome b (CybS) of the larval complex II differ from those of adult enzyme, while two complex IIs share a common iron-sulfur cluster subunit (Ip). In the present study, A. suum larval complex II was highly purified to characterize the larval cytochrome b subunits in more detail. Peptide mass fingerprinting and N-terminal amino acid sequencing showed that the larval and adult cytochrome b (CybL) proteins are identical. In contrast, cDNA sequences revealed that the small subunit of larval cytochrome b (CybS(L)) is distinct from the adult CybS (CybS(A)). Furthermore, Northern analysis and immunoblotting showed stage-specific expression of CybS(L) and CybS(A) in larval and adult mitochondria, respectively. Enzymatic assays revealed that the ratio of rhodoquinol-fumarate reductase (RQFR) to succinate-ubiquinone reductase (SQR) activities and the K(m) values for quinones are almost identical for the adult and larval complex IIs, but that the fumarate reductase (FRD) activity is higher for the adult form than for the larval form. These results indicate that the adult and larval A. suum complex IIs have different properties than the complex II of the mammalian host and that the larval complex II is able to function as a RQFR. Such RQFR activity of the larval complex II would be essential for rapid adaptation to the dramatic change of oxygen availability during infection of the host.

Clinical outcomes in real-world patients with small vessel disease treated with XIENCE V® everolimus-eluting stents: one year results from the XIENCE V® USA condition of approval post-market study.

PubMed

Hermiller, James B; Rutledge, David R; Mao, Vivian W; Zhao, Weiying; Wang, Jin; Gruberg, Luis; Lombardi, William; Sharma, Samin K; Krucoff, Mitchell W

2014-07-01

The purpose of this study was to evaluate the 1-year clinical outcomes of more complex XIENCE V USA real-world patients with small versus nonsmall vessel lesions. Patients with small vessel lesions undergoing coronary stent placement are at higher risk of major adverse cardiac events. Improved safety and efficacy of XIENCE V everolimus eluting stents (EES) have been previously demonstrated in selected low-risk small vessel populations in randomized clinical trials. The XIENCE V USA study was a condition of approval, single-arm study in unselected real-world patients. Baseline and 1-year clinical outcomes were compared between XIENCE V USA patients who received a single 2.5 mm stent (small vessel group, N = 838) and patients implanted with a single >2.5 mm stent (non-small vessel group, N = 2,015). Mean reference vessel diameter was 2.55 ± 0.36 and 3.25 ± 0.46 mm in the small and non-small vessel groups, respectively (P < 0.001). Small vessel group had more females, presented with a higher rate of diabetes, and had more complex lesion characteristics. The definite or probable ST rates analyzed using Kaplan-Meier method were low and not significantly different between the groups at 0.37 and 0.40% for the small and nonsmall vessel group (P = 0.88), respectively. The composite rate of cardiac death or MI was comparable at 4.5% for the small and 5.1% for the non-small vessel 1 groups (P = 0.57). The 1-year target lesion revascularization rate was also comparable in the small vessel group (3.8% vs. 3.0%, P = 0.35). Despite gender difference, higher prevalence of diabetes and more complex lesions in the small vessel groups, the 1-year clinical outcomes were similar in both small and nonsmall vessel groups. These results demonstrate the therapeutic benefit of XIENCE V EES in a real-world all inclusive patient population with small vessel disease. © 2013 Wiley Periodicals, Inc.

Chronic Intestinal Pseudo-obstruction: Clinical and Manometric Characteristics in the Chilean Population

PubMed Central

de Arce, Edith Pérez; Landskron, Glauben; Hirsch, Sandra; Defilippi, Carlos; Madrid, Ana María

2017-01-01

Background/Aims Chronic intestinal pseudo-obstruction (CIPO) is a rare syndrome characterized by a failure of the propulsion of intraluminal contents and recurrent symptoms of partial bowel obstruction in the absence of mechanical obstruction. Regional variations of the intestinal compromise have been described. Intestinal manometry can indicate the pathophysiology and prognosis. Our objective is to establish the demographic and clinical characteristics of group Chilean patients and analyze the motility of the small intestine and its prognostic value. Methods Patients with symptoms of intestinal pseudo-obstruction with dilated bowel loops were included, in all of whom a manometry of the small intestine was performed using perfused catheters. Results Of the 64 patients included, 51 women (average age 41.5 ± 17.6 years), 54 primary and 10 secondary CIPO were included. Dilatation of the small intestine was the only finding in 38 patients; in the remaining, the compromise was associated with other segments, primarily the colon. Forty-nine patients underwent 65 surgeries, mainly exploratory laparotomies and colectomies. Intestinal manometry was performed on all patients; 4 “patterns” were observed: neuropathic (n = 26), myopathic (n = 3), mixed (n = 24), and a group without motor activity (n = 11). The most relevant findings were the complex migrating motor disorders and decreased frequency and propagation of contractions. The 9 patients who died had a severe myopathic compromise. Conclusions In our series, isolated small bowel compromise was the most common disorder. Neuropathic motor compromise was observed in most of the patients. Mortality was associated with severe myopathic compromise. PMID:27669829

12 CFR 25.26 - Small bank performance standards.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 12 Banks and Banking 1 2011-01-01 2011-01-01 false Small bank performance standards. 25.26 Section... REINVESTMENT ACT AND INTERSTATE DEPOSIT PRODUCTION REGULATIONS Regulations Standards for Assessing Performance § 25.26 Small bank performance standards. (a) Performance criteria—(1) Small banks that are not...

12 CFR 25.26 - Small bank performance standards.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 1 2010-01-01 2010-01-01 false Small bank performance standards. 25.26 Section... REINVESTMENT ACT AND INTERSTATE DEPOSIT PRODUCTION REGULATIONS Regulations Standards for Assessing Performance § 25.26 Small bank performance standards. (a) Performance criteria—(1) Small banks that are not...

The Retrospective Iterated Analysis Scheme for Nonlinear Chaotic Dynamics

NASA Technical Reports Server (NTRS)

Todling, Ricardo

2002-01-01

Atmospheric data assimilation is the name scientists give to the techniques of blending atmospheric observations with atmospheric model results to obtain an accurate idea of what the atmosphere looks like at any given time. Because two pieces of information are used, observations and model results, the outcomes of data assimilation procedure should be better than what one would get by using one of these two pieces of information alone. There is a number of different mathematical techniques that fall under the data assimilation jargon. In theory most these techniques accomplish about the same thing. In practice, however, slight differences in the approaches amount to faster algorithms in some cases, more economical algorithms in other cases, and even give better overall results in yet some other cases because of practical uncertainties not accounted for by theory. Therefore, the key is to find the most adequate data assimilation procedure for the problem in hand. In our Data Assimilation group we have been doing extensive research to try and find just such data assimilation procedure. One promising possibility is what we call retrospective iterated analysis (RIA) scheme. This procedure has recently been implemented and studied in the context of a very large data assimilation system built to help predict and study weather and climate. Although the results from that study suggest that the RIA scheme produces quite reasonable results, a complete evaluation of the scheme is very difficult due to the complexity of that problem. The present work steps back a little bit and studies the behavior of the RIA scheme in the context of a small problem. The problem is small enough to allow full assessment of the quality of the RIA scheme, but it still has some of the complexity found in nature, namely, its chaotic-type behavior. We find that the RIA performs very well for this small but still complex problem which is a result that seconds the results of our early studies.

A Study of Ship Acquisition Cost Estimating in the Naval Sea Systems Command. Appendices

DTIC Science & Technology

1977-10-01

Shipbuilding Is A Heovy Fabrication Industry Pro- ducing Small Numbers Of Expensive, Complex Units Of Output PAGE A-2 (1) Due to its heavy ...estimate future ship construction costs. - A-l 1. SHIPBUILDING IS A HEAVY FABRICATION INDUSTRY PRODUCING SMALL NUMBERS OF EXPENSIVE, COMPLEX...extensively in production line industries such as automotive products and the airframe industry. (1) Due To Its Heavy Construction Orientation

Greased Lightning (GL-10) Performance Flight Research: Flight Data Report

NASA Technical Reports Server (NTRS)

McSwain, Robert G.; Glaab, Louis J.; Theodore, Colin R.; Rhew, Ray D. (Editor); North, David D. (Editor)

2017-01-01

Modern aircraft design methods have produced acceptable designs for large conventional aircraft performance. With revolutionary electronic propulsion technologies fueled by the growth in the small UAS (Unmanned Aerial Systems) industry, these same prediction models are being applied to new smaller, and experimental design concepts requiring a VTOL (Vertical Take Off and Landing) capability for ODM (On Demand Mobility). A 50% sub-scale GL-10 flight model was built and tested to demonstrate the transition from hover to forward flight utilizing DEP (Distributed Electric Propulsion)[1][2]. In 2016 plans were put in place to conduct performance flight testing on the 50% sub-scale GL-10 flight model to support a NASA project called DELIVER (Design Environment for Novel Vertical Lift Vehicles). DELIVER was investigating the feasibility of including smaller and more experimental aircraft configurations into a NASA design tool called NDARC (NASA Design and Analysis of Rotorcraft)[3]. This report covers the performance flight data collected during flight testing of the GL-10 50% sub-scale flight model conducted at Beaver Dam Airpark, VA. Overall the flight test data provides great insight into how well our existing conceptual design tools predict the performance of small scale experimental DEP concepts. Low fidelity conceptual design tools estimated the (L/D)( sub max)of the GL-10 50% sub-scale flight model to be 16. Experimentally measured (L/D)( sub max) for the GL-10 50% scale flight model was 7.2. The aerodynamic performance predicted versus measured highlights the complexity of wing and nacelle interactions which is not currently accounted for in existing low fidelity tools.

DFT Performance Prediction in FFTW

NASA Astrophysics Data System (ADS)

Gu, Liang; Li, Xiaoming

Fastest Fourier Transform in the West (FFTW) is an adaptive FFT library that generates highly efficient Discrete Fourier Transform (DFT) implementations. It is one of the fastest FFT libraries available and it outperforms many adaptive or hand-tuned DFT libraries. Its success largely relies on the huge search space spanned by several FFT algorithms and a set of compiler generated C code (called codelets) for small size DFTs. FFTW empirically finds the best algorithm by measuring the performance of different algorithm combinations. Although the empirical search works very well for FFTW, the search process does not explain why the best plan found performs best, and the search overhead grows polynomially as the DFT size increases. The opposite of empirical search is model-driven optimization. However, it is widely believed that model-driven optimization is inferior to empirical search and is particularly powerless to solve problems as complex as the optimization of DFT.

Visualizing request-flow comparison to aid performance diagnosis in distributed systems.

PubMed

Sambasivan, Raja R; Shafer, Ilari; Mazurek, Michelle L; Ganger, Gregory R

2013-12-01

Distributed systems are complex to develop and administer, and performance problem diagnosis is particularly challenging. When performance degrades, the problem might be in any of the system's many components or could be a result of poor interactions among them. Recent research efforts have created tools that automatically localize the problem to a small number of potential culprits, but research is needed to understand what visualization techniques work best for helping distributed systems developers understand and explore their results. This paper compares the relative merits of three well-known visualization approaches (side-by-side, diff, and animation) in the context of presenting the results of one proven automated localization technique called request-flow comparison. Via a 26-person user study, which included real distributed systems developers, we identify the unique benefits that each approach provides for different problem types and usage modes.

Phase behavior and structure of stable complexes between a long polyanion and a branched polycation

NASA Astrophysics Data System (ADS)

Mengarelli, Valentina; Zeghal, Mehdi; Auvray, Loïc; Clemens, Daniel

2011-08-01

The association between oppositely charged branched polyethylenimine (BPEI) and polymethacrylic acid (PMA) in the dilute regime is investigated using turbidimetric titration and electrophoretic mobility measurements. The complexation is controlled by tuning continuously the pH-sensitive charge of the polyacid in acidic solution. The formation of soluble and stable positively charged complexes is a cooperative process characterized by the existence of two regimes of weak and strong complexation. In the regime of weak complexation, a long PMA chain overcharged by several BPEI molecules forms a binary complex. As the charge of the polyacid increases, these binary complexes condense at a well defined charge ratio of the mixture to form large positively charged aggregates. The overcharging and the existence of two regimes of complexation are analyzed in the light of recent theories. The structure of the polyelectrolytes is investigated at higher polymer concentration by small angle neutron scattering. Binary complexes of finite size present an open structure where the polyacid chains connecting a small number of BPEI molecules have shrunk slightly. In the condensed complexes, BPEI molecules, wrapped by polyacid chains, form networks of stretched necklaces.

Realtime Compositing of Procedural Facade Textures on the Gpu

NASA Astrophysics Data System (ADS)

Krecklau, L.; Kobbelt, L.

2011-09-01

The real time rendering of complex virtual city models has become more important in the last few years for many practical applications like realistic navigation or urban planning. For maximum rendering performance, the complexity of the geometry or textures can be reduced by decreasing the resolution until the data set can fully reside on the memory of the graphics card. This typically results in a low quality of the virtual city model. Alternatively, a streaming algorithm can load the high quality data set from the hard drive. However, this approach requires a large amount of persistent storage providing several gigabytes of static data. We present a system that uses a texture atlas containing atomic tiles like windows, doors or wall patterns, and that combines those elements on-the-fly directly on the graphics card. The presented approach benefits from a sophisticated randomization approach that produces lots of different facades while the grammar description itself remains small. By using a ray casting apporach, we are able to trace through transparent windows revealing procedurally generated rooms which further contributes to the realism of the rendering. The presented method enables real time rendering of city models with a high level of detail for facades while still relying on a small memory footprint.

[Craniometrical study of the species complex of Meriones shawii-grandis (Mammalia: Rodentia) in Morocco, in Algeria and in Tunisia].

PubMed

Djelaila, Yassine; Denys, Christiane; Stoetzel, Emmanuelle; Cornette, Raphaël; Lalis, Aude; Adamou-Djerbaoui, Malika; Boukhemza, Mohamed

2018-01-01

In North Africa, the rodents of the species complex Meriones shawii-grandis have a considerable ecological, economic and epidemiological importance. Until now, the systematics of these species was subject to discussion due to the presence of populations displaying high morphological variability. By means of an approach of traditional morphometrics based on cranial distances and by using the method of the log shape-ratio, we attempt to characterize morphologically these two taxa. The results show significant differences in size and shape between the specimens of Morocco, on the one hand, and those of Algeria and Tunisia, on the other hand. The samples of Morocco that have been molecularly typed and attributed to M. grandis have larger tooth rows and narrower skulls, as well as relatively small tympanic bullae. On the other hand, those of Algeria and Tunisia assigned to M. shawii are characterized by small tooth rows and wide skulls with well-developed tympanic bullae. The morphological distance is relatively strong between both clades (79.5%), which corresponds to the molecular distance. However, the discriminant analysis performed after molecularly-typed specimens allows the correct classification of only 91.8% of the individuals. Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Biologically inspired collision avoidance system for unmanned vehicles

NASA Astrophysics Data System (ADS)

Ortiz, Fernando E.; Graham, Brett; Spagnoli, Kyle; Kelmelis, Eric J.

2009-05-01

In this project, we collaborate with researchers in the neuroscience department at the University of Delaware to develop an Field Programmable Gate Array (FPGA)-based embedded computer, inspired by the brains of small vertebrates (fish). The mechanisms of object detection and avoidance in fish have been extensively studied by our Delaware collaborators. The midbrain optic tectum is a biological multimodal navigation controller capable of processing input from all senses that convey spatial information, including vision, audition, touch, and lateral-line (water current sensing in fish). Unfortunately, computational complexity makes these models too slow for use in real-time applications. These simulations are run offline on state-of-the-art desktop computers, presenting a gap between the application and the target platform: a low-power embedded device. EM Photonics has expertise in developing of high-performance computers based on commodity platforms such as graphic cards (GPUs) and FPGAs. FPGAs offer (1) high computational power, low power consumption and small footprint (in line with typical autonomous vehicle constraints), and (2) the ability to implement massively-parallel computational architectures, which can be leveraged to closely emulate biological systems. Combining UD's brain modeling algorithms and the power of FPGAs, this computer enables autonomous navigation in complex environments, and further types of onboard neural processing in future applications.

Comparing reactive and memory-one strategies of direct reciprocity

NASA Astrophysics Data System (ADS)

Baek, Seung Ki; Jeong, Hyeong-Chai; Hilbe, Christian; Nowak, Martin A.

2016-05-01

Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player’s previous move, and memory-one strategies, which take into account the own and the co-player’s previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation.

Comparing the Properties of Electrochemical-Based DNA Sensors Employing Different Redox Tags

PubMed Central

Kang, Di; Zuo, Xiaolei; Yang, Renqiang; Xia, Fan; Plaxco, Kevin W.; White, Ryan J.

2009-01-01

Many electrochemical biosensor approaches developed in recent years utilize redox labeled (most commonly methylene blue or ferrocene) oligonucleotide probes site-specifically attached to an interrogating electrode. Sensors in this class have been reported employing a range of probe architectures, including single- and double-stranded DNA, more complex DNA structures, DNA and RNA aptamers and, most recently, DNA-small molecule chimeras. Signaling in this class of sensors is generally predicated on binding-induced changes in the efficiency with which the covalently attached redox label transfers electrons with the interrogating electrode. Here we have investigated how the properties of the redox tag affect the performance of such sensors. Specifically, we compare the differences in signaling and stability of electrochemical DNA sensors (E-DNA sensors) fabricated using either ferrocene or methylene blue as the signaling redox moiety. We find that while both tags support efficient E-DNA signaling, ferrocene produces slightly improved signal gain and target affinity. These small advantages, however, come at a potentially significant price: the ferrocene-based sensors are far less stable than their methylene blue counterparts, particularly with regards to stability to long-term storage, repeated electrochemical interrogations, repeated sensing/regeneration iterations, and employment in complex sample matrices such as blood serum. PMID:19810694

Comparing reactive and memory-one strategies of direct reciprocity

PubMed Central

Baek, Seung Ki; Jeong, Hyeong-Chai; Hilbe, Christian; Nowak, Martin A.

2016-01-01

Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player’s previous move, and memory-one strategies, which take into account the own and the co-player’s previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation. PMID:27161141

Lightweight Solar Power for Small Satellites

NASA Technical Reports Server (NTRS)

Nabors, Sammy A.

2015-01-01

The innovation targets small satellites or CubeSats for which conventional deployable arrays are not feasible due to their size, weight and complexity. This novel solar cell array includes a thin and flexible photovoltaic cell applied to an inflatable structure to create a high surface area array for collecting solar energy in a lightweight, simple and deployable structure. The inflatable array, with its high functional surface area, eliminates the need and the mechanisms required to point the system toward the sun. The power density achievable in these small arrays is similar to that of conventional high-power deployable/pointable arrays used on large satellites or space vehicles. Although inflatable solar arrays have been previously considered by others, the arrays involved the use of traditional rigid solar cells. Researchers are currently working with thin film photovoltaics from various suppliers so that the NASA innovation is not limited to any particular solar cell technology. NASA has built prototypes and tested functionality before and after inflation. As shown in the current-voltage currents below, deployment does not damage the cell performance.

On the use of infrasound for constraining global climate models

NASA Astrophysics Data System (ADS)

Millet, Christophe; Ribstein, Bruno; Lott, Francois; Cugnet, David

2017-11-01

Numerical prediction of infrasound is a complex issue due to constantly changing atmospheric conditions and to the random nature of small-scale flows. Although part of the upward propagating wave is refracted at stratospheric levels, where gravity waves significantly affect the temperature and the wind, yet the process by which the gravity wave field changes the infrasound arrivals remains poorly understood. In the present work, we use a stochastic parameterization to represent the subgrid scale gravity wave field from the atmospheric specifications provided by the European Centre for Medium-Range Weather Forecasts. It is shown that regardless of whether the gravity wave field possesses relatively small or large features, the sensitivity of acoustic waveforms to atmospheric disturbances can be extremely different. Using infrasound signals recorded during campaigns of ammunition destruction explosions, a new set of tunable parameters is proposed which more accurately predicts the small-scale content of gravity wave fields in the middle atmosphere. Climate simulations are performed using the updated parameterization. Numerical results demonstrate that a network of ground-based infrasound stations is a promising technology for dynamically tuning the gravity wave parameterization.

Indexing and retrieving DICOM data in disperse and unstructured archives.

PubMed

Costa, Carlos; Freitas, Filipe; Pereira, Marco; Silva, Augusto; Oliveira, José L

2009-01-01

This paper proposes an indexing and retrieval solution to gather information from distributed DICOM documents by allowing searches and access to the virtual data repository using a Google-like process. The medical imaging modalities are becoming more powerful and less expensive. The result is the proliferation of equipment acquisition by imaging centers, including the small ones. With this dispersion of data, it is not easy to take advantage of all the information that can be retrieved from these studies. Furthermore, many of these small centers do not have large enough requirements to justify the acquisition of a traditional PACS. A peer-to-peer PACS platform to index and query DICOM files over a set of distributed repositories that are logically viewed as a single federated unit. The solution is based on a public domain document-indexing engine and extends traditional PACS query and retrieval mechanisms. This proposal deals well with complex searching requirements, from a single desktop environment to distributed scenarios. The solution performance and robustness were demonstrated in trials. The characteristics of presented PACS platform make it particularly important for small institutions, including educational and research groups.

DOE-FG02-00ER62797 Final Report

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

Sweedler, J.V.

2004-12-01

Specific Aims The overall goal of this proposal has been to develop and interface a new technology, molecular gates, with microfabricated systems to add an important capability to microfabricated DNA measurement systems. This project specifically focused on demonstrating how molecular gates could be used to capture a single analyte band, among a stream of bands from a separation or a flow injection analysis experiment, and release it for later measurement, thus allowing further manipulations on the selected analyte. Since the original proposal, the molecular gate concept has been greatly expanded to allow the gates to be used as externally controllablemore » intelligent interconnects in multilayer microfluidic networks. We have demonstrated: (1) the ability of the molecular gates to work with a much wider range of biological molecules including DNA, proteins and small metabolites; and (2) the capability of performing an electrophoretic separation and sequestering individual picoliter volume components (or even classes of components) into separate channels for further analysis. Both capabilities will enable characterization of small mass amounts of complex mixtures of DNA, proteins and even small molecules--allowing them to be further separated and chemically characterized.« less

Study on Iron Distribution and Electrical Activities at Grain Boundaries in Polycrystalline Silicon Substrate for Solar Cells

NASA Astrophysics Data System (ADS)

Arafune, Koji; Ohishi, Eichiro; Sai, Hitoshi; Terada, Yasuko; Ohshita, Yoshio; Yamaguchi, Masafumi

2006-08-01

To clarify the role of grain boundaries in iron sinks and carrier recombination centers, iron distributions and their chemical states were studied before and after gettering. They were measured by the X-ray microprobe fluorescence and the X-ray absorption in the near-edge structure using the beamline 37XU at the SPring-8 third-generation synchrotron facility. To determine the crystallographic orientation of the grain boundaries, electron backscatter diffraction measurements were performed. The distribution of electric active defects was characterized by electron-beam-induced current measurements. Before gettering, the iron was distributed in the small grain and its chemical state was similar to that of iron oxide. After gettering, the iron was redistributed along the small angle grain boundary, and its chemical state was similar to the iron silicide complexed with the iron oxide. Regarding the electrical activity, high carrier recombination was observed along the small-angle grain boundary. On the contrary, Σ 3 grain boundaries were relatively weak impurity sinks and showed low recombination activity.

Small-angle X-Ray analysis of macromolecular structure: the structure of protein NS2 (NEP) in solution

NASA Astrophysics Data System (ADS)

Shtykova, E. V.; Bogacheva, E. N.; Dadinova, L. A.; Jeffries, C. M.; Fedorova, N. V.; Golovko, A. O.; Baratova, L. A.; Batishchev, O. V.

2017-11-01

A complex structural analysis of nuclear export protein NS2 (NEP) of influenza virus A has been performed using bioinformatics predictive methods and small-angle X-ray scattering data. The behavior of NEP molecules in a solution (their aggregation, oligomerization, and dissociation, depending on the buffer composition) has been investigated. It was shown that stable associates are formed even in a conventional aqueous salt solution at physiological pH value. For the first time we have managed to get NEP dimers in solution, to analyze their structure, and to compare the models obtained using the method of the molecular tectonics with the spatial protein structure predicted by us using the bioinformatics methods. The results of the study provide a new insight into the structural features of nuclear export protein NS2 (NEP) of the influenza virus A, which is very important for viral infection development.

Small-signal modeling with direct parameter extraction for impact ionization effect in high-electron-mobility transistors

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

Guan, He; Lv, Hongliang; Guo, Hui, E-mail: hguan@stu.xidian.edu.cn

2015-11-21

Impact ionization affects the radio-frequency (RF) behavior of high-electron-mobility transistors (HEMTs), which have narrow-bandgap semiconductor channels, and this necessitates complex parameter extraction procedures for HEMT modeling. In this paper, an enhanced small-signal equivalent circuit model is developed to investigate the impact ionization, and an improved method is presented in detail for direct extraction of intrinsic parameters using two-step measurements in low-frequency and high-frequency regimes. The practicability of the enhanced model and the proposed direct parameter extraction method are verified by comparing the simulated S-parameters with published experimental data from an InAs/AlSb HEMT operating over a wide frequency range. The resultsmore » demonstrate that the enhanced model with optimal intrinsic parameter values that were obtained by the direct extraction approach can effectively characterize the effects of impact ionization on the RF performance of HEMTs.« less

Utility of Small Animal Models of Developmental Programming.

PubMed

Reynolds, Clare M; Vickers, Mark H

2018-01-01

Any effective strategy to tackle the global obesity and rising noncommunicable disease epidemic requires an in-depth understanding of the mechanisms that underlie these conditions that manifest as a consequence of complex gene-environment interactions. In this context, it is now well established that alterations in the early life environment, including suboptimal nutrition, can result in an increased risk for a range of metabolic, cardiovascular, and behavioral disorders in later life, a process preferentially termed developmental programming. To date, most of the mechanistic knowledge around the processes underpinning development programming has been derived from preclinical research performed mostly, but not exclusively, in laboratory mouse and rat strains. This review will cover the utility of small animal models in developmental programming, the limitations of such models, and potential future directions that are required to fully maximize information derived from preclinical models in order to effectively translate to clinical use.

Arthroscopic Broström repair with Gould augmentation via an accessory anterolateral port for lateral instability of the ankle.

PubMed

Matsui, Kentaro; Takao, Masato; Miyamoto, Wataru; Innami, Ken; Matsushita, Takashi

2014-10-01

Although several arthroscopic surgical techniques for the treatment of lateral instability of the ankle have been introduced recently, some concern remains over their procedural complexity, complications, and unclear clinical outcomes. We have simplified the arthroscopic technique of Broström repair with Gould augmentation. This technique requires only two small skin incisions for two ports (medial midline and accessory anterolateral ports), without needing a percutaneous procedure or extension of the skin incisions. The anterior talofibular ligament is reattached to its anatomical footprint on the fibula with suture anchor, under arthroscopic view. The inferior extensor retinaculum is directly visualized through the accessory anterolateral port and is attached to the fibula with another suture anchor under arthroscopic view via the anterolateral port. The use of two small ports offers a procedure that is simple to perform and less morbid for patients.

Applying Principles from Complex Systems to Studying the Efficacy of CAM Therapies

PubMed Central

Nahin, Richard L.; Calabrese, Carlo; Folkman, Susan; Kimbrough, Elizabeth; Shoham, Jacob; Haramati, Aviad

2010-01-01

Abstract In October 2007, a National Center for Complementary and Alternative Medicine (NCCAM)–sponsored workshop, entitled “Applying Principles from Complex Systems to Studying the Efficacy of CAM Therapies,” was held at Georgetown University in Washington, DC. Over a 2-day period, the workshop engaged a small group of experts from the fields of complementary and alternative medicine (CAM) research and complexity science to discuss and examine ways in which complexity science can be applied to CAM research. After didactic presentations and small-group discussions, a number of salient themes and ideas emerged. This paper article describes the workshop program and summarizes these emergent ideas, which are divided into five broad categories: (1) introduction to complexity; (2) challenges to CAM research; (3) applications of complexity science to CAM; (4) CAM as a model of complexity applied to medicine; and (5) future directions. This discusses possible benefits and challenges associated with applying complexity science to CAM research. By providing an introductory framework for this collaboration and exchange, it is hoped that this article may stimulate further inquiry into this largely unexplored area of research. PMID:20715978

Petascale self-consistent electromagnetic computations using scalable and accurate algorithms for complex structures

NASA Astrophysics Data System (ADS)

Cary, John R.; Abell, D.; Amundson, J.; Bruhwiler, D. L.; Busby, R.; Carlsson, J. A.; Dimitrov, D. A.; Kashdan, E.; Messmer, P.; Nieter, C.; Smithe, D. N.; Spentzouris, P.; Stoltz, P.; Trines, R. M.; Wang, H.; Werner, G. R.

2006-09-01

As the size and cost of particle accelerators escalate, high-performance computing plays an increasingly important role; optimization through accurate, detailed computermodeling increases performance and reduces costs. But consequently, computer simulations face enormous challenges. Early approximation methods, such as expansions in distance from the design orbit, were unable to supply detailed accurate results, such as in the computation of wake fields in complex cavities. Since the advent of message-passing supercomputers with thousands of processors, earlier approximations are no longer necessary, and it is now possible to compute wake fields, the effects of dampers, and self-consistent dynamics in cavities accurately. In this environment, the focus has shifted towards the development and implementation of algorithms that scale to large numbers of processors. So-called charge-conserving algorithms evolve the electromagnetic fields without the need for any global solves (which are difficult to scale up to many processors). Using cut-cell (or embedded) boundaries, these algorithms can simulate the fields in complex accelerator cavities with curved walls. New implicit algorithms, which are stable for any time-step, conserve charge as well, allowing faster simulation of structures with details small compared to the characteristic wavelength. These algorithmic and computational advances have been implemented in the VORPAL7 Framework, a flexible, object-oriented, massively parallel computational application that allows run-time assembly of algorithms and objects, thus composing an application on the fly.

Next generation communications satellites: multiple access and network studies

NASA Technical Reports Server (NTRS)

Meadows, H. E.; Schwartz, M.; Stern, T. E.; Ganguly, S.; Kraimeche, B.; Matsuo, K.; Gopal, I.

1982-01-01

Efficient resource allocation and network design for satellite systems serving heterogeneous user populations with large numbers of small direct-to-user Earth stations are discussed. Focus is on TDMA systems involving a high degree of frequency reuse by means of satellite-switched multiple beams (SSMB) with varying degrees of onboard processing. Algorithms for the efficient utilization of the satellite resources were developed. The effect of skewed traffic, overlapping beams and batched arrivals in packet-switched SSMB systems, integration of stream and bursty traffic, and optimal circuit scheduling in SSMB systems: performance bounds and computational complexity are discussed.

Analysis of the dynamics of movement of the landing vehicle with an inflatable braking device on the final trajectory under the influence of wind load

NASA Astrophysics Data System (ADS)

Koryanov, V.; Kazakovtsev, V.; Harri, A.-M.; Heilimo, J.; Haukka, H.; Aleksashkin, S.

2015-10-01

This research work is devoted to analysis of angular motion of the landing vehicle (LV) with an inflatable braking device (IBD), taking into account the influence of the wind load on the final stage of the movement. Using methods to perform a calculation of parameters of angular motion of the landing vehicle with an inflatable braking device based on the availability of small asymmetries, which are capable of complex dynamic phenomena, analyzes motion of the landing vehicle at the final stage of motion in the atmosphere.

Hexahistidine (6xHis) fusion-based assays for protein-protein interactions.

PubMed

Puckett, Mary C

2015-01-01

Fusion-protein tags provide a useful method to study protein-protein interactions. One widely used fusion tag is hexahistidine (6xHis). This tag has unique advantages over others due to its small size and the relatively low abundance of naturally occurring consecutive histidine repeats. 6xHis tags can interact with immobilized metal cations to provide for the capture of proteins and protein complexes of interest. In this chapter, a description of the benefits and uses of 6xHis-fusion proteins as well as a detailed method for performing a 6xHis-pulldown assay are described.

KSC-05PD-1086

NASA Technical Reports Server (NTRS)

2005-01-01

KENNEDY SPACE CENTER, FLA. At Launch Complex 39B, technicians in Space Shuttle Discovery's payload bay perform a borescope inspection of the retract link assembly on the orbiter's main landing gear door. The inspection is a precautionary measure after a small crack was found in a retract link assembly on the right-hand main landing gear on orbiter Atlantis. An initial review of the closeout photos of the link assembly on Discovery did not reveal any cracks. Discovery is scheduled to return the Space Shuttle fleet to operational status on mission STS-114. This additional work does not impact the launch planning window of July 13-31.

Cotton-Mouton polarimeter with HCN laser on CHS

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

Akiyama, T.; Kawahata, K.; Ito, Y.

Polarimeters based on the Cotton-Mouton effect hold promise for electron density measurements. We have designed and installed a Cotton-Mouton polarimeter on the Compact Helical System. The Cotton-Mouton effect is measured as the phase difference between probe and reference beams. In this system, an interferometric measurement can be performed simultaneously with the same probe chord. The light source is a HCN laser (wavelength of 337 {mu}m). Digital complex demodulation is adopted for small phase analysis. The line averaged density evaluated from the polarimeter along a plasma center chord is almost consistent with that from the interferometer.

The Cost-Utility Analysis of PET-Scan in Diagnosis and Treatment of Non-Small Cell Lung Carcinoma in Iran.

PubMed

Akbari Sari, Ali; Ravaghi, Hamid; Mobinizadeh, Mohammadreza; Sarvari, Sima

2013-06-01

PET scan is a non-invasive, complex and expensive medical imaging technology that is normally used for the diagnosis and treatment of various diseases including lung cancer. The purpose of this study is to assess the cost effectiveness of this technology in the diagnosis and treatment of non- small cell lung carcinoma (NSCLC) in Iran. The main electronic databases including The Cochrane Library and Medline were searched to identify available evidence about the performance and effectiveness of technology. A standard decision tree model with seven strategies was used to perform the economic evaluation. Retrieved studies and expert opinion were used to estimate the cost of each treatment strategy in Iran. The costs were divided into three categories including capital costs (depreciation costs of buildings and equipment), staff costs and other expenses (including cost of consumables, running and maintenance costs). The costs were estimated in both IR-Rials and US-Dollars with an exchange rate of 10.000 IR Rials per one US Dollar according to the exchange rate in 2008. The total annual running cost of a PET scan was about 8850 to 13000 million Rials, (0.9 to 1.3 million US$). The average cost of performing a PET scan varied between 3 and 4.5 million Rials (300 to 450US$). The strategies 3 (mediastinoscopy alone) and 7 (mediastinoscopy after PET scan) were more cost-effective than other strategies, especially when the result of the CT-scan performed before PET scan was negative. The technical performance of PET scan is significantly higher than similar technologies for staging and treatment of NSCLC. In addition, it might slightly improve the treatment process and lead to a small level of increase in the quality adjusted life year (QALY) gained by these patients making it cost-effective for the treatment of NSCLC.

Geo-PET: A novel generic organ-pet for small animal organs and tissues

NASA Astrophysics Data System (ADS)

Sensoy, Levent

Reconstructed tomographic image resolution of small animal PET imaging systems is improving with advances in radiation detector development. However the trend towards higher resolution systems has come with an increase in price and system complexity. Recent developments in the area of solid-state photomultiplication devices like silicon photomultiplier arrays (SPMA) are creating opportunities for new high performance tools for PET scanner design. Imaging of excised small animal organs and tissues has been used as part of post-mortem studies in order to gain detailed, high-resolution anatomical information on sacrificed animals. However, this kind of ex-vivo specimen imaging has largely been limited to ultra-high resolution muCT. The inherent limitations to PET resolution have, to date, excluded PET imaging from these ex-vivo imaging studies. In this work, we leverage the diminishing physical size of current generation SPMA designs to create a very small, simple, and high-resolution prototype detector system targeting ex-vivo tomographic imaging of small animal organs and tissues. We investigate sensitivity, spatial resolution, and the reconstructed image quality of a prototype small animal PET scanner designed specifically for imaging of excised murine tissue and organs. We aim to demonstrate that a cost-effective silicon photomultiplier (SiPM) array based design with thin crystals (2 mm) to minimize depth of interaction errors might be able to achieve sub-millimeter resolution. We hypothesize that the substantial decrease in sensitivity associated with the thin crystals can be compensated for with increased solid angle detection, longer acquisitions, higher activity and wider acceptance energy windows (due to minimal scatter from excised organs). The constructed system has a functional field of view (FoV) of 40 mm diameter, which is adequate for most small animal specimen studies. We perform both analytical (3D-FBP) and iterative (ML-EM) methods in order to reconstruct tomographic images. Results demonstrate good agreement between the simulation and the prototype. Our detector system with pixelated crystals is able to separate small objects as close as 1.25 mm apart, whereas spatial resolution converges to the theoretical limit of 1.6 mm (half the size of the smallest detecting element), which is to comparable to the spatial resolution of the existing commercial small animal PET systems. Better system spatial resolution is achievable with new generation SiPM detector boards with 1 mm x 1 mm cell dimensions. We demonstrate through Monte Carlo simulations that it is possible to achieve sub-millimeter spatial image resolution (0.7 mm for our scanner) in complex objects using monolithic crystals and exploiting the light-sharing mechanism among the neighboring detector cells. Results also suggest that scanner (or object) rotation minimizes artifacts arising from poor angular sampling, which is even more significant in smaller PET designs as the gaps between the sensitive regions of the detector have a more exaggerated effect on the overall reconstructed image quality when the design is more compact. Sensitivity of the system, on the other hand, can be doubled by adding two additional detector heads resulting in a, fully closed, 4? geometry.

A Comparison of Cognitive Function in Former Rugby Union Players Compared with Former Non-Contact-Sport Players and the Impact of Concussion History.

PubMed

Hume, Patria A; Theadom, Alice; Lewis, Gwyn N; Quarrie, Kenneth L; Brown, Scott R; Hill, Rosamund; Marshall, Stephen W

2017-06-01

This study investigated differences in cognitive function between former rugby and non-contact-sport players, and assessed the association between concussion history and cognitive function. Overall, 366 former players (mean ± standard deviation [SD] age 43.3 ± 8.2 years) were recruited from October 2012 to April 2014. Engagement in sport, general health, sports injuries and concussion history, and demographic information were obtained from an online self-report questionnaire. Cognitive functioning was assessed using the online CNS Vital Signs neuropsychological test battery. Cohen's d effect size statistics were calculated for comparisons across player groups, concussion groups (one or more self-reported concussions versus no concussions) and between those groups with CNS Vital Signs age-matched norms (US norms). Individual differences within groups were represented as SDs. The elite-rugby group (n = 103) performed worse on tests of complex attention, processing speed, executive functioning, and cognitive flexibility than the non-contact-sport group (n = 65), and worse than the community-rugby group (n = 193) on complex attention. The community-rugby group performed worse than the non-contact group on executive functioning and cognitive flexibility. Compared with US norms, all three former player groups performed worse on verbal memory and reaction time; rugby groups performed worse on processing speed, cognitive flexibility and executive functioning; and the community-rugby group performed worse on composite memory. The community-rugby group and non-contact-sport group performed slightly better than US norms on complex attention, as did the elite-rugby group for motor speed. All three player groups had greater individual differences than US norms on composite memory, verbal memory and reaction time. The elite-rugby group had greater individual differences on processing speed and complex attention, and the community-rugby group had greater individual differences on psychomotor speed and motor speed. The average number of concussions recalled per player was greater for elite rugby and community rugby than non-contact sport. Former players who recalled one or more concussions (elite rugby, 85 %; community rugby, 77 %; non-contact sport, 23 %) had worse scores on cognitive flexibility, executive functioning, and complex attention than players who did not recall experiencing a concussion. Past participation in rugby or a history of concussion were associated with small to moderate neurocognitive deficits (as indicated by worse CNS Vital Signs scores) in athletes post retirement from competitive sport.

A general electrochemical method for label-free screening of protein–small molecule interactions†

PubMed Central

Cash, Kevin J.; Ricci, Francesco

2010-01-01

Here we report a versatile method by which the interaction between a protein and a small molecule, and the disruption of that interaction by competition with other small molecules, can be monitored electrochemically directly in complex sample matrices. PMID:19826675

A liquid jet setup for x-ray scattering experiments on complex liquids at free-electron laser sources

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

Steinke, I.; Lehmkühler, F., E-mail: felix.lehmkuehler@desy.de; Schroer, M. A.

2016-06-15

In this paper we describe a setup for x-ray scattering experiments on complex fluids using a liquid jet. The setup supports Small and Wide Angle X-ray Scattering (SAXS/WAXS) geometries. The jet is formed by a gas-dynamic virtual nozzle (GDVN) allowing for diameters ranging between 1 μm and 20 μm at a jet length of several hundred μm. To control jet properties such as jet length, diameter, or flow rate, the instrument is equipped with several diagnostic tools. Three microscopes are installed to quantify jet dimensions and stability in situ. The setup has been used at several beamlines performing both SAXSmore » and WAXS experiments. As a typical example we show an experiment on a colloidal dispersion in a liquid jet at the X-ray Correlation Spectroscopy instrument at the Linac Coherent Light Source free-electron laser.« less

Complex absorbing potentials within EOM-CC family of methods: Theory, implementation, and benchmarks

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

Zuev, Dmitry; Jagau, Thomas-C.; Krylov, Anna I.

2014-07-14

A production-level implementation of equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) for electron attachment and excitation energies augmented by a complex absorbing potential (CAP) is presented. The new method enables the treatment of metastable states within the EOM-CC formalism in a similar manner as bound states. The numeric performance of the method and the sensitivity of resonance positions and lifetimes to the CAP parameters and the choice of one-electron basis set are investigated. A protocol for studying molecular shape resonances based on the use of standard basis sets and a universal criterion for choosing the CAP parameters are presented. Our resultsmore » for a variety of π{sup *} shape resonances of small to medium-size molecules demonstrate that CAP-augmented EOM-CCSD is competitive relative to other theoretical approaches for the treatment of resonances and is often able to reproduce experimental results.« less

A selective-update affine projection algorithm with selective input vectors

NASA Astrophysics Data System (ADS)

Kong, NamWoong; Shin, JaeWook; Park, PooGyeon

2011-10-01

This paper proposes an affine projection algorithm (APA) with selective input vectors, which based on the concept of selective-update in order to reduce estimation errors and computations. The algorithm consists of two procedures: input- vector-selection and state-decision. The input-vector-selection procedure determines the number of input vectors by checking with mean square error (MSE) whether the input vectors have enough information for update. The state-decision procedure determines the current state of the adaptive filter by using the state-decision criterion. As the adaptive filter is in transient state, the algorithm updates the filter coefficients with the selected input vectors. On the other hand, as soon as the adaptive filter reaches the steady state, the update procedure is not performed. Through these two procedures, the proposed algorithm achieves small steady-state estimation errors, low computational complexity and low update complexity for colored input signals.

The mechanism of enantioselective ketone reduction with Noyori and Noyori–Ikariya bifunctional catalysts

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

Dub, Pavel A.; Gordon, John C.

2016-03-21

The catalytic hydrogenation of prochiral ketones with second and third-row transition metal complexes bearing chelating chiral ligands containing at least one N–H functionality has achieved unparalleled performance, delivering, in the best cases, chiral alcohols with up to 99.9% ee using extremely small catalyst loadings (~10 -5 mol%). Hence the efficacy of this reaction has closely approached that of natural enzymatic systems and the reaction itself has become one of the most efficient artificial catalytic reactions developed to date. This paper describes the current level of understanding of the mechanism of enantioselective hydrogenation and transfer hydrogenation of aromatic ketones with pioneeringmore » prototypes of bifunctional catalysts, the Noyori and Noyori–Ikariya complexes. Finally, analysis presented herein expands the concept of “metal–ligand cooperation”, redefines the term “cooperative ligand” and introduces “H –/H + outer-sphere hydrogenation” as a novel paradigm in outer-sphere hydrogenation.« less

Overarching framework for data-based modelling

NASA Astrophysics Data System (ADS)

Schelter, Björn; Mader, Malenka; Mader, Wolfgang; Sommerlade, Linda; Platt, Bettina; Lai, Ying-Cheng; Grebogi, Celso; Thiel, Marco

2014-02-01

One of the main modelling paradigms for complex physical systems are networks. When estimating the network structure from measured signals, typically several assumptions such as stationarity are made in the estimation process. Violating these assumptions renders standard analysis techniques fruitless. We here propose a framework to estimate the network structure from measurements of arbitrary non-linear, non-stationary, stochastic processes. To this end, we propose a rigorous mathematical theory that underlies this framework. Based on this theory, we present a highly efficient algorithm and the corresponding statistics that are immediately sensibly applicable to measured signals. We demonstrate its performance in a simulation study. In experiments of transitions between vigilance stages in rodents, we infer small network structures with complex, time-dependent interactions; this suggests biomarkers for such transitions, the key to understand and diagnose numerous diseases such as dementia. We argue that the suggested framework combines features that other approaches followed so far lack.

TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics.

PubMed

Hou, Yue; Konen, Jessica; Brat, Daniel J; Marcus, Adam I; Cooper, Lee A D

2018-05-08

Spheroid cultures derived from explanted cancer specimens are an increasingly utilized resource for studying complex biological processes like tumor cell invasion and metastasis, representing an important bridge between the simplicity and practicality of 2-dimensional monolayer cultures and the complexity and realism of in vivo animal models. Temporal imaging of spheroids can capture the dynamics of cell behaviors and microenvironments, and when combined with quantitative image analysis methods, enables deep interrogation of biological mechanisms. This paper presents a comprehensive open-source software framework for Temporal Analysis of Spheroid Imaging (TASI) that allows investigators to objectively characterize spheroid growth and invasion dynamics. TASI performs spatiotemporal segmentation of spheroid cultures, extraction of features describing spheroid morpho-phenotypes, mathematical modeling of spheroid dynamics, and statistical comparisons of experimental conditions. We demonstrate the utility of this tool in an analysis of non-small cell lung cancer spheroids that exhibit variability in metastatic and proliferative behaviors.

Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation.

PubMed

Naitow, Hisashi; Matsuura, Yoshinori; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Tanaka, Rie; Tanaka, Tomoyuki; Sugahara, Michihiro; Kobayashi, Jun; Nango, Eriko; Iwata, So; Kunishima, Naoki

2017-08-01

Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein-ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results. In a comparison of the SFX and SR structures, clear differences were observed in the unit-cell parameters, in the alternate conformation of side chains, in the degree of water coordination and in the ligand-binding mode.

A liquid jet setup for x-ray scattering experiments on complex liquids at free-electron laser sources

DOE PAGES

Steinke, I.; Walther, M.; Lehmkühler, F.; ...

2016-06-01

In this study we describe a setup for x-ray scattering experiments on complex fluids using a liquid jet. The setup supports Small and Wide Angle X-ray Scattering (SAXS/WAXS) geometries. The jet is formed by a gas-dynamic virtual nozzle (GDVN) allowing for diameters ranging between 1 μm and 20 μm at a jet length of several hundred μm. To control jet properties such as jet length, diameter, or flow rate, the instrument is equipped with several diagnostic tools. Three microscopes are installed to quantify jet dimensions and stability in situ. The setup has been used at several beamlines performing both SAXSmore » and WAXS experiments. Finally, as a typical example we show an experiment on a colloidal dispersion in a liquid jet at the X-ray Correlation Spectroscopy instrument at the Linac Coherent Light Source free-electron laser.« less

Stability Analysis and Internal Heating Effect on Oscillatory Convection in a Viscoelastic Fluid Saturated Porous Medium Under Gravity Modulation

NASA Astrophysics Data System (ADS)

Bhadauria, B. S.; Singh, M. K.; Singh, A.; Singh, B. K.; Kiran, P.

2016-12-01

In this paper, we investigate the combined effect of internal heating and time periodic gravity modulation in a viscoelastic fluid saturated porous medium by reducing the problem into a complex non-autonomous Ginzgburg-Landau equation. Weak nonlinear stability analysis has been performed by using power series expansion in terms of the amplitude of gravity modulation, which is assumed to be small. The Nusselt number is obtained in terms of the amplitude for oscillatory mode of convection. The influence of viscoelastic parameters on heat transfer has been discussed. Gravity modulation is found to have a destabilizing effect at low frequencies and a stabilizing effect at high frequencies. Finally, it is found that overstability advances the onset of convection, more with internal heating. The conditions for which the complex Ginzgburg-Landau equation undergoes Hopf bifurcation and the amplitude equation undergoes supercritical pitchfork bifurcation are studied.

Hardware-efficient implementation of digital FIR filter using fast first-order moment algorithm

NASA Astrophysics Data System (ADS)

Cao, Li; Liu, Jianguo; Xiong, Jun; Zhang, Jing

2018-03-01

As the digital finite impulse response (FIR) filter can be transformed into the shift-add form of multiple small-sized firstorder moments, based on the existing fast first-order moment algorithm, this paper presents a novel multiplier-less structure to calculate any number of sequential filtering results in parallel. The theoretical analysis on its hardware and time-complexities reveals that by appropriately setting the degree of parallelism and the decomposition factor of a fixed word width, the proposed structure may achieve better area-time efficiency than the existing two-dimensional (2-D) memoryless-based filter. To evaluate the performance concretely, the proposed designs for different taps along with the existing 2-D memoryless-based filters, are synthesized by Synopsys Design Compiler with 0.18-μm SMIC library. The comparisons show that the proposed design has less area-time complexity and power consumption when the number of filter taps is larger than 48.

Whole-cell biocomputing

NASA Technical Reports Server (NTRS)

Simpson, M. L.; Sayler, G. S.; Fleming, J. T.; Applegate, B.

2001-01-01

The ability to manipulate systems on the molecular scale naturally leads to speculation about the rational design of molecular-scale machines. Cells might be the ultimate molecular-scale machines and our ability to engineer them is relatively advanced when compared with our ability to control the synthesis and direct the assembly of man-made materials. Indeed, engineered whole cells deployed in biosensors can be considered one of the practical successes of molecular-scale devices. However, these devices explore only a small portion of cellular functionality. Individual cells or self-organized groups of cells perform extremely complex functions that include sensing, communication, navigation, cooperation and even fabrication of synthetic nanoscopic materials. In natural systems, these capabilities are controlled by complex genetic regulatory circuits, which are only partially understood and not readily accessible for use in engineered systems. Here, we focus on efforts to mimic the functionality of man-made information-processing systems within whole cells.

Creating targeted initial populations for genetic product searches in heterogeneous markets

NASA Astrophysics Data System (ADS)

Foster, Garrett; Turner, Callaway; Ferguson, Scott; Donndelinger, Joseph

2014-12-01

Genetic searches often use randomly generated initial populations to maximize diversity and enable a thorough sampling of the design space. While many of these initial configurations perform poorly, the trade-off between population diversity and solution quality is typically acceptable for small-scale problems. Navigating complex design spaces, however, often requires computationally intelligent approaches that improve solution quality. This article draws on research advances in market-based product design and heuristic optimization to strategically construct 'targeted' initial populations. Targeted initial designs are created using respondent-level part-worths estimated from discrete choice models. These designs are then integrated into a traditional genetic search. Two case study problems of differing complexity are presented to illustrate the benefits of this approach. In both problems, targeted populations lead to computational savings and product configurations with improved market share of preferences. Future research efforts to tailor this approach and extend it towards multiple objectives are also discussed.

Two-dimensional turbulent flow chromatography coupled on-line to liquid chromatography-mass spectrometry for solution-based ligand screening against multiple proteins.

PubMed

Zhou, Jian-Liang; An, Jing-Jing; Li, Ping; Li, Hui-Jun; Jiang, Yan; Cheng, Jie-Fei

2009-03-20

We present herein a novel bioseparation/chemical analysis strategy for protein-ligand screening and affinity ranking in compound mixtures, designed to increase screening rates and improve sensitivity and ruggedness in performance. The strategy is carried out by combining on-line two-dimensional turbulent flow chromatography (2D-TFC) with liquid chromatography-mass spectrometry (LC-MS), and accomplished through the following steps: (1) a reversed-phase TFC stage to separate the protein/ligand complex from the unbound free molecules, (2) an on-line dissociation process to release the bound ligands from the complexes, and (3) a second mixed-mode cation-exchange/reversed-phase TFC stage to trap the bound ligands and to remove the proteins and salts, followed by LC-MS analysis for identification and determination of the binding affinities. The technique can implement an ultra-fast isolation of protein/ligand complex with the retention time of a complex peak in about 5s, and on-line prepare the "clean" sample to be directly compatible with the LC-MS analysis. The improvement in performance of this 2D-TFC/LC-MS approach over the conventional approach has been demonstrated by determining affinity-selected ligands of the target proteins acetylcholinesterase and butyrylcholinesterase from a small library with known binding affinities and a steroidal alkaloid library composed of structurally similar compounds. Our results show that 2D-TFC/LC-MS is a generic and efficient tool for high-throughput screening of ligands with low-to-high binding affinities, and structure-activity relationship evaluation.

Elucidating the role of surface chemistry on cationic phosphorus dendrimer-siRNA complexation.

PubMed

Deriu, Marco A; Tsapis, Nicolas; Noiray, Magali; Grasso, Gianvito; El Brahmi, Nabil; Mignani, Serge; Majoral, Jean-Pierre; Fattal, Elias; Danani, Andrea

2018-06-14

In the field of dendrimers targeting small interfering RNA (siRNA) delivery, dendrimer structural properties, such as the flexibility/rigidity ratio, play a crucial role in the efficiency of complexation. However, advances in organic chemistry have enabled the development of dendrimers that differ only by a single atom on their surface terminals. This is the case for cationic phosphorus dendrimers functionalized with either pyrrolidinium (DP) or morpholinium (DM) terminal groups. This small change was shown to strongly affect the dendrimer-siRNA complexation, leading to more efficient anti-inflammatory effects in the case of DP. Reasons for this different behavior can hardly be inferred only by biological in vitro and in vivo experiments due to the high number of variables and complexity of the investigated biological system. However, an understanding of how small chemical surface changes may completely modify the overall dendrimer-siRNA complexation is a significant breakthrough towards the design of efficient dendrimers for nucleic acid delivery. Herein, we present experimental and computational approaches based on isothermal titration calorimetry and molecular dynamics simulations to elucidate the molecular reasons behind different efficiencies and activities of DP and DM. Results of the present research highlight how chemical surface modifications may drive the overall dendrimer-siRNA affinity by influencing enthalpic and entropic contributions of binding free energy. Moreover, this study elucidates molecular reasons related to complexation stoichiometry that may be crucial in determining the dendrimer complexation efficiency.

Characterizing octagonal and rectangular fibers for MAROON-X

NASA Astrophysics Data System (ADS)

Sutherland, Adam P.; Stuermer, Julian; Miller, Katrina R.; Seifahrt, Andreas; Bean, Jacob L.

2016-07-01

We report on the scrambling performance and focal-ratio-degradation (FRD) of various octagonal and rectangular fibers considered for MAROON-X. Our measurements demonstrate the detrimental effect of thin claddings on the FRD of octagonal and rectangular fibers and that stress induced at the connectors can further increase the FRD. We find that fibers with a thick, round cladding show low FRD. We further demonstrate that the scrambling behavior of non-circular fibers is often complex and introduce a new metric to fully capture non-linear scrambling performance, leading to much lower scrambling gain values than are typically reported in the literature (<=1000 compared to 10,000 or more). We find that scrambling gain measurements for small-core, non-circular fibers are often speckle dominated if the fiber is not agitated.

Streaming simplification of tetrahedral meshes.

PubMed

Vo, Huy T; Callahan, Steven P; Lindstrom, Peter; Pascucci, Valerio; Silva, Cláudio T

2007-01-01

Unstructured tetrahedral meshes are commonly used in scientific computing to represent scalar, vector, and tensor fields in three dimensions. Visualization of these meshes can be difficult to perform interactively due to their size and complexity. By reducing the size of the data, we can accomplish real-time visualization necessary for scientific analysis. We propose a two-step approach for streaming simplification of large tetrahedral meshes. Our algorithm arranges the data on disk in a streaming, I/O-efficient format that allows coherent access to the tetrahedral cells. A quadric-based simplification is sequentially performed on small portions of the mesh in-core. Our output is a coherent streaming mesh which facilitates future processing. Our technique is fast, produces high quality approximations, and operates out-of-core to process meshes too large for main memory.

Minimizing makespan in a two-stage flow shop with parallel batch-processing machines and re-entrant jobs

NASA Astrophysics Data System (ADS)

Huang, J. D.; Liu, J. J.; Chen, Q. X.; Mao, N.

2017-06-01

Against a background of heat-treatment operations in mould manufacturing, a two-stage flow-shop scheduling problem is described for minimizing makespan with parallel batch-processing machines and re-entrant jobs. The weights and release dates of jobs are non-identical, but job processing times are equal. A mixed-integer linear programming model is developed and tested with small-scale scenarios. Given that the problem is NP hard, three heuristic construction methods with polynomial complexity are proposed. The worst case of the new constructive heuristic is analysed in detail. A method for computing lower bounds is proposed to test heuristic performance. Heuristic efficiency is tested with sets of scenarios. Compared with the two improved heuristics, the performance of the new constructive heuristic is superior.

Mapping TES Temperature Sensitivity and Current Sensitivity as a Function of Temperature, Current, and Magnetic Field with IV Curve and Complex Admittance Measurements

NASA Astrophysics Data System (ADS)

Zhou, Y.; Ambarish, C. V.; Gruenke, R.; Jaeckel, F. T.; Kripps, K. L.; McCammon, D.; Morgan, K. M.; Wulf, D.; Zhang, S.; Adams, J. S.; Bandler, S. R.; Chervenak, J. A.; Datesman, A. M.; Eckart, M. E.; Ewin, A. J.; Finkbeiner, F. M.; Kelley, R. L.; Kilbourne, C. A.; Miniussi, A. R.; Porter, F. S.; Sadleir, J. E.; Sakai, K.; Smith, S. J.; Wakeham, N. A.; Wassell, E. J.; Yoon, W.

2018-05-01

We have specialized astronomical applications for X-ray microcalorimeters with superconducting transition edge sensors (TESs) that require exceptionally good TES performance, but which operate in the small-signal regime. We have therefore begun a program to carefully characterize the entire transition surface of TESs with and without the usual zebra stripes to see if there are reproducible local "sweet spots" where the performance is much better than average. These measurements require precise knowledge of the circuit parameters. Here, we show how the Shapiro effect can be used to precisely calibrate the value of the shunt resistor. We are also investigating the effects of stress and external magnetic fields to better understand reproducibility problems.

Generalized binomial τ-leap method for biochemical kinetics incorporating both delay and intrinsic noise

NASA Astrophysics Data System (ADS)

Leier, André; Marquez-Lago, Tatiana T.; Burrage, Kevin

2008-05-01

The delay stochastic simulation algorithm (DSSA) by Barrio et al. [Plos Comput. Biol. 2, 117(E) (2006)] was developed to simulate delayed processes in cell biology in the presence of intrinsic noise, that is, when there are small-to-moderate numbers of certain key molecules present in a chemical reaction system. These delayed processes can faithfully represent complex interactions and mechanisms that imply a number of spatiotemporal processes often not explicitly modeled such as transcription and translation, basic in the modeling of cell signaling pathways. However, for systems with widely varying reaction rate constants or large numbers of molecules, the simulation time steps of both the stochastic simulation algorithm (SSA) and the DSSA can become very small causing considerable computational overheads. In order to overcome the limit of small step sizes, various τ-leap strategies have been suggested for improving computational performance of the SSA. In this paper, we present a binomial τ-DSSA method that extends the τ-leap idea to the delay setting and avoids drawing insufficient numbers of reactions, a common shortcoming of existing binomial τ-leap methods that becomes evident when dealing with complex chemical interactions. The resulting inaccuracies are most evident in the delayed case, even when considering reaction products as potential reactants within the same time step in which they are produced. Moreover, we extend the framework to account for multicellular systems with different degrees of intercellular communication. We apply these ideas to two important genetic regulatory models, namely, the hes1 gene, implicated as a molecular clock, and a Her1/Her 7 model for coupled oscillating cells.

First 101 Robotic General Surgery Cases in a Community Hospital

PubMed Central

Robertson, Jarrod C.; Alrajhi, Sharifah

2016-01-01

Background and Objectives: The general surgeon's robotic learning curve may improve if the experience is classified into categories based on the complexity of the procedures in a small community hospital. The intraoperative time should decrease and the incidence of complications should be comparable to conventional laparoscopy. The learning curve of a single robotic general surgeon in a small community hospital using the da Vinci S platform was analyzed. Methods: Measured parameters were operative time, console time, conversion rates, complications, surgical site infections (SSIs), surgical site occurrences (SSOs), length of stay, and patient demographics. Results: Between March 2014 and August 2015, 101 robotic general surgery cases were performed by a single surgeon in a 266-bed community hospital, including laparoscopic cholecystectomies, inguinal hernia repairs; ventral, incisional, and umbilical hernia repairs; and colorectal, foregut, bariatric, and miscellaneous procedures. Ninety-nine of the cases were completed robotically. Seven patients were readmitted within 30 days. There were 8 complications (7.92%). There were no mortalities and all complications were resolved with good outcomes. The mean operative time was 233.0 minutes. The mean console operative time was 117.6 minutes. Conclusion: A robotic general surgery program can be safely implemented in a small community hospital with extensive training of the surgical team through basic robotic skills courses as well as supplemental educational experiences. Although the use of the robotic platform in general surgery could be limited to complex procedures such as foregut and colorectal surgery, it can also be safely used in a large variety of operations with results similar to those of conventional laparoscopy. PMID:27667913

First 101 Robotic General Surgery Cases in a Community Hospital.

PubMed

Oviedo, Rodolfo J; Robertson, Jarrod C; Alrajhi, Sharifah

2016-01-01

The general surgeon's robotic learning curve may improve if the experience is classified into categories based on the complexity of the procedures in a small community hospital. The intraoperative time should decrease and the incidence of complications should be comparable to conventional laparoscopy. The learning curve of a single robotic general surgeon in a small community hospital using the da Vinci S platform was analyzed. Measured parameters were operative time, console time, conversion rates, complications, surgical site infections (SSIs), surgical site occurrences (SSOs), length of stay, and patient demographics. Between March 2014 and August 2015, 101 robotic general surgery cases were performed by a single surgeon in a 266-bed community hospital, including laparoscopic cholecystectomies, inguinal hernia repairs; ventral, incisional, and umbilical hernia repairs; and colorectal, foregut, bariatric, and miscellaneous procedures. Ninety-nine of the cases were completed robotically. Seven patients were readmitted within 30 days. There were 8 complications (7.92%). There were no mortalities and all complications were resolved with good outcomes. The mean operative time was 233.0 minutes. The mean console operative time was 117.6 minutes. A robotic general surgery program can be safely implemented in a small community hospital with extensive training of the surgical team through basic robotic skills courses as well as supplemental educational experiences. Although the use of the robotic platform in general surgery could be limited to complex procedures such as foregut and colorectal surgery, it can also be safely used in a large variety of operations with results similar to those of conventional laparoscopy.

Feral Cats Are Better Killers in Open Habitats, Revealed by Animal-Borne Video.

PubMed

McGregor, Hugh; Legge, Sarah; Jones, Menna E; Johnson, Christopher N

2015-01-01

One of the key gaps in understanding the impacts of predation by small mammalian predators on prey is how habitat structure affects the hunting success of small predators, such as feral cats. These effects are poorly understood due to the difficulty of observing actual hunting behaviours. We attached collar-mounted video cameras to feral cats living in a tropical savanna environment in northern Australia, and measured variation in hunting success among different microhabitats (open areas, dense grass and complex rocks). From 89 hours of footage, we recorded 101 hunting events, of which 32 were successful. Of these kills, 28% were not eaten. Hunting success was highly dependent on microhabitat structure surrounding prey, increasing from 17% in habitats with dense grass or complex rocks to 70% in open areas. This research shows that habitat structure has a profound influence on the impacts of small predators on their prey. This has broad implications for management of vegetation and disturbance processes (like fire and grazing) in areas where feral cats threaten native fauna. Maintaining complex vegetation cover can reduce predation rates of small prey species from feral cat predation.

Looking Behavior and Audiovisual Speech Understanding in Children With Normal Hearing and Children With Mild Bilateral or Unilateral Hearing Loss.

PubMed

Lewis, Dawna E; Smith, Nicholas A; Spalding, Jody L; Valente, Daniel L

Visual information from talkers facilitates speech intelligibility for listeners when audibility is challenged by environmental noise and hearing loss. Less is known about how listeners actively process and attend to visual information from different talkers in complex multi-talker environments. This study tracked looking behavior in children with normal hearing (NH), mild bilateral hearing loss (MBHL), and unilateral hearing loss (UHL) in a complex multi-talker environment to examine the extent to which children look at talkers and whether looking patterns relate to performance on a speech-understanding task. It was hypothesized that performance would decrease as perceptual complexity increased and that children with hearing loss would perform more poorly than their peers with NH. Children with MBHL or UHL were expected to demonstrate greater attention to individual talkers during multi-talker exchanges, indicating that they were more likely to attempt to use visual information from talkers to assist in speech understanding in adverse acoustics. It also was of interest to examine whether MBHL, versus UHL, would differentially affect performance and looking behavior. Eighteen children with NH, eight children with MBHL, and 10 children with UHL participated (8-12 years). They followed audiovisual instructions for placing objects on a mat under three conditions: a single talker providing instructions via a video monitor, four possible talkers alternately providing instructions on separate monitors in front of the listener, and the same four talkers providing both target and nontarget information. Multi-talker background noise was presented at a 5 dB signal-to-noise ratio during testing. An eye tracker monitored looking behavior while children performed the experimental task. Behavioral task performance was higher for children with NH than for either group of children with hearing loss. There were no differences in performance between children with UHL and children with MBHL. Eye-tracker analysis revealed that children with NH looked more at the screens overall than did children with MBHL or UHL, though individual differences were greater in the groups with hearing loss. Listeners in all groups spent a small proportion of time looking at relevant screens as talkers spoke. Although looking was distributed across all screens, there was a bias toward the right side of the display. There was no relationship between overall looking behavior and performance on the task. The present study examined the processing of audiovisual speech in the context of a naturalistic task. Results demonstrated that children distributed their looking to a variety of sources during the task, but that children with NH were more likely to look at screens than were those with MBHL/UHL. However, all groups looked at the relevant talkers as they were speaking only a small proportion of the time. Despite variability in looking behavior, listeners were able to follow the audiovisual instructions and children with NH demonstrated better performance than children with MBHL/UHL. These results suggest that performance on some challenging multi-talker audiovisual tasks is not dependent on visual fixation to relevant talkers for children with NH or with MBHL/UHL.

Factors Modulating Post-Activation Potentiation of Jump, Sprint, Throw, and Upper-Body Ballistic Performances: A Systematic Review with Meta-Analysis.

PubMed

Seitz, Laurent B; Haff, G Gregory

2016-02-01

Although post-activation potentiation (PAP) has been extensively examined following the completion of a conditioning activity (CA), the precise effects on subsequent jump, sprint, throw, and upper-body ballistic performances and the factors modulating these effects have yet to be determined. Moreover, weaker and stronger individuals seem to exhibit different PAP responses; however, how they respond to the different components of a strength-power-potentiation complex remains to be elucidated. This meta-analysis determined (1) the effect of performing a CA on subsequent jump, sprint, throw, and upper-body ballistic performances; (2) the influence of different types of CA, squat depths during the CA, rest intervals, volumes of CA, and loads during the CA on PAP; and (3) how individuals of different strength levels respond to these various strength-power-potentiation complex components. A computerized search was conducted in ADONIS, ERIC, SPORTDiscus, EBSCOhost, Google Scholar, MEDLINE, and PubMed databases up to March 2015. The analysis comprised 47 studies and 135 groups of participants for a total of 1954 participants. The PAP effect is small for jump (effect size [ES] = 0.29), throw (ES = 0.26), and upper-body ballistic (ES = 0.23) performance activities, and moderate for sprint (ES = 0.51) performance activity. A larger PAP effect is observed among stronger individuals and those with more experience in resistance training. Plyometric (ES = 0.47) CAs induce a slightly larger PAP effect than traditional high-intensity (ES = 0.41), traditional moderate-intensity (ES = 0.19), and maximal isometric (ES = -0.09) CAs, and a greater effect after shallower (ES = 0.58) versus deeper (ES = 0.25) squat CAs, longer (ES = 0.44 and 0.49) versus shorter (ES = 0.17) recovery intervals, multiple- (ES = 0.69) versus single- (ES = 0.24) set CAs, and repetition maximum (RM) (ES = 0.51) versus sub-maximal (ES = 0.34) loads during the CA. It is noteworthy that a greater PAP effect can be realized earlier after a plyometric CA than with traditional high- and moderate-intensity CAs. Additionally, shorter recovery intervals, single-set CAs, and RM CAs are more effective at inducing PAP in stronger individuals, while weaker individuals respond better to longer recovery intervals, multiple-set CAs, and sub-maximal CAs. Finally, both weaker and stronger individuals express greater PAP after shallower squat CAs. Performing a CA elicits small PAP effects for jump, throw, and upper-body ballistic performance activities, and a moderate effect for sprint performance activity. The level of potentiation is dependent on the individual's level of strength and resistance training experience, the type of CA, the depth of the squat when this exercise is employed to elicit PAP, the rest period between the CA and subsequent performance, the number of set(s) of the CA, and the type of load used during the CA. Finally, some components of the strength-power-potentiation complex modulate the PAP response of weaker and stronger individuals in a different way.

State estimation for autopilot control of small unmanned aerial vehicles in windy conditions

NASA Astrophysics Data System (ADS)

Poorman, David Paul

The use of small unmanned aerial vehicles (UAVs) both in the military and civil realms is growing. This is largely due to the proliferation of inexpensive sensors and the increase in capability of small computers that has stemmed from the personal electronic device market. Methods for performing accurate state estimation for large scale aircraft have been well known and understood for decades, which usually involve a complex array of expensive high accuracy sensors. Performing accurate state estimation for small unmanned aircraft is a newer area of study and often involves adapting known state estimation methods to small UAVs. State estimation for small UAVs can be more difficult than state estimation for larger UAVs due to small UAVs employing limited sensor suites due to cost, and the fact that small UAVs are more susceptible to wind than large aircraft. The purpose of this research is to evaluate the ability of existing methods of state estimation for small UAVs to accurately capture the states of the aircraft that are necessary for autopilot control of the aircraft in a Dryden wind field. The research begins by showing which aircraft states are necessary for autopilot control in Dryden wind. Then two state estimation methods that employ only accelerometer, gyro, and GPS measurements are introduced. The first method uses assumptions on aircraft motion to directly solve for attitude information and smooth GPS data, while the second method integrates sensor data to propagate estimates between GPS measurements and then corrects those estimates with GPS information. The performance of both methods is analyzed with and without Dryden wind, in straight and level flight, in a coordinated turn, and in a wings level ascent. It is shown that in zero wind, the first method produces significant steady state attitude errors in both a coordinated turn and in a wings level ascent. In Dryden wind, it produces large noise on the estimates for its attitude states, and has a non-zero mean error that increases when gyro bias is increased. The second method is shown to not exhibit any steady state error in the tested scenarios that is inherent to its design. The second method can correct for attitude errors that arise from both integration error and gyro bias states, but it suffers from lack of attitude error observability. The attitude errors are shown to be more observable in wind, but increased integration error in wind outweighs the increase in attitude corrections that such increased observability brings, resulting in larger attitude errors in wind. Overall, this work highlights many technical deficiencies of both of these methods of state estimation that could be improved upon in the future to enhance state estimation for small UAVs in windy conditions.

Optimizing classification performance in an object-based very-high-resolution land use-land cover urban application

NASA Astrophysics Data System (ADS)

Georganos, Stefanos; Grippa, Tais; Vanhuysse, Sabine; Lennert, Moritz; Shimoni, Michal; Wolff, Eléonore

2017-10-01

This study evaluates the impact of three Feature Selection (FS) algorithms in an Object Based Image Analysis (OBIA) framework for Very-High-Resolution (VHR) Land Use-Land Cover (LULC) classification. The three selected FS algorithms, Correlation Based Selection (CFS), Mean Decrease in Accuracy (MDA) and Random Forest (RF) based Recursive Feature Elimination (RFE), were tested on Support Vector Machine (SVM), K-Nearest Neighbor, and Random Forest (RF) classifiers. The results demonstrate that the accuracy of SVM and KNN classifiers are the most sensitive to FS. The RF appeared to be more robust to high dimensionality, although a significant increase in accuracy was found by using the RFE method. In terms of classification accuracy, SVM performed the best using FS, followed by RF and KNN. Finally, only a small number of features is needed to achieve the highest performance using each classifier. This study emphasizes the benefits of rigorous FS for maximizing performance, as well as for minimizing model complexity and interpretation.

Social learning strategies modify the effect of network structure on group performance.

PubMed

Barkoczi, Daniel; Galesic, Mirta

2016-10-07

The structure of communication networks is an important determinant of the capacity of teams, organizations and societies to solve policy, business and science problems. Yet, previous studies reached contradictory results about the relationship between network structure and performance, finding support for the superiority of both well-connected efficient and poorly connected inefficient network structures. Here we argue that understanding how communication networks affect group performance requires taking into consideration the social learning strategies of individual team members. We show that efficient networks outperform inefficient networks when individuals rely on conformity by copying the most frequent solution among their contacts. However, inefficient networks are superior when individuals follow the best member by copying the group member with the highest payoff. In addition, groups relying on conformity based on a small sample of others excel at complex tasks, while groups following the best member achieve greatest performance for simple tasks. Our findings reconcile contradictory results in the literature and have broad implications for the study of social learning across disciplines.

Social learning strategies modify the effect of network structure on group performance

NASA Astrophysics Data System (ADS)

Barkoczi, Daniel; Galesic, Mirta

2016-10-01

The structure of communication networks is an important determinant of the capacity of teams, organizations and societies to solve policy, business and science problems. Yet, previous studies reached contradictory results about the relationship between network structure and performance, finding support for the superiority of both well-connected efficient and poorly connected inefficient network structures. Here we argue that understanding how communication networks affect group performance requires taking into consideration the social learning strategies of individual team members. We show that efficient networks outperform inefficient networks when individuals rely on conformity by copying the most frequent solution among their contacts. However, inefficient networks are superior when individuals follow the best member by copying the group member with the highest payoff. In addition, groups relying on conformity based on a small sample of others excel at complex tasks, while groups following the best member achieve greatest performance for simple tasks. Our findings reconcile contradictory results in the literature and have broad implications for the study of social learning across disciplines.

Multi-Objective Control Optimization for Greenhouse Environment Using Evolutionary Algorithms

PubMed Central

Hu, Haigen; Xu, Lihong; Wei, Ruihua; Zhu, Bingkun

2011-01-01

This paper investigates the issue of tuning the Proportional Integral and Derivative (PID) controller parameters for a greenhouse climate control system using an Evolutionary Algorithm (EA) based on multiple performance measures such as good static-dynamic performance specifications and the smooth process of control. A model of nonlinear thermodynamic laws between numerous system variables affecting the greenhouse climate is formulated. The proposed tuning scheme is tested for greenhouse climate control by minimizing the integrated time square error (ITSE) and the control increment or rate in a simulation experiment. The results show that by tuning the gain parameters the controllers can achieve good control performance through step responses such as small overshoot, fast settling time, and less rise time and steady state error. Besides, it can be applied to tuning the system with different properties, such as strong interactions among variables, nonlinearities and conflicting performance criteria. The results implicate that it is a quite effective and promising tuning method using multi-objective optimization algorithms in the complex greenhouse production. PMID:22163927

Temporal Decompostion of a Distribution System Quasi-Static Time-Series Simulation

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

Mather, Barry A; Hunsberger, Randolph J

This paper documents the first phase of an investigation into reducing runtimes of complex OpenDSS models through parallelization. As the method seems promising, future work will quantify - and further mitigate - errors arising from this process. In this initial report, we demonstrate how, through the use of temporal decomposition, the run times of a complex distribution-system-level quasi-static time series simulation can be reduced roughly proportional to the level of parallelization. Using this method, the monolithic model runtime of 51 hours was reduced to a minimum of about 90 minutes. As expected, this comes at the expense of control- andmore » voltage-errors at the time-slice boundaries. All evaluations were performed using a real distribution circuit model with the addition of 50 PV systems - representing a mock complex PV impact study. We are able to reduce induced transition errors through the addition of controls initialization, though small errors persist. The time savings with parallelization are so significant that we feel additional investigation to reduce control errors is warranted.« less

Complex plane integration in the modelling of electromagnetic fields in layered media: part 1. Application to a very large loop

NASA Astrophysics Data System (ADS)

Silva, Valdelírio da Silva e.; Régis, Cícero; Howard, Allen Q., Jr.

2014-02-01

This paper analyses the details of a procedure for the numerical integration of Hankel transforms in the calculation of the electromagnetic fields generated by a large horizontal loop over a 1D earth. The method performs the integration by deforming the integration path into the complex plane and applying Cauchy's theorem on a modified version of the integrand. The modification is the replacement of the Bessel functions J0 and J1 by the Hankel functions H_0^{(1)} and H_1^{(1)} respectively. The integration in the complex plane takes advantage of the exponentially decaying behaviour of the Hankel functions, allowing calculation on very small segments, instead of the infinite line of the original improper integrals. A crucial point in this problem is the location of the poles. The companion paper shows two methods to estimate the pole locations. We have used this method to calculate the fields of very large loops. Our results show that this method allows the estimation of the integrals with fewer evaluations of the integrand functions than other methods.

Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking.

PubMed

Makeneni, Spandana; Thieker, David F; Woods, Robert J

2018-03-26

In this work, we developed a computational protocol that employs multiple molecular docking experiments, followed by pose clustering, molecular dynamic simulations (10 ns), and energy rescoring to produce reliable 3D models of antibody-carbohydrate complexes. The protocol was applied to 10 antibody-carbohydrate co-complexes and three unliganded (apo) antibodies. Pose clustering significantly reduced the number of potential poses. For each system, 15 or fewer clusters out of 100 initial poses were generated and chosen for further analysis. Molecular dynamics (MD) simulations allowed the docked poses to either converge or disperse, and rescoring increased the likelihood that the best-ranked pose was an acceptable pose. This approach is amenable to automation and can be a valuable aid in determining the structure of antibody-carbohydrate complexes provided there is no major side chain rearrangement or backbone conformational change in the H3 loop of the CDR regions. Further, the basic protocol of docking a small ligand to a known binding site, clustering the results, and performing MD with a suitable force field is applicable to any protein ligand system.

The system with zwitterionic lactose-based surfactant for complexation and delivery of small interfering ribonucleic acid—A structural and spectroscopic study

NASA Astrophysics Data System (ADS)

Skupin, Michalina; Sobczak, Krzysztof; Zieliński, Ryszard; Kozak, Maciej

2016-05-01

Systems suitable for the effective preparation of complexes with siRNA (small interfering RNA) are at the center of interest in the area of research work on the delivery of the RNA-based drugs (RNA-therapeutics). This article presents results of a study on the structural effects associated with siRNA complexation by a surfactant comprising a lactose group (N-(3-propanesulfone)-N-dodecyl-amino-beta-D-lactose hydrochloride, LA12). The double stranded siRNA oligomer (21 base pairs) used in this study is responsible for silencing a gene that can be important in the therapy of myotonic dystrophy type 1. The obtained siRNA/LA12 lipoplexes were studied using the methods of small angle scattering of synchrotron radiation, circular dichroism spectroscopy, Fourier transform infrared spectroscopy, and electrophoretic mobility tests. Lipoplexes form in solution stable lamellar or cubic phases. The surfactant selected for the study shows much lower cytotoxicity and good complexation abilities of siRNA than dicationic or polycationic surfactants.

The system with zwitterionic lactose-based surfactant for complexation and delivery of small interfering ribonucleic acid—A structural and spectroscopic study

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

Skupin, Michalina; Sobczak, Krzysztof; Zieliński, Ryszard

Systems suitable for the effective preparation of complexes with siRNA (small interfering RNA) are at the center of interest in the area of research work on the delivery of the RNA-based drugs (RNA-therapeutics). This article presents results of a study on the structural effects associated with siRNA complexation by a surfactant comprising a lactose group (N-(3-propanesulfone)-N-dodecyl-amino-beta-D-lactose hydrochloride, LA12). The double stranded siRNA oligomer (21 base pairs) used in this study is responsible for silencing a gene that can be important in the therapy of myotonic dystrophy type 1. The obtained siRNA/LA12 lipoplexes were studied using the methods of small anglemore » scattering of synchrotron radiation, circular dichroism spectroscopy, Fourier transform infrared spectroscopy, and electrophoretic mobility tests. Lipoplexes form in solution stable lamellar or cubic phases. The surfactant selected for the study shows much lower cytotoxicity and good complexation abilities of siRNA than dicationic or polycationic surfactants.« less

Identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex

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

Andersen, Jacob Lauwring, E-mail: jla@mb.au.dk; Schrøder, Tenna Juul; Christensen, Søren

2014-02-01

The identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex are reported. Sortilin is a type I membrane glycoprotein belonging to the vacuolar protein sorting 10 protein (Vps10p) family of sorting receptors and is most abundantly expressed in the central nervous system. Sortilin has emerged as a key player in the regulation of neuronal viability and has been implicated as a possible therapeutic target in a range of disorders. Here, the identification of AF40431, the first reported small-molecule ligand of sortilin, is reported. Crystals of the sortilin–AF40431 complex were obtained bymore » co-crystallization and the structure of the complex was solved to 2.7 Å resolution. AF40431 is bound in the neurotensin-binding site of sortilin, with the leucine moiety of AF40431 mimicking the binding mode of the C-terminal leucine of neurotensin and the 4-methylumbelliferone moiety of AF40431 forming π-stacking with a phenylalanine.« less

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

Mainzer, A.; Masiero, J.; Hand, E.

The NEOWISE data set offers the opportunity to study the variations in albedo for asteroid classification schemes based on visible and near-infrared observations for a large sample of minor planets. We have determined the albedos for nearly 1900 asteroids classified by the Tholen, Bus, and Bus-DeMeo taxonomic classification schemes. We find that the S-complex spans a broad range of bright albedos, partially overlapping the low albedo C-complex at small sizes. As expected, the X-complex covers a wide range of albedos. The multiwavelength infrared coverage provided by NEOWISE allows determination of the reflectivity at 3.4 and 4.6 {mu}m relative to themore » visible albedo. The direct computation of the reflectivity at 3.4 and 4.6 {mu}m enables a new means of comparing the various taxonomic classes. Although C, B, D, and T asteroids all have similarly low visible albedos, the D and T types can be distinguished from the C and B types by examining their relative reflectance at 3.4 and 4.6 {mu}m. All of the albedo distributions are strongly affected by selection biases against small, low albedo objects, as all objects selected for taxonomic classification were chosen according to their visible light brightness. Due to these strong selection biases, we are unable to determine whether or not there are correlations between size, albedo, and space weathering. We argue that the current set of classified asteroids makes any such correlations difficult to verify. A sample of taxonomically classified asteroids drawn without significant albedo bias is needed in order to perform such an analysis.« less

Deuterium Labeling Together with Contrast Variation Small-angle Neutron Scattering Suggests How Skp Captures and Releases Unfolded Outer Membrane Proteins

PubMed Central

Zaccai, Nathan R.; Sandlin, Clifford W.; Hoopes, James T.; Curtis, Joseph E.; Fleming, Patrick J.; Fleming, Karen G.; Krueger, Susan

2016-01-01

In gram-negative bacteria, the chaperone protein Skp forms specific and stable complexes with membrane proteins while they are transported across the periplasm to the outer membrane. The jellyfish-like architecture of Skp is similar to the eukaryotic and archeal prefoldins and the mitochondrial Tim chaperones, that is α-helical ‘tentacles’ extend from a β-strand ‘body’ to create an internal cavity. Contrast variation small-angle neutron scattering (SANS) experiments on Skp alone in solution and bound in two different complexes to unfolded outer membrane proteins (uOMPs), OmpA and OmpW, demonstrate that the helical tentacles of Skp bind their substrate in a clamp-like mechanism in a conformation similar to that previously observed in the apo crystal structure of Skp. Deuteration of the uOMP component combined with contrast variation analysis allowed the shapes of Skp and uOMP as well as the location of uOMP with respect to Skp to be determined in both complexes. This represents unique information that could not be obtained without deuterium labeling of the uOMPs. The data yield the first direct structural evidence that the α-helical Skp tentacles move closer together on binding its substrate and that the structure of Skp is different when binding different uOMPs. This work presents, by example, a tutorial on performing SANS experiments using both deuterium labeling and contrast variation, including SANS theory, sample preparation, data collection, sample quality validation, data analysis and structure modeling. PMID:26791979

Free-Energy Landscape of Protein-Ligand Interactions Coupled with Protein Structural Changes.

PubMed

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2017-02-02

Protein-ligand interactions are frequently coupled with protein structural changes. Focusing on the coupling, we present the free-energy surface (FES) of the ligand-binding process for glutamine-binding protein (GlnBP) and its ligand, glutamine, in which glutamine binding accompanies large-scale domain closure. All-atom simulations were performed in explicit solvents by multiscale enhanced sampling (MSES), which adopts a multicopy and multiscale scheme to achieve enhanced sampling of systems with a large number of degrees of freedom. The structural ensemble derived from the MSES simulation yielded the FES of the coupling, described in terms of both the ligand's and protein's degrees of freedom at atomic resolution, and revealed the tight coupling between the two degrees of freedom. The derived FES led to the determination of definite structural states, which suggested the dominant pathways of glutamine binding to GlnBP: first, glutamine migrates via diffusion to form a dominant encounter complex with Arg75 on the large domain of GlnBP, through strong polar interactions. Subsequently, the closing motion of GlnBP occurs to form ligand interactions with the small domain, finally completing the native-specific complex structure. The formation of hydrogen bonds between glutamine and the small domain is considered to be a rate-limiting step, inducing desolvation of the protein-ligand interface to form the specific native complex. The key interactions to attain high specificity for glutamine, the "door keeper" existing between the two domains (Asp10-Lys115) and the "hydrophobic sandwich" formed between the ligand glutamine and Phe13/Phe50, have been successfully mapped on the pathway derived from the FES.

Activation of beta-major globin gene transcription is associated with recruitment of NF-E2 to the beta-globin LCR and gene promoter.

PubMed

Sawado, T; Igarashi, K; Groudine, M

2001-08-28

The mouse beta-globin gene locus control region (LCR), located upstream of the beta-globin gene cluster, is essential for the activated transcription of genes in the cluster. The LCR contains multiple binding sites for transactivators, including Maf-recognition elements (MAREs). However, little is known about the specific proteins that bind to these sites or the time at which they bind during erythroid differentiation. We have performed chromatin immunoprecipitation experiments to determine the recruitment of the erythroid-specific transactivator p45 NF-E2/MafK (p18 NF-E2) heterodimer and small Maf proteins to various regions in the globin gene locus before and after the induction of murine erythroleukemia (MEL) cell differentiation. We report that, before induction, the LCR is occupied by small Maf proteins, and, on erythroid maturation, the NF-E2 complex is recruited to the LCR and the active globin promoters, even though the promoters do not contain MAREs. This differentiation-coupled recruitment of NF-E2 complex correlates with a greater than 100-fold increase in beta-major globin transcription, but is not associated with a significant change in locus-wide histone H3 acetylation. These findings suggest that the beta-globin gene locus exists in a constitutively open chromatin conformation before terminal differentiation, and we speculate that recruitment of NF-E2 complex to the LCR and active promoters may be a rate-limiting step in the activation of beta-globin gene expression.

Deuterium Labeling Together with Contrast Variation Small-Angle Neutron Scattering Suggests How Skp Captures and Releases Unfolded Outer Membrane Proteins.

PubMed

Zaccai, Nathan R; Sandlin, Clifford W; Hoopes, James T; Curtis, Joseph E; Fleming, Patrick J; Fleming, Karen G; Krueger, Susan

2016-01-01

In Gram-negative bacteria, the chaperone protein Skp forms specific and stable complexes with membrane proteins while they are transported across the periplasm to the outer membrane. The jellyfish-like architecture of Skp is similar to the eukaryotic and archaeal prefoldins and the mitochondrial Tim chaperones, that is the α-helical "tentacles" extend from a β-strand "body" to create an internal cavity. Contrast variation small-angle neutron scattering (SANS) experiments on Skp alone in solution and bound in two different complexes to unfolded outer membrane proteins (uOMPs), OmpA and OmpW, demonstrate that the helical tentacles of Skp bind their substrate in a clamp-like mechanism in a conformation similar to that previously observed in the apo crystal structure of Skp. Deuteration of the uOMP component combined with contrast variation analysis allowed the shapes of Skp and uOMP as well as the location of uOMP with respect to Skp to be determined in both complexes. This represents unique information that could not be obtained without deuterium labeling of the uOMPs. The data yield the first direct structural evidence that the α-helical Skp tentacles move closer together on binding its substrate and that the structure of Skp is different when binding different uOMPs. This work presents, by example, a tutorial on performing SANS experiments using both deuterium labeling and contrast variation, including SANS theory, sample preparation, data collection, sample quality validation, data analysis, and structure modeling. © 2016 Elsevier Inc. All rights reserved.

Creation of parallel algorithms for the solution of problems of gas dynamics on multi-core computers and GPU

NASA Astrophysics Data System (ADS)

Rybakin, B.; Bogatencov, P.; Secrieru, G.; Iliuha, N.

2013-10-01

The paper deals with a parallel algorithm for calculations on multiprocessor computers and GPU accelerators. The calculations of shock waves interaction with low-density bubble results and the problem of the gas flow with the forces of gravity are presented. This algorithm combines a possibility to capture a high resolution of shock waves, the second-order accuracy for TVD schemes, and a possibility to observe a low-level diffusion of the advection scheme. Many complex problems of continuum mechanics are numerically solved on structured or unstructured grids. To improve the accuracy of the calculations is necessary to choose a sufficiently small grid (with a small cell size). This leads to the drawback of a substantial increase of computation time. Therefore, for the calculations of complex problems it is reasonable to use the method of Adaptive Mesh Refinement. That is, the grid refinement is performed only in the areas of interest of the structure, where, e.g., the shock waves are generated, or a complex geometry or other such features exist. Thus, the computing time is greatly reduced. In addition, the execution of the application on the resulting sequence of nested, decreasing nets can be parallelized. Proposed algorithm is based on the AMR method. Utilization of AMR method can significantly improve the resolution of the difference grid in areas of high interest, and from other side to accelerate the processes of the multi-dimensional problems calculating. Parallel algorithms of the analyzed difference models realized for the purpose of calculations on graphic processors using the CUDA technology [1].

Screening large-scale association study data: exploiting interactions using random forests.

PubMed

Lunetta, Kathryn L; Hayward, L Brooke; Segal, Jonathan; Van Eerdewegh, Paul

2004-12-10

Genome-wide association studies for complex diseases will produce genotypes on hundreds of thousands of single nucleotide polymorphisms (SNPs). A logical first approach to dealing with massive numbers of SNPs is to use some test to screen the SNPs, retaining only those that meet some criterion for further study. For example, SNPs can be ranked by p-value, and those with the lowest p-values retained. When SNPs have large interaction effects but small marginal effects in a population, they are unlikely to be retained when univariate tests are used for screening. However, model-based screens that pre-specify interactions are impractical for data sets with thousands of SNPs. Random forest analysis is an alternative method that produces a single measure of importance for each predictor variable that takes into account interactions among variables without requiring model specification. Interactions increase the importance for the individual interacting variables, making them more likely to be given high importance relative to other variables. We test the performance of random forests as a screening procedure to identify small numbers of risk-associated SNPs from among large numbers of unassociated SNPs using complex disease models with up to 32 loci, incorporating both genetic heterogeneity and multi-locus interaction. Keeping other factors constant, if risk SNPs interact, the random forest importance measure significantly outperforms the Fisher Exact test as a screening tool. As the number of interacting SNPs increases, the improvement in performance of random forest analysis relative to Fisher Exact test for screening also increases. Random forests perform similarly to the univariate Fisher Exact test as a screening tool when SNPs in the analysis do not interact. In the context of large-scale genetic association studies where unknown interactions exist among true risk-associated SNPs or SNPs and environmental covariates, screening SNPs using random forest analyses can significantly reduce the number of SNPs that need to be retained for further study compared to standard univariate screening methods.

Analysis of thin fractures with GPR: from theory to practice

NASA Astrophysics Data System (ADS)

Arosio, Diego; Zanzi, Luigi; Longoni, Laura; Papini, Monica

2017-04-01

Whenever we perform a GPR survey to investigate a rocky medium, being the ultimate purpose of the survey either to study the stability of a rock slope or to determine the soundness of a quarried rock block, we would like mainly to detect any fracture within the investigated medium and, possibly, to estimate the parameters of the fractures, namely thickness and filling material. In most of the practical cases, rock fracture thicknesses are very small when compared to the wavelength of the electromagnetic radiation generated by the GPR systems. In such cases, fractures are to be considered as thin beds, i.e. two interfaces whose distance is smaller than GPR resolving capability, and the reflected signal is the sum of the electromagnetic reverberation within the bed. According to this, fracture parameters are encoded in the thin bed complex response and in this work we propose a methodology based on deterministic deconvolution to process amplitude and phase information in the frequency domain to estimate fracture parameters. We first present some theoretical aspects related to thin bed response and a sensitivity analysis concerning fracture thickness and filling. Secondly, we deal with GPR datasets collected both during laboratory experiments and in the facilities of quarrying activities. In the lab tests fractures were simulated by placing materials with known electromagnetic parameters and controlled thickness in between two small marble blocks, whereas field GPR surveys were performed on bigger quarried ornamental stone blocks before they were submitted to the cutting process. We show that, with basic pre-processing and the choice of a proper deconvolving signal, results are encouraging although an ambiguity between thickness and filling estimates exists when no a-priori information is available. Results can be improved by performing CMP radar surveys that are able to provide additional information (i.e., variation of thin bed response versus offset) at the expense of acquisition effort and of more complex and tricky pre-processing sequences.

III. FROM SMALL TO BIG: METHODS FOR INCORPORATING LARGE SCALE DATA INTO DEVELOPMENTAL SCIENCE.

PubMed

Davis-Kean, Pamela E; Jager, Justin

2017-06-01

For decades, developmental science has been based primarily on relatively small-scale data collections with children and families. Part of the reason for the dominance of this type of data collection is the complexity of collecting cognitive and social data on infants and small children. These small data sets are limited in both power to detect differences and the demographic diversity to generalize clearly and broadly. Thus, in this chapter we will discuss the value of using existing large-scale data sets to tests the complex questions of child development and how to develop future large-scale data sets that are both representative and can answer the important questions of developmental scientists. © 2017 The Society for Research in Child Development, Inc.

Rapid and simultaneous detection of ricin, staphylococcal enterotoxin B and saxitoxin by chemiluminescence-based microarray immunoassay.

PubMed

Szkola, A; Linares, E M; Worbs, S; Dorner, B G; Dietrich, R; Märtlbauer, E; Niessner, R; Seidel, M

2014-11-21

Simultaneous detection of small and large molecules on microarray immunoassays is a challenge that limits some applications in multiplex analysis. This is the case for biosecurity, where fast, cheap and reliable simultaneous detection of proteotoxins and small toxins is needed. Two highly relevant proteotoxins, ricin (60 kDa) and bacterial toxin staphylococcal enterotoxin B (SEB, 30 kDa) and the small phycotoxin saxitoxin (STX, 0.3 kDa) are potential biological warfare agents and require an analytical tool for simultaneous detection. Proteotoxins are successfully detected by sandwich immunoassays, whereas competitive immunoassays are more suitable for small toxins (<1 kDa). Based on this need, this work provides a novel and efficient solution based on anti-idiotypic antibodies for small molecules to combine both assay principles on one microarray. The biotoxin measurements are performed on a flow-through chemiluminescence microarray platform MCR3 in 18 minutes. The chemiluminescence signal was amplified by using a poly-horseradish peroxidase complex (polyHRP), resulting in low detection limits: 2.9 ± 3.1 μg L(-1) for ricin, 0.1 ± 0.1 μg L(-1) for SEB and 2.3 ± 1.7 μg L(-1) for STX. The developed multiplex system for the three biotoxins is completely novel, relevant in the context of biosecurity and establishes the basis for research on anti-idiotypic antibodies for microarray immunoassays.

Laparoscopic approach is feasible in Crohn's complex enterovisceral fistulas: a case-match review.

PubMed

Beyer-Berjot, Laura; Mancini, Julien; Bege, Thierry; Moutardier, Vincent; Brunet, Christian; Grimaud, Jean-Charles; Berdah, Stéphane

2013-02-01

Complex enterovisceral fistulas are internal fistulas joining a "diseased" organ to any intra-abdominal "victim" organ, with the exception of ileoileal fistulas. Few publications have addressed laparoscopic surgery for complex fistulas in Crohn's disease. The aim of this study was to evaluate the feasibility of such an approach. This study is a retrospective, case-match review. This study was conducted at a tertiary academic hospital. : All patients who underwent a laparoscopic ileocecal resection for complex enterovisceral fistulas between January 2004 and August 2011 were included. They were matched to a control group undergoing operation for nonfistulizing Crohn's disease according to age, sex, nutritional state, preoperative use of steroids, and type of resection performed. Matching was performed blind to the peri- and postoperative results of each patient. The 2 groups were compared in terms of operative time, conversion to open surgery, morbidity and mortality rates, and length of stay. Eleven patients presenting with 13 complex fistulas were included and matched with 22 controls. Group 1 contained 5 ileosigmoid fistulas (38%), 3 ileotransverse fistulas (23%), 3 ileovesical fistulas (23%), 1 colocolic fistula (8%), and 1 ileosalpingeal fistula (8%). There were no significant differences between the groups in terms of operative time (120 (range, 75-270) vs 120 (range, 50-160) minutes, p = 0.65), conversion to open surgery (9% vs 0%, p = 0.33), stoma creation (9% vs 14%, p = 1), global postoperative morbidity (18% vs 32%, p = 0.68), and major complications (Dindo III: 0% vs 9%, p = 0.54; Dindo IV: 0% vs 0%, p = 1), as well as in terms of length of stay (8 (range, 7-32) vs 9 (range, 5-17) days, p = 0.72). No patients died. This is a retrospective review with a small sample size. A laparoscopic approach for complex fistulas is feasible in Crohn's disease, with outcomes similar to those reported for nonfistulizing forms.

An Exploratory Study of the Butterfly Effect Using Agent-Based Modeling

NASA Technical Reports Server (NTRS)

Khasawneh, Mahmoud T.; Zhang, Jun; Shearer, Nevan E. N.; Rodriquez-Velasquez, Elkin; Bowling, Shannon R.

2010-01-01

This paper provides insights about the behavior of chaotic complex systems, and the sensitive dependence of the system on the initial starting conditions. How much does a small change in the initial conditions of a complex system affect it in the long term? Do complex systems exhibit what is called the "Butterfly Effect"? This paper uses an agent-based modeling approach to address these questions. An existing model from NetLogo library was extended in order to compare chaotic complex systems with near-identical initial conditions. Results show that small changes in initial starting conditions can have a huge impact on the behavior of chaotic complex systems. The term the "butterfly effect" is attributed to the work of Edward Lorenz [1]. It is used to describe the sensitive dependence of the behavior of chaotic complex systems on the initial conditions of these systems. The metaphor refers to the notion that a butterfly flapping its wings somewhere may cause extreme changes in the ecological system's behavior in the future, such as a hurricane.

[Intra-abdominal desmoplastic small round cell tumour].

PubMed

Briseño-Hernández, Andrés Alejandro; Quezada-López, Deissy Roxana; Corona-Cobián, Lilia Edith; Castañeda-Chávez, Agar; Duarte-Ojeda, Alfonso Tonatiuh; Macías-Amezcua, Michel Dassaejv

2015-01-01

The desmoplastic small round cell tumour is a rare and aggressive intra-abdominal neoplasia, with only 200 cases reported, and a higher incidence in men and predilection for the second decade of life. Histologically characterized by the presence of small nests of undifferentiated tumour cells, wrapped in fibrous desmoplastic stroma. A 24 year old male started with abdominal pain of 4 weeks onset in the right upper quadrant, colic type, sporadic, self-limiting and accompanied by early satiety, decreased appetite, and involuntary weight loss of 10 kg in 3 months. At the time of admission the abdomen was globular, with decreased peristalsis, soft, depressible. Computed tomography of the abdomen showed multiple enlarged lymph nodes in the abdominal-pelvic cavity. A laparotomy was performed, with a subsequent omentum resection due to the presence of multiple tumours, which microscopically were characterised by groups of small, round, blue cells, separated by a desmoplastic stroma. The immunohistochemistry was positive for desmin (> 75%), epithelial membrane antigen (> 75%), CD99 (> 50%), and S100 (25%), concluding with an abdominal tumour of small, round, blue cells as a diagnosis. Chemotherapy treatment was initiated based on IMAP plus GM-CSF. The desmoplastic small round cell tumour is a rare neoplasia, with diagnostic complexity and a lethal course. Its clinical presentation is unspecific. Histologically, it is classified as an aggressive soft tissue sarcoma that shares similar characteristics with the family of the small and blue cells tumours. Copyright © 2015 Academia Mexicana de Cirugía A.C. Published by Masson Doyma México S.A. All rights reserved.

POSTMAN: Point of Sail Tacking for Maritime Autonomous Navigation

NASA Technical Reports Server (NTRS)

Huntsberger, Terrance L.; Reinhart, Felix

2012-01-01

Waves apply significant forces to small boats, in particular when such vessels are moving at a high speed in severe sea conditions. In addition, small high-speed boats run the risk of diving with the bow into the next wave crest during operations in the wavelengths and wave speeds that are typical for shallow water. In order to mitigate the issues of autonomous navigation in rough water, a hybrid controller called POSTMAN combines the concept of POS (point of sail) tack planning from the sailing domain with a standard PID (proportional-integral-derivative) controller that implements reliable target reaching for the motorized small boat control task. This is an embedded, adaptive software controller that uses look-ahead sensing in a closed loop method to perform path planning for safer navigation in rough waters. State-of-the-art controllers for small boats are based on complex models of the vessel's kinematics and dynamics. They enable the vessel to follow preplanned paths accurately and can theoretically control all of the small boat s six degrees of freedom. However, the problems of bow diving and other undesirable incidents are not addressed, and it is questionable if a six-DOF controller with basically a single actuator is possible at all. POSTMAN builds an adaptive capability into the controller based on sensed wave characteristics. This software will bring a muchneeded capability to unmanned small boats moving at high speeds. Previously, this class of boat was limited to wave heights of less than one meter in the sea states in which it could operate. POSTMAN is a major advance in autonomous safety for small maritime craft.

Dynamic Frequency Shifts of Complexed Ligands: An NMR Study of D-[1- 13C,1- 2H]Glucose Complexed to the Escherichia coliPeriplasmic Glucose/Galactose Receptor

NASA Astrophysics Data System (ADS)

Gabel, Scott A.; Luck, Linda A.; Werbelow, Lawrence G.; London, Robert E.

1997-10-01

The13C multiplet structure ofD-[1-13C,1-2H]glucose complexed to theEscherichia coliperiplasmic glucose/galactose receptor has been studied as a function of temperature. Asymmetric multiplet patterns observed are shown to arise from dynamic frequency shifts. Multiplet asymmetry contributions resulting from shift anisotropy-dipolar cross correlations were found to be small, with optimal fits of the data corresponding to small, negative values of the correlation factor, χCD-CSA. Additional broadening at higher temperatures most probably results from ligand exchange between free and complexed states. Effects of internal motion are also considered theoretically, and indicate that the order parameter for the bound glucose is ≥0.9.

Theoretical study of structure and stability of small gadolinium carboxylate complexes in liquid scintillator solvents.

PubMed

Huang, Pin-Wen

2014-09-01

The structural properties of three small gadolinium carboxylate complexes in three liquid scintillator solvents (pseudocumene, linear alkylbenzene, and phenyl xylylethane) were theoretically investigated using density functional theory (B3LYP/LC-RECP) and polarizable continuum model (PCM). The average interaction energy between gadolinium atom and carboxylate ligand (E(int)) and the energy difference of the highest singly occupied molecular orbital and lowest unoccupied molecular orbital (Δ(SL)) were calculated to evaluate and compare the relative stability of these complexes in solvents. The calculation results show that the larger (with a longer alkyl chain) gadolinium carboxylate complex has greater stability than the smaller one, while these gadolinium carboxylates in linear alkylbenzene were found to have greater stability than those in the other two solvents.

Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity

PubMed Central

Rand, Tim A.; Ginalski, Krzysztof; Grishin, Nick V.; Wang, Xiaodong

2004-01-01

RNA interference is carried out by the small double-stranded RNA-induced silencing complex (RISC). The RISC-bound small RNA guides the RISC complex to identify and cleave mRNAs with complementary sequences. The proteins that make up the RISC complex and cleave mRNA have not been unequivocally defined. Here, we report the biochemical purification of RISC activity to homogeneity from Drosophila Schnieder 2 cell extracts. Argonaute 2 (Ago-2) is the sole protein component present in the purified, functional RISC. By using a bioinformatics method that combines sequence-profile analysis with predicted protein secondary structure, we found homology between the PIWI domain of Ago-2 and endonuclease V and identified potential active-site amino acid residues within the PIWI domain of Ago-2. PMID:15452342

Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity.

PubMed

Rand, Tim A; Ginalski, Krzysztof; Grishin, Nick V; Wang, Xiaodong

2004-10-05

RNA interference is carried out by the small double-stranded RNA-induced silencing complex (RISC). The RISC-bound small RNA guides the RISC complex to identify and cleave mRNAs with complementary sequences. The proteins that make up the RISC complex and cleave mRNA have not been unequivocally defined. Here, we report the biochemical purification of RISC activity to homogeneity from Drosophila Schnieder 2 cell extracts. Argonaute 2 (Ago-2) is the sole protein component present in the purified, functional RISC. By using a bioinformatics method that combines sequence-profile analysis with predicted protein secondary structure, we found homology between the PIWI domain of Ago-2 and endonuclease V and identified potential active-site amino acid residues within the PIWI domain of Ago-2.

A simple model clarifies the complicated relationships of complex networks

PubMed Central

Zheng, Bojin; Wu, Hongrun; Kuang, Li; Qin, Jun; Du, Wenhua; Wang, Jianmin; Li, Deyi

2014-01-01

Real-world networks such as the Internet and WWW have many common traits. Until now, hundreds of models were proposed to characterize these traits for understanding the networks. Because different models used very different mechanisms, it is widely believed that these traits origin from different causes. However, we find that a simple model based on optimisation can produce many traits, including scale-free, small-world, ultra small-world, Delta-distribution, compact, fractal, regular and random networks. Moreover, by revising the proposed model, the community-structure networks are generated. By this model and the revised versions, the complicated relationships of complex networks are illustrated. The model brings a new universal perspective to the understanding of complex networks and provide a universal method to model complex networks from the viewpoint of optimisation. PMID:25160506

A fast Chebyshev method for simulating flexible-wing propulsion

NASA Astrophysics Data System (ADS)

Moore, M. Nicholas J.

2017-09-01

We develop a highly efficient numerical method to simulate small-amplitude flapping propulsion by a flexible wing in a nearly inviscid fluid. We allow the wing's elastic modulus and mass density to vary arbitrarily, with an eye towards optimizing these distributions for propulsive performance. The method to determine the wing kinematics is based on Chebyshev collocation of the 1D beam equation as coupled to the surrounding 2D fluid flow. Through small-amplitude analysis of the Euler equations (with trailing-edge vortex shedding), the complete hydrodynamics can be represented by a nonlocal operator that acts on the 1D wing kinematics. A class of semi-analytical solutions permits fast evaluation of this operator with O (Nlog ⁡ N) operations, where N is the number of collocation points on the wing. This is in contrast to the minimum O (N2) cost of a direct 2D fluid solver. The coupled wing-fluid problem is thus recast as a PDE with nonlocal operator, which we solve using a preconditioned iterative method. These techniques yield a solver of near-optimal complexity, O (Nlog ⁡ N) , allowing one to rapidly search the infinite-dimensional parameter space of all possible material distributions and even perform optimization over this space.

Investigating the relative permeability behavior of microporosity-rich carbonates and tight sandstones with multiscale pore network models

NASA Astrophysics Data System (ADS)

Bultreys, Tom; Stappen, Jeroen Van; Kock, Tim De; Boever, Wesley De; Boone, Marijn A.; Hoorebeke, Luc Van; Cnudde, Veerle

2016-11-01

The relative permeability behavior of rocks with wide ranges of pore sizes is in many cases still poorly understood and is difficult to model at the pore scale. In this work, we investigate the capillary pressure and relative permeability behavior of three outcrop carbonates and two tight reservoir sandstones with wide, multimodal pore size distributions. To examine how the drainage and imbibition properties of these complex rock types are influenced by the connectivity of macropores to each other and to zones with unresolved small-scale porosity, we apply a previously presented microcomputed-tomography-based multiscale pore network model to these samples. The sensitivity to the properties of the small-scale porosity is studied by performing simulations with different artificial sphere-packing-based networks as a proxy for these pores. Finally, the mixed-wet water-flooding behavior of the samples is investigated, assuming different wettability distributions for the microporosity and macroporosity. While this work is not an attempt to perform predictive modeling, it seeks to qualitatively explain the behavior of the investigated samples and illustrates some of the most recent developments in multiscale pore network modeling.

Optimal Phase Oscillatory Network

NASA Astrophysics Data System (ADS)

Follmann, Rosangela

2013-03-01

Important topics as preventive detection of epidemics, collective self-organization, information flow and systemic robustness in clusters are typical examples of processes that can be studied in the context of the theory of complex networks. It is an emerging theory in a field, which has recently attracted much interest, involving the synchronization of dynamical systems associated to nodes, or vertices, of the network. Studies have shown that synchronization in oscillatory networks depends not only on the individual dynamics of each element, but also on the combination of the topology of the connections as well as on the properties of the interactions of these elements. Moreover, the response of the network to small damages, caused at strategic points, can enhance the global performance of the whole network. In this presentation we explore an optimal phase oscillatory network altered by an additional term in the coupling function. The application to associative-memory network shows improvement on the correct information retrieval as well as increase of the storage capacity. The inclusion of some small deviations on the nodes, when solutions are attracted to a false state, results in additional enhancement of the performance of the associative-memory network. Supported by FAPESP - Sao Paulo Research Foundation, grant number 2012/12555-4

Discrete Event Modeling and Massively Parallel Execution of Epidemic Outbreak Phenomena

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

Perumalla, Kalyan S; Seal, Sudip K

2011-01-01

In complex phenomena such as epidemiological outbreaks, the intensity of inherent feedback effects and the significant role of transients in the dynamics make simulation the only effective method for proactive, reactive or post-facto analysis. The spatial scale, runtime speed, and behavioral detail needed in detailed simulations of epidemic outbreaks make it necessary to use large-scale parallel processing. Here, an optimistic parallel execution of a new discrete event formulation of a reaction-diffusion simulation model of epidemic propagation is presented to facilitate in dramatically increasing the fidelity and speed by which epidemiological simulations can be performed. Rollback support needed during optimistic parallelmore » execution is achieved by combining reverse computation with a small amount of incremental state saving. Parallel speedup of over 5,500 and other runtime performance metrics of the system are observed with weak-scaling execution on a small (8,192-core) Blue Gene / P system, while scalability with a weak-scaling speedup of over 10,000 is demonstrated on 65,536 cores of a large Cray XT5 system. Scenarios representing large population sizes exceeding several hundreds of millions of individuals in the largest cases are successfully exercised to verify model scalability.« less

Multiscale modelling for tokamak pedestals

NASA Astrophysics Data System (ADS)

Abel, I. G.

2018-04-01

Pedestal modelling is crucial to predict the performance of future fusion devices. Current modelling efforts suffer either from a lack of kinetic physics, or an excess of computational complexity. To ameliorate these problems, we take a first-principles multiscale approach to the pedestal. We will present three separate sets of equations, covering the dynamics of edge localised modes (ELMs), the inter-ELM pedestal and pedestal turbulence, respectively. Precisely how these equations should be coupled to each other is covered in detail. This framework is completely self-consistent; it is derived from first principles by means of an asymptotic expansion of the fundamental Vlasov-Landau-Maxwell system in appropriate small parameters. The derivation exploits the narrowness of the pedestal region, the smallness of the thermal gyroradius and the low plasma (the ratio of thermal to magnetic pressures) typical of current pedestal operation to achieve its simplifications. The relationship between this framework and gyrokinetics is analysed, and possibilities to directly match our systems of equations onto multiscale gyrokinetics are explored. A detailed comparison between our model and other models in the literature is performed. Finally, the potential for matching this framework onto an open-field-line region is briefly discussed.

Small intestinal bacterial overgrowth syndrome

PubMed Central

Bures, Jan; Cyrany, Jiri; Kohoutova, Darina; Förstl, Miroslav; Rejchrt, Stanislav; Kvetina, Jaroslav; Vorisek, Viktor; Kopacova, Marcela

2010-01-01

Human intestinal microbiota create a complex polymicrobial ecology. This is characterised by its high population density, wide diversity and complexity of interaction. Any dysbalance of this complex intestinal microbiome, both qualitative and quantitative, might have serious health consequence for a macro-organism, including small intestinal bacterial overgrowth syndrome (SIBO). SIBO is defined as an increase in the number and/or alteration in the type of bacteria in the upper gastrointestinal tract. There are several endogenous defence mechanisms for preventing bacterial overgrowth: gastric acid secretion, intestinal motility, intact ileo-caecal valve, immunoglobulins within intestinal secretion and bacteriostatic properties of pancreatic and biliary secretion. Aetiology of SIBO is usually complex, associated with disorders of protective antibacterial mechanisms (e.g. achlorhydria, pancreatic exocrine insufficiency, immunodeficiency syndromes), anatomical abnormalities (e.g. small intestinal obstruction, diverticula, fistulae, surgical blind loop, previous ileo-caecal resections) and/or motility disorders (e.g. scleroderma, autonomic neuropathy in diabetes mellitus, post-radiation enteropathy, small intestinal pseudo-obstruction). In some patients more than one factor may be involved. Symptoms related to SIBO are bloating, diarrhoea, malabsorption, weight loss and malnutrition. The gold standard for diagnosing SIBO is still microbial investigation of jejunal aspirates. Non-invasive hydrogen and methane breath tests are most commonly used for the diagnosis of SIBO using glucose or lactulose. Therapy for SIBO must be complex, addressing all causes, symptoms and complications, and fully individualised. It should include treatment of the underlying disease, nutritional support and cyclical gastro-intestinal selective antibiotics. Prognosis is usually serious, determined mostly by the underlying disease that led to SIBO. PMID:20572300

Disentangling the complexity of tropical small-scale fisheries dynamics using supervised Self-Organizing Maps.

PubMed

Mendoza-Carranza, Manuel; Ejarque, Elisabet; Nagelkerke, Leopold A J

2018-01-01

Tropical small-scale fisheries are typical for providing complex multivariate data, due to their diversity in fishing techniques and highly diverse species composition. In this paper we used for the first time a supervised Self-Organizing Map (xyf-SOM), to recognize and understand the internal heterogeneity of a tropical marine small-scale fishery, using as model the fishery fleet of San Pedro port, Tabasco, Mexico. We used multivariate data from commercial logbooks, including the following four factors: fish species (47), gear types (bottom longline, vertical line+shark longline and vertical line), season (cold, warm), and inter-annual variation (2007-2012). The size of the xyf-SOM, a fundamental characteristic to improve its predictive quality, was optimized for the minimum distance between objects and the maximum prediction rate. The xyf-SOM successfully classified individual fishing trips in relation to the four factors included in the model. Prediction percentages were high (80-100%) for bottom longline and vertical line + shark longline, but lower prediction values were obtained for vertical line (51-74%) fishery. A confusion matrix indicated that classification errors occurred within the same fishing gear. Prediction rates were validated by generating confidence interval using bootstrap. The xyf-SOM showed that not all the fishing trips were targeting the most abundant species and the catch rates were not symmetrically distributed around the mean. Also, the species composition is not homogeneous among fishing trips. Despite the complexity of the data, the xyf-SOM proved to be an excellent tool to identify trends in complex scenarios, emphasizing the diverse and complex patterns that characterize tropical small scale-fishery fleets.

a Sensor Aided H.264/AVC Video Encoder for Aerial Video Sequences with in the Loop Metadata Correction

NASA Astrophysics Data System (ADS)

Cicala, L.; Angelino, C. V.; Ruatta, G.; Baccaglini, E.; Raimondo, N.

2015-08-01

Unmanned Aerial Vehicles (UAVs) are often employed to collect high resolution images in order to perform image mosaicking and/or 3D reconstruction. Images are usually stored on board and then processed with on-ground desktop software. In such a way the computational load, and hence the power consumption, is moved on ground, leaving on board only the task of storing data. Such an approach is important in the case of small multi-rotorcraft UAVs because of their low endurance due to the short battery life. Images can be stored on board with either still image or video data compression. Still image system are preferred when low frame rates are involved, because video coding systems are based on motion estimation and compensation algorithms which fail when the motion vectors are significantly long and when the overlapping between subsequent frames is very small. In this scenario, UAVs attitude and position metadata from the Inertial Navigation System (INS) can be employed to estimate global motion parameters without video analysis. A low complexity image analysis can be still performed in order to refine the motion field estimated using only the metadata. In this work, we propose to use this refinement step in order to improve the position and attitude estimation produced by the navigation system in order to maximize the encoder performance. Experiments are performed on both simulated and real world video sequences.

Radiation Hardness Assurance (RHA) for Small Missions

NASA Technical Reports Server (NTRS)

Campola, Michael J.

2016-01-01

Varied mission life and complexity is growing for small spacecraft. Small missions benefit from detailed hazard definition and evaluation as done in the past. Requirements need to flow from the system down to the parts level and aid system level radiation tolerance. RHA is highlighted with increasing COTS usage.

The Complexities of Operating Multiple Small Schools in a High School Conversion

ERIC Educational Resources Information Center

Wallach, Catherine A.

2010-01-01

School reformers hope that converting comprehensive high schools into collections of small schools will produce results similar to those realized in freestanding small schools. Three themes--personalization, professional community, and shared decision making--exemplify the early successes in conversions. But the challenge of sustaining these gains…

Cellular manganese content is developmentally regulated in human dopaminergic neurons

NASA Astrophysics Data System (ADS)

Kumar, Kevin K.; Lowe, Edward W., Jr.; Aboud, Asad A.; Neely, M. Diana; Redha, Rey; Bauer, Joshua A.; Odak, Mihir; Weaver, C. David; Meiler, Jens; Aschner, Michael; Bowman, Aaron B.

2014-10-01

Manganese (Mn) is both an essential biological cofactor and neurotoxicant. Disruption of Mn biology in the basal ganglia has been implicated in the pathogenesis of neurodegenerative disorders, such as parkinsonism and Huntington's disease. Handling of other essential metals (e.g. iron and zinc) occurs via complex intracellular signaling networks that link metal detection and transport systems. However, beyond several non-selective transporters, little is known about the intracellular processes regulating neuronal Mn homeostasis. We hypothesized that small molecules that modulate intracellular Mn could provide insight into cell-level Mn regulatory mechanisms. We performed a high throughput screen of 40,167 small molecules for modifiers of cellular Mn content in a mouse striatal neuron cell line. Following stringent validation assays and chemical informatics, we obtained a chemical `toolbox' of 41 small molecules with diverse structure-activity relationships that can alter intracellular Mn levels under biologically relevant Mn exposures. We utilized this toolbox to test for differential regulation of Mn handling in human floor-plate lineage dopaminergic neurons, a lineage especially vulnerable to environmental Mn exposure. We report differential Mn accumulation between developmental stages and stage-specific differences in the Mn-altering activity of individual small molecules. This work demonstrates cell-level regulation of Mn content across neuronal differentiation.

SMEs, IT, and the Third Space: Colonization and Creativity in the Theatre Industry

NASA Astrophysics Data System (ADS)

Kendall, Julie E.; Kendall, Kenneth E.

We examine how small and medium-sized, professional, nonprofit performing arts theatres in the US can improve the strategic use of information technology (IT), as well as other aspects of theatre management for large, commercial theatre productions in the West End of London and on Broadway in New York City. In this article we use the epistemology of the third space developed by Bhabha (1994) and extended by Frenkel (2008). Although both authors were discussing knowledge transfer, we use their conceptualizations to characterize and explore more deeply the transfer process of culture (and thereby useful practices and worthwhile lessons) from small and medium-sized professional, nonprofit theaters to large-scale commercial theatres. We include a discussion of Nonaka’s (1991) concept of ba, and how it relates to the third space. We specifically employ the metaphor of the third space developed by Bhabha (1994) to critique and understand the verbal and nonverbal cultural transmissions between small and large theatres. One of our contributions is to use the conceptualization and metaphor of the third space to understand the complex exchanges and relationships between small to medium-sized nonprofit professional theatres and large commercial theatres, and to identify what large commercial productions can learn from nonprofit theatres from these exchanges.

Novel Regulatory Small RNAs in Streptococcus pyogenes

PubMed Central

Tesorero, Rafael A.; Yu, Ning; Wright, Jordan O.; Svencionis, Juan P.; Cheng, Qiang; Kim, Jeong-Ho; Cho, Kyu Hong

2013-01-01

Streptococcus pyogenes (Group A Streptococcus or GAS) is a Gram-positive bacterial pathogen that has shown complex modes of regulation of its virulence factors to cause diverse diseases. Bacterial small RNAs are regarded as novel widespread regulators of gene expression in response to environmental signals. Recent studies have revealed that several small RNAs (sRNAs) have an important role in S. pyogenes physiology and pathogenesis by regulating gene expression at the translational level. To search for new sRNAs in S. pyogenes, we performed a genomewide analysis through computational prediction followed by experimental verification. To overcome the limitation of low accuracy in computational prediction, we employed a combination of three different computational algorithms (sRNAPredict, eQRNA and RNAz). A total of 45 candidates were chosen based on the computational analysis, and their transcription was analyzed by reverse-transcriptase PCR and Northern blot. Through this process, we discovered 7 putative novel trans-acting sRNAs. Their abundance varied between different growth phases, suggesting that their expression is influenced by environmental or internal signals. Further, to screen target mRNAs of an sRNA, we employed differential RNA sequencing analysis. This study provides a significant resource for future study of small RNAs and their roles in physiology and pathogenesis of S. pyogenes. PMID:23762235

Distributional potential of the Triatoma brasiliensis species complex at present and under scenarios of future climate conditions

PubMed Central

2014-01-01

Background The Triatoma brasiliensis complex is a monophyletic group, comprising three species, one of which includes two subspecific taxa, distributed across 12 Brazilian states, in the caatinga and cerrado biomes. Members of the complex are diverse in terms of epidemiological importance, morphology, biology, ecology, and genetics. Triatoma b. brasiliensis is the most disease-relevant member of the complex in terms of epidemiology, extensive distribution, broad feeding preferences, broad ecological distribution, and high rates of infection with Trypanosoma cruzi; consequently, it is considered the principal vector of Chagas disease in northeastern Brazil. Methods We used ecological niche models to estimate potential distributions of all members of the complex, and evaluated the potential for suitable adjacent areas to be colonized; we also present first evaluations of potential for climate change-mediated distributional shifts. Models were developed using the GARP and Maxent algorithms. Results Models for three members of the complex (T. b. brasiliensis, N = 332; T. b. macromelasoma, N = 35; and T. juazeirensis, N = 78) had significant distributional predictivity; however, models for T. sherlocki and T. melanica, both with very small sample sizes (N = 7), did not yield predictions that performed better than random. Model projections onto future-climate scenarios indicated little broad-scale potential for change in the potential distribution of the complex through 2050. Conclusions This study suggests that T. b. brasiliensis is the member of the complex with the greatest distributional potential to colonize new areas: overall; however, the distribution of the complex appears relatively stable. These analyses offer key information to guide proactive monitoring and remediation activities to reduce risk of Chagas disease transmission. PMID:24886587

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates.

PubMed

Leung, Kaston; Klaus, Anders; Lin, Bill K; Laks, Emma; Biele, Justina; Lai, Daniel; Bashashati, Ali; Huang, Yi-Fei; Aniba, Radhouane; Moksa, Michelle; Steif, Adi; Mes-Masson, Anne-Marie; Hirst, Martin; Shah, Sohrab P; Aparicio, Samuel; Hansen, Carl L

2016-07-26

The genomes of large numbers of single cells must be sequenced to further understanding of the biological significance of genomic heterogeneity in complex systems. Whole genome amplification (WGA) of single cells is generally the first step in such studies, but is prone to nonuniformity that can compromise genomic measurement accuracy. Despite recent advances, robust performance in high-throughput single-cell WGA remains elusive. Here, we introduce droplet multiple displacement amplification (MDA), a method that uses commercially available liquid dispensing to perform high-throughput single-cell MDA in nanoliter volumes. The performance of droplet MDA is characterized using a large dataset of 129 normal diploid cells, and is shown to exceed previously reported single-cell WGA methods in amplification uniformity, genome coverage, and/or robustness. We achieve up to 80% coverage of a single-cell genome at 5× sequencing depth, and demonstrate excellent single-nucleotide variant (SNV) detection using targeted sequencing of droplet MDA product to achieve a median allelic dropout of 15%, and using whole genome sequencing to achieve false and true positive rates of 9.66 × 10(-6) and 68.8%, respectively, in a G1-phase cell. We further show that droplet MDA allows for the detection of copy number variants (CNVs) as small as 30 kb in single cells of an ovarian cancer cell line and as small as 9 Mb in two high-grade serous ovarian cancer samples using only 0.02× depth. Droplet MDA provides an accessible and scalable method for performing robust and accurate CNV and SNV measurements on large numbers of single cells.

A methodology for spacecraft technology insertion analysis balancing benefit, cost, and risk

NASA Astrophysics Data System (ADS)

Bearden, David Allen

Emerging technologies are changing the way space missions are developed and implemented. Technology development programs are proceeding with the goal of enhancing spacecraft performance and reducing mass and cost. However, it is often the case that technology insertion assessment activities, in the interest of maximizing performance and/or mass reduction, do not consider synergistic system-level effects. Furthermore, even though technical risks are often identified as a large cost and schedule driver, many design processes ignore effects of cost and schedule uncertainty. This research is based on the hypothesis that technology selection is a problem of balancing interrelated (and potentially competing) objectives. Current spacecraft technology selection approaches are summarized, and a Methodology for Evaluating and Ranking Insertion of Technology (MERIT) that expands on these practices to attack otherwise unsolved problems is demonstrated. MERIT combines the modern techniques of technology maturity measures, parametric models, genetic algorithms, and risk assessment (cost and schedule) in a unique manner to resolve very difficult issues including: user-generated uncertainty, relationships between cost/schedule and complexity, and technology "portfolio" management. While the methodology is sufficiently generic that it may in theory be applied to a number of technology insertion problems, this research focuses on application to the specific case of small (<500 kg) satellite design. Small satellite missions are of particular interest because they are often developed under rigid programmatic (cost and schedule) constraints and are motivated to introduce advanced technologies into the design. MERIT is demonstrated for programs procured under varying conditions and constraints such as stringent performance goals, not-to-exceed costs, or hard schedule requirements. MERIT'S contributions to the engineering community are its: unique coupling of the aspects of performance, cost, and schedule; assessment of system level impacts of technology insertion; procedures for estimating uncertainties (risks) associated with advanced technology; and application of heuristics to facilitate informed system-level technology utilization decisions earlier in the conceptual design phase. MERIT extends the state of the art in technology insertion assessment selection practice and, if adopted, may aid designers in determining the configuration of complex systems that meet essential requirements in a timely, cost-effective manner.

Multi-stage decoding for multi-level block modulation codes

NASA Technical Reports Server (NTRS)

Lin, Shu

1991-01-01

In this paper, we investigate various types of multi-stage decoding for multi-level block modulation codes, in which the decoding of a component code at each stage can be either soft-decision or hard-decision, maximum likelihood or bounded-distance. Error performance of codes is analyzed for a memoryless additive channel based on various types of multi-stage decoding, and upper bounds on the probability of an incorrect decoding are derived. Based on our study and computation results, we find that, if component codes of a multi-level modulation code and types of decoding at various stages are chosen properly, high spectral efficiency and large coding gain can be achieved with reduced decoding complexity. In particular, we find that the difference in performance between the suboptimum multi-stage soft-decision maximum likelihood decoding of a modulation code and the single-stage optimum decoding of the overall code is very small: only a fraction of dB loss in SNR at the probability of an incorrect decoding for a block of 10(exp -6). Multi-stage decoding of multi-level modulation codes really offers a way to achieve the best of three worlds, bandwidth efficiency, coding gain, and decoding complexity.

MiR-21 is enriched in the RNA-induced silencing complex and targets COL4A1 in human granulosa cell lines.

PubMed

Mase, Yuri; Ishibashi, Osamu; Ishikawa, Tomoko; Takizawa, Takami; Kiguchi, Kazushige; Ohba, Takashi; Katabuchi, Hidetaka; Takeshita, Toshiyuki; Takizawa, Toshihiro

2012-10-01

MicroRNAs (miRNAs) are noncoding small RNAs that play important roles in a variety of physiological and pathological events. In this study, we performed large-scale profiling of EIF2C2-bound miRNAs in 3 human granulosa-derived cell lines (ie, KGN, HSOGT, and GC1a) by high-throughput sequencing and found that miR-21 accounted for more than 80% of EIF2C2-bound miRNAs, suggesting that it was enriched in the RNA-induced silencing complex (RISC) and played a functional role in human granulosa cell (GC) lines. We also found high expression levels of miR-21 in primary human GCs. Assuming that miR-21 target mRNAs are enriched in RISC, we performed cDNA cloning of EIF2C2-bound mRNAs in KGN cells. We identified COL4A1 mRNA as a miR-21 target in the GC lines. These data suggest that miR-21 is involved in the regulation of the synthesis of COL4A1, a component of the basement membrane surrounding the GC layer and granulosa-embedded extracellular structure.

Going Up. A GPS Receiver Adapts to Space

NASA Technical Reports Server (NTRS)

Lightsey, E. Glenn; Simpson, James E.

2000-01-01

Current plans for the space station call for the GPS receiver to be installed on the U.S. lab module of the station in early 2001 (ISS Assembly Flight SA), followed by the attachment of the antenna array in late 2001 (Flight 8A). At that point the U.S. ISS guidance and control system will be operational. The flight of SIGI on the space station represents a "coming of age" for GPS technology on spacecraft. For at least a decade, the promise of using GPS receivers to automate spacecraft operations, simplify satellite design, and reduce mission costs has enticed satellite designers. Integration of this technology onto spacecraft has been slower than some originally anticipated. However, given the complexity of the GPS sensor, and the importance of the functions it performs, its incorporation into mainstream satellite design has probably occurred at a very reasonable pace. Going from providing experimental payloads on small, unmanned satellites to performing critical operational functions on manned vehicles has been a major evolution. If all goes as planned in the next few months, GPS receivers will soon provide those critical functions on one of the most complex spacecraft in history, the International Space Station.

[The evolution of Chilean universities from 1981 to 2004].

PubMed

Cruz-Coke, Ricardo

2004-12-01

In 1981, a supreme decree allowed the creation of private universities in Chile. As a consequence, 50 new universities were created in one decade, under the surveillance of the Council for Superior Education. This paper analyzes the evolution of this expansion process, that resulted in an admission of 370,000 students to 60 universities along the country, during 2004. At the moment, 42% of the universities, designed as traditional, receive state financing and 58% are private. Twenty six percent are owned by the state, 52% are secular and 22% are confessional. The 25 traditional universities are complex organizations of a high academic level. New private universities are only devoted to teaching and some have obtained their autonomy. Some have improved the quality of their academic staff, perform research and impart doctorate degrees. However, most are small and with a limited academic staff. Traditional universities are stratified in a superior level. Eight private universities and some regional institutions, that are becoming complex and performing research activities, are stratified in a middle level. Two thirds of the private universities are in the lower level. The expansion of superior education is a sign of the social and cultural progress that Chile has experienced.

Inhibiting diffusion of complex contagions in social networks: theoretical and experimental results

PubMed Central

Anil Kumar, V.S.; Marathe, Madhav V.; Ravi, S.S.; Rosenkrantz, Daniel J.

2014-01-01

We consider the problem of inhibiting undesirable contagions (e.g. rumors, spread of mob behavior) in social networks. Much of the work in this context has been carried out under the 1-threshold model, where diffusion occurs when a node has just one neighbor with the contagion. We study the problem of inhibiting more complex contagions in social networks where nodes may have thresholds larger than 1. The goal is to minimize the propagation of the contagion by removing a small number of nodes (called critical nodes) from the network. We study several versions of this problem and prove that, in general, they cannot even be efficiently approximated to within any factor ρ ≥ 1, unless P = NP. We develop efficient and practical heuristics for these problems and carry out an experimental study of their performance on three well known social networks, namely epinions, wikipedia and slashdot. Our results show that these heuristics perform significantly better than five other known methods. We also establish an efficiently computable upper bound on the number of nodes to which a contagion can spread and evaluate this bound on many real and synthetic networks. PMID:25750583

The Unknown Oldowan: ~1.7-Million-Year-Old Standardized Obsidian Small Tools from Garba IV, Melka Kunture, Ethiopia

PubMed Central

2015-01-01

The Oldowan Industrial Complex has long been thought to have been static, with limited internal variability, embracing techno-complexes essentially focused on small-to-medium flake production. The flakes were rarely modified by retouch to produce small tools, which do not show any standardized pattern. Usually, the manufacture of small standardized tools has been interpreted as a more complex behavior emerging with the Acheulean technology. Here we report on the ~1.7 Ma Oldowan assemblages from Garba IVE-F at Melka Kunture in the Ethiopian highland. This industry is structured by technical criteria shared by the other East African Oldowan assemblages. However, there is also evidence of a specific technical process never recorded before, i.e. the systematic production of standardized small pointed tools strictly linked to the obsidian exploitation. Standardization and raw material selection in the manufacture of small tools disappear at Melka Kunture during the Lower Pleistocene Acheulean. This proves that 1) the emergence of a certain degree of standardization in tool-kits does not reflect in itself a major step in cultural evolution; and that 2) the Oldowan knappers, when driven by functional needs and supported by a highly suitable raw material, were occasionally able to develop specific technical solutions. The small tool production at ~1.7 Ma, at a time when the Acheulean was already emerging elsewhere in East Africa, adds to the growing amount of evidence of Oldowan techno-economic variability and flexibility, further challenging the view that early stone knapping was static over hundreds of thousands of years. PMID:26690569

The Unknown Oldowan: ~1.7-Million-Year-Old Standardized Obsidian Small Tools from Garba IV, Melka Kunture, Ethiopia.

PubMed

Gallotti, Rosalia; Mussi, Margherita

2015-01-01

The Oldowan Industrial Complex has long been thought to have been static, with limited internal variability, embracing techno-complexes essentially focused on small-to-medium flake production. The flakes were rarely modified by retouch to produce small tools, which do not show any standardized pattern. Usually, the manufacture of small standardized tools has been interpreted as a more complex behavior emerging with the Acheulean technology. Here we report on the ~1.7 Ma Oldowan assemblages from Garba IVE-F at Melka Kunture in the Ethiopian highland. This industry is structured by technical criteria shared by the other East African Oldowan assemblages. However, there is also evidence of a specific technical process never recorded before, i.e. the systematic production of standardized small pointed tools strictly linked to the obsidian exploitation. Standardization and raw material selection in the manufacture of small tools disappear at Melka Kunture during the Lower Pleistocene Acheulean. This proves that 1) the emergence of a certain degree of standardization in tool-kits does not reflect in itself a major step in cultural evolution; and that 2) the Oldowan knappers, when driven by functional needs and supported by a highly suitable raw material, were occasionally able to develop specific technical solutions. The small tool production at ~1.7 Ma, at a time when the Acheulean was already emerging elsewhere in East Africa, adds to the growing amount of evidence of Oldowan techno-economic variability and flexibility, further challenging the view that early stone knapping was static over hundreds of thousands of years.

Boosting-Based Optimization as a Generic Framework for Novelty and Fraud Detection in Complex Strategies

NASA Astrophysics Data System (ADS)

Gavrishchaka, Valeriy V.; Kovbasinskaya, Maria; Monina, Maria

2008-11-01

Novelty detection is a very desirable additional feature of any practical classification or forecasting system. Novelty and rare patterns detection is the main objective in such applications as fault/abnormality discovery in complex technical and biological systems, fraud detection and risk management in financial and insurance industry. Although many interdisciplinary approaches for rare event modeling and novelty detection have been proposed, significant data incompleteness due to the nature of the problem makes it difficult to find a universal solution. Even more challenging and much less formalized problem is novelty detection in complex strategies and models where practical performance criteria are usually multi-objective and the best state-of-the-art solution is often not known due to the complexity of the task and/or proprietary nature of the application area. For example, it is much more difficult to detect a series of small insider trading or other illegal transactions mixed with valid operations and distributed over long time period according to a well-designed strategy than a single, large fraudulent transaction. Recently proposed boosting-based optimization was shown to be an effective generic tool for the discovery of stable multi-component strategies/models from the existing parsimonious base strategies/models in financial and other applications. Here we outline how the same framework can be used for novelty and fraud detection in complex strategies and models.