Modeling of chromosome intermingling by partially overlapping uniform random polygons.

PubMed

Blackstone, T; Scharein, R; Borgo, B; Varela, R; Diao, Y; Arsuaga, J

2011-03-01

During the early phase of the cell cycle the eukaryotic genome is organized into chromosome territories. The geometry of the interface between any two chromosomes remains a matter of debate and may have important functional consequences. The Interchromosomal Network model (introduced by Branco and Pombo) proposes that territories intermingle along their periphery. In order to partially quantify this concept we here investigate the probability that two chromosomes form an unsplittable link. We use the uniform random polygon as a crude model for chromosome territories and we model the interchromosomal network as the common spatial region of two overlapping uniform random polygons. This simple model allows us to derive some rigorous mathematical results as well as to perform computer simulations easily. We find that the probability that one uniform random polygon of length n that partially overlaps a fixed polygon is bounded below by 1 − O(1/√n). We use numerical simulations to estimate the dependence of the linking probability of two uniform random polygons (of lengths n and m, respectively) on the amount of overlapping. The degree of overlapping is parametrized by a parameter [Formula: see text] such that [Formula: see text] indicates no overlapping and [Formula: see text] indicates total overlapping. We propose that this dependence relation may be modeled as f (ε, m, n) = [Formula: see text]. Numerical evidence shows that this model works well when [Formula: see text] is relatively large (ε ≥ 0.5). We then use these results to model the data published by Branco and Pombo and observe that for the amount of overlapping observed experimentally the URPs have a non-zero probability of forming an unsplittable link.

Piecemeal Rupture of the Mentawai Patch, Sumatra: The 2008 Mw 7.2 North Pagai Earthquake Sequence

NASA Astrophysics Data System (ADS)

Salman, Rino; Hill, Emma M.; Feng, Lujia; Lindsey, Eric O.; Mele Veedu, Deepa; Barbot, Sylvain; Banerjee, Paramesh; Hermawan, Iwan; Natawidjaja, Danny H.

2017-11-01

The 25 February 2008 Mw 7.2 North Pagai earthquake partially ruptured the middle section of the Mentawai patch of the Sunda megathrust, offshore Sumatra. The patch has been forecast to generate a great earthquake in the next few decades. However, in the current cycle the patch has so far broken in a sequence of partial ruptures, one of which was the 2008 event, illustrating the potential of the patch to generate a spectrum of earthquake sizes. We estimate the coseismic slip distribution of the 2008 event by jointly inverting coseismic offsets from GPS and interferometric synthetic aperture radar. We then estimate afterslip with 5.6 years of cumulative GPS displacements. Our results suggest that the estimated afterslip partially overlaps the coseismic rupture. The overlap of coseismic rupture and afterslip can be explained conceptually by a simple rate-and-state model where the degree of overlapping is controlled by the dynamic weakening and the critical nucleation size in the velocity-weakening area. Comparing our rate-and-state model results with our geodetic inversion results, we suggest that the part of the coseismic rupture that does not overlap with the afterslip may represent a velocity-weakening region, while the overlapping part may represent a velocity-strengthening region.

Locating hardware faults in a parallel computer

DOEpatents

Archer, Charles J.; Megerian, Mark G.; Ratterman, Joseph D.; Smith, Brian E.

2010-04-13

Locating hardware faults in a parallel computer, including defining within a tree network of the parallel computer two or more sets of non-overlapping test levels of compute nodes of the network that together include all the data communications links of the network, each non-overlapping test level comprising two or more adjacent tiers of the tree; defining test cells within each non-overlapping test level, each test cell comprising a subtree of the tree including a subtree root compute node and all descendant compute nodes of the subtree root compute node within a non-overlapping test level; performing, separately on each set of non-overlapping test levels, an uplink test on all test cells in a set of non-overlapping test levels; and performing, separately from the uplink tests and separately on each set of non-overlapping test levels, a downlink test on all test cells in a set of non-overlapping test levels.

Cylinder stitching interferometry: with and without overlap regions

NASA Astrophysics Data System (ADS)

Peng, Junzheng; Chen, Dingfu; Yu, Yingjie

2017-06-01

Since the cylinder surface is closed and periodic in the azimuthal direction, existing stitching methods cannot be used to yield the 360° form map. To address this problem, this paper presents two methods for stitching interferometry of cylinder: one requires overlap regions, and the other does not need the overlap regions. For the former, we use the first order approximation of cylindrical coordinate transformation to build the stitching model. With it, the relative parameters between the adjacent sub-apertures can be calculated by the stitching model. For the latter, a set of orthogonal polynomials, termed Legendre Fourier (LF) polynomials, was developed. With these polynomials, individual sub-aperture data can be expanded as composition of inherent form of partial cylinder surface and additional misalignment parameters. Then the 360° form map can be acquired by simultaneously fitting all sub-aperture data with LF polynomials. Finally the two proposed methods are compared under various conditions. The merits and drawbacks of each stitching method are consequently revealed to provide suggestion in acquisition of 360° form map for a precision cylinder.

Avoiding and tolerating latency in large-scale next-generation shared-memory multiprocessors

NASA Technical Reports Server (NTRS)

Probst, David K.

1993-01-01

A scalable solution to the memory-latency problem is necessary to prevent the large latencies of synchronization and memory operations inherent in large-scale shared-memory multiprocessors from reducing high performance. We distinguish latency avoidance and latency tolerance. Latency is avoided when data is brought to nearby locales for future reference. Latency is tolerated when references are overlapped with other computation. Latency-avoiding locales include: processor registers, data caches used temporally, and nearby memory modules. Tolerating communication latency requires parallelism, allowing the overlap of communication and computation. Latency-tolerating techniques include: vector pipelining, data caches used spatially, prefetching in various forms, and multithreading in various forms. Relaxing the consistency model permits increased use of avoidance and tolerance techniques. Each model is a mapping from the program text to sets of partial orders on program operations; it is a convention about which temporal precedences among program operations are necessary. Information about temporal locality and parallelism constrains the use of avoidance and tolerance techniques. Suitable architectural primitives and compiler technology are required to exploit the increased freedom to reorder and overlap operations in relaxed models.

Radial sets: interactive visual analysis of large overlapping sets.

PubMed

Alsallakh, Bilal; Aigner, Wolfgang; Miksch, Silvia; Hauser, Helwig

2013-12-01

In many applications, data tables contain multi-valued attributes that often store the memberships of the table entities to multiple sets such as which languages a person masters, which skills an applicant documents, or which features a product comes with. With a growing number of entities, the resulting element-set membership matrix becomes very rich of information about how these sets overlap. Many analysis tasks targeted at set-typed data are concerned with these overlaps as salient features of such data. This paper presents Radial Sets, a novel visual technique to analyze set memberships for a large number of elements. Our technique uses frequency-based representations to enable quickly finding and analyzing different kinds of overlaps between the sets, and relating these overlaps to other attributes of the table entities. Furthermore, it enables various interactions to select elements of interest, find out if they are over-represented in specific sets or overlaps, and if they exhibit a different distribution for a specific attribute compared to the rest of the elements. These interactions allow formulating highly-expressive visual queries on the elements in terms of their set memberships and attribute values. As we demonstrate via two usage scenarios, Radial Sets enable revealing and analyzing a multitude of overlapping patterns between large sets, beyond the limits of state-of-the-art techniques.

The evaluation of partial binocular overlap on car maneuverability: A pilot study

NASA Technical Reports Server (NTRS)

Tsou, Brian H.; Rogers-Adams, Beth M.; Goodyear, Charles D.

1992-01-01

An engineering approach to enlarge the helmet mounted display (HMD) field of view (FOV) and maintain resolution and weight by partially overlapping the binocular FOV has received renewed interest among human factors scientists. It is evident, based on the brief literature review, that any panoramic display with a binocular overlap, less than a minimum amount, annoys the viewer, degrades performance, and elicits undesirable behavior. The major finding is that across the 60 deg conditions, subjects moved their heads a greater distance (by about 5 degs on each side) than in the 180 deg condition, presumably to compensate for the lack of FOV. It is quite clear that the study, based on simple car maneuverability and two subjects, reveals differences in FOV, but nothing significant between binocular overlap levels and configurations. This tentatively indicates that some tradeoffs of binocular vision for a larger overall display FOV are acceptable.

Wide coverage biomedical event extraction using multiple partially overlapping corpora

PubMed Central

2013-01-01

Background Biomedical events are key to understanding physiological processes and disease, and wide coverage extraction is required for comprehensive automatic analysis of statements describing biomedical systems in the literature. In turn, the training and evaluation of extraction methods requires manually annotated corpora. However, as manual annotation is time-consuming and expensive, any single event-annotated corpus can only cover a limited number of semantic types. Although combined use of several such corpora could potentially allow an extraction system to achieve broad semantic coverage, there has been little research into learning from multiple corpora with partially overlapping semantic annotation scopes. Results We propose a method for learning from multiple corpora with partial semantic annotation overlap, and implement this method to improve our existing event extraction system, EventMine. An evaluation using seven event annotated corpora, including 65 event types in total, shows that learning from overlapping corpora can produce a single, corpus-independent, wide coverage extraction system that outperforms systems trained on single corpora and exceeds previously reported results on two established event extraction tasks from the BioNLP Shared Task 2011. Conclusions The proposed method allows the training of a wide-coverage, state-of-the-art event extraction system from multiple corpora with partial semantic annotation overlap. The resulting single model makes broad-coverage extraction straightforward in practice by removing the need to either select a subset of compatible corpora or semantic types, or to merge results from several models trained on different individual corpora. Multi-corpus learning also allows annotation efforts to focus on covering additional semantic types, rather than aiming for exhaustive coverage in any single annotation effort, or extending the coverage of semantic types annotated in existing corpora. PMID:23731785

Polysomnography versus limited respiratory monitoring and nurse-led titration to optimise non-invasive ventilation set-up: a pilot randomised clinical trial.

PubMed

Patout, Maxime; Arbane, Gill; Cuvelier, Antoine; Muir, Jean Francois; Hart, Nicholas; Murphy, Patrick Brian

2018-03-30

Polysomnography (PSG) is recommended for non-invasive ventilation (NIV) set-up in patients with chronic respiratory failure. In this pilot randomised clinical trial, we compared the physiological effectiveness of NIV set-up guided by PSG to limited respiratory monitoring (LRM) and nurse-led titration in patients with COPD-obstructive sleep apnoea (OSA) overlap. The principal outcome of interest was change in daytime arterial partial pressure of carbon dioxide (PaCO 2 ) at 3 months. Fourteen patients with daytime PaCO 2 >6 kPa and body mass index >30 kg/m 2 were recruited. At 3 months, PaCO 2 was reduced by -0.88 kPa (95% CI -1.52 to -0.24 kPa) in the LRM group and by -0.36 kPa (95% CI -0.96 to 0.24 kPa) in the PSG group. These pilot data provide support to undertake a clinical trial investigating the clinical effectiveness of attended limited respiratory monitoring and PSG to establish NIV in patients with COPD-OSA overlap. Results, NCT02444806. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Peculiarities of Forming a Multiband Transmission Function Based on Multifrequency Acousto-Optic Diffraction

NASA Astrophysics Data System (ADS)

Proklov, V. V.; Rezvov, Yu. G.

2018-01-01

An analytical solution for the transmission function of noncoherent wideband radiation is obtained under acousto-optic (AO) filtering using a discrete set of monochromatic AO waves with a small spectral overlap. We studied characteristics of the AO transformation of a continuous spectrum of noncoherent radiation into a given set of discrete narrow bands of spectral transmission by excitation of a discrete set of sound frequencies. We carried out the analysis of transmission functions of individual channels taking into account a partial overlap of their spectra and possible intermodulation distortions. It is shown that a stationary value of the root-mean-square light power is found at the electronic output due to the photoelectric transformation and detecting diffracted light. Based on this, a necessary stationary, multiband, and nearly equidistant transmission function of a device can be formed by using a relevant spectrum of acoustic excitation. Peculiarities of this way of forming the multiband transmission function are revealed: the limitation of diffraction efficiency for an individual channel, the possibility of decoupling side lobes of adjacent channels, etc. A multiband acousto-optic filter (MAOF) was simulated that was based on a paratellurite monocrystal (TeO2), which was previously used for experimental optical encoding. The theoretical and experimental results are in gratifying agreement.

Temporal coherence for pure tones in budgerigars (Melopsittacus undulatus) and humans (Homo sapiens).

PubMed

Neilans, Erikson G; Dent, Micheal L

2015-02-01

Auditory scene analysis has been suggested as a universal process that exists across all animals. Relative to humans, however, little work has been devoted to how animals perceptually isolate different sound sources. Frequency separation of sounds is arguably the most common parameter studied in auditory streaming, but it is not the only factor contributing to how the auditory scene is perceived. Researchers have found that in humans, even at large frequency separations, synchronous tones are heard as a single auditory stream, whereas asynchronous tones with the same frequency separations are perceived as 2 distinct sounds. These findings demonstrate how both the timing and frequency separation of sounds are important for auditory scene analysis. It is unclear how animals, such as budgerigars (Melopsittacus undulatus), perceive synchronous and asynchronous sounds. In this study, budgerigars and humans (Homo sapiens) were tested on their perception of synchronous, asynchronous, and partially overlapping pure tones using the same psychophysical procedures. Species differences were found between budgerigars and humans in how partially overlapping sounds were perceived, with budgerigars more likely to segregate overlapping sounds and humans more apt to fuse the 2 sounds together. The results also illustrated that temporal cues are particularly important for stream segregation of overlapping sounds. Lastly, budgerigars were found to segregate partially overlapping sounds in a manner predicted by computational models of streaming, whereas humans were not. PsycINFO Database Record (c) 2015 APA, all rights reserved.

A comparative study of novel spectrophotometric resolution techniques applied for pharmaceutical mixtures with partially or severely overlapped spectra

NASA Astrophysics Data System (ADS)

Lotfy, Hayam M.; Tawakkol, Shereen M.; Fahmy, Nesma M.; Shehata, Mostafa A.

2015-02-01

Simultaneous determination of mixtures of lidocaine hydrochloride (LH), flucortolone pivalate (FCP), in presence of chlorquinaldol (CQ) without prior separation steps was applied using either successive or progressive resolution techniques. According to the concentration of CQ the extent of overlapping changed so it can be eliminated from the mixture to get the binary mixture of LH and FCP using ratio subtraction method for partially overlapped spectra or constant value via amplitude difference followed by ratio subtraction or constant center followed by spectrum subtraction spectrum subtraction for severely overlapped spectra. Successive ratio subtraction was coupled with extended ratio subtraction, constant multiplication, derivative subtraction coupled constant multiplication, and spectrum subtraction can be applied for the analysis of partially overlapped spectra. On the other hand severely overlapped spectra can be analyzed by constant center and the novel methods namely differential dual wavelength (D1 DWL) for CQ, ratio difference and differential derivative ratio (D1 DR) for FCP, while LH was determined by applying constant value via amplitude difference followed by successive ratio subtraction, and successive derivative subtraction. The spectra of the cited drugs can be resolved and their concentrations are determined progressively from the same ratio spectrum using amplitude modulation method. The specificity of the developed methods was investigated by analyzing laboratory prepared mixtures and were successfully applied for the analysis of pharmaceutical formulations containing the cited drugs with no interference from additives. The proposed methods were validated according to the ICH guidelines. The obtained results were statistically compared with those of the official or reported methods; using student t-test, F-test, and one way ANOVA, showing no significant difference with respect to accuracy and precision.

Forensic Discrimination of Latent Fingerprints Using Laser-Induced Breakdown Spectroscopy (LIBS) and Chemometric Approaches.

PubMed

Yang, Jun-Ho; Yoh, Jack J

2018-01-01

A novel technique is reported for separating overlapping latent fingerprints using chemometric approaches that combine laser-induced breakdown spectroscopy (LIBS) and multivariate analysis. The LIBS technique provides the capability of real time analysis and high frequency scanning as well as the data regarding the chemical composition of overlapping latent fingerprints. These spectra offer valuable information for the classification and reconstruction of overlapping latent fingerprints by implementing appropriate statistical multivariate analysis. The current study employs principal component analysis and partial least square methods for the classification of latent fingerprints from the LIBS spectra. This technique was successfully demonstrated through a classification study of four distinct latent fingerprints using classification methods such as soft independent modeling of class analogy (SIMCA) and partial least squares discriminant analysis (PLS-DA). The novel method yielded an accuracy of more than 85% and was proven to be sufficiently robust. Furthermore, through laser scanning analysis at a spatial interval of 125 µm, the overlapping fingerprints were reconstructed as separate two-dimensional forms.

a Non-Overlapping Discretization Method for Partial Differential Equations

NASA Astrophysics Data System (ADS)

Rosas-Medina, A.; Herrera, I.

2013-05-01

Mathematical models of many systems of interest, including very important continuous systems of Engineering and Science, lead to a great variety of partial differential equations whose solution methods are based on the computational processing of large-scale algebraic systems. Furthermore, the incredible expansion experienced by the existing computational hardware and software has made amenable to effective treatment problems of an ever increasing diversity and complexity, posed by engineering and scientific applications. The emergence of parallel computing prompted on the part of the computational-modeling community a continued and systematic effort with the purpose of harnessing it for the endeavor of solving boundary-value problems (BVPs) of partial differential equations. Very early after such an effort began, it was recognized that domain decomposition methods (DDM) were the most effective technique for applying parallel computing to the solution of partial differential equations, since such an approach drastically simplifies the coordination of the many processors that carry out the different tasks and also reduces very much the requirements of information-transmission between them. Ideally, DDMs intend producing algorithms that fulfill the DDM-paradigm; i.e., such that "the global solution is obtained by solving local problems defined separately in each subdomain of the coarse-mesh -or domain-decomposition-". Stated in a simplistic manner, the basic idea is that, when the DDM-paradigm is satisfied, full parallelization can be achieved by assigning each subdomain to a different processor. When intensive DDM research began much attention was given to overlapping DDMs, but soon after attention shifted to non-overlapping DDMs. This evolution seems natural when the DDM-paradigm is taken into account: it is easier to uncouple the local problems when the subdomains are separated. However, an important limitation of non-overlapping domain decompositions, as that concept is usually understood today, is that interface nodes are shared by two or more subdomains of the coarse-mesh and, therefore, even non-overlapping DDMs are actually overlapping when seen from the perspective of the nodes used in the discretization. In this talk we present and discuss a discretization method in which the nodes used are non-overlapping, in the sense that each one of them belongs to one and only one subdomain of the coarse-mesh.

Overlap Spectrum Fiber Bragg Grating Sensor Based on Light Power Demodulation

PubMed Central

Zhang, Hao; Jiang, Junzhen; Liu, Shuang; Chen, Huaixi; Zheng, Xiaoqian; Qiu, Yishen

2018-01-01

Demodulation is a bottleneck for applications involving fiber Bragg gratings (FBGs). An overlap spectrum FBG sensor based on a light power demodulation method is presented in this paper. The demodulation method uses two chirp FBGs (cFBGs) of which the reflection spectra partially overlap each other. The light power variation of the overlap spectrum can be linked to changes in the measurand, and the sensor function can be realized via this relationship. A temperature experiment showed that the relationship between the overlap power spectrum of the FBG sensor and temperature had good linearity and agreed with the theoretical analysis. PMID:29772793

Termination of String Rewriting Rules that have One Pair of Overlaps

NASA Technical Reports Server (NTRS)

Geser, Alfons; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

This paper presents a partial solution to the long standing open problem of termination of one-rule string rewriting. Overlaps between the two sides of the rule play a central role in existing termination criteria. We characterize termination of all one-rule string rewriting systems that have one such overlap at either end. This both completes a result of Kurth and generalizes a result of Shikishima-Tsuji et al.

Motor Execution Affects Action Prediction

ERIC Educational Resources Information Center

Springer, Anne; Brandstadter, Simone; Liepelt, Roman; Birngruber, Teresa; Giese, Martin; Mechsner, Franz; Prinz, Wolfgang

2011-01-01

Previous studies provided evidence of the claim that the prediction of occluded action involves real-time simulation. We report two experiments that aimed to study how real-time simulation is affected by simultaneous action execution under conditions of full, partial or no overlap between observed and executed actions. This overlap was analysed by…

A Galerkin formulation of the MIB method for three dimensional elliptic interface problems

PubMed Central

Xia, Kelin; Wei, Guo-Wei

2014-01-01

We develop a three dimensional (3D) Galerkin formulation of the matched interface and boundary (MIB) method for solving elliptic partial differential equations (PDEs) with discontinuous coefficients, i.e., the elliptic interface problem. The present approach builds up two sets of elements respectively on two extended subdomains which both include the interface. As a result, two sets of elements overlap each other near the interface. Fictitious solutions are defined on the overlapping part of the elements, so that the differentiation operations of the original PDEs can be discretized as if there was no interface. The extra coefficients of polynomial basis functions, which furnish the overlapping elements and solve the fictitious solutions, are determined by interface jump conditions. Consequently, the interface jump conditions are rigorously enforced on the interface. The present method utilizes Cartesian meshes to avoid the mesh generation in conventional finite element methods (FEMs). We implement the proposed MIB Galerkin method with three different elements, namely, rectangular prism element, five-tetrahedron element and six-tetrahedron element, which tile the Cartesian mesh without introducing any new node. The accuracy, stability and robustness of the proposed 3D MIB Galerkin are extensively validated over three types of elliptic interface problems. In the first type, interfaces are analytically defined by level set functions. These interfaces are relatively simple but admit geometric singularities. In the second type, interfaces are defined by protein surfaces, which are truly arbitrarily complex. The last type of interfaces originates from multiprotein complexes, such as molecular motors. Near second order accuracy has been confirmed for all of these problems. To our knowledge, it is the first time for an FEM to show a near second order convergence in solving the Poisson equation with realistic protein surfaces. Additionally, the present work offers the first known near second order accurate method for C1 continuous or H2 continuous solutions associated with a Lipschitz continuous interface in a 3D setting. PMID:25309038

Partially-overlapped viewing zone based integral imaging system with super wide viewing angle.

PubMed

Xiong, Zhao-Long; Wang, Qiong-Hua; Li, Shu-Li; Deng, Huan; Ji, Chao-Chao

2014-09-22

In this paper, we analyze the relationship between viewer and viewing zones of integral imaging (II) system and present a partially-overlapped viewing zone (POVZ) based integral imaging system with a super wide viewing angle. In the proposed system, the viewing angle can be wider than the viewing angle of the conventional tracking based II system. In addition, the POVZ can eliminate the flipping and time delay of the 3D scene as well. The proposed II system has a super wide viewing angle of 120° without flipping effect about twice as wide as the conventional one.

Scope of partial least-squares regression applied to the enantiomeric composition determination of ketoprofen from strongly overlapped chromatographic profiles.

PubMed

Padró, Juan M; Osorio-Grisales, Jaiver; Arancibia, Juan A; Olivieri, Alejandro C; Castells, Cecilia B

2015-07-01

Valuable quantitative information could be obtained from strongly overlapped chromatographic profiles of two enantiomers by using proper chemometric methods. Complete separation profiles where the peaks are fully resolved are difficult to achieve in chiral separation methods, and this becomes a particularly severe problem in case that the analyst needs to measure the chiral purity, i.e., when one of the enantiomers is present in the sample in very low concentrations. In this report, we explore the scope of a multivariate chemometric technique based on unfolded partial least-squares regression, as a mathematical tool to solve this quite frequent difficulty. This technique was applied to obtain quantitative results from partially overlapped chromatographic profiles of R- and S-ketoprofen, with different values of enantioresolution factors (from 0.81 down to less than 0.2 resolution units), and also at several different S:R enantiomeric ratios. Enantiomeric purity below 1% was determined with excellent precision even from almost completely overlapped signals. All these assays were tested on the most demanding condition, i.e., when the minor peak elutes immediately after the main peak. The results were validated using univariate calibration of completely resolved profiles and the method applied to the determination of enantiomeric purity of commercial pharmaceuticals. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum entanglement of identical particles by standard information-theoretic notions

PubMed Central

Lo Franco, Rosario; Compagno, Giuseppe

2016-01-01

Quantum entanglement of identical particles is essential in quantum information theory. Yet, its correct determination remains an open issue hindering the general understanding and exploitation of many-particle systems. Operator-based methods have been developed that attempt to overcome the issue. Here we introduce a state-based method which, as second quantization, does not label identical particles and presents conceptual and technical advances compared to the previous ones. It establishes the quantitative role played by arbitrary wave function overlaps, local measurements and particle nature (bosons or fermions) in assessing entanglement by notions commonly used in quantum information theory for distinguishable particles, like partial trace. Our approach furthermore shows that bringing identical particles into the same spatial location functions as an entangling gate, providing fundamental theoretical support to recent experimental observations with ultracold atoms. These results pave the way to set and interpret experiments for utilizing quantum correlations in realistic scenarios where overlap of particles can count, as in Bose-Einstein condensates, quantum dots and biological molecular aggregates. PMID:26857475

B{sub K} with two flavors of dynamical overlap fermions

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

Aoki, S.; Riken BNL Research Center, Brookhaven National Laboratory, Upton, New York 11973; Fukaya, H.

2008-05-01

We present a two-flavor QCD calculation of B{sub K} on a 16{sup 3}x32 lattice at a{approx}0.12 fm (or equivalently a{sup -1}=1.67 GeV). Both valence and sea quarks are described by the overlap fermion formulation. The matching factor is calculated nonperturbatively with the so-called RI/MOM scheme. We find that the lattice data are well described by the next-to-leading order (NLO) partially quenched chiral perturbation theory (PQChPT) up to around a half of the strange quark mass (m{sub s}{sup phys}/2). The data at quark masses heavier than m{sub s}{sup phys}/2 are fitted including a part of next-to-next-to-leading order terms. We obtain B{submore » K}{sup MS}(2 GeV)=0.537(4)(40), where the first error is statistical and the second is an estimate of systematic uncertainties from finite volume, fixing topology, the matching factor, and the scale setting.« less

Blind separation of overlapping partials in harmonic musical notes using amplitude and phase reconstruction

NASA Astrophysics Data System (ADS)

de León, Jesús Ponce; Beltrán, José Ramón

2012-12-01

In this study, a new method of blind audio source separation (BASS) of monaural musical harmonic notes is presented. The input (mixed notes) signal is processed using a flexible analysis and synthesis algorithm (complex wavelet additive synthesis, CWAS), which is based on the complex continuous wavelet transform. When the harmonics from two or more sources overlap in a certain frequency band (or group of bands), a new technique based on amplitude similarity criteria is used to obtain an approximation to the original partial information. The aim is to show that the CWAS algorithm can be a powerful tool in BASS. Compared with other existing techniques, the main advantages of the proposed algorithm are its accuracy in the instantaneous phase estimation, its synthesis capability and that the only input information needed is the mixed signal itself. A set of synthetically mixed monaural isolated notes have been analyzed using this method, in eight different experiments: the same instrument playing two notes within the same octave and two harmonically related notes (5th and 12th intervals), two different musical instruments playing 5th and 12th intervals, two different instruments playing non-harmonic notes, major and minor chords played by the same musical instrument, three different instruments playing non-harmonically related notes and finally the mixture of a inharmonic instrument (piano) and one harmonic instrument. The results obtained show the strength of the technique.

Neural-net-based image matching

NASA Astrophysics Data System (ADS)

Jerebko, Anna K.; Barabanov, Nikita E.; Luciv, Vadim R.; Allinson, Nigel M.

2000-04-01

The paper describes a neural-based method for matching spatially distorted image sets. The matching of partially overlapping images is important in many applications-- integrating information from images formed from different spectral ranges, detecting changes in a scene and identifying objects of differing orientations and sizes. Our approach consists of extracting contour features from both images, describing the contour curves as sets of line segments, comparing these sets, determining the corresponding curves and their common reference points, calculating the image-to-image co-ordinate transformation parameters on the basis of the most successful variant of the derived curve relationships. The main steps are performed by custom neural networks. The algorithms describe in this paper have been successfully tested on a large set of images of the same terrain taken in different spectral ranges, at different seasons and rotated by various angles. In general, this experimental verification indicates that the proposed method for image fusion allows the robust detection of similar objects in noisy, distorted scenes where traditional approaches often fail.

Track with overlapping links for dry coal extrusion pumps

DOEpatents

Saunders, Timothy; Brady, John D

2014-01-21

A chain for a particulate material extrusion pump includes a plurality of links, each of the plurality of links having a link body and a link ledge, wherein each link ledge of the plurality of links at least partially overlaps the link body of an adjacent one of the plurality of links.

Tunable overlapping long-period fiber grating and its bending vector sensing application

NASA Astrophysics Data System (ADS)

Hu, Wei; Zhang, Weigang; Chen, Lei; Wang, Song; Zhang, Yunshan; Zhang, Yanxin; Kong, Lingxin; Yu, Lin; Yan, Tieyi; Li, Yanping

2018-03-01

A novel overlapping long-period fiber grating (OLPFG) is proposed and experimentally demonstrated in this paper. The OLPFG is composed of two partially overlapping long-period fiber gratings (LPFG). Based on the coupled model theory and transfer matrix method, it is found that the phase shift LPFG and LPFGs interference are two special situations of the proposed OLPFG. Moreover, the confirmation experiments verified that the proposed OLPFG has a high bending sensitivity in opposite directions, and the temperature crosstalk can be compensated spontaneously.

Nucleus detection using gradient orientation information and linear least squares regression

NASA Astrophysics Data System (ADS)

Kwak, Jin Tae; Hewitt, Stephen M.; Xu, Sheng; Pinto, Peter A.; Wood, Bradford J.

2015-03-01

Computerized histopathology image analysis enables an objective, efficient, and quantitative assessment of digitized histopathology images. Such analysis often requires an accurate and efficient detection and segmentation of histological structures such as glands, cells and nuclei. The segmentation is used to characterize tissue specimens and to determine the disease status or outcomes. The segmentation of nuclei, in particular, is challenging due to the overlapping or clumped nuclei. Here, we propose a nuclei seed detection method for the individual and overlapping nuclei that utilizes the gradient orientation or direction information. The initial nuclei segmentation is provided by a multiview boosting approach. The angle of the gradient orientation is computed and traced for the nuclear boundaries. Taking the first derivative of the angle of the gradient orientation, high concavity points (junctions) are discovered. False junctions are found and removed by adopting a greedy search scheme with the goodness-of-fit statistic in a linear least squares sense. Then, the junctions determine boundary segments. Partial boundary segments belonging to the same nucleus are identified and combined by examining the overlapping area between them. Using the final set of the boundary segments, we generate the list of seeds in tissue images. The method achieved an overall precision of 0.89 and a recall of 0.88 in comparison to the manual segmentation.

Effects of Modality on the Neural Correlates of Encoding Processes Supporting Recollection and Familiarity

ERIC Educational Resources Information Center

Gottlieb, Lauren J.; Rugg, Michael D.

2011-01-01

Prior research has demonstrated that the neural correlates of successful encoding ("subsequent memory effects") partially overlap with neural regions selectively engaged by the on-line demands of the study task. The primary goal of the present experiment was to determine whether this overlap is associated solely with encoding processes supporting…

An Exercise on Calibration: DRIFTS Study of Binary Mixtures of Calcite and Dolomite with Partially Overlapping Spectral Features

ERIC Educational Resources Information Center

De Lorenzi Pezzolo, Alessandra

2013-01-01

Unlike most spectroscopic calibrations that are based on the study of well-separated features ascribable to the different components, this laboratory experience is especially designed to exploit spectral features that are nearly overlapping. The investigated system consists of a binary mixture of two commonly occurring minerals, calcite and…

Overlapping double potential wells in a single optical microtube cavity with vernier-scale-like tuning effect

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

Madani, A.; Schmidt, O. G.; Material Systems for Nanoelectronics, Chemnitz University of Technology, Reichenhainer Str. 70, 09107 Chemnitz

2016-04-25

Spatially and temporally overlapping double potential wells are realized in a hybrid optical microtube cavity due to the coexistence of an aggregate of luminescent quantum dots embedded in the tube wall and the cone-shaped tube's geometry. The double potential wells produce two independent sets of optical modes with different sets of mode numbers, indicating phase velocity separation for the modes overlapping at the same frequency. The overlapping mode position can be tuned by modifying the tube cavity, where these mode sets shift with different magnitudes, allowing for a vernier-scale-like tuning effect.

Consistency of forest presence and biomass predictions modeled across overlapping spatial and temporal extents

Treesearch

Mark D. Nelson; Sean Healey; W. Keith Moser; J.G. Masek; Warren Cohen

2011-01-01

We assessed the consistency across space and time of spatially explicit models of forest presence and biomass in southern Missouri, USA, for adjacent, partially overlapping satellite image Path/Rows, and for coincident satellite images from the same Path/Row acquired in different years. Such consistency in satellite image-based classification and estimation is critical...

Visual search for emotional expressions: Effect of stimulus set on anger and happiness superiority.

PubMed

Savage, Ruth A; Becker, Stefanie I; Lipp, Ottmar V

2016-01-01

Prior reports of preferential detection of emotional expressions in visual search have yielded inconsistent results, even for face stimuli that avoid obvious expression-related perceptual confounds. The current study investigated inconsistent reports of anger and happiness superiority effects using face stimuli drawn from the same database. Experiment 1 excluded procedural differences as a potential factor, replicating a happiness superiority effect in a procedure that previously yielded an anger superiority effect. Experiments 2a and 2b confirmed that image colour or poser gender did not account for prior inconsistent findings. Experiments 3a and 3b identified stimulus set as the critical variable, revealing happiness or anger superiority effects for two partially overlapping sets of face stimuli. The current results highlight the critical role of stimulus selection for the observation of happiness or anger superiority effects in visual search even for face stimuli that avoid obvious expression related perceptual confounds and are drawn from a single database.

Chironomidae larvae (Diptera) of Neotropical floodplain: overlap niche in different habitats.

PubMed

Butakka, C M M; Ragonha, F H; Takeda, A M

2014-05-01

The niche overlap between trophic groups of Chironomidae larvae in different habitats was observed between trophic groups and between different environments in Neotropical floodplain. For the evaluation we used the index of niche overlap (CXY) and analysis of trophic networks, both from the types and amount of food items identified in the larval alimentary canal. In all environments, the larvae fed on mainly organic matter such as plants fragments and algae, but there were many omnivore larvae. Species that have high values of food items occurred in diverse environments as generalists with great overlap niche and those with a low amount of food items with less overlap niche were classified as specialists. The largest number of trophic niche overlap was observed among collector-gatherers in connected floodplain lakes. The lower values of index niche overlap were predators. The similarity in the diet of different taxa in the same niche does not necessarily imply competition between them, but coexistence when the food resource is not scarce in the environment even in partially overlapping niches.

Determination of enantiomeric composition of ibuprofen in pharmaceutical formulations by partial least-squares regression of strongly overlapped chromatographic profiles.

PubMed

Grisales, Jaiver Osorio; Arancibia, Juan A; Castells, Cecilia B; Olivieri, Alejandro C

2012-12-01

In this report, we demonstrate how chiral liquid chromatography combined with multivariate chemometric techniques, specifically unfolded-partial least-squares regression (U-PLS), provides a powerful analytical methodology. Using U-PLS, strongly overlapped enantiomer profiles in a sample could be successfully processed and enantiomeric purity could be accurately determined without requiring baseline enantioresolution between peaks. The samples were partially enantioseparated with a permethyl-β-cyclodextrin chiral column under reversed-phase conditions. Signals detected with a diode-array detector within a wavelength range from 198 to 241 nm were recorded, and the data were processed by a second-order multivariate algorithm to decrease detection limits. The R-(-)-enantiomer of ibuprofen in tablet formulation samples could be determined at the level of 0.5 mg L⁻¹ in the presence of 99.9% of the S-(+)-enantiomorph with relative prediction error within ±3%. Copyright © 2012 Elsevier B.V. All rights reserved.

Advanced brain aging: relationship with epidemiologic and genetic risk factors, and overlap with Alzheimer disease atrophy patterns.

PubMed

Habes, M; Janowitz, D; Erus, G; Toledo, J B; Resnick, S M; Doshi, J; Van der Auwera, S; Wittfeld, K; Hegenscheid, K; Hosten, N; Biffar, R; Homuth, G; Völzke, H; Grabe, H J; Hoffmann, W; Davatzikos, C

2016-04-05

We systematically compared structural imaging patterns of advanced brain aging (ABA) in the general-population, herein defined as significant deviation from typical BA to those found in Alzheimer disease (AD). The hypothesis that ABA would show different patterns of structural change compared with those found in AD was tested via advanced pattern analysis methods. In particular, magnetic resonance images of 2705 participants from the Study of Health in Pomerania (aged 20-90 years) were analyzed using an index that captures aging atrophy patterns (Spatial Pattern of Atrophy for Recognition of BA (SPARE-BA)), and an index previously shown to capture atrophy patterns found in clinical AD (Spatial Patterns of Abnormality for Recognition of Early Alzheimer's Disease (SPARE-AD)). We studied the association between these indices and risk factors, including an AD polygenic risk score. Finally, we compared the ABA-associated atrophy with typical AD-like patterns. We observed that SPARE-BA had significant association with: smoking (P<0.05), anti-hypertensive (P<0.05), anti-diabetic drug use (men P<0.05, women P=0.06) and waist circumference for the male cohort (P<0.05), after adjusting for age. Subjects with ABA had spatially extensive gray matter loss in the frontal, parietal and temporal lobes (false-discovery-rate-corrected q<0.001). ABA patterns of atrophy were partially overlapping with, but notably deviating from those typically found in AD. Subjects with ABA had higher SPARE-AD values; largely due to the partial spatial overlap of associated patterns in temporal regions. The AD polygenic risk score was significantly associated with SPARE-AD but not with SPARE-BA. Our findings suggest that ABA is likely characterized by pathophysiologic mechanisms that are distinct from, or only partially overlapping with those of AD.

Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease.

PubMed

Azuaje, Francisco; Zheng, Huiru; Camargo, Anyela; Wang, Haiying

2011-08-01

The discovery of novel disease biomarkers is a crucial challenge for translational bioinformatics. Demonstration of both their classification power and reproducibility across independent datasets are essential requirements to assess their potential clinical relevance. Small datasets and multiplicity of putative biomarker sets may explain lack of predictive reproducibility. Studies based on pathway-driven discovery approaches have suggested that, despite such discrepancies, the resulting putative biomarkers tend to be implicated in common biological processes. Investigations of this problem have been mainly focused on datasets derived from cancer research. We investigated the predictive and functional concordance of five methods for discovering putative biomarkers in four independently-generated datasets from the cardiovascular disease domain. A diversity of biosignatures was identified by the different methods. However, we found strong biological process concordance between them, especially in the case of methods based on gene set analysis. With a few exceptions, we observed lack of classification reproducibility using independent datasets. Partial overlaps between our putative sets of biomarkers and the primary studies exist. Despite the observed limitations, pathway-driven or gene set analysis can predict potentially novel biomarkers and can jointly point to biomedically-relevant underlying molecular mechanisms. Copyright © 2011 Elsevier Inc. All rights reserved.

Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences.

PubMed

Aguilera-Mendoza, Longendri; Marrero-Ponce, Yovani; Tellez-Ibarra, Roberto; Llorente-Quesada, Monica T; Salgado, Jesús; Barigye, Stephen J; Liu, Jun

2015-08-01

The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are included in CAMP_Patent. However, the majority of databases have their own set of unique sequences, as well as some overlap with other databases. The complete set of non-duplicate sequences comprises 16 990 cases, which is almost half of the total number of reported peptides. On the other hand, the diversity analysis identifies the most and least diverse databases and proves that all databases exhibit some level of redundancy. Finally, we present a new parallel-free software, named Dover Analyzer, developed to compute the overlap and diversity between any number of databases and compile a set of non-redundant sequences. These results are useful for selecting or building a suitable representative set of AMPs, according to specific needs. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Real-time edge-enhanced optical correlator

NASA Astrophysics Data System (ADS)

Shihabi, Mazen M.; Hinedi, Sami M.; Shah, Biren N.

1992-08-01

The performance of five symbol lock detectors are compared. They are the square-law detector with overlapping (SQOD) and non-overlapping (SQNOD) integrators, the absolute value detectors with overlapping and non-overlapping (AVNOD) integrators and the signal power estimator detector (SPED). The analysis considers various scenarios when the observation interval is much larger or equal to the symbol synchronizer loop bandwidth, which has not been considered in previous analyses. Also, the case of threshold setting in the absence of signal is considered. It is shown that the SQOD outperforms all others when the threshold is set in the presence of signal, independent of the relationship between loop bandwidth and observation period. On the other hand, the SPED outperforms all others when the threshold is set in the presence of noise only.

Real-time edge-enhanced optical correlator

NASA Technical Reports Server (NTRS)

Shihabi, Mazen M. (Inventor); Hinedi, Sami M. (Inventor); Shah, Biren N. (Inventor)

1992-01-01

The performance of five symbol lock detectors are compared. They are the square-law detector with overlapping (SQOD) and non-overlapping (SQNOD) integrators, the absolute value detectors with overlapping and non-overlapping (AVNOD) integrators and the signal power estimator detector (SPED). The analysis considers various scenarios when the observation interval is much larger or equal to the symbol synchronizer loop bandwidth, which has not been considered in previous analyses. Also, the case of threshold setting in the absence of signal is considered. It is shown that the SQOD outperforms all others when the threshold is set in the presence of signal, independent of the relationship between loop bandwidth and observation period. On the other hand, the SPED outperforms all others when the threshold is set in the presence of noise only.

Some new results on the central overlap problem in astrometry

NASA Astrophysics Data System (ADS)

Rapaport, M.

1998-07-01

The central overlap problem in astrometry has been revisited in the recent last years by Eichhorn (1988) who explicitly inverted the matrix of a constrained least squares problem. In this paper, the general explicit solution of the unconstrained central overlap problem is given. We also give the explicit solution for an other set of constraints; this result is a confirmation of a conjecture expressed by Eichhorn (1988). We also consider the use of iterative methods to solve the central overlap problem. A surprising result is obtained when the classical Gauss Seidel method is used; the iterations converge immediately to the general solution of the equations; we explain this property writing the central overlap problem in a new set of variables.

Specific surface area of overlapping spheres in the presence of obstructions

NASA Astrophysics Data System (ADS)

Jenkins, D. R.

2013-02-01

This study considers the random placement of uniform sized spheres, which may overlap, in the presence of another set of randomly placed (hard) spheres, which do not overlap. The overlapping spheres do not intersect the hard spheres. It is shown that the specific surface area of the collection of overlapping spheres is affected by the hard spheres, such that there is a minimum in the specific surface area as a function of the relative size of the two sets of spheres. The occurrence of the minimum is explained in terms of the break-up of pore connectivity. The configuration can be considered to be a simple model of the structure of a porous composite material. In particular, the overlapping particles represent voids while the hard particles represent fillers. Example materials are pervious concrete, metallurgical coke, ice cream, and polymer composites. We also show how the material properties of such composites are affected by the void structure.

Specific surface area of overlapping spheres in the presence of obstructions.

PubMed

Jenkins, D R

2013-02-21

This study considers the random placement of uniform sized spheres, which may overlap, in the presence of another set of randomly placed (hard) spheres, which do not overlap. The overlapping spheres do not intersect the hard spheres. It is shown that the specific surface area of the collection of overlapping spheres is affected by the hard spheres, such that there is a minimum in the specific surface area as a function of the relative size of the two sets of spheres. The occurrence of the minimum is explained in terms of the break-up of pore connectivity. The configuration can be considered to be a simple model of the structure of a porous composite material. In particular, the overlapping particles represent voids while the hard particles represent fillers. Example materials are pervious concrete, metallurgical coke, ice cream, and polymer composites. We also show how the material properties of such composites are affected by the void structure.

Characterization of a cis-Golgi matrix protein, GM130

PubMed Central

1995-01-01

Antisera raised to a detergent- and salt-resistant matrix fraction from rat liver Golgi stacks were used to screen an expression library from rat liver cDNA. A full-length clone was obtained encoding a protein of 130 kD (termed GM130), the COOH-terminal domain of which was highly homologous to a Golgi human auto-antigen, golgin-95 (Fritzler et al., 1993). Biochemical data showed that GM130 is a peripheral cytoplasmic protein that is tightly bound to Golgi membranes and part of a larger oligomeric complex. Predictions from the protein sequence suggest that GM130 is an extended rod-like protein with coiled-coil domains. Immunofluorescence microscopy showed partial overlap with medial- and trans-Golgi markers but almost complete overlap with the cis-Golgi network (CGN) marker, syntaxin5. Immunoelectron microscopy confirmed this location showing that most of the GM130 was located in the CGN and in one or two cisternae on the cis-side of the Golgi stack. GM130 was not re-distributed to the ER in the presence of brefeldin A but maintained its overlap with syntaxin5 and a partial overlap with the ER- Golgi intermediate compartment marker, p53. Together these results suggest that GM130 is part of a cis-Golgi matrix and has a role in maintaining cis-Golgi structure. PMID:8557739

A Comparison of Item Selection Techniques and Exposure Control Mechanisms in CATs Using the Generalized Partial Credit Model.

ERIC Educational Resources Information Center

Pastor, Dena A.; Dodd, Barbara G.; Chang, Hua-Hua

2002-01-01

Studied the impact of using five different exposure control algorithms in two sizes of item pool calibrated using the generalized partial credit model. Simulation results show that the a-stratified design, in comparison to a no-exposure control condition, could be used to reduce item exposure and overlap and increase pool use, while degrading…

Community Structure of a Bank-Firm Credit Network in Japan

NASA Astrophysics Data System (ADS)

Iyetomi, Hiroshi; Matsuura, Yuki

2014-03-01

We study temporal change of community structure in a Japanese credit network formed by banks and listed firms through their financial relations over the last 30 years. The credit connectedness is regarded as a potenital source of systemic risk. Our network is a bipartite graph consisting of two species of nodes connected with bidirectional links. The direction of links is identified with that of risk flows and their weights are relative credit/loan with respect to the targets. In a partial credit network obtained only with the links pointing from firms toward banks, the city banks forms one major community in most of the time period to share risk when firms go wrong. On the other hand, a partial network only with the links from banks toward firms is decomposed into communities of similar size each of which has its own city bank, reflecting the main-bank system in Japan. Finally we take overlapping parts of the two community sets to find cores of the risk concentration in the credit network. This work was supported by JSPS KAKENHI Grant Number 22300080.

Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses

PubMed Central

Chen, Hongjun; Ye, Jianqiang; Xu, Kemin; Angel, Matthew; Shao, Hongxia; Ferrero, Andrea; Sutton, Troy; Perez, Daniel R.

2012-01-01

Since 1999, plasmid-based reverse genetics (RG) systems have revolutionized the way influenza viruses are studied. However, it is not unusual to encounter cloning difficulties for one or more influenza genes while attempting to recover virus de novo. To overcome some of these shortcomings we sought to develop partial or full plasmid-free RG systems. The influenza gene of choice is assembled into a RG competent unit by virtue of overlapping PCR reactions containing a cDNA copy of the viral gene segment under the control of RNA polymerase I promoter (pol1) and termination (t1) signals – herein referred to as Flu PCR amplicons. Transfection of tissue culture cells with either HA or NA Flu PCR amplicons and 7 plasmids encoding the remaining influenza RG units, resulted in efficient virus rescue. Likewise, transfections including both HA and NA Flu PCR amplicons and 6 RG plasmids also resulted in efficient virus rescue. In addition, influenza viruses were recovered from a full set of Flu PCR amplicons without the use of plasmids. PMID:23029501

SU-G-JeP3-03: Effect of Robot Pose On Beam Blocking for Ultrasound Guided SBRT of the Prostate

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

Gerlach, S; Schlaefer, A; Kuhlemann, I

Purpose: Ultrasound presents a fast, volumetric image modality for real-time tracking of abdominal organ motion. How-ever, ultrasound transducer placement during radiation therapy is challenging. Recently, approaches using robotic arms for intra-treatment ultrasound imaging have been proposed. Good and reliable imaging requires placing the transducer close to the PTV. We studied the effect of a seven degrees of freedom robot on the fea-sible beam directions. Methods: For five CyberKnife prostate treatment plans we established viewports for the transducer, i.e., points on the patient surface with a soft tissue view towards the PTV. Choosing a feasible transducer pose and using the kinematicmore » redundancy of the KUKA LBR iiwa robot, we considered three robot poses. Poses 1 to 3 had the elbow point anterior, superior, and inferior, respectively. For each pose and each beam starting point, the pro-jections of robot and PTV were computed. We added a 20 mm margin accounting for organ / beam motion. The number of nodes for which the PTV was partially of fully blocked were established. Moreover, the cumula-tive overlap for each of the poses and the minimum overlap over all poses were computed. Results: The fully and partially blocked nodes ranged from 12% to 20% and 13% to 27%, respectively. Typically, pose 3 caused the fewest blocked nodes. The cumulative overlap ranged from 19% to 29%. Taking the minimum overlap, i.e., considering moving the robot’s elbow while maintaining the transducer pose, the cumulative over-lap was reduced to 16% to 18% and was 3% to 6% lower than for the best individual pose. Conclusion: Our results indicate that it is possible to identify feasible ultrasound transducer poses and to use the kinematic redundancy of a 7 DOF robot to minimize the impact of the imaging subsystem on the feasible beam directions for ultrasound guided and motion compensated SBRT. Research partially funded by DFG grants ER 817/1-1 and SCHL 1844/3-1.« less

Markov models for fMRI correlation structure: Is brain functional connectivity small world, or decomposable into networks?

PubMed

Varoquaux, G; Gramfort, A; Poline, J B; Thirion, B

2012-01-01

Correlations in the signal observed via functional Magnetic Resonance Imaging (fMRI), are expected to reveal the interactions in the underlying neural populations through hemodynamic response. In particular, they highlight distributed set of mutually correlated regions that correspond to brain networks related to different cognitive functions. Yet graph-theoretical studies of neural connections give a different picture: that of a highly integrated system with small-world properties: local clustering but with short pathways across the complete structure. We examine the conditional independence properties of the fMRI signal, i.e. its Markov structure, to find realistic assumptions on the connectivity structure that are required to explain the observed functional connectivity. In particular we seek a decomposition of the Markov structure into segregated functional networks using decomposable graphs: a set of strongly-connected and partially overlapping cliques. We introduce a new method to efficiently extract such cliques on a large, strongly-connected graph. We compare methods learning different graph structures from functional connectivity by testing the goodness of fit of the model they learn on new data. We find that summarizing the structure as strongly-connected networks can give a good description only for very large and overlapping networks. These results highlight that Markov models are good tools to identify the structure of brain connectivity from fMRI signals, but for this purpose they must reflect the small-world properties of the underlying neural systems. Copyright © 2012 Elsevier Ltd. All rights reserved.

A fully-automated multiscale kernel graph cuts based particle localization scheme for temporal focusing two-photon microscopy

NASA Astrophysics Data System (ADS)

Huang, Xia; Li, Chunqiang; Xiao, Chuan; Sun, Wenqing; Qian, Wei

2017-03-01

The temporal focusing two-photon microscope (TFM) is developed to perform depth resolved wide field fluorescence imaging by capturing frames sequentially. However, due to strong nonignorable noises and diffraction rings surrounding particles, further researches are extremely formidable without a precise particle localization technique. In this paper, we developed a fully-automated scheme to locate particles positions with high noise tolerance. Our scheme includes the following procedures: noise reduction using a hybrid Kalman filter method, particle segmentation based on a multiscale kernel graph cuts global and local segmentation algorithm, and a kinematic estimation based particle tracking method. Both isolated and partial-overlapped particles can be accurately identified with removal of unrelated pixels. Based on our quantitative analysis, 96.22% isolated particles and 84.19% partial-overlapped particles were successfully detected.

Aspects and the Overlap Function.

ERIC Educational Resources Information Center

Levine, Marilyn M.; Levine, Leonard P.

1984-01-01

Presents system for automatic handling of ordered sets, states based on these sets, and differing points of view regarding Universe of Discourse. Aspects are represented by new logical "overlap" function with examples taken from Ranganathan's horse and carriage parable and several books involving four main concepts (history, geography,…

Communication: molecular dynamics and (1)H NMR of n-hexane in liquid crystals.

PubMed

Weber, Adrian C J; Burnell, E Elliott; Meerts, W Leo; de Lange, Cornelis A; Dong, Ronald Y; Muccioli, Luca; Pizzirusso, Antonio; Zannoni, Claudio

2015-07-07

The NMR spectrum of n-hexane orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy (CMA-ES). The spectrum contains over 150 000 transitions, with many sharp features appearing above a broad, underlying background signal that results from the plethora of overlapping transitions from the n-hexane as well as from the liquid crystal. The CMA-ES requires initial search ranges for NMR spectral parameters, notably the direct dipolar couplings. Several sets of such ranges were utilized, including three from MD simulations and others from the modified chord model that is specifically designed to predict hydrocarbon-chain dipolar couplings. In the end, only inaccurate dipolar couplings from an earlier study utilizing proton-proton double quantum 2D-NMR techniques on partially deuterated n-hexane provided the necessary estimates. The precise set of dipolar couplings obtained can now be used to investigate conformational averaging of n-hexane in a nematic environment.

Communication: Molecular dynamics and {sup 1}H NMR of n-hexane in liquid crystals

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

Weber, Adrian C. J., E-mail: WeberA@BrandonU.CA; Burnell, E. Elliott, E-mail: elliott.burnell@ubc.ca; Meerts, W. Leo, E-mail: leo.meerts@science.ru.nl

The NMR spectrum of n-hexane orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy (CMA-ES). The spectrum contains over 150 000 transitions, with many sharp features appearing above a broad, underlying background signal that results from the plethora of overlapping transitions from the n-hexane as well as from the liquid crystal. The CMA-ES requires initial search ranges for NMR spectral parameters, notably the direct dipolar couplings. Several sets of such ranges were utilized, including three from MD simulations and others from the modified chord model that is specifically designed to predict hydrocarbon-chain dipolar couplings.more » In the end, only inaccurate dipolar couplings from an earlier study utilizing proton-proton double quantum 2D-NMR techniques on partially deuterated n-hexane provided the necessary estimates. The precise set of dipolar couplings obtained can now be used to investigate conformational averaging of n-hexane in a nematic environment.« less

Advanced stability indicating chemometric methods for quantitation of amlodipine and atorvastatin in their quinary mixture with acidic degradation products

NASA Astrophysics Data System (ADS)

Darwish, Hany W.; Hassan, Said A.; Salem, Maissa Y.; El-Zeany, Badr A.

2016-02-01

Two advanced, accurate and precise chemometric methods are developed for the simultaneous determination of amlodipine besylate (AML) and atorvastatin calcium (ATV) in the presence of their acidic degradation products in tablet dosage forms. The first method was Partial Least Squares (PLS-1) and the second was Artificial Neural Networks (ANN). PLS was compared to ANN models with and without variable selection procedure (genetic algorithm (GA)). For proper analysis, a 5-factor 5-level experimental design was established resulting in 25 mixtures containing different ratios of the interfering species. Fifteen mixtures were used as calibration set and the other ten mixtures were used as validation set to validate the prediction ability of the suggested models. The proposed methods were successfully applied to the analysis of pharmaceutical tablets containing AML and ATV. The methods indicated the ability of the mentioned models to solve the highly overlapped spectra of the quinary mixture, yet using inexpensive and easy to handle instruments like the UV-VIS spectrophotometer.

A combined experimental and DFT investigation of disazo dye having pyrazole skeleton

NASA Astrophysics Data System (ADS)

Şener, Nesrin; Bayrakdar, Alpaslan; Kart, Hasan Hüseyin; Şener, İzzet

2017-02-01

Disazo dye containing pyrazole skeleton has been synthesized. The structure of the dye has been confirmed by using FT-IR, 1H NMR, 13C NMR, HRMS spectral technique and elemental analysis. The molecular geometry and infrared spectrum are also calculated by the Density Functional Theory (DFT) employing B3LYP level with 6-311G (d,p) basis set. The chemical shifts calculation for 1H NMR of the title molecule is done by using by Gauge-Invariant Atomic Orbital (GIAO) method by utilizing the same basis sets. The total density of state, the partial density of state and the overlap population density of state diagram analysis are done via Gauss Sum 3.0 program. Frontier molecular orbitals such as highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and molecular electrostatic potential surface on the title molecule are predicted for various intramolecular interactions that are responsible for the stabilization of the molecule. The experimental results and theoretical values have been compared.

Functional Specialization and Flexibility in Human Association Cortex

PubMed Central

Yeo, B. T. Thomas; Krienen, Fenna M.; Eickhoff, Simon B.; Yaakub, Siti N.; Fox, Peter T.; Buckner, Randy L.; Asplund, Christopher L.; Chee, Michael W.L.

2015-01-01

The association cortex supports cognitive functions enabling flexible behavior. Here, we explored the organization of human association cortex by mathematically formalizing the notion that a behavioral task engages multiple cognitive components, which are in turn supported by multiple overlapping brain regions. Application of the model to a large data set of neuroimaging experiments (N = 10 449) identified complex zones of frontal and parietal regions that ranged from being highly specialized to highly flexible. The network organization of the specialized and flexible regions was explored with an independent resting-state fMRI data set (N = 1000). Cortical regions specialized for the same components were strongly coupled, suggesting that components function as partially isolated networks. Functionally flexible regions participated in multiple components to different degrees. This heterogeneous selectivity was predicted by the connectivity between flexible and specialized regions. Functionally flexible regions might support binding or integrating specialized brain networks that, in turn, contribute to the ability to execute multiple and varied tasks. PMID:25249407

Predicting 3D pose in partially overlapped X-ray images of knee prostheses using model-based Roentgen stereophotogrammetric analysis (RSA).

PubMed

Hsu, Chi-Pin; Lin, Shang-Chih; Shih, Kao-Shang; Huang, Chang-Hung; Lee, Chian-Her

2014-12-01

After total knee replacement, the model-based Roentgen stereophotogrammetric analysis (RSA) technique has been used to monitor the status of prosthetic wear, misalignment, and even failure. However, the overlap of the prosthetic outlines inevitably increases errors in the estimation of prosthetic poses due to the limited amount of available outlines. In the literature, quite a few studies have investigated the problems induced by the overlapped outlines, and manual adjustment is still the mainstream. This study proposes two methods to automate the image processing of overlapped outlines prior to the pose registration of prosthetic models. The outline-separated method defines the intersected points and segments the overlapped outlines. The feature-recognized method uses the point and line features of the remaining outlines to initiate registration. Overlap percentage is defined as the ratio of overlapped to non-overlapped outlines. The simulated images with five overlapping percentages are used to evaluate the robustness and accuracy of the proposed methods. Compared with non-overlapped images, overlapped images reduce the number of outlines available for model-based RSA calculation. The maximum and root mean square errors for a prosthetic outline are 0.35 and 0.04 mm, respectively. The mean translation and rotation errors are 0.11 mm and 0.18°, respectively. The errors of the model-based RSA results are increased when the overlap percentage is beyond about 9%. In conclusion, both outline-separated and feature-recognized methods can be seamlessly integrated to automate the calculation of rough registration. This can significantly increase the clinical practicability of the model-based RSA technique.

Detecting overlapping instances in microscopy images using extremal region trees.

PubMed

Arteta, Carlos; Lempitsky, Victor; Noble, J Alison; Zisserman, Andrew

2016-01-01

In many microscopy applications the images may contain both regions of low and high cell densities corresponding to different tissues or colonies at different stages of growth. This poses a challenge to most previously developed automated cell detection and counting methods, which are designed to handle either the low-density scenario (through cell detection) or the high-density scenario (through density estimation or texture analysis). The objective of this work is to detect all the instances of an object of interest in microscopy images. The instances may be partially overlapping and clustered. To this end we introduce a tree-structured discrete graphical model that is used to select and label a set of non-overlapping regions in the image by a global optimization of a classification score. Each region is labeled with the number of instances it contains - for example regions can be selected that contain two or three object instances, by defining separate classes for tuples of objects in the detection process. We show that this formulation can be learned within the structured output SVM framework and that the inference in such a model can be accomplished using dynamic programming on a tree structured region graph. Furthermore, the learning only requires weak annotations - a dot on each instance. The candidate regions for the selection are obtained as extremal region of a surface computed from the microscopy image, and we show that the performance of the model can be improved by considering a proxy problem for learning the surface that allows better selection of the extremal regions. Furthermore, we consider a number of variations for the loss function used in the structured output learning. The model is applied and evaluated over six quite disparate data sets of images covering: fluorescence microscopy, weak-fluorescence molecular images, phase contrast microscopy and histopathology images, and is shown to exceed the state of the art in performance. Copyright © 2015 Elsevier B.V. All rights reserved.

A Brain Centred View of Psychiatric Comorbidity in Tinnitus: From Otology to Hodology

PubMed Central

Minichino, Amedeo; Panico, Roberta; Testugini, Valeria; Altissimi, Giancarlo; Cianfrone, Giancarlo

2014-01-01

Introduction. Comorbid psychiatric disorders are frequent among patients affected by tinnitus. There are mutual clinical influences between tinnitus and psychiatric disorders, as well as neurobiological relations based on partially overlapping hodological and neuroplastic phenomena. The aim of the present paper is to review the evidence of alterations in brain networks underlying tinnitus physiopathology and to discuss them in light of the current knowledge of the neurobiology of psychiatric disorders. Methods. Relevant literature was identified through a search on Medline and PubMed; search terms included tinnitus, brain, plasticity, cortex, network, and pathways. Results. Tinnitus phenomenon results from systemic-neurootological triggers followed by neuronal remapping within several auditory and nonauditory pathways. Plastic reorganization and white matter alterations within limbic system, arcuate fasciculus, insula, salience network, dorsolateral prefrontal cortex, auditory pathways, ffrontocortical, and thalamocortical networks are discussed. Discussion. Several overlapping brain network alterations do exist between tinnitus and psychiatric disorders. Tinnitus, initially related to a clinicoanatomical approach based on a cortical localizationism, could be better explained by an holistic or associationist approach considering psychic functions and tinnitus as emergent properties of partially overlapping large-scale neural networks. PMID:25018882

Inexpensive Masks for Film Deposition

NASA Technical Reports Server (NTRS)

Conley, W. R.

1986-01-01

Sputtered sprayed lines less than 2 millimeters wide made by superimposing masks with partially overlapping openings. Slits first cut in masks by stamping or other economical process. Masks superimposed so slits define new openings narrower than original slits.

White matter microstructural abnormalities in girls with chromosome 22q11.2 deletion syndrome, Fragile X or Turner syndrome as evidenced by diffusion tensor imaging

PubMed Central

Villalon, Julio; Jahanshad, Neda; Beaton, Elliott; Toga, Arthur W.; Thompson, Paul M.; Simon, Tony J.

2014-01-01

Children with chromosome 22q11.2 Deletion Syndrome (22q11.2DS), Fragile X Syndrome (FXS), or Turner Syndrome (TS) are considered to belong to distinct genetic groups, as each disorder is caused by separate genetic alterations. Even so, they have similar cognitive and behavioral dysfunctions, particularly in visuospatial and numerical abilities. To assess evidence for common underlying neural microstructural alterations, we set out to determine whether these groups have partially overlapping white matter abnormalities, relative to typically developing controls. We scanned 101 female children between 7 and 14 years old: 25 with 22q11.2DS, 18 with FXS, 17 with TS, and 41 aged-matched controls using diffusion tensor imaging (DTI). Anisotropy and diffusivity measures were calculated and all brain scans were nonlinearly aligned to population and site-specific templates. We performed voxel-based statistical comparisons of the DTI-derived metrics between each disease group and the controls, while adjusting for age. Girls with 22q11.2DS showed lower fractional anisotropy (FA) than controls in the association fibers of the superior and inferior longitudinal fasciculi, the splenium of the corpus callosum, and the corticospinal tract. FA was abnormally lower in girls with FXS in the posterior limbs of the internal capsule, posterior thalami, and precentral gyrus. Girls with TS had lower FA in the inferior longitudinal fasciculus, right internal capsule and left cerebellar peduncle. Partially overlapping neurodevelopmental anomalies were detected in all three neurogenetic disorders. Altered white matter integrity in the superior and inferior longitudinal fasciculi and thalamic to frontal tracts may contribute to the behavioral characteristics of all of these disorders. PMID:23602925

Novel absorptivity centering method utilizing normalized and factorized spectra for analysis of mixtures with overlapping spectra in different matrices using built-in spectrophotometer software

NASA Astrophysics Data System (ADS)

Lotfy, Hayam Mahmoud; Omran, Yasmin Rostom

2018-07-01

A novel, simple, rapid, accurate, and economical spectrophotometric method, namely absorptivity centering (a-Centering) has been developed and validated for the simultaneous determination of mixtures with partially and completely overlapping spectra in different matrices using either normalized or factorized spectrum using built-in spectrophotometer software without a need of special purchased program. Mixture I (Mix I) composed of Simvastatin (SM) and Ezetimibe (EZ) is the one with partial overlapping spectra formulated as tablets, while mixture II (Mix II) formed by Chloramphenicol (CPL) and Prednisolone acetate (PA) is that with complete overlapping spectra formulated as eye drops. These procedures do not require any separation steps. Resolution of spectrally overlapping binary mixtures has been achieved getting recovered zero-order (D0) spectrum of each drug, then absorbance was recorded at their maxima 238, 233.5, 273 and 242.5 nm for SM, EZ, CPL and PA, respectively. Calibration graphs were established with good correlation coefficients. The method shows significant advantages as simplicity, minimal data manipulation besides maximum reproducibility and robustness. Moreover, it was validated according to ICH guidelines. Selectivity was tested using laboratory-prepared mixtures. Accuracy, precision and repeatability were found to be within the acceptable limits. The proposed method is good enough to be applied to an assay of drugs in their combined formulations without any interference from excipients. The obtained results were statistically compared with those of the reported and official methods by applying t-test and F-test at 95% confidence level concluding that there is no significant difference with regard to accuracy and precision. Generally, this method could be used successfully for the routine quality control testing.

Novel absorptivity centering method utilizing normalized and factorized spectra for analysis of mixtures with overlapping spectra in different matrices using built-in spectrophotometer software.

PubMed

Lotfy, Hayam Mahmoud; Omran, Yasmin Rostom

2018-07-05

A novel, simple, rapid, accurate, and economical spectrophotometric method, namely absorptivity centering (a-Centering) has been developed and validated for the simultaneous determination of mixtures with partially and completely overlapping spectra in different matrices using either normalized or factorized spectrum using built-in spectrophotometer software without a need of special purchased program. Mixture I (Mix I) composed of Simvastatin (SM) and Ezetimibe (EZ) is the one with partial overlapping spectra formulated as tablets, while mixture II (Mix II) formed by Chloramphenicol (CPL) and Prednisolone acetate (PA) is that with complete overlapping spectra formulated as eye drops. These procedures do not require any separation steps. Resolution of spectrally overlapping binary mixtures has been achieved getting recovered zero-order (D 0 ) spectrum of each drug, then absorbance was recorded at their maxima 238, 233.5, 273 and 242.5 nm for SM, EZ, CPL and PA, respectively. Calibration graphs were established with good correlation coefficients. The method shows significant advantages as simplicity, minimal data manipulation besides maximum reproducibility and robustness. Moreover, it was validated according to ICH guidelines. Selectivity was tested using laboratory-prepared mixtures. Accuracy, precision and repeatability were found to be within the acceptable limits. The proposed method is good enough to be applied to an assay of drugs in their combined formulations without any interference from excipients. The obtained results were statistically compared with those of the reported and official methods by applying t-test and F-test at 95% confidence level concluding that there is no significant difference with regard to accuracy and precision. Generally, this method could be used successfully for the routine quality control testing. Copyright © 2018 Elsevier B.V. All rights reserved.

Robust, Globally Consistent, and Fully-automatic Multi-image Registration and Montage Synthesis for 3-D Multi-channel Images

PubMed Central

Tsai, Chia-Ling; Lister, James P.; Bjornsson, Christopher J; Smith, Karen; Shain, William; Barnes, Carol A.; Roysam, Badrinath

2013-01-01

The need to map regions of brain tissue that are much wider than the field of view of the microscope arises frequently. One common approach is to collect a series of overlapping partial views, and align them to synthesize a montage covering the entire region of interest. We present a method that advances this approach in multiple ways. Our method (1) produces a globally consistent joint registration of an unorganized collection of 3-D multi-channel images with or without stage micrometer data; (2) produces accurate registrations withstanding changes in scale, rotation, translation and shear by using a 3-D affine transformation model; (3) achieves complete automation, and does not require any parameter settings; (4) handles low and variable overlaps (5 – 15%) between adjacent images, minimizing the number of images required to cover a tissue region; (5) has the self-diagnostic ability to recognize registration failures instead of delivering incorrect results; (6) can handle a broad range of biological images by exploiting generic alignment cues from multiple fluorescence channels without requiring segmentation; and (7) is computationally efficient enough to run on desktop computers regardless of the number of images. The algorithm was tested with several tissue samples of at least 50 image tiles, involving over 5,000 image pairs. It correctly registered all image pairs with an overlap greater than 7%, correctly recognized all failures, and successfully joint-registered all images for all tissue samples studied. This algorithm is disseminated freely to the community as included with the FARSIGHT toolkit for microscopy (www.farsight-toolkit.org). PMID:21361958

Overlapping meta-analyses on the same topic: survey of published studies.

PubMed

Siontis, Konstantinos C; Hernandez-Boussard, Tina; Ioannidis, John P A

2013-07-19

To assess how common it is to have multiple overlapping meta-analyses of randomized trials published on the same topic. Survey of published meta-analyses. PubMed. Meta-analyses published in 2010 were identified, and 5% of them were randomly selected. We further selected those that included randomized trials and examined effectiveness of any medical intervention. For eligible meta-analyses, we searched for other meta-analyses on the same topic (covering the same comparisons, indications/settings, and outcomes or overlapping subsets of them) published until February 2013. Of 73 eligible meta-analyses published in 2010, 49 (67%) had at least one other overlapping meta-analysis (median two meta-analyses per topic, interquartile range 1-4, maximum 13). In 17 topics at least one author was involved in at least two of the overlapping meta-analyses. No characteristics of the index meta-analyses were associated with the potential for overlapping meta-analyses. Among pairs of overlapping meta-analyses in 20 randomly selected topics, 13 of the more recent meta-analyses did not include any additional outcomes. In three of the four topics with eight or more published meta-analyses, many meta-analyses examined only a subset of the eligible interventions or indications/settings covered by the index meta-analysis. Conversely, for statins in the prevention of atrial fibrillation after cardiac surgery, 11 meta-analyses were published with similar eligibility criteria for interventions and setting: there was still variability on which studies were included, but the results were always similar or even identical across meta-analyses. While some independent replication of meta-analyses by different teams is possibly useful, the overall picture suggests that there is a waste of efforts with many topics covered by multiple overlapping meta-analyses.

A comparative analysis of biclustering algorithms for gene expression data

PubMed Central

Eren, Kemal; Deveci, Mehmet; Küçüktunç, Onur; Çatalyürek, Ümit V.

2013-01-01

The need to analyze high-dimension biological data is driving the development of new data mining methods. Biclustering algorithms have been successfully applied to gene expression data to discover local patterns, in which a subset of genes exhibit similar expression levels over a subset of conditions. However, it is not clear which algorithms are best suited for this task. Many algorithms have been published in the past decade, most of which have been compared only to a small number of algorithms. Surveys and comparisons exist in the literature, but because of the large number and variety of biclustering algorithms, they are quickly outdated. In this article we partially address this problem of evaluating the strengths and weaknesses of existing biclustering methods. We used the BiBench package to compare 12 algorithms, many of which were recently published or have not been extensively studied. The algorithms were tested on a suite of synthetic data sets to measure their performance on data with varying conditions, such as different bicluster models, varying noise, varying numbers of biclusters and overlapping biclusters. The algorithms were also tested on eight large gene expression data sets obtained from the Gene Expression Omnibus. Gene Ontology enrichment analysis was performed on the resulting biclusters, and the best enrichment terms are reported. Our analyses show that the biclustering method and its parameters should be selected based on the desired model, whether that model allows overlapping biclusters, and its robustness to noise. In addition, we observe that the biclustering algorithms capable of finding more than one model are more successful at capturing biologically relevant clusters. PMID:22772837

The association of color memory and the enumeration of multiple spatially overlapping sets.

PubMed

Poltoratski, Sonia; Xu, Yaoda

2013-07-09

Using dot displays, Halberda, Sires, and Feigenson (2006) showed that observers could simultaneously encode the numerosity of two spatially overlapping sets and the superset of all items at a glance. With the brief display and the masking used in Halberda et al., the task required observers to encode the colors of each set in order to select and enumerate all the dots in that set. As such, the observed capacity limit for set enumeration could reflect a limit in visual short-term memory (VSTM) capacity for the set color rather than a limit in set enumeration per se. Here, we largely replicated Halberda et al. and found successful enumeration of approximately two sets (the superset was not probed). We also found that only about two and a half colors could be remembered from the colored dot displays whether or not the enumeration task was performed concurrently with the color VSTM task. Because observers must remember the color of a set prior to enumerating it, the under three-item VSTM capacity for color necessarily dictates that set enumeration capacity in this paradigm could not exceed two sets. Thus, the ability to enumerate multiple spatially overlapping sets is likely limited by VSTM capacity to retain the discriminating feature of these sets. This relationship suggests that the capacity for set enumeration cannot be considered independently from the capacity for the set's defining features.

Facial expression recognition under partial occlusion based on fusion of global and local features

NASA Astrophysics Data System (ADS)

Wang, Xiaohua; Xia, Chen; Hu, Min; Ren, Fuji

2018-04-01

Facial expression recognition under partial occlusion is a challenging research. This paper proposes a novel framework for facial expression recognition under occlusion by fusing the global and local features. In global aspect, first, information entropy are employed to locate the occluded region. Second, principal Component Analysis (PCA) method is adopted to reconstruct the occlusion region of image. After that, a replace strategy is applied to reconstruct image by replacing the occluded region with the corresponding region of the best matched image in training set, Pyramid Weber Local Descriptor (PWLD) feature is then extracted. At last, the outputs of SVM are fitted to the probabilities of the target class by using sigmoid function. For the local aspect, an overlapping block-based method is adopted to extract WLD features, and each block is weighted adaptively by information entropy, Chi-square distance and similar block summation methods are then applied to obtain the probabilities which emotion belongs to. Finally, fusion at the decision level is employed for the data fusion of the global and local features based on Dempster-Shafer theory of evidence. Experimental results on the Cohn-Kanade and JAFFE databases demonstrate the effectiveness and fault tolerance of this method.

[A functional orthodontic magnetic appliance (FOMA) after Vardimon. 1. A three-dimensional analysis of the force system of the attractive magnets].

PubMed

Bourauel, C; Vardimon, A D; Drescher, D; Schmuth, G P

1995-09-01

The functional magnetic system (FMS) is a removable functional appliance which induces mandibular advance by means of mandibular and maxillary magnets in an attracting configuration. The maxillary and mandibular plates are each equipped with 2 cylindrically shaped cobalt-samarium magnets, 4 mm in diameter and 3 mm in height, which are welded into stainless steel housings. The force system of this magnetic configuration was analyzed using the orthodontic measurement and simulation system (OMSS). OMSS simulated the mandibular jaw movements by separating the installed magnets vertically, corresponding to a mouth opening of X = -10 mm, transversally (right excursion, +/left excursion, -) at Y = +/- 10 mm and sagittally (anterior displacement, +/posterior displacement, -) at Z = +/- 10 mm. The resulting 2D and 3D force/displacement diagrams elucidate the outstanding centripetal-spatial orientation characteristics of the functional magnetic appliance in reference to the full overlap brought about by the attraction of the mandibular magnet by the maxillary magnet. The maximum centripetal forces reached a value of approximately FY, max = 0.65 N for the vertical attracting force at full overlap of the mandibular and maxillary magnets (X = 0.55 mm, Y = Z = 0 mm), a value of FY, max = 0.65 N for the medial shearing force at a partial transversal overlap Z = 0, Y = +/- 2 mm and Y = +/- 6 mm), and for the sagittal shearing force a value of FZ, max = 1.2 N at a partial sagittal overlap of the magnets (Y = 0 mm, Z = +/- 2 mm).(ABSTRACT TRUNCATED AT 250 WORDS)

Reflections on Rational-Emotive Therapy.

ERIC Educational Resources Information Center

Ellis, Albert

1993-01-01

Reflects rational-emotive therapy (RET) in 1955 and discusses some of its recent constructivist and humanist theories and practice. Distinguishes between general RET, called synonymous with general cognitive-behavioral therapy, from preferential RET, called unique kind of cognitive therapy that partially overlaps with general cognitive-behavioral…

Efficient measurement of point-to-set correlations and overlap fluctuations in glass-forming liquids

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

Berthier, Ludovic; Charbonneau, Patrick; Department of Physics, Duke University, Durham, North Carolina 27708

Cavity point-to-set correlations are real-space tools to detect the roughening of the free-energy landscape that accompanies the dynamical slowdown of glass-forming liquids. Measuring these correlations in model glass formers remains, however, a major computational challenge. Here, we develop a general parallel-tempering method that provides orders-of-magnitude improvement for sampling and equilibrating configurations within cavities. We apply this improved scheme to the canonical Kob-Andersen binary Lennard-Jones model for temperatures down to the mode-coupling theory crossover. Most significant improvements are noted for small cavities, which have thus far been the most difficult to study. This methodological advance also enables us to study amore » broader range of physical observables associated with thermodynamic fluctuations. We measure the probability distribution of overlap fluctuations in cavities, which displays a non-trivial temperature evolution. The corresponding overlap susceptibility is found to provide a robust quantitative estimate of the point-to-set length scale requiring no fitting. By resolving spatial fluctuations of the overlap in the cavity, we also obtain quantitative information about the geometry of overlap fluctuations. We can thus examine in detail how the penetration length as well as its fluctuations evolve with temperature and cavity size.« less

Ras proteins have multiple functions in vegetative cells of Dictyostelium.

PubMed

Bolourani, Parvin; Spiegelman, George; Weeks, Gerald

2010-11-01

During the aggregation of Dictyostelium cells, signaling through RasG is more important in regulating cyclic AMP (cAMP) chemotaxis, whereas signaling through RasC is more important in regulating the cAMP relay. However, RasC is capable of substituting for RasG for chemotaxis, since rasG⁻ cells are only partially deficient in chemotaxis, whereas rasC⁻/rasG⁻ cells are totally incapable of chemotaxis. In this study we have examined the possible functional overlap between RasG and RasC in vegetative cells by comparing the vegetative cell properties of rasG⁻, rasC⁻, and rasC⁻/rasG⁻ cells. In addition, since RasD, a protein not normally found in vegetative cells, is expressed in vegetative rasG⁻ and rasC⁻/rasG⁻ cells and appears to partially compensate for the absence of RasG, we have also examined the possible functional overlap between RasG and RasD by comparing the properties of rasG⁻ and rasC⁻/rasG⁻ cells with those of the mutant cells expressing higher levels of RasD. The results of these two lines of investigation show that RasD is capable of totally substituting for RasG for cytokinesis and growth in suspension, whereas RasC is without effect. In contrast, for chemotaxis to folate, RasC is capable of partially substituting for RasG, but RasD is totally without effect. Finally, neither RasC nor RasD is able to substitute for the role that RasG plays in regulating actin distribution and random motility. These specificity studies therefore delineate three distinct and none-overlapping functions for RasG in vegetative cells.

Advanced stability indicating chemometric methods for quantitation of amlodipine and atorvastatin in their quinary mixture with acidic degradation products.

PubMed

Darwish, Hany W; Hassan, Said A; Salem, Maissa Y; El-Zeany, Badr A

2016-02-05

Two advanced, accurate and precise chemometric methods are developed for the simultaneous determination of amlodipine besylate (AML) and atorvastatin calcium (ATV) in the presence of their acidic degradation products in tablet dosage forms. The first method was Partial Least Squares (PLS-1) and the second was Artificial Neural Networks (ANN). PLS was compared to ANN models with and without variable selection procedure (genetic algorithm (GA)). For proper analysis, a 5-factor 5-level experimental design was established resulting in 25 mixtures containing different ratios of the interfering species. Fifteen mixtures were used as calibration set and the other ten mixtures were used as validation set to validate the prediction ability of the suggested models. The proposed methods were successfully applied to the analysis of pharmaceutical tablets containing AML and ATV. The methods indicated the ability of the mentioned models to solve the highly overlapped spectra of the quinary mixture, yet using inexpensive and easy to handle instruments like the UV-VIS spectrophotometer. Copyright © 2015 Elsevier B.V. All rights reserved.

Network neighborhood analysis with the multi-node topological overlap measure.

PubMed

Li, Ai; Horvath, Steve

2007-01-15

The goal of neighborhood analysis is to find a set of genes (the neighborhood) that is similar to an initial 'seed' set of genes. Neighborhood analysis methods for network data are important in systems biology. If individual network connections are susceptible to noise, it can be advantageous to define neighborhoods on the basis of a robust interconnectedness measure, e.g. the topological overlap measure. Since the use of multiple nodes in the seed set may lead to more informative neighborhoods, it can be advantageous to define multi-node similarity measures. The pairwise topological overlap measure is generalized to multiple network nodes and subsequently used in a recursive neighborhood construction method. A local permutation scheme is used to determine the neighborhood size. Using four network applications and a simulated example, we provide empirical evidence that the resulting neighborhoods are biologically meaningful, e.g. we use neighborhood analysis to identify brain cancer related genes. An executable Windows program and tutorial for multi-node topological overlap measure (MTOM) based analysis can be downloaded from the webpage (http://www.genetics.ucla.edu/labs/horvath/MTOM/).

Reading in two alphabets.

PubMed

Lukatela, G; Turvey, M T

1998-09-01

Many speakers of Serbo-Croatian read the language in two phonemically precise and partially overlapping alphabets. Twenty years of experiments directed toward this ability have led to deeper understandings of the role of speech-related processes in reading and the contrasts and similarities among the world's alphabetic writing systems.

Leakage current suppression with a combination of planarized gate and overlap/off-set structure in metal-induced laterally crystallized polycrystalline-silicon thin-film transistors

NASA Astrophysics Data System (ADS)

Chae, Hee Jae; Seok, Ki Hwan; Lee, Sol Kyu; Joo, Seung Ki

2018-04-01

A novel inverted staggered metal-induced laterally crystallized (MILC) polycrystalline-silicon (poly-Si) thin-film transistors (TFTs) with a combination of a planarized gate and an overlap/off-set at the source-gate/drain-gate structure were fabricated and characterized. While the MILC process is advantageous for fabricating inverted staggered poly-Si TFTs, MILC TFTs reveal higher leakage current than TFTs crystallized by other processes due to their high trap density of Ni contamination. Due to this drawback, the planarized gate and overlap/off-set structure were applied to inverted staggered MILC TFTs. The proposed device shows drastic suppression of leakage current and pinning phenomenon by reducing the lateral electric field and the space-charge limited current from the gate to the drain.

Trophic overlap between expanding and contracting fish predators in a range margin undergoing change.

PubMed

Westerbom, Mats; Lappalainen, Antti; Mustonen, Olli; Norkko, Alf

2018-05-21

Climate change is predicted to cause a freshening of the Baltic Sea, facilitating range expansions of freshwater species and contractions of marine. Resident marine flounders (Platichthys flesus) and expansive freshwater roach (Rutilus rutilus) are dominant consumers in the Baltic Sea sublittoral where they occur in partial sympatry. By comparing patterns of resource use by flounders and roach along a declining resource gradient of blue mussels (Mytilus trossulus) our aim was to explore predator functional responses and the degree of trophic overlap. Understanding the nature of density-dependent prey acquisition has important implications for predicting population dynamics of both predators and their shared prey. Results showed a highly specialized diet for both species, high reliance on blue mussels throughout the range, similar prey size preference and high trophic overlap. Highest overlap occurred where blue mussels were abundant but overlap was also high where they were scarce. Our results highlight the importance of a single food item - the blue mussel - for both species, likely promoting high population size and range expansion of roach. Findings also suggest that range expansion of roach may have a top-down structuring force on mussels that differ in severity and location from that originating from resident flounders.

Parallel Newton-Krylov-Schwarz algorithms for the transonic full potential equation

NASA Technical Reports Server (NTRS)

Cai, Xiao-Chuan; Gropp, William D.; Keyes, David E.; Melvin, Robin G.; Young, David P.

1996-01-01

We study parallel two-level overlapping Schwarz algorithms for solving nonlinear finite element problems, in particular, for the full potential equation of aerodynamics discretized in two dimensions with bilinear elements. The overall algorithm, Newton-Krylov-Schwarz (NKS), employs an inexact finite-difference Newton method and a Krylov space iterative method, with a two-level overlapping Schwarz method as a preconditioner. We demonstrate that NKS, combined with a density upwinding continuation strategy for problems with weak shocks, is robust and, economical for this class of mixed elliptic-hyperbolic nonlinear partial differential equations, with proper specification of several parameters. We study upwinding parameters, inner convergence tolerance, coarse grid density, subdomain overlap, and the level of fill-in in the incomplete factorization, and report their effect on numerical convergence rate, overall execution time, and parallel efficiency on a distributed-memory parallel computer.

A 2D MTF approach to evaluate and guide dynamic imaging developments.

PubMed

Chao, Tzu-Cheng; Chung, Hsiao-Wen; Hoge, W Scott; Madore, Bruno

2010-02-01

As the number and complexity of partially sampled dynamic imaging methods continue to increase, reliable strategies to evaluate performance may prove most useful. In the present work, an analytical framework to evaluate given reconstruction methods is presented. A perturbation algorithm allows the proposed evaluation scheme to perform robustly without requiring knowledge about the inner workings of the method being evaluated. A main output of the evaluation process consists of a two-dimensional modulation transfer function, an easy-to-interpret visual rendering of a method's ability to capture all combinations of spatial and temporal frequencies. Approaches to evaluate noise properties and artifact content at all spatial and temporal frequencies are also proposed. One fully sampled phantom and three fully sampled cardiac cine datasets were subsampled (R = 4 and 8) and reconstructed with the different methods tested here. A hybrid method, which combines the main advantageous features observed in our assessments, was proposed and tested in a cardiac cine application, with acceleration factors of 3.5 and 6.3 (skip factors of 4 and 8, respectively). This approach combines features from methods such as k-t sensitivity encoding, unaliasing by Fourier encoding the overlaps in the temporal dimension-sensitivity encoding, generalized autocalibrating partially parallel acquisition, sensitivity profiles from an array of coils for encoding and reconstruction in parallel, self, hybrid referencing with unaliasing by Fourier encoding the overlaps in the temporal dimension and generalized autocalibrating partially parallel acquisition, and generalized autocalibrating partially parallel acquisition-enhanced sensitivity maps for sensitivity encoding reconstructions.

'Stent in a stent'--an alternative technique for removing partially covered stents following sleeve gastrectomy complications.

PubMed

Vasilikostas, Georgios; Sanmugalingam, Nimalan; Khan, Omar; Reddy, Marcus; Groves, Chris; Wan, Andrew

2014-03-01

Endoscopic stenting is a relatively new technique for the treatment of post sleeve gastrectomy complications. Partially covered stents are used in this method to minimise the risk of migration but they are associated with difficulties with removal. Patients requiring emergency stenting following sleeve gastrectomy underwent insertion of a partially covered metallic stent. One month later, if the stent was not easily removable, a fully covered overlapping stent was inserted and the patient was readmitted 2 weeks later for removal of both stents. Four patients required stenting following sleeve gastrectomy leaks, and one patient required stenting for a stricture. In these cases, a 'stent in a stent' technique was used for removal. This technique allows the safe removal of partially covered stents inserted following sleeve gastrectomy complications.

LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.

PubMed

Nagraj, V P; Magee, Neal E; Sheffield, Nathan C

2018-06-06

The past few years have seen an explosion of interest in understanding the role of regulatory DNA. This interest has driven large-scale production of functional genomics data and analytical methods. One popular analysis is to test for enrichment of overlaps between a query set of genomic regions and a database of region sets. In this way, new genomic data can be easily connected to annotations from external data sources. Here, we present an interactive interface for enrichment analysis of genomic locus overlaps using a web server called LOLAweb. LOLAweb accepts a set of genomic ranges from the user and tests it for enrichment against a database of region sets. LOLAweb renders results in an R Shiny application to provide interactive visualization features, enabling users to filter, sort, and explore enrichment results dynamically. LOLAweb is built and deployed in a Linux container, making it scalable to many concurrent users on our servers and also enabling users to download and run LOLAweb locally.

A variational approach to multi-phase motion of gas, liquid and solid based on the level set method

NASA Astrophysics Data System (ADS)

Yokoi, Kensuke

2009-07-01

We propose a simple and robust numerical algorithm to deal with multi-phase motion of gas, liquid and solid based on the level set method [S. Osher, J.A. Sethian, Front propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi formulation, J. Comput. Phys. 79 (1988) 12; M. Sussman, P. Smereka, S. Osher, A level set approach for capturing solution to incompressible two-phase flow, J. Comput. Phys. 114 (1994) 146; J.A. Sethian, Level Set Methods and Fast Marching Methods, Cambridge University Press, 1999; S. Osher, R. Fedkiw, Level Set Methods and Dynamics Implicit Surface, Applied Mathematical Sciences, vol. 153, Springer, 2003]. In Eulerian framework, to simulate interaction between a moving solid object and an interfacial flow, we need to define at least two functions (level set functions) to distinguish three materials. In such simulations, in general two functions overlap and/or disagree due to numerical errors such as numerical diffusion. In this paper, we resolved the problem using the idea of the active contour model [M. Kass, A. Witkin, D. Terzopoulos, Snakes: active contour models, International Journal of Computer Vision 1 (1988) 321; V. Caselles, R. Kimmel, G. Sapiro, Geodesic active contours, International Journal of Computer Vision 22 (1997) 61; G. Sapiro, Geometric Partial Differential Equations and Image Analysis, Cambridge University Press, 2001; R. Kimmel, Numerical Geometry of Images: Theory, Algorithms, and Applications, Springer-Verlag, 2003] introduced in the field of image processing.

Design and Optimization of a Chemometric-Assisted Spectrophotometric Determination of Telmisartan and Hydrochlorothiazide in Pharmaceutical Dosage Form

PubMed Central

Lakshmi, KS; Lakshmi, S

2010-01-01

Two chemometric methods were developed for the simultaneous determination of telmisartan and hydrochlorothiazide. The chemometric methods applied were principal component regression (PCR) and partial least square (PLS-1). These approaches were successfully applied to quantify the two drugs in the mixture using the information included in the UV absorption spectra of appropriate solutions in the range of 200-350 nm with the intervals Δλ = 1 nm. The calibration of PCR and PLS-1 models was evaluated by internal validation (prediction of compounds in its own designed training set of calibration) and by external validation over laboratory prepared mixtures and pharmaceutical preparations. The PCR and PLS-1 methods require neither any separation step, nor any prior graphical treatment of the overlapping spectra of the two drugs in a mixture. The results of PCR and PLS-1 methods were compared with each other and a good agreement was found. PMID:21331198

Design and optimization of a chemometric-assisted spectrophotometric determination of telmisartan and hydrochlorothiazide in pharmaceutical dosage form.

PubMed

Lakshmi, Ks; Lakshmi, S

2010-01-01

Two chemometric methods were developed for the simultaneous determination of telmisartan and hydrochlorothiazide. The chemometric methods applied were principal component regression (PCR) and partial least square (PLS-1). These approaches were successfully applied to quantify the two drugs in the mixture using the information included in the UV absorption spectra of appropriate solutions in the range of 200-350 nm with the intervals Δλ = 1 nm. The calibration of PCR and PLS-1 models was evaluated by internal validation (prediction of compounds in its own designed training set of calibration) and by external validation over laboratory prepared mixtures and pharmaceutical preparations. The PCR and PLS-1 methods require neither any separation step, nor any prior graphical treatment of the overlapping spectra of the two drugs in a mixture. The results of PCR and PLS-1 methods were compared with each other and a good agreement was found.

Simultaneous determination of three herbicides by differential pulse voltammetry and chemometrics.

PubMed

Ni, Yongnian; Wang, Lin; Kokot, Serge

2011-01-01

A novel differential pulse voltammetry method (DPV) was researched and developed for the simultaneous determination of Pendimethalin, Dinoseb and sodium 5-nitroguaiacolate (5NG) with the aid of chemometrics. The voltammograms of these three compounds overlapped significantly, and to facilitate the simultaneous determination of the three analytes, chemometrics methods were applied. These included classical least squares (CLS), principal component regression (PCR), partial least squares (PLS) and radial basis function-artificial neural networks (RBF-ANN). A separately prepared verification data set was used to confirm the calibrations, which were built from the original and first derivative data matrices of the voltammograms. On the basis relative prediction errors and recoveries of the analytes, the RBF-ANN and the DPLS (D - first derivative spectra) models performed best and are particularly recommended for application. The DPLS calibration model was applied satisfactorily for the prediction of the three analytes from market vegetables and lake water samples.

Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers

NASA Astrophysics Data System (ADS)

Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Cho, Kwang-Jin; Dolino, Drew M.; Chen, Wei; Li, Hongyang; Grant, Barry J.; Hancock, John F.; Gorfe, Alemayehu A.

2017-01-01

Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers. For validation we used mutagenesis, electron microscopy and biochemical assays under non-denaturing conditions. We show that partial disruption of a predicted interface through charge reversal mutation of apposed residues reduces oligomerization while introduction of cysteines at these positions enhanced dimerization likely through the formation of an intermolecular disulfide bond. Free energy calculations indicated that K-Ras dimerization involves direct but weak protein-protein interactions in solution, consistent with the notion that dimerization is facilitated by membrane binding. Taken together, our atomically detailed analyses provide unique mechanistic insights into K-Ras dimer formation and membrane organization as well as the conformational fluctuations and equilibrium thermodynamics underlying these processes.

Some New Sets of Sequences of Fuzzy Numbers with Respect to the Partial Metric

PubMed Central

Ozluk, Muharrem

2015-01-01

In this paper, we essentially deal with Köthe-Toeplitz duals of fuzzy level sets defined using a partial metric. Since the utilization of Zadeh's extension principle is quite difficult in practice, we prefer the idea of level sets in order to construct some classical notions. In this paper, we present the sets of bounded, convergent, and null series and the set of sequences of bounded variation of fuzzy level sets, based on the partial metric. We examine the relationships between these sets and their classical forms and give some properties including definitions, propositions, and various kinds of partial metric spaces of fuzzy level sets. Furthermore, we study some of their properties like completeness and duality. Finally, we obtain the Köthe-Toeplitz duals of fuzzy level sets with respect to the partial metric based on a partial ordering. PMID:25695102

Grid pattern of nanothick microgel network.

PubMed

Chen, Guoping; Kawazoe, Naoki; Fan, Yujiang; Ito, Yoshihiro; Tateishi, Tetsuya

2007-05-22

A novel grid pattern of two kinds of nanothick microgels was developed by alternate patterning using photolithography. At first, 100-microm-wide nanothick PAAm microgel stripes were grafted on a polystyrene surface by UV irradiation of the photoreactive azidobenzoyl-derivatized polyallylamine-coated surface through a photomask with 100-microm-wide stripes. Then, a second set of 100-microm-wide nanothick PAAc microgel stripes were grafted across the PAAm-grated polystyrene surface by UV irradiation of the photoreactive azidophenyl-derivatized poly(acrylic acid)-coated surface through a photomask placed perpendicularly to the first set of PAAm microgel stripes. The PAAc microgel stripe pattern was formed over the PAAm microgel stripe pattern. The cross angle of the two microgel stripes could be controlled by adjusting the position of the photomask when the second microgel pattern was prepared. Swelling and shrinking of the microgels were investigated by scanning probe microscopy (SPM) in an aqueous solution. SPM observation indicated that the thickness of the gel network was 100 to 500 nm. The regions containing PAAm, PAAc, and the PAAc-PAAm overlapping microgels showed different swelling and shrinking properties when the pH was changed. The PAAm microgel swelled at low pH and shrank at high pH whereas the PAAc microgel swelled at high pH and shrank at low pH. However, the PAAc-PAAm overlapping microgel did not change as significantly as did the two microgels, indicating that the swelling and shrinking of the two gels was partially offset. The pH-induced structural change was repeatedly reversible. The novel grid pattern of nanothick microgels will find applications in various fields such as smart actuators, artificial muscles, sensors, and drug delivery systems as well as in tissue engineering and so forth.

The moral affiliations of disgust: a functional MRI study.

PubMed

Moll, Jorge; de Oliveira-Souza, Ricardo; Moll, Fernanda Tovar; Ignácio, Fátima Azevedo; Bramati, Ivanei E; Caparelli-Dáquer, Egas M; Eslinger, Paul J

2005-03-01

Recent investigations in cognitive neuroscience have shown that ordinary human behavior is guided by emotions that are uniquely human in their experiential and interpersonal aspects. These "moral emotions" contribute importantly to human social behavior and derive from the neurobehavioral reorganization of the basic plan of emotions that pervade mammalian life. Disgust is one prototypic emotion with multiple domains that include viscerosomatic reaction patterns and subjective experiences linked to (a) the sensory properties of a class of natural stimuli, (b) a set of aversive experiences and (c) a unique mode of experiencing morality. In the current investigation, we tested the hypotheses that (a) the experience of disgust devoid of moral connotations ("pure disgust") can be subjectively and behaviorally differentiated from the experience of disgust disguised in the moral emotion of "indignation" and that (b) pure disgust and indignation may have partially overlapping neural substrates. Thirteen normal adult volunteers were investigated with functional magnetic resonance imaging as they read a series of statements depicting scenarios of pure disgust, indignation, and neutral emotion. After the scanning procedure, they assigned one basic and one moral emotion to each stimulus from an array of six basic and seven moral emotions. Results indicated that (a) emotional stimuli may evoke pure disgust with or without indignation, (b) these different aspects of the experience of disgust could be elicited by a set of written statements, and (c) pure disgust and indignation recruited both overlapping and distinct brain regions, mainly in the frontal and temporal lobes. This work underscores the importance of the prefrontal and orbitofrontal cortices in moral judgment and in the automatic attribution of morality to social events. Human disgust encompasses a variety of emotional experiences that are ingrained in frontal, temporal, and limbic networks.

Multiple zonal projections of the nucleus reticularis tegmenti pontis to the cerebellar cortex of the rat.

PubMed

Serapide, M F; Parenti, R; Pantò, M R; Zappalà, A; Cicirata, F

2002-06-01

Compartmentalization (alternating labelled and unlabelled stripes) of mossy fibre terminals was found in the cerebellar cortex after iontophoretic injections of biotinylated dextran amine into discrete regions of the nucleus reticularis tegmenti pontis (NRTP). The zonal pattern was only observed when volumes of nuclear tissue ranging from 4.5 x 106 to 17.66 x 106 microm3 were impregnated. Up to nine compartments (i.e. up to five stripes separated by four interstripes) were found in crus I and in vermal lobule VI. Up to seven compartments (four stripes and three interstripes) were found in crus II; up to five compartments (three stripes and two interstripes) were identified in the lobulus simplex, the paraflocculus and vermal lobules IV, V and VII; up to three compartments (two stripes and one interstripe) were identified in the paramedian lobule and, finally, up to two compartments (one stripe and one interstripe) were identified in the copula pyramidis, in the flocculus and in vermal lobules II, III, VIII and IX. The projections of the NRTP are arranged according to a divergent/convergent projection pattern. From single injections in the NRTP, projections were traced to a set of cortical stripes widely distributed over the cerebellar cortex. The set of stripes labelled from different regions of the NRTP partially overlapped but complete overlap was never found. This finding revealed that the topographic combination of the projections of the NRTP to the cerebellar cortex is specific for each region of the NRTP. Finally, the projections to single cortical areas were arranged according to a pattern of compartmentalization that is specific for each cortical area, independent of the site of injection in the NRTP and of the number of stripes evident in the cortex.

Innate responses to gene knockouts impact overlapping gene networks and vary with respect to resistance to viral infection.

PubMed

Liu, Yonghong; Liu, Yuanyuan; Wu, Jiaming; Roizman, Bernard; Zhou, Grace Guoying

2018-04-03

Analyses of the levels of mRNAs encoding IFIT1, IFI16, RIG-1, MDA5, CXCL10, LGP2, PUM1, LSD1, STING, and IFNβ in cell lines from which the gene encoding LGP2, LSD1, PML, HDAC4, IFI16, PUM1, STING, MDA5, IRF3, or HDAC 1 had been knocked out, as well as the ability of these cell lines to support the replication of HSV-1, revealed the following: ( i ) Cell lines lacking the gene encoding LGP2, PML, or HDAC4 (cluster 1) exhibited increased levels of expression of partially overlapping gene networks. Concurrently, these cell lines produced from 5 fold to 12 fold lower yields of HSV-1 than the parental cells. ( ii ) Cell lines lacking the genes encoding STING, LSD1, MDA5, IRF3, or HDAC 1 (cluster 2) exhibited decreased levels of mRNAs of partially overlapping gene networks. Concurrently, these cell lines produced virus yields that did not differ from those produced by the parental cell line. The genes up-regulated in cell lines forming cluster 1, overlapped in part with genes down-regulated in cluster 2. The key conclusions are that gene knockouts and subsequent selection for growth causes changes in expression of multiple genes, and hence the phenotype of the cell lines cannot be ascribed to a single gene; the patterns of gene expression may be shared by multiple knockouts; and the enhanced immunity to viral replication by cluster 1 knockout cell lines but not by cluster 2 cell lines suggests that in parental cells, the expression of innate resistance to infection is specifically repressed.

Skn-1a/Oct-11 and {Delta}Np63{alpha} exert antagonizing effects on human keratin expression

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

Lena, Anna Maria; Cipollone, Rita; Amelio, Ivano

2010-10-29

Research highlights: {yields} Skn-1a markedly downregulates {Delta}Np63-driven K14 expression. {yields} {Delta}Np63 inhibits Skn-1a-mediated K10 expression. {yields} {Delta}Np63, mutated in SAM domain, is less effecting in K10 downregulation. {yields} Immunolocalization in human skin of the two transcription factors is partially overlapping. {yields} The antagonistic effects of Skn-1a and p63 is through competition for overlapping responsive elements or through an indirect interaction. -- Abstract: The formation of a stratified epidermis requires a carefully controlled balance between keratinocyte proliferation and differentiation. Here, we report the reciprocal effect on keratin expression of {Delta}Np63, pivotal in normal epidermal morphogenesis and maintenance, and Skn-1a/Oct-11, a POUmore » transcription factor that triggers and regulates the differentiation of keratinocytes. The expression of Skn-1a markedly downregulated {Delta}Np63-driven K14 expression in luciferase reporter assays. The extent of downregulation was comparable to the inhibition of Skn-1a-mediated K10 expression upon expression of {Delta}Np63. {Delta}Np63, mutated in the protein-protein interaction domain (SAM domain; mutated in human ectodermal dysplasia syndrome), was significantly less effecting in downregulating K10, raising the possibility of a direct interaction among Skn-1a and {Delta}Np63. Immunolocalization in human skin biopsies revealed that the expression of the two transcription factors is partially overlapping. Co-immunoprecipitation experiments did not, however, demonstrate a direct interaction between {Delta}Np63 and Skn-1a, suggesting that the antagonistic effects of Skn-1a and p63 on keratin promoter transactivation is probably through competition for overlapping binding sites on target gene promoter or through an indirect interaction.« less

Genetic overlap between impulsivity and alcohol dependence: a large-scale national twin study.

PubMed

Khemiri, L; Kuja-Halkola, R; Larsson, H; Jayaram-Lindström, N

2016-04-01

Alcohol dependence is associated with increased levels of impulsivity, but the genetic and environmental underpinnings of this overlap remain unclear. The purpose of the current study was to investigate the degree to which genetic and environmental factors contribute to the overlap between alcohol dependence and impulsivity. Univariate and bivariate twin model fitting was conducted for alcohol dependence and impulsivity in a national sample of 16 819 twins born in Sweden from 1959 to 1985. The heritability estimate for alcohol dependence was 44% [95% confidence interval (CI) 31-57%] for males and 62% (95% CI 52-72%) for females. For impulsivity, the heritability was 33% (95% CI 30-36%) in males and females. The bivariate twin analysis indicated a statistically significant genetic correlation between alcohol dependence and impulsivity of 0.40 (95% CI 0.23-0.58) in males and 0.20 (95% CI 0.07-0.33) in females. The phenotypic correlation between alcohol dependence and impulsivity was 0.20 and 0.17 for males and females, respectively, and the bivariate heritability was 80% (95% CI 47-117%) for males and 53% (95% CI 19-86%) for females. The remaining variance in all models was accounted for by non-shared environmental factors. The association between alcohol dependence and impulsivity can be partially accounted for by shared genetic factors. The genetic correlation was greater in men compared with women, which may indicate different pathways to the development of alcohol dependence between sexes. The observed genetic overlap has clinical implications regarding treatment and prevention, and partially explains the substantial co-morbidity between alcohol dependence and psychiatric disorders characterized by impulsive behaviour.

The role of self-math overlap in understanding math anxiety and the relation between math anxiety and performance

PubMed Central

Necka, Elizabeth A.; Sokolowski, H. Moriah; Lyons, Ian M.

2015-01-01

Recent work has demonstrated that math anxiety is more than just the product of poor math skills. Psychosocial factors may play a key role in understanding what it means to be math anxious, and hence may aid in attempts to sever the link between math anxiety and poor math performance. One such factor may be the extent to which individuals integrate math into their sense of self. We adapted a well-established measure of this degree of integration (i.e., self-other overlap) to assess individuals’ self-math overlap. This non-verbal single-item measure showed that identifying oneself with math (having higher self-math overlap) was strongly associated with lower math anxiety (r = -0.610). We also expected that having higher self-math overlap would leave one especially susceptible to the threat of poor math performance to the self. We identified two competing hypotheses regarding how this plays out in terms of math anxiety. Those higher in self-math overlap might be more likely to worry about poor math performance, exacerbating the negative relation between math anxiety and math ability. Alternatively, those higher in self-math overlap might exhibit self-serving biases regarding their math ability, which would instead predict a decoupling of the relation between their perceived and actual math ability, and in turn the relation between their math ability and math anxiety. Results clearly favored the latter hypothesis: those higher in self-math overlap exhibited almost no relation between math anxiety and math ability, whereas those lower in self-math overlap showed a strong negative relation between math anxiety and math ability. This was partially explained by greater self-serving biases among those higher in self-math overlap. In sum, these results reveal that the degree to which one integrates math into one’s self – self-math overlap – may provide insight into how the pernicious negative relation between math anxiety and math ability may be ameliorated. PMID:26528210

The role of self-math overlap in understanding math anxiety and the relation between math anxiety and performance.

PubMed

Necka, Elizabeth A; Sokolowski, H Moriah; Lyons, Ian M

2015-01-01

Recent work has demonstrated that math anxiety is more than just the product of poor math skills. Psychosocial factors may play a key role in understanding what it means to be math anxious, and hence may aid in attempts to sever the link between math anxiety and poor math performance. One such factor may be the extent to which individuals integrate math into their sense of self. We adapted a well-established measure of this degree of integration (i.e., self-other overlap) to assess individuals' self-math overlap. This non-verbal single-item measure showed that identifying oneself with math (having higher self-math overlap) was strongly associated with lower math anxiety (r = -0.610). We also expected that having higher self-math overlap would leave one especially susceptible to the threat of poor math performance to the self. We identified two competing hypotheses regarding how this plays out in terms of math anxiety. Those higher in self-math overlap might be more likely to worry about poor math performance, exacerbating the negative relation between math anxiety and math ability. Alternatively, those higher in self-math overlap might exhibit self-serving biases regarding their math ability, which would instead predict a decoupling of the relation between their perceived and actual math ability, and in turn the relation between their math ability and math anxiety. Results clearly favored the latter hypothesis: those higher in self-math overlap exhibited almost no relation between math anxiety and math ability, whereas those lower in self-math overlap showed a strong negative relation between math anxiety and math ability. This was partially explained by greater self-serving biases among those higher in self-math overlap. In sum, these results reveal that the degree to which one integrates math into one's self - self-math overlap - may provide insight into how the pernicious negative relation between math anxiety and math ability may be ameliorated.

Areas activated during naturalistic reading comprehension overlap topological visual, auditory, and somatotomotor maps

PubMed Central

2016-01-01

Abstract Cortical mapping techniques using fMRI have been instrumental in identifying the boundaries of topological (neighbor‐preserving) maps in early sensory areas. The presence of topological maps beyond early sensory areas raises the possibility that they might play a significant role in other cognitive systems, and that topological mapping might help to delineate areas involved in higher cognitive processes. In this study, we combine surface‐based visual, auditory, and somatomotor mapping methods with a naturalistic reading comprehension task in the same group of subjects to provide a qualitative and quantitative assessment of the cortical overlap between sensory‐motor maps in all major sensory modalities, and reading processing regions. Our results suggest that cortical activation during naturalistic reading comprehension overlaps more extensively with topological sensory‐motor maps than has been heretofore appreciated. Reading activation in regions adjacent to occipital lobe and inferior parietal lobe almost completely overlaps visual maps, whereas a significant portion of frontal activation for reading in dorsolateral and ventral prefrontal cortex overlaps both visual and auditory maps. Even classical language regions in superior temporal cortex are partially overlapped by topological visual and auditory maps. By contrast, the main overlap with somatomotor maps is restricted to a small region on the anterior bank of the central sulcus near the border between the face and hand representations of M‐I. Hum Brain Mapp 37:2784–2810, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. PMID:27061771

Intra-Cyclic Phases of Arm-Leg Movement and Index of Coordination in Relation to Sprint Breaststroke Swimming in Young Swimmers

PubMed Central

Strzala, Marek; Krezalek, Piotr; Glab, Grzegorz; Kaca, Marcin; Ostrowski, Andrzej; Stanula, Arkadiusz; Tyka, Anna K.

2013-01-01

Despite the limitations set by FINA regulations, execution technique in breaststroke swimming is being improved thanks to more and more advanced analyses of the efficiency of the swimmer’s movements. The aim of this study was to detect the parameters of the time structure of the cycle correlated with the maximal swimming speed at the of 50 meters distance, in order to focus to specific technical aspects in the breaststroke training. In the group of 23 participants, between the age of 15.0 ± 1.17, the breaststroke cycle movement of the arms and legs was divided into two phases: propulsive or non-propulsive. In addition, indices characterizing the temporal coordination of movements of the upper limbs in relation to the lower limbs were distinguished: 1) Arm-Leg Lag - determines the interval between the phases of propulsion generated by upper and lower limbs; 2) Glide or Overlap - the inter-cyclic glide or overlap of the propulsive movement of the upper on lower limbs. Significant dependence was noted between the swim speed (V50surface breast) and the percentage of time of the arm propulsive in-sweep phase 0.64, p < 0.01. A significant correlation was observed between the V50surface breast with the percentage of partially surfaced hand phase of arm recovery 0.54, p < 0.01. Correlation between total leg propulsion and non-propulsion phases with V50surface breast was 0.49 and -0.49 respectively, both p < 0.01. The Glide or Overlap index was significantly related to the swimming speed V50surface breast 0.48, p < 0.05. This type of analysis suggests how to refine the swimming technique, with the goal to improve the current speed capabilities; furthermore the results also indicate the direction of its development in the future swimmers of the group studied. Key Points This study investigated the influence of the inter- and intra-cyclic time structure of the movements in sprint breaststroke swimming. The distinction of the operations phases of the upper limbs in the propulsive movement shows significant correlation 0.64, p <0.01 between the swimming speed V50surface breast and the execution time of the in-sweep phase in the movement cycle. Significant relationship was noted between minimizing the first non-propulsive phase of arm recovery with higher contribution of the next, partially immersed sliding phase of arm recovery. The specification of the inter-cyclic coordination index of the upper and lower limbs during the movement cycle shows influence of the overlap of the propulsive movement of the upper limbs on the propulsive movement of the lower limbs on V50surface breast with correlation 0.48, p <0.05 for young swimmers. PMID:24421728

76 FR 29215 - Notice of Intent To Prepare Draft Environmental Impact Statements/Environmental Impact Reports...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-20

... because they partially overlap in their study areas, purpose, potential improvements, potential effects... that an EIS/EIR will be prepared to describe alternatives, potential environmental effects, and... funding toward flood management improvements. These funds may be matched with those from the Early...

A graphical method to evaluate spectral preprocessing in multivariate regression calibrations: example with Savitzky-Golay filters and partial least squares regression

USDA-ARS?s Scientific Manuscript database

In multivariate regression analysis of spectroscopy data, spectral preprocessing is often performed to reduce unwanted background information (offsets, sloped baselines) or accentuate absorption features in intrinsically overlapping bands. These procedures, also known as pretreatments, are commonly ...

Education Policy and Intergenerational Transfers in Equilibrium. NBER Working Paper No. 18782

ERIC Educational Resources Information Center

Abbott, Brant; Gallipoli, Giovanni; Meghir, Costas; Violante, Giovanni L.

2013-01-01

This paper compares partial and general equilibrium effects of alternative financial aid policies intended to promote college participation. We build an overlapping generations life-cycle, heterogeneous-agent, incomplete-markets model with education, labor supply, and consumption/saving decisions. Altruistic parents make inter vivos transfers to…

Electron thermal confinement in a partially stochastic magnetic structure

NASA Astrophysics Data System (ADS)

Morton, L. A.; Young, W. C.; Hegna, C. C.; Parke, E.; Reusch, J. A.; Den Hartog, D. J.

2018-04-01

Using a high-repetition-rate Thomson scattering diagnostic, we observe a peak in electron temperature Te coinciding with the location of a large magnetic island in the Madison Symmetric Torus. Magnetohydrodynamic modeling of this quasi-single helicity plasma indicates that smaller adjacent islands overlap with and destroy the large island flux surfaces. The estimated stochastic electron thermal conductivity ( ≈30 m 2/s ) is consistent with the conductivity inferred from the observed Te gradient and ohmic heating power. Island-shaped Te peaks can result from partially stochastic magnetic islands.

Automatic segmentation software in locally advanced rectal cancer: READY (REsearch program in Auto Delineation sYstem)-RECTAL 02: prospective study.

PubMed

Gambacorta, Maria A; Boldrini, Luca; Valentini, Chiara; Dinapoli, Nicola; Mattiucci, Gian C; Chiloiro, Giuditta; Pasini, Danilo; Manfrida, Stefania; Caria, Nicola; Minsky, Bruce D; Valentini, Vincenzo

2016-07-05

To validate autocontouring software (AS) in a clinical practice including a two steps delineation quality assurance (QA) procedure.The existing delineation agreement among experts for rectal cancer and the overlap and time criteria that have to be verified to allow the use of AS were defined.Median Dice Similarity Coefficient (MDSC), Mean slicewise Hausdorff Distances (MSHD) and Total-Time saving (TT) were analyzed.Two expert Radiation Oncologists reviewed CT-scans of 44 patients and agreed the reference-CTV: the first 14 consecutive cases were used to populate the software Atlas and 30 were used as Test.Each expert performed a manual (group A) and an automatic delineation (group B) of 15 Test patients.The delineations were compared with the reference contours.The overlap between the manual and automatic delineations with MDSC and MSHD and the TT were analyzed.Three acceptance criteria were set: MDSC ≥ 0.75, MSHD ≤1mm and TT sparing ≥ 50%.At least 2 criteria had to be met, one of which had to be TT saving, to validate the system.The MDSC was 0.75, MSHD 2.00 mm and the TT saving 55.5% between group A and group B. MDSC among experts was 0.84.Autosegmentation systems in rectal cancer partially met acceptability criteria with the present version.

Detection of Tampering Inconsistencies on Mobile Photos

NASA Astrophysics Data System (ADS)

Cao, Hong; Kot, Alex C.

Fast proliferation of mobile cameras and the deteriorating trust on digital images have created needs in determining the integrity of photos captured by mobile devices. As tampering often creates some inconsistencies, we propose in this paper a novel framework to statistically detect the image tampering inconsistency using accurately detected demosaicing weights features. By first cropping four non-overlapping blocks, each from one of the four quadrants in the mobile photo, we extract a set of demosaicing weights features from each block based on a partial derivative correlation model. Through regularizing the eigenspectrum of the within-photo covariance matrix and performing eigenfeature transformation, we further derive a compact set of eigen demosaicing weights features, which are sensitive to image signal mixing from different photo sources. A metric is then proposed to quantify the inconsistency based on the eigen weights features among the blocks cropped from different regions of the mobile photo. Through comparison, we show our eigen weights features perform better than the eigen features extracted from several other conventional sets of statistical forensics features in detecting the presence of tampering. Experimentally, our method shows a good confidence in tampering detection especially when one of the four cropped blocks is from a different camera model or brand with different demosaicing process.

A systematic study of acupuncture practice: acupoint usage in an outpatient setting in Beijing, China.

PubMed

Napadow, Vitaly; Liu, Jing; Kaptchuk, Ted J

2004-12-01

Acupuncture textbooks mention a wide assortment of indications for each acupuncture point and, conversely, each disease or indication can be treated by a wide assortment of acupoints. However, little systematic information exists on how acupuncture is actually used in practice: i.e. which points are actually selected and for which conditions. This study prospectively gathered data on acupuncture point usage in two primarily acupuncture hospital clinics in Beijing, China. Of the more than 150 unique acupoints, the 30 most commonly used points represented 68% of the total number of acupoints needled at the first clinic, and 63% of points needled at the second clinic. While acupuncturists use a similar set of most prevalent points, such as LI-4 (used in >65% of treatments at both clinic sites), this core of points only partially overlaps. These results support the hypothesis that while the most commonly used points are similar from one acupuncturist to another, each practitioner tends to have certain acupoints, which are favorites as core points or to round out the point prescription. In addition, the results of this study are consistent with the recent development of "manualized" protocols in randomized controlled trials of acupuncture where a fixed set of acupoints are augmented depending on individualized signs and symptoms (TCM patterns).

Investigating the discrimination potential of linear and nonlinear spectral multivariate calibrations for analysis of phenolic compounds in their binary and ternary mixtures and calculation pKa values.

PubMed

Rasouli, Zolaikha; Ghavami, Raouf

2016-08-05

Vanillin (VA), vanillic acid (VAI) and syringaldehyde (SIA) are important food additives as flavor enhancers. The current study for the first time is devote to the application of partial least square (PLS-1), partial robust M-regression (PRM) and feed forward neural networks (FFNNs) as linear and nonlinear chemometric methods for the simultaneous detection of binary and ternary mixtures of VA, VAI and SIA using data extracted directly from UV-spectra with overlapped peaks of individual analytes. Under the optimum experimental conditions, for each compound a linear calibration was obtained in the concentration range of 0.61-20.99 [LOD=0.12], 0.67-23.19 [LOD=0.13] and 0.73-25.12 [LOD=0.15] μgmL(-1) for VA, VAI and SIA, respectively. Four calibration sets of standard samples were designed by combination of a full and fractional factorial designs with the use of the seven and three levels for each factor for binary and ternary mixtures, respectively. The results of this study reveal that both the methods of PLS-1 and PRM are similar in terms of predict ability each binary mixtures. The resolution of ternary mixture has been accomplished by FFNNs. Multivariate curve resolution-alternating least squares (MCR-ALS) was applied for the description of spectra from the acid-base titration systems each individual compound, i.e. the resolution of the complex overlapping spectra as well as to interpret the extracted spectral and concentration profiles of any pure chemical species identified. Evolving factor analysis (EFA) and singular value decomposition (SVD) were used to distinguish the number of chemical species. Subsequently, their corresponding dissociation constants were derived. Finally, FFNNs has been used to detection active compounds in real and spiked water samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Investigating the discrimination potential of linear and nonlinear spectral multivariate calibrations for analysis of phenolic compounds in their binary and ternary mixtures and calculation pKa values

NASA Astrophysics Data System (ADS)

Rasouli, Zolaikha; Ghavami, Raouf

2016-08-01

Vanillin (VA), vanillic acid (VAI) and syringaldehyde (SIA) are important food additives as flavor enhancers. The current study for the first time is devote to the application of partial least square (PLS-1), partial robust M-regression (PRM) and feed forward neural networks (FFNNs) as linear and nonlinear chemometric methods for the simultaneous detection of binary and ternary mixtures of VA, VAI and SIA using data extracted directly from UV-spectra with overlapped peaks of individual analytes. Under the optimum experimental conditions, for each compound a linear calibration was obtained in the concentration range of 0.61-20.99 [LOD = 0.12], 0.67-23.19 [LOD = 0.13] and 0.73-25.12 [LOD = 0.15] μg mL- 1 for VA, VAI and SIA, respectively. Four calibration sets of standard samples were designed by combination of a full and fractional factorial designs with the use of the seven and three levels for each factor for binary and ternary mixtures, respectively. The results of this study reveal that both the methods of PLS-1 and PRM are similar in terms of predict ability each binary mixtures. The resolution of ternary mixture has been accomplished by FFNNs. Multivariate curve resolution-alternating least squares (MCR-ALS) was applied for the description of spectra from the acid-base titration systems each individual compound, i.e. the resolution of the complex overlapping spectra as well as to interpret the extracted spectral and concentration profiles of any pure chemical species identified. Evolving factor analysis (EFA) and singular value decomposition (SVD) were used to distinguish the number of chemical species. Subsequently, their corresponding dissociation constants were derived. Finally, FFNNs has been used to detection active compounds in real and spiked water samples.

Comparative study on gene set and pathway topology-based enrichment methods.

PubMed

Bayerlová, Michaela; Jung, Klaus; Kramer, Frank; Klemm, Florian; Bleckmann, Annalen; Beißbarth, Tim

2015-10-22

Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions. In contrast, the new group of so called pathway topology-based methods integrates the topological structure of a pathway into the analysis. We comparatively investigated gene set and pathway topology-based enrichment approaches, considering three gene set and four topological methods. These methods were compared in two extensive simulation studies and on a benchmark of 36 real datasets, providing the same pathway input data for all methods. In the benchmark data analysis both types of methods showed a comparable ability to detect enriched pathways. The first simulation study was conducted with KEGG pathways, which showed considerable gene overlaps between each other. In this study with original KEGG pathways, none of the topology-based methods outperformed the gene set approach. Therefore, a second simulation study was performed on non-overlapping pathways created by unique gene IDs. Here, methods accounting for pathway topology reached higher accuracy than the gene set methods, however their sensitivity was lower. We conducted one of the first comprehensive comparative works on evaluating gene set against pathway topology-based enrichment methods. The topological methods showed better performance in the simulation scenarios with non-overlapping pathways, however, they were not conclusively better in the other scenarios. This suggests that simple gene set approach might be sufficient to detect an enriched pathway under realistic circumstances. Nevertheless, more extensive studies and further benchmark data are needed to systematically evaluate these methods and to assess what gain and cost pathway topology information introduces into enrichment analysis. Both types of methods for enrichment analysis require further improvements in order to deal with the problem of pathway overlaps.

Hyperphagia and Obesity in Prader⁻Willi Syndrome: PCSK1 Deficiency and Beyond?

PubMed

Ramos-Molina, Bruno; Molina-Vega, María; Fernández-García, José C; Creemers, John W

2018-06-07

Prader⁻Willi syndrome (PWS) is a complex genetic disorder that, besides cognitive impairments, is characterized by hyperphagia, obesity, hypogonadism, and growth impairment. Proprotein convertase subtilisin/kexin type 1 ( PCSK1 ) deficiency, a rare recessive congenital disorder, partially overlaps phenotypically with PWS, but both genetic disorders show clear dissimilarities as well. The recent observation that PCSK1 is downregulated in a model of human PWS suggests that overlapping pathways are affected. In this review we will not only discuss the mechanisms by which PWS and PCSK1 deficiency could lead to hyperphagia but also the therapeutic interventions to treat obesity in both genetic disorders.

Shared neural processes support semantic control and action understanding

PubMed Central

Davey, James; Rueschemeyer, Shirley-Ann; Costigan, Alison; Murphy, Nik; Krieger-Redwood, Katya; Hallam, Glyn; Jefferies, Elizabeth

2015-01-01

Executive–semantic control and action understanding appear to recruit overlapping brain regions but existing evidence from neuroimaging meta-analyses and neuropsychology lacks spatial precision; we therefore manipulated difficulty and feature type (visual vs. action) in a single fMRI study. Harder judgements recruited an executive–semantic network encompassing medial and inferior frontal regions (including LIFG) and posterior temporal cortex (including pMTG). These regions partially overlapped with brain areas involved in action but not visual judgements. In LIFG, the peak responses to action and difficulty were spatially identical across participants, while these responses were overlapping yet spatially distinct in posterior temporal cortex. We propose that the co-activation of LIFG and pMTG allows the flexible retrieval of semantic information, appropriate to the current context; this might be necessary both for semantic control and understanding actions. Feature selection in difficult trials also recruited ventral occipital–temporal areas, not implicated in action understanding. PMID:25658631

Augmented Reality in a Simulated Tower Environment: Effect of Field of View on Aircraft Detection

NASA Technical Reports Server (NTRS)

Ellis, Stephen R.; Adelstein, Bernard D.; Reisman, Ronald J.; Schmidt-Ott, Joelle R.; Gips, Jonathan; Krozel, Jimmy; Cohen, Malcolm (Technical Monitor)

2002-01-01

An optical see-through, augmented reality display was used to study subjects' ability to detect aircraft maneuvering and landing at the Dallas Ft. Worth International airport in an ATC Tower simulation. Subjects monitored the traffic patterns as if from the airport's western control tower. Three binocular fields of view (14 deg, 28 deg and 47 deg) were studied in an independent groups' design to measure the degradation in detection performance associated with the visual field restrictions. In a second experiment the 14 deg and 28 deg fields were presented either with 46% binocular overlap or 100% overlap for separate groups. The near asymptotic results of the first experiment suggest that binocular fields of view much greater than 47% are unlikely to dramatically improve performance; and those of the second experiment suggest that partial binocular overlap is feasible for augmented reality displays such as may be used for ATC tower applications.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.

PubMed

Xu, Qifang; Dunbrack, Roland L

2012-11-01

Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed. We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM-HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly.

Examining care navigation: librarian participation in a team-based approach?

PubMed

Nix, A Tyler; Huber, Jeffrey T; Shapiro, Robert M; Pfeifle, Andrea

2016-04-01

This study investigated responsibilities, skill sets, degrees, and certifications required of health care navigators in order to identify areas of potential overlap with health sciences librarianship. The authors conducted a content analysis of health care navigator position announcements and developed and assigned forty-eight category terms to represent the sample's responsibilities and skill sets. Coordination of patient care and a bachelor's degree were the most common responsibility and degree requirements, respectively. Results also suggest that managing and providing health information resources is an area of overlap between health care navigators and health sciences librarians, and that librarians are well suited to serve on navigation teams. Such overlap may provide an avenue for collaboration between navigators and health sciences librarians.

Compressive Detection of Highly Overlapped Spectra Using Walsh-Hadamard-Based Filter Functions.

PubMed

Corcoran, Timothy C

2018-03-01

In the chemometric context in which spectral loadings of the analytes are already known, spectral filter functions may be constructed which allow the scores of mixtures of analytes to be determined in on-the-fly fashion directly, by applying a compressive detection strategy. Rather than collecting the entire spectrum over the relevant region for the mixture, a filter function may be applied within the spectrometer itself so that only the scores are recorded. Consequently, compressive detection shrinks data sets tremendously. The Walsh functions, the binary basis used in Walsh-Hadamard transform spectroscopy, form a complete orthonormal set well suited to compressive detection. A method for constructing filter functions using binary fourfold linear combinations of Walsh functions is detailed using mathematics borrowed from genetic algorithm work, as a means of optimizing said functions for a specific set of analytes. These filter functions can be constructed to automatically strip the baseline from analysis. Monte Carlo simulations were performed with a mixture of four highly overlapped Raman loadings and with ten excitation-emission matrix loadings; both sets showed a very high degree of spectral overlap. Reasonable estimates of the true scores were obtained in both simulations using noisy data sets, proving the linearity of the method.

Genome-wide association study of borderline personality disorder reveals genetic overlap with bipolar disorder, major depression and schizophrenia.

PubMed

Witt, S H; Streit, F; Jungkunz, M; Frank, J; Awasthi, S; Reinbold, C S; Treutlein, J; Degenhardt, F; Forstner, A J; Heilmann-Heimbach, S; Dietl, L; Schwarze, C E; Schendel, D; Strohmaier, J; Abdellaoui, A; Adolfsson, R; Air, T M; Akil, H; Alda, M; Alliey-Rodriguez, N; Andreassen, O A; Babadjanova, G; Bass, N J; Bauer, M; Baune, B T; Bellivier, F; Bergen, S; Bethell, A; Biernacka, J M; Blackwood, D H R; Boks, M P; Boomsma, D I; Børglum, A D; Borrmann-Hassenbach, M; Brennan, P; Budde, M; Buttenschøn, H N; Byrne, E M; Cervantes, P; Clarke, T-K; Craddock, N; Cruceanu, C; Curtis, D; Czerski, P M; Dannlowski, U; Davis, T; de Geus, E J C; Di Florio, A; Djurovic, S; Domenici, E; Edenberg, H J; Etain, B; Fischer, S B; Forty, L; Fraser, C; Frye, M A; Fullerton, J M; Gade, K; Gershon, E S; Giegling, I; Gordon, S D; Gordon-Smith, K; Grabe, H J; Green, E K; Greenwood, T A; Grigoroiu-Serbanescu, M; Guzman-Parra, J; Hall, L S; Hamshere, M; Hauser, J; Hautzinger, M; Heilbronner, U; Herms, S; Hitturlingappa, S; Hoffmann, P; Holmans, P; Hottenga, J-J; Jamain, S; Jones, I; Jones, L A; Juréus, A; Kahn, R S; Kammerer-Ciernioch, J; Kirov, G; Kittel-Schneider, S; Kloiber, S; Knott, S V; Kogevinas, M; Landén, M; Leber, M; Leboyer, M; Li, Q S; Lissowska, J; Lucae, S; Martin, N G; Mayoral-Cleries, F; McElroy, S L; McIntosh, A M; McKay, J D; McQuillin, A; Medland, S E; Middeldorp, C M; Milaneschi, Y; Mitchell, P B; Montgomery, G W; Morken, G; Mors, O; Mühleisen, T W; Müller-Myhsok, B; Myers, R M; Nievergelt, C M; Nurnberger, J I; O'Donovan, M C; Loohuis, L M O; Ophoff, R; Oruc, L; Owen, M J; Paciga, S A; Penninx, B W J H; Perry, A; Pfennig, A; Potash, J B; Preisig, M; Reif, A; Rivas, F; Rouleau, G A; Schofield, P R; Schulze, T G; Schwarz, M; Scott, L; Sinnamon, G C B; Stahl, E A; Strauss, J; Turecki, G; Van der Auwera, S; Vedder, H; Vincent, J B; Willemsen, G; Witt, C C; Wray, N R; Xi, H S; Tadic, A; Dahmen, N; Schott, B H; Cichon, S; Nöthen, M M; Ripke, S; Mobascher, A; Rujescu, D; Lieb, K; Roepke, S; Schmahl, C; Bohus, M; Rietschel, M

2017-06-20

Borderline personality disorder (BOR) is determined by environmental and genetic factors, and characterized by affective instability and impulsivity, diagnostic symptoms also observed in manic phases of bipolar disorder (BIP). Up to 20% of BIP patients show comorbidity with BOR. This report describes the first case-control genome-wide association study (GWAS) of BOR, performed in one of the largest BOR patient samples worldwide. The focus of our analysis was (i) to detect genes and gene sets involved in BOR and (ii) to investigate the genetic overlap with BIP. As there is considerable genetic overlap between BIP, major depression (MDD) and schizophrenia (SCZ) and a high comorbidity of BOR and MDD, we also analyzed the genetic overlap of BOR with SCZ and MDD. GWAS, gene-based tests and gene-set analyses were performed in 998 BOR patients and 1545 controls. Linkage disequilibrium score regression was used to detect the genetic overlap between BOR and these disorders. Single marker analysis revealed no significant association after correction for multiple testing. Gene-based analysis yielded two significant genes: DPYD (P=4.42 × 10 -7 ) and PKP4 (P=8.67 × 10 -7 ); and gene-set analysis yielded a significant finding for exocytosis (GO:0006887, P FDR =0.019; FDR, false discovery rate). Prior studies have implicated DPYD, PKP4 and exocytosis in BIP and SCZ. The most notable finding of the present study was the genetic overlap of BOR with BIP (r g =0.28 [P=2.99 × 10 -3 ]), SCZ (r g =0.34 [P=4.37 × 10 -5 ]) and MDD (r g =0.57 [P=1.04 × 10 -3 ]). We believe our study is the first to demonstrate that BOR overlaps with BIP, MDD and SCZ on the genetic level. Whether this is confined to transdiagnostic clinical symptoms should be examined in future studies.

Overlapping bio-absorbable scaffolds: Aim for D2D technique?

PubMed

Khan, Asaad A; Dangas, George D

2018-06-01

The results of overlapping metallic stents have been concerning but this practice is often unavoidable in the setting of long or tortuous lesions, diameter discrepancy of proximal and distal vessel, and for residual dissections. Theoretically, bio-absorbable scaffolds may carry an advantage over metallic stents due to the progressive resorption of the scaffold theoretically rendering the overlap a non-issue; this has not been clinically evident. Since stent/scaffold overlap cannot be entirely avoided, improved stent delivery/deployment and scaffold design modification may reduce complications in this complex patient subset. © 2018 Wiley Periodicals, Inc.

48 CFR 19.502-3 - Partial set-asides.

Code of Federal Regulations, 2010 CFR

2010-10-01

... non-set-aside part of the acquisition shall have first priority with respect to negotiations for the... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Partial set-asides. 19.502... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 19.502-3 Partial set-asides. (a...

Serial or overlapping processing in multitasking as individual preference: Effects of stimulus preview on task switching and concurrent dual-task performance.

PubMed

Reissland, Jessika; Manzey, Dietrich

2016-07-01

Understanding the mechanisms and performance consequences of multitasking has long been in focus of scientific interest, but has been investigated by three research lines more or less isolated from each other. Studies in the fields of the psychological refractory period, task switching, and interruptions have scored with a high experimental control, but usually do not give participants many degrees of freedom to self-organize the processing of two concurrent tasks. Individual strategies as well as their impact on efficiency have mainly been neglected. Self-organized multitasking has been investigated in the field of human factors, but primarily with respect to overall performance without detailed investigation of how the tasks are processed. The current work attempts to link aspects of these research lines. All of them, explicitly or implicitly, provide hints about an individually preferred type of task organization, either more cautious trying to work strictly serially on only one task at a time or more daring with a focus on task interleaving and, if possible, also partially overlapping (parallel) processing. In two experiments we investigated different strategies of task organization and their impact on efficiency using a new measure of overall multitasking efficiency. Experiment 1 was based on a classical task switching paradigm with two classification tasks, but provided one group of participants with a stimulus preview of the task to switch to next, enabling at least partial overlapping processing. Indeed, this preview led to a reduction of switch costs and to an increase of dual-task efficiency, but only for a subgroup of participants. They obviously exploited the possibility of overlapping processing, while the others worked mainly serially. While task-sequence was externally guided in the first experiment, Experiment 2 extended the approach by giving the participants full freedom of task organization in concurrent performance of the same tasks. Fine-grained analyses of response scheduling again revealed individual differences regarding the preference for strictly serial processing vs. some sort of task interleaving and overlapping processing. However, neither group showed a striking benefit in dual-task efficiency, although the results show that the costs of multitasking can partly be compensated by overlapping processing. Copyright © 2016 Elsevier B.V. All rights reserved.

Closed form unsupervised registration of multi-temporal structure from motion-multiview stereo data using non-linearly weighted image features

NASA Astrophysics Data System (ADS)

Seers, T. D.; Hodgetts, D.

2013-12-01

Seers, T. D. & Hodgetts, D. School of Earth, Atmospheric and Environmental Sciences, University of Manchester, UK. M13 9PL. The detection of topological change at the Earth's surface is of considerable scholarly interest, allowing the quantification of the rates of geomorphic processes whilst providing lucid insights into the underlying mechanisms driving landscape evolution. In this regard, the past decade has witnessed the ever increasing proliferation of studies employing multi-temporal topographic data in within the geosciences, bolstered by continuing technical advancements in the acquisition and processing of prerequisite datasets. Provided by workers within the field of Computer Vision, multiview stereo (MVS) dense surface reconstructions, primed by structure-from-motion (SfM) based camera pose estimation represents one such development. Providing a cost effective, operationally efficient data capture medium, the modest requirement of a consumer grade camera for data collection coupled with the minimal user intervention required during post-processing makes SfM-MVS an attractive alternative to terrestrial laser scanners for collecting multi-temporal topographic datasets. However, in similitude to terrestrial scanner derived data, the co-registration of spatially coincident or partially overlapping scans produced by SfM-MVS presents a major technical challenge, particularly in the case of semi non-rigid scenes produced during topographic change detection studies. Moreover, the arbitrary scaling resulting from SfM ambiguity requires that a scale matrix must be estimated during the transformation, introducing further complexity into its formulation. Here, we present a novel, fully unsupervised algorithm which utilises non-linearly weighted image features for the solving the similarity transform (scale, translation rotation) between partially overlapping scans produced by SfM-MVS image processing. With the only initialization condition being partial intersection between input image sets, our method has major advantages over conventional iterative least squares minimization based methods (e.g. Iterative Closest Point variants), acting only on rigid areas of target scenes, being capable of reliably estimating the scaling factor and requiring no incipient estimation of the transformation to initialize (i.e. manual rough alignment). Moreover, because the solution is closed form, convergence is considerably more expedient that most iterative methods. It is hoped that the availability of improved co-registration routines, such as the one presented here, will facilitate the routine collection of multi-temporal topographic datasets by a wider range of geoscience practitioners.

Areas activated during naturalistic reading comprehension overlap topological visual, auditory, and somatotomotor maps.

PubMed

Sood, Mariam R; Sereno, Martin I

2016-08-01

Cortical mapping techniques using fMRI have been instrumental in identifying the boundaries of topological (neighbor-preserving) maps in early sensory areas. The presence of topological maps beyond early sensory areas raises the possibility that they might play a significant role in other cognitive systems, and that topological mapping might help to delineate areas involved in higher cognitive processes. In this study, we combine surface-based visual, auditory, and somatomotor mapping methods with a naturalistic reading comprehension task in the same group of subjects to provide a qualitative and quantitative assessment of the cortical overlap between sensory-motor maps in all major sensory modalities, and reading processing regions. Our results suggest that cortical activation during naturalistic reading comprehension overlaps more extensively with topological sensory-motor maps than has been heretofore appreciated. Reading activation in regions adjacent to occipital lobe and inferior parietal lobe almost completely overlaps visual maps, whereas a significant portion of frontal activation for reading in dorsolateral and ventral prefrontal cortex overlaps both visual and auditory maps. Even classical language regions in superior temporal cortex are partially overlapped by topological visual and auditory maps. By contrast, the main overlap with somatomotor maps is restricted to a small region on the anterior bank of the central sulcus near the border between the face and hand representations of M-I. Hum Brain Mapp 37:2784-2810, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Status, distribution, and movements of martens in northeastern Minnesota.

Treesearch

L. David Mech; Lynn L. Rogers

1977-01-01

The decline of martens in Minnesota is reviewed and a recent increase documented. Adjacent and partially overlapping home ranges of 4.3 to 19.9 km2 were determined by telemetry for a female and three males. Habitat use is described. If current trapping and timber management practices persist, martens should continue to increase.

Microprocessor-Based Neural-Pulse-Wave Analyzer

NASA Technical Reports Server (NTRS)

Kojima, G. K.; Bracchi, F.

1983-01-01

Microprocessor-based system analyzes amplitudes and rise times of neural waveforms. Displaying histograms of measured parameters helps researchers determine how many nerves contribute to signal and specify waveform characteristics of each. Results are improved noise rejection, full or partial separation of overlapping peaks, and isolation and identification of related peaks in different histograms. 2

Southern Tomato Virus: The Link between the Families Totiviridae and Partitiviridae

USDA-ARS?s Scientific Manuscript database

A dsRNA virus with a genome of 3.5 kb was isolated from field and greenhouse-grown tomato plants of different cultivars and geographic locations in North America. Cloning and sequencing of the viral genome showed the presence of two partially overlapping open reading frames (ORFs) and a genomic orga...

Schizophrenia and epilepsy: is there a shared susceptibility?

PubMed

Cascella, Nicola G; Schretlen, David J; Sawa, Akira

2009-04-01

Individuals with epilepsy are at increased risk of having psychotic symptoms that resemble those of schizophrenia. More controversial and less searched is if schizophrenia is a risk factor for epilepsy. Here we review overlapping epidemiological, clinical, neuropathological and neuroimaging features of these two diseases. We discuss the role of temporal and other brain areas in the development of schizophrenia-like psychosis of epilepsy. We underline the importance of ventricular enlargement in both conditions as a phenotypic manifestation of a shared biologic liability that might relate to abnormalities in neurodevelopment. We suggest that genes implicated in neurodevelopment may play a common role in both conditions and speculate that recently identified causative genes for partial complex seizures with auditory features might help explain the pathophysiology of schizophrenia. These particularly include the leucine-rich glioma inactivated (LGI) family gene loci overlap with genes of interest for psychiatric diseases like schizophrenia. Finally, we conclude that LGI genes associated with partial epilepsy with auditory features might also represent genes of interest for schizophrenia, especially among patients with prominent auditory hallucinations and formal thought disorder.

On the ground state of Yang-Mills theory

NASA Astrophysics Data System (ADS)

Bakry, Ahmed S.; Leinweber, Derek B.; Williams, Anthony G.

2011-08-01

We investigate the overlap of the ground state meson potential with sets of mesonic-trial wave functions corresponding to different gluonic distributions. We probe the transverse structure of the flux tube through the creation of non-uniform smearing profiles for the string of glue connecting two color sources in Wilson loop operator. The non-uniformly UV-regulated flux-tube operators are found to optimize the overlap with the ground state and display interesting features in the ground state overlap.

Anatomy of Shoulder Girdle Muscle Modifications and Walking Adaptation in the Scaly Chinese Pangolin (Manis Pentadactyla Pentadactyla: Pholidota) Compared with the Partially Osteoderm-Clad Armadillos (Dasypodidae).

PubMed

Kawashima, Tomokazu; Thorington, Richard W; Bohaska, Paula W; Chen, Yen-Jean; Sato, Fumi

2015-07-01

Because pangolins are unique mammals with a body and limbs almost entirely sheathed in hard keratinous overlapping scales and with digging and climbing abilities, the shoulder girdle muscles may differ significantly from those of other mammals including the partially osteoderm-clad armadillos. Therefore, we conducted a functional anatomical study of the shoulder girdle muscles in Chinese pangolins (Manis pentadactyla pentadactyla, Pholidota) and some armadillo species (Dasypodidae). Our CT scans revealed that the pangolin's overlapping scales are hard structures completely encasing the limbs. The armadillo's limbs, however, are covered with small relatively soft non-overlapping scales embedded in the skin, and articulate completely free of the hard osteodermal carapace. The attachments of some shoulder girdle muscles in the pangolin have moved from the surrounding edges of the scapula to the spine, and they, therefore, fully cover the scapula. In addition, some pangolin shoulder girdle muscles cross the shoulder joint to insert on the distal humerus, but this does not occur in armadillos. We cannot rule out the possibility that these muscle modifications represent adaptations for digging and/or climbing in pangolins. Our results and previous literature do not establish specific links between them and locomotive modes. However, we propose that the Chinese pangolin may use its derived muscular features when walking to move its armor-restricted forelimbs more effectively by swinging its head from side to side. © 2015 Wiley Periodicals, Inc.

Robust face alignment under occlusion via regional predictive power estimation.

PubMed

Heng Yang; Xuming He; Xuhui Jia; Patras, Ioannis

2015-08-01

Face alignment has been well studied in recent years, however, when a face alignment model is applied on facial images with heavy partial occlusion, the performance deteriorates significantly. In this paper, instead of training an occlusion-aware model with visibility annotation, we address this issue via a model adaptation scheme that uses the result of a local regression forest (RF) voting method. In the proposed scheme, the consistency of the votes of the local RF in each of several oversegmented regions is used to determine the reliability of predicting the location of the facial landmarks. The latter is what we call regional predictive power (RPP). Subsequently, we adapt a holistic voting method (cascaded pose regression based on random ferns) by putting weights on the votes of each fern according to the RPP of the regions used in the fern tests. The proposed method shows superior performance over existing face alignment models in the most challenging data sets (COFW and 300-W). Moreover, it can also estimate with high accuracy (72.4% overlap ratio) which image areas belong to the face or nonface objects, on the heavily occluded images of the COFW data set, without explicit occlusion modeling.

Application of lap laser welding technology on stainless steel railway vehicles

NASA Astrophysics Data System (ADS)

Wang, Hongxiao; Wang, Chunsheng; He, Guangzhong; Li, Wei; Liu, Liguo

2016-10-01

Stainless steel railway vehicles with so many advantages, such as lightweight, antirust, low cost of maintenance and simple manufacturing process, so the production of high level stainless steel railway vehicles has become the development strategy of European, American and other developed nations. The current stainless steel railway vehicles body and structure are usually assembled by resistance spot welding process. The weak points of this process are the poor surface quality and bad airtight due to the pressure of electrodes. In this study, the partial penetration lap laser welding process was investigated to resolve the problems, by controlling the laser to stop at the second plate in the appropriate penetration. The lap laser welding joint of stainless steel railway vehicle car body with partial penetration has higher strength and surface quality than those of resistance spot welding joint. The biggest problem of lap laser welding technology is to find the balance of the strength and surface quality with different penetrations. The mechanism of overlap laser welding of stainless steel, mechanical tests, microstructure analysis, the optimization of welding parameters, analysis of fatigue performance, the design of laser welding stainless steel railway vehicles structure and the development of non-destructive testing technology were systematically studied before lap laser welding process to be applied in manufacture of railway vehicles. The results of the experiments and study show that high-quality surface state and higher fatigue strength can be achieved by the partial penetration overlap laser welding of the side panel structure, and the structure strength of the car body can be higher than the requirements of En12663, the standard of structural requirements of railway vehicles bodies. Our company has produced the stainless steel subway and high way railway vehicles by using overlap laser welding technology. The application of lap laser welding will be a big change of railway vehicles manufacturing technology.

Familial translocation t(6;20)(p21;p13) resulting in partial trisomy 6p and partial monosomy 20p: report of a new case and review of the literature.

PubMed

Berner, A L; Bağci, S; Wohlleber, E; Engels, E; Müller, A; Bartmann, P; Weber, R G; Reutter, H

2012-01-01

Carriers of completely balanced chromosomal translocations have all necessary genetic information. Nevertheless, because of the possibility of maldistribution during gametogenesis, they are at increased risk for infertility, miscarriage, stillbirth or having a child with congenital anomalies including mental retardation. As postnatal clinical reports are infrequent, prediction of clinical course for specific unbalanced karyotypes diagnosed during pregnancy remains difficult. Here, we report the 6th case of partial trisomy 6p and partial monosomy 20p due to an unbalanced adjacent-1 segregation of the rare familial translocation t(6;20)(p21;p13). We give a thorough clinical description of the present case, demonstrating broad phenotypic overlap with the 5 previously published cases reviewed here, providing important data on postnatal outcome. Copyright © 2012 S. Karger AG, Basel.

Design optimization of continuous partially prestressed concrete beams

NASA Astrophysics Data System (ADS)

Al-Gahtani, A. S.; Al-Saadoun, S. S.; Abul-Feilat, E. A.

1995-04-01

An effective formulation for optimum design of two-span continuous partially prestressed concrete beams is described in this paper. Variable prestressing forces along the tendon profile, which may be jacked from one end or both ends with flexibility in the overlapping range and location, and the induced secondary effects are considered. The imposed constraints are on flexural stresses, ultimate flexural strength, cracking moment, ultimate shear strength, reinforcement limits cross-section dimensions, and cable profile geometries. These constraints are formulated in accordance with ACI (American Concrete Institute) code provisions. The capabilities of the program to solve several engineering problems are presented.

Mof-Tree: A Spatial Access Method To Manipulate Multiple Overlapping Features.

ERIC Educational Resources Information Center

Manolopoulos, Yannis; Nardelli, Enrico; Papadopoulos, Apostolos; Proietti, Guido

1997-01-01

Investigates the manipulation of large sets of two-dimensional data representing multiple overlapping features, and presents a new access method, the MOF-tree. Analyzes storage requirements and time with respect to window query operations involving multiple features. Examines both the pointer-based and pointerless MOF-tree representations.…

Idiopathic inflammatory myopathies overlapping with systemic diseases

PubMed Central

Lepreux, Sébastien; Hainfellner, Johannes A.; Vital, Anne

2018-01-01

A muscle biopsy is currently requested to assess the diagnosis of an idiopathic inflammatory myopathy overlapping with a systemic disease. During the past few years, the classification of inflammatory myopathy subtypes has been revisited progressively on the basis of correlations between clinical phenotypes, autoantibodies and histological data. Several syndromic entities are now more clearly defined, and the aim of the present review is to clarify the contribution of muscle biopsy in a setting of idiopathic inflammatory myopathies overlapping with systemic diseases. PMID:29154752

A Systematic Analysis of Term Reuse and Term Overlap across Biomedical Ontologies

PubMed Central

Kamdar, Maulik R.; Tudorache, Tania; Musen, Mark A.

2016-01-01

Reusing ontologies and their terms is a principle and best practice that most ontology development methodologies strongly encourage. Reuse comes with the promise to support the semantic interoperability and to reduce engineering costs. In this paper, we present a descriptive study of the current extent of term reuse and overlap among biomedical ontologies. We use the corpus of biomedical ontologies stored in the BioPortal repository, and analyze different types of reuse and overlap constructs. While we find an approximate term overlap between 25–31%, the term reuse is only <9%, with most ontologies reusing fewer than 5% of their terms from a small set of popular ontologies. Clustering analysis shows that the terms reused by a common set of ontologies have >90% semantic similarity, hinting that ontology developers tend to reuse terms that are sibling or parent–child nodes. We validate this finding by analysing the logs generated from a Protégé plugin that enables developers to reuse terms from BioPortal. We find most reuse constructs were 2-level subtrees on the higher levels of the class hierarchy. We developed a Web application that visualizes reuse dependencies and overlap among ontologies, and that proposes similar terms from BioPortal for a term of interest. We also identified a set of error patterns that indicate that ontology developers did intend to reuse terms from other ontologies, but that they were using different and sometimes incorrect representations. Our results stipulate the need for semi-automated tools that augment term reuse in the ontology engineering process through personalized recommendations. PMID:28819351

Parents' Past Experiences as a Mediational Tool for Understanding Their Child's Current Mathematical Learning

ERIC Educational Resources Information Center

O'Toole, Sarah; de Abreu, Guida

2005-01-01

This article explores the ways in which parents use their own past experiences as a mediational tool for understanding their child's current school learning. Following a sociocultural approach parents' past experiences were examined drawing on the notions of (1) heterochronicity, which looks at the partially overlapping histories of the individual…

On The Origin Of Two-Shell Supernova Remnants

NASA Astrophysics Data System (ADS)

Gvaramadze, Vasilii

2007-07-01

The proper motion of massive stars could cause them to explode far from the geometric centers of their wind-driven bubbles and thereby could affect the symmetry of the resulting diffuse supernova remnants (SNRs). We use this fact to explain the origin of SNRs consisting of two partially overlapping shells (e.g. Cygnus Loop, 3C 400.2, etc.).

Multimodal Image Analysis in Alzheimer’s Disease via Statistical Modelling of Non-local Intensity Correlations

NASA Astrophysics Data System (ADS)

Lorenzi, Marco; Simpson, Ivor J.; Mendelson, Alex F.; Vos, Sjoerd B.; Cardoso, M. Jorge; Modat, Marc; Schott, Jonathan M.; Ourselin, Sebastien

2016-04-01

The joint analysis of brain atrophy measured with magnetic resonance imaging (MRI) and hypometabolism measured with positron emission tomography with fluorodeoxyglucose (FDG-PET) is of primary importance in developing models of pathological changes in Alzheimer’s disease (AD). Most of the current multimodal analyses in AD assume a local (spatially overlapping) relationship between MR and FDG-PET intensities. However, it is well known that atrophy and hypometabolism are prominent in different anatomical areas. The aim of this work is to describe the relationship between atrophy and hypometabolism by means of a data-driven statistical model of non-overlapping intensity correlations. For this purpose, FDG-PET and MRI signals are jointly analyzed through a computationally tractable formulation of partial least squares regression (PLSR). The PLSR model is estimated and validated on a large clinical cohort of 1049 individuals from the ADNI dataset. Results show that the proposed non-local analysis outperforms classical local approaches in terms of predictive accuracy while providing a plausible description of disease dynamics: early AD is characterised by non-overlapping temporal atrophy and temporo-parietal hypometabolism, while the later disease stages show overlapping brain atrophy and hypometabolism spread in temporal, parietal and cortical areas.

Ethical issues in nanomedicine: Tempest in a teapot?

PubMed

Allon, Irit; Ben-Yehudah, Ahmi; Dekel, Raz; Solbakk, Jan-Helge; Weltring, Klaus-Michael; Siegal, Gil

2017-03-01

Nanomedicine offers remarkable options for new therapeutic avenues. As methods in nanomedicine advance, ethical questions conjunctly arise. Nanomedicine is an exceptional niche in several aspects as it reflects risks and uncertainties not encountered in other areas of medical research or practice. Nanomedicine partially overlaps, partially interlocks and partially exceeds other medical disciplines. Some interpreters agree that advances in nanotechnology may pose varied ethical challenges, whilst others argue that these challenges are not new and that nanotechnology basically echoes recurrent bioethical dilemmas. The purpose of this article is to discuss some of the ethical issues related to nanomedicine and to reflect on the question whether nanomedicine generates ethical challenges of new and unique nature. Such a determination should have implications on regulatory processes and professional conducts and protocols in the future.

Technology initiatives with government/business overlap

NASA Astrophysics Data System (ADS)

Knapp, Robert H., Jr.

2015-03-01

Three important present-day technology development settings involve significant overlap between government and private sectors. The Advanced Research Project Agency for Energy (ARPA-E) supports a wide range of "high risk, high return" projects carried out in academic, non-profit or private business settings. The Materials Genome Initiative (MGI), based in the White House, aims at radical acceleration of the development process for advanced materials. California public utilities such as Pacific Gas & Electric operate under a structure of financial returns and political program mandates that make them arms of public policy as much as independent businesses.

The Functional Genetics of Handedness and Language Lateralization: Insights from Gene Ontology, Pathway and Disease Association Analyses.

PubMed

Schmitz, Judith; Lor, Stephanie; Klose, Rena; Güntürkün, Onur; Ocklenburg, Sebastian

2017-01-01

Handedness and language lateralization are partially determined by genetic influences. It has been estimated that at least 40 (and potentially more) possibly interacting genes may influence the ontogenesis of hemispheric asymmetries. Recently, it has been suggested that analyzing the genetics of hemispheric asymmetries on the level of gene ontology sets, rather than at the level of individual genes, might be more informative for understanding the underlying functional cascades. Here, we performed gene ontology, pathway and disease association analyses on genes that have previously been associated with handedness and language lateralization. Significant gene ontology sets for handedness were anatomical structure development, pattern specification (especially asymmetry formation) and biological regulation. Pathway analysis highlighted the importance of the TGF-beta signaling pathway for handedness ontogenesis. Significant gene ontology sets for language lateralization were responses to different stimuli, nervous system development, transport, signaling, and biological regulation. Despite the fact that some authors assume that handedness and language lateralization share a common ontogenetic basis, gene ontology sets barely overlap between phenotypes. Compared to genes involved in handedness, which mostly contribute to structural development, genes involved in language lateralization rather contribute to activity-dependent cognitive processes. Disease association analysis revealed associations of genes involved in handedness with diseases affecting the whole body, while genes involved in language lateralization were specifically engaged in mental and neurological diseases. These findings further support the idea that handedness and language lateralization are ontogenetically independent, complex phenotypes.

The Functional Genetics of Handedness and Language Lateralization: Insights from Gene Ontology, Pathway and Disease Association Analyses

PubMed Central

Schmitz, Judith; Lor, Stephanie; Klose, Rena; Güntürkün, Onur; Ocklenburg, Sebastian

2017-01-01

Handedness and language lateralization are partially determined by genetic influences. It has been estimated that at least 40 (and potentially more) possibly interacting genes may influence the ontogenesis of hemispheric asymmetries. Recently, it has been suggested that analyzing the genetics of hemispheric asymmetries on the level of gene ontology sets, rather than at the level of individual genes, might be more informative for understanding the underlying functional cascades. Here, we performed gene ontology, pathway and disease association analyses on genes that have previously been associated with handedness and language lateralization. Significant gene ontology sets for handedness were anatomical structure development, pattern specification (especially asymmetry formation) and biological regulation. Pathway analysis highlighted the importance of the TGF-beta signaling pathway for handedness ontogenesis. Significant gene ontology sets for language lateralization were responses to different stimuli, nervous system development, transport, signaling, and biological regulation. Despite the fact that some authors assume that handedness and language lateralization share a common ontogenetic basis, gene ontology sets barely overlap between phenotypes. Compared to genes involved in handedness, which mostly contribute to structural development, genes involved in language lateralization rather contribute to activity-dependent cognitive processes. Disease association analysis revealed associations of genes involved in handedness with diseases affecting the whole body, while genes involved in language lateralization were specifically engaged in mental and neurological diseases. These findings further support the idea that handedness and language lateralization are ontogenetically independent, complex phenotypes. PMID:28729848

Simultaneous estimation of ramipril, acetylsalicylic acid and atorvastatin calcium by chemometrics assisted UV-spectrophotometric method in capsules.

PubMed

Sankar, A S Kamatchi; Vetrichelvan, Thangarasu; Venkappaya, Devashya

2011-09-01

In the present work, three different spectrophotometric methods for simultaneous estimation of ramipril, aspirin and atorvastatin calcium in raw materials and in formulations are described. Overlapped data was quantitatively resolved by using chemometric methods, viz. inverse least squares (ILS), principal component regression (PCR) and partial least squares (PLS). Calibrations were constructed using the absorption data matrix corresponding to the concentration data matrix. The linearity range was found to be 1-5, 10-50 and 2-10 μg mL-1 for ramipril, aspirin and atorvastatin calcium, respectively. The absorbance matrix was obtained by measuring the zero-order absorbance in the wavelength range between 210 and 320 nm. A training set design of the concentration data corresponding to the ramipril, aspirin and atorvastatin calcium mixtures was organized statistically to maximize the information content from the spectra and to minimize the error of multivariate calibrations. By applying the respective algorithms for PLS 1, PCR and ILS to the measured spectra of the calibration set, a suitable model was obtained. This model was selected on the basis of RMSECV and RMSEP values. The same was applied to the prediction set and capsule formulation. Mean recoveries of the commercial formulation set together with the figures of merit (calibration sensitivity, selectivity, limit of detection, limit of quantification and analytical sensitivity) were estimated. Validity of the proposed approaches was successfully assessed for analyses of drugs in the various prepared physical mixtures and formulations.

Overlapping Modularity at the Critical Point of k-Clique Percolation

NASA Astrophysics Data System (ADS)

Tóth, Bálint; Vicsek, Tamás; Palla, Gergely

2013-05-01

One of the most remarkable social phenomena is the formation of communities in social networks corresponding to families, friendship circles, work teams, etc. Since people usually belong to several different communities at the same time, the induced overlaps result in an extremely complicated web of the communities themselves. Thus, uncovering the intricate community structure of social networks is a non-trivial task with great potential for practical applications, gaining a notable interest in the recent years. The Clique Percolation Method (CPM) is one of the earliest overlapping community finding methods, which was already used in the analysis of several different social networks. In this approach the communities correspond to k-clique percolation clusters, and the general heuristic for setting the parameters of the method is to tune the system just below the critical point of k-clique percolation. However, this rule is based on simple physical principles and its validity was never subject to quantitative analysis. Here we examine the quality of the partitioning in the vicinity of the critical point using recently introduced overlapping modularity measures. According to our results on real social and other networks, the overlapping modularities show a maximum close to the critical point, justifying the original criteria for the optimal parameter settings.

Mental reinstatement of encoding context improves episodic remembering.

PubMed

Bramão, Inês; Karlsson, Anna; Johansson, Mikael

2017-09-01

This study investigates context-dependent memory retrieval. Previous work has shown that physically re-experiencing the encoding context at retrieval improves memory accessibility. The current study examined if mental reconstruction of the original encoding context would yield parallel memory benefits. Participants performed a cued-recall memory task, preceded either by a mental or by a physical context reinstatement task, and we manipulated whether the context reinstated at retrieval overlapped with the context of the target episode. Both behavioral and electrophysiological measures of brain activity showed strong encoding-retrieval (E-R) overlap effects, with facilitated episodic retrieval when the encoding and retrieval contexts overlapped. The electrophysiological E-R overlap effect was more sustained and involved more posterior regions when context was mentally compared with physically reinstated. Additionally, a time-frequency analysis revealed that context reinstatement alone engenders recollection of the target episode. However, while recollection of the target memory is readily prompted by a physical reinstatement, target recollection during mental reinstatement is delayed and depends on the gradual reconstruction of the context. Taken together, our results show facilitated episodic remembering also when mentally reinstating the encoding context; and that such benefits are supported by both shared and partially non-overlapping neural mechanisms when the encoding context is mentally reconstructed as compared with physically presented at the time of retrieval. Copyright © 2017 Elsevier Ltd. All rights reserved.

T-cell memory responses elicited by yellow fever vaccine are targeted to overlapping epitopes containing multiple HLA-I and -II binding motifs.

PubMed

de Melo, Andréa Barbosa; Nascimento, Eduardo J M; Braga-Neto, Ulisses; Dhalia, Rafael; Silva, Ana Maria; Oelke, Mathias; Schneck, Jonathan P; Sidney, John; Sette, Alessandro; Montenegro, Silvia M L; Marques, Ernesto T A

2013-01-01

The yellow fever vaccines (YF-17D-204 and 17DD) are considered to be among the safest vaccines and the presence of neutralizing antibodies is correlated with protection, although other immune effector mechanisms are known to be involved. T-cell responses are known to play an important role modulating antibody production and the killing of infected cells. However, little is known about the repertoire of T-cell responses elicited by the YF-17DD vaccine in humans. In this report, a library of 653 partially overlapping 15-mer peptides covering the envelope (Env) and nonstructural (NS) proteins 1 to 5 of the vaccine was utilized to perform a comprehensive analysis of the virus-specific CD4(+) and CD8(+) T-cell responses. The T-cell responses were screened ex-vivo by IFN-γ ELISPOT assays using blood samples from 220 YF-17DD vaccinees collected two months to four years after immunization. Each peptide was tested in 75 to 208 separate individuals of the cohort. The screening identified sixteen immunodominant antigens that elicited activation of circulating memory T-cells in 10% to 33% of the individuals. Biochemical in-vitro binding assays and immunogenetic and immunogenicity studies indicated that each of the sixteen immunogenic 15-mer peptides contained two or more partially overlapping epitopes that could bind with high affinity to molecules of different HLAs. The prevalence of the immunogenicity of a peptide in the cohort was correlated with the diversity of HLA-II alleles that they could bind. These findings suggest that overlapping of HLA binding motifs within a peptide enhances its T-cell immunogenicity and the prevalence of the response in the population. In summary, the results suggests that in addition to factors of the innate immunity, "promiscuous" T-cell antigens might contribute to the high efficacy of the yellow fever vaccines.

T-Cell Memory Responses Elicited by Yellow Fever Vaccine are Targeted to Overlapping Epitopes Containing Multiple HLA-I and -II Binding Motifs

PubMed Central

de Melo, Andréa Barbosa; Nascimento, Eduardo J. M.; Braga-Neto, Ulisses; Dhalia, Rafael; Silva, Ana Maria; Oelke, Mathias; Schneck, Jonathan P.; Sidney, John; Sette, Alessandro; Montenegro, Silvia M. L.; Marques, Ernesto T. A.

2013-01-01

The yellow fever vaccines (YF-17D-204 and 17DD) are considered to be among the safest vaccines and the presence of neutralizing antibodies is correlated with protection, although other immune effector mechanisms are known to be involved. T-cell responses are known to play an important role modulating antibody production and the killing of infected cells. However, little is known about the repertoire of T-cell responses elicited by the YF-17DD vaccine in humans. In this report, a library of 653 partially overlapping 15-mer peptides covering the envelope (Env) and nonstructural (NS) proteins 1 to 5 of the vaccine was utilized to perform a comprehensive analysis of the virus-specific CD4+ and CD8+ T-cell responses. The T-cell responses were screened ex-vivo by IFN-γ ELISPOT assays using blood samples from 220 YF-17DD vaccinees collected two months to four years after immunization. Each peptide was tested in 75 to 208 separate individuals of the cohort. The screening identified sixteen immunodominant antigens that elicited activation of circulating memory T-cells in 10% to 33% of the individuals. Biochemical in-vitro binding assays and immunogenetic and immunogenicity studies indicated that each of the sixteen immunogenic 15-mer peptides contained two or more partially overlapping epitopes that could bind with high affinity to molecules of different HLAs. The prevalence of the immunogenicity of a peptide in the cohort was correlated with the diversity of HLA-II alleles that they could bind. These findings suggest that overlapping of HLA binding motifs within a peptide enhances its T-cell immunogenicity and the prevalence of the response in the population. In summary, the results suggests that in addition to factors of the innate immunity, “promiscuous” T-cell antigens might contribute to the high efficacy of the yellow fever vaccines. PMID:23383350

Appeals Court Gives MIT Another Chance to Prove Benefits of Overlap Group.

ERIC Educational Resources Information Center

Jaschik, Scott

1993-01-01

A federal appeals court has given the Massachusetts Institute of Technology another chance to prove in court that the Overlap Group, of which MIT was a member, did not violate antitrust laws. The group of 23 colleges set common financial-aid awards for students admitted to more than one institution. (MSE)

The species-area relationship, self-similarity, and the true meaning of the z-value.

PubMed

Tjørve, Even; Tjørve, Kathleen M Calf

2008-12-01

The power model, S= cA(z) (where S is number of species, A is area, and c and z are fitted constants), is the model most commonly fitted to species-area data assessing species diversity. We use the self-similarity properties of this model to reveal patterns implicated by the z parameter. We present the basic arithmetic leading both to the fraction of new species added when two areas are combined and to species overlap between two areas of the same size, given a continuous sampling scheme. The fraction of new species resulting from expansion of an area can be expressed as alpha(z)-1, where alpha is the expansion factor. Consequently, z-values can be converted to a scale-invariant species overlap between two equally sized areas, since the proportion of species in common between the two areas is 2-2(z). Calculating overlap when adding areas of the same size reveals the intrinsic effect of distance assumed by the bisectional scheme. We use overlap area relationships from empirical data sets to illustrate how answers to the single large or several small reserves (SLOSS) question vary between data sets and with scale. We conclude that species overlap and the effect of distance between sample areas or isolates should be addressed when discussing species area relationships, and lack of fit to the power model can be caused by its assumption of a scale-invariant overlap relationship.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB

PubMed Central

Dunbrack, Roland L.

2012-01-01

Motivation: Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed. Results: We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM–HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. Availability: The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly. Contact: Roland.Dunbracks@fccc.edu PMID:22942020

Seeding for pervasively overlapping communities

NASA Astrophysics Data System (ADS)

Lee, Conrad; Reid, Fergal; McDaid, Aaron; Hurley, Neil

2011-06-01

In some social and biological networks, the majority of nodes belong to multiple communities. It has recently been shown that a number of the algorithms specifically designed to detect overlapping communities do not perform well in such highly overlapping settings. Here, we consider one class of these algorithms, those which optimize a local fitness measure, typically by using a greedy heuristic to expand a seed into a community. We perform synthetic benchmarks which indicate that an appropriate seeding strategy becomes more important as the extent of community overlap increases. We find that distinct cliques provide the best seeds. We find further support for this seeding strategy with benchmarks on a Facebook network and the yeast interactome.

Regular approximate factorization of a class of matrix-function with an unstable set of partial indices

PubMed Central

Rogosin, S.

2018-01-01

From the classic work of Gohberg & Krein (1958 Uspekhi Mat. Nauk. XIII, 3–72. (Russian).), it is well known that the set of partial indices of a non-singular matrix function may change depending on the properties of the original matrix. More precisely, it was shown that if the difference between the largest and the smallest partial indices is larger than unity then, in any neighbourhood of the original matrix function, there exists another matrix function possessing a different set of partial indices. As a result, the factorization of matrix functions, being an extremely difficult process itself even in the case of the canonical factorization, remains unresolvable or even questionable in the case of a non-stable set of partial indices. Such a situation, in turn, has became an unavoidable obstacle to the application of the factorization technique. This paper sets out to answer a less ambitious question than that of effective factorizing matrix functions with non-stable sets of partial indices, and instead focuses on determining the conditions which, when having known factorization of the limiting matrix function, allow to construct another family of matrix functions with the same origin that preserves the non-stable partial indices and is close to the original set of the matrix functions. PMID:29434502

Regular approximate factorization of a class of matrix-function with an unstable set of partial indices.

PubMed

Mishuris, G; Rogosin, S

2018-01-01

From the classic work of Gohberg & Krein (1958 Uspekhi Mat. Nauk. XIII , 3-72. (Russian).), it is well known that the set of partial indices of a non-singular matrix function may change depending on the properties of the original matrix. More precisely, it was shown that if the difference between the largest and the smallest partial indices is larger than unity then, in any neighbourhood of the original matrix function, there exists another matrix function possessing a different set of partial indices. As a result, the factorization of matrix functions, being an extremely difficult process itself even in the case of the canonical factorization, remains unresolvable or even questionable in the case of a non-stable set of partial indices. Such a situation, in turn, has became an unavoidable obstacle to the application of the factorization technique. This paper sets out to answer a less ambitious question than that of effective factorizing matrix functions with non-stable sets of partial indices, and instead focuses on determining the conditions which, when having known factorization of the limiting matrix function, allow to construct another family of matrix functions with the same origin that preserves the non-stable partial indices and is close to the original set of the matrix functions.

How Long Do Satellites Need to Overlap? Evaluation of Climate Data Stability from Overlapping Satellite Records

NASA Technical Reports Server (NTRS)

Weatherhead, Elizabeth C.; Harder, Jerald; Araujo-Pradere, Eduardo A.; Bodeker, Greg; English, Jason M.; Flynn, Lawrence E.; Frith, Stacey M.; Lazo, Jeffrey K.; Pilewskie, Peter; Weber, Mark;

How long do satellites need to overlap? Evaluation of climate data stability from overlapping satellite records

NASA Astrophysics Data System (ADS)

Weatherhead, Elizabeth C.; Harder, Jerald; Araujo-Pradere, Eduardo A.; Bodeker, Greg; English, Jason M.; Flynn, Lawrence E.; Frith, Stacey M.; Lazo, Jeffrey K.; Pilewskie, Peter; Weber, Mark; Woods, Thomas N.

2017-12-01

Sensors on satellites provide unprecedented understanding of the Earth's climate system by measuring incoming solar radiation, as well as both passive and active observations of the entire Earth with outstanding spatial and temporal coverage. A common challenge with satellite observations is to quantify their ability to provide well-calibrated, long-term, stable records of the parameters they measure. Ground-based intercomparisons offer some insight, while reference observations and internal calibrations give further assistance for understanding long-term stability. A valuable tool for evaluating and developing long-term records from satellites is the examination of data from overlapping satellite missions. This paper addresses how the length of overlap affects the ability to identify an offset or a drift in the overlap of data between two sensors. Ozone and temperature data sets are used as examples showing that overlap data can differ by latitude and can change over time. New results are presented for the general case of sensor overlap by using Solar Radiation and Climate Experiment (SORCE) Spectral Irradiance Monitor (SIM) and Solar Stellar Irradiance Comparison Experiment (SOLSTICE) solar irradiance data as an example. To achieve a 1 % uncertainty in estimating the offset for these two instruments' measurement of the Mg II core (280 nm) requires approximately 5 months of overlap. For relative drift to be identified within 0.1 % yr-1 uncertainty (0.00008 W m-2 nm-1 yr-1), the overlap for these two satellites would need to be 2.5 years. Additional overlap of satellite measurements is needed if, as is the case for solar monitoring, unexpected jumps occur adding uncertainty to both offsets and drifts; the additional length of time needed to account for a single jump in the overlap data may be as large as 50 % of the original overlap period in order to achieve the same desired confidence in the stability of the merged data set. Results presented here are directly applicable to satellite Earth observations. Approaches for Earth observations offer additional challenges due to the complexity of the observations, but Earth observations may also benefit from ancillary observations taken from ground-based and in situ sources. Difficult choices need to be made when monitoring approaches are considered; we outline some attempts at optimizing networks based on economic principles. The careful evaluation of monitoring overlap is important to the appropriate application of observational resources and to the usefulness of current and future observations.

Improving mortality outcomes of Stevens Johnson syndrome/toxic epidermal necrolysis: A regional burns centre experience.

PubMed

Nizamoglu, M; Ward, J A; Frew, Q; Gerrish, H; Martin, N; Shaw, A; Barnes, D; Shelly, O; Philp, B; El-Muttardi, N; Dziewulski, P

2018-05-01

Stevens Johnson Syndrome/toxic epidermal necrolysis (SJS/TEN) are rare, potentially fatal desquamative disorders characterised by large areas of partial thickness skin and mucosal loss. The degree of epidermal detachment that occurs has led to SJS/TEN being described as a burn-like condition. These patients benefit from judicious critical care, early debridement and meticulous wound care. This is best undertaken within a multidisciplinary setting led by clinicians experienced in the management of massive skin loss and its sequelae. In this study, we examined the clinical outcomes of SJS/TEN overlap & TEN patients managed by our regional burns service over a 12-year period. We present our treatment model for other burn centres treating SJS/TEN patients. A retrospective case review was performed for all patients with a clinical diagnosis of TEN or SJS/TEN overlap admitted to our paediatric and adult burns centre between June 2004 and December 2016. Patient demographics, percentage total body surface area (%TBSA), mucosal involvement, causation, severity of illness score (SCORTEN), length of stay and survival were appraised with appropriate statistical analysis performed using Graph Pad Prism 7.02 Software. During the study period, 42 patients (M26; F: 16) with TEN (n=32) and SJS/TEN overlap (n=10) were managed within our burns service. Mean %TBSA of cutaneous involvement was 57% (range 10-100%) and mean length of stay (LOS) was 27 days (range 1-144 days). We observed 4 deaths in our series compared to 16 predicted by SCORTEN giving a standardised mortality ratio (SMR) of 24%. Management in our burns service with an aggressive wound care protocol involving debridement of blistered epidermis and wound closure with synthetic and biological dressings seems to have produced benefits in mortality when compared to predicted outcomes. Copyright © 2017 Elsevier Ltd and ISBI. All rights reserved.

Evidence for partial overlap of male olfactory cues in lampreys

USGS Publications Warehouse

Buchinger, Tyler J.; Li, Ke; Huertas, Mar; Baker, Cindy F.; Jia, Liang; Hayes, Michael C.; Li, Weiming; Johnson, Nicholas S.

2016-01-01

Animals rely on a mosaic of complex information to find and evaluate mates. Pheromones, often comprised of multiple components, are considered to be particularly important for species-recognition in many species. While the evolution of species-specific pheromone blends is well-described in many insects, very few vertebrate pheromones have been studied in a macro-evolutionary context. Here, we report a phylogenetic comparison of multi-component male odours that guide reproduction in lampreys. Chemical profiling of sexually mature males from eleven species of lamprey, representing six of ten genera and two of three families, indicated the chemical profiles of sexually mature male odours are partially shared among species. Behavioural assays conducted with four species sympatric in the Laurentian Great Lakes indicated asymmetric female responses to heterospecific odours, where Petromyzon marinus were attracted to male odour collected from all species tested but other species generally preferred only the odour of conspecifics. Electro-olfactogram recordings from P. marinusindicated that although P. marinus exhibited behavioural responses to odours from males of all species, at least some of the compounds that elicited olfactory responses were different in conspecific male odours compared to heterospecific male odours. We conclude that some of the compounds released by sexually mature males are shared among species and elicit olfactory and behavioural responses in P. marinus, and suggest that our results provide evidence for partial overlap of male olfactory cues among lampreys. Further characterization of the chemical identities of odour components is needed to confirm shared pheromones among species.

Impaired Recognition and Regulation of Disgust Is Associated with Distinct but Partially Overlapping Patterns of Decreased Gray Matter Volume in the Ventroanterior Insula.

PubMed

Woolley, Josh D; Strobl, Eric V; Sturm, Virginia E; Shany-Ur, Tal; Poorzand, Pardis; Grossman, Scott; Nguyen, Lauren; Eckart, Janet A; Levenson, Robert W; Seeley, William W; Miller, Bruce L; Rankin, Katherine P

2015-10-01

The ventroanterior insula is implicated in the experience, expression, and recognition of disgust; however, whether this brain region is required for recognizing disgust or regulating disgusting behaviors remains unknown. We examined the brain correlates of the presence of disgusting behavior and impaired recognition of disgust using voxel-based morphometry in a sample of 305 patients with heterogeneous patterns of neurodegeneration. Permutation-based analyses were used to determine regions of decreased gray matter volume at a significance level p <= .05 corrected for family-wise error across the whole brain and within the insula. Patients with behavioral variant frontotemporal dementia and semantic variant primary progressive aphasia were most likely to exhibit disgusting behaviors and were, on average, the most impaired at recognizing disgust in others. Imaging analysis revealed that patients who exhibited disgusting behaviors had significantly less gray matter volume bilaterally in the ventral anterior insula. A region of interest analysis restricted to behavioral variant frontotemporal dementia and semantic variant primary progressive aphasia patients alone confirmed this result. Moreover, impaired recognition of disgust was associated with decreased gray matter volume in the bilateral ventroanterior and ventral middle regions of the insula. There was an area of overlap in the bilateral anterior insula where decreased gray matter volume was associated with both the presence of disgusting behavior and impairments in recognizing disgust. These findings suggest that regulating disgusting behaviors and recognizing disgust in others involve two partially overlapping neural systems within the insula. Moreover, the ventral anterior insula is required for both processes. Published by Elsevier Inc.

Impaired recognition and regulation of disgust is associated with distinct but partially overlapping patterns of decreased gray matter volume in the ventroanterior insula

PubMed Central

Woolley, Joshua; Strobl, Eric V; Sturm, Virginia E; Shany-Ur, Tal; Poorzand, Pardis; Grossman, Scott; Nguyen, Lauren; Eckart, Janet A; Levenson, Robert W; Seeley, William W; Miller, Bruce L; Rankin, Katherine P

2015-01-01

Background The ventroanterior insula is implicated in the experience, expression, and recognition of disgust; however, whether this brain region is required for recognizing disgust or regulating disgusting behaviors remains unknown. Methods We examined the brain correlates of the presence of disgusting behavior and impaired recognition of disgust using voxel-based morphometry in a sample of 305 patients with heterogeneous patterns of neurodegeneration. Permutation-based analyses were used to determine regions of decreased grey matter volume at a significance level p<0.05 corrected for family-wise error across the whole brain and within the insula. Results Patients with behavioral variant frontotemporal dementia (bvFTD) and semantic variant primary progressive aphasia (svPPA) were most likely to exhibit disgusting behaviors and were, on average, the most impaired at recognizing disgust in others. Imaging analysis revealed that patients who exhibited disgusting behaviors had significantly less grey matter volume bilaterally in the ventral anterior insula. A region of interest analysis restricted to bvFTD and svPPA patients alone confirmed this result. Moreover, impaired recognition of disgust was associated with decreased grey matter volume in the bilateral ventroanterior and ventral middle regions of the insula. There was an area of overlap in the bilateral anterior insula where decreased grey matter volume was associated with both the presence of disgusting behavior and impairments in recognizing disgust. Conclusion These findings suggest that regulating disgusting behaviors and recognizing disgust in others involve two partially overlapping neural systems within the insula. Moreover, the ventral anterior insula is required for both processes. PMID:25890642

Differentiation of uric acid versus non-uric acid kidney stones in the presence of iodine using dual-energy CT

NASA Astrophysics Data System (ADS)

Wang, J.; Qu, M.; Leng, S.; McCollough, C. H.

2010-04-01

In this study, the feasibility of differentiating uric acid from non-uric acid kidney stones in the presence of iodinated contrast material was evaluated using dual-energy CT (DECT). Iodine subtraction was accomplished with a commercial three material decomposition algorithm to create a virtual non-contrast (VNC) image set. VNC images were then used to segment stone regions from tissue background. The DE ratio of each stone was calculated using the CT images acquired at two different energies with DECT using the stone map generated from the VNC images. The performance of DE ratio-based stone differentiation was evaluated at five different iodine concentrations (21, 42, 63, 84 and 105 mg/ml). The DE ratio of stones in iodine solution was found larger than those obtained in non-iodine cases. This is mainly caused by the partial volume effect around the boundary between the stone and iodine solution. The overestimation of the DE ratio leads to substantial overlap between different stone types. To address the partial volume effect, an expectation-maximization (EM) approach was implemented to estimate the contribution of iodine and stone within each image pixel in their mixture area. The DE ratio of each stone was corrected to maximally remove the influence of iodine solutions. The separation of uric-acid and non-uric-acid stone was improved in the presence of iodine solution.

Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation

NASA Astrophysics Data System (ADS)

Wu, Di; Kofke, David A.

2005-08-01

We consider ways to quantify the overlap of the parts of phase space important to two systems, labeled A and B. Of interest is how much of the A-important phase space lies in that important to B, and how much of B lies in A. Two measures are proposed. The first considers four total-energy distributions, formed from all combinations made by tabulating either the A-system or the B-system energy when sampling either the A or B system. Measures for A in B and B in A are given by two overlap integrals defined on pairs of these distributions. The second measure is based on information theory, and defines two relative entropies which are conveniently expressed in terms of the dissipated work for free-energy perturbation (FEP) calculations in the A →B and B →A directions, respectively. Phase-space overlap is an important consideration in the performance of free-energy calculations. To demonstrate this connection, we examine bias in FEP calculations applied to a system of independent particles in a harmonic potential. Systems are selected to represent a range of overlap situations, including extreme subset, subset, partial overlap, and nonoverlap. The magnitude and symmetry of the bias (A →B vs B →A) are shown to correlate well with the overlap, and consequently with the overlap measures. The relative entropies are used to scale the amount of sampling to obtain a universal bias curve. This result leads to develop a simple heuristic that can be applied to determine whether a work-based free-energy measurement is free of bias. The heuristic is based in part on the measured free energy, but we argue that it is fail-safe inasmuch as any bias in the measurement will not promote a false indication of accuracy.

Automatic Activation of Phonological Code during Visual Word Recognition in Children: A Masked Priming Study in Grades 3 and 5

ERIC Educational Resources Information Center

Sauval, Karinne; Perre, Laetitia; Casalis, Séverine

2017-01-01

The present study aimed to investigate the development of automatic phonological processes involved in visual word recognition during reading acquisition in French. A visual masked priming lexical decision experiment was carried out with third, fifth graders and adult skilled readers. Three different types of partial overlap between the prime and…

Underdominant KCC3b R31I association with blood sodium concentration in domestic sheep suggests role in oligomer function

USDA-ARS?s Scientific Manuscript database

KCC3 and KCC1 are potassium chloride transporters with partially overlapping function, and KCC3 knockout mice exhibit hypertension. Two KCC3 isoforms differ by alternate promoters and first coding exons: KCC3a is widely expressed, and KCC3b is highly expressed in kidney proximal convoluted tubule. W...

Fully automatic multi-atlas segmentation of CTA for partial volume correction in cardiac SPECT/CT

NASA Astrophysics Data System (ADS)

Liu, Qingyi; Mohy-ud-Din, Hassan; Boutagy, Nabil E.; Jiang, Mingyan; Ren, Silin; Stendahl, John C.; Sinusas, Albert J.; Liu, Chi

2017-05-01

Anatomical-based partial volume correction (PVC) has been shown to improve image quality and quantitative accuracy in cardiac SPECT/CT. However, this method requires manual segmentation of various organs from contrast-enhanced computed tomography angiography (CTA) data. In order to achieve fully automatic CTA segmentation for clinical translation, we investigated the most common multi-atlas segmentation methods. We also modified the multi-atlas segmentation method by introducing a novel label fusion algorithm for multiple organ segmentation to eliminate overlap and gap voxels. To evaluate our proposed automatic segmentation, eight canine 99mTc-labeled red blood cell SPECT/CT datasets that incorporated PVC were analyzed, using the leave-one-out approach. The Dice similarity coefficient of each organ was computed. Compared to the conventional label fusion method, our proposed label fusion method effectively eliminated gaps and overlaps and improved the CTA segmentation accuracy. The anatomical-based PVC of cardiac SPECT images with automatic multi-atlas segmentation provided consistent image quality and quantitative estimation of intramyocardial blood volume, as compared to those derived using manual segmentation. In conclusion, our proposed automatic multi-atlas segmentation method of CTAs is feasible, practical, and facilitates anatomical-based PVC of cardiac SPECT/CT images.

48 CFR 52.219-7 - Notice of Partial Small Business Set-Aside.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Clauses 52.219-7 Notice of Partial Small Business Set-Aside. As prescribed in 19.508(d), insert the following clause: Notice of Partial Small Business Set-Aside (JUN 2003) (a) Definitions. Small business..., and qualified as a small business under the size standards in this solicitation. (b) General. (1) A...

48 CFR 52.219-7 - Notice of Partial Small Business Set-Aside.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Clauses 52.219-7 Notice of Partial Small Business Set-Aside. As prescribed in 19.508(d), insert the following clause: Notice of Partial Small Business Set-Aside (JUN 2003) (a) Definitions. Small business..., and qualified as a small business under the size standards in this solicitation. (b) General. (1) A...

48 CFR 52.219-7 - Notice of Partial Small Business Set-Aside.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Clauses 52.219-7 Notice of Partial Small Business Set-Aside. As prescribed in 19.508(d), insert the following clause: Notice of Partial Small Business Set-Aside (JUN 2003) (a) Definitions. Small business..., and qualified as a small business under the size standards in this solicitation. (b) General. (1) A...

48 CFR 52.219-7 - Notice of Partial Small Business Set-Aside.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Clauses 52.219-7 Notice of Partial Small Business Set-Aside. As prescribed in 19.508(d), insert the following clause: Notice of Partial Small Business Set-Aside (JUN 2003) (a) Definitions. Small business..., and qualified as a small business under the size standards in this solicitation. (b) General. (1) A...

48 CFR 52.219-7 - Notice of Partial Small Business Set-Aside.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Clauses 52.219-7 Notice of Partial Small Business Set-Aside. As prescribed in 19.508(d), insert the following clause: Notice of Partial Small Business Set-Aside (JUN 2003) (a) Definitions. Small business..., and qualified as a small business under the size standards in this solicitation. (b) General. (1) A...

Cultivating Computational Thinking Practices and Mathematical Habits of Mind in Lattice Land

ERIC Educational Resources Information Center

Pei, Christina; Weintrop, David; Wilensky, Uri

2018-01-01

There is a great deal of overlap between the set of practices collected under the term "computational thinking" and the mathematical habits of mind that are the focus of much mathematics instruction. Despite this overlap, the links between these two desirable educational outcomes are rarely made explicit, either in classrooms or in the…

Error Estimation Techniques to Refine Overlapping Aerial Image Mosaic Processes via Detected Parameters

ERIC Educational Resources Information Center

Bond, William Glenn

2012-01-01

In this paper, I propose to demonstrate a means of error estimation preprocessing in the assembly of overlapping aerial image mosaics. The mosaic program automatically assembles several hundred aerial images from a data set by aligning them, via image registration using a pattern search method, onto a GIS grid. The method presented first locates…

Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

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

Thompson, Michael C.; Cascio, Duilio; Yeates, Todd O.

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the datamore » sets, and it was found that the 18 data sets separated into two distinct groups, with largeRvalues (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.« less

A new CT collimator for producing two simultaneous overlapping slices from one scan. [for biomedical applications

NASA Technical Reports Server (NTRS)

Kwoh, Y. S.; Glenn, W. V., Jr.; Reed, I. S.; Truong, T. K.

1981-01-01

A new CT collimator is developed which is capable of producing two simultaneous successive overlapping images from a single scan. The collimator represents a modification of the standard EMI 5005 collimator achieved by alternately masking one end or portions of both ends of the X-ray detectors at a 13-mm beamwidth so that a set of 540 filtered projections is obtained for each scan which can be separated into two sets of interleaved projections corresponding to views 3 mm apart. Tests have demonstrated that the quality of the images produced from these two projections almost equals the quality of those produced by the standard collimator from two separate scans. The new collimator may thus be used to achieve a speed improvement in the generation of overlapping sections as well as a reduction in X-ray dosage.

Sub-Audible Speech Recognition Based upon Electromyographic Signals

NASA Technical Reports Server (NTRS)

Jorgensen, Charles C. (Inventor); Agabon, Shane T. (Inventor); Lee, Diana D. (Inventor)

2012-01-01

Method and system for processing and identifying a sub-audible signal formed by a source of sub-audible sounds. Sequences of samples of sub-audible sound patterns ("SASPs") for known words/phrases in a selected database are received for overlapping time intervals, and Signal Processing Transforms ("SPTs") are formed for each sample, as part of a matrix of entry values. The matrix is decomposed into contiguous, non-overlapping two-dimensional cells of entries, and neural net analysis is applied to estimate reference sets of weight coefficients that provide sums with optimal matches to reference sets of values. The reference sets of weight coefficients are used to determine a correspondence between a new (unknown) word/phrase and a word/phrase in the database.

Partial trisomy 5q resulting from chromosome 7 insertion: An expansion of the phenotype

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

Fries, M.H.; Reilly, P.A.; Williams, T.C.

Partial trisomy 5q has been categorized into three separate phenotypes; however, a distinctive phenotype has not been described for duplications spanning 5q23-q35. We report a case of partial trisomy 5q for this region as a result of a ins(7,5)(q31.3;q23.2q35.1)mat. The liveborn male infant was delivered by emergency cesarean section at 37 weeks after a pregnancy notable for oligohydramnios, with birth weight 1792 g (<3%). Postnatal course was marked by psychomotor delay, failure to thrive, and biopsy demonstrated neonatal giant cell hepatitis with a paucity of intrahepatic bile ducts. His appearance was remarkable for lack of subcutaneous fat, midline displaced hairmore » whorl, bitemporal narrowing with frontal bossing, wide anterior fontanel, widow`s peak, protuberant eyes with periorbital and lid edema, short flat nasal bridge with broad flattened nasal tip, long smooth philtrum, wide mouth with thin lips, wide gingival ridges, micrognathia, posteriorly rotated low-set ears, hepatomegaly, flexion contractions of elbows, and generalized hypertonicity. Urine organic acids, oligosaccharide/mucopolysaccharide screen, and plasma amino acids were negative. GTG-banding on prometaphase chromosomes showed an unbalanced translocation involving chr. 7. This was identified as an insertion of chr. 5 (q23.2q35.1) into distal 7q after FISH using chr. 5 and chr. 7 painting probes. The infant`s mother carries the balanced insertional rearrangement: 46,XX,dir ins(7,5)(q31.3;q23.2q35.1). This phenotype overlaps that of previously described duplications with the addition of giant cell hepatitis, coarsened facial features, gingival thickening, and flexion contractures, suggestive of a yet undiagnosed storage disorder.« less

The Subject of Data in Submissions to the CLCS: Documenting the outer limits of the Northern Continental Shelf of the Faroe Islands

NASA Astrophysics Data System (ADS)

Vang Heinesen, Martin; Mørk, Finn

2017-04-01

The first partial submissions made by the Kingdom of Denmark, in respect of the continental shelf north of the Faroe Islands (North Faroe Margin, NFM), was submitted to the Commission on the Limits of the Continental Shelf in April 2009 as the result of 7 years of preparation which also included 4 additional continental shelf regions around the Faroe Islands and Greenland, on which individual partial submissions were made subsequently. The NFM covers parts of the NW European continental margin, it continues onto the Faroe-Iceland Ridge and the extinct Ægir (spreading) Ridge and overlaps with the continental margin of Iceland and Norway in the sediment rich Ægir Basin located between the European margin to the south and south-east, and the Jan Mayen Micro-continental margin to the west and north-west. Prior to the onset of the continental shelf project of the Kingdom of Denmark, arrangements had already been made with Norway and Iceland regarding the sharing of existing data and acquisition of new seismic data in the overlapping regions. Before that, the main database in the area included a comprehensive multi-beam bathymetric data set covering large parts of the Ægir Ridge with scattered single beam bathymetric lines in the remaining regions. It also comprised a number of single- and multi-channel seismic lines and a long refraction seismic line transecting the entire eastern part of the basin, from the Norwegian shelf to the Ægir Ridge, in addition to local side scan sonar and regional potential field data. During the project, additional high quality multi-channel seismic data, extensive multi-beam bathymetric data, and a comprehensive high resolution aeromagnetic dataset were acquired, allowing detailed mapping of the morphological and geological nature of the margin, including accurate identification of the base of the continental slope and mapping of the sediment thickness and sediment continuation in the basin. This data proved to be crucial for the documentation to the CLCS of the outer limits of the continental shelf to the north of the Faroe Islands.

Foraging range movements of the endangered Hawaiian hoary bat, Lasiurus cinereus semotus (Chiroptera: Vespertilionidae)

USGS Publications Warehouse

Bonaccorso, Frank J.; Todd, Christopher M.; Miles, Adam C.; Gorresen, P. Marcos

2015-01-01

We documented nightly movements of Hawaiian hoary bats (Lasiurus cinereus semotus) on the island of Hawai’i. Based on data from 28 radiotagged individuals mean foraging range (FR) was 230.7±72.3 ha, core-use area (CUA) was 25.5±6.9 ha (or 11.1% of mean FR), and the mean long axis (LAX) across the FR was 3,390.8±754.3 m. There was almost no overlap in CUAs among 4 adult males having overlapping foraging areas and tracked simultaneously or within a 90-day window of each other. CUAs of subadults partially overlapped with multiple adult males or with one other subadult. High variance in FRs, cores use areas, and LAX across the FR perhaps reflect localized stochastic variables such as weather, habitat, and food resources. Hawaiian hoary bats use moderately large FRs among insectivorous bats studied with comparable methodologies; however, foraging activity indicated by documentation of acoustic feeding buzzes is concentrated within one or a few disjunct areas cumulatively forming the 50% fixed kernel of CUA. The concentration of feeding activity, low values of individual overlap, and agonistic chasing behavior within CUAs all demonstrate a structured use of individual space by Hawaiian hoary bats.

Brain gray matter phenotypes across the psychosis dimension

PubMed Central

Ivleva, Elena I.; Bidesi, Anup S.; Thomas, Binu P.; Meda, Shashwath A.; Francis, Alan; Moates, Amanda F.; Witte, Bradley; Keshavan, Matcheri S.; Tamminga, Carol A.

2013-01-01

This study sought to examine whole brain and regional gray matter (GM) phenotypes across the schizophrenia (SZ)–bipolar disorder psychosis dimension using voxel-based morphometry (VBM 8.0 with DARTEL segmentation/normalization) and semi-automated regional parcellation, FreeSurfer (FS 4.3.1/64 bit). 3T T1 MPRAGE images were acquired from 19 volunteers with schizophrenia (SZ), 16 with schizoaffective disorder (SAD), 17 with psychotic bipolar I disorder (BD-P) and 10 healthy controls (HC). Contrasted with HC, SZ showed extensive cortical GM reductions, most pronounced in fronto-temporal regions; SAD had GM reductions overlapping with SZ, albeit less extensive; and BD-P demonstrated no GM differences from HC. Within the psychosis dimension, BD-P showed larger volumes in fronto-temporal and other cortical/subcortical regions compared with SZ, whereas SAD showed intermediate GM volumes. The two volumetric methodologies, VBM and FS, revealed highly overlapping results for cortical GM, but partially divergent results for subcortical volumes (basal ganglia, amygdala). Overall, these findings suggest that individuals across the psychosis dimension show both overlapping and unique GM phenotypes: decreased GM, predominantly in fronto-temporal regions, is characteristic of SZ but not of psychotic BD-P, whereas SAD display GM deficits overlapping with SZ, albeit less extensive. PMID:23177922

Brain gray matter phenotypes across the psychosis dimension.

PubMed

Ivleva, Elena I; Bidesi, Anup S; Thomas, Binu P; Meda, Shashwath A; Francis, Alan; Moates, Amanda F; Witte, Bradley; Keshavan, Matcheri S; Tamminga, Carol A

2012-10-30

This study sought to examine whole brain and regional gray matter (GM) phenotypes across the schizophrenia (SZ)-bipolar disorder psychosis dimension using voxel-based morphometry (VBM 8.0 with DARTEL segmentation/normalization) and semi-automated regional parcellation, FreeSurfer (FS 4.3.1/64 bit). 3T T1 MPRAGE images were acquired from 19 volunteers with schizophrenia (SZ), 16 with schizoaffective disorder (SAD), 17 with psychotic bipolar I disorder (BD-P) and 10 healthy controls (HC). Contrasted with HC, SZ showed extensive cortical GM reductions, most pronounced in fronto-temporal regions; SAD had GM reductions overlapping with SZ, albeit less extensive; and BD-P demonstrated no GM differences from HC. Within the psychosis dimension, BD-P showed larger volumes in fronto-temporal and other cortical/subcortical regions compared with SZ, whereas SAD showed intermediate GM volumes. The two volumetric methodologies, VBM and FS, revealed highly overlapping results for cortical GM, but partially divergent results for subcortical volumes (basal ganglia, amygdala). Overall, these findings suggest that individuals across the psychosis dimension show both overlapping and unique GM phenotypes: decreased GM, predominantly in fronto-temporal regions, is characteristic of SZ but not of psychotic BD-P, whereas SAD display GM deficits overlapping with SZ, albeit less extensive. Published by Elsevier Ireland Ltd.

Reduction of astrographic catalogues

NASA Technical Reports Server (NTRS)

Stock, J.; Prugna, F. D.; Cova, J.

1984-01-01

An automatic program for the reduction of overlapping Carte du Ciel plates is described. The projection and transformation equations are given and the RAA subprogram flow is outlined. The program was applied to two different sets of data, namely to nine overlapping plates of the Cape Zone of the CdC, and to fifteen plates taken with the CIDA-refractor of the open cluster Tr10.

QSAR analysis of nicotinamidic compounds and design of potential Bruton's tyrosine kinase (Btk) inhibitors.

PubMed

Santos-Garcia, Letícia; Assis, Letícia C; Silva, Daniela R; Ramalho, Teodorico C; da Cunha, Elaine F F

2016-07-01

Bruton's tyrosine kinase (Btk) is an important enzyme in B-lymphocyte development and differentiation. Furthermore, Btk expression is considered essential for the proliferation and survival of these cells. Btk inhibition has become an attractive strategy for treating autoimmune diseases, B-cell leukemia, and lymphomas. With the objective of proposing new candidates for Btk inhibitors, we applied receptor-dependent four-dimensional quantitative structure-activity relationship (QSAR) methodology to a series of 96 nicotinamide analogs useful as Btk modulators. The QSAR models were developed using 71 compounds, the training set, and externally validated using 25 compounds, the test set. The conformations obtained by molecular dynamics simulation were overlapped in a virtual three-dimensional cubic box comprised of 2 and 5 Å cells, according to the six trial alignments. The models were generated by combining genetic function approximation and partial least squares regression technique. The analyses suggest that Model 1a yields the best results. The best equation shows [Formula: see text], r(2) = .743, RMSEC = .831, RMSECV = .879. Given the importance of the Tyr551, this residue could become a strategic target for the design of novel Btk inhibitors with improved potency. In addition, the good potency predicted for the proposed M2 compound indicates this compound as a potential Btk inhibitor candidate.

Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes

PubMed Central

VanderKraats, Nathan D.; Hiken, Jeffrey F.; Decker, Keith F.; Edwards, John R.

2013-01-01

Methylation of the CpG-rich region (CpG island) overlapping a gene’s promoter is a generally accepted mechanism for silencing expression. While recent technological advances have enabled measurement of DNA methylation and expression changes genome-wide, only modest correlations between differential methylation at gene promoters and expression have been found. We hypothesize that stronger associations are not observed because existing analysis methods oversimplify their representation of the data and do not capture the diversity of existing methylation patterns. Recently, other patterns such as CpG island shore methylation and long partially hypomethylated domains have also been linked with gene silencing. Here, we detail a new approach for discovering differential methylation patterns associated with expression change using genome-wide high-resolution methylation data: we represent differential methylation as an interpolated curve, or signature, and then identify groups of genes with similarly shaped signatures and corresponding expression changes. Our technique uncovers a diverse set of patterns that are conserved across embryonic stem cell and cancer data sets. Overall, we find strong associations between these methylation patterns and expression. We further show that an extension of our method also outperforms other approaches by generating a longer list of genes with higher quality associations between differential methylation and expression. PMID:23748561

Interacting epidemics on overlay networks

NASA Astrophysics Data System (ADS)

Funk, Sebastian; Jansen, Vincent A. A.

2010-03-01

The interaction between multiple pathogens spreading on networks connecting a given set of nodes presents an ongoing theoretical challenge. Here, we aim to understand such interactions by studying bond percolation of two different processes on overlay networks of arbitrary joint degree distribution. We find that an outbreak of a first pathogen providing immunity to another one spreading subsequently on a second network connecting the same set of nodes does so most effectively if the degrees on the two networks are positively correlated. In that case, the protection is stronger the more heterogeneous the degree distributions of the two networks are. If, on the other hand, the degrees are uncorrelated or negatively correlated, increasing heterogeneity reduces the potential of the first process to prevent the second one from reaching epidemic proportions. We generalize these results to cases where the edges of the two networks overlap to arbitrary amount, or where the immunity granted is only partial. If both processes grant immunity to each other, we find a wide range of possible situations of coexistence or mutual exclusion, depending on the joint degree distribution of the underlying networks and the amount of immunity granted mutually. These results generalize the concept of a coexistence threshold and illustrate the impact of large-scale network structure on the interaction between multiple spreading agents.

A Three-Attribute Transfer Skills Framework--Part I: Establishing the Model and Its Relation to Chemical Education

ERIC Educational Resources Information Center

Dori, Yehudit Judy; Sasson, Irit

2013-01-01

This paper presents Part I of a two-part study. This first part reviews the literature of transfer of learning as one of the major goals of instruction. Transfer refers to students' ability to apply knowledge and skills in new learning contexts. The literature suggests partially or non-overlapping definitions, and empirical studies on transfer…

What Are the Underlying Skills of Silent Reading Acquisition? A Developmental Study from Kindergarten to the 2nd Grade

ERIC Educational Resources Information Center

Bar-Kochva, Irit

2013-01-01

Research on reading acquisition and on the processes underlying it usually examined reading orally, while silent reading, which is the more common mode of reading, has been rather neglected. As accumulated data suggests that these two modes of reading only partially overlap, our understanding of the natural mode of reading may still be limited.…

Recombinant human interleukin-3 (rhIL-3) enhances the mobilization of peripheral blood progenitor cells by recombinant human granulocyte colony-stimulating factor (rhG-CSF) in normal volunteers.

PubMed

Huhn, R D; Yurkow, E J; Tushinski, R; Clarke, L; Sturgill, M G; Hoffman, R; Sheay, W; Cody, R; Philipp, C; Resta, D; George, M

1996-06-01

To identify a precisely timed and safe protocol for progenitor cell mobilization, we studied the effects of rhIL-3 and rhG-CSF administration to normal volunteers. rhG-CSF 5 micrograms/kg/d was administered subcutaneously (s.c.) for 7 consecutive days either alone or preceded by rhIL-3 5 micrograms/kg/d s.c. for 4 consecutive days in sequential or partially overlapping schedules. The combined cytokines were well-tolerated--adverse effects were similar to those of the individual agents. Total white blood cell (WBC) and neutrophil counts rose briskly in response to rhG-CSF, and peak mean values were similar between treatment cohorts. Mean platelet counts were modestly elevated during rhG-CSF treatment only in the cohorts receiving rhIL-3 and rhG-CSF. Mean circulating CD34+ cells peaked on day 5 in the rhG-CSF group (38.9+/-14.3/microliter), day 6 in the sequential rhIL-3/rhG-CSF group (56.4+/-12.4/microliter), and day 6 in the partial overlap group (46.1+/-10.9/microliter). On day 3, mean CD34+ cell counts of the subjects who received sequential treatment were markedly higher than observed in the other groups (p<0.05) and were estimated to have been sufficient for collection of adequate grafts by single 10-L leukapheresis procedures in 60% of subjects. Circulating clonogenic cells (CFU-GM and/or BFU-E) were substantially higher in the sequential group than the rhG-CSF group on days 3-6 but were only minimally elevated above baseline in the partial overlap group. The numbers of circulating CD34+/Lin-/Thy-1+ cells (putative stem cells) were increased substantially, especially in the sequential group. On the basis of this pilot trial, we conclude that priming with rhIL-3 is a safe and well-tolerated method for enhancing the mobilization of human blood progenitors and stem cells by rhG-CSF.

Efficient methods for overlapping group lasso.

PubMed

Yuan, Lei; Liu, Jun; Ye, Jieping

2013-09-01

The group Lasso is an extension of the Lasso for feature selection on (predefined) nonoverlapping groups of features. The nonoverlapping group structure limits its applicability in practice. There have been several recent attempts to study a more general formulation where groups of features are given, potentially with overlaps between the groups. The resulting optimization is, however, much more challenging to solve due to the group overlaps. In this paper, we consider the efficient optimization of the overlapping group Lasso penalized problem. We reveal several key properties of the proximal operator associated with the overlapping group Lasso, and compute the proximal operator by solving the smooth and convex dual problem, which allows the use of the gradient descent type of algorithms for the optimization. Our methods and theoretical results are then generalized to tackle the general overlapping group Lasso formulation based on the l(q) norm. We further extend our algorithm to solve a nonconvex overlapping group Lasso formulation based on the capped norm regularization, which reduces the estimation bias introduced by the convex penalty. We have performed empirical evaluations using both a synthetic and the breast cancer gene expression dataset, which consists of 8,141 genes organized into (overlapping) gene sets. Experimental results show that the proposed algorithm is more efficient than existing state-of-the-art algorithms. Results also demonstrate the effectiveness of the nonconvex formulation for overlapping group Lasso.

Ubiquitous information for ubiquitous computing: expressing clinical data sets with openEHR archetypes.

PubMed

Garde, Sebastian; Hovenga, Evelyn; Buck, Jasmin; Knaup, Petra

2006-01-01

Ubiquitous computing requires ubiquitous access to information and knowledge. With the release of openEHR Version 1.0 there is a common model available to solve some of the problems related to accessing information and knowledge by improving semantic interoperability between clinical systems. Considerable work has been undertaken by various bodies to standardise Clinical Data Sets. Notwithstanding their value, several problems remain unsolved with Clinical Data Sets without the use of a common model underpinning them. This paper outlines these problems like incompatible basic data types and overlapping and incompatible definitions of clinical content. A solution to this based on openEHR archetypes is motivated and an approach to transform existing Clinical Data Sets into archetypes is presented. To avoid significant overlaps and unnecessary effort during archetype development, archetype development needs to be coordinated nationwide and beyond and also across the various health professions in a formalized process.

A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa.

PubMed

Ficklin, Stephen P; Feltus, Frank Alex

2013-01-01

Many traits of biological and agronomic significance in plants are controlled in a complex manner where multiple genes and environmental signals affect the expression of the phenotype. In Oryza sativa (rice), thousands of quantitative genetic signals have been mapped to the rice genome. In parallel, thousands of gene expression profiles have been generated across many experimental conditions. Through the discovery of networks with real gene co-expression relationships, it is possible to identify co-localized genetic and gene expression signals that implicate complex genotype-phenotype relationships. In this work, we used a knowledge-independent, systems genetics approach, to discover a high-quality set of co-expression networks, termed Gene Interaction Layers (GILs). Twenty-two GILs were constructed from 1,306 Affymetrix microarray rice expression profiles that were pre-clustered to allow for improved capture of gene co-expression relationships. Functional genomic and genetic data, including over 8,000 QTLs and 766 phenotype-tagged SNPs (p-value < = 0.001) from genome-wide association studies, both covering over 230 different rice traits were integrated with the GILs. An online systems genetics data-mining resource, the GeneNet Engine, was constructed to enable dynamic discovery of gene sets (i.e. network modules) that overlap with genetic traits. GeneNet Engine does not provide the exact set of genes underlying a given complex trait, but through the evidence of gene-marker correspondence, co-expression, and functional enrichment, site visitors can identify genes with potential shared causality for a trait which could then be used for experimental validation. A set of 2 million SNPs was incorporated into the database and serve as a potential set of testable biomarkers for genes in modules that overlap with genetic traits. Herein, we describe two modules found using GeneNet Engine, one with significant overlap with the trait amylose content and another with significant overlap with blast disease resistance.

A Systems-Genetics Approach and Data Mining Tool to Assist in the Discovery of Genes Underlying Complex Traits in Oryza sativa

PubMed Central

Ficklin, Stephen P.; Feltus, Frank Alex

2013-01-01

Many traits of biological and agronomic significance in plants are controlled in a complex manner where multiple genes and environmental signals affect the expression of the phenotype. In Oryza sativa (rice), thousands of quantitative genetic signals have been mapped to the rice genome. In parallel, thousands of gene expression profiles have been generated across many experimental conditions. Through the discovery of networks with real gene co-expression relationships, it is possible to identify co-localized genetic and gene expression signals that implicate complex genotype-phenotype relationships. In this work, we used a knowledge-independent, systems genetics approach, to discover a high-quality set of co-expression networks, termed Gene Interaction Layers (GILs). Twenty-two GILs were constructed from 1,306 Affymetrix microarray rice expression profiles that were pre-clustered to allow for improved capture of gene co-expression relationships. Functional genomic and genetic data, including over 8,000 QTLs and 766 phenotype-tagged SNPs (p-value < = 0.001) from genome-wide association studies, both covering over 230 different rice traits were integrated with the GILs. An online systems genetics data-mining resource, the GeneNet Engine, was constructed to enable dynamic discovery of gene sets (i.e. network modules) that overlap with genetic traits. GeneNet Engine does not provide the exact set of genes underlying a given complex trait, but through the evidence of gene-marker correspondence, co-expression, and functional enrichment, site visitors can identify genes with potential shared causality for a trait which could then be used for experimental validation. A set of 2 million SNPs was incorporated into the database and serve as a potential set of testable biomarkers for genes in modules that overlap with genetic traits. Herein, we describe two modules found using GeneNet Engine, one with significant overlap with the trait amylose content and another with significant overlap with blast disease resistance. PMID:23874666

Redundancy control in pathway databases (ReCiPa): an application for improving gene-set enrichment analysis in Omics studies and "Big data" biology.

PubMed

Vivar, Juan C; Pemu, Priscilla; McPherson, Ruth; Ghosh, Sujoy

2013-08-01

Abstract Unparalleled technological advances have fueled an explosive growth in the scope and scale of biological data and have propelled life sciences into the realm of "Big Data" that cannot be managed or analyzed by conventional approaches. Big Data in the life sciences are driven primarily via a diverse collection of 'omics'-based technologies, including genomics, proteomics, metabolomics, transcriptomics, metagenomics, and lipidomics. Gene-set enrichment analysis is a powerful approach for interrogating large 'omics' datasets, leading to the identification of biological mechanisms associated with observed outcomes. While several factors influence the results from such analysis, the impact from the contents of pathway databases is often under-appreciated. Pathway databases often contain variously named pathways that overlap with one another to varying degrees. Ignoring such redundancies during pathway analysis can lead to the designation of several pathways as being significant due to high content-similarity, rather than truly independent biological mechanisms. Statistically, such dependencies also result in correlated p values and overdispersion, leading to biased results. We investigated the level of redundancies in multiple pathway databases and observed large discrepancies in the nature and extent of pathway overlap. This prompted us to develop the application, ReCiPa (Redundancy Control in Pathway Databases), to control redundancies in pathway databases based on user-defined thresholds. Analysis of genomic and genetic datasets, using ReCiPa-generated overlap-controlled versions of KEGG and Reactome pathways, led to a reduction in redundancy among the top-scoring gene-sets and allowed for the inclusion of additional gene-sets representing possibly novel biological mechanisms. Using obesity as an example, bioinformatic analysis further demonstrated that gene-sets identified from overlap-controlled pathway databases show stronger evidence of prior association to obesity compared to pathways identified from the original databases.

A non-orthogonal decomposition of flows into discrete events

NASA Astrophysics Data System (ADS)

Boxx, Isaac; Lewalle, Jacques

1998-11-01

This work is based on the formula for the inverse Hermitian wavelet transform. A signal can be interpreted as a (non-unique) superposition of near-singular, partially overlapping events arising from Dirac functions and/or its derivatives combined with diffusion.( No dynamics implied: dimensionless diffusion is related to the definition of the analyzing wavelets.) These events correspond to local maxima of spectral energy density. We successfully fitted model events of various orders on a succession of fields, ranging from elementary signals to one-dimensional hot-wire traces. We document edge effects, event overlap and its implications on the algorithm. The interpretation of the discrete singularities as flow events (such as coherent structures) and the fundamental non-uniqueness of the decomposition are discussed. The dynamics of these events will be examined in the companion paper.

A simple spatiotemporal rabies model for skunk and bat interaction in northeast Texas.

PubMed

Borchering, Rebecca K; Liu, Hao; Steinhaus, Mara C; Gardner, Carl L; Kuang, Yang

2012-12-07

We formulate a simple partial differential equation model in an effort to qualitatively reproduce the spread dynamics and spatial pattern of rabies in northeast Texas with overlapping reservoir species (skunks and bats). Most existing models ignore reservoir species or model them with patchy models by ordinary differential equations. In our model, we incorporate interspecies rabies infection in addition to rabid population random movement. We apply this model to the confirmed case data from northeast Texas with most parameter values obtained or computed from the literature. Results of simulations using both our skunk-only model and our skunk and bat model demonstrate that the model with overlapping reservoir species more accurately reproduces the progression of rabies spread in northeast Texas. Copyright © 2012 Elsevier Ltd. All rights reserved.

Holographic measurement of distortion during laser melting: Additive distortion from overlapping pulses

NASA Astrophysics Data System (ADS)

Haglund, Peter; Frostevarg, Jan; Powell, John; Eriksson, Ingemar; Kaplan, Alexander F. H.

2018-03-01

Laser - material interactions such as welding, heat treatment and thermal bending generate thermal gradients which give rise to thermal stresses and strains which often result in a permanent distortion of the heated object. This paper investigates the thermal distortion response which results from pulsed laser surface melting of a stainless steel sheet. Pulsed holography has been used to accurately monitor, in real time, the out-of-plane distortion of stainless steel samples melted on one face by with both single and multiple laser pulses. It has been shown that surface melting by additional laser pulses increases the out of plane distortion of the sample without significantly increasing the melt depth. The distortion differences between the primary pulse and subsequent pulses has also been analysed for fully and partially overlapping laser pulses.

Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction.

PubMed

Palmer, Lance E; Dejori, Mathaeus; Bolanos, Randall; Fasulo, Daniel

2010-01-15

With the rapid expansion of DNA sequencing databases, it is now feasible to identify relevant information from prior sequencing projects and completed genomes and apply it to de novo sequencing of new organisms. As an example, this paper demonstrates how such extra information can be used to improve de novo assemblies by augmenting the overlapping step. Finding all pairs of overlapping reads is a key task in many genome assemblers, and to this end, highly efficient algorithms have been developed to find alignments in large collections of sequences. It is well known that due to repeated sequences, many aligned pairs of reads nevertheless do not overlap. But no overlapping algorithm to date takes a rigorous approach to separating aligned but non-overlapping read pairs from true overlaps. We present an approach that extends the Minimus assembler by a data driven step to classify overlaps as true or false prior to contig construction. We trained several different classification models within the Weka framework using various statistics derived from overlaps of reads available from prior sequencing projects. These statistics included percent mismatch and k-mer frequencies within the overlaps as well as a comparative genomics score derived from mapping reads to multiple reference genomes. We show that in real whole-genome sequencing data from the E. coli and S. aureus genomes, by providing a curated set of overlaps to the contigging phase of the assembler, we nearly doubled the median contig length (N50) without sacrificing coverage of the genome or increasing the number of mis-assemblies. Machine learning methods that use comparative and non-comparative features to classify overlaps as true or false can be used to improve the quality of a sequence assembly.

DVS-SOFTWARE: An Effective Tool for Applying Highly Parallelized Hardware To Computational Geophysics

NASA Astrophysics Data System (ADS)

Herrera, I.; Herrera, G. S.

2015-12-01

Most geophysical systems are macroscopic physical systems. The behavior prediction of such systems is carried out by means of computational models whose basic models are partial differential equations (PDEs) [1]. Due to the enormous size of the discretized version of such PDEs it is necessary to apply highly parallelized super-computers. For them, at present, the most efficient software is based on non-overlapping domain decomposition methods (DDM). However, a limiting feature of the present state-of-the-art techniques is due to the kind of discretizations used in them. Recently, I. Herrera and co-workers using 'non-overlapping discretizations' have produced the DVS-Software which overcomes this limitation [2]. The DVS-software can be applied to a great variety of geophysical problems and achieves very high parallel efficiencies (90%, or so [3]). It is therefore very suitable for effectively applying the most advanced parallel supercomputers available at present. In a parallel talk, in this AGU Fall Meeting, Graciela Herrera Z. will present how this software is being applied to advance MOD-FLOW. Key Words: Parallel Software for Geophysics, High Performance Computing, HPC, Parallel Computing, Domain Decomposition Methods (DDM)REFERENCES [1]. Herrera Ismael and George F. Pinder, Mathematical Modelling in Science and Engineering: An axiomatic approach", John Wiley, 243p., 2012. [2]. Herrera, I., de la Cruz L.M. and Rosas-Medina A. "Non Overlapping Discretization Methods for Partial, Differential Equations". NUMER METH PART D E, 30: 1427-1454, 2014, DOI 10.1002/num 21852. (Open source) [3]. Herrera, I., & Contreras Iván "An Innovative Tool for Effectively Applying Highly Parallelized Software To Problems of Elasticity". Geofísica Internacional, 2015 (In press)

Efficient and Flexible Computation of Many-Electron Wave Function Overlaps.

PubMed

Plasser, Felix; Ruckenbauer, Matthias; Mai, Sebastian; Oppel, Markus; Marquetand, Philipp; González, Leticia

2016-03-08

A new algorithm for the computation of the overlap between many-electron wave functions is described. This algorithm allows for the extensive use of recurring intermediates and thus provides high computational efficiency. Because of the general formalism employed, overlaps can be computed for varying wave function types, molecular orbitals, basis sets, and molecular geometries. This paves the way for efficiently computing nonadiabatic interaction terms for dynamics simulations. In addition, other application areas can be envisaged, such as the comparison of wave functions constructed at different levels of theory. Aside from explaining the algorithm and evaluating the performance, a detailed analysis of the numerical stability of wave function overlaps is carried out, and strategies for overcoming potential severe pitfalls due to displaced atoms and truncated wave functions are presented.

Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation

PubMed Central

Kozhuharova, Ana; Sharma, Harshita; Ohyama, Takako; Fasolo, Francesca; Yamazaki, Toshio; Cotella, Diego; Santoro, Claudio; Zucchelli, Silvia; Gustincich, Stefano; Carninci, Piero

2018-01-01

SINEUPs are antisense long noncoding RNAs, in which an embedded SINE B2 element UP-regulates translation of partially overlapping target sense mRNAs. SINEUPs contain two functional domains. First, the binding domain (BD) is located in the region antisense to the target, providing specific targeting to the overlapping mRNA. Second, the inverted SINE B2 represents the effector domain (ED) and enhances translation. To adapt SINEUP technology to a broader number of targets, we took advantage of a high-throughput, semi-automated imaging system to optimize synthetic SINEUP BD and ED design in HEK293T cell lines. Using SINEUP-GFP as a model SINEUP, we extensively screened variants of the BD to map features needed for optimal design. We found that most active SINEUPs overlap an AUG-Kozak sequence. Moreover, we report our screening of the inverted SINE B2 sequence to identify active sub-domains and map the length of the minimal active ED. Our synthetic SINEUP-GFP screening of both BDs and EDs constitutes a broad test with flexible applications to any target gene of interest. PMID:29414979

Improved Wallis Dodging Algorithm for Large-Scale Super-Resolution Reconstruction Remote Sensing Images.

PubMed

Fan, Chong; Chen, Xushuai; Zhong, Lei; Zhou, Min; Shi, Yun; Duan, Yulin

2017-03-18

A sub-block algorithm is usually applied in the super-resolution (SR) reconstruction of images because of limitations in computer memory. However, the sub-block SR images can hardly achieve a seamless image mosaicking because of the uneven distribution of brightness and contrast among these sub-blocks. An effectively improved weighted Wallis dodging algorithm is proposed, aiming at the characteristic that SR reconstructed images are gray images with the same size and overlapping region. This algorithm can achieve consistency of image brightness and contrast. Meanwhile, a weighted adjustment sequence is presented to avoid the spatial propagation and accumulation of errors and the loss of image information caused by excessive computation. A seam line elimination method can share the partial dislocation in the seam line to the entire overlapping region with a smooth transition effect. Subsequently, the improved method is employed to remove the uneven illumination for 900 SR reconstructed images of ZY-3. Then, the overlapping image mosaic method is adopted to accomplish a seamless image mosaic based on the optimal seam line.

Strategies for controlling item exposure in computerized adaptive testing with the partial credit model.

PubMed

Davis, Laurie Laughlin; Dodd, Barbara G

2008-01-01

Exposure control research with polytomous item pools has determined that randomization procedures can be very effective for controlling test security in computerized adaptive testing (CAT). The current study investigated the performance of four procedures for controlling item exposure in a CAT under the partial credit model. In addition to a no exposure control baseline condition, the Kingsbury-Zara, modified-within-.10-logits, Sympson-Hetter, and conditional Sympson-Hetter procedures were implemented to control exposure rates. The Kingsbury-Zara and the modified-within-.10-logits procedures were implemented with 3 and 6 item candidate conditions. The results show that the Kingsbury-Zara and modified-within-.10-logits procedures with 6 item candidates performed as well as the conditional Sympson-Hetter in terms of exposure rates, overlap rates, and pool utilization. These two procedures are strongly recommended for use with partial credit CATs due to their simplicity and strength of their results.

Novel rabies virus-neutralizing epitope recognized by human monoclonal antibody: fine mapping and escape mutant analysis.

PubMed

Marissen, Wilfred E; Kramer, R Arjen; Rice, Amy; Weldon, William C; Niezgoda, Michael; Faber, Milosz; Slootstra, Jerry W; Meloen, Rob H; Clijsters-van der Horst, Marieke; Visser, Therese J; Jongeneelen, Mandy; Thijsse, Sandra; Throsby, Mark; de Kruif, John; Rupprecht, Charles E; Dietzschold, Bernhard; Goudsmit, Jaap; Bakker, Alexander B H

2005-04-01

Anti-rabies virus immunoglobulin combined with rabies vaccine protects humans from lethal rabies infections. For cost and safety reasons, replacement of the human or equine polyclonal immunoglobulin is advocated, and the use of rabies virus-specific monoclonal antibodies (MAbs) is recommended. We produced two previously described potent rabies virus-neutralizing human MAbs, CR57 and CRJB, in human PER.C6 cells. The two MAbs competed for binding to rabies virus glycoprotein. Using CR57 and a set of 15-mer overlapping peptides covering the glycoprotein ectodomain, a neutralization domain was identified between amino acids (aa) 218 and 240. The minimal binding region was identified as KLCGVL (aa 226 to 231), with key residues K-CGV- identified by alanine replacement scanning. The critical binding region of this novel nonconformational rabies virus epitope is highly conserved within rabies viruses of genotype 1. Subsequently, we generated six rabies virus variants escaping neutralization by CR57 and six variants escaping CRJB. The CR57 escape mutants were only partially covered by CRJB, and all CRJB-resistant variants completely escaped neutralization by CR57. Without exception, the CR57-resistant variants showed a mutation at key residues within the defined minimal binding region, while the CRJB escape viruses showed a single mutation distant from the CR57 epitope (N182D) combined with mutations in the CR57 epitope. The competition between CR57 and CRJB, the in vitro escape profile, and the apparent overlap between the recognized epitopes argues against including both CR57 and CRJB in a MAb cocktail aimed at replacing classical immunoglobulin preparations.

Managing overlapping federal FMLA and state leave regulations.

PubMed

Grebowski, Lucinda S

2002-03-01

The overlap between the Family and Medical Leave Act and state leave laws can create complications. Employers, particularly those with multistate operations, may wish to consider an outsourced absence management system, which can remove the burden of day-to-day administration and the need to stay abreast of changing state regulations. However, employers cannot outsource the responsibility to set broad policy toward absence management.

Relative-Error-Covariance Algorithms

NASA Technical Reports Server (NTRS)

Bierman, Gerald J.; Wolff, Peter J.

1991-01-01

Two algorithms compute error covariance of difference between optimal estimates, based on data acquired during overlapping or disjoint intervals, of state of discrete linear system. Provides quantitative measure of mutual consistency or inconsistency of estimates of states. Relative-error-covariance concept applied, to determine degree of correlation between trajectories calculated from two overlapping sets of measurements and construct real-time test of consistency of state estimates based upon recently acquired data.

A New Method for Estimating the Variance Overlap between the Short and the Long Form of a Psychological Test

ERIC Educational Resources Information Center

Pfeiffer, Nils; Hagemann, Dirk; Backenstrass, Matthias

2011-01-01

In response to the low standards in short form development, Smith, McCarthy, and Anderson (2000) introduced a set of guidelines for the construction and evaluation of short forms of psychological tests. One of their recommendations requires researches to show that the variance overlap between the short form and its long form is adequate. This…

How many atoms are required to characterize accurately trajectory fluctuations of a protein?

NASA Astrophysics Data System (ADS)

Cukier, Robert I.

2010-06-01

Large molecules, whose thermal fluctuations sample a complex energy landscape, exhibit motions on an extended range of space and time scales. Principal component analysis (PCA) is often used to extract dominant motions that in proteins are typically domain motions. These motions are captured in the large eigenvalue (leading) principal components. There is also information in the small eigenvalues, arising from approximate linear dependencies among the coordinates. These linear dependencies suggest that instead of using all the atom coordinates to represent a trajectory, it should be possible to use a reduced set of coordinates with little loss in the information captured by the large eigenvalue principal components. In this work, methods that can monitor the correlation (overlap) between a reduced set of atoms and any number of retained principal components are introduced. For application to trajectory data generated by simulations, where the overall translational and rotational motion needs to be eliminated before PCA is carried out, some difficulties with the overlap measures arise and methods are developed to overcome them. The overlap measures are evaluated for a trajectory generated by molecular dynamics for the protein adenylate kinase, which consists of a stable, core domain, and two more mobile domains, referred to as the LID domain and the AMP-binding domain. The use of reduced sets corresponding, for the smallest set, to one-eighth of the alpha carbon (CA) atoms relative to using all the CA atoms is shown to predict the dominant motions of adenylate kinase. The overlap between using all the CA atoms and all the backbone atoms is essentially unity for a sum over PCA modes that effectively capture the exact trajectory. A reduction to a few atoms (three in the LID and three in the AMP-binding domain) shows that at least the first principal component, characterizing a large part of the LID-binding and AMP-binding motion, is well described. Based on these results, the overlap criterion should be applicable as a guide to postulating and validating coarse-grained descriptions of generic biomolecular assemblies.

Genomic analysis of filoviruses associated with four viral hemorrhagic fever outbreaks in Uganda and the Democratic Republic of the Congo in 2012.

PubMed

Albariño, C G; Shoemaker, T; Khristova, M L; Wamala, J F; Muyembe, J J; Balinandi, S; Tumusiime, A; Campbell, S; Cannon, D; Gibbons, A; Bergeron, E; Bird, B; Dodd, K; Spiropoulou, C; Erickson, B R; Guerrero, L; Knust, B; Nichol, S T; Rollin, P E; Ströher, U

2013-08-01

In 2012, an unprecedented number of four distinct, partially overlapping filovirus-associated viral hemorrhagic fever outbreaks were detected in equatorial Africa. Analysis of complete virus genome sequences confirmed the reemergence of Sudan virus and Marburg virus in Uganda, and the first emergence of Bundibugyo virus in the Democratic Republic of the Congo. Published by Elsevier Inc.

Implicit finite difference methods on composite grids

NASA Technical Reports Server (NTRS)

Mastin, C. Wayne

1987-01-01

Techniques for eliminating time lags in the implicit finite-difference solution of partial differential equations are investigated analytically, with a focus on transient fluid dynamics problems on overlapping multicomponent grids. The fundamental principles of the approach are explained, and the method is shown to be applicable to both rectangular and curvilinear grids. Numerical results for sample problems are compared with exact solutions in graphs, and good agreement is demonstrated.

CRISPR Detection From Short Reads Using Partial Overlap Graphs.

PubMed

Ben-Bassat, Ilan; Chor, Benny

2016-06-01

Clustered regularly interspaced short palindromic repeats (CRISPR) are structured regions in bacterial and archaeal genomes, which are part of an adaptive immune system against phages. CRISPRs are important for many microbial studies and are playing an essential role in current gene editing techniques. As such, they attract substantial research interest. The exponential growth in the amount of bacterial sequence data in recent years enables the exploration of CRISPR loci in more and more species. Most of the automated tools that detect CRISPR loci rely on fully assembled genomes. However, many assemblers do not handle repetitive regions successfully. The first tool to work directly on raw sequence data is Crass, which requires reads that are long enough to contain two copies of the same repeat. We present a method to identify CRISPR repeats from raw sequence data of short reads. The algorithm is based on an observation differentiating CRISPR repeats from other types of repeats, and it involves a series of partial constructions of the overlap graph. This enables us to avoid many of the difficulties that assemblers face, as we merely aim to identify the repeats that belong to CRISPR loci. A preliminary implementation of the algorithm shows good results and detects CRISPR repeats in cases where other existing tools fail to do so.

Speaking-rate-induced variability in F2 trajectories.

PubMed

Tjaden, K; Weismer, G

1998-10-01

This study examined speaking-rate-induced spectral and temporal variability of F2 formant trajectories for target words produced in a carrier phrase at speaking rates ranging from fast to slow. F2 onset frequency measured at the first glottal pulse following the stop consonant release in target words was used to quantify the extent to which adjacent consonantal and vocalic gestures overlapped; F2 target frequency was operationally defined as the first occurrence of a frequency minimum or maximum following F2 onset frequency. Regression analyses indicated 70% of functions relating F2 onset and vowel duration were statistically significant. The strength of the effect was variable, however, and the direction of significant functions often differed from that predicted by a simple model of overlapping, sliding gestures. Results of a partial correlation analysis examining interrelationships among F2 onset, F2 target frequency, and vowel duration across the speaking rate range indicated that covariation of F2 target with vowel duration may obscure the relationship between F2 onset and vowel duration across rate. The results further suggested that a sliding based model of acoustic variability associated with speaking rate change only partially accounts for the present data, and that such a view accounts for some speakers' data better than others.

Densities of L-Glutamic Acid HCl Drug in Aqueous NaCl and KCl Solutions at Different Temperatures

NASA Astrophysics Data System (ADS)

Ryshetti, Suresh; Raghuram, Noothi; Rani, Emmadi Jayanthi; Tangeda, Savitha Jyostna

2016-04-01

Densities (ρ ) of (0.01 to 0.07) {mol}{\\cdot } {kg}^{-1} L-Glutamic acid HCl (L-HCl) drug in water, and in aqueous NaCl and KCl (0.5 and 1.0) {mol}{\\cdot } {kg}^{-1} solutions have been reported as a function of temperature at T = (298.15, 303.15, 308.15, and 313.15) K and atmospheric pressure. The accurate density (ρ ) values are used to estimate the various parameters such as the apparent molar volume (V_{2,{\\upphi }}), the partial molar volume (V2^{∞}), the isobaric thermal expansion coefficient (α 2), the partial molar expansion (E2^{∞}), and Hepler's constant (partial 2V2^{∞}/partial T2)P. The Cosphere overlap model is used to understand the solute-solvent interactions in a ternary mixture (L-HCl drug + NaCl or KCl + water). Hepler's constant (partial 2V2^{∞}/partial T2)_P is utilized to interpret the structure-making or -breaking ability of L-HCl drug in aqueous NaCl and KCl solutions, and the results are inferred that L-HCl drug acts as a structure maker, i.e., kosmotrope in aqueous NaCl solutions and performs as a structure breaker, i.e., chaotrope in aqueous KCl solutions.

Percolation in multiplex networks with overlap.

PubMed

Cellai, Davide; López, Eduardo; Zhou, Jie; Gleeson, James P; Bianconi, Ginestra

2013-11-01

From transportation networks to complex infrastructures, and to social and communication networks, a large variety of systems can be described in terms of multiplexes formed by a set of nodes interacting through different networks (layers). Multiplexes may display an increased fragility with respect to the single layers that constitute them. However, so far the overlap of the links in different layers has been mostly neglected, despite the fact that it is an ubiquitous phenomenon in most multiplexes. Here, we show that the overlap among layers can improve the robustness of interdependent multiplex systems and change the critical behavior of the percolation phase transition in a complex way.

A reassessment of the evolutionary timescale of bat rabies viruses based upon glycoprotein gene sequences.

PubMed

Kuzmina, Natalia A; Kuzmin, Ivan V; Ellison, James A; Taylor, Steven T; Bergman, David L; Dew, Beverly; Rupprecht, Charles E

2013-10-01

Rabies, an acute progressive encephalomyelitis caused by viruses in the genus Lyssavirus, is one of the oldest known infectious diseases. Although dogs and other carnivores represent the greatest threat to public health as rabies reservoirs, it is commonly accepted that bats are the primary evolutionary hosts of lyssaviruses. Despite early historical documentation of rabies, molecular clock analyses indicate a quite young age of lyssaviruses, which is confusing. For example, the results obtained for partial and complete nucleoprotein gene sequences of rabies viruses (RABV), or for a limited number of glycoprotein gene sequences, indicated that the time of the most recent common ancestor (TMRCA) for current bat RABV diversity in the Americas lies in the seventeenth to eighteenth centuries and might be directly or indirectly associated with the European colonization. Conversely, several other reports demonstrated high genetic similarity between lyssavirus isolates, including RABV, obtained within a time interval of 25-50 years. In the present study, we attempted to re-estimate the age of several North American bat RABV lineages based on the largest set of complete and partial glycoprotein gene sequences compiled to date (n = 201) employing a codon substitution model. Although our results overlap with previous estimates in marginal areas of the 95 % high probability density (HPD), they suggest a longer evolutionary history of American bat RABV lineages (TMRCA at least 732 years, with a 95 % HPD 436-1107 years).

Overlapping Networks Engaged during Spoken Language Production and Its Cognitive Control

PubMed Central

Wise, Richard J.S.; Mehta, Amrish; Leech, Robert

2014-01-01

Spoken language production is a complex brain function that relies on large-scale networks. These include domain-specific networks that mediate language-specific processes, as well as domain-general networks mediating top-down and bottom-up attentional control. Language control is thought to involve a left-lateralized fronto-temporal-parietal (FTP) system. However, these regions do not always activate for language tasks and similar regions have been implicated in nonlinguistic cognitive processes. These inconsistent findings suggest that either the left FTP is involved in multidomain cognitive control or that there are multiple spatially overlapping FTP systems. We present evidence from an fMRI study using multivariate analysis to identify spatiotemporal networks involved in spoken language production in humans. We compared spoken language production (Speech) with multiple baselines, counting (Count), nonverbal decision (Decision), and “rest,” to pull apart the multiple partially overlapping networks that are involved in speech production. A left-lateralized FTP network was activated during Speech and deactivated during Count and nonverbal Decision trials, implicating it in cognitive control specific to sentential spoken language production. A mirror right-lateralized FTP network was activated in the Count and Decision trials, but not Speech. Importantly, a second overlapping left FTP network showed relative deactivation in Speech. These three networks, with distinct time courses, overlapped in the left parietal lobe. Contrary to the standard model of the left FTP as being dominant for speech, we revealed a more complex pattern within the left FTP, including at least two left FTP networks with competing functional roles, only one of which was activated in speech production. PMID:24966373

Overlapping networks engaged during spoken language production and its cognitive control.

PubMed

Geranmayeh, Fatemeh; Wise, Richard J S; Mehta, Amrish; Leech, Robert

2014-06-25

Spoken language production is a complex brain function that relies on large-scale networks. These include domain-specific networks that mediate language-specific processes, as well as domain-general networks mediating top-down and bottom-up attentional control. Language control is thought to involve a left-lateralized fronto-temporal-parietal (FTP) system. However, these regions do not always activate for language tasks and similar regions have been implicated in nonlinguistic cognitive processes. These inconsistent findings suggest that either the left FTP is involved in multidomain cognitive control or that there are multiple spatially overlapping FTP systems. We present evidence from an fMRI study using multivariate analysis to identify spatiotemporal networks involved in spoken language production in humans. We compared spoken language production (Speech) with multiple baselines, counting (Count), nonverbal decision (Decision), and "rest," to pull apart the multiple partially overlapping networks that are involved in speech production. A left-lateralized FTP network was activated during Speech and deactivated during Count and nonverbal Decision trials, implicating it in cognitive control specific to sentential spoken language production. A mirror right-lateralized FTP network was activated in the Count and Decision trials, but not Speech. Importantly, a second overlapping left FTP network showed relative deactivation in Speech. These three networks, with distinct time courses, overlapped in the left parietal lobe. Contrary to the standard model of the left FTP as being dominant for speech, we revealed a more complex pattern within the left FTP, including at least two left FTP networks with competing functional roles, only one of which was activated in speech production. Copyright © 2014 Geranmayeh et al.

Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach

DTIC Science & Technology

2012-01-01

target representatives. Target profiles were then generated for a given query molecule by computing maximal shape/ chemistry overlap between the query...molecule and the drug sets assigned to each protein target. The overlap was computed using the program ROCS (Rapid Overlay of Chemical Structures ). We...approaches in off-target prediction has been reviewed.9,10 Many structure -based target fishing (SBTF) approaches, such as INVDOCK11 and Target Fishing Dock

Volumetric applications for spiral CT in the thorax

NASA Astrophysics Data System (ADS)

Rubin, Geoffrey D.; Napel, Sandy; Leung, Ann N.

1994-05-01

Spiral computed tomography (CT) is a new technique for rapidly acquiring volumetric data within the body. By combining a continuous gantry rotation and table feed, it is possible to image the entire thorax within a single breath-hold. This eliminates the ventilatory misregistration seen with conventional thoracic CT, which can result in small pulmonary lesions being undetected. An additional advantage of a continuous data set is that axial sections can be reconstructed at arbitrary intervals along the spiral path, resulting in the generation of overlapping sections which diminish partial volume effects resulting from lesions that straddle adjacent sections. The rapid acquisition of spiral CT enables up to a 50% reduction in the total iodinated contrast dose required for routine thoracic CT scanning. This can be very important for imaging patients with cardiac and renal diseases and could reduce the cost of thoracic CT scanning. Alternatively, by combining a high flow peripheral intravenous iodinated contrast injection with a spiral CT acquisition, it is possible to obtain images of the vasculature, which demonstrate pulmonary arterial thrombi, aortic aneurysms and dissections, and congenital vascular anomalies in detail previously unattainable without direct arterial access.

Analysis of the polarization observables H and P for γ-> p -> ->π+ n

NASA Astrophysics Data System (ADS)

Lee, Robert J.; Ritchie, B. G.; Dugger, M.; CLAS Collaboration

2017-09-01

A search is underway to find baryon resonances that have been predicted, but yet remain unobserved. Nucleon resonances, due to their broad energy widths, overlap and must be disentangled in order to be identified. Meson photoproduction observables related to the orientation of the spin of the incoming photon and the spin of the target proton are useful tools to deconvolute the nucleon resonance spectrum. These observables are particularly sensitive to interference between phases of the complex amplitudes. A set of these observables has been measured using the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab with linearly-polarized photons having energies from 725 to 2100 MeV with polar angle values of cos (θC . M .) between 1 and -0.8 and transversely-polarized protons in the Jefferson Lab FRozen Spin Target (FROST). By fitting π+ yields over azimuthal scattering angle, the observables H and P have been extracted. Preliminary results for these observables will be presented and compared with predictions provided by SAID Partial-Wave Analysis Facility. Work at ASU is supported by the U.S. National Science Foundation.

Biological adaptations for functional features of language in the face of cultural evolution.

PubMed

Christiansen, Morten H; Reali, Florencia; Chater, Nick

2011-04-01

Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely to be an innate universal grammar evolved through biological adaptations for arbitrary linguistic features. Instead, it has been suggested that the patterns of resemblance emerge because language has been shaped by the brain, with individual languages representing different but partially overlapping solutions to the same set of nonlinguistic constraints. Here, we use computational simulations to investigate whether biological adaptation for functional features of language, deriving from cognitive and communicative constraints, may nonetheless be possible alongside rapid cultural evolution. Specifically, we focus on the Baldwin effect as an evolutionary mechanism by which previously learned linguistic features might become innate through natural selection across many generations of language users. The results indicate that cultural evolution of language does not necessarily prevent functional features of language from becoming genetically fixed, thus potentially providing a particularly informative source of constraints on cross-linguistic resemblance patterns.

A search for pre-main-sequence stars in high-latitude molecular clouds. 3: A survey of the Einstein database

NASA Technical Reports Server (NTRS)

Caillault, Jean-Pierre; Magnani, Loris; Fryer, Chris

1995-01-01

In order to discern whether the high-latitude molecular clouds are regions of ongoing star formation, we have used X-ray emission as a tracer of youthful stars. The entire Einstein database yields 18 images which overlap 10 of the clouds mapped partially or completely in the CO (1-0) transition, providing a total of approximately 6 deg squared of overlap. Five previously unidentified X-ray sources were detected: one has an optical counterpart which is a pre-main-sequence (PMS) star, and two have normal main-sequence stellar counterparts, while the other two are probably extragalactic sources. The PMS star is located in a high Galactic latitude Lynds dark cloud, so this result is not too suprising. The translucent clouds, though, have yet to reveal any evidence of star formation.

Ray tracing a three dimensional scene using a grid

DOEpatents

Wald, Ingo; Ize, Santiago; Parker, Steven G; Knoll, Aaron

2013-02-26

Ray tracing a three-dimensional scene using a grid. One example embodiment is a method for ray tracing a three-dimensional scene using a grid. In this example method, the three-dimensional scene is made up of objects that are spatially partitioned into a plurality of cells that make up the grid. The method includes a first act of computing a bounding frustum of a packet of rays, and a second act of traversing the grid slice by slice along a major traversal axis. Each slice traversal includes a first act of determining one or more cells in the slice that are overlapped by the frustum and a second act of testing the rays in the packet for intersection with any objects at least partially bounded by the one or more cells overlapped by the frustum.

STBase: one million species trees for comparative biology.

PubMed

McMahon, Michelle M; Deepak, Akshay; Fernández-Baca, David; Boss, Darren; Sanderson, Michael J

2015-01-01

Comprehensively sampled phylogenetic trees provide the most compelling foundations for strong inferences in comparative evolutionary biology. Mismatches are common, however, between the taxa for which comparative data are available and the taxa sampled by published phylogenetic analyses. Moreover, many published phylogenies are gene trees, which cannot always be adapted immediately for species level comparisons because of discordance, gene duplication, and other confounding biological processes. A new database, STBase, lets comparative biologists quickly retrieve species level phylogenetic hypotheses in response to a query list of species names. The database consists of 1 million single- and multi-locus data sets, each with a confidence set of 1000 putative species trees, computed from GenBank sequence data for 413,000 eukaryotic taxa. Two bodies of theoretical work are leveraged to aid in the assembly of multi-locus concatenated data sets for species tree construction. First, multiply labeled gene trees are pruned to conflict-free singly-labeled species-level trees that can be combined between loci. Second, impacts of missing data in multi-locus data sets are ameliorated by assembling only decisive data sets. Data sets overlapping with the user's query are ranked using a scheme that depends on user-provided weights for tree quality and for taxonomic overlap of the tree with the query. Retrieval times are independent of the size of the database, typically a few seconds. Tree quality is assessed by a real-time evaluation of bootstrap support on just the overlapping subtree. Associated sequence alignments, tree files and metadata can be downloaded for subsequent analysis. STBase provides a tool for comparative biologists interested in exploiting the most relevant sequence data available for the taxa of interest. It may also serve as a prototype for future species tree oriented databases and as a resource for assembly of larger species phylogenies from precomputed trees.

Controlled Teleportation of a Qudit State by Partially Entangled GHZ States

NASA Astrophysics Data System (ADS)

Wang, Jin-wei; Shu, Lan; Mo, Zhi-wen; Zhang, Zhi-hua

2014-08-01

In this paper, we propose a controlled teleportation scheme which communicates an arbitrary ququart state via two sets of partially entangled GHZ state. The necessary measurements and operations are given detailedly. Furthmore the scheme is generalized to teleport a qudit state via s sets of partially entangled GHZ state.

Impact of flavor attributes on consumer liking of Swiss cheese.

PubMed

Liggett, R E; Drake, M A; Delwiche, J F

2008-02-01

Although Swiss cheese is growing in popularity, no research has examined what flavor characteristics consumers desire in Swiss cheese, which was the main objective of this study. To this end, a large group of commercially available Swiss-type cheeses (10 domestic Swiss cheeses, 4 domestic Baby Swiss cheeses, and one imported Swiss Emmenthal) were assessed both by 12 trained panelists for flavor and feeling factors and by 101 consumers for overall liking. In addition, a separate panel of 24 consumers rated the same cheeses for dissimilarity. On the basis of liking ratings, the 101 consumers were segmented by cluster analysis into 2 groups: nondistinguishers (n = 40) and varying responders (n = 61). Partial least squares regression, a statistical modeling technique that relates 2 data sets (in this case, a set of descriptive analysis data and a set of consumer liking data), was used to determine which flavor attributes assessed by the trained panel were important variables in overall liking of the cheeses for the varying responders. The model explained 93% of the liking variance on 3 normally distributed components and had 49% predictability. Diacetyl, whey, milk fat, and umami were found to be drivers of liking, whereas cabbage, cooked, and vinegar were drivers of disliking. Nutty flavor was not particularly important to liking and it was present in only 2 of the cheeses. The dissimilarity ratings were combined with the liking ratings of both segments and analyzed by probabilistic multidimensional scaling. The ideals of each segment completely overlapped, with the variance of the varying responders being smaller than the variance of the non-distinguishers. This model indicated that the Baby Swiss cheeses were closer to the consumers' ideals than were the other cheeses. Taken together, the 2 models suggest that the partial least squares regression failed to capture one or more attributes that contribute to consumer acceptance, although the descriptive analysis of flavor and feeling factors was able to account for 93% of the variance in the liking ratings. These findings indicate the flavor characteristics Swiss cheese producers should optimize, and minimize, to create cheeses that best match consumer desires.

Towards developing robust algorithms for solving partial differential equations on MIMD machines

NASA Technical Reports Server (NTRS)

Saltz, Joel H.; Naik, Vijay K.

1988-01-01

Methods for efficient computation of numerical algorithms on a wide variety of MIMD machines are proposed. These techniques reorganize the data dependency patterns to improve the processor utilization. The model problem finds the time-accurate solution to a parabolic partial differential equation discretized in space and implicitly marched forward in time. The algorithms are extensions of Jacobi and SOR. The extensions consist of iterating over a window of several timesteps, allowing efficient overlap of computation with communication. The methods increase the degree to which work can be performed while data are communicated between processors. The effect of the window size and of domain partitioning on the system performance is examined both by implementing the algorithm on a simulated multiprocessor system.

Towards developing robust algorithms for solving partial differential equations on MIMD machines

NASA Technical Reports Server (NTRS)

Saltz, J. H.; Naik, V. K.

1985-01-01

Methods for efficient computation of numerical algorithms on a wide variety of MIMD machines are proposed. These techniques reorganize the data dependency patterns to improve the processor utilization. The model problem finds the time-accurate solution to a parabolic partial differential equation discretized in space and implicitly marched forward in time. The algorithms are extensions of Jacobi and SOR. The extensions consist of iterating over a window of several timesteps, allowing efficient overlap of computation with communication. The methods increase the degree to which work can be performed while data are communicated between processors. The effect of the window size and of domain partitioning on the system performance is examined both by implementing the algorithm on a simulated multiprocessor system.

Top-d Rank Aggregation in Web Meta-search Engine

NASA Astrophysics Data System (ADS)

Fang, Qizhi; Xiao, Han; Zhu, Shanfeng

In this paper, we consider the rank aggregation problem for information retrieval over Web making use of a kind of metric, the coherence, which considers both the normalized Kendall-τ distance and the size of overlap between two partial rankings. In general, the top-d coherence aggregation problem is defined as: given collection of partial rankings Π = {τ 1,τ 2, ⋯ , τ K }, how to find a final ranking π with specific length d, which maximizes the total coherence Φ(π,Pi)=sum_{i=1}^K Φ(π,tau_i). The corresponding complexity and algorithmic issues are discussed in this paper. Our main technical contribution is a polynomial time approximation scheme (PTAS) for a restricted top-d coherence aggregation problem.

On the optimization of mitred overlaps in transformer cores

NASA Astrophysics Data System (ADS)

Bengtsson, C.; Pfützner, H.; Schönhuber, P.

1989-05-01

The influence of the overlap length a on the no-load loss P and excitation power S of single phase model cores was measured for different sheet widths w. It was found that the optimum overlap length a0 shows a non-linear increase with w. The appearance of such minima, however, was irregular, and in many cases, the lowest no-load loss was obtained at the smallest investigated overlap length, an effect which may result from the assembling conditions. Minima in P will appear as a consequence of a balance between loss contributions resulting from normal flux in the overlap region, from increased longitudinal flux due to flux transfer between sheets, and from the triangular cut-outs at the inner corners of the cores. However, the dependence of a0 on w is attributed only to the triangular cut-outs. The flatness of the minima in combination with their irregular appearance, makes the effect difficult to be used in practice. It is concluded that in power transformers, the overlap length should be chosen as small as possible within the limitations set by stability requirements of the core. This is especially important in cores with a high operating flux density.

Scoring the correlation of genes by their shared properties using OScal, an improved overlap quantification model.

PubMed

Liu, Hui; Liu, Wei; Lin, Ying; Liu, Teng; Ma, Zhaowu; Li, Mo; Zhang, Hong-Mei; Kenneth Wang, Qing; Guo, An-Yuan

2015-05-27

Scoring the correlation between two genes by their shared properties is a common and basic work in biological study. A prospective way to score this correlation is to quantify the overlap between the two sets of homogeneous properties of the two genes. However the proper model has not been decided, here we focused on studying the quantification of overlap and proposed a more effective model after theoretically compared 7 existing models. We defined three characteristic parameters (d, R, r) of an overlap, which highlight essential differences among the 7 models and grouped them into two classes. Then the pros and cons of the two groups of model were fully examined by their solution space in the (d, R, r) coordinate system. Finally we proposed a new model called OScal (Overlap Score calculator), which was modified on Poisson distribution (one of 7 models) to avoid its disadvantages. Tested in assessing gene relation using different data, OScal performs better than existing models. In addition, OScal is a basic mathematic model, with very low computation cost and few restrictive conditions, so it can be used in a wide-range of research areas to measure the overlap or similarity of two entities.

Tuning the overlap and the cross-layer correlations in two-layer networks: Application to a susceptible-infectious-recovered model with awareness dissemination

NASA Astrophysics Data System (ADS)

Juher, David; Saldaña, Joan

2018-03-01

We study the properties of the potential overlap between two networks A ,B sharing the same set of N nodes (a two-layer network) whose respective degree distributions pA(k ) ,pB(k ) are given. Defining the overlap coefficient α as the Jaccard index, we prove that α is very close to 0 when A and B are random and independently generated. We derive an upper bound αM for the maximum overlap coefficient permitted in terms of pA(k ) , pB(k ) , and N . Then we present an algorithm based on cross rewiring of links to obtain a two-layer network with any prescribed α inside the range (0 ,αM) . A refined version of the algorithm allows us to minimize the cross-layer correlations that unavoidably appear for values of α beyond a critical overlap αc<αM . Finally, we present a very simple example of a susceptible-infectious-recovered epidemic model with information dissemination and use the algorithms to determine the impact of the overlap on the final outbreak size predicted by the model.

Correcting Evaluation Bias of Relational Classifiers with Network Cross Validation

DTIC Science & Technology

2010-01-01

classi- fication algorithms: simple random resampling (RRS), equal-instance random resampling (ERS), and network cross-validation ( NCV ). The first two... NCV procedure that eliminates overlap between test sets altogether. The procedure samples for k disjoint test sets that will be used for evaluation...propLabeled ∗ S) nodes from train Pool in f erenceSet =network − trainSet F = F ∪ < trainSet, test Set, in f erenceSet > end for output: F NCV addresses

Coherent Radiative Control of Chemical Reactions

DTIC Science & Technology

1992-01-01

calculation. The criterion used i Cm to resrict the number of states to be included was that the overlaps Figure 10. Case i: Stimulated emission spectrum...is reflected in the fluorescence emission as quantum beats. It is well known that both the state created by photon excitation and any subsequent...Combining eqs. (4) and (5) gives the general expression for the fluo- rescence emission spectrum associated with a state created by a partially coherent

Towards Determination of Visual Requirements for Augmented Reality Displays and Virtual Environments for the Airport Tower

DTIC Science & Technology

2006-06-01

allowing substantial see-around capability. Regions of visual suppression due to binocular rivalry ( luning ) are shown along the shaded flanks of...that the visual suppression of binocular rivalry, luning , (Velger, 1998, p.56-58) associated with the partial overlap conditions did not materially...tags were displayed. Thus, the frequency of conflicting binocular contours was reduced. In any case, luning does not seem to introduce major

The multi-resolution capability of Tchebichef moments and its applications to the analysis of fluorescence excitation-emission spectra

NASA Astrophysics Data System (ADS)

Li, Bao Qiong; Wang, Xue; Li Xu, Min; Zhai, Hong Lin; Chen, Jing; Liu, Jin Jin

2018-01-01

Fluorescence spectroscopy with an excitation-emission matrix (EEM) is a fast and inexpensive technique and has been applied to the detection of a very wide range of analytes. However, serious scattering and overlapping signals hinder the applications of EEM spectra. In this contribution, the multi-resolution capability of Tchebichef moments was investigated in depth and applied to the analysis of two EEM data sets (data set 1 consisted of valine-tyrosine-valine, tryptophan-glycine and phenylalanine, and data set 2 included vitamin B1, vitamin B2 and vitamin B6) for the first time. By means of the Tchebichef moments with different orders, the different information in the EEM spectra can be represented. It is owing to this multi-resolution capability that the overlapping problem was solved, and the information of chemicals and scatterings were separated. The obtained results demonstrated that the Tchebichef moment method is very effective, which provides a promising tool for the analysis of EEM spectra. It is expected that the applications of Tchebichef moment method could be developed and extended in complex systems such as biological fluids, food, environment and others to deal with the practical problems (overlapped peaks, unknown interferences, baseline drifts, and so on) with other spectra.

Effect of Overlapping Operations on Outcomes in Microvascular Reconstructions of the Head and Neck.

PubMed

Sweeny, Larissa; Rosenthal, Eben L; Light, Tyler; Grayson, Jessica; Petrisor, Daniel; Troob, Scott H; Greene, Benjamin J; Carroll, William R; Wax, Mark K

2017-04-01

Objective To compare outcomes after microvascular reconstructions of head and neck defects between overlapping and nonoverlapping operations. Study Design Retrospective cohort study. Setting Tertiary care center. Subjects and Methods Patients undergoing microvascular free tissue transfer operations between January 2010 and February 2015 at 2 tertiary care institutions were included (n = 1315). Patients were divided into 2 cohorts by whether the senior authors performed a single or consecutive microvascular reconstruction (nonoverlapping; n = 773, 59%) vs performing overlapping microvascular reconstructions (overlapping; n = 542, 41%). Variables reviewed were as follows: defect location, indication, T classification, surgical details, duration of the operation and hospitalization, and complications (major, minor, medical). Results Microvascular free tissue transfers performed included radial forearm (49%, n = 639), osteocutaneous radial forearm (14%, n = 182), anterior lateral thigh (12%, n = 153), fibula (10%, n = 135), rectus abdominis (7%, n = 92), latissimus dorsi (6%, n = 78), and scapula (<1%, n = 4). The mean duration of the overlapping operations was 21 minutes longer than nonoverlapping operations ( P = .003). Mean duration of hospitalization was similar for nonoverlapping (9.5 days) and overlapping (9.1 days) cohorts ( P = .39). There was no difference in complication rates when stratified by overlapping (45%, n = 241) and nonoverlapping (45%, n = 344) ( P = .99). Subset analysis yielded similar results when minor, major, and medical complications between groups were assessed. The overall survival rate of free tissue transfers was 96%, and this was same for overlapping (96%) and nonoverlapping (96%) operations ( P = .71). Conclusions Patients had similar complication rates and durations of hospitalization for overlapping and nonoverlapping operations.

Long-range analysis of density fitting in extended systems

NASA Astrophysics Data System (ADS)

Varga, Scarontefan

Density fitting scheme is analyzed for the Coulomb problem in extended systems from the correctness of long-range behavior point of view. We show that for the correct cancellation of divergent long-range Coulomb terms it is crucial for the density fitting scheme to reproduce the overlap matrix exactly. It is demonstrated that from all possible fitting metric choices the Coulomb metric is the only one which inherently preserves the overlap matrix for infinite systems with translational periodicity. Moreover, we show that by a small additional effort any non-Coulomb metric fit can be made overlap-preserving as well. The problem is analyzed for both ordinary and Poisson basis set choices.

Drosophila innate immunity: regional and functional specialization of prophenoloxidases.

PubMed

Dudzic, Jan P; Kondo, Shu; Ueda, Ryu; Bergman, Casey M; Lemaitre, Bruno

2015-10-01

The diversification of immune systems during evolution involves the expansion of particular gene families in given phyla. A better understanding of the metazoan immune system requires an analysis of the logic underlying such immune gene amplification. This analysis is now within reach due to the ease with which we can generate multiple mutations in an organism. In this paper, we analyze the contribution of the three Drosophila prophenoloxidases (PPOs) to host defense by generating single, double and triple mutants. PPOs are enzymes that catalyze the production of melanin at the site of infection and around parasites. They are the rate-limiting enzymes that contribute to the melanization reaction, a major immune mechanism of arthropods. The number of PPO-encoding genes is variable among insects, ranging from one in the bee to ten in the mosquito. By analyzing mutations alone and in combination, we ascribe a specific function to each of the three PPOs of Drosophila. Our study confirms that two PPOs produced by crystal cells, PPO1 and PPO2, contribute to the bulk of melanization in the hemolymph, upon septic or clean injury. In contrast, PPO3, a PPO restricted to the D. melanogaster group, is expressed in lamellocytes and contributes to melanization during the encapsulation process. Interestingly, another overlapping set of PPOs, PPO2 and PPO3, achieve melanization of the capsule upon parasitoid wasp infection. The use of single or combined mutations allowed us to show that each PPO mutant has a specific phenotype, and that knocking out two of three genes is required to abolish fully a particular function. Thus, Drosophila PPOs have partially overlapping functions to optimize melanization in at least two conditions: following injury or during encapsulation. Since PPO3 is restricted to the D. melanogaster group, this suggests that production of PPO by lamellocytes emerged as a recent defense mechanism against parasitoid wasps. We conclude that differences in spatial localization, immediate or late availability, and mode of activation underlie the functional diversification of the three Drosophila PPOs, with each of them having non-redundant but overlapping functions.

Unified User Interface to Support Effective and Intuitive Data Discovery, Dissemination, and Analysis at NASA GES DISC

NASA Technical Reports Server (NTRS)

Petrenko, M.; Hegde, M.; Bryant, K.; Johnson, J. E.; Ritrivi, A.; Shen, S.; Volmer, B.; Pham, L. B.

2015-01-01

Goddard Earth Sciences Data and Information Services Center (GES DISC) has been providing access to scientific data sets since 1990s. Beginning as one of the first Earth Observing System Data and Information System (EOSDIS) archive centers, GES DISC has evolved to offer a wide range of science-enabling services. With a growing understanding of needs and goals of its science users, GES DISC continues to improve and expand on its broad set of data discovery and access tools, sub-setting services, and visualization tools. Nonetheless, the multitude of the available tools, a partial overlap of functionality, and independent and uncoupled interfaces employed by these tools often leave the end users confused as of what tools or services are the most appropriate for a task at hand. As a result, some the services remain underutilized or largely unknown to the users, significantly reducing the availability of the data and leading to a great loss of scientific productivity. In order to improve the accessibility of GES DISC tools and services, we have designed and implemented UUI, the Unified User Interface. UUI seeks to provide a simple, unified, and intuitive one-stop shop experience for the key services available at GES DISC, including sub-setting (Simple Subset Wizard), granule file search (Mirador), plotting (Giovanni), and other services. In this poster, we will discuss the main lessons, obstacles, and insights encountered while designing the UUI experience. We will also present the architecture and technology behind UUI, including NodeJS, Angular, and Mongo DB, as well as speculate on the future of the tool at GES DISC as well as in a broader context of the Space Science Informatics.

Advantages of continuous genotype values over genotype classes for GWAS in higher polyploids: a comparative study in hexaploid chrysanthemum.

PubMed

Grandke, Fabian; Singh, Priyanka; Heuven, Henri C M; de Haan, Jorn R; Metzler, Dirk

2016-08-24

Association studies are an essential part of modern plant breeding, but are limited for polyploid crops. The increased number of possible genotype classes complicates the differentiation between them. Available methods are limited with respect to the ploidy level or data producing technologies. While genotype classification is an established noise reduction step in diploids, it gains complexity with increasing ploidy levels. Eventually, the errors produced by misclassifications exceed the benefits of genotype classes. Alternatively, continuous genotype values can be used for association analysis in higher polyploids. We associated continuous genotypes to three different traits and compared the results to the output of the genotype caller SuperMASSA. Linear, Bayesian and partial least squares regression were applied, to determine if the use of continuous genotypes is limited to a specific method. A disease, a flowering and a growth trait with h (2) of 0.51, 0.78 and 0.91 were associated with a hexaploid chrysanthemum genotypes. The data set consisted of 55,825 probes and 228 samples. We were able to detect associating probes using continuous genotypes for multiple traits, using different regression methods. The identified probe sets were overlapping, but not identical between the methods. Baysian regression was the most restrictive method, resulting in ten probes for one trait and none for the others. Linear and partial least squares regression led to numerous associating probes. Association based on genotype classes resulted in similar values, but missed several significant probes. A simulation study was used to successfully validate the number of associating markers. Association of various phenotypic traits with continuous genotypes is successful with both uni- and multivariate regression methods. Genotype calling does not improve the association and shows no advantages in this study. Instead, use of continuous genotypes simplifies the analysis, saves computational time and results more potential markers.

Trichuris spp. (Nematoda: Trichuridae) from two rodents, Mastomys natalensis and Gerbilliscus vicinus in Tanzania.

PubMed

Ribas, Alexis; López, Sergi; Makundi, Rhodes H; Leirs, Herwig; de Bellocq, Joëlle Goüy

2013-10-01

During a survey of the helminth community of several rodent species in the Morogoro region (Tanzania), Trichuris whipworms (Nematoda: Trichuridae) were found in the ceca of the Natal multimammate mouse, Mastomys natalensis and a gerbil, Gerbilliscus vicinus (both Rodentia: Muridae). The taxonomic literature regarding Trichuris from African native rodents describes 10 species, but includes few metric and morphologic characters that discriminate between some of the pairs. The whipworms we sampled in Tanzanian Natal multimammate mice and gerbils were morphologically identified, respectively, as Trichuris mastomysi Verster, 1960 and Trichuris carlieri Gedoelst, 1916 sensu lato, but with characters that overlap or partially overlap with the cosmopolitan Murinae whipworm, Trichuris muris , already reported from several rodents in Africa. To clarify our identification, we sequenced the ITS-1, 5.8S, and ITS-2 ribosomal DNA region of the worms' nuclear genome. The genetic analyses clearly distinguish the whipworms we found in M. natalensis from those found in the gerbil, and both of these from T. muris whipworm reference sequences. The overlap of morphological characters between rodent whipworms suggests that reports of T. muris from rodent species not closely related to Murinae in other parts of Africa should be treated with caution.

Spacecraft Antennas

NASA Technical Reports Server (NTRS)

Jamnejad, Vahraz; Manshadi, Farzin; Rahmat-Samii, Yahya; Cramer, Paul

1990-01-01

Some of the various categories of issues that must be considered in the selection and design of spacecraft antennas for a Personal Access Satellite System (PASS) are addressed, and parametric studies for some of the antenna concepts to help the system designer in making the most appropriate antenna choice with regards to weight, size, and complexity, etc. are provided. The question of appropriate polarization for the spacecraft as well as for the User Terminal Antenna required particular attention and was studied in some depth. Circular polarization seems to be the favored outcome of this study. Another problem that has generally been a complicating factor in designing the multiple beam reflector antennas, is the type of feeds (single vs. multiple element and overlapping vs. non-overlapping clusters) needed for generating the beams. This choice is dependent on certain system design factors, such as the required frequency reuse, acceptable interbeam isolation, antenna efficiency, number of beams scanned, and beam-forming network (BFN) complexity. This issue is partially addressed, but is not completely resolved. Indications are that it may be possible to use relatively simple non-overlapping clusters of only a few elements, unless a large frequency reuse and very stringent isolation levels are required.

Recruitment and Consolidation of Cell Assemblies for Words by Way of Hebbian Learning and Competition in a Multi-Layer Neural Network

PubMed Central

Garagnani, Max; Wennekers, Thomas; Pulvermüller, Friedemann

2009-01-01

Current cognitive theories postulate either localist representations of knowledge or fully overlapping, distributed ones. We use a connectionist model that closely replicates known anatomical properties of the cerebral cortex and neurophysiological principles to show that Hebbian learning in a multi-layer neural network leads to memory traces (cell assemblies) that are both distributed and anatomically distinct. Taking the example of word learning based on action-perception correlation, we document mechanisms underlying the emergence of these assemblies, especially (i) the recruitment of neurons and consolidation of connections defining the kernel of the assembly along with (ii) the pruning of the cell assembly’s halo (consisting of very weakly connected cells). We found that, whereas a learning rule mapping covariance led to significant overlap and merging of assemblies, a neurobiologically grounded synaptic plasticity rule with fixed LTP/LTD thresholds produced minimal overlap and prevented merging, exhibiting competitive learning behaviour. Our results are discussed in light of current theories of language and memory. As simulations with neurobiologically realistic neural networks demonstrate here spontaneous emergence of lexical representations that are both cortically dispersed and anatomically distinct, both localist and distributed cognitive accounts receive partial support. PMID:20396612

Recruitment and Consolidation of Cell Assemblies for Words by Way of Hebbian Learning and Competition in a Multi-Layer Neural Network.

PubMed

Garagnani, Max; Wennekers, Thomas; Pulvermüller, Friedemann

2009-06-01

Current cognitive theories postulate either localist representations of knowledge or fully overlapping, distributed ones. We use a connectionist model that closely replicates known anatomical properties of the cerebral cortex and neurophysiological principles to show that Hebbian learning in a multi-layer neural network leads to memory traces (cell assemblies) that are both distributed and anatomically distinct. Taking the example of word learning based on action-perception correlation, we document mechanisms underlying the emergence of these assemblies, especially (i) the recruitment of neurons and consolidation of connections defining the kernel of the assembly along with (ii) the pruning of the cell assembly's halo (consisting of very weakly connected cells). We found that, whereas a learning rule mapping covariance led to significant overlap and merging of assemblies, a neurobiologically grounded synaptic plasticity rule with fixed LTP/LTD thresholds produced minimal overlap and prevented merging, exhibiting competitive learning behaviour. Our results are discussed in light of current theories of language and memory. As simulations with neurobiologically realistic neural networks demonstrate here spontaneous emergence of lexical representations that are both cortically dispersed and anatomically distinct, both localist and distributed cognitive accounts receive partial support.

Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps

PubMed Central

Huang, Hailiang; Jedynak, Bruno M; Bader, Joel S

2007-01-01

Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins. The fraction of interactions detected in independent screens can be very small, and an outstanding challenge is to determine the reason for the low overlap. Low overlap can arise from either a high false-discovery rate (interaction sets have low overlap because each set is contaminated by a large number of stochastic false-positive interactions) or a high false-negative rate (interaction sets have low overlap because each misses many true interactions). We extend capture–recapture theory to provide the first unified model for false-positive and false-negative rates for two-hybrid screens. Analysis of yeast, worm, and fly data indicates that 25% to 45% of the reported interactions are likely false positives. Membrane proteins have higher false-discovery rates on average, and signal transduction proteins have lower rates. The overall false-negative rate ranges from 75% for worm to 90% for fly, which arises from a roughly 50% false-negative rate due to statistical undersampling and a 55% to 85% false-negative rate due to proteins that appear to be systematically lost from the assays. Finally, statistical model selection conclusively rejects the Erdös-Rényi network model in favor of the power law model for yeast and the truncated power law for worm and fly degree distributions. Much as genome sequencing coverage estimates were essential for planning the human genome sequencing project, the coverage estimates developed here will be valuable for guiding future proteomic screens. All software and datasets are available in Datasets S1 and S2, Figures S1–S5, and Tables S1−S6, and are also available from our Web site, http://www.baderzone.org. PMID:18039026

A 3D Kinematic Measurement of Knee Prosthesis Using X-ray Projection Images

NASA Astrophysics Data System (ADS)

Hirokawa, Shunji; Ariyoshi, Shogo; Hossain, Mohammad Abrar

We have developed a technique for estimating 3D motion of knee prosthesis from its 2D perspective projections. As Fourier descriptors were used for compact representation of library templates and contours extracted from the prosthetic X-ray images, the entire silhouette contour of each prosthetic component was required. This caused such a problem as our algorithm did not function when the silhouettes of tibio and femoral components overlapped with each other. Here we planned a novel method to overcome it; which was processed in two steps. First, the missing part of silhouette contour due to overlap was interpolated using a free-formed curvature such as Bezier. Then the first step position/orientation estimation was performed. In the next step, a clipping window was set in the projective coordinate so as to separate the overlapped silhouette drawn using the first step estimates. After that the localized library whose templates were clipped in shape was prepared and the second step estimation was performed. Computer model simulation demonstrated sufficient accuracies of position/orientation estimation even for overlapped silhouettes; equivalent to those without overlap.

Parentage of overlapping offspring of an arboreal-breeding frog with no nest defense: implications for nest site selection and reproductive strategy.

PubMed

Tung, Wan-Ping; Chen, Yi-Huey; Cheng, Wei-Chun; Chuang, Ming-Feng; Hsu, Wan-Tso; Kam, Yeong-Choy; Lehtinen, Richard M

2015-01-01

Overlapping offspring occurs when eggs are laid in a nest containing offspring from earlier reproduction. Earlier studies showed that the parentage is not always obvious due to difficulties in field observation and/or alternative breeding tactics. To unveil the parentage between overlapping offspring and parents is critical in understanding oviposition site selection and the reproductive strategies of parents. Amplectant pairs of an arboreal-breeding frog, Kurixalus eiffingeri, lay eggs in tadpole-occupied nests where offspring of different life stages (embryos and tadpoles) coexist. We used five microsatellite DNA markers to assess the parentage between parents and overlapping offspring. We also tested the hypothesis that the male or female frog would breed in the same breeding site because of the scarcity of nest sites. Results showed varied parentage patterns, which may differ from the phenomenon of overlapping egg clutches reported earlier. Parentage analyses showed that only 58 and 25% of the tadpole-occupied stumps were reused by the same male and female respectively, partially confirming our prediction. Re-nesting by the same individual was more common in males than females, which is most likely related to the cost of tadpole feeding and/or feeding schemes of females. On the other hand, results of parentage analyses showed that about 42 and 75% of male and female respectively bred in tadpole-occupied stumps where tadpoles were genetically unrelated. Results of a nest-choice experiment revealed that 40% of frogs chose tadpole-occupied bamboo cups when we presented identical stumps, without or with tadpoles, suggesting that the habitat saturation hypothesis does not fully explain why frogs used the tadpole-occupied stumps. Several possible benefits of overlapping offspring with different life stages were proposed. Our study highlights the importance of integrating molecular data with field observations to better understand the reproductive biology and nest site selection of anuran amphibians.

Recovering Wood and McCarthy's ERP-prototypes by means of ERP-specific procrustes-rotation.

PubMed

Beauducel, André

2018-02-01

The misallocation of treatment-variance on the wrong component has been discussed in the context of temporal principal component analysis of event-related potentials. There is, until now, no rotation-method that can perfectly recover Wood and McCarthy's prototypes without making use of additional information on treatment-effects. In order to close this gap, two new methods: for component rotation were proposed. After Varimax-prerotation, the first method identifies very small slopes of successive loadings. The corresponding loadings are set to zero in a target-matrix for event-related orthogonal partial Procrustes- (EPP-) rotation. The second method generates Gaussian normal distributions around the peaks of the Varimax-loadings and performs orthogonal Procrustes-rotation towards these Gaussian distributions. Oblique versions of this Gaussian event-related Procrustes- (GEP) rotation and of EPP-rotation are based on Promax-rotation. A simulation study revealed that the new orthogonal rotations recover Wood and McCarthy's prototypes and eliminate misallocation of treatment-variance. In an additional simulation study with a more pronounced overlap of the prototypes GEP Promax-rotation reduced the variance misallocation slightly more than EPP Promax-rotation. Comparison with Existing Method(s): Varimax- and conventional Promax-rotations resulted in substantial misallocations of variance in simulation studies when components had temporal overlap. A substantially reduced misallocation of variance occurred with the EPP-, EPP Promax-, GEP-, and GEP Promax-rotations. Misallocation of variance can be minimized by means of the new rotation methods: Making use of information on the temporal order of the loadings may allow for improvements of the rotation of temporal PCA components. Copyright © 2017 Elsevier B.V. All rights reserved.

Effectiveness of computer aided detection for solitary pulmonary nodules

NASA Astrophysics Data System (ADS)

Yan, Jiayong; Li, Wenjie; Du, Xiangying; Lu, Huihai; Xu, Jianrong; Xu, Mantao; Rong, Dongdong

2009-02-01

This study is to investigate the incremental effect of using a high performance computer-aided detection (CAD) system in detection of solitary pulmonary nodules in chest radiographs. The Kodak Chest CAD system was evaluated by a panel of six radiologists at different levels of experience. The observer study consisted of two independent phases: readings without CAD and readings with assistance of CAD. The study was conducted over a set of chest radiographs comprising 150 cancer cases and 150 cancer-free cases. The actual sensitivity of the CAD system is 72% with 3.7 false positives per case. Receiver operating characteristic (ROC) analysis was used to assess the overall observer performance. The AUZ (area under ROC curve) showed a significantly improvement (P=0.0001) from 0.844 to 0.884 after using CAD. The ROC analysis was also applied for observer performances on nodules in different sizes and visibilities. The average AUZs are improved from 0.798 to 0.835 (P=0.0003) for 5-10mm nodules, 0.853 to 0.907 (P=0.001) for 10-15mm nodules, 0.864 to 0.897 (P=0.051) for 15-20 mm nodules and 0.859 to 0.896 (P=0.0342) for 20-30mm nodules, respectively. For different visibilities, the average AUZs are improved from 0.886 to 0.915 (P=0.0337), 0.803 to 0.840 (P=0.063), 0.830 to 0.893 (P=0.0001), and 0.813 to 0.847 (P=0.152), for nodules clearly visible, hidden by ribs, partially overlap with ribs, and overlap with other structures, respectively. These results showed that observer performance could be greatly improved when the CAD system is employed as a second reader, especially for small nodules and nodules occluded by ribs.

Novel Rabies Virus-Neutralizing Epitope Recognized by Human Monoclonal Antibody: Fine Mapping and Escape Mutant Analysis†

PubMed Central

Marissen, Wilfred E.; Kramer, R. Arjen; Rice, Amy; Weldon, William C.; Niezgoda, Michael; Faber, Milosz; Slootstra, Jerry W.; Meloen, Rob H.; Clijsters-van der Horst, Marieke; Visser, Therese J.; Jongeneelen, Mandy; Thijsse, Sandra; Throsby, Mark; de Kruif, John; Rupprecht, Charles E.; Dietzschold, Bernhard; Goudsmit, Jaap; Bakker, Alexander B. H.

2005-01-01

Anti-rabies virus immunoglobulin combined with rabies vaccine protects humans from lethal rabies infections. For cost and safety reasons, replacement of the human or equine polyclonal immunoglobulin is advocated, and the use of rabies virus-specific monoclonal antibodies (MAbs) is recommended. We produced two previously described potent rabies virus-neutralizing human MAbs, CR57 and CRJB, in human PER.C6 cells. The two MAbs competed for binding to rabies virus glycoprotein. Using CR57 and a set of 15-mer overlapping peptides covering the glycoprotein ectodomain, a neutralization domain was identified between amino acids (aa) 218 and 240. The minimal binding region was identified as KLCGVL (aa 226 to 231), with key residues K-CGV- identified by alanine replacement scanning. The critical binding region of this novel nonconformational rabies virus epitope is highly conserved within rabies viruses of genotype 1. Subsequently, we generated six rabies virus variants escaping neutralization by CR57 and six variants escaping CRJB. The CR57 escape mutants were only partially covered by CRJB, and all CRJB-resistant variants completely escaped neutralization by CR57. Without exception, the CR57-resistant variants showed a mutation at key residues within the defined minimal binding region, while the CRJB escape viruses showed a single mutation distant from the CR57 epitope (N182D) combined with mutations in the CR57 epitope. The competition between CR57 and CRJB, the in vitro escape profile, and the apparent overlap between the recognized epitopes argues against including both CR57 and CRJB in a MAb cocktail aimed at replacing classical immunoglobulin preparations. PMID:15795253

Studies of quantum dots in the quantum Hall regime

NASA Astrophysics Data System (ADS)

Goldmann, Eyal

We present two studies of quantum dots in the quantum Hall regime. In the first study, presented in Chapter 3, we investigate the edge reconstruction phenomenon believed to occur when the quantum dot filling fraction is n≲1 . Our approach involves the examination of large dots (≤40 electrons) using a partial diagonalization technique in which the occupancies of the deep interior orbitals are frozen. To interpret the results of this calculation, we evaluate the overlap between the diagonalized ground state and a set of trial wavefunctions which we call projected necklace (PN) states. A PN state is simply the angular momentum projection of a maximum density droplet surrounded by a ring of localized electrons. Our calculations reveal that PN states have up to 99% overlap with the diagonalized ground states, and are lower in energy than the states identified in Chamon and Wen's study of the edge reconstruction. In the second study, presented in Chapter 4, we investigate quantum dots in the fractional quantum Hall regime using a Hartree formulation of composite fermion theory. We find that under appropriate conditions, the chemical potential of the dots oscillates periodically with B due to the transfer of composite fermions between quasi-Landau bands. This effect is analogous the addition spectrum oscillations which occur in quantum dots in the integer quantum Hall regime. Period f0 oscillations are found in sharply confined dots with filling factors nu = 2/5 and nu = 2/3. Period 3 f0 oscillations are found in a parabolically confined nu = 2/5 dot. More generally, we argue that the oscillation period of dots with band pinning should vary continuously with B, whereas the period of dots without band pinning is f0 .

Magnetic positioner having a single moving part

DOEpatents

Trumper, David L.; Kim, Won-Jong

1999-01-01

A magnetic positioner is provided which is capable of providing long travel in two dimension and short travel in the remaining four dimensions. The positioner has a movable stage and a stator oriented adjacent and substantially parallel to this stage. At least three sets of first magnetic elements, which for preferred embodiments are winding sets capable of generating forces in two directions, are on the portion of the stator adjacent to the stage at any given time, and at least two second magnetic elements, which are magnet arrays for the preferred embodiment, are on the stage adjacent to the stator. At least one of the second magnetic elements overlaps multiple first magnetic elements for all positions of the stage relative to the stator, with one magnet overlapping multiple windings for one preferred embodiment of the invention and two magnets on the stage overlapping multiple windings on the stator for a second embodiment. The windings form a linear motor providing forces in both a corresponding long travel dimension and in a dimension perpendicular to both long travel dimensions.

Pollination niche overlap between a parasitic plant and its host.

PubMed

Ollerton, Jeff; Stott, Adrian; Allnutt, Emma; Shove, Sam; Taylor, Chloe; Lamborn, Ellen

2007-03-01

Niche theory predicts that species which share resources should evolve strategies to minimise competition for those resources, or the less competitive species would be extirpated. Some plant species are constrained to co-occur, for example parasitic plants and their hosts, and may overlap in their pollination niche if they flower at the same time and attract the same pollinators. Using field observations and experiments between 1996 and 2006, we tested a series of hypotheses regarding pollination niche overlap between a specialist parasitic plant Orobanche elatior (Orobanchaceae) and its host Centaurea scabiosa (Asteraceae). These species flower more or less at the same time, with some year-to-year variation. The host is pollinated by a diverse range of insects, which vary in their effectiveness, whilst the parasite is pollinated by a single species of bumblebee, Bombus pascuorum, which is also an effective pollinator of the host plant. The two species therefore have partially overlapping pollination niches. These niches are not finely subdivided by differential pollen placement, or by diurnal segregation of the niches. We therefore found no evidence of character displacement within the pollination niches of these species, possibly because pollinators are not a limiting resource for these plants. Direct observation of pollinator movements, coupled with experimental manipulations of host plant inflorescence density, showed that Bombus pascuorum only rarely moves between inflorescences of the host and the parasite and therefore the presence of one plant is unlikely to be facilitating pollination in the other. This is the first detailed examination of pollination niche overlap in a plant parasite system and we suggest avenues for future research in relation to pollination and other shared interactions between parasitic plants and their hosts.

A network-based method to evaluate quality of reproducibility of differential expression in cancer genomics studies

PubMed Central

Geng, Haijiang; Li, Zhihui; Li, Jiabing; Lu, Tao; Yan, Fangrong

2015-01-01

BACKGROUND Personalized cancer treatments depend on the determination of a patient's genetic status according to known genetic profiles for which targeted treatments exist. Such genetic profiles must be scientifically validated before they is applied to general patient population. Reproducibility of findings that support such genetic profiles is a fundamental challenge in validation studies. The percentage of overlapping genes (POG) criterion and derivative methods produce unstable and misleading results. Furthermore, in a complex disease, comparisons between different tumor subtypes can produce high POG scores that do not capture the consistencies in the functions. RESULTS We focused on the quality rather than the quantity of the overlapping genes. We defined the rank value of each gene according to importance or quality by PageRank on basis of a particular topological structure. Then, we used the p-value of the rank-sum of the overlapping genes (PRSOG) to evaluate the quality of reproducibility. Though the POG scores were low in different studies of the same disease, the PRSOG was statistically significant, which suggests that sets of differentially expressed genes might be highly reproducible. CONCLUSIONS Evaluations of eight datasets from breast cancer, lung cancer and four other disorders indicate that quality-based PRSOG method performs better than a quantity-based method. Our analysis of the components of the sets of overlapping genes supports the utility of the PRSOG method. PMID:26556852

Attention please: evaluative priming effects in a valent/non-valent categorisation task (reply to Werner & Rothermund, 2013).

PubMed

Spruyt, Adriaan

2014-04-01

It has previously been argued (a) that automatic evaluative stimulus processing is dependent upon feature-specific attention allocation (FSAA) and (b) that evaluative priming effects can arise in the absence of dimensional overlap between the prime set and the response set. In opposition to these claims, Werner and Rothermund (2013) recently reported that they were unable to replicate the evaluative priming effect in a valent/non-valent categorisation task. In this manuscript, I report the results of a conceptual replication of the studies by Werner and Rothermund (2013). A clear-cut evaluative priming effect was found, thus supporting the initial claims about FSAA and dimensional overlap. An explanation for these divergent findings is discussed.

Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology.

PubMed

Pessôa, Rodrigo; Watanabe, Jaqueline Tomoko; Nukui, Youko; Pereira, Juliana; Casseb, Jorge; Kasseb, Jorge; de Oliveira, Augusto César Penalva; Segurado, Aluisio Cotrim; Sanabani, Sabri Saeed

2014-01-01

Here, we report on the partial and full-length genomic (FLG) variability of HTLV-1 sequences from 90 well-characterized subjects, including 48 HTLV-1 asymptomatic carriers (ACs), 35 HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and 7 adult T-cell leukemia/lymphoma (ATLL) patients, using an Illumina paired-end protocol. Blood samples were collected from 90 individuals, and DNA was extracted from the PBMCs to measure the proviral load and to amplify the HTLV-1 FLG from two overlapping fragments. The amplified PCR products were subjected to deep sequencing. The sequencing data were assembled, aligned, and mapped against the HTLV-1 genome with sufficient genetic resemblance and utilized for further phylogenetic analysis. A high-throughput sequencing-by-synthesis instrument was used to obtain an average of 3210- and 5200-fold coverage of the partial (n = 14) and FLG (n = 76) data from the HTLV-1 strains, respectively. The results based on the phylogenetic trees of consensus sequences from partial and FLGs revealed that 86 (95.5%) individuals were infected with the transcontinental sub-subtypes of the cosmopolitan subtype (aA) and that 4 individuals (4.5%) were infected with the Japanese sub-subtypes (aB). A comparison of the nucleotide and amino acids of the FLG between the three clinical settings yielded no correlation between the sequenced genotype and clinical outcomes. The evolutionary relationships among the HTLV sequences were inferred from nucleotide sequence, and the results are consistent with the hypothesis that there were multiple introductions of the transcontinental subtype in Brazil. This study has increased the number of subtype aA full-length genomes from 8 to 81 and HTLV-1 aB from 2 to 5 sequences. The overall data confirmed that the cosmopolitan transcontinental sub-subtypes were the most prevalent in the Brazilian population. It is hoped that this valuable genomic data will add to our current understanding of the evolutionary history of this medically important virus.

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

PubMed Central

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

2011-01-01

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

Value of Robotically Assisted Surgery for Mitral Valve Disease

PubMed Central

Mihaljevic, Tomislav; Koprivanac, Marijan; Kelava, Marta; Goodman, Avi; Jarrett, Craig; Williams, Sarah J.; Gillinov, A. Marc; Bajwa, Gurjyot; Mick, Stephanie L.; Bonatti, Johannes; Blackstone, Eugene H.

2014-01-01

Importance The value of robotically assisted surgery for mitral valve disease is questioned because the high cost of care associated with robotic technology may outweigh its clinical benefits. Objective To investigate conditions under which benefits of robotic surgery mitigate high technology costs. Design Clinical cohort study comparing costs of robotic vs. three contemporaneous conventional surgical approaches for degenerative mitral disease. Surgery was performed from 2006–2011, and comparisons were based on intent-to-treat, with propensity-matching used to reduce selection bias. Setting Large multi-specialty academic medical center. Participants 1,290 patients aged 57±11 years, 27% women, underwent mitral repair for regurgitation from posterior leaflet prolapse. Robotic surgery was used in 473, complete sternotomy in 227, partial sternotomy in 349, and anterolateral thoracotomy in 241. Three propensity-matched groups were formed based on demographics, symptoms, cardiac and noncardiac comorbidities, valve pathophysiology, and echocardiographic measurements: robotic vs. sternotomy (n=198 pairs) vs. partial sternotomy (n=293 pairs) vs. thoracotomy (n=224 pairs). Interventions Mitral valve repair. Main Outcome Measures Cost of care, expressed as robotic capital investment, maintenance, and direct technical hospital cost, and benefit of care, based on differences in recovery time. Results Median cost of care for robotically assisted surgery exceeded the cost of alternative approaches by 27% (−5%, 68%), 32% (−6%, 70%), and 21% (−2%, 54%) (median [15th, 85th percentiles]) for complete sternotomy, partial sternotomy, and anterolateral thoracotomy, respectively. Higher operative costs were partially offset by lower postoperative costs and earlier return to work: median 35 days for robotic surgery, 49 for complete sternotomy, 56 for partial sternotomy, and 42 for anterolateral thoracotomy. Resulting net differences in cost of robotic surgery vs. the three alternatives were 16% (−15%, 55%), 16% (−19%, 51%), and 15% (−7%, 49%), respectively. Beyond a volume threshold of 55–100 robotic cases per year, confidence limits for the cost of robotic surgery broadly overlapped those of conventional approaches. Conclusions In exchange for higher procedural costs, robotically assisted mitral valve surgery offers the clinical benefit of least invasive surgery, lowest postoperative cost, and fastest return to work. The value of robotically assisted surgery comparable to conventional approaches can only be realized in high-volume centers. PMID:24848944

Simultaneous spectrophotometric determination of four metals by two kinds of partial least squares methods

NASA Astrophysics Data System (ADS)

Gao, Ling; Ren, Shouxin

2005-10-01

Simultaneous determination of Ni(II), Cd(II), Cu(II) and Zn(II) was studied by two methods, kernel partial least squares (KPLS) and wavelet packet transform partial least squares (WPTPLS), with xylenol orange and cetyltrimethyl ammonium bromide as reagents in the medium pH = 9.22 borax-hydrochloric acid buffer solution. Two programs, PKPLS and PWPTPLS, were designed to perform the calculations. Data reduction was performed using kernel matrices and wavelet packet transform, respectively. In the KPLS method, the size of the kernel matrix is only dependent on the number of samples, thus the method was suitable for the data matrix with many wavelengths and fewer samples. Wavelet packet representations of signals provide a local time-frequency description, thus in the wavelet packet domain, the quality of the noise removal can be improved. In the WPTPLS by optimization, wavelet function and decomposition level were selected as Daubeches 12 and 5, respectively. Experimental results showed both methods to be successful even where there was severe overlap of spectra.

Prevention of overlapping prescriptions of psychotropic drugs by community pharmacists.

PubMed

Shimane, Takuya; Matsumoto, Toshihiko; Wada, Kiyoshi

2012-10-01

The nonmedical use or abuse of prescription drugs, including psychotropic medicines, is a growing health problem in Japan. Patient access to psychotropic drugs, specifically from the oversupply of medications due to overlapping prescriptions, may increase the risk of drug abuse and dependence. However, very little is known about such overlapping prescriptions. Today, the dispensing of prescriptions is generally moving from inside to outside of hospitals, with psychotropic drugs mainly dispensed at community pharmacies. In this study, we used health insurance claims (i.e., receipts) for dispensing as the main source of information in an investigation of overlapping prescriptions of psychotropic drugs. A total of 119 patients were found to have received overlapping prescriptions, as identified by community pharmacists who were members of the Saitama Pharmaceutical Association, using patient medication records, followed by medication counseling and prescription notes for the patient. According to our findings, the most frequently overlapping medication was etizolam. Etizolam can be prescribed for more than 30 days since it is not regulated under Japanese law as a "psychotropic drug." Generally, when a drug can be prescribed for a greater number of days, it increases the likelihood of an overlapping prescription during the same period. As a result, the long-term prescription of etizolam increases the risk of overlapping prescriptions. We also found that the patients who received overlapping prescriptions of etizolam were mostly elderly and the most common pattern was prescription from both internal medicine and orthopedics physicians. Etizolam has wide range of indications that are covered by health insurance. Our results suggest that patients who received overlapping prescriptions of etizolam may receive prescriptions from different prescribers for different purposes. Therefore, it may be appropriate to regulate etizolam as a "psychotropic drug" under Japanese law, thus setting a limit on the period for which it can be prescribed in order to help prevent long-term and overlapping prescriptions.

Chromatographic multivariate quality control of pharmaceuticals giving strongly overlapped peaks based on the chromatogram profile.

PubMed

Escuder-Gilabert, L; Ruiz-Roch, D; Villanueva-Camañas, R M; Medina-Hernández, M J; Sagrado, S

2004-03-12

In the present paper, the simultaneous quantification of two analytes showing strongly overlapped chromatographic peaks (alpha = 1.02), under the assumption that both available equipment and training of the laboratory staff are basic, is studied. A pharmaceutical preparation (Mutabase) containing two drugs of similar physicochemical properties (amitriptyline and perphenazine) is selected as case of study. The assays are carried out under realistic working conditions (i.e. routine testing laboratories). Uncertainty considerations are introduced in the study. A partial least squares model is directly applied to the chromatographic data (with no previous signal transformation) to perform quality control of the pharmaceutical formulation. Under the adequate protocol, the relative error in prediction of analytes is within the tolerances found in the pharmacopeia (10%). For spiked samples simulating formulation mistakes, the errors found have the same magnitude and sign to those provoked.

Comparative analysis of Six 3 and Six 6 distribution in the developing and adult mouse brain.

PubMed

Conte, Ivan; Morcillo, Julian; Bovolenta, Paola

2005-11-01

Six 3 and Six 6 genes are two closely related members of the Six/sine oculis family of homeobox containing transcription factors. Their expression and function at early stages of embryonic development has been widely addressed in a variety of species. However, their mRNA distribution during late embryonic, postnatal, and adult brain barely has been analyzed. Here, we show that despite their initial overlap in the anterior neural plate, the expression of Six 3 and Six 6 progressively segregates to different regions during mammalian brain development, maintaining only few areas of partial overlap in the thalamic and hypothalamic regions. Six 3, but not Six 6, is additionally expressed in the olfactory bulb, cerebral cortex, hippocampus, midbrain, and cerebellum. These distinct patterns support the idea that Six 3 and Six 6 are differentially required during forebrain development. Developmental Dynamics 234:718-725, 2005. (c) 2005 Wiley-Liss, Inc.

Sensitive and selective cocaine electrochemical detection using disposable sensors.

PubMed

Asturias-Arribas, Laura; Alonso-Lomillo, M Asunción; Domínguez-Renedo, Olga; Arcos-Martínez, M Julia

2014-06-27

This paper describes the voltammetric determination of cocaine in presence of three different interferences that could be found in street samples using disposable sensors. The electrochemical analysis of this alkaloid can be affected by the presence of codeine, paracetamol or caffeine, whose oxidation peaks may overlap and lead to false positives. This work describes two different solutions to this problem. On one hand, the modification of disposable carbon sensors with carbon nanotubes allows the voltammetric quantification of cocaine by using ordinary least squares regressions in the concentration range from 10 to 155 μmol L(-1), with a reproducibility of 5.6% (RSD, n = 7. On the other hand, partial least squares regressions are used for the resolution of the overlapped voltammetric signals when using screen-printed carbon electrodes without any modification. Both procedures have been successfully applied to the evaluation of the purity of cocaine street samples. Copyright © 2014 Elsevier B.V. All rights reserved.

Simultaneous determination of rifampicin, isoniazid and pyrazinamide in tablet preparations by multivariate spectrophotometric calibration.

PubMed

Goicoechea, H C; Olivieri, A C

1999-08-01

The use of multivariate spectrophotometric calibration is presented for the simultaneous determination of the active components of tablets used in the treatment of pulmonary tuberculosis. The resolution of ternary mixtures of rifampicin, isoniazid and pyrazinamide has been accomplished by using partial least squares (PLS-1) regression analysis. Although the components show an important degree of spectral overlap, they have been simultaneously determined with high accuracy and precision, rapidly and with no need of nonaqueous solvents for dissolving the samples. No interference has been observed from the tablet excipients. A comparison is presented with the related multivariate method of classical least squares (CLS) analysis, which is shown to yield less reliable results due to the severe spectral overlap among the studied compounds. This is highlighted in the case of isoniazid, due to the small absorbances measured for this component.

Endovascular treatment of the extracranial carotid pseudoaneurysms resulting from stab penetrating injury using overlapping bare stents.

PubMed

Pan, Yao-hua; Lin, Yong; Ding, Sheng-hao; Chen, Lei; Liang, Yu-ming; Yin, Yu-hua; Bao, Ying-hui; Gao, Guo-Yi; Qiu, Yong-ming; Jiang, Ji-yao

2014-05-01

Injury pertaining to the common carotid artery may result in complete or partial arterial transection, pseudoaneurysms, or arteriovenous connections. Endovascular treatment option of the pseudoaneurysm has already been established with favorable success rate and minimal morbidity. Our purpose is to report one 18-year-old male patient having 2 traumatic pseudoaneurysms as a result of penetrating stab injury in the extracranial common carotid. The patient was successfully treated using 2 overlapping bare-metal stents. The 2 common carotid pseudoaneurysms had different degree inflow angles defined as the space between the lines indicating the direction of blood flow from the parent artery and through the aneurysmal neck to the dome. Computed tomography angiography was utilized to follow the evolution of the pseudoaneurysms until total occlusion was demonstrated. The treatment modality used in this report represents an alternative approach of the endovascular treatment for the extracranial carotid pseudoaneurysm.

Robust Statistical Fusion of Image Labels

PubMed Central

Landman, Bennett A.; Asman, Andrew J.; Scoggins, Andrew G.; Bogovic, John A.; Xing, Fangxu; Prince, Jerry L.

2011-01-01

Image labeling and parcellation (i.e. assigning structure to a collection of voxels) are critical tasks for the assessment of volumetric and morphometric features in medical imaging data. The process of image labeling is inherently error prone as images are corrupted by noise and artifacts. Even expert interpretations are subject to subjectivity and the precision of the individual raters. Hence, all labels must be considered imperfect with some degree of inherent variability. One may seek multiple independent assessments to both reduce this variability and quantify the degree of uncertainty. Existing techniques have exploited maximum a posteriori statistics to combine data from multiple raters and simultaneously estimate rater reliabilities. Although quite successful, wide-scale application has been hampered by unstable estimation with practical datasets, for example, with label sets with small or thin objects to be labeled or with partial or limited datasets. As well, these approaches have required each rater to generate a complete dataset, which is often impossible given both human foibles and the typical turnover rate of raters in a research or clinical environment. Herein, we propose a robust approach to improve estimation performance with small anatomical structures, allow for missing data, account for repeated label sets, and utilize training/catch trial data. With this approach, numerous raters can label small, overlapping portions of a large dataset, and rater heterogeneity can be robustly controlled while simultaneously estimating a single, reliable label set and characterizing uncertainty. The proposed approach enables many individuals to collaborate in the construction of large datasets for labeling tasks (e.g., human parallel processing) and reduces the otherwise detrimental impact of rater unavailability. PMID:22010145

Cerebral Economics: Resource Competition within but not Between Hemispheres.

DTIC Science & Technology

1981-06-01

the Office of Naval Research and by the Air Force Office of Scientific Research. 19. KEY WORDS (Continue on reveree side ifneceset, and Identify by...consistent RVF advantage on the naming task when it LI 6 was performed alone, the effect of adding the memory load made left hemisphere resources so...might be argued that the equivalent tradeoff effects we found when comparing the complete with the partial overlap situation might be evidence for some

Solution structure of biopolymers: a new method of constructing a bead model.

PubMed Central

Banachowicz, E; Gapiński, J; Patkowski, A

2000-01-01

We propose a new, automated method of converting crystallographic data into a bead model used for the calculations of hydrodynamic properties of rigid macromolecules. Two types of molecules are considered: nucleic acids and small proteins. A bead model of short DNA fragments has been constructed in which each nucleotide is represented by two identical, partially overlapping spheres: one for the base and one for the sugar and phosphate group. The optimum radius sigma = 5.0 A was chosen on the basis of a comparison of the calculated translational diffusion coefficients (D(T)) and the rotational relaxation times (tau(R)) with the corresponding experimental data for B-DNA fragments of 8, 12, and 20 basepairs. This value was assumed for the calculation D(T) and tau(R) of tRNA(Phe). Better agreement with the experimental data was achieved for slightly larger sigma = 5.7 A. A similar procedure was applied to small proteins. Bead models were constructed such that each amino acid was represented by a single sphere or a pair of identical, partially overlapping spheres, depending on the amino acid's size. Experimental data of D(T) of small proteins were used to establish the optimum value of sigma = 4.5 A for amino acids. The lack of experimental data on tau(R) for proteins restricted the tests to the translational diffusion properties. PMID:10620274

Signaling pathway for phagocyte priming upon encounter with apoptotic cells

PubMed Central

Ando, Yuki; Kanetani, Takuto; Hoshi, Chiharu; Nakai, Yuji

2017-01-01

The phagocytic elimination of cells undergoing apoptosis is an evolutionarily conserved innate immune mechanism for eliminating unnecessary cells. Previous studies showed an increase in the level of engulfment receptors in phagocytes after the phagocytosis of apoptotic cells, which leads to the enhancement of their phagocytic activity. However, precise mechanisms underlying this phenomenon require further clarification. We found that the pre-incubation of a Drosophila phagocyte cell line with the fragments of apoptotic cells enhanced the subsequent phagocytosis of apoptotic cells, accompanied by an augmented expression of the engulfment receptors Draper and integrin αPS3. The DNA-binding activity of the transcription repressor Tailless was transiently raised in those phagocytes, depending on two partially overlapping signal-transduction pathways for the induction of phagocytosis as well as the occurrence of engulfment. The RNAi knockdown of tailless in phagocytes abrogated the enhancement of both phagocytosis and engulfment receptor expression. Furthermore, the hemocyte-specific RNAi of tailless reduced apoptotic cell clearance in Drosophila embryos. Taken together, we propose the following mechanism for the activation of Drosophila phagocytes after an encounter with apoptotic cells: two partially overlapping signal-transduction pathways for phagocytosis are initiated; transcription repressor Tailless is activated; expression of engulfment receptors is stimulated; and phagocytic activity is enhanced. This phenomenon most likely ensures the phagocytic elimination of apoptotic cells by stimulated phagocytes and is thus considered as a mechanism to prime phagocytes in innate immunity. PMID:28325838

75 FR 25844 - Class Deviation From FAR 52.219-7, Notice of Partial Small Business Set-Aside

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-10

... Small Business Set-Aside AGENCY: Defense Logistics Agency, DoD. ACTION: Notice. SUMMARY: This is to...) regarding partial small business set-asides for Defense Logistics Agency (DLA), Defense Energy Support Center (DESC) bulk fuels solicitations and resulting contract awards. DLA is requesting Department of...

Comparative mRNA analysis of behavioral and genetic mouse models of aggression.

PubMed

Malki, Karim; Tosto, Maria G; Pain, Oliver; Sluyter, Frans; Mineur, Yann S; Crusio, Wim E; de Boer, Sietse; Sandnabba, Kenneth N; Kesserwani, Jad; Robinson, Edward; Schalkwyk, Leonard C; Asherson, Philip

2016-04-01

Mouse models of aggression have traditionally compared strains, most notably BALB/cJ and C57BL/6. However, these strains were not designed to study aggression despite differences in aggression-related traits and distinct reactivity to stress. This study evaluated expression of genes differentially regulated in a stress (behavioral) mouse model of aggression with those from a recent genetic mouse model aggression. The study used a discovery-replication design using two independent mRNA studies from mouse brain tissue. The discovery study identified strain (BALB/cJ and C57BL/6J) × stress (chronic mild stress or control) interactions. Probe sets differentially regulated in the discovery set were intersected with those uncovered in the replication study, which evaluated differences between high and low aggressive animals from three strains specifically bred to study aggression. Network analysis was conducted on overlapping genes uncovered across both studies. A significant overlap was found with the genetic mouse study sharing 1,916 probe sets with the stress model. Fifty-one probe sets were found to be strongly dysregulated across both studies mapping to 50 known genes. Network analysis revealed two plausible pathways including one centered on the UBC gene hub which encodes ubiquitin, a protein well-known for protein degradation, and another on P38 MAPK. Findings from this study support the stress model of aggression, which showed remarkable molecular overlap with a genetic model. The study uncovered a set of candidate genes including the Erg2 gene, which has previously been implicated in different psychopathologies. The gene networks uncovered points at a Redox pathway as potentially being implicated in aggressive related behaviors. © 2016 Wiley Periodicals, Inc.

Critical Points and Traveling Wave in Locomotion: Experimental Evidence and Some Theoretical Considerations.

PubMed

Saltiel, Philippe; d'Avella, Andrea; Tresch, Matthew C; Wyler, Kuno; Bizzi, Emilio

2017-01-01

The central pattern generator (CPG) architecture for rhythm generation remains partly elusive. We compare cat and frog locomotion results, where the component unrelated to pattern formation appears as a temporal grid, and traveling wave respectively. Frog spinal cord microstimulation with N-methyl-D-Aspartate (NMDA), a CPG activator, produced a limited set of force directions, sometimes tonic, but more often alternating between directions similar to the tonic forces. The tonic forces were topographically organized, and sites evoking rhythms with different force subsets were located close to the constituent tonic force regions. Thus CPGs consist of topographically organized modules. Modularity was also identified as a limited set of muscle synergies whose combinations reconstructed the EMGs. The cat CPG was investigated using proprioceptive inputs during fictive locomotion. Critical points identified both as abrupt transitions in the effect of phasic perturbations, and burst shape transitions, had biomechanical correlates in intact locomotion. During tonic proprioceptive perturbations, discrete shifts between these critical points explained the burst durations changes, and amplitude changes occurred at one of these points. Besides confirming CPG modularity, these results suggest a fixed temporal grid of anchoring points, to shift modules onsets and offsets. Frog locomotion, reconstructed with the NMDA synergies, showed a partially overlapping synergy activation sequence. Using the early synergy output evoked by NMDA at different spinal sites, revealed a rostrocaudal topographic organization, where each synergy is preferentially evoked from a few, albeit overlapping, cord regions. Comparing the locomotor synergy sequence with this topography suggests that a rostrocaudal traveling wave would activate the synergies in the proper sequence for locomotion. This output was reproduced in a two-layer model using this topography and a traveling wave. Together our results suggest two CPG components: modules, i.e., synergies; and temporal patterning, seen as a temporal grid in the cat, and a traveling wave in the frog. Animal and limb navigation have similarities. Research relating grid cells to the theta rhythm and on segmentation during navigation may relate to our temporal grid and traveling wave results. Winfree's mathematical work, combining critical phases and a traveling wave, also appears important. We conclude suggesting tracing, and imaging experiments to investigate our CPG model.

Combined node and link partitions method for finding overlapping communities in complex networks

PubMed Central

Jin, Di; Gabrys, Bogdan; Dang, Jianwu

2015-01-01

Community detection in complex networks is a fundamental data analysis task in various domains, and how to effectively find overlapping communities in real applications is still a challenge. In this work, we propose a new unified model and method for finding the best overlapping communities on the basis of the associated node and link partitions derived from the same framework. Specifically, we first describe a unified model that accommodates node and link communities (partitions) together, and then present a nonnegative matrix factorization method to learn the parameters of the model. Thereafter, we infer the overlapping communities based on the derived node and link communities, i.e., determine each overlapped community between the corresponding node and link community with a greedy optimization of a local community function conductance. Finally, we introduce a model selection method based on consensus clustering to determine the number of communities. We have evaluated our method on both synthetic and real-world networks with ground-truths, and compared it with seven state-of-the-art methods. The experimental results demonstrate the superior performance of our method over the competing ones in detecting overlapping communities for all analysed data sets. Improved performance is particularly pronounced in cases of more complicated networked community structures. PMID:25715829

One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy

PubMed Central

Casini, Arturo; MacDonald, James T.; Jonghe, Joachim De; Christodoulou, Georgia; Freemont, Paul S.; Baldwin, Geoff S.; Ellis, Tom

2014-01-01

Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer this, we present MODAL: a Modular Overlap-Directed Assembly with Linkers strategy that brings modularity to overlap-directed methods, allowing assembly of an initial set of DNA parts into a variety of arrangements in one-pot reactions. MODAL is accompanied by a custom software tool that designs overlap linkers to guide assembly, allowing parts to be assembled in any specified order and orientation. The in silico design of synthetic orthogonal overlapping junctions allows for much greater efficiency in DNA assembly for a variety of different methods compared with using non-designed sequence. In tests with three different assembly technologies, the MODAL strategy gives assembly of both yeast and bacterial plasmids, composed of up to five DNA parts in the kilobase range with efficiencies of between 75 and 100%. It also seamlessly allows mutagenesis to be performed on any specified DNA parts during the process, allowing the one-step creation of construct libraries valuable for synthetic biology applications. PMID:24153110

Stress Reactivity in Traditional Chinese Medicine–Based Subgroups of Patients with Irritable Bowel Syndrome

PubMed Central

Chang, Megan C.; Shapiro, David; Joshi, Aditi; Shahabi, Leila; Tan, Steven; Smith, Suzanne; Hui, Ka Kit; Tillisch, Kirsten; Mayer, Emeran A.

2014-01-01

Abstract Objectives: This study aimed to examine differences in autonomic responses to stress, pain perception, and the role of negative affect in these responses in individuals with irritable bowel syndrome (IBS) according to Traditional Chinese Medicine (TCM) classifications. Design: Fifty-nine female patients with IBS age 18–65 years diagnosed by TCM practitioners as showing primarily an excess (n=32) or an overlap (n=27) pattern (mixed excess and deficiency) were assessed for symptom differences, heart rate, and skin conductance responses to a psychosocial stressor and pain perception. Settings/Locations: University of California in Los Angeles, California. Results: Compared with the excess group, the overlap group showed significantly greater overall gastrointestinal symptom severity, abdominal pain, and negative affect. The excess group with higher levels of negative affect showed greater reactivity to stress, whereas the overlap group showed an opposite response pattern. The overlap group showed increased cold sensitivity. Conclusions: IBS patients with the overlap pattern have greater disease severity and comorbidity than those with excess alone. Those with excess showed a pattern of increased stress response with greater negative affect, whereas the overlap group with greater deficiency showed lower physiologic arousal with greater negative affect, consistent with depletion resulting from allostatic load. PMID:24256027

Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes.

PubMed

Jin, Ya; Yuan, Qi; Zhang, Jun; Manabe, Takashi; Tan, Wen

2015-09-01

Human bronchial smooth muscle cell soluble proteins were analyzed by a combined method of nondenaturing micro 2DE, grid gel-cutting, and quantitative LC-MS/MS and a native protein map was prepared for each of the identified 4323 proteins [1]. A method to evaluate the degree of similarity between the protein maps was developed since we expected the proteins comprising a protein complex would be separated together under nondenaturing conditions. The following procedure was employed using Excel macros; (i) maps that have three or more squares with protein quantity data were selected (2328 maps), (ii) within each map, the quantity values of the squares were normalized setting the highest value to be 1.0, (iii) in comparing a map with another map, the smaller normalized quantity in two corresponding squares was taken and summed throughout the map to give an "overlap score," (iv) each map was compared against all the 2328 maps and the largest overlap score, obtained when a map was compared with itself, was set to be 1.0 thus providing 2328 "overlap factors," (v) step (iv) was repeated for all maps providing 2328 × 2328 matrix of overlap factors. From the matrix, protein pairs that showed overlap factors above 0.65 from both protein sides were selected (431 protein pairs). Each protein pair was searched in a database (UniProtKB) on complex formation and 301 protein pairs, which comprise 35 protein complexes, were found to be documented. These results demonstrated that native protein maps and their similarity search would enable simultaneous analysis of multiple protein complexes in cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Information-optimal genome assembly via sparse read-overlap graphs.

PubMed

Shomorony, Ilan; Kim, Samuel H; Courtade, Thomas A; Tse, David N C

2016-09-01

In the context of third-generation long-read sequencing technologies, read-overlap-based approaches are expected to play a central role in the assembly step. A fundamental challenge in assembling from a read-overlap graph is that the true sequence corresponds to a Hamiltonian path on the graph, and, under most formulations, the assembly problem becomes NP-hard, restricting practical approaches to heuristics. In this work, we avoid this seemingly fundamental barrier by first setting the computational complexity issue aside, and seeking an algorithm that targets information limits In particular, we consider a basic feasibility question: when does the set of reads contain enough information to allow unambiguous reconstruction of the true sequence? Based on insights from this information feasibility question, we present an algorithm-the Not-So-Greedy algorithm-to construct a sparse read-overlap graph. Unlike most other assembly algorithms, Not-So-Greedy comes with a performance guarantee: whenever information feasibility conditions are satisfied, the algorithm reduces the assembly problem to an Eulerian path problem on the resulting graph, and can thus be solved in linear time. In practice, this theoretical guarantee translates into assemblies of higher quality. Evaluations on both simulated reads from real genomes and a PacBio Escherichia coli K12 dataset demonstrate that Not-So-Greedy compares favorably with standard string graph approaches in terms of accuracy of the resulting read-overlap graph and contig N50. Available at github.com/samhykim/nsg courtade@eecs.berkeley.edu or dntse@stanford.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

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

MacArthur, Stewart; Li, Xiao-Yong; Li, Jingyi

2009-05-15

BACKGROUND: We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less conserved non-coding DNA, suggesting that many are likely non-functional. RESULTS: Here we show that an additional 15 transcription factors that regulate other aspects of embryo patterning show a similar quantitative continuum of functionmore » and binding to thousands of genomic regions in vivo. Collectively, the 21 regulators show a surprisingly high overlap in the regions they bind given that they belong to 11 DNA binding domain families, specify distinct developmental fates, and can act via different cis-regulatory modules. We demonstrate, however, that quantitative differences in relative levels of binding to shared targets correlate with the known biological and transcriptional regulatory specificities of these factors. CONCLUSIONS: It is likely that the overlap in binding of biochemically and functionally unrelated transcription factors arises from the high concentrations of these proteins in nuclei, which, coupled with their broad DNA binding specificities, directs them to regions of open chromatin. We suggest that most animal transcription factors will be found to show a similar broad overlapping pattern of binding in vivo, with specificity achieved by modulating the amount, rather than the identity, of bound factor.« less

77 FR 64737 - Partial Approval and Partial Disapproval of Air Quality State Implementation Plans; Nevada...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-23

... standard was set at 15 micrograms per cubic meter ([mu]g/m\\3\\), based on the 3-year average of annual... 2.5 standard was set at 65 [mu]g/m\\3\\, based on the 3- year average of the 98th percentile of 24... partially approve the submittal based on EPA's independent evaluation of Nevada's impact on receptor states...

The effect of monetary punishment on error evaluation in a Go/No-go task.

PubMed

Maruo, Yuya; Sommer, Werner; Masaki, Hiroaki

2017-10-01

Little is known about the effects of the motivational significance of errors in Go/No-go tasks. We investigated the impact of monetary punishment on the error-related negativity (ERN) and error positivity (Pe) for both overt errors and partial errors, that is, no-go trials without overt responses but with covert muscle activities. We compared high and low punishment conditions where errors were penalized with 50 or 5 yen, respectively, and a control condition without monetary consequences for errors. Because we hypothesized that the partial-error ERN might overlap with the no-go N2, we compared ERPs between correct rejections (i.e., successful no-go trials) and partial errors in no-go trials. We also expected that Pe amplitudes should increase with the severity of the penalty for errors. Mean error rates were significantly lower in the high punishment than in the control condition. Monetary punishment did not influence the overt-error ERN and partial-error ERN in no-go trials. The ERN in no-go trials did not differ between partial errors and overt errors; in addition, ERPs for correct rejections in no-go trials without partial errors were of the same size as in go-trial. Therefore the overt-error ERN and the partial-error ERN may share similar error monitoring processes. Monetary punishment increased Pe amplitudes for overt errors, suggesting enhanced error evaluation processes. For partial errors an early Pe was observed, presumably representing inhibition processes. Interestingly, even partial errors elicited the Pe, suggesting that covert erroneous activities could be detected in Go/No-go tasks. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Down-weighting overlapping genes improves gene set analysis

PubMed Central

2012-01-01

Background The identification of gene sets that are significantly impacted in a given condition based on microarray data is a crucial step in current life science research. Most gene set analysis methods treat genes equally, regardless how specific they are to a given gene set. Results In this work we propose a new gene set analysis method that computes a gene set score as the mean of absolute values of weighted moderated gene t-scores. The gene weights are designed to emphasize the genes appearing in few gene sets, versus genes that appear in many gene sets. We demonstrate the usefulness of the method when analyzing gene sets that correspond to the KEGG pathways, and hence we called our method Pathway Analysis with Down-weighting of Overlapping Genes (PADOG). Unlike most gene set analysis methods which are validated through the analysis of 2-3 data sets followed by a human interpretation of the results, the validation employed here uses 24 different data sets and a completely objective assessment scheme that makes minimal assumptions and eliminates the need for possibly biased human assessments of the analysis results. Conclusions PADOG significantly improves gene set ranking and boosts sensitivity of analysis using information already available in the gene expression profiles and the collection of gene sets to be analyzed. The advantages of PADOG over other existing approaches are shown to be stable to changes in the database of gene sets to be analyzed. PADOG was implemented as an R package available at: http://bioinformaticsprb.med.wayne.edu/PADOG/or http://www.bioconductor.org. PMID:22713124

Sliding perspectives: dissociating ownership from self-location during full body illusions in virtual reality

PubMed Central

Maselli, Antonella; Slater, Mel

2014-01-01

Bodily illusions have been used to study bodily self-consciousness and disentangle its various components, among other the sense of ownership and self-location. Congruent multimodal correlations between the real body and a fake humanoid body can in fact trigger the illusion that the fake body is one's own and/or disrupt the unity between the perceived self-location and the position of the physical body. However, the extent to which changes in self-location entail changes in ownership is still matter of debate. Here we address this problem with the support of immersive virtual reality. Congruent visuotactile stimulation was delivered on healthy participants to trigger full body illusions from different visual perspectives, each resulting in a different degree of overlap between real and virtual body. Changes in ownership and self-location were measured with novel self-posture assessment tasks and with an adapted version of the cross-modal congruency task. We found that, despite their strong coupling, self-location and ownership can be selectively altered: self-location was affected when having a third person perspective over the virtual body, while ownership toward the virtual body was experienced only in the conditions with total or partial overlap. Thus, when the virtual body is seen in the far extra-personal space, changes in self-location were not coupled with changes in ownership. If a partial spatial overlap is present, ownership was instead typically experienced with a boosted change in the perceived self-location. We discussed results in the context of the current knowledge of the multisensory integration mechanisms contributing to self-body perception. We argue that changes in the perceived self-location are associated to the dynamical representation of peripersonal space encoded by visuotactile neurons. On the other hand, our results speak in favor of visuo-proprioceptive neuronal populations being a driving trigger in full body ownership illusions. PMID:25309383

Novel pure component contribution, mean centering of ratio spectra and factor based algorithms for simultaneous resolution and quantification of overlapped spectral signals: An application to recently co-formulated tablets of chlorzoxazone, aceclofenac and paracetamol

NASA Astrophysics Data System (ADS)

Toubar, Safaa S.; Hegazy, Maha A.; Elshahed, Mona S.; Helmy, Marwa I.

2016-06-01

In this work, resolution and quantitation of spectral signals are achieved by several univariate and multivariate techniques. The novel pure component contribution algorithm (PCCA) along with mean centering of ratio spectra (MCR) and the factor based partial least squares (PLS) algorithms were developed for simultaneous determination of chlorzoxazone (CXZ), aceclofenac (ACF) and paracetamol (PAR) in their pure form and recently co-formulated tablets. The PCCA method allows the determination of each drug at its λmax. While, the mean centered values at 230, 302 and 253 nm, were used for quantification of CXZ, ACF and PAR, respectively, by MCR method. Partial least-squares (PLS) algorithm was applied as a multivariate calibration method. The three methods were successfully applied for determination of CXZ, ACF and PAR in pure form and tablets. Good linear relationships were obtained in the ranges of 2-50, 2-40 and 2-30 μg mL- 1 for CXZ, ACF and PAR, in order, by both PCCA and MCR, while the PLS model was built for the three compounds each in the range of 2-10 μg mL- 1. The results obtained from the proposed methods were statistically compared with a reported one. PCCA and MCR methods were validated according to ICH guidelines, while PLS method was validated by both cross validation and an independent data set. They are found suitable for the determination of the studied drugs in bulk powder and tablets.

Study of the modes of adsorption and electronic structure of hydrogen peroxide and ethanol over TiO2 rutile (110) surface within the context of water splitting

NASA Astrophysics Data System (ADS)

Alghamdi, H.; Idriss, H.

2018-03-01

While photocatalytic water splitting over many materials is favourable thermodynamically the kinetic of the reaction is very slow. One of the proposed reasons linked to the slow oxidation reaction rate is H2O2 formation as a reaction intermediate. Using Density Functional Theory (DFT) H2O2 is investigated on TiO2 rutile (110) surface to determine its most stable adsorption modes: molecular, (H)O(H)O - (a), partially dissociated, (H)OO - (a), and fully dissociated (a) - OO - (a). We then compare H2O2 interaction to that of a fast hole scavenger molecule, ethanol. Geometry, electronic structure, charge density difference and work function determination of both adsorbates are presented and compared using DFT with different functionals (PBE, PBE-D, PBE-U, and HSE + D). H2O2 is found to be strongly adsorbed on TiO2 rutile (110) surface with adsorption energies reaching 0.95 eV, comparable to that of ethanol (0.89 eV); using GGA PBE. The negative changes in the work function upon adsorption were found to be highest for molecular adsorption ( - 1.23 eV) and lowest for the fully dissociated mode ( - 0.54 eV) of H2O2. This may indicate that electrons flow from the surface to the adsorbate in order to make O(s)-H partially offset the overall magnitude of the oxygen lone pair interaction (of H2O2) with Ti4+ cations. Examination of the electronic structure through density of states (DOS) at the PBE level of computation, indicates that the H2O2 highest occupied molecular orbital (HOMO) level is not overlapping with oxygen atoms of TiO2 surface at any of its adsorption modes and at any of the computation methods. Some overlap is seen using the HSE + D computational method. On the other hand the dissociated mode of ethanol (ethoxides) does overlap with all computational methods used. The high adsorption energy and the absence of overlapping of the HOMO level of H2O2 with TiO2 rutile (110) surface may explain why water splitting is slow.

Asynchronous partial contact motion due to internal resonance in multiple degree-of-freedom rotordynamics

NASA Astrophysics Data System (ADS)

Shaw, A. D.; Champneys, A. R.; Friswell, M. I.

2016-08-01

Sudden onset of violent chattering or whirling rotor-stator contact motion in rotational machines can cause significant damage in many industrial applications. It is shown that internal resonance can lead to the onset of bouncing-type partial contact motion away from primary resonances. These partial contact limit cycles can involve any two modes of an arbitrarily high degree-of-freedom system, and can be seen as an extension of a synchronization condition previously reported for a single disc system. The synchronization formula predicts multiple drivespeeds, corresponding to different forms of mode-locked bouncing orbits. These results are backed up by a brute-force bifurcation analysis which reveals numerical existence of the corresponding family of bouncing orbits at supercritical drivespeeds, provided the damping is sufficiently low. The numerics reveal many overlapping families of solutions, which leads to significant multi-stability of the response at given drive speeds. Further, secondary bifurcations can also occur within each family, altering the nature of the response and ultimately leading to chaos. It is illustrated how stiffness and damping of the stator have a large effect on the number and nature of the partial contact solutions, illustrating the extreme sensitivity that would be observed in practice.

Fast Metabolite Identification in Nuclear Magnetic Resonance Metabolomic Studies: Statistical Peak Sorting and Peak Overlap Detection for More Reliable Database Queries.

PubMed

Hoijemberg, Pablo A; Pelczer, István

2018-01-05

A lot of time is spent by researchers in the identification of metabolites in NMR-based metabolomic studies. The usual metabolite identification starts employing public or commercial databases to match chemical shifts thought to belong to a given compound. Statistical total correlation spectroscopy (STOCSY), in use for more than a decade, speeds the process by finding statistical correlations among peaks, being able to create a better peak list as input for the database query. However, the (normally not automated) analysis becomes challenging due to the intrinsic issue of peak overlap, where correlations of more than one compound appear in the STOCSY trace. Here we present a fully automated methodology that analyzes all STOCSY traces at once (every peak is chosen as driver peak) and overcomes the peak overlap obstacle. Peak overlap detection by clustering analysis and sorting of traces (POD-CAST) first creates an overlap matrix from the STOCSY traces, then clusters the overlap traces based on their similarity and finally calculates a cumulative overlap index (COI) to account for both strong and intermediate correlations. This information is gathered in one plot to help the user identify the groups of peaks that would belong to a single molecule and perform a more reliable database query. The simultaneous examination of all traces reduces the time of analysis, compared to viewing STOCSY traces by pairs or small groups, and condenses the redundant information in the 2D STOCSY matrix into bands containing similar traces. The COI helps in the detection of overlapping peaks, which can be added to the peak list from another cross-correlated band. POD-CAST overcomes the generally overlooked and underestimated presence of overlapping peaks and it detects them to include them in the search of all compounds contributing to the peak overlap, enabling the user to accelerate the metabolite identification process with more successful database queries and searching all tentative compounds in the sample set.

On the Automaticity of the Evaluative Priming Effect in the Valent/Non-Valent Categorization Task

PubMed Central

Spruyt, Adriaan; Tibboel, Helen

2015-01-01

It has previously been argued (a) that automatic evaluative stimulus processing is critically dependent upon feature-specific attention allocation and (b) that evaluative priming effects can arise in the absence of dimensional overlap between the prime set and the response set. In line with both claims, research conducted at our lab revealed that the evaluative priming effect replicates in the valent/non-valent categorization task. This research was criticized, however, because non-automatic, strategic processes may have contributed to the emergence of this effect. We now report the results of a replication study in which the operation of non-automatic, strategic processes was controlled for. A clear-cut evaluative priming effect emerged, thus supporting initial claims concerning feature-specific attention allocation and dimensional overlap. PMID:25803444

On the automaticity of the evaluative priming effect in the valent/non-valent categorization task.

PubMed

Spruyt, Adriaan; Tibboel, Helen

2015-01-01

It has previously been argued (a) that automatic evaluative stimulus processing is critically dependent upon feature-specific attention allocation and (b) that evaluative priming effects can arise in the absence of dimensional overlap between the prime set and the response set. In line with both claims, research conducted at our lab revealed that the evaluative priming effect replicates in the valent/non-valent categorization task. This research was criticized, however, because non-automatic, strategic processes may have contributed to the emergence of this effect. We now report the results of a replication study in which the operation of non-automatic, strategic processes was controlled for. A clear-cut evaluative priming effect emerged, thus supporting initial claims concerning feature-specific attention allocation and dimensional overlap.

Rejection Sensitivity Mediates the Relationship between Social Anxiety and Body Dysmorphic Concerns

PubMed Central

Fang, Angela; Asnaani, Anu; Gutner, Cassidy; Cook, Courtney; Wilhelm, Sabine; Hofmann, Stefan G.

2011-01-01

The goal of this study was to examine the role of rejection sensitivity in the relationship between social anxiety and body dysmorphic concerns. To test our hypothesis that rejection sensitivity mediates the link between social anxiety and body dysmorphic concerns, we administered self-report questionnaires to 209 student volunteers. Consistent with our prediction, rejection sensitivity partially mediated the relationship between social anxiety symptoms and body dysmorphic concerns. The implications of the overlap between these constructs are discussed. PMID:21741203

Stitching of near-nulled subaperture measurements

NASA Technical Reports Server (NTRS)

Devries, Gary (Inventor); Brophy, Christopher (Inventor); Forbes, Greg (Inventor); Murphy, Paul (Inventor)

2012-01-01

A metrology system for measuring aspheric test objects by subaperture stitching. A wavefront-measuring gauge having a limited capture range of wavefront shapes collects partially overlapping subaperture measurements over the test object. A variable optical aberrator reshapes the measurement wavefront with between a limited number of the measurements to maintain the measurement wavefront within the capture range of the wavefront-measuring gauge. Various error compensators are incorporated into a stitching operation to manage residual errors associated with the use of the variable optical aberrator.

Controlling the Electronic Structure of Graphene Using Surface-Adsorbate Interactions

DTIC Science & Technology

2015-07-21

after adsorption of Na the propensity of graphene bonding to Ni is much lower due to reduced overlap of atomic orbitals, which results from n- doping of...subse- quent intercalation of the Na underneath graphene. The ability to partially decouple graphene from a Ni substrate via n- doping (with or without...interactions with the substrate or adsorbates, which can modify the energy of the Dirac cone through doping , or cause a band gap to open at the K

Development and Testing of a New Area Search Model with Partially Overlapping Target and Searcher Patrol Areas

DTIC Science & Technology

2008-12-01

1, /(2 ) T T VR A t A VR f t t F t VRt A t A VR t A VR ∈⎧ = ⎨ ⎩ <⎧ ⎪= ∈⎨ ⎪ >⎩ (2) The mean time to detection is given by...follows: Exhaustive Search (Black line): ( ) (2 ) /T sF t VRt A= . Random Search (Pink line): 2( ) 1 (1 / ) exp( 2 / )T s sF t R A RVt Aπ

Revised Mechanism and Improved Efficiency of the QuikChange Site-Directed Mutagenesis Method.

PubMed

Xia, Yongzhen; Xun, Luying

2017-01-01

Site-directed mutagenesis has been widely used for the substitution, addition or deletion of nucleotide residues in a defined DNA sequence. QuikChange™ site-directed mutagenesis and its related protocols have been widely used for this purpose because of convenience and efficiency. We have recently demonstrated that the mechanism of the QuikChange™ site-directed mutagenesis process is different from that being proposed. The new mechanism promotes the use of partially overlapping primers and commercial PCR enzymes for efficient PCR and mutagenesis.

STBase: One Million Species Trees for Comparative Biology

PubMed Central

McMahon, Michelle M.; Deepak, Akshay; Fernández-Baca, David; Boss, Darren; Sanderson, Michael J.

2015-01-01

Comprehensively sampled phylogenetic trees provide the most compelling foundations for strong inferences in comparative evolutionary biology. Mismatches are common, however, between the taxa for which comparative data are available and the taxa sampled by published phylogenetic analyses. Moreover, many published phylogenies are gene trees, which cannot always be adapted immediately for species level comparisons because of discordance, gene duplication, and other confounding biological processes. A new database, STBase, lets comparative biologists quickly retrieve species level phylogenetic hypotheses in response to a query list of species names. The database consists of 1 million single- and multi-locus data sets, each with a confidence set of 1000 putative species trees, computed from GenBank sequence data for 413,000 eukaryotic taxa. Two bodies of theoretical work are leveraged to aid in the assembly of multi-locus concatenated data sets for species tree construction. First, multiply labeled gene trees are pruned to conflict-free singly-labeled species-level trees that can be combined between loci. Second, impacts of missing data in multi-locus data sets are ameliorated by assembling only decisive data sets. Data sets overlapping with the user’s query are ranked using a scheme that depends on user-provided weights for tree quality and for taxonomic overlap of the tree with the query. Retrieval times are independent of the size of the database, typically a few seconds. Tree quality is assessed by a real-time evaluation of bootstrap support on just the overlapping subtree. Associated sequence alignments, tree files and metadata can be downloaded for subsequent analysis. STBase provides a tool for comparative biologists interested in exploiting the most relevant sequence data available for the taxa of interest. It may also serve as a prototype for future species tree oriented databases and as a resource for assembly of larger species phylogenies from precomputed trees. PMID:25679219

Using partial site aggregation to reduce bias in random utility travel cost models

NASA Astrophysics Data System (ADS)

Lupi, Frank; Feather, Peter M.

1998-12-01

We propose a "partial aggregation" strategy for defining the recreation sites that enter choice sets in random utility models. Under the proposal, the most popular sites and sites that will be the subject of policy analysis enter choice sets as individual sites while remaining sites are aggregated into groups of similar sites. The scheme balances the desire to include all potential substitute sites in the choice sets with practical data and modeling constraints. Unlike fully aggregate models, our analysis and empirical applications suggest that the partial aggregation approach reasonably approximates the results of a disaggregate model. The partial aggregation approach offers all of the data and computational advantages of models with aggregate sites but does not suffer from the same degree of bias as fully aggregate models.

Overlapping Chronic Pain Conditions: Implications for Diagnosis and Classification.

PubMed

Maixner, William; Fillingim, Roger B; Williams, David A; Smith, Shad B; Slade, Gary D

2016-09-01

There is increasing recognition that many if not most common chronic pain conditions are heterogeneous with a high degree of overlap or coprevalence of other common pain conditions along with influences from biopsychosocial factors. At present, very little attention is given to the high degree of overlap of many common pain conditions when recruiting for clinical trials. As such, many if not most patients enrolled into clinical studies are not representative of most chronic pain patients. The failure to account for the heterogeneous and overlapping nature of most common pain conditions may result in treatment responses of small effect size when these treatments are administered to patients with chronic overlapping pain conditions (COPCs) represented in the general population. In this brief review we describe the concept of COPCs and the putative mechanisms underlying COPCs. Finally, we present a series of recommendations that will advance our understanding of COPCs. This brief review describes the concept of COPCs. A mechanism-based heuristic model is presented and current knowledge and evidence for COPCs are presented. Finally, a set of recommendations is provided to advance our understanding of COPCs. Copyright © 2016 American Pain Society. Published by Elsevier Inc. All rights reserved.

Locating overlapping dense subgraphs in gene (protein) association networks and predicting novel protein functional groups among these subgraphs

NASA Astrophysics Data System (ADS)

Palla, Gergely; Derenyi, Imre; Farkas, Illes J.; Vicsek, Tamas

2006-03-01

Most tasks in a cell are performed not by individual proteins, but by functional groups of proteins (either physically interacting with each other or associated in other ways). In gene (protein) association networks these groups show up as sets of densely connected nodes. In the yeast, Saccharomyces cerevisiae, known physically interacting groups of proteins (called protein complexes) strongly overlap: the total number of proteins contained by these complexes by far underestimates the sum of their sizes (2750 vs. 8932). Thus, most functional groups of proteins, both physically interacting and other, are likely to share many of their members with other groups. However, current algorithms searching for dense groups of nodes in networks usually exclude overlaps. With the aim to discover both novel functions of individual proteins and novel protein functional groups we combine in protein association networks (i) a search for overlapping dense subgraphs based on the Clique Percolation Method (CPM) (Palla, G., et.al. Nature 435, 814-818 (2005), http://angel.elte.hu/clustering), which explicitly allows for overlaps among the groups, and (ii) a verification and characterization of the identified groups of nodes (proteins) with the help of standard annotation databases listing known functions.

An RGB colour image steganography scheme using overlapping block-based pixel-value differencing

PubMed Central

Pal, Arup Kumar

2017-01-01

This paper presents a steganographic scheme based on the RGB colour cover image. The secret message bits are embedded into each colour pixel sequentially by the pixel-value differencing (PVD) technique. PVD basically works on two consecutive non-overlapping components; as a result, the straightforward conventional PVD technique is not applicable to embed the secret message bits into a colour pixel, since a colour pixel consists of three colour components, i.e. red, green and blue. Hence, in the proposed scheme, initially the three colour components are represented into two overlapping blocks like the combination of red and green colour components, while another one is the combination of green and blue colour components, respectively. Later, the PVD technique is employed on each block independently to embed the secret data. The two overlapping blocks are readjusted to attain the modified three colour components. The notion of overlapping blocks has improved the embedding capacity of the cover image. The scheme has been tested on a set of colour images and satisfactory results have been achieved in terms of embedding capacity and upholding the acceptable visual quality of the stego-image. PMID:28484623

13 CFR 121.412 - What are the size procedures for partial small business set-asides?

Code of Federal Regulations, 2010 CFR

2010-01-01

... Requirements for Government Procurement § 121.412 What are the size procedures for partial small business set... portion of a procurement, and is not required to qualify as a small business for the unrestricted portion. ...

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

Papajak, Ewa; Truhlar, Donald G.

We present sets of convergent, partially augmented basis set levels corresponding to subsets of the augmented “aug-cc-pV(n+d)Z” basis sets of Dunning and co-workers. We show that for many molecular properties a basis set fully augmented with diffuse functions is computationally expensive and almost always unnecessary. On the other hand, unaugmented cc-pV(n+d)Z basis sets are insufficient for many properties that require diffuse functions. Therefore, we propose using intermediate basis sets. We developed an efficient strategy for partial augmentation, and in this article, we test it and validate it. Sequentially deleting diffuse basis functions from the “aug” basis sets yields the “jul”,more » “jun”, “may”, “apr”, etc. basis sets. Tests of these basis sets for Møller-Plesset second-order perturbation theory (MP2) show the advantages of using these partially augmented basis sets and allow us to recommend which basis sets offer the best accuracy for a given number of basis functions for calculations on large systems. Similar truncations in the diffuse space can be performed for the aug-cc-pVxZ, aug-cc-pCVxZ, etc. basis sets.« less

Comparison of clinical knowledge bases for summarization of electronic health records.

PubMed

McCoy, Allison B; Sittig, Dean F; Wright, Adam

2013-01-01

Automated summarization tools that create condition-specific displays may improve clinician efficiency. These tools require new kinds of knowledge that is difficult to obtain. We compared five problem-medication pair knowledge bases generated using four previously described knowledge base development approaches. The number of pairs in the resulting mapped knowledge bases varied widely due to differing mapping techniques from the source terminologies, ranging from 2,873 to 63,977,738 pairs. The number of overlapping pairs across knowledge bases was low, with one knowledge base having half of the pairs overlapping with another knowledge base, and most having less than a third overlapping. Further research is necessary to better evaluate the knowledge bases independently in additional settings, and to identify methods to integrate the knowledge bases.

Dopaminergic neurons encode a distributed, asymmetric representation of temperature in Drosophila.

PubMed

Tomchik, Seth M

2013-01-30

Dopaminergic circuits modulate a wide variety of innate and learned behaviors in animals, including olfactory associative learning, arousal, and temperature-preference behavior. It is not known whether distinct or overlapping sets of dopaminergic neurons modulate these behaviors. Here, I have functionally characterized the dopaminergic circuits innervating the Drosophila mushroom body with in vivo calcium imaging and conditional silencing of genetically defined subsets of neurons. Distinct subsets of PPL1 dopaminergic neurons innervating the vertical lobes of the mushroom body responded to decreases in temperature, but not increases, with rapidly adapting bursts of activity. PAM neurons innervating the horizontal lobes did not respond to temperature shifts. Ablation of the antennae and maxillary palps reduced, but did not eliminate, the responses. Genetic silencing of dopaminergic neurons innervating the vertical mushroom body lobes substantially reduced behavioral cold avoidance, but silencing smaller subsets of these neurons had no effect. These data demonstrate that overlapping dopaminergic circuits encode a broadly distributed, asymmetric representation of temperature that overlays regions implicated previously in learning, memory, and forgetting. Thus, diverse behaviors engage overlapping sets of dopaminergic neurons that encode multimodal stimuli and innervate a single anatomical target, the mushroom body.

Determining attenuation properties of interfering fast and slow ultrasonic waves in cancellous bone.

PubMed

Nelson, Amber M; Hoffman, Joseph J; Anderson, Christian C; Holland, Mark R; Nagatani, Yoshiki; Mizuno, Katsunori; Matsukawa, Mami; Miller, James G

2011-10-01

Previous studies have shown that interference between fast waves and slow waves can lead to observed negative dispersion in cancellous bone. In this study, the effects of overlapping fast and slow waves on measurements of the apparent attenuation as a function of propagation distance are investigated along with methods of analysis used to determine the attenuation properties. Two methods are applied to simulated data that were generated based on experimentally acquired signals taken from a bovine specimen. The first method uses a time-domain approach that was dictated by constraints imposed by the partial overlap of fast and slow waves. The second method uses a frequency-domain log-spectral subtraction technique on the separated fast and slow waves. Applying the time-domain analysis to the broadband data yields apparent attenuation behavior that is larger in the early stages of propagation and decreases as the wave travels deeper. In contrast, performing frequency-domain analysis on the separated fast waves and slow waves results in attenuation coefficients that are independent of propagation distance. Results suggest that features arising from the analysis of overlapping two-mode data may represent an alternate explanation for the previously reported apparent dependence on propagation distance of the attenuation coefficient of cancellous bone. © 2011 Acoustical Society of America

Determining attenuation properties of interfering fast and slow ultrasonic waves in cancellous bone

PubMed Central

Nelson, Amber M.; Hoffman, Joseph J.; Anderson, Christian C.; Holland, Mark R.; Nagatani, Yoshiki; Mizuno, Katsunori; Matsukawa, Mami; Miller, James G.

2011-01-01

Previous studies have shown that interference between fast waves and slow waves can lead to observed negative dispersion in cancellous bone. In this study, the effects of overlapping fast and slow waves on measurements of the apparent attenuation as a function of propagation distance are investigated along with methods of analysis used to determine the attenuation properties. Two methods are applied to simulated data that were generated based on experimentally acquired signals taken from a bovine specimen. The first method uses a time-domain approach that was dictated by constraints imposed by the partial overlap of fast and slow waves. The second method uses a frequency-domain log-spectral subtraction technique on the separated fast and slow waves. Applying the time-domain analysis to the broadband data yields apparent attenuation behavior that is larger in the early stages of propagation and decreases as the wave travels deeper. In contrast, performing frequency-domain analysis on the separated fast waves and slow waves results in attenuation coefficients that are independent of propagation distance. Results suggest that features arising from the analysis of overlapping two-mode data may represent an alternate explanation for the previously reported apparent dependence on propagation distance of the attenuation coefficient of cancellous bone. PMID:21973378

SCF-Xα-SW electron densities with the overlapping sphere approximation

NASA Astrophysics Data System (ADS)

McMaster, Blair N.; Smith, Vedene H., Jr.; Salahub, Dennis R.

Self consistent field-Xα-scattered wave (SCF-Xα-SW) calculations have been performed for a series of eight first and second row homonuclear diatomic molecules using both the touching (TS) and 25 per cent overlapping sphere (OS) versions. The OS deformation density maps exhibit much better quantitative agreement with those from other Xα methods, which do not employ the spherical muffin-tin (MT) potential approximation, than do the TS maps. The OS version thus compensates very effectively for the errors involved in the MT approximation in computing electron densities. A detailed comparison between the TS- and OS-Xα-SW orbitals reveals that the reasons for this improvement are surprisingly specific. The dominant effect of the OS approximation is to increase substantially the electron density near the midpoint of bonding σ orbitals, with a consequent reduction of the density behind the atoms. A similar effect occurs for the bonding π orbitals but is less pronounced. These effects are due to a change in hybridization of the orbitals, with the OS approximation increasing the proportion of the subdominant partial waves and hence changing the shapes of the orbitals. It is this increased orbital polarization which so effectively compensates for the lack of (non-spherically symmetric) polarization components in the MT potential, when overlapping spheres are used.

Evolution of learning in fluctuating environments: when selection favors both social and exploratory individual learning.

PubMed

Borenstein, Elhanan; Feldman, Marcus W; Aoki, Kenichi

2008-03-01

Cumulative cultural change requires organisms that are capable of both exploratory individual learning and faithful social learning. In our model, an organism's phenotype is initially determined innately (by its genotypic value) or by social learning (copying a phenotype from the parental generation), and then may or may not be modified by individual learning (exploration around the initial phenotype). The environment alternates periodically between two states, each defined as a certain range of phenotypes that can survive. These states may overlap, in which case the same phenotype can survive in both states, or they may not. We find that a joint social and exploratory individual learning strategy-the strategy that supports cumulative culture-is likely to spread when the environmental states do not overlap. In particular, when the environmental states are contiguous and mutation is allowed among the genotypic values, this strategy will spread in either moderately or highly stable environments, depending on the exact nature of the individual learning applied. On the other hand, natural selection often favors a social learning strategy without exploration when the environmental states overlap. We find only partial support for the "consensus" view, which holds that individual learning, social learning, and innate determination of behavior will evolve at short, intermediate, and long environmental periodicities, respectively.

Markers of Psychological Differences and Social and Health Inequalities: Possible Genetic and Phenotypic Overlaps.

PubMed

Mõttus, René; Marioni, Riccardo; Deary, Ian J

2017-02-01

Associations between markers of ostensible psychological characteristics and social and health inequalities are pervasive but difficult to explain. In some cases, there may be causal influence flowing from social and health inequalities to psychological differences, whereas sometimes it may be the other way around. Here, we focus on the possibility that some markers that we often consider as indexing different domains of individual differences may in fact reflect at least partially overlapping genetic and/or phenotypic bases. For example, individual differences in cognitive abilities and educational attainment appear to reflect largely overlapping genetic influences, whereas cognitive abilities and health literacy may be almost identical phenomena at the phenotypic, never mind genetic, level. We make the case for employing molecular genetic data and quantitative genetic techniques to better understand the associations of psychological individual differences with social and health inequalities. We illustrate these arguments by using published findings from the Lothian Birth Cohort and the Generation Scotland studies. We also present novel findings pertaining to longitudinal stability and change in older age personality traits and some correlates of the change, molecular genetic data-based heritability estimates of Neuroticism and Extraversion, and the genetic correlations of these personality traits with markers of social and health inequalities. © 2015 The Authors. Journal of Personality published by Wiley Periodicals, Inc.

Electromyographic activity associated with spontaneous functional recovery after spinal cord injury in rats.

PubMed

Kaegi, Sibille; Schwab, Martin E; Dietz, Volker; Fouad, Karim

2002-07-01

This investigation was designed to study the spontaneous functional recovery of adult rats with incomplete spinal cord injury (SCI) at thoracic level during a time course of 2 weeks. Daily testing sessions included open field locomotor examination and electromyographic (EMG) recordings from a knee extensor (vastus lateralis, VL) and an ankle flexor muscle (tibialis anterior, TA) in the hindlimbs of treadmill walking rats. The BBB score (a locomotor score named after Basso et al., 1995, J. Neurotrauma, 12, 1-21) and various measures from EMG recordings were analysed (i.e. step cycle duration, rhythmicity of limb movements, flexor and extensor burst duration, EMG amplitude, root-mean-square, activity overlap between flexor and extensor muscles and hindlimb coupling). Directly after SCI, a marked drop in locomotor ability occurred in all rats with subsequent partial recovery over 14 days. The recovery was most pronounced during the first week. Significant changes were noted in the recovery of almost all analysed EMG measures. Within the 14 days of recovery, many of these measures approached control levels. Persistent abnormalities included a prolonged flexor burst and increased activity overlap between flexor and extensor muscles. Activity overlap between flexor and extensor muscles might be directly caused by altered descending input or by maladaptation of central pattern generating networks and/or sensory feedback.

Diet overlap between harbour porpoise and bottlenose dolphin: An argument in favour of interference competition for food?

NASA Astrophysics Data System (ADS)

Spitz, Jérôme; Rousseau, Yann; Ridoux, Vincent

2006-10-01

In aquatic ecosystems, competitive interactions are occasionally described. Violent attacks on harbour porpoises by bottlenose dolphins were reported and it was proposed that this behavior could result from competitive interactions for food. This hypothesis implies that the two predators should share all or part of they prey range. In this work, we describe the diets of each predator in the Bay of Biscay and adjacent areas from stomach content analysis of stranded animals. The diet of the harbour porpoise was mostly composed of small schooling fish living close to the seafloor (98 percent by mass). The diet of the bottlenose dolphin was characterised by the presence of large specimens of demersal fish (91 percent by mass) and cephalopods. Several prey species are common in the two diets and even the length distributions of some of them, such as sardine or scads, are very similar. However, global indices such as the Mantel test or the Pianka's index indicate no or weak overlap. The dietary results suggest that the two predators show partial dietary overlap over several major dimensions of the foraging niche: prey profile, foraging habitats, prey species and size range. We suggest interference competition is plausible at the scale of a prey school that would be exploited jointly by groups of the two predators.

Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes.

PubMed

Taylor, Louis J; Strebel, Klaus

2017-01-07

Gene knockouts are a common tool used to study gene function in various organisms. However, designing gene knockouts is complicated in viruses, which frequently contain sequences that code for multiple overlapping genes. Designing mutants that can be traced by the creation of new or elimination of existing restriction sites further compounds the difficulty in experimental design of knockouts of overlapping genes. While software is available to rapidly identify restriction sites in a given nucleotide sequence, no existing software addresses experimental design of mutations involving multiple overlapping amino acid sequences in generating gene knockouts. Pyviko performed well on a test set of over 240,000 gene pairs collected from viral genomes deposited in the National Center for Biotechnology Information Nucleotide database, identifying a point mutation which added a premature stop codon within the first 20 codons of the target gene in 93.2% of all tested gene-overprinted gene pairs. This shows that Pyviko can be used successfully in a wide variety of contexts to facilitate the molecular cloning and study of viral overprinted genes. Pyviko is an extensible and intuitive Python tool for designing knockouts of overlapping genes. Freely available as both a Python package and a web-based interface ( http://louiejtaylor.github.io/pyViKO/ ), Pyviko simplifies the experimental design of gene knockouts in complex viruses with overlapping genes.

Reliable Transition State Searches Integrated with the Growing String Method.

PubMed

Zimmerman, Paul

2013-07-09

The growing string method (GSM) is highly useful for locating reaction paths connecting two molecular intermediates. GSM has often been used in a two-step procedure to locate exact transition states (TS), where GSM creates a quality initial structure for a local TS search. This procedure and others like it, however, do not always converge to the desired transition state because the local search is sensitive to the quality of the initial guess. This article describes an integrated technique for simultaneous reaction path and exact transition state search. This is achieved by implementing an eigenvector following optimization algorithm in internal coordinates with Hessian update techniques. After partial convergence of the string, an exact saddle point search begins under the constraint that the maximized eigenmode of the TS node Hessian has significant overlap with the string tangent near the TS. Subsequent optimization maintains connectivity of the string to the TS as well as locks in the TS direction, all but eliminating the possibility that the local search leads to the wrong TS. To verify the robustness of this approach, reaction paths and TSs are found for a benchmark set of more than 100 elementary reactions.

Structural investigation of a self-assembled monolayer material 5-[(3-methylphenyl) (phenyl) amino] isophthalic acid for organic light-emitting devices.

PubMed

Saş, E Babur; Kurt, M; Can, M; Okur, S; İçli, S; Demiç, S

2014-12-10

The molecular structure and vibrations of 5-[(3-methylphenyl) (phenyl) amino] isophthalic acid (MePIFA) were investigated by infrared and Raman spectroscopies, UV-Vis, (1)H and (13)C NMR spectroscopic techniques and NBO analysis. FT-IR, FT-Raman and dispersive Raman spectra were recorded in the solid phase. (1)H and (13)C NMR spectra and UV-Vis spectrum were recorded in DMSO solution. HOMO-LUMO analysis and molecular electrostatic potential (MEP) analysis were performed. The theoretical calculations for the molecular structure and spectroscopies were performed with DFT (B3LYP) and 6-311G(d,p) basis set calculations using the Gaussian 09 program. After the geometry of the molecule was optimized, vibration wavenumbers and fundamental vibration wavenumbers were assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with VEDA 4 program. The total (TDOS), partial (PDOS) density of state and overlap population density of state (OPDOS) diagrams analysis were made using GaussSum 2.2 program. The results of theoretical calculations for the spectra of the title compound were compared with the observed spectra. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural investigation of a self-assembled monolayer material 5-[(3-methylphenyl) (phenyl) amino] isophthalic acid for organic light-emitting devices

NASA Astrophysics Data System (ADS)

Saş, E. Babur; Kurt, M.; Can, M.; Okur, S.; İçli, S.; Demiç, S.

2014-12-01

The molecular structure and vibrations of 5-[(3-methylphenyl) (phenyl) amino] isophthalic acid (MePIFA) were investigated by infrared and Raman spectroscopies, UV-Vis, 1H and 13C NMR spectroscopic techniques and NBO analysis. FT-IR, FT-Raman and dispersive Raman spectra were recorded in the solid phase. 1H and 13C NMR spectra and UV-Vis spectrum were recorded in DMSO solution. HOMO-LUMO analysis and molecular electrostatic potential (MEP) analysis were performed. The theoretical calculations for the molecular structure and spectroscopies were performed with DFT (B3LYP) and 6-311G(d,p) basis set calculations using the Gaussian 09 program. After the geometry of the molecule was optimized, vibration wavenumbers and fundamental vibration wavenumbers were assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with VEDA 4 program. The total (TDOS), partial (PDOS) density of state and overlap population density of state (OPDOS) diagrams analysis were made using GaussSum 2.2 program. The results of theoretical calculations for the spectra of the title compound were compared with the observed spectra.

Fear extinction in the human brain: A meta-analysis of fMRI studies in healthy participants.

PubMed

Fullana, Miquel A; Albajes-Eizagirre, Anton; Soriano-Mas, Carles; Vervliet, Bram; Cardoner, Narcís; Benet, Olívia; Radua, Joaquim; Harrison, Ben J

2018-05-01

The study of fear extinction represents an important example of translational neuroscience in psychiatry and promises to improve the understanding and treatment of anxiety and fear-related disorders. We present the results of a set of meta-analyses of human fear extinction studies in healthy participants, conducted with functional magnetic resonance imaging (fMRI) and reporting whole-brain results. Meta-analyses of fear extinction learning primarily implicate consistent activation of brain regions linked to threat appraisal and experience, including the dorsal anterior cingulate and anterior insular cortices. An overlapping anatomical result was obtained from the meta-analysis of extinction recall studies, except when studies directly compared an extinguished threat stimulus to an unextinguished threat stimulus (instead of a safety stimulus). In this latter instance, more consistent activation was observed in dorsolateral and ventromedial prefrontal cortex regions, together with other areas including the hippocampus. While our results partially support the notion of a shared neuroanatomy between human and rodent models of extinction processes, they also encourage an expanded account of the neural basis of human fear extinction. Copyright © 2018 Elsevier Ltd. All rights reserved.

High Diversity of Genes for Nonhost Resistance of Barley to Heterologous Rust Fungi

PubMed Central

Jafary, Hossein; Albertazzi, Giorgia; Marcel, Thierry C.; Niks, Rients E.

2008-01-01

Inheritance studies on the nonhost resistance of plants would normally require interspecific crosses that suffer from sterility and abnormal segregation. Therefore, we developed the barley–Puccinia rust model system to study, using forward genetics, the specificity, number, and diversity of genes involved in nonhost resistance. We developed two mapping populations by crossing the line SusPtrit, with exceptional susceptibility to heterologous rust species, with the immune barley cultivars Vada and Cebada Capa. These two mapping populations along with the Oregon Wolfe Barley population, which showed unexpected segregation for resistance to heterologous rusts, were phenotyped with four heterologous rust fungal species. Positions of QTL conferring nonhost resistance in the three mapping populations were compared using an integrated consensus map. The results confirmed that nonhost resistance in barley to heterologous rust species is controlled by QTL with different and overlapping specificities and by an occasional contribution of an R-gene for hypersensitivity. In each population, different sets of loci were implicated in resistance. Few genes were common between the populations, suggesting a high diversity of genes conferring nonhost resistance to heterologous pathogens. These loci were significantly associated with QTL for partial resistance to the pathogen Puccinia hordei and with defense-related genes. PMID:18430953

Synchrotron-based multiple-beam FTIR chemical imaging of a multi-layered polymer in transmission and reflection: towards cultural heritage applications

NASA Astrophysics Data System (ADS)

Unger, Miriam; Mattson, Eric; Schmidt Patterson, Catherine; Alavi, Zahrasadet; Carson, David; Hirschmugl, Carol J.

2013-04-01

IRENI (infrared environmental imaging) is a recently commissioned Fourier transform infrared (FTIR) chemical imaging beamline at the Synchrotron Radiation Center in Madison, WI, USA. This novel beamline extracts 320 mrad of radiation, horizontally, from one bending magnet. The optical transport separates and recombines the beam into 12 parallel collimated beams to illuminate a commercial FTIR microspectrometer (Bruker Hyperion 3000) equipped with a focal plane array detector where single pixels in the detector image a projected sample area of either 0.54×0.54 μm2 or 2×2 μm2, depending in the measurement geometry. The 12 beams are partially overlapped and defocused, similar to wide-field microscopy, homogeneously illuminating a relatively large sample area compared to single-beam arrangements. Both transmission and reflection geometries are used to examine a model cross section from a layered polymer material. The compromises for sample preparation and measurement strategies are discussed, and the chemical composition and spatial definition of the layers are distinguished in chemical images generated from data sets. Deconvolution methods that may allow more detailed data analysis are also discussed.

A calculation model to half-life estimate of two-proton radioactive decay process

NASA Astrophysics Data System (ADS)

Tavares, O. A. P.; Medeiros, E. L.

2018-04-01

Partial half-life of the radioactive decay by the two-proton emission mode has been estimated for proton-rich nuclei of mass number 18 < A < 68 by a model based on the quantum mechanical tunneling mechanism through a potential barrier. The Coulomb, centrifugal and overlapping contributions to the barrier have been considered within the spherical nucleus approximation. The present calculation method has been shown to be adequate in reproducing the existing experimental half-life data for 19Mg, 45Fe, 48Ni, and 54Zn 2p-emitter nuclides within a factor six. For 67Kr parent nucleus the calculated partial 2p-decay half-life has been found to be ten times greater than the recent, unique measured value at RIKEN Nishina Center. Prediction for new, yet unmeasured cases of two-proton radioactivity are also reported.

Relationship between locked modes and thermal quenches in DIII-D

NASA Astrophysics Data System (ADS)

Sweeney, R.; Choi, W.; Austin, M.; Brookman, M.; Izzo, V.; Knolker, M.; La Haye, R. J.; Leonard, A.; Strait, E.; Volpe, F. A.; The DIII-D Team

2018-05-01

Locked modes are known to be one of the major causes of disruptions, but the physical mechanisms by which locking leads to disruptions are not well understood. Here we analyze the evolution of the temperature profile in the presence of multiple coexisting locked modes during partial and full thermal quenches. Partial quenches are often observed to be an initial, distinct stage in the full thermal quench. Near the onset of partial quenches, locked island O-points are observed to align with each other on the midplane, and their widths are sufficient to overlap each other, as indicated by the Chirikov parameter. Energy conservation analysis of one partial thermal quench shows that the energy lost is both radiated in the divertor region, and conducted or convected to the divertor. Nonlinear resistive magnetohydrodynamic simulations support the interpretation of stochastic fields causing a partial axisymmetric collapse, though the simulated temperature profile exhibits less degradation than the experimental profiles. In discharges with minimum values of the safety factor above  ∼1.2, locked modes are observed to self-stabilize by inducing, possibly via double tearing modes, a minor disruption that removes their neoclassical drive. These high q min discharges often exhibit relatively low ratios of the plasma internal inductance to the safety factor at 95% of the poloidal flux, which might imply classical stability, in agreement with the decay of the mode when the neoclassical drive is removed.

Implications of climatic seasonality on activity patterns and resource use by sympatric peccaries in northern Pantanal.

PubMed

Hofmann, Gabriel Selbach; Coelho, Igor Pfeifer; Bastazini, Vinicius Augusto Galvão; Cordeiro, José Luís Passos; de Oliveira, Luiz Flamarion Barbosa

2016-03-01

We evaluated the effects of climate seasonality from a thermal and water availability perspective on the activity patterns and resource use of Pecari tajacu and Tayassu pecari during wet and dry seasons in the northeastern Brazilian Pantanal. We used camera traps and temperature sensors to record species activity patterns in relation to temperature, established five habitat categories based on flooding intensity and local vegetation characteristics, assessed the activity patterns of each species in dry and wet periods and in artificial water bodies using circular statistical metrics, and calculated niche amplitude and overlap on three axes (temperature, time, and habitat) in both periods. Peccaries shared a strong resemblance in resource use and in their responses to seasonal variations in the tested gradients. The activity patterns of both species exhibited a significant correlation with air temperature on all the evaluated measures, and both species strongly reduced their activity when the air temperature exceeded 35 °C. High temperatures associated with low water availability were most likely responsible for the changes in species activity patterns, which resulted in an increased temporal overlap in habitat use throughout the dry season. However, the peccaries avoided intensively flooded habitats; therefore, the habitat gradient overlap was greater during the wet period. Our results show that an increase in niche overlap on the environmental gradient as a result of climatic seasonality may be partially compensated by a reduction in other niche dimensions. In this case, temporal partitioning appears to be an important, viable mechanism to reduce competition by potentially competing species.

Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.

PubMed

Lu, Jonathan; Trnka, Michael J; Roh, Soung-Hun; Robinson, Philip J J; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L; Guan, Shenheng

2015-12-01

Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise. Graphical Abstract ᅟ.

Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes.

PubMed

Aref-Eshghi, Erfan; Rodenhiser, David I; Schenkel, Laila C; Lin, Hanxin; Skinner, Cindy; Ainsworth, Peter; Paré, Guillaume; Hood, Rebecca L; Bulman, Dennis E; Kernohan, Kristin D; Boycott, Kym M; Campeau, Philippe M; Schwartz, Charles; Sadikovic, Bekim

2018-01-04

Pediatric developmental syndromes present with systemic, complex, and often overlapping clinical features that are not infrequently a consequence of Mendelian inheritance of mutations in genes involved in DNA methylation, establishment of histone modifications, and chromatin remodeling (the "epigenetic machinery"). The mechanistic cross-talk between histone modification and DNA methylation suggests that these syndromes might be expected to display specific DNA methylation signatures that are a reflection of those primary errors associated with chromatin dysregulation. Given the interrelated functions of these chromatin regulatory proteins, we sought to identify DNA methylation epi-signatures that could provide syndrome-specific biomarkers to complement standard clinical diagnostics. In the present study, we examined peripheral blood samples from a large cohort of individuals encompassing 14 Mendelian disorders displaying mutations in the genes encoding proteins of the epigenetic machinery. We demonstrated that specific but partially overlapping DNA methylation signatures are associated with many of these conditions. The degree of overlap among these epi-signatures is minimal, further suggesting that, consistent with the initial event, the downstream changes are unique to every syndrome. In addition, by combining these epi-signatures, we have demonstrated that a machine learning tool can be built to concurrently screen for multiple syndromes with high sensitivity and specificity, and we highlight the utility of this tool in solving ambiguous case subjects presenting with variants of unknown significance, along with its ability to generate accurate predictions for subjects presenting with the overlapping clinical and molecular features associated with the disruption of the epigenetic machinery. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Evaluation of 1H NMR metabolic profiling using biofluid mixture design.

PubMed

Athersuch, Toby J; Malik, Shahid; Weljie, Aalim; Newton, Jack; Keun, Hector C

2013-07-16

A strategy for evaluating the performance of quantitative spectral analysis tools in conditions that better approximate background variation in a metabonomics experiment is presented. Three different urine samples were mixed in known proportions according to a {3, 3} simplex lattice experimental design and analyzed in triplicate by 1D (1)H NMR spectroscopy. Fifty-four urinary metabolites were subsequently quantified from the sample spectra using two methods common in metabolic profiling studies: (1) targeted spectral fitting and (2) targeted spectral integration. Multivariate analysis using partial least-squares (PLS) regression showed the latent structure of the spectral set recapitulated the experimental mixture design. The goodness-of-prediction statistic (Q(2)) of each metabolite variable in a PLS model was calculated as a metric for the reliability of measurement, across the sample compositional space. Several metabolites were observed to have low Q(2) values, largely as a consequence of their spectral resonances having low s/n or strong overlap with other sample components. This strategy has the potential to allow evaluation of spectral features obtained from metabolic profiling platforms in the context of the compositional background found in real biological sample sets, which may be subject to considerable variation. We suggest that it be incorporated into metabolic profiling studies to improve the estimation of matrix effects that confound accurate metabolite measurement. This novel method provides a rational basis for exploiting information from several samples in an efficient manner and avoids the use of multiple spike-in authentic standards, which may be difficult to obtain.

Evaluation of the efficiency of continuous wavelet transform as processing and preprocessing algorithm for resolution of overlapped signals in univariate and multivariate regression analyses; an application to ternary and quaternary mixtures

NASA Astrophysics Data System (ADS)

Hegazy, Maha A.; Lotfy, Hayam M.; Mowaka, Shereen; Mohamed, Ekram Hany

2016-07-01

Wavelets have been adapted for a vast number of signal-processing applications due to the amount of information that can be extracted from a signal. In this work, a comparative study on the efficiency of continuous wavelet transform (CWT) as a signal processing tool in univariate regression and a pre-processing tool in multivariate analysis using partial least square (CWT-PLS) was conducted. These were applied to complex spectral signals of ternary and quaternary mixtures. CWT-PLS method succeeded in the simultaneous determination of a quaternary mixture of drotaverine (DRO), caffeine (CAF), paracetamol (PAR) and p-aminophenol (PAP, the major impurity of paracetamol). While, the univariate CWT failed to simultaneously determine the quaternary mixture components and was able to determine only PAR and PAP, the ternary mixtures of DRO, CAF, and PAR and CAF, PAR, and PAP. During the calculations of CWT, different wavelet families were tested. The univariate CWT method was validated according to the ICH guidelines. While for the development of the CWT-PLS model a calibration set was prepared by means of an orthogonal experimental design and their absorption spectra were recorded and processed by CWT. The CWT-PLS model was constructed by regression between the wavelet coefficients and concentration matrices and validation was performed by both cross validation and external validation sets. Both methods were successfully applied for determination of the studied drugs in pharmaceutical formulations.

PARP Inhibitors in Ovarian Cancer.

PubMed

Mittica, Gloria; Ghisoni, Eleonora; Giannone, Gaia; Genta, Sofia; Aglietta, Massimo; Sapino, Anna; Valabrega, Giorgio

2018-03-05

Treatment of Epithelial Ovarian Cancer (EOC), historically based on surgery and platinum doublet chemotherapy, is associated with high risk of relapse and poor prognosis for recurrent disease. In this landscape, the innovative treatment with PARP inhibitors (PARPis) demonstrated an outstanding activity in EOC, and is currently changing clinical practice in BRCA mutant patients. To highlight the mechanism of action, pharmacokinetics, clinical activity, indications and current strategies of development of Olaparib, Niraparib, Rucaparib, Talazoparib and Veliparib, the 5 most relevant PARPis. We performed a review on Pubmed using 'ovarian cancer' and the name of each PARPi (PARP inhibitor) discussed in the review as Medical Subject Headings (MeSH) keywords. The same search was performed on "clinicaltrial.gov" to identify ongoing clinical trials and on "google.com/patents" and "uspto.gov" for recent patents exploring PARPIs in ovarian cancer. Olaparib, Niraparib and Rucaparib are already approved for treatment of recurrent EOC and their indications are partially overlapping. Talazoparib and Veliparib are promising PARPis, but currently under investigation in early phase trials. Several studies are evaluating PARPis in monotherapy or in associations, in a wide range of settings (i.e. first line, neoadjuvant, platinum-sensitive and resistant disease). PARPis are valuable options in patients with recurrent ovarian cancer with promising activity in different stages of this disease. Further studies are required to better define optimal clinical settings, predictors of response beyond BRCA mutations and strategies to overcome secondary resistance of PARPis therapy in EOC. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Effects of oral exposure to bisphenol A on gene expression and global genomic DNA methylation in the prostate, female mammary gland, and uterus of NCTR Sprague-Dawley rats

PubMed Central

Camacho, Luísa; Basavarajappa, Mallikarjuna S.; Chang, Ching-Wei; Han, Tao; Kobets, Tetyana; Koturbash, Igor; Surratt, Gordon; Lewis, Sherry M.; Vanlandingham, Michelle M.; Fuscoe, James C.; da Costa, Gonçalo Gamboa; Pogribny, Igor P.; Delclos, K. Barry

2015-01-01

Bisphenol A (BPA), an industrial chemical used in the manufacture of polycarbonate and epoxy resins, binds to the nuclear estrogen receptor with an affinity 4–5 orders of magnitude lower than that of estradiol. We reported previously that “high BPA” (100,000 and 300,000 μg/kg body weight (bw)/day), but not “low BPA” [2.5–2700 μg/kg bw/day], induced clear adverse effects in NCTR Sprague-Dawley rats gavaged daily from gestation day 6 through postnatal day 90. The “high BPA” effects partially overlapped those of ethinyl estradiol (EE2, 0.5 and 5.0 μg/kg bw/day). To evaluate further the potential of “low BPA” to induce biological effects, here we assessed the global genomic DNA methylation and gene expression in the prostate and female mammary glands, tissues identified previously as potential targets of BPA, and uterus, a sensitive estrogen-responsive tissue. Both doses of EE2 modulated gene expression, including of known estrogen-responsive genes, and PND 4 global gene expression data showed a partial overlap of the “high BPA” effects with those of EE2. The “low BPA” doses modulated the expression of several genes; however, the absence of a dose response reduces the likelihood that these changes were causally linked to the treatment. These results are consistent with the toxicity outcomes. PMID:25862956

Development of an immersive virtual reality head-mounted display with high performance.

PubMed

Wang, Yunqi; Liu, Weiqi; Meng, Xiangxiang; Fu, Hanyi; Zhang, Daliang; Kang, Yusi; Feng, Rui; Wei, Zhonglun; Zhu, Xiuqing; Jiang, Guohua

2016-09-01

To resolve the contradiction between large field of view and high resolution in immersive virtual reality (VR) head-mounted displays (HMDs), an HMD monocular optical system with a large field of view and high resolution was designed. The system was fabricated by adopting aspheric technology with CNC grinding and a high-resolution LCD as the image source. With this monocular optical system, an HMD binocular optical system with a wide-range continuously adjustable interpupillary distance was achieved in the form of partially overlapping fields of view (FOV) combined with a screw adjustment mechanism. A fast image processor-centered LCD driver circuit and an image preprocessing system were also built to address binocular vision inconsistency in the partially overlapping FOV binocular optical system. The distortions of the HMD optical system with a large field of view were measured. Meanwhile, the optical distortions in the display and the trapezoidal distortions introduced during image processing were corrected by a calibration model for reverse rotations and translations. A high-performance not-fully-transparent VR HMD device with high resolution (1920×1080) and large FOV [141.6°(H)×73.08°(V)] was developed. The full field-of-view average value of angular resolution is 18.6  pixels/degree. With the device, high-quality VR simulations can be completed under various scenarios, and the device can be utilized for simulated trainings in aeronautics, astronautics, and other fields with corresponding platforms. The developed device has positive practical significance.

The urinary excretion of metformin, ceftizoxime and ofloxacin in high serum creatinine rats: Can creatinine predict renal tubular elimination?

PubMed

Ma, Yan-Rong; Zhou, Yan; Huang, Jing; Qin, Hong-Yan; Wang, Pei; Wu, Xin-An

2018-03-01

The renal excretion of creatinine and most drugs are the net result of glomerular filtration and tubular secretion, and their tubular secretions are mediated by individual transporters. Thus, we hypothesized that the increase of serum creatinine (SCr) levels attributing to inhibiting tubular transporters but not glomerular filtration rate (GFR) could be used to evaluate the tubular excretion of drugs mediated by identical or partial overlap transporter with creatinine. In this work, we firstly developed the creatinine excretion inhibition model with normal GFR by competitively inhibiting tubular transporters, and investigated the renal excretion of metformin, ceftizoxime and ofloxacin in vivo and in vitro. The results showed that the 24-hour urinary excretion of metformin and ceftizoxime in model rats were decreased by 25% and 17% compared to that in control rats, respectively. The uptake amount and urinary excretion of metformin and ceftizoxime could be inhibited by creatinine in renal cortical slices and isolated kidney perfusion. However, the urinary excretion of ofloxacin was not affected by high SCr. These results showed that the inhibition of tubular creatinine transporters by high SCr resulted to the decrease of urinary excretion of metformin and ceftizoxime, but not ofloxacin, which implied that the increase of SCr could also be used to evaluate the tubular excretion of drugs mediated by identical or partial overlap transporter with creatinine in normal GFR rats. Copyright © 2018 Elsevier Inc. All rights reserved.

Sense and antisense transcripts of the developmentally regulated murine hsp70.2 gene are expressed in distinct and only partially overlapping areas in the adult brain

NASA Technical Reports Server (NTRS)

Murashov, A. K.; Wolgemuth, D. J.

1996-01-01

We have examined the spatial pattern of expression of a member of the hsp70 gene family, hsp70.2, in the mouse central nervous system. Surprisingly, RNA blot analysis and in situ hybridization revealed abundant expression of an 'antisense' hsp70.2 transcript in several areas of adult mouse brain. Two different transcripts recognized by sense and antisense riboprobes for the hsp70.2 gene were expressed in distinct and only partially overlapping neuronal populations. RNA blot analysis revealed low levels of the 2.7 kb transcript of hsp70.2 in several areas of the brain, with highest signal in the hippocampus. Abundant expression of a slightly larger (approximately 2.8 kb) 'antisense' transcript was detected in several brain regions, notably in the brainstem, cerebellum, mesencephalic tectum, thalamus, cortex, and hippocampus. In situ hybridization revealed that the sense and antisense transcripts were both predominantly neuronal and localized to the same cell types in the granular layer of the cerebellum, trapezoid nucleus of the superior olivary complex, locus coeruleus and hippocampus. The hsp70.2 antisense transcripts were particularly abundant in the frontal cortex, dentate gyrus, subthalamic nucleus, zona incerta, superior and inferior colliculi, central gray, brainstem, and cerebellar Purkinje cells. Our findings have revealed a distinct cellular and spatial localization of both sense and antisense transcripts, demonstrating a new level of complexity in the function of the heat shock genes.

Signaling pathway for phagocyte priming upon encounter with apoptotic cells.

PubMed

Nonaka, Saori; Ando, Yuki; Kanetani, Takuto; Hoshi, Chiharu; Nakai, Yuji; Nainu, Firzan; Nagaosa, Kaz; Shiratsuchi, Akiko; Nakanishi, Yoshinobu

2017-05-12

The phagocytic elimination of cells undergoing apoptosis is an evolutionarily conserved innate immune mechanism for eliminating unnecessary cells. Previous studies showed an increase in the level of engulfment receptors in phagocytes after the phagocytosis of apoptotic cells, which leads to the enhancement of their phagocytic activity. However, precise mechanisms underlying this phenomenon require further clarification. We found that the pre-incubation of a Drosophila phagocyte cell line with the fragments of apoptotic cells enhanced the subsequent phagocytosis of apoptotic cells, accompanied by an augmented expression of the engulfment receptors Draper and integrin αPS3. The DNA-binding activity of the transcription repressor Tailless was transiently raised in those phagocytes, depending on two partially overlapping signal-transduction pathways for the induction of phagocytosis as well as the occurrence of engulfment. The RNAi knockdown of tailless in phagocytes abrogated the enhancement of both phagocytosis and engulfment receptor expression. Furthermore, the hemocyte-specific RNAi of tailless reduced apoptotic cell clearance in Drosophila embryos. Taken together, we propose the following mechanism for the activation of Drosophila phagocytes after an encounter with apoptotic cells: two partially overlapping signal-transduction pathways for phagocytosis are initiated; transcription repressor Tailless is activated; expression of engulfment receptors is stimulated; and phagocytic activity is enhanced. This phenomenon most likely ensures the phagocytic elimination of apoptotic cells by stimulated phagocytes and is thus considered as a mechanism to prime phagocytes in innate immunity. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Exacerbations and health care resource utilization in patients with airflow limitation diseases attending a primary care setting: the PUMA study

PubMed Central

Montes de Oca, Maria; Aguirre, Carlos; Lopez Varela, Maria Victorina; Laucho-Contreras, Maria E; Casas, Alejandro; Surmont, Filip

2016-01-01

Background COPD, asthma, and asthma–COPD overlap increase health care resource consumption, predominantly because of hospitalization for exacerbations and also increased visits to general practitioners (GPs) or specialists. Little information is available regarding this in the primary care setting. Objectives To describe the prevalence and number of GP and specialist visits for any cause or due to exacerbations in patients with COPD, asthma, and asthma–COPD overlap. Methods COPD was defined as post-bronchodilator forced expiratory volume in 1 second/forced vital capacity (FEV1/FVC) ratio <0.70; asthma was defined as prior medical diagnosis, wheezing in the last 12 months, or wheezing plus reversibility (post-bronchodilator FEV1 or FVC increase ≥200 mL and ≥12%); asthma–COPD overlap was defined as post-bronchodilator FEV1/FVC <0.70 plus prior asthma diagnosis. Health care utilization was evaluated as GP and/or specialist visits in the previous year. Results Among the 1,743 individuals who completed the questionnaire, 1,540 performed acceptable spirometry. COPD patients had a higher prevalence of any medical visits to any physician versus those without COPD (37.2% vs 21.8%, respectively) and exacerbations doubled the number of visits. The prevalence of any medical visits to any physician was also higher in asthma patients versus those without asthma (wheezing: 47.2% vs 22.7%; medical diagnosis: 54.6% vs 21.6%; wheezing plus reversibility: 46.2% vs 23.8%, respectively). Asthma patients with exacerbations had twice the number of visits versus those without an exacerbation. The number of visits was higher (2.8 times) in asthma–COPD overlap, asthma (1.9 times), or COPD (1.4 times) patients versus those without these respiratory diseases; the number of visits due to exacerbation was also higher (4.9 times) in asthma–COPD overlap, asthma (3.5 times), and COPD (3.8 times) patients. Conclusion COPD, asthma, and asthma–COPD overlap increase the prevalence of medical visits and, therefore, health care resource utilization. Attempts to reduce health care resource use in these patients require interventions aimed at preventing exacerbations. PMID:27994446

Exacerbations and health care resource utilization in patients with airflow limitation diseases attending a primary care setting: the PUMA study.

PubMed

Montes de Oca, Maria; Aguirre, Carlos; Lopez Varela, Maria Victorina; Laucho-Contreras, Maria E; Casas, Alejandro; Surmont, Filip

2016-01-01

COPD, asthma, and asthma-COPD overlap increase health care resource consumption, predominantly because of hospitalization for exacerbations and also increased visits to general practitioners (GPs) or specialists. Little information is available regarding this in the primary care setting. To describe the prevalence and number of GP and specialist visits for any cause or due to exacerbations in patients with COPD, asthma, and asthma-COPD overlap. COPD was defined as post-bronchodilator forced expiratory volume in 1 second/forced vital capacity (FEV 1 /FVC) ratio <0.70; asthma was defined as prior medical diagnosis, wheezing in the last 12 months, or wheezing plus reversibility (post-bronchodilator FEV 1 or FVC increase ≥200 mL and ≥12%); asthma-COPD overlap was defined as post-bronchodilator FEV 1 /FVC <0.70 plus prior asthma diagnosis. Health care utilization was evaluated as GP and/or specialist visits in the previous year. Among the 1,743 individuals who completed the questionnaire, 1,540 performed acceptable spirometry. COPD patients had a higher prevalence of any medical visits to any physician versus those without COPD (37.2% vs 21.8%, respectively) and exacerbations doubled the number of visits. The prevalence of any medical visits to any physician was also higher in asthma patients versus those without asthma (wheezing: 47.2% vs 22.7%; medical diagnosis: 54.6% vs 21.6%; wheezing plus reversibility: 46.2% vs 23.8%, respectively). Asthma patients with exacerbations had twice the number of visits versus those without an exacerbation. The number of visits was higher (2.8 times) in asthma-COPD overlap, asthma (1.9 times), or COPD (1.4 times) patients versus those without these respiratory diseases; the number of visits due to exacerbation was also higher (4.9 times) in asthma-COPD overlap, asthma (3.5 times), and COPD (3.8 times) patients. COPD, asthma, and asthma-COPD overlap increase the prevalence of medical visits and, therefore, health care resource utilization. Attempts to reduce health care resource use in these patients require interventions aimed at preventing exacerbations.

A Fast, Automatic Segmentation Algorithm for Locating and Delineating Touching Cell Boundaries in Imaged Histopathology

PubMed Central

Qi, Xin; Xing, Fuyong; Foran, David J.; Yang, Lin

2013-01-01

Summary Background Automated analysis of imaged histopathology specimens could potentially provide support for improved reliability in detection and classification in a range of investigative and clinical cancer applications. Automated segmentation of cells in the digitized tissue microarray (TMA) is often the prerequisite for quantitative analysis. However overlapping cells usually bring significant challenges for traditional segmentation algorithms. Objectives In this paper, we propose a novel, automatic algorithm to separate overlapping cells in stained histology specimens acquired using bright-field RGB imaging. Methods It starts by systematically identifying salient regions of interest throughout the image based upon their underlying visual content. The segmentation algorithm subsequently performs a quick, voting based seed detection. Finally, the contour of each cell is obtained using a repulsive level set deformable model using the seeds generated in the previous step. We compared the experimental results with the most current literature, and the pixel wise accuracy between human experts' annotation and those generated using the automatic segmentation algorithm. Results The method is tested with 100 image patches which contain more than 1000 overlapping cells. The overall precision and recall of the developed algorithm is 90% and 78%, respectively. We also implement the algorithm on GPU. The parallel implementation is 22 times faster than its C/C++ sequential implementation. Conclusion The proposed overlapping cell segmentation algorithm can accurately detect the center of each overlapping cell and effectively separate each of the overlapping cells. GPU is proven to be an efficient parallel platform for overlapping cell segmentation. PMID:22526139

A Time Series of Mean Global Sea Surface Temperature from the Along-Track Scanning Radiometers

NASA Astrophysics Data System (ADS)

Veal, Karen L.; Corlett, Gary; Remedios, John; Llewellyn-Jones, David

2010-12-01

A climate data set requires a long time series of consistently processed data with suitably long periods of overlap of different instruments which allows characterization of any inter-instrument biases. The data obtained from ESA's three Along-Track Scanning Radiometers (ATSRs) together comprise an 18 year record of SST with overlap periods of at least 6 months. The data from all three ATSRs has been consistently processed. These factors together with the stability of the instruments and the precision of the derived SST makes this data set eminently suitable for the construction of a time series of SST that complies with many of the GCOS requirements for a climate data set. A time series of global and regional average SST anomalies has been constructed from the ATSR version 2 data set. An analysis of the overlap periods of successive instruments was used to remove intra-series biases and align the series to a common reference. An ATSR climatology has been developed and has been used to calculate the SST anomalies. The ATSR-1 time series and the AATSR time series have been aligned to ATSR-2. The largest adjustment is ~0.2 K between ATSR-2 and AATSR which is suspected to be due to a shift of the 12 μm filter function for AATSR. An uncertainty of 0.06 K is assigned to the relative anomaly record that is derived from the dual three-channel night-time data. A relative uncertainty of 0.07 K is assigned to the dual night-time two-channel record, except in the ATSR-1 period (1994-1996) where it is larger.

Hospital mergers and market overlap.

PubMed Central

Brooks, G R; Jones, V G

1997-01-01

OBJECTIVE: To address two questions: What are the characteristics of hospitals that affect the likelihood of their being involved in a merger? What characteristics of particular pairs of hospitals affect the likelihood of the pair engaging in a merger? DATA SOURCES/STUDY SETTING: Hospitals in the 12 county region surrounding the San Francisco Bay during the period 1983 to 1992 were the focus of the study. Data were drawn from secondary sources, including the Lexis/Nexis database, the American Hospital Association, and the Office of Statewide Health Planning and Development of the State of California. STUDY DESIGN: Seventeen hospital mergers during the study period were identified. A random sample of pairs of hospitals that did not merge was drawn to establish a statistically efficient control set. Models constructed from hypotheses regarding hospital and market characteristics believed to be related to merger likelihood were tested using logistic regression analysis. DATA COLLECTION: See Data Sources/Study Setting. PRINCIPAL FINDINGS: The analysis shows that the likelihood of a merger between a particular pair of hospitals is positively related to the degree of market overlap that exists between them. Furthermore, market overlap and performance difference interact in their effect on merger likelihood. In an analysis of individual hospitals, conditions of rivalry, hospital market share, and hospital size were not found to influence the likelihood that a hospital will engage in a merger. CONCLUSIONS: Mergers between hospitals are not driven directly by considerations of market power or efficiency as much as by the existence of specific merger opportunities in the hospitals' local markets. Market overlap is a condition that enables a merger to occur, but other factors, such as the relative performance levels of the hospitals in question and their ownership and teaching status, also play a role in influencing the likelihood that a merger will in fact take place. PMID:9018212

Conformational analysis, spectroscopic study (FT-IR, FT-Raman, UV, 1H and 13C NMR), molecular orbital energy and NLO properties of 5-iodosalicylic acid

NASA Astrophysics Data System (ADS)

Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

2015-02-01

In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n = 1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts (1H and 13C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results.

Remembering what could have happened: Neural correlates of episodic counterfactual thinking

PubMed Central

De Brigard, F; Addis, D.R.; Ford, J.H.; Schacter, D.L.; Giovanello, K.S

2014-01-01

Recent evidence suggests that our capacities to remember the past and to imagine what might happen in the future largely depend on the same core brain network that includes the middle temporal lobe, the posterior cingulate/retrosplenial cortex, the inferior parietal lobe, the medial prefrontal cortex, and the lateral temporal cortex. However, the extent to which regions of this core brain network are also responsible for our capacity to think about what could have happened in our past, yet did not occur (i.e., episodic counterfactual thinking), is still unknown. The present study examined this issue. Using a variation of the experimental recombination paradigm (Addis et al., 2009), participants were asked both to remember personal past events and to envision alternative outcomes to such events while undergoing functional magnetic resonance imaging. Three sets of analyses were performed on the imaging data in order to investigate two related issues. First, a mean-centered spatiotemporal partial least square (PLS) analysis identified a pattern of brain activity across regions of the core network that was common to episodic memory and episodic counterfactual thinking. Second, a non-rotated PLS analysis identified two different patterns of brain activity for likely and unlikely episodic counterfactual thoughts, with the former showing significant overlap with the set of regions engaged during episodic recollection. Finally, a parametric modulation was conducted to explore the differential engagement of brain regions during counterfactual thinking, revealing that areas such as the parahippocampal gyrus and the right hippocampus were modulated by the subjective likelihood of counterfactual simulations. These results suggest that episodic counterfactual thinking engages regions that form the core brain network, and also that the subjective likelihood of our counterfactual thoughts modulates the engagement of different areas within this set of regions. PMID:23376052

Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation

PubMed Central

Mihalik, Ágoston; Csermely, Peter

2011-01-01

Network analysis became a powerful tool giving new insights to the understanding of cellular behavior. Heat shock, the archetype of stress responses, is a well-characterized and simple model of cellular dynamics. S. cerevisiae is an appropriate model organism, since both its protein-protein interaction network (interactome) and stress response at the gene expression level have been well characterized. However, the analysis of the reorganization of the yeast interactome during stress has not been investigated yet. We calculated the changes of the interaction-weights of the yeast interactome from the changes of mRNA expression levels upon heat shock. The major finding of our study is that heat shock induced a significant decrease in both the overlaps and connections of yeast interactome modules. In agreement with this the weighted diameter of the yeast interactome had a 4.9-fold increase in heat shock. Several key proteins of the heat shock response became centers of heat shock-induced local communities, as well as bridges providing a residual connection of modules after heat shock. The observed changes resemble to a ‘stratus-cumulus’ type transition of the interactome structure, since the unstressed yeast interactome had a globally connected organization, similar to that of stratus clouds, whereas the heat shocked interactome had a multifocal organization, similar to that of cumulus clouds. Our results showed that heat shock induces a partial disintegration of the global organization of the yeast interactome. This change may be rather general occurring in many types of stresses. Moreover, other complex systems, such as single proteins, social networks and ecosystems may also decrease their inter-modular links, thus develop more compact modules, and display a partial disintegration of their global structure in the initial phase of crisis. Thus, our work may provide a model of a general, system-level adaptation mechanism to environmental changes. PMID:22022244

Phase modulated 2D HSQC-TOCSY for unambiguous assignment of overlapping spin systems

NASA Astrophysics Data System (ADS)

Singh, Amrinder; Dubey, Abhinav; Adiga, Satish K.; Atreya, Hanudatta S.

2018-01-01

We present a new method that allows one to unambiguously resolve overlapping spin systems often encountered in biomolecular systems such as peptides and proteins or in samples containing a mixture of different molecules such as in metabolomics. We address this problem using the recently proposed phase modulation approach. By evolving the 1H chemical shifts in a conventional two dimensional (2D) HSQC-TOCSY experiment for a fixed delay period, the phase/intensity of set of cross peaks belonging to one spin system are modulated differentially relative to those of its overlapping counterpart, resulting in their discrimination and recognition. The method thus accelerates the process of identification and resonance assignment of individual compounds in complex mixtures. This approach facilitated the assignment of molecules in the embryo culture medium used in human assisted reproductive technology.

Epidemic spreading and immunization strategy in multiplex networks

NASA Astrophysics Data System (ADS)

Alvarez Zuzek, Lucila G.; Buono, Camila; Braunstein, Lidia A.

2015-09-01

A more connected world has brought major consequences such as facilitate the spread of diseases all over the world to quickly become epidemics, reason why researchers are concentrated in modeling the propagation of epidemics and outbreaks in multilayer networks. In this networks all nodes interact in different layers with different type of links. However, in many scenarios such as in the society, a multiplex network framework is not completely suitable since not all individuals participate in all layers. In this paper, we use a partially overlapped, multiplex network where only a fraction of the individuals are shared by the layers. We develop a mitigation strategy for stopping a disease propagation, considering the Susceptible-Infected- Recover model, in a system consisted by two layers. We consider a random immunization in one of the layers and study the effect of the overlapping fraction in both, the propagation of the disease and the immunization strategy. Using branching theory, we study this scenario theoretically and via simulations and find a lower epidemic threshold than in the case without strategy.

Shared neurocircuitry underlying feeding and drugs of abuse in Drosophila.

PubMed

Landayan, Dan; Wolf, Fred W

2015-12-01

The neural circuitry and molecules that control the rewarding properties of food and drugs of abuse appear to partially overlap in the mammalian brain. This has raised questions about the extent of the overlap and the precise role of specific circuit elements in reward and in other behaviors associated with feeding regulation and drug responses. The much simpler brain of invertebrates including the fruit fly Drosophila, offers an opportunity to make high-resolution maps of the circuits and molecules that govern behavior. Recent progress in Drosophila has revealed not only some common substrates for the actions of drugs of abuse and for the regulation of feeding, but also a remarkable level of conservation with vertebrates for key neuromodulatory transmitters. We speculate that Drosophila may serve as a model for distinguishing the neural mechanisms underlying normal and pathological motivational states that will be applicable to mammals. Copyright © 2016 Chang Gung University. Published by Elsevier B.V. All rights reserved.

Sensitive analytical method for simultaneous analysis of some vasoconstrictors with highly overlapped analytical signals

NASA Astrophysics Data System (ADS)

Nikolić, G. S.; Žerajić, S.; Cakić, M.

2011-10-01

Multivariate calibration method is a powerful mathematical tool that can be applied in analytical chemistry when the analytical signals are highly overlapped. The method with regression by partial least squares is proposed for the simultaneous spectrophotometric determination of adrenergic vasoconstrictors in decongestive solution containing two active components: phenyleprine hydrochloride and trimazoline hydrochloride. These sympathomimetic agents are that frequently associated in pharmaceutical formulations against the common cold. The proposed method, which is, simple and rapid, offers the advantages of sensitivity and wide range of determinations without the need for extraction of the vasoconstrictors. In order to minimize the optimal factors necessary to obtain the calibration matrix by multivariate calibration, different parameters were evaluated. The adequate selection of the spectral regions proved to be important on the number of factors. In order to simultaneously quantify both hydrochlorides among excipients, the spectral region between 250 and 290 nm was selected. A recovery for the vasoconstrictor was 98-101%. The developed method was applied to assay of two decongestive pharmaceutical preparations.

Mathematical analysis of a multiple strain, multi-locus-allele system for antigenically variable infectious diseases revisited.

PubMed

Cherif, Alhaji

2015-09-01

Many important pathogens such as HIV/AIDS, influenza, malaria, dengue and meningitis generally exist in phenotypically distinct serotypes that compete for hosts. Models used to study these diseases appear as meta-population systems. Herein, we revisit one of the multiple strain models that have been used to investigate the dynamics of infectious diseases with co-circulating serotypes or strains, and provide analytical results underlying the numerical investigations. In particular, we establish the necessary conditions for the local asymptotic stability of the steady states and for the existence of oscillatory behaviors via Hopf bifurcation. In addition, we show that the existence of discrete antigenic forms among pathogens can either fully or partially self-organize, where (i) strains exhibit no strain structures and coexist or (ii) antigenic variants sort into non-overlapping or minimally overlapping clusters that either undergo the principle of competitive exclusion exhibiting discrete strain structures, or co-exist cyclically. Copyright © 2015. Published by Elsevier Inc.

Prenatal diagnosis of a fetus with unbalanced translocation (4;13)(p16;q32) with overlapping features of Patau and Wolf-Hirschhorn syndromes.

PubMed

Tapper, Jill K; Zhang, Shuliu; Harirah, Hassan M; Panova, Neli I; Merryman, Linda S; Hawkins, Judy C; Lockhart, Lillian H; Gei, Alfredo B; Velagaleti, Gopalrao V N

2002-01-01

Wolf-Hirschhorn syndrome (WHS) and Patau syndrome are two of the most severe conditions resulting from chromosome abnormalities. WHS is caused by a deletion of 4p16, while Patau syndrome is caused by trisomy for some or all regions of chromosome 13. Though the etiologies of these syndromes differ, they share several features including pre- and postnatal growth retardation, microcephaly, cleft lip and palate, and cardiac anomalies. We present here a female fetus with deletion of 4p16 --> pter and duplication of 13q32 --> qter due to unbalanced segregation of t(4;13)(p16;q32) in the father. She displayed overlapping features of both of these syndromes on ultrasound. To the best of our knowledge, this is the first report of a fetus with both partial trisomy 13 and deletion of 4p16, the critical region for WHS. Copyright 2002 S. Karger AG, Basel

Numerical study of magnetohydrodynamic pulsatile flow of Sutterby fluid through an inclined overlapping arterial stenosis in the presence of periodic body acceleration

NASA Astrophysics Data System (ADS)

Abbas, Z.; Shabbir, M. S.; Ali, N.

2018-06-01

In the present theoretical investigation, we have numerically simulated the problem of blood flow through an overlapping stenosed arterial blood vessel under the action of externally applied body acceleration and the periodic pressure gradient. The rheology of blood is characterized by the Sutterby fluid model. The blood is considered as an electrically conducting fluid. A steady uniform magnetic field is applied in the radial direction of the blood vessel. The governing nonlinear partial differential equations of the present flow together with prescribed boundary conditions are solved by employing explicit finite difference scheme. Results concerning the temporal distribution of velocity, flow rate, shear stress and resistance to the flow are displayed through graphs. The effects of various emerging parameters on the flow variables are analyzed and discussed in detail. The analysis reveals that the applied magnetic field and periodic body acceleration have considerable effects on the flow field.

Triangle network motifs predict complexes by complementing high-error interactomes with structural information.

PubMed

Andreopoulos, Bill; Winter, Christof; Labudde, Dirk; Schroeder, Michael

2009-06-27

A lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs) were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs) representing binding evidence on proteins, forming PPI-SDDI-PPI triangles. We find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from Munich Information center for Protein Sequences (MIPS). PPI-SDDI-PPI triangles have ~20 times higher overlap with MIPS complexes than using second-level neighbors in PPINs without SDDIs. The biological interpretation for triangles is that a SDDI causes two proteins to be observed with common interaction partners in high-throughput experiments. The relatively few SDDIs overlapping with PPINs are part of highly connected SDDI components, and are more likely to be detected in experimental studies. We demonstrate the utility of PPI-SDDI-PPI triangles by reconstructing myosin-actin processes in the nucleus, cytoplasm, and cytoskeleton, which were not obvious in the original PPIN. Using other complementary datatypes in place of SDDIs to form triangles, such as PubMed co-occurrences or threading information, results in a similar ability to find protein complexes. Given high-error PPINs with missing information, triangles of mixed datatypes are a promising direction for finding protein complexes. Integrating PPINs with SDDIs improves finding complexes. Structural SDDIs partially explain the high functional similarity of second-level neighbors in PPINs. We estimate that relatively little structural information would be sufficient for finding complexes involving most of the proteins and interactions in a typical PPIN.

Triangle network motifs predict complexes by complementing high-error interactomes with structural information

PubMed Central

Andreopoulos, Bill; Winter, Christof; Labudde, Dirk; Schroeder, Michael

2009-01-01

Background A lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs) were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs) representing binding evidence on proteins, forming PPI-SDDI-PPI triangles. Results We find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from Munich Information center for Protein Sequences (MIPS). PPI-SDDI-PPI triangles have ~20 times higher overlap with MIPS complexes than using second-level neighbors in PPINs without SDDIs. The biological interpretation for triangles is that a SDDI causes two proteins to be observed with common interaction partners in high-throughput experiments. The relatively few SDDIs overlapping with PPINs are part of highly connected SDDI components, and are more likely to be detected in experimental studies. We demonstrate the utility of PPI-SDDI-PPI triangles by reconstructing myosin-actin processes in the nucleus, cytoplasm, and cytoskeleton, which were not obvious in the original PPIN. Using other complementary datatypes in place of SDDIs to form triangles, such as PubMed co-occurrences or threading information, results in a similar ability to find protein complexes. Conclusion Given high-error PPINs with missing information, triangles of mixed datatypes are a promising direction for finding protein complexes. Integrating PPINs with SDDIs improves finding complexes. Structural SDDIs partially explain the high functional similarity of second-level neighbors in PPINs. We estimate that relatively little structural information would be sufficient for finding complexes involving most of the proteins and interactions in a typical PPIN. PMID:19558694

Impact of oppositional defiant disorder dimensions on the temporal ordering of conduct problems and depression across childhood and adolescence in girls.

PubMed

Hipwell, Alison E; Stepp, Stephanie; Feng, Xin; Burke, Jeff; Battista, Deena R; Loeber, Rolf; Keenan, Kate

2011-10-01

Little is known about the role of oppositional defiant disorder (ODD) dimensions on the temporal unfolding of conduct disorder (CD) and depression in girls between childhood and adolescence. The year-to-year associations between CD and depressive symptomatology were examined using nine waves of annually collected data (ages 8 through 16 years) from 1215 participants of the Pittsburgh Girls Study. A series of autoregressive path models were tested that included ODD-Emotion Dysregulation (ODD-ED) and ODD-Defiance, as time-varying covariates on CD predicting depression severity in the following year, and vice versa. Conduct problems, depression, and ODD dimensions were relatively stable throughout childhood and adolescence, and a moderate degree of covariance was observed between these variables. Path analyses showed that CD often preceded depression across this developmental period, although the effect sizes were small. There was less consistent prediction from depression to CD. The overlap between ODD-ED and CD partially explained the prospective relations from CD to depression, whereas these paths were fully explained by the overlap between ODD-ED and depression. The overlap between ODD-Defiance and CD did not account for the prospective relations from CD to depression. In contrast, the overlap between ODD-Defiance and depression accounted for virtually all paths from CD to depression. Accounting for the overlap between ODD dimensions and both CD and depression eliminated all significant predictive paths. Symptoms of CD tend to precede depression in girls during childhood and adolescence. However, covariance between depression and both ODD-ED and ODD-Defiance accounts for these prospective relations. ODD dimensions should be assessed when evaluating risk for comorbid depression in girls with conduct problems, and emotion dysregulation and defiance aspects of ODD should be identified as targets for treatment in order to prevent depression in the future. © 2011 The Authors. Journal of Child Psychology and Psychiatry © 2011 Association for Child and Adolescent Mental Health.

Detecting Malaria Hotspots: A Comparison of Rapid Diagnostic Test, Microscopy, and Polymerase Chain Reaction

PubMed Central

Mogeni, Polycarp; Williams, Thomas N; Omedo, Irene; Kimani, Domtila; Ngoi, Joyce M; Mwacharo, Jedida; Morter, Richard; Nyundo, Christopher; Wambua, Juliana; Nyangweso, George; Kapulu, Melissa; Fegan, Gregory; Bejon, Philip

2017-01-01

Abstract Background Malaria control strategies need to respond to geographical hotspots of transmission. Detection of hotspots depends on the sensitivity of the diagnostic tool used. Methods We conducted cross-sectional surveys in 3 sites within Kilifi County, Kenya, that had variable transmission intensities. Rapid diagnostic test (RDT), microscopy, and polymerase chain reaction (PCR) were used to detect asymptomatic parasitemia, and hotspots were detected using the spatial scan statistic. Results Eight thousand five hundred eighty-one study participants were surveyed in 3 sites. There were statistically significant malaria hotspots by RDT, microscopy, and PCR for all sites except by microscopy in 1 low transmission site. Pooled data analysis of hotspots by PCR overlapped with hotspots by microscopy at a moderate setting but not at 2 lower transmission settings. However, variations in degree of overlap were noted when data were analyzed by year. Hotspots by RDT were predictive of PCR/microscopy at the moderate setting, but not at the 2 low transmission settings. We observed long-term stability of hotspots by PCR and microscopy but not RDT. Conclusion Malaria control programs may consider PCR testing to guide asymptomatic malaria hotspot detection once the prevalence of infection falls. PMID:28973672

Evolutionary fuzzy ARTMAP neural networks for classification of semiconductor defects.

PubMed

Tan, Shing Chiang; Watada, Junzo; Ibrahim, Zuwairie; Khalid, Marzuki

2015-05-01

Wafer defect detection using an intelligent system is an approach of quality improvement in semiconductor manufacturing that aims to enhance its process stability, increase production capacity, and improve yields. Occasionally, only few records that indicate defective units are available and they are classified as a minority group in a large database. Such a situation leads to an imbalanced data set problem, wherein it engenders a great challenge to deal with by applying machine-learning techniques for obtaining effective solution. In addition, the database may comprise overlapping samples of different classes. This paper introduces two models of evolutionary fuzzy ARTMAP (FAM) neural networks to deal with the imbalanced data set problems in a semiconductor manufacturing operations. In particular, both the FAM models and hybrid genetic algorithms are integrated in the proposed evolutionary artificial neural networks (EANNs) to classify an imbalanced data set. In addition, one of the proposed EANNs incorporates a facility to learn overlapping samples of different classes from the imbalanced data environment. The classification results of the proposed evolutionary FAM neural networks are presented, compared, and analyzed using several classification metrics. The outcomes positively indicate the effectiveness of the proposed networks in handling classification problems with imbalanced data sets.

Film excerpts shown to specifically elicit various affects lead to overlapping activation foci in a large set of symmetrical brain regions in males.

PubMed

Karama, Sherif; Armony, Jorge; Beauregard, Mario

2011-01-01

While the limbic system theory continues to be part of common scientific parlance, its validity has been questioned on multiple grounds. Nonetheless, the issue of whether or not there exists a set of brain areas preferentially dedicated to emotional processing remains central within affective neuroscience. Recently, a widespread neural reference space for emotion which includes limbic as well as other regions was characterized in a large meta-analysis. As methodologically heterogeneous studies go into such meta-analyses, showing in an individual study in which all parameters are kept constant, the involvement of overlapping areas for various emotion conditions in keeping with the neural reference space for emotion, would serve as valuable confirmatory evidence. Here, using fMRI, 20 young adult men were scanned while viewing validated neutral and effective emotion-eliciting short film excerpts shown to quickly and specifically elicit disgust, amusement, or sexual arousal. Each emotion-specific run included, in random order, multiple neutral and emotion condition blocks. A stringent conjunction analysis revealed a large overlap across emotion conditions that fit remarkably well with the neural reference space for emotion. This overlap included symmetrical bilateral activation of the medial prefrontal cortex, the anterior cingulate, the temporo-occipital junction, the basal ganglia, the brainstem, the amygdala, the hippocampus, the thalamus, the subthalamic nucleus, the posterior hypothalamus, the cerebellum, as well as the frontal operculum extending towards the anterior insula. This study clearly confirms for the visual modality, that processing emotional stimuli leads to widespread increases in activation that cluster within relatively confined areas, regardless of valence.

Patient goal setting as a method for program improvement/development in partial hospitalization programs.

PubMed

Gates, A

1991-12-01

Data were collected from a study of 49 patients in 1990 and 106 patients in 1991 admitted into Country View Treatment Center and Green Country Counseling Center. Country View is a 30-bed chemical dependency residential center operating under St. John Medical Center in Tulsa, Oklahoma. Green Country is an evening partial hospital chemical dependency program operating under St. John Medical Center in Tulsa, Oklahoma, The tools used in this study were the Country View Patient Self-Reporting Questionnaire, the global Rating Scale, and the Model of Recovering Alcoholics Behavior Stages and Goal Setting (Wing, 1990). These assessments were specifically designed to measure the patient's perceptions of goal setting and the patient's perspective on treatment outcome. The study outcome resulted in program improvement (Green Country evening partial hospital program) and the development of the Country View Substance Abuse Intermediate Link (SAIL) Program (day partial hospital).

Optical filter selection for high confidence discrimination of strongly overlapping infrared chemical spectra.

PubMed

Major, Kevin J; Poutous, Menelaos K; Ewing, Kenneth J; Dunnill, Kevin F; Sanghera, Jasbinder S; Aggarwal, Ishwar D

2015-09-01

Optical filter-based chemical sensing techniques provide a new avenue to develop low-cost infrared sensors. These methods utilize multiple infrared optical filters to selectively measure different response functions for various chemicals, dependent on each chemical's infrared absorption. Rather than identifying distinct spectral features, which can then be used to determine the identity of a target chemical, optical filter-based approaches rely on measuring differences in the ensemble response between a given filter set and specific chemicals of interest. Therefore, the results of such methods are highly dependent on the original optical filter choice, which will dictate the selectivity, sensitivity, and stability of any filter-based sensing method. Recently, a method has been developed that utilizes unique detection vector operations defined by optical multifilter responses, to discriminate between volatile chemical vapors. This method, comparative-discrimination spectral detection (CDSD), is a technique which employs broadband optical filters to selectively discriminate between chemicals with highly overlapping infrared absorption spectra. CDSD has been shown to correctly distinguish between similar chemicals in the carbon-hydrogen stretch region of the infrared absorption spectra from 2800-3100 cm(-1). A key challenge to this approach is how to determine which optical filter sets should be utilized to achieve the greatest discrimination between target chemicals. Previous studies used empirical approaches to select the optical filter set; however this is insufficient to determine the optimum selectivity between strongly overlapping chemical spectra. Here we present a numerical approach to systematically study the effects of filter positioning and bandwidth on a number of three-chemical systems. We describe how both the filter properties, as well as the chemicals in each set, affect the CDSD results and subsequent discrimination. These results demonstrate the importance of choosing the proper filter set and chemicals for comparative discrimination, in order to identify the target chemical of interest in the presence of closely matched chemical interferents. These findings are an integral step in the development of experimental prototype sensors, which will utilize CDSD.

Local–global overlap in diversity informs mechanisms of bacterial biogeography

PubMed Central

Livermore, Joshua A; Jones, Stuart E

2015-01-01

Spatial variation in environmental conditions and barriers to organism movement are thought to be important factors for generating endemic species, thus enhancing global diversity. Recent microbial ecology research suggested that the entire diversity of bacteria in the global oceans could be recovered at a single site, thus inferring a lack of bacterial endemism. We argue this is not the case in the global ocean, but might be in other bacterial ecosystems with higher dispersal rates and lower global diversity, like the human gut. We quantified the degree to which local and global bacterial diversity overlap in a diverse set of ecosystems. Upon comparison of observed local–global diversity overlap with predictions from a neutral biogeography model, human-associated microbiomes (gut, skin, mouth) behaved much closer to neutral expectations whereas soil, lake and marine communities deviated strongly from the neutral expectations. This is likely a result of differences in dispersal rate among ‘patches', global diversity of these systems, and local densities of bacterial cells. It appears that overlap of local and global bacterial diversity is surprisingly large (but likely not one-hundred percent), and most importantly this overlap appears to be predictable based upon traditional biogeographic parameters like community size, global diversity, inter-patch environmental heterogeneity and patch connectivity. PMID:25848869

Min-cut segmentation of cursive handwriting in tabular documents

NASA Astrophysics Data System (ADS)

Davis, Brian L.; Barrett, William A.; Swingle, Scott D.

2015-01-01

Handwritten tabular documents, such as census, birth, death and marriage records, contain a wealth of information vital to genealogical and related research. Much work has been done in segmenting freeform handwriting, however, segmentation of cursive handwriting in tabular documents is still an unsolved problem. Tabular documents present unique segmentation challenges caused by handwriting overlapping cell-boundaries and other words, both horizontally and vertically, as "ascenders" and "descenders" overlap into adjacent cells. This paper presents a method for segmenting handwriting in tabular documents using a min-cut/max-flow algorithm on a graph formed from a distance map and connected components of handwriting. Specifically, we focus on line, word and first letter segmentation. Additionally, we include the angles of strokes of the handwriting as a third dimension to our graph to enable the resulting segments to share pixels of overlapping letters. Word segmentation accuracy is 89.5% evaluating lines of the data set used in the ICDAR2013 Handwriting Segmentation Contest. Accuracy is 92.6% for a specific application of segmenting first and last names from noisy census records. Accuracy for segmenting lines of names from noisy census records is 80.7%. The 3D graph cutting shows promise in segmenting overlapping letters, although highly convoluted or overlapping handwriting remains an ongoing challenge.

Partially Overlapping Brain Networks for Singing and Cello Playing.

PubMed

Segado, Melanie; Hollinger, Avrum; Thibodeau, Joseph; Penhune, Virginia; Zatorre, Robert J

2018-01-01

This research uses an MR-Compatible cello to compare functional brain activation during singing and cello playing within the same individuals to determine the extent to which arbitrary auditory-motor associations, like those required to play the cello, co-opt functional brain networks that evolved for singing. Musical instrument playing and singing both require highly specific associations between sounds and movements. Because these are both used to produce musical sounds, it is often assumed in the literature that their neural underpinnings are highly similar. However, singing is an evolutionarily old human trait, and the auditory-motor associations used for singing are also used for speech and non-speech vocalizations. This sets it apart from the arbitrary auditory-motor associations required to play musical instruments. The pitch range of the cello is similar to that of the human voice, but cello playing is completely independent of the vocal apparatus, and can therefore be used to dissociate the auditory-vocal network from that of the auditory-motor network. While in the MR-Scanner, 11 expert cellists listened to and subsequently produced individual tones either by singing or cello playing. All participants were able to sing and play the target tones in tune (<50C deviation from target). We found that brain activity during cello playing directly overlaps with brain activity during singing in many areas within the auditory-vocal network. These include primary motor, dorsal pre-motor, and supplementary motor cortices (M1, dPMC, SMA),the primary and periprimary auditory cortices within the superior temporal gyrus (STG) including Heschl's gyrus, anterior insula (aINS), anterior cingulate cortex (ACC), and intraparietal sulcus (IPS), and Cerebellum but, notably, exclude the periaqueductal gray (PAG) and basal ganglia (Putamen). Second, we found that activity within the overlapping areas is positively correlated with, and therefore likely contributing to, both singing and playing in tune determined with performance measures. Third, we found that activity in auditory areas is functionally connected with activity in dorsal motor and pre-motor areas, and that the connectivity between them is positively correlated with good performance on this task. This functional connectivity suggests that the brain areas are working together to contribute to task performance and not just coincidently active. Last, our findings showed that cello playing may directly co-opt vocal areas (including larynx area of motor cortex), especially if musical training begins before age 7.

Partially Overlapping Brain Networks for Singing and Cello Playing

PubMed Central

Segado, Melanie; Hollinger, Avrum; Thibodeau, Joseph; Penhune, Virginia; Zatorre, Robert J.

2018-01-01

This research uses an MR-Compatible cello to compare functional brain activation during singing and cello playing within the same individuals to determine the extent to which arbitrary auditory-motor associations, like those required to play the cello, co-opt functional brain networks that evolved for singing. Musical instrument playing and singing both require highly specific associations between sounds and movements. Because these are both used to produce musical sounds, it is often assumed in the literature that their neural underpinnings are highly similar. However, singing is an evolutionarily old human trait, and the auditory-motor associations used for singing are also used for speech and non-speech vocalizations. This sets it apart from the arbitrary auditory-motor associations required to play musical instruments. The pitch range of the cello is similar to that of the human voice, but cello playing is completely independent of the vocal apparatus, and can therefore be used to dissociate the auditory-vocal network from that of the auditory-motor network. While in the MR-Scanner, 11 expert cellists listened to and subsequently produced individual tones either by singing or cello playing. All participants were able to sing and play the target tones in tune (<50C deviation from target). We found that brain activity during cello playing directly overlaps with brain activity during singing in many areas within the auditory-vocal network. These include primary motor, dorsal pre-motor, and supplementary motor cortices (M1, dPMC, SMA),the primary and periprimary auditory cortices within the superior temporal gyrus (STG) including Heschl's gyrus, anterior insula (aINS), anterior cingulate cortex (ACC), and intraparietal sulcus (IPS), and Cerebellum but, notably, exclude the periaqueductal gray (PAG) and basal ganglia (Putamen). Second, we found that activity within the overlapping areas is positively correlated with, and therefore likely contributing to, both singing and playing in tune determined with performance measures. Third, we found that activity in auditory areas is functionally connected with activity in dorsal motor and pre-motor areas, and that the connectivity between them is positively correlated with good performance on this task. This functional connectivity suggests that the brain areas are working together to contribute to task performance and not just coincidently active. Last, our findings showed that cello playing may directly co-opt vocal areas (including larynx area of motor cortex), especially if musical training begins before age 7. PMID:29892211

Evaluating the role of fronts in habitat overlaps between cold and warm water species in the western North Pacific: A proof of concept

NASA Astrophysics Data System (ADS)

Mugo, Robinson M.; Saitoh, Sei-Ichi; Takahashi, Fumihiro; Nihira, Akira; Kuroyama, Tadaaki

2014-09-01

Cold- and warm-water species' fishing grounds show a spatial synchrony around fronts in the western North Pacific (WNP). However, it is not yet clear whether a front (thermal, salinity or chlorophyll) acts as an absolute barrier to fish migration on either side or its structure allows interaction of species with different physiological requirements. Our objective was to assess potential areas of overlap between cold- and warm-water species using probabilities of presence derived from fishery datasets and remotely sensed environment data in the Kuroshio-Oyashio region in the WNP. Fishery data comprised skipjack tuna (Katsuwonus pelamis) fishing locations and proxy presences (derived from fishing night light images) for neon flying squid (Ommastrephes bartrami) and Pacific saury (Cololabis saira). Monthly (August-November) satellite remotely sensed sea-surface temperature, chlorophyll-a and sea-surface height anomaly images were used as environment data. Maximum entropy (MaxEnt) models were used to determine probabilities of presence (PoP) for each set of fishery and environment data for the area 35-45°N and 140-160°E. Maps of both sets of PoPs were compared and areas of overlap identified using a combined probability map. Results indicated that areas of spatial overlap existed among the species habitats, which gradually widened from September to November. The reasons for these overlaps include the presence of strong thermal/ocean-color gradients between cold Oyashio and warm Kuroshio waters, and also the presence of the sub-arctic front. Due to the high abundance of food along frontal zones, the species use the fronts as foraging grounds while confining within physiologically tolerable waters on either side of the front. The interaction zone around the front points to areas that might be accessible to both species for foraging, which suggests intense prey-predator interaction zones.

Critical discussion of evaluation parameters for inter-observer variability in target definition for radiation therapy.

PubMed

Fotina, I; Lütgendorf-Caucig, C; Stock, M; Pötter, R; Georg, D

2012-02-01

Inter-observer studies represent a valid method for the evaluation of target definition uncertainties and contouring guidelines. However, data from the literature do not yet give clear guidelines for reporting contouring variability. Thus, the purpose of this work was to compare and discuss various methods to determine variability on the basis of clinical cases and a literature review. In this study, 7 prostate and 8 lung cases were contoured on CT images by 8 experienced observers. Analysis of variability included descriptive statistics, calculation of overlap measures, and statistical measures of agreement. Cross tables with ratios and correlations were established for overlap parameters. It was shown that the minimal set of parameters to be reported should include at least one of three volume overlap measures (i.e., generalized conformity index, Jaccard coefficient, or conformation number). High correlation between these parameters and scatter of the results was observed. A combination of descriptive statistics, overlap measure, and statistical measure of agreement or reliability analysis is required to fully report the interrater variability in delineation.

Relation of Cloud Occurrence Frequency, Overlap, and Effective Thickness Derived from CALIPSO and CloudSat Merged Cloud Vertical Profiles

NASA Technical Reports Server (NTRS)

Kato, Seiji; Sun-Mack, Sunny; Miller, Walter F.; Rose, Fred G.; Chen, Yan; Minnis, Patrick; Wielicki, Bruce A.

2009-01-01

A cloud frequency of occurrence matrix is generated using merged cloud vertical profile derived from Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) and Cloud Profiling Radar (CPR). The matrix contains vertical profiles of cloud occurrence frequency as a function of the uppermost cloud top. It is shown that the cloud fraction and uppermost cloud top vertical pro les can be related by a set of equations when the correlation distance of cloud occurrence, which is interpreted as an effective cloud thickness, is introduced. The underlying assumption in establishing the above relation is that cloud overlap approaches the random overlap with increasing distance separating cloud layers and that the probability of deviating from the random overlap decreases exponentially with distance. One month of CALIPSO and CloudSat data support these assumptions. However, the correlation distance sometimes becomes large, which might be an indication of precipitation. The cloud correlation distance is equivalent to the de-correlation distance introduced by Hogan and Illingworth [2000] when cloud fractions of both layers in a two-cloud layer system are the same.

Parametrization study of the land multiparameter VTI elastic waveform inversion

NASA Astrophysics Data System (ADS)

He, W.; Plessix, R.-É.; Singh, S.

2018-06-01

Multiparameter inversion of seismic data remains challenging due to the trade-off between the different elastic parameters and the non-uniqueness of the solution. The sensitivity of the seismic data to a given subsurface elastic parameter depends on the source and receiver ray/wave path orientations at the subsurface point. In a high-frequency approximation, this is commonly analysed through the study of the radiation patterns that indicate the sensitivity of each parameter versus the incoming (from the source) and outgoing (to the receiver) angles. In practice, this means that the inversion result becomes sensitive to the choice of parametrization, notably because the null-space of the inversion depends on this choice. We can use a least-overlapping parametrization that minimizes the overlaps between the radiation patterns, in this case each parameter is only sensitive in a restricted angle domain, or an overlapping parametrization that contains a parameter sensitive to all angles, in this case overlaps between the radiation parameters occur. Considering a multiparameter inversion in an elastic vertically transverse isotropic medium and a complex land geological setting, we show that the inversion with the least-overlapping parametrization gives less satisfactory results than with the overlapping parametrization. The difficulties come from the complex wave paths that make difficult to predict the areas of sensitivity of each parameter. This shows that the parametrization choice should not only be based on the radiation pattern analysis but also on the angular coverage at each subsurface point that depends on geology and the acquisition layout.

The double polarization program of CBELSA/TAPS

NASA Astrophysics Data System (ADS)

Thiel, Annika

2014-06-01

The excitation spectrum of the proton consists of resonances with substancial width which are often strongly overlapping and are therefore difficult to disentangle. To determine the exact contributions and identify these resonances, a partial wave analysis solution has to be found. For a complete experiment, which leads to an unambiguous solution, several single and double polarization observables are needed. With the Crystal Barrel/TAPS experiment at ELSA, the measurement of double polarization observables in different reactions is possible by using a circularly or linearly polarized photon beam on a transversely or longitudinally polarized butanol target.

Two-dimensional imaging of molecular hydrogen in H2-air diffusion flames using two-photon laser-induced fluorescence

NASA Technical Reports Server (NTRS)

Lempert, W.; Kumar, V.; Glesk, I.; Miles, R.; Diskin, G.

1991-01-01

The use of a tunable ArF laser at 193.26 nm to record simultaneous single-laser-shot, planar images of molecular hydrogen and hot oxygen in a turbulent H2-air diffusion flame. Excitation spectra of fuel and oxidant-rich flame zones confirm a partial overlap of the two-photon H2 and single-photon O2 Schumann-Runge absorption bands. UV Rayleigh scattering images of flame structure and estimated detection limits for the H2 two-photon imaging are also presented.

Semantic amnesia without dementia: documentation of a case.

PubMed

Rusconi, M L; Zago, S; Basso, A

1997-06-01

We described the case of a patient affected by a progressive semantic memory disorder associated with prevalent temporal lobe atrophy. This deficit seems to be "pure" in the sense that it has not been found to overlap with other cognitive deficits (intellectual, linguistic, perceptual, visuo-spatial etc.) for a long time. Furthermore, despite his impaired semantic knowledge, the autobiographical memory of the patient was largely intact. This case therefore represents a form of "semantic amnesia" without dementia, and supports the hypothesis that there is a partial distinction between "semantic" and "episodic" memory.

Molecular Cytogenetic Analysis of One African and Five Asian Macaque Species Reveals Identical Karyotypes as in Mandrill.

PubMed

Sangpakdee, Wiwat; Tanomtong, Alongkoad; Chaveerach, Arunrat; Pinthong, Krit; Trifonov, Vladimir; Loth, Kristina; Hensel, Christiana; Liehr, Thomas; Weise, Anja; Fan, Xiaobo

2018-04-01

The question how evolution and speciation work is one of the major interests of biology. Especially, genetic including karyotypic evolution within primates is of special interest due to the close phylogenetic position of Macaca and Homo sapiens and the role as in vivo models in medical research, neuroscience, behavior, pharmacology, reproduction and Acquired Immune Deficiency Syndrome (AIDS). Karyotypes of five macaque species from South East Asia and of one macaque species as well as mandrill from Africa were analyzed by high resolution molecular cytogenetics to obtain new insights into karyotypic evolution of old world monkeys. Molecular cytogenetics applying human probes and probe sets was applied in chromosomes of Macaca arctoides, M. fascicularis, M. nemestrina, M. assamensis, M. sylvanus, M. mulatta and Mandrillus sphinx. Established two- to multicolor-fluorescence in situ hybridization (FISH) approaches were applied. Locus-specific probes, whole and partial chromosome paint probes were hybridized. Especially the FISH-banding approach multicolor-banding (MCB) as well as probes oriented towards heterochromatin turned out to be highly efficient for interspecies comparison. Karyotypes of all seven studied species could be characterized in detail. Surprisingly, no evolutionary conserved differences were found among macaques, including mandrill. Between the seven here studied and phenotypically so different species we expected several via FISH detectable karyoypic and submicroscopic changes and were surprised to find none of them on a molecular cytogenetic level. Spatial separation, may explain the speciation and different evolution for some of them, like African M. sylvanus, Mandrillus sphinx and the South Asian macaques. However, for the partially or completely overlapping habitats of the five studied South Asian macaques the species separation process can also not be deduced to karyotypic separation.

Misfit dislocation patterns of Mg-Nb interfaces

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

Chen, Youxing; Shao, Shuai; Liu, Xiang-Yang

The role of heterogeneous interfaces in improving mechanical properties of polycrystalline aggregates and laminated composites has been well recognized with interface structure being of fundamental importance in designing composites containing multiple interfaces. In this paper, taking the Mg (hexagonal close-packed (hcp))/Nb (body-centered cubic (bcc)) interface as an example, we develop Mg-Nb interatomic potentials for predicting atomic configurations of Mg/Nb interfaces. We systematically characterize interface dislocations of Mg/Nb interfaces with Nishiyama-Wassermann (NW) and Kurdjumov-Sachs (KS) orientation relationships and propose a generalized procedure of characterizing interface structure by combining atomistic simulation and interface dislocation theory, which is applicable for not only hcp/bccmore » interfaces, but also other systems with complicated interface dislocation configurations.Here, in Mg/Nb, interface dislocation networks of two types of interfaces are significantly different although they originate from partial dislocations of similar character: the NW interface is composed of three sets of partial dislocations, while the KS interface is composed of four sets of interface dislocations - three sets of partial dislocations and one set of full dislocations that forms from the reaction of two close partial dislocations.« less

Accessible Information for Equally-Distant Partially-Entangled Alphabet State Resource

NASA Astrophysics Data System (ADS)

Hao, San-Ru; Hou, Bo-Yu; Xi, Xiao-Qiang; Yue, Rui-Hong

2002-02-01

We have proposed a quantum system with equally-distant partially-entangled alphabet states which has the minimal mutual overlap and the highly distinguishability, these quantum states are used as the "signal states" of the quantum communication. We have also constructed the positive operator-valued measure for these "signal states" and discussed their entanglement properties and measurement of entanglement. We calculate the accessible information for these alphabet states and show that the accessible information is closely related to the entanglement of the "signal states": the higher the entanglement of the "signal states", the better the accessible information of the quantum system, and the accessible information reaches its maximal value when the alphabet states have their maximal entanglement. The project supported in part by Foundation of the Science and Technology Committee of China, and Foundation of the Science and Technology Committee of Hunan Province of China under the contract FSTCH-21000205

Electrostatic interactions guide the active site face of a structure-specific ribonuclease to its RNA substrate.

PubMed

Plantinga, Matthew J; Korennykh, Alexei V; Piccirilli, Joseph A; Correll, Carl C

2008-08-26

Restrictocin, a member of the alpha-sarcin family of site-specific endoribonucleases, uses electrostatic interactions to bind to the ribosome and to RNA oligonucleotides, including the minimal specific substrate, the sarcin/ricin loop (SRL) of 23S-28S rRNA. Restrictocin binds to the SRL by forming a ground-state E:S complex that is stabilized predominantly by Coulomb interactions and depends on neither the sequence nor structure of the RNA, suggesting a nonspecific complex. The 22 cationic residues of restrictocin are dispersed throughout this protein surface, complicating a priori identification of a Coulomb interacting surface. Structural studies have identified an enzyme-substrate interface, which is expected to overlap with the electrostatic E:S interface. Here, we identified restrictocin residues that contribute to binding in the E:S complex by determining the salt dependence [partial differential log(k 2/ K 1/2)/ partial differential log[KCl

Gauge Physics of Spin Hall Effect

PubMed Central

Tan, Seng Ghee; Jalil, Mansoor B. A.; Ho, Cong Son; Siu, Zhuobin; Murakami, Shuichi

2015-01-01

Spin Hall effect (SHE) has been discussed in the context of Kubo formulation, geometric physics, spin orbit force, and numerous semi-classical treatments. It can be confusing if the different pictures have partial or overlapping claims of contribution to the SHE. In this article, we present a gauge-theoretic, time-momentum elucidation, which provides a general SHE equation of motion, that unifies under one theoretical framework, all contributions of SHE conductivity due to the kinetic, the spin orbit force (Yang-Mills), and the geometric (Murakami-Fujita) effects. Our work puts right an ambiguity surrounding previously partial treatments involving the Kubo, semiclassical, Berry curvatures, or the spin orbit force. Our full treatment shows the Rashba 2DEG SHE conductivity to be instead of −, and Rashba heavy hole instead of −. This renewed treatment suggests a need to re-derive and re-calculate previously studied SHE conductivity. PMID:26689260

Diffraction of entangled particles by light gratings

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

Sancho, Pedro, E-mail: psanchos@aemet.es

We analyze the diffraction regime of the Kapitza–Dirac effect for particles entangled in momentum. The detection patterns show two-particle interferences. In the single-mode case we identify a discontinuity in the set of joint detection probabilities, associated with the disconnected character of the space of non-separable states. For Gaussian multi-mode states we derive the diffraction patterns, providing an example of the dependence of the light–matter interaction on entanglement. When the particles are identical, we can explore the relation between exchange and entanglement effects. We find a complementary behavior between overlapping and Schmidt’s number. In particular, symmetric entanglement can cancel the exchangemore » effects. - Highlights: • Kapitza–Dirac diffraction of entangled particles shows multiparticle interference. • There is a discontinuity in the set of joint detection patterns of entangled states. • We find a complementary behavior between overlapping and Schmidt’s number. • Symmetric entanglement can cancel the exchange effects.« less

Generalised power graph compression reveals dominant relationship patterns in complex networks

PubMed Central

Ahnert, Sebastian E.

2014-01-01

We introduce a framework for the discovery of dominant relationship patterns in complex networks, by compressing the networks into power graphs with overlapping power nodes. When paired with enrichment analysis of node classification terms, the most compressible sets of edges provide a highly informative sketch of the dominant relationship patterns that define the network. In addition, this procedure also gives rise to a novel, link-based definition of overlapping node communities in which nodes are defined by their relationships with sets of other nodes, rather than through connections within the community. We show that this completely general approach can be applied to undirected, directed, and bipartite networks, yielding valuable insights into the large-scale structure of real-world networks, including social networks and food webs. Our approach therefore provides a novel way in which network architecture can be studied, defined and classified. PMID:24663099

Experimental design approach to the process parameter optimization for laser welding of martensitic stainless steels in a constrained overlap configuration

NASA Astrophysics Data System (ADS)

Khan, M. M. A.; Romoli, L.; Fiaschi, M.; Dini, G.; Sarri, F.

2011-02-01

This paper presents an experimental design approach to process parameter optimization for the laser welding of martensitic AISI 416 and AISI 440FSe stainless steels in a constrained overlap configuration in which outer shell was 0.55 mm thick. To determine the optimal laser-welding parameters, a set of mathematical models were developed relating welding parameters to each of the weld characteristics. These were validated both statistically and experimentally. The quality criteria set for the weld to determine optimal parameters were the minimization of weld width and the maximization of weld penetration depth, resistance length and shearing force. Laser power and welding speed in the range 855-930 W and 4.50-4.65 m/min, respectively, with a fiber diameter of 300 μm were identified as the optimal set of process parameters. However, the laser power and welding speed can be reduced to 800-840 W and increased to 4.75-5.37 m/min, respectively, to obtain stronger and better welds.

Randomly picked cosmid clones overlap the pyrB and oriC gap in the physical map of the E. coli chromosome.

PubMed Central

Knott, V; Rees, D J; Cheng, Z; Brownlee, G G

1988-01-01

Sets of overlapping cosmid clones generated by random sampling and fingerprinting methods complement data at pyrB (96.5') and oriC (84') in the published physical map of E. coli. A new cloning strategy using sheared DNA, and a low copy, inducible cosmid vector were used in order to reduce bias in libraries, in conjunction with micro-methods for preparing cosmid DNA from a large number of clones. Our results are relevant to the design of the best approach to the physical mapping of large genomes. PMID:2834694

Digital Mammography and Digital Breast Tomosynthesis.

PubMed

Moseley, Tanya W

2016-06-01

Breast imaging technology has advanced significantly from the 1930s until the present. American women have a 1 in 8 chance of developing breast cancer. Mammography has been proven in multiple clinical trials to reduce breast cancer mortality. Although a mainstay of breast imaging and improved from film-screen mammography, digital mammography is not a perfect examination. Overlapping obscuring breast tissue limits mammographic interpretation. Breast digital tomosynthesis reduces and/or eliminates overlapping obscuring breast tissue. Although there are some disadvantages with digital breast tomosynthesis, this relatively lost-cost technology may be used effectively in the screening and diagnostic settings.

7. (Second sheet of a twosheet set entitled 'Kongensgade 5154') ...

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

7. (Second sheet of a two-sheet set entitled 'Kongensgade 51-54') KONGENSGADE (FRONT) ELEVATIONS OF KONGENSGADE 53 (only part of this elevation shown, for full elevation overlap with complementary photograph VI-50-6), & KONGENSGADE 54 (LEFT TO RIGHT) - King Street Area Study, Kongensgade 5-18, 36, 37B, 51-58 (Houses), 5-18, 36-37B, 51-58 King Street, Frederiksted, St. Croix, VI

Non-specific filtering of beta-distributed data.

PubMed

Wang, Xinhui; Laird, Peter W; Hinoue, Toshinori; Groshen, Susan; Siegmund, Kimberly D

2014-06-19

Non-specific feature selection is a dimension reduction procedure performed prior to cluster analysis of high dimensional molecular data. Not all measured features are expected to show biological variation, so only the most varying are selected for analysis. In DNA methylation studies, DNA methylation is measured as a proportion, bounded between 0 and 1, with variance a function of the mean. Filtering on standard deviation biases the selection of probes to those with mean values near 0.5. We explore the effect this has on clustering, and develop alternate filter methods that utilize a variance stabilizing transformation for Beta distributed data and do not share this bias. We compared results for 11 different non-specific filters on eight Infinium HumanMethylation data sets, selected to span a variety of biological conditions. We found that for data sets having a small fraction of samples showing abnormal methylation of a subset of normally unmethylated CpGs, a characteristic of the CpG island methylator phenotype in cancer, a novel filter statistic that utilized a variance-stabilizing transformation for Beta distributed data outperformed the common filter of using standard deviation of the DNA methylation proportion, or its log-transformed M-value, in its ability to detect the cancer subtype in a cluster analysis. However, the standard deviation filter always performed among the best for distinguishing subgroups of normal tissue. The novel filter and standard deviation filter tended to favour features in different genome contexts; for the same data set, the novel filter always selected more features from CpG island promoters and the standard deviation filter always selected more features from non-CpG island intergenic regions. Interestingly, despite selecting largely non-overlapping sets of features, the two filters did find sample subsets that overlapped for some real data sets. We found two different filter statistics that tended to prioritize features with different characteristics, each performed well for identifying clusters of cancer and non-cancer tissue, and identifying a cancer CpG island hypermethylation phenotype. Since cluster analysis is for discovery, we would suggest trying both filters on any new data sets, evaluating the overlap of features selected and clusters discovered.

Local structural change in zircon following radiation damage accumulation. Observation by 29Si nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Farnan, I.; Trachenko, K.

2003-04-01

29Si nuclear magnetic resonance (NMR) is a one of the most useful probes of the local structure of silicates. One of the results of recent studies of naturally radiation damaged zircons is that there is an evolution of the local structure in both crystalline and amorphous fractions of partially metamict zircon as a function of accumulated α-dose. We have examined the evolution of this local structure within the framework of several models of damage accumulation. The total number of displaced atoms produced per α-decay as function of accumulated dose, as measured by NMR, is not consistent with the idea of multiple overlap events being responsible for the evolution of the total damaged fraction. However, increased connectivity in the damaged region as the number of α-events increases is correlated to the degree of cascade overlap. The results of large scale atomistic (MD) simulations of heavy nuclei recoils at realistic energies (70keV) are consistent with the NMR quantification and also with TEM estimates of the diameters of damaged regions. The local heterogeneity (density and bonding) in the damaged area in the simulations is consistent with the existence of connected silicate tetrahedra. Detailed experiments on the annealing of damaged zircons at 500 and 600^oC have been performed. These show that a significant energetic barrier to the recrystallisation exists at these temperatures once a small fraction of damaged material has been recrystallised. This correlates well with the degree of cascade overlap. Indicating that the more connected SiO_4 tetrahedra present this barrier. A sample with very little cascade overlap can be annealed to ˜97% crystallinity at these temperatures.

Relationship between locked modes and thermal quenches in DIII-D

DOE PAGES

Sweeney, R.; Choi, W.; Austin, M.; ...

2018-03-28

Locked modes are known to be one of the major causes of disruptions, but the physical mechanisms by which locking leads to disruptions are not well understood. For this study, we analyze the evolution of the temperature profile in the presence of multiple coexisting locked modes during partial and full thermal quenches. Partial quenches are often observed to be an initial, distinct stage in the full thermal quench. Near the onset of partial quenches, locked island O-points are observed to align with each other on the midplane, and their widths are sufficient to overlap each other, as indicated by themore » Chirikov parameter. Energy conservation analysis of one partial thermal quench shows that the energy lost is both radiated in the divertor region, and conducted or convected to the divertor. Nonlinear resistive magnetohydrodynamic simulations support the interpretation of stochastic fields causing a partial axisymmetric collapse, though the simulated temperature profile exhibits less degradation than the experimental profiles. In discharges with minimum values of the safety factor above ~1.2, locked modes are observed to self-stabilize by inducing, possibly via double tearing modes, a minor disruption that removes their neoclassical drive. These high q min discharges often exhibit relatively low ratios of the plasma internal inductance to the safety factor at 95% of the poloidal flux, which might imply classical stability, in agreement with the decay of the mode when the neoclassical drive is removed.« less

Improving Speech Perception in Noise with Current Focusing in Cochlear Implant Users

PubMed Central

Srinivasan, Arthi G.; Padilla, Monica; Shannon, Robert V.; Landsberger, David M.

2013-01-01

Cochlear implant (CI) users typically have excellent speech recognition in quiet but struggle with understanding speech in noise. It is thought that broad current spread from stimulating electrodes causes adjacent electrodes to activate overlapping populations of neurons which results in interactions across adjacent channels. Current focusing has been studied as a way to reduce spread of excitation, and therefore, reduce channel interactions. In particular, partial tripolar stimulation has been shown to reduce spread of excitation relative to monopolar stimulation. However, the crucial question is whether this benefit translates to improvements in speech perception. In this study, we compared speech perception in noise with experimental monopolar and partial tripolar speech processing strategies. The two strategies were matched in terms of number of active electrodes, microphone, filterbanks, stimulation rate and loudness (although both strategies used a lower stimulation rate than typical clinical strategies). The results of this study showed a significant improvement in speech perception in noise with partial tripolar stimulation. All subjects benefited from the current focused speech processing strategy. There was a mean improvement in speech recognition threshold of 2.7 dB in a digits in noise task and a mean improvement of 3 dB in a sentences in noise task with partial tripolar stimulation relative to monopolar stimulation. Although the experimental monopolar strategy was worse than the clinical, presumably due to different microphones, frequency allocations and stimulation rates, the experimental partial-tripolar strategy, which had the same changes, showed no acute deficit relative to the clinical. PMID:23467170

Relationship between locked modes and thermal quenches in DIII-D

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

Sweeney, R.; Choi, W.; Austin, M.

Locked modes are known to be one of the major causes of disruptions, but the physical mechanisms by which locking leads to disruptions are not well understood. For this study, we analyze the evolution of the temperature profile in the presence of multiple coexisting locked modes during partial and full thermal quenches. Partial quenches are often observed to be an initial, distinct stage in the full thermal quench. Near the onset of partial quenches, locked island O-points are observed to align with each other on the midplane, and their widths are sufficient to overlap each other, as indicated by themore » Chirikov parameter. Energy conservation analysis of one partial thermal quench shows that the energy lost is both radiated in the divertor region, and conducted or convected to the divertor. Nonlinear resistive magnetohydrodynamic simulations support the interpretation of stochastic fields causing a partial axisymmetric collapse, though the simulated temperature profile exhibits less degradation than the experimental profiles. In discharges with minimum values of the safety factor above ~1.2, locked modes are observed to self-stabilize by inducing, possibly via double tearing modes, a minor disruption that removes their neoclassical drive. These high q min discharges often exhibit relatively low ratios of the plasma internal inductance to the safety factor at 95% of the poloidal flux, which might imply classical stability, in agreement with the decay of the mode when the neoclassical drive is removed.« less

Effects of oxygen on responses to heating in two lizard species sampled along an elevational gradient.

PubMed

DuBois, P Mason; Shea, Tanner K; Claunch, Natalie M; Taylor, Emily N

2017-08-01

Thermal tolerance is an important variable in predictive models about the effects of global climate change on species distributions, yet the physiological mechanisms responsible for reduced performance at high temperatures in air-breathing vertebrates are not clear. We conducted an experiment to examine how oxygen affects three variables exhibited by ectotherms as they heat-gaping threshold, panting threshold, and loss of righting response (the latter indicating the critical thermal maximum)-in two lizard species along an elevational (and therefore environmental oxygen partial pressure) gradient. Oxygen partial pressure did not impact these variables in either species. We also exposed lizards at each elevation to severely hypoxic gas to evaluate their responses to hypoxia. Severely low oxygen partial pressure treatments significantly reduced the gaping threshold, panting threshold, and critical thermal maximum. Further, under these extreme hypoxic conditions, these variables were strongly and positively related to partial pressure of oxygen. In an elevation where both species overlapped, the thermal tolerance of the high elevation species was less affected by hypoxia than that of the low elevation species, suggesting the high elevation species may be adapted to lower oxygen partial pressures. In the high elevation species, female lizards had higher thermal tolerance than males. Our data suggest that oxygen impacts the thermal tolerance of lizards, but only under severely hypoxic conditions, possibly as a result of hypoxia-induced anapyrexia. Copyright © 2017. Published by Elsevier Ltd.

UNDERSTANDING POLYSPECIFICITY WITHIN THE SUBSTRATE-BINDING CAVITY OF THE HUMAN MULTIDRUG RESISTANCE P-GLYCOPROTEIN

PubMed Central

Martinez, Lorena; Arnaud, Ophélie; Henin, Emilie; Tao, Houchao; Chaptal, Vincent; Doshi, Rupak; Andrieu, Thibaud; Dussurgey, Sébastien; Tod, Michel; Di Pietro, Attilio; Zhang, Qinghai; Chang, Geoffrey; Falson, Pierre

2015-01-01

Human P-glycoprotein (P-gp) controls drugs bioavailability by pumping out of the cells many structurally-unrelated drugs. The x-ray structure of the mouse P-gp ortholog was solved with two SSS- and one RRR-enantiomers of the selenohexapeptide inhibitor QZ59, found within the putative drug-binding pocket of the membrane domain outer leaflet. This offered the first opportunity to localize the well-known H- and R- drug-substrate sites in light of QZ59 inhibition mechanisms that were characterized here in cellulo and modelled towards Hoechst 33342 and daunorubicin transport. We found that QZ59-SSS competes efficiently with both substrates, displaying KI,app values of 0.15 and 0.3 μM, respectively 13 and 2 times lower than corresponding Km,app. In contrast, QZ59-RRR non-competitively inhibited daunorubicin transport with moderate efficacy (KI,app = 1.9 μM) and displayed a mixed-type inhibition towards Hoechst 33342 transport, resulting from a mainly non-competitive (Ki2,app = 1.6 μM) and a poor but significant competitive tendency (Ki1,app = 5 μM). These results suppose a positional overlap of QZ59 – drug-transport sites, total for the SSS enantiomer and partial for the RRR one. Crystal structures analysis suggests that the H site overlaps both QZ59-SSS locations while the R-site overlaps the most embedded one. PMID:24219411

First-principles studies of electric field effects on the electronic structure of trilayer graphene

NASA Astrophysics Data System (ADS)

Wang, Yun-Peng; Li, Xiang-Guo; Fry, James N.; Cheng, Hai-Ping

2016-10-01

A gate electric field is a powerful way to manipulate the physical properties of nanojunctions made of two-dimensional crystals. To simulate field effects on the electronic structure of trilayer graphene, we used density functional theory in combination with the effective screening medium method, which enables us to understand the field-dependent layer-layer interactions and the fundamental physics underlying band gap variations and the resulting band modifications. Two different graphene stacking orders, Bernal (or ABC) and rhombohedral (or ABA), were considered. In addition to confirming the experimentally observed band gap opening in ABC-stacked and the band overlap in ABA-stacked trilayer systems, our results reveal rich physics in these fascinating systems, where layer-layer couplings are present but some characteristics features of single-layer graphene are partially preserved. For ABC stacking, the electric-field-induced band gap size can be tuned by charge doping, while for ABA band the tunable quantity is the band overlap. Our calculations show that the electronic structures of the two stacking orders respond very differently to charge doping. We find that in the ABA stacking hole doping can reopen a band gap in the band-overlapping region, a phenomenon distinctly different from electron doping. The physical origins of the observed behaviors were fully analyzed, and we conclude that the dual-gate configuration greatly enhances the tunability of the trilayer systems.

A review of West Nile and Usutu virus co-circulation in Europe: how much do transmission cycles overlap?

PubMed

Nikolay, Birgit

2015-10-01

Due to the increasing global spread of arboviruses, the geographic extent of virus co-circulation is expanding. This complicates the diagnosis of febrile conditions and can have direct effects on the epidemiology. As previously demonstrated, subsequent infections by two closely related viruses, such as those belonging to the Japanese encephalitis virus (JEV) serocomplex, can lead to partial or complete cross-immunity, altering the risk of infections or the outcome of disease. Two flaviviruses that may interact at population level are West Nile virus (WNV) and Usutu virus (USUV). These pathogens have antigenic cross-reactivity and affect human and animal populations throughout Europe. This systematic review investigates the overlap of WNV and USUV transmission cycles, not only geographically but also in terms of host and vector ranges. Co-circulation of WNV and USUV was reported in 10 countries and the viruses were found to infect 34 common bird species belonging to 11 orders. Moreover, four mosquito species are potential vectors for both viruses. Taken together, these data suggest that WNV and USUV transmission overlaps substantially in Europe and highlight the importance of further studies investigating the interactions between the two viruses within host and vector populations. © The Author 2015. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Orthogonality catastrophe and fractional exclusion statistics

NASA Astrophysics Data System (ADS)

Ares, Filiberto; Gupta, Kumar S.; de Queiroz, Amilcar R.

2018-02-01

We show that the N -particle Sutherland model with inverse-square and harmonic interactions exhibits orthogonality catastrophe. For a fixed value of the harmonic coupling, the overlap of the N -body ground state wave functions with two different values of the inverse-square interaction term goes to zero in the thermodynamic limit. When the two values of the inverse-square coupling differ by an infinitesimal amount, the wave function overlap shows an exponential suppression. This is qualitatively different from the usual power law suppression observed in the Anderson's orthogonality catastrophe. We also obtain an analytic expression for the wave function overlaps for an arbitrary set of couplings, whose properties are analyzed numerically. The quasiparticles constituting the ground state wave functions of the Sutherland model are known to obey fractional exclusion statistics. Our analysis indicates that the orthogonality catastrophe may be valid in systems with more general kinds of statistics than just the fermionic type.

Orthogonality catastrophe and fractional exclusion statistics.

PubMed

Ares, Filiberto; Gupta, Kumar S; de Queiroz, Amilcar R

2018-02-01

We show that the N-particle Sutherland model with inverse-square and harmonic interactions exhibits orthogonality catastrophe. For a fixed value of the harmonic coupling, the overlap of the N-body ground state wave functions with two different values of the inverse-square interaction term goes to zero in the thermodynamic limit. When the two values of the inverse-square coupling differ by an infinitesimal amount, the wave function overlap shows an exponential suppression. This is qualitatively different from the usual power law suppression observed in the Anderson's orthogonality catastrophe. We also obtain an analytic expression for the wave function overlaps for an arbitrary set of couplings, whose properties are analyzed numerically. The quasiparticles constituting the ground state wave functions of the Sutherland model are known to obey fractional exclusion statistics. Our analysis indicates that the orthogonality catastrophe may be valid in systems with more general kinds of statistics than just the fermionic type.

SU-F-T-592: A Delivery QA-Free Approach for Adaptive Therapy of Prostate Cancer with Static Intensity Modulated Radiotherapy

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

Roth, T; Dooley, J; Zhu, T

2016-06-15

Purpose: Clinical implementations of adaptive radiotherapy (ART) are limited mainly by the requirement of delivery QA (DQA) prior to the treatment. Small segment size and small segment MU are two dominant factors causing failures of DQA. The aim of this project is to explore the feasibility of ART treatment without DQA by using a partial optimization approach. Methods: A retrospective simulation study was performed on two prostate cancer patients treated with SMLC-IMRT. The prescription was 180cGx25 fractions with daily CT-on-rail imaging for target alignment. For each patient, seven daily CTs were selected randomly across treatment course. The contours were deformablelymore » transferred from the simulation CT onto the daily CTs and modified appropriately. For each selected treatment, dose distributions from original beams were calculated on the daily treatment CTs (DCT plan). An ART plan was also created by optimizing the segmental MU only, while the segment shapes were preserved and the minimum MU constraint was respected. The overlaps, between PTV and the rectum, between PTV and the bladder, were normalized by the PTV volume. This ratio was used to characterize the difficulty of organs-at-risk (OAR) sparing. Results: Comparing to the original plan, PTV coverage was compromised significantly in DCT plans (82% ± 7%) while all ART plans preserved PTV coverage. ART plans showed similar OAR sparing as the original plan, such as V40Gy=11.2cc (ART) vs 11.4cc (original) for the rectum and D10cc=4580cGy vs 4605cGy for the bladder. The sparing of the rectum/bladder depends on overlap ratios. The sparing in ART was either similar or improved when overlap ratios in treatment CTs were smaller than those in original plan. Conclusion: A partial optimization method is developed that may make the real-time ART feasible on selected patients. Future research is warranted to quantify the applicability of the proposed method.« less

A Comparison of Graded Response and Rasch Partial Credit Models with Subjective Well-Being.

ERIC Educational Resources Information Center

Baker, John G.; Rounds, James B.; Zevon, Michael A.

2000-01-01

Compared two multiple category item response theory models using a data set of 52 mood terms with 713 undergraduate psychology students. Comparative model fit for the Samejima (F. Samejima, 1966) logistic model for graded responses and the Masters (G. Masters, 1982) partial credit model favored the former model for this data set. (SLD)

Robust Point Set Matching for Partial Face Recognition.

PubMed

Weng, Renliang; Lu, Jiwen; Tan, Yap-Peng

2016-03-01

Over the past three decades, a number of face recognition methods have been proposed in computer vision, and most of them use holistic face images for person identification. In many real-world scenarios especially some unconstrained environments, human faces might be occluded by other objects, and it is difficult to obtain fully holistic face images for recognition. To address this, we propose a new partial face recognition approach to recognize persons of interest from their partial faces. Given a pair of gallery image and probe face patch, we first detect keypoints and extract their local textural features. Then, we propose a robust point set matching method to discriminatively match these two extracted local feature sets, where both the textural information and geometrical information of local features are explicitly used for matching simultaneously. Finally, the similarity of two faces is converted as the distance between these two aligned feature sets. Experimental results on four public face data sets show the effectiveness of the proposed approach.

Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach

PubMed Central

Ruderfer, Douglas M; Charney, Alexander W; Readhead, Ben; Kidd, Brian A; Kähler, Anna K; Kenny, Paul J; Keiser, Michael J; Moran, Jennifer L; Hultman, Christina M; Scott, Stuart A; Sullivan, Patrick F; Purcell, Shaun M; Dudley, Joel T; Sklar, Pamela

2016-01-01

Summary Background Therapeutic treatments for schizophrenia do not alleviate symptoms for all patients and efficacy is limited by common, often severe, side-effects. Genetic studies of disease can identify novel drug targets, and drugs for which the mechanism has direct genetic support have increased likelihood of clinical success. Large-scale genetic studies of schizophrenia have increased the number of genes and gene sets associated with risk. We aimed to examine the overlap between schizophrenia risk loci and gene targets of a comprehensive set of medications to potentially inform and improve treatment of schizophrenia. Methods We defined schizophrenia risk loci as genomic regions reaching genome-wide significance in the latest Psychiatric Genomics Consortium schizophrenia genome-wide association study (GWAS) of 36 989 cases and 113 075 controls and loss of function variants observed only once among 5079 individuals in an exome-sequencing study of 2536 schizophrenia cases and 2543 controls (Swedish Schizophrenia Study). Using two large and orthogonally created databases, we collated drug targets into 167 gene sets targeted by pharmacologically similar drugs and examined enrichment of schizophrenia risk loci in these sets. We further linked the exome-sequenced data with a national drug registry (the Swedish Prescribed Drug Register) to assess the contribution of rare variants to treatment response, using clozapine prescription as a proxy for treatment resistance. Findings We combined results from testing rare and common variation and, after correction for multiple testing, two gene sets were associated with schizophrenia risk: agents against amoebiasis and other protozoal diseases (106 genes, p=0·00046, pcorrected =0·024) and antipsychotics (347 genes, p=0·00078, pcorrected=0·046). Further analysis pointed to antipsychotics as having independent enrichment after removing genes that overlapped these two target sets. We noted significant enrichment both in known targets of antipsychotics (70 genes, p=0·0078) and novel predicted targets (277 genes, p=0·019). Patients with treatment-resistant schizophrenia had an excess of rare disruptive variants in gene targets of antipsychotics (347 genes, p=0·0067) and in genes with evidence for a role in antipsychotic efficacy (91 genes, p=0·0029). Interpretation Our results support genetic overlap between schizophrenia pathogenesis and antipsychotic mechanism of action. This finding is consistent with treatment efficacy being polygenic and suggests that single-target therapeutics might be insufficient. We provide evidence of a role for rare functional variants in antipsychotic treatment response, pointing to a subset of patients where their genetic information could inform treatment. Finally, we present a novel framework for identifying treatments from genetic data and improving our understanding of therapeutic mechanism. PMID:26915512

Spatial capture–recapture with partial identity: An application to camera traps

USGS Publications Warehouse

Augustine, Ben C.; Royle, J. Andrew; Kelly, Marcella J.; Satter, Christopher B.; Alonso, Robert S.; Boydston, Erin E.; Crooks, Kevin R.

2018-01-01

Camera trapping surveys frequently capture individuals whose identity is only known from a single flank. The most widely used methods for incorporating these partial identity individuals into density analyses discard some of the partial identity capture histories, reducing precision, and, while not previously recognized, introducing bias. Here, we present the spatial partial identity model (SPIM), which uses the spatial location where partial identity samples are captured to probabilistically resolve their complete identities, allowing all partial identity samples to be used in the analysis. We show that the SPIM outperforms other analytical alternatives. We then apply the SPIM to an ocelot data set collected on a trapping array with double-camera stations and a bobcat data set collected on a trapping array with single-camera stations. The SPIM improves inference in both cases and, in the ocelot example, individual sex is determined from photographs used to further resolve partial identities—one of which is resolved to near certainty. The SPIM opens the door for the investigation of trapping designs that deviate from the standard two camera design, the combination of other data types between which identities cannot be deterministically linked, and can be extended to the problem of partial genotypes.

Film Excerpts Shown to Specifically Elicit Various Affects Lead to Overlapping Activation Foci in a Large Set of Symmetrical Brain Regions in Males

PubMed Central

Karama, Sherif; Armony, Jorge; Beauregard, Mario

2011-01-01

While the limbic system theory continues to be part of common scientific parlance, its validity has been questioned on multiple grounds. Nonetheless, the issue of whether or not there exists a set of brain areas preferentially dedicated to emotional processing remains central within affective neuroscience. Recently, a widespread neural reference space for emotion which includes limbic as well as other regions was characterized in a large meta-analysis. As methodologically heterogeneous studies go into such meta-analyses, showing in an individual study in which all parameters are kept constant, the involvement of overlapping areas for various emotion conditions in keeping with the neural reference space for emotion, would serve as valuable confirmatory evidence. Here, using fMRI, 20 young adult men were scanned while viewing validated neutral and effective emotion-eliciting short film excerpts shown to quickly and specifically elicit disgust, amusement, or sexual arousal. Each emotion-specific run included, in random order, multiple neutral and emotion condition blocks. A stringent conjunction analysis revealed a large overlap across emotion conditions that fit remarkably well with the neural reference space for emotion. This overlap included symmetrical bilateral activation of the medial prefrontal cortex, the anterior cingulate, the temporo-occipital junction, the basal ganglia, the brainstem, the amygdala, the hippocampus, the thalamus, the subthalamic nucleus, the posterior hypothalamus, the cerebellum, as well as the frontal operculum extending towards the anterior insula. This study clearly confirms for the visual modality, that processing emotional stimuli leads to widespread increases in activation that cluster within relatively confined areas, regardless of valence. PMID:21818311

A Bifurcation Problem for a Nonlinear Partial Differential Equation of Parabolic Type,

DTIC Science & Technology

NONLINEAR DIFFERENTIAL EQUATIONS, INTEGRATION), (*PARTIAL DIFFERENTIAL EQUATIONS, BOUNDARY VALUE PROBLEMS), BANACH SPACE , MAPPING (TRANSFORMATIONS), SET THEORY, TOPOLOGY, ITERATIONS, STABILITY, THEOREMS

Design of partially supervised classifiers for multispectral image data

NASA Technical Reports Server (NTRS)

Jeon, Byeungwoo; Landgrebe, David

1993-01-01

A partially supervised classification problem is addressed, especially when the class definition and corresponding training samples are provided a priori only for just one particular class. In practical applications of pattern classification techniques, a frequently observed characteristic is the heavy, often nearly impossible requirements on representative prior statistical class characteristics of all classes in a given data set. Considering the effort in both time and man-power required to have a well-defined, exhaustive list of classes with a corresponding representative set of training samples, this 'partially' supervised capability would be very desirable, assuming adequate classifier performance can be obtained. Two different classification algorithms are developed to achieve simplicity in classifier design by reducing the requirement of prior statistical information without sacrificing significant classifying capability. The first one is based on optimal significance testing, where the optimal acceptance probability is estimated directly from the data set. In the second approach, the partially supervised classification is considered as a problem of unsupervised clustering with initially one known cluster or class. A weighted unsupervised clustering procedure is developed to automatically define other classes and estimate their class statistics. The operational simplicity thus realized should make these partially supervised classification schemes very viable tools in pattern classification.

Mathematics for Gifted Students in an Arts- and Technology-Rich Setting

ERIC Educational Resources Information Center

Gadanidis, George; Hughes, Janette; Cordy, Michelle

2011-01-01

In this paper we report on a study of a short-term mathematics program for grade 7-8 gifted students that integrated open-ended mathematics tasks with the arts (poetry and drama) and with technology. The program was offered partially online and partially in a classroom setting. The study sought to investigate (a) students' perceptions of their…

Geochemical and Depth Variations at the Galápagos 93.25˚W Propagating Rift

NASA Astrophysics Data System (ADS)

Rotella, M.; Sinton, J.; Mahoney, J.; Chazey, W.

2006-12-01

The 93.25°W propagating rift on the Galápagos Spreading Center (GSC) differs markedly from the better-known propagator at 95.5°W in having the morphology of a classic overlapping spreading center (~24 km of overlap and 7.5 km of offset). It has a higher propagation rate (70 vs 48 mm/yr) [Wilson & Hey, JGR v. 100, 1995] and is breaking through younger crust (260 vs 910 ka); overall magma supply is ~20% greater, as the area is closer to the Galápagos hotspot. The overlapping limbs lack pronounced bathymetric lows, instead they are up to 150 m shallower than the surrounding axial ridges away from the offset. Lavas are T-MORB; failing rift lavas show a slight increase in Mg within the overlap zone but propagating rift lavas lack the strong fractionation anomaly that characterizes the propagating limb at 95.5°W and many other propagating rifts. New major and trace element data on 28 samples from 24 dredge stations along a 175 km section of the GSC spanning the 93.25°W offset indicate significant, systematic variations in mantle sources and melting processes on each limb of the system. Fractionation-corrected ratios of highly to moderately incompatible elements (e.g. La/Yb, Sm/Yb, Zr/Y) show constant values along the propagating rift east of 93.2°W, but within the overlap zone these ratios increase sharply up to a factor of 1.5, then gradually decline to the west. In contrast, the failing rift shows constant to moderately increasing ratios as the overlap zone is approached from the west, with lower overall ratios within the zone. These variations could be interpreted to reflect a counter-intuitive relationship of gradually increasing extent of partial melting with progressive failure of the dying rift, consistent with the striking shoaling of the failing limb, or melting of incompatible-element depleted mantle. Variations along the eastern, propagating rift suggest either a sharp decrease in extent of melting or tapping of a more incompatible-element-enriched mantle source within the overlap zone. Limited Nd-Pb-Sr isotopic data suggest source variations are required in addition to variations in extent of melting. Thus, in contrast to other well-documented propagators where geochemical variations are dominated by magma chamber effects, variations around the 93.25°W system appear to be dominated by melting and source.

Effect of variation in self-incompatibility on pollen limitation and inbreeding depression in Flourensia cernua (Asteraceae) scrubs of contrasting density

PubMed Central

Ferrer, Miriam M.; Good-Avila, Sara V.; Montaña, Carlos; Domínguez, César A.; Eguiarte, Luis E.

2009-01-01

Background and Aims Selection may favour a partial or complete loss of self-incompatibility (SI) if it increases the reproductive output of individuals in the presence of low mate availability. The reproductive output of individuals varying in their strength of SI may also be affected by population density via its affect on the spatial structuring and number of S-alleles in populations. Modifiers increasing levels of self-compatibility can be selected when self-compatible individuals receive reproductive compensation by, for example, increasing seed set and/or when they become associated with high fitness genotypes. Methods The effect of variation in the strength of SI and scrub density (low versus high) on seed set, seed germination and inbreeding depression in seed germination (δgerm) was investigated in the partially self-incompatible species Flourensia cernua by analysing data from self-, cross- and open-pollinated florets. Key Results Examination of 100 plants in both high and low scrub densities revealed that 51% of plants were strongly self-incompatible and 49 % varied from being self-incompatible to self-compatible. Seed set after hand cross-pollination was higher than after open-pollination for self-incompatible, partially self-incompatible and self-compatible plants but was uniformly low for strongly self-incompatible plants. Strongly self-incompatible and self-incompatible plants exhibited lower seed set, seed germination and multiplicative female fitness (floral display × seed set × seed germination) in open-pollinated florets compared with partially self-incompatible and self-compatible plants. Scrub density also had an effect on seed set and inbreeding depression: in low-density scrubs seed set was higher after open-pollination and δgerm was lower. Conclusions These data suggest that (a) plants suffered outcross pollen limitation, (b) female fitness in partially self-incompatible and self-compatible plants is enhanced by increased mate-compatibility and (c) plants in low-density scrubs received higher quality pollen via open-pollination than plants in high-density scrubs. PMID:19218580

6. (First sheet of a twosheet set entitled 'Kongensgade 5154') ...

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

6. (First sheet of a two-sheet set entitled 'Kongensgade 51-54') KONGENSGADE (FRONT) ELEVATIONS OF KONGENSGADE 51, 52 & 53 (only part of Kongensgade 53 elevation shown, for full elevation overlap with complementary photograph VI-50-7) (LEFT TO RIGHT) - King Street Area Study, Kongensgade 5-18, 36, 37B, 51-58 (Houses), 5-18, 36-37B, 51-58 King Street, Frederiksted, St. Croix, VI

Detecting Malaria Hotspots: A Comparison of Rapid Diagnostic Test, Microscopy, and Polymerase Chain Reaction.

PubMed

Mogeni, Polycarp; Williams, Thomas N; Omedo, Irene; Kimani, Domtila; Ngoi, Joyce M; Mwacharo, Jedida; Morter, Richard; Nyundo, Christopher; Wambua, Juliana; Nyangweso, George; Kapulu, Melissa; Fegan, Gregory; Bejon, Philip

2017-11-27

Malaria control strategies need to respond to geographical hotspots of transmission. Detection of hotspots depends on the sensitivity of the diagnostic tool used. We conducted cross-sectional surveys in 3 sites within Kilifi County, Kenya, that had variable transmission intensities. Rapid diagnostic test (RDT), microscopy, and polymerase chain reaction (PCR) were used to detect asymptomatic parasitemia, and hotspots were detected using the spatial scan statistic. Eight thousand five hundred eighty-one study participants were surveyed in 3 sites. There were statistically significant malaria hotspots by RDT, microscopy, and PCR for all sites except by microscopy in 1 low transmission site. Pooled data analysis of hotspots by PCR overlapped with hotspots by microscopy at a moderate setting but not at 2 lower transmission settings. However, variations in degree of overlap were noted when data were analyzed by year. Hotspots by RDT were predictive of PCR/microscopy at the moderate setting, but not at the 2 low transmission settings. We observed long-term stability of hotspots by PCR and microscopy but not RDT. Malaria control programs may consider PCR testing to guide asymptomatic malaria hotspot detection once the prevalence of infection falls. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

Application of visible and near-infrared spectroscopy to classification of Miscanthus species

DOE PAGES

Jin, Xiaoli; Chen, Xiaoling; Xiao, Liang; ...

2017-04-03

Here, the feasibility of visible and near infrared (NIR) spectroscopy as tool to classify Miscanthus samples was explored in this study. Three types of Miscanthus plants, namely, M. sinensis, M. sacchariflorus and M. fIoridulus, were analyzed using a NIR spectrophotometer. Several classification models based on the NIR spectra data were developed using line discriminated analysis (LDA), partial least squares (PLS), least squares support vector machine regression (LSSVR), radial basis function (RBF) and neural network (NN). The principal component analysis (PCA) presented rough classification with overlapping samples, while the models of Line_LSSVR, RBF_LSSVR and RBF_NN presented almost same calibration and validationmore » results. Due to the higher speed of Line_LSSVR than RBF_LSSVR and RBF_NN, we selected the line_LSSVR model as a representative. In our study, the model based on line_LSSVR showed higher accuracy than LDA and PLS models. The total correct classification rates of 87.79 and 96.51% were observed based on LDA and PLS model in the testing set, respectively, while the line_LSSVR showed 99.42% of total correct classification rate. Meanwhile, the lin_LSSVR model in the testing set showed correct classification rate of 100, 100 and 96.77% for M. sinensis, M. sacchariflorus and M. fIoridulus, respectively. The lin_LSSVR model assigned 99.42% of samples to the right groups, except one M. fIoridulus sample. The results demonstrated that NIR spectra combined with a preliminary morphological classification could be an effective and reliable procedure for the classification of Miscanthus species.« 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

Application of visible and near-infrared spectroscopy to classification of Miscanthus species

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

Jin, Xiaoli; Chen, Xiaoling; Xiao, Liang

Here, the feasibility of visible and near infrared (NIR) spectroscopy as tool to classify Miscanthus samples was explored in this study. Three types of Miscanthus plants, namely, M. sinensis, M. sacchariflorus and M. fIoridulus, were analyzed using a NIR spectrophotometer. Several classification models based on the NIR spectra data were developed using line discriminated analysis (LDA), partial least squares (PLS), least squares support vector machine regression (LSSVR), radial basis function (RBF) and neural network (NN). The principal component analysis (PCA) presented rough classification with overlapping samples, while the models of Line_LSSVR, RBF_LSSVR and RBF_NN presented almost same calibration and validationmore » results. Due to the higher speed of Line_LSSVR than RBF_LSSVR and RBF_NN, we selected the line_LSSVR model as a representative. In our study, the model based on line_LSSVR showed higher accuracy than LDA and PLS models. The total correct classification rates of 87.79 and 96.51% were observed based on LDA and PLS model in the testing set, respectively, while the line_LSSVR showed 99.42% of total correct classification rate. Meanwhile, the lin_LSSVR model in the testing set showed correct classification rate of 100, 100 and 96.77% for M. sinensis, M. sacchariflorus and M. fIoridulus, respectively. The lin_LSSVR model assigned 99.42% of samples to the right groups, except one M. fIoridulus sample. The results demonstrated that NIR spectra combined with a preliminary morphological classification could be an effective and reliable procedure for the classification of Miscanthus species.« less

Application of visible and near-infrared spectroscopy to classification of Miscanthus species.

PubMed

Jin, Xiaoli; Chen, Xiaoling; Xiao, Liang; Shi, Chunhai; Chen, Liang; Yu, Bin; Yi, Zili; Yoo, Ji Hye; Heo, Kweon; Yu, Chang Yeon; Yamada, Toshihiko; Sacks, Erik J; Peng, Junhua

2017-01-01

The feasibility of visible and near infrared (NIR) spectroscopy as tool to classify Miscanthus samples was explored in this study. Three types of Miscanthus plants, namely, M. sinensis, M. sacchariflorus and M. fIoridulus, were analyzed using a NIR spectrophotometer. Several classification models based on the NIR spectra data were developed using line discriminated analysis (LDA), partial least squares (PLS), least squares support vector machine regression (LSSVR), radial basis function (RBF) and neural network (NN). The principal component analysis (PCA) presented rough classification with overlapping samples, while the models of Line_LSSVR, RBF_LSSVR and RBF_NN presented almost same calibration and validation results. Due to the higher speed of Line_LSSVR than RBF_LSSVR and RBF_NN, we selected the line_LSSVR model as a representative. In our study, the model based on line_LSSVR showed higher accuracy than LDA and PLS models. The total correct classification rates of 87.79 and 96.51% were observed based on LDA and PLS model in the testing set, respectively, while the line_LSSVR showed 99.42% of total correct classification rate. Meanwhile, the lin_LSSVR model in the testing set showed correct classification rate of 100, 100 and 96.77% for M. sinensis, M. sacchariflorus and M. fIoridulus, respectively. The lin_LSSVR model assigned 99.42% of samples to the right groups, except one M. fIoridulus sample. The results demonstrated that NIR spectra combined with a preliminary morphological classification could be an effective and reliable procedure for the classification of Miscanthus species.

Application of visible and near-infrared spectroscopy to classification of Miscanthus species

PubMed Central

Shi, Chunhai; Chen, Liang; Yu, Bin; Yi, Zili; Yoo, Ji Hye; Heo, Kweon; Yu, Chang Yeon; Yamada, Toshihiko; Sacks, Erik J.; Peng, Junhua

2017-01-01

The feasibility of visible and near infrared (NIR) spectroscopy as tool to classify Miscanthus samples was explored in this study. Three types of Miscanthus plants, namely, M. sinensis, M. sacchariflorus and M. fIoridulus, were analyzed using a NIR spectrophotometer. Several classification models based on the NIR spectra data were developed using line discriminated analysis (LDA), partial least squares (PLS), least squares support vector machine regression (LSSVR), radial basis function (RBF) and neural network (NN). The principal component analysis (PCA) presented rough classification with overlapping samples, while the models of Line_LSSVR, RBF_LSSVR and RBF_NN presented almost same calibration and validation results. Due to the higher speed of Line_LSSVR than RBF_LSSVR and RBF_NN, we selected the line_LSSVR model as a representative. In our study, the model based on line_LSSVR showed higher accuracy than LDA and PLS models. The total correct classification rates of 87.79 and 96.51% were observed based on LDA and PLS model in the testing set, respectively, while the line_LSSVR showed 99.42% of total correct classification rate. Meanwhile, the lin_LSSVR model in the testing set showed correct classification rate of 100, 100 and 96.77% for M. sinensis, M. sacchariflorus and M. fIoridulus, respectively. The lin_LSSVR model assigned 99.42% of samples to the right groups, except one M. fIoridulus sample. The results demonstrated that NIR spectra combined with a preliminary morphological classification could be an effective and reliable procedure for the classification of Miscanthus species. PMID:28369059

The groESL Chaperone Operon of Lactobacillus johnsonii†

PubMed Central

Walker, D. Carey; Girgis, Hany S.; Klaenhammer, Todd R.

1999-01-01

The Lactobacillus johnsonii VPI 11088 groESL operon was localized on the chromosome near the insertion element IS1223. The operon was initially cloned as a series of three overlapping PCR fragments, which were sequenced and used to design primers to amplify the entire operon. The amplified fragment was used as a probe to recover the chromosomal copy of the groESL operon from a partial library of L. johnsonii VPI 11088 (NCK88) DNA, cloned in the shuttle vector pTRKH2. The 2,253-bp groESL fragment contained three putative open reading frames, two of which encoded the ubiquitous GroES and GroEL chaperone proteins. Analysis of the groESL promoter region revealed three transcription initiation sites, as well as three sets of inverted repeats (IR) positioned between the transcription and translation start sites. Two of the three IR sets bore significant homology to the CIRCE elements, implicated in negative regulation of the heat shock response in many bacteria. Northern analysis and primer extension revealed that multiple temperature-sensitive promoters preceded the groESL chaperone operon, suggesting that stress protein production in L. johnsonii is strongly regulated. Maximum groESL transcription activity was observed following a shift to 55°C, and a 15 to 30-min exposure of log-phase cells to this temperature increased the recovery of freeze-thawed L. johnsonii VPI 11088. These results suggest that a brief, preconditioning heat shock can be used to trigger increased chaperone production and provide significant cross-protection from the stresses imposed during the production of frozen culture concentrates. PMID:10388700

Evaluation of the efficiency of continuous wavelet transform as processing and preprocessing algorithm for resolution of overlapped signals in univariate and multivariate regression analyses; an application to ternary and quaternary mixtures.

PubMed

Hegazy, Maha A; Lotfy, Hayam M; Mowaka, Shereen; Mohamed, Ekram Hany

2016-07-05

Wavelets have been adapted for a vast number of signal-processing applications due to the amount of information that can be extracted from a signal. In this work, a comparative study on the efficiency of continuous wavelet transform (CWT) as a signal processing tool in univariate regression and a pre-processing tool in multivariate analysis using partial least square (CWT-PLS) was conducted. These were applied to complex spectral signals of ternary and quaternary mixtures. CWT-PLS method succeeded in the simultaneous determination of a quaternary mixture of drotaverine (DRO), caffeine (CAF), paracetamol (PAR) and p-aminophenol (PAP, the major impurity of paracetamol). While, the univariate CWT failed to simultaneously determine the quaternary mixture components and was able to determine only PAR and PAP, the ternary mixtures of DRO, CAF, and PAR and CAF, PAR, and PAP. During the calculations of CWT, different wavelet families were tested. The univariate CWT method was validated according to the ICH guidelines. While for the development of the CWT-PLS model a calibration set was prepared by means of an orthogonal experimental design and their absorption spectra were recorded and processed by CWT. The CWT-PLS model was constructed by regression between the wavelet coefficients and concentration matrices and validation was performed by both cross validation and external validation sets. Both methods were successfully applied for determination of the studied drugs in pharmaceutical formulations. Copyright © 2016 Elsevier B.V. All rights reserved.

Membrane Introduction Mass Spectrometry Combined with an Orthogonal Partial-Least Squares Calibration Model for Mixture Analysis.

PubMed

Li, Min; Zhang, Lu; Yao, Xiaolong; Jiang, Xingyu

2017-01-01

The emerging membrane introduction mass spectrometry technique has been successfully used to detect benzene, toluene, ethyl benzene and xylene (BTEX), while overlapped spectra have unfortunately hindered its further application to the analysis of mixtures. Multivariate calibration, an efficient method to analyze mixtures, has been widely applied. In this paper, we compared univariate and multivariate analyses for quantification of the individual components of mixture samples. The results showed that the univariate analysis creates poor models with regression coefficients of 0.912, 0.867, 0.440 and 0.351 for BTEX, respectively. For multivariate analysis, a comparison to the partial-least squares (PLS) model shows that the orthogonal partial-least squares (OPLS) regression exhibits an optimal performance with regression coefficients of 0.995, 0.999, 0.980 and 0.976, favorable calibration parameters (RMSEC and RMSECV) and a favorable validation parameter (RMSEP). Furthermore, the OPLS exhibits a good recovery of 73.86 - 122.20% and relative standard deviation (RSD) of the repeatability of 1.14 - 4.87%. Thus, MIMS coupled with the OPLS regression provides an optimal approach for a quantitative BTEX mixture analysis in monitoring and predicting water pollution.

Experimental verification of the model for formation of double Shockley stacking faults in highly doped regions of PVT-grown 4H–SiC wafers

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

Yang, Yu; Guo, Jianqiu; Goue, Ouloide

Recently, we reported on the formation of overlapping rhombus-shaped stacking faults from scratches left over by the chemical mechanical polishing during high temperature annealing of PVT-grown 4H–SiC wafer. These stacking faults are restricted to regions with high N-doped areas of the wafer. The type of these stacking faults were determined to be Shockley stacking faults by analyzing the behavior of their area contrast using synchrotron white beam X-ray topography studies. A model was proposed to explain the formation mechanism of the rhombus shaped stacking faults based on double Shockley fault nucleation and propagation. In this paper, we have experimentally verifiedmore » this model by characterizing the configuration of the bounding partials of the stacking faults on both surfaces using synchrotron topography in back reflection geometry. As predicted by the model, on both the Si and C faces, the leading partials bounding the rhombus-shaped stacking faults are 30° Si-core and the trailing partials are 30° C-core. Finally, using high resolution transmission electron microscopy, we have verified that the enclosed stacking fault is a double Shockley type.« less

Architecture and dynamics of overlapped RNA regulatory networks.

PubMed

Lapointe, Christopher P; Preston, Melanie A; Wilinski, Daniel; Saunders, Harriet A J; Campbell, Zachary T; Wickens, Marvin

2017-11-01

A single protein can bind and regulate many mRNAs. Multiple proteins with similar specificities often bind and control overlapping sets of mRNAs. Yet little is known about the architecture or dynamics of overlapped networks. We focused on three proteins with similar structures and related RNA-binding specificities-Puf3p, Puf4p, and Puf5p of S. cerevisiae Using RNA Tagging, we identified a "super-network" comprised of four subnetworks: Puf3p, Puf4p, and Puf5p subnetworks, and one controlled by both Puf4p and Puf5p. The architecture of individual subnetworks, and thus the super-network, is determined by competition among particular PUF proteins to bind mRNAs, their affinities for binding elements, and the abundances of the proteins. The super-network responds dramatically: The remaining network can either expand or contract. These strikingly opposite outcomes are determined by an interplay between the relative abundance of the RNAs and proteins, and their affinities for one another. The diverse interplay between overlapping RNA-protein networks provides versatile opportunities for regulation and evolution. © 2017 Lapointe et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

An Efficient Method to Detect Mutual Overlap of a Large Set of Unordered Images for Structure-From

NASA Astrophysics Data System (ADS)

Wang, X.; Zhan, Z. Q.; Heipke, C.

2017-05-01

Recently, low-cost 3D reconstruction based on images has become a popular focus of photogrammetry and computer vision research. Methods which can handle an arbitrary geometric setup of a large number of unordered and convergent images are of particular interest. However, determining the mutual overlap poses a considerable challenge. We propose a new method which was inspired by and improves upon methods employing random k-d forests for this task. Specifically, we first derive features from the images and then a random k-d forest is used to find the nearest neighbours in feature space. Subsequently, the degree of similarity between individual images, the image overlaps and thus images belonging to a common block are calculated as input to a structure-from-motion (sfm) pipeline. In our experiments we show the general applicability of the new method and compare it with other methods by analyzing the time efficiency. Orientations and 3D reconstructions were successfully conducted with our overlap graphs by sfm. The results show a speed-up of a factor of 80 compared to conventional pairwise matching, and of 8 and 2 compared to the VocMatch approach using 1 and 4 CPU, respectively.

Profiles of sedentary and non-sedentary young men - a population-based MOPO study.

PubMed

Pyky, Riitta; Jauho, Anna-Maiju; Ahola, Riikka; Ikäheimo, Tiina M; Koivumaa-Honkanen, Heli; Mäntysaari, Matti; Jämsä, Timo; Korpelainen, Raija

2015-11-23

Sedentary behavior is associated with poor well-being in youth with adverse trajectories spanning to adulthood. Still, its determinants are poorly known. Our aim was to profile sedentary and non-sedentary young men and to clarify their differences in a population-based setting. A total of 616 men (mean age 17.9, SD 0.6) attending compulsory conscription for military service completed a questionnaire on health, health behavior, socioeconomic situation and media use. They underwent a physical (body composition, muscle and aerobic fitness) and medical examination. Profiles were formed by principal component analysis (PCA). A total of 30.1 % men were sedentary (daily leisure-time sitting ≥5 h) and 28.9 % non-sedentary (sitting ≤2 h). The sedentary men had more body fat, more depressive symptoms, but lower fitness and life satisfaction than non-sedentary men. However, according to PCA, profiles of unhealthy eating, life-dissatisfaction, and gaming were detected both among sedentary and non-sedentary men, as well as high self-rated PA and motives to exercise. Determinants of sedentary and non-sedentary lifestyles were multiple and partially overlapping. Recognizing individual patterns and underlying factors of the sedentary lifestyle is essential for tailored health promotion and interventions.

A relational extension of the notion of motifs: application to the common 3D protein substructures searching problem.

PubMed

Pisanti, Nadia; Soldano, Henry; Carpentier, Mathilde; Pothier, Joel

2009-12-01

The geometrical configurations of atoms in protein structures can be viewed as approximate relations among them. Then, finding similar common substructures within a set of protein structures belongs to a new class of problems that generalizes that of finding repeated motifs. The novelty lies in the addition of constraints on the motifs in terms of relations that must hold between pairs of positions of the motifs. We will hence denote them as relational motifs. For this class of problems, we present an algorithm that is a suitable extension of the KMR paradigm and, in particular, of the KMRC as it uses a degenerate alphabet. Our algorithm contains several improvements that become especially useful when-as it is required for relational motifs-the inference is made by partially overlapping shorter motifs, rather than concatenating them. The efficiency, correctness and completeness of the algorithm is ensured by several non-trivial properties that are proven in this paper. The algorithm has been applied in the important field of protein common 3D substructure searching. The methods implemented have been tested on several examples of protein families such as serine proteases, globins and cytochromes P450 additionally. The detected motifs have been compared to those found by multiple structural alignments methods.

Quantum chemical calculation (electronic and topologic) and experimental (FT-IR, FT-Raman and UV) analysis of isonicotinic acid N-oxide

NASA Astrophysics Data System (ADS)

Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

2015-04-01

In this work, the molecular conformation, vibrational and electronic analysis of isonicotinic acid N-oxide (iso-NANO) were presented in the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. The geometry optimization and energies associated possible two conformers (Rot-I and Rot-II) were computed. The vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The obtained structures were analyzed with the Atoms in Molecules (AIMs) methodology. The computational results diagnose the most stable conformer of iso-NANO as the Rot-I form. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (OPDOS) diagrams analysis for the most stable conformer (Rot-I) were calculated using the same method. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated. As a result, the optimized geometry and calculated spectroscopic data show a good agreement with the experimental results.

Left-ventricle segmentation in real-time 3D echocardiography using a hybrid active shape model and optimal graph search approach

NASA Astrophysics Data System (ADS)

Zhang, Honghai; Abiose, Ademola K.; Campbell, Dwayne N.; Sonka, Milan; Martins, James B.; Wahle, Andreas

2010-03-01

Quantitative analysis of the left ventricular shape and motion patterns associated with left ventricular mechanical dyssynchrony (LVMD) is essential for diagnosis and treatment planning in congestive heart failure. Real-time 3D echocardiography (RT3DE) used for LVMD analysis is frequently limited by heavy speckle noise or partially incomplete data, thus a segmentation method utilizing learned global shape knowledge is beneficial. In this study, the endocardial surface of the left ventricle (LV) is segmented using a hybrid approach combining active shape model (ASM) with optimal graph search. The latter is used to achieve landmark refinement in the ASM framework. Optimal graph search translates the 3D segmentation into the detection of a minimum-cost closed set in a graph and can produce a globally optimal result. Various information-gradient, intensity distributions, and regional-property terms-are used to define the costs for the graph search. The developed method was tested on 44 RT3DE datasets acquired from 26 LVMD patients. The segmentation accuracy was assessed by surface positioning error and volume overlap measured for the whole LV as well as 16 standard LV regions. The segmentation produced very good results that were not achievable using ASM or graph search alone.

Glass promotes the differentiation of neuronal and non-neuronal cell types in the Drosophila eye

PubMed Central

Morrison, Carolyn A.; Chen, Hao; Cook, Tiffany; Brown, Stuart

2018-01-01

Transcriptional regulators can specify different cell types from a pool of equivalent progenitors by activating distinct developmental programs. The Glass transcription factor is expressed in all progenitors in the developing Drosophila eye, and is maintained in both neuronal and non-neuronal cell types. Glass is required for neuronal progenitors to differentiate as photoreceptors, but its role in non-neuronal cone and pigment cells is unknown. To determine whether Glass activity is limited to neuronal lineages, we compared the effects of misexpressing it in neuroblasts of the larval brain and in epithelial cells of the wing disc. Glass activated overlapping but distinct sets of genes in these neuronal and non-neuronal contexts, including markers of photoreceptors, cone cells and pigment cells. Coexpression of other transcription factors such as Pax2, Eyes absent, Lozenge and Escargot enabled Glass to induce additional genes characteristic of the non-neuronal cell types. Cell type-specific glass mutations generated in cone or pigment cells using somatic CRISPR revealed autonomous developmental defects, and expressing Glass specifically in these cells partially rescued glass mutant phenotypes. These results indicate that Glass is a determinant of organ identity that acts in both neuronal and non-neuronal cells to promote their differentiation into functional components of the eye. PMID:29324767

CONVERGENT TRANSCRIPTOMICS AND PROTEOMICS OF ENVIRONMENTAL ENRICHMENT AND COCAINE IDENTIFIES NOVEL THERAPEUTIC STRATEGIES FOR ADDICTION

PubMed Central

ZHANG, YAFANG; CROFTON, ELIZABETH J.; FAN, XIUZHEN; LI, DINGGE; KONG, FANPING; SINHA, MALA; LUXON, BRUCE A.; SPRATT, HEIDI M.; LICHTI, CHERYL F.; GREEN, THOMAS A.

2016-01-01

Transcriptomic and proteomic approaches have separately proven effective at identifying novel mechanisms affecting addiction-related behavior; however, it is difficult to prioritize the many promising leads from each approach. A convergent secondary analysis of proteomic and transcriptomic results can glean additional information to help prioritize promising leads. The current study is a secondary analysis of the convergence of recently published separate transcriptomic and proteomic analyses of nucleus accumbens (NAc) tissue from rats subjected to environmental enrichment vs. isolation and cocaine self-administration vs. saline. Multiple bioinformatics approaches (e.g. Gene Ontology (GO) analysis, Ingenuity Pathway Analysis (IPA), and Gene Set Enrichment Analysis (GSEA)) were used to interrogate these rich data sets. Although there was little correspondence between mRNA vs. protein at the individual target level, good correspondence was found at the level of gene/protein sets, particularly for the environmental enrichment manipulation. These data identify gene sets where there is a positive relationship between changes in mRNA and protein (e.g. glycolysis, ATP synthesis, translation elongation factor activity, etc.) and gene sets where there is an inverse relationship (e.g. ribosomes, Rho GTPase signaling, protein ubiquitination, etc.). Overall environmental enrichment produced better correspondence than cocaine self-administration. The individual targets contributing to mRNA and protein effects were largely not overlapping. As a whole, these results confirm that robust transcriptomic and proteomic data sets can provide similar results at the gene/protein set level even when there is little correspondence at the individual target level and little overlap in the targets contributing to the effects. PMID:27717806

Communities and classes in symmetric fractals

NASA Astrophysics Data System (ADS)

Krawczyk, Małgorzata J.

2015-07-01

Two aspects of fractal networks are considered: the community structure and the class structure, where classes of nodes appear as a consequence of a local symmetry of nodes. The analyzed systems are the networks constructed for two selected symmetric fractals: the Sierpinski triangle and the Koch curve. Communities are searched for by means of a set of differential equations. Overlapping nodes which belong to two different communities are identified by adding some noise to the initial connectivity matrix. Then, a node can be characterized by a spectrum of probabilities of belonging to different communities. Our main goal is that the overlapping nodes with the same spectra belong to the same class.

Stereo imaging with spaceborne radars

NASA Technical Reports Server (NTRS)

Leberl, F.; Kobrick, M.

1983-01-01

Stereo viewing is a valuable tool in photointerpretation and is used for the quantitative reconstruction of the three dimensional shape of a topographical surface. Stereo viewing refers to a visual perception of space by presenting an overlapping image pair to an observer so that a three dimensional model is formed in the brain. Some of the observer's function is performed by machine correlation of the overlapping images - so called automated stereo correlation. The direct perception of space with two eyes is often called natural binocular vision; techniques of generating three dimensional models of the surface from two sets of monocular image measurements is the topic of stereology.

Measurement of plasma sheath overlap above a trench

NASA Astrophysics Data System (ADS)

Sheridan, T. E.; Steinberger, Thomas E.

2017-06-01

The plasma sheath above a rectangular trench has been experimentally characterized as the trench width is varied in a radio frequency (rf) plasma discharge for two different rf powers giving two different sets of plasma parameters. Measurements were made using the positions and all six normal mode frequencies of two dust particles floating just inside the sheath edge above the center of the trench. We find that sheath overlap occurs when the trench width ≲ 3 s 0 for a trench depth ≈0.7s0, where s0 is the planar sheath width. The electric field gradient inside the sheath edge increases with rf power.

Tools for model-building with cryo-EM maps

DOE PAGES

Terwilliger, Thomas Charles

2018-01-01

There are new tools available to you in Phenix for interpreting cryo-EM maps. You can automatically sharpen (or blur) a map with phenix.auto_sharpen and you can segment a map with phenix.segment_and_split_map. If you have overlapping partial models for a map, you can merge them with phenix.combine_models. If you have a protein-RNA complex and protein chains have been accidentally built in the RNA region, you can try to remove them with phenix.remove_poor_fragments. You can put these together and automatically sharpen, segment and build a map with phenix.map_to_model.

FOXG1 Is Responsible for the Congenital Variant of Rett Syndrome

PubMed Central

Ariani, Francesca; Hayek, Giuseppe; Rondinella, Dalila; Artuso, Rosangela; Mencarelli, Maria Antonietta; Spanhol-Rosseto, Ariele; Pollazzon, Marzia; Buoni, Sabrina; Spiga, Ottavia; Ricciardi, Sara; Meloni, Ilaria; Longo, Ilaria; Mari, Francesca; Broccoli, Vania; Zappella, Michele; Renieri, Alessandra

2008-01-01

Rett syndrome is a severe neurodevelopmental disease caused by mutations in the X-linked gene encoding for the methyl-CpG-binding protein MeCP2. Here, we report the identification of FOXG1-truncating mutations in two patients affected by the congenital variant of Rett syndrome. FOXG1 encodes a brain-specific transcriptional repressor that is essential for early development of the telencephalon. Molecular analysis revealed that Foxg1 might also share common molecular mechanisms with MeCP2 during neuronal development, exhibiting partially overlapping expression domain in postnatal cortex and neuronal subnuclear localization. PMID:18571142

First Use of Heads-up Display for Astronomy Education

NASA Astrophysics Data System (ADS)

Mumford, Holly; Hintz, E. G.; Jones, M.; Lawler, J.; Fisler, A.

2013-01-01

As part of our work on deaf education in a planetarium environment we are exploring the use of heads-up display systems. This allows us to overlap an ASL interpreter with our educational videos. The overall goal is to allow a student to watch a full-dome planetarium show and have the interpreter tracking to any portion of the video. We will present the first results of using a heads-up display to provide an ASL ‘sound-track’ for a deaf audience. This work is partially funded by an NSF IIS-1124548 grant and funding from the Sorenson Foundation.

Tools for model-building with cryo-EM maps

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

Terwilliger, Thomas Charles

There are new tools available to you in Phenix for interpreting cryo-EM maps. You can automatically sharpen (or blur) a map with phenix.auto_sharpen and you can segment a map with phenix.segment_and_split_map. If you have overlapping partial models for a map, you can merge them with phenix.combine_models. If you have a protein-RNA complex and protein chains have been accidentally built in the RNA region, you can try to remove them with phenix.remove_poor_fragments. You can put these together and automatically sharpen, segment and build a map with phenix.map_to_model.

High-Resolution Photo-Mosaicing of the Rosebud Hydrothermal Vent Site and Surrounding Lava Flows, Galapagos Rift 86W: Techniques and Interpretations

NASA Astrophysics Data System (ADS)

Rzhanov, Y.; Mayer, L.; Fornari, D.; Shank, T.; Humphris, S.; Scheirer, D.; Kinsey, J.; Whitcomb, L.

2003-12-01

The Rosebud hydrothermal vent field was discovered in May 2002 in the Galapagos Rift near 86W during a series of Alvin dives and ABE autonomous vehicle surveys. Vertical-incidence digital imaging using a 3.1 Mpixel digital camera and strobe illumination from altitudes of 3-5m was carried out during the Alvin dives. A complete survey of the Rosebud vent site was carried out on Alvin Dive 3790. Submersible position was determined by post-cruise integration of 1.2 MHz bottom-lock Doppler sonar velocity data logged at 5Hz, integrated with heading and attitude data from a north-seeking fiber-optic gyroscope logged at 10Hz, and initialized with a surveyed-in long-baseline transponder navigation system providing geodetic position fixes at 15s intervals. The photo-mosaicing process consisted of three main stages: pre-processing, pair-wise image co-registration, and global alignment. Excellent image quality allowed us to avoid lens distortion correction, so images only underwent histogram equalization. Pair-wise co-registration of sequential frames was done partially automatically (where overlap exceeded 70 percent we employed a frequency-domain based technique), and partially manually (when overlap did not exceed 15 percent and manual feature extraction was the only way to find transformations relating the frames). Partial mosaics allowed us to determine which non-sequential frames had substantial overlap, and the corresponding transformations were found via feature extraction. Global alignment of the images consisted of construction of a sparse, nonlinear over-constrained system of equations reflecting positions of the frames in real-world coordinates. This system was solved using least squares, and the solution provided globally optimal positions of the frames in the overall mosaic. Over 700 images were mosaiced resulting in resolution of ~3 mm per pixel. The mosaiced area covers approximately 50 m x 60 m and clearly shows several biological zonations and distribution of lava flow morphologies, including what is interpreted as the contact between older lobate lava and the young sheet flow that hosts Rosebud vent communities. Recruitment of tubeworms, mussels, and clams is actively occurring at more than five locations oriented on a NE-SW trend where vent emissions occur through small cracks in the sheet flow. Large-scale views of seafloor hydrothermal vent sites, such as the one produced for Rosebud, are critical to properly understanding spatial relationships between hydrothermal biological communities, sites of focused and diffuse fluid flow, and the complex array of volcanic and tectonic features at mid-ocean ridge crests. These high-resolution perspectives are also critical to time-series studies where quantitative documentation of changes can be related to variations in hydrothermal, magmatic and tectonic processes.

Informal Institutions and the Weaknesses of Human Behavior

DTIC Science & Technology

2005-01-01

der Wirtschafispolitik 2, 2001, S.185-210. * Haucap, Justus, Uwe Pauly & Christian Wey, Collective Wage Setting When Wages Are Generally Binding: An...in an Overlapping Generations Model, Nr. 8/1999. " Henning, Andreas & Wolfgang Greiner, Organknappheit im Transplantationswesen - L6sungs- ansditze aus

Terrestrial biodiversity analyses in Dalmatia (Croatia): a complementary approach using diversity and rarity.

PubMed

Jelaska, Sven D; Nikolić, Toni; Serić Jelaska, Lucija; Kusan, Vladimir; Peternel, Hrvoje; Guzvica, Goran; Major, Zoran

2010-03-01

Here we present the methodology used for terrestrial biodiversity analysis and site selection in Phase B of the UNDP/GEF COAST project. The analysis was focused on the problem of biodiversity evaluation in four Croatian counties stretching from sea level to the highest mountain in Croatia. Data on habitats, vascular flora, and fauna (mammals, birds, reptiles, amphibians, butterflies, ground beetles, and underground invertebrates) were collected and analyzed for each of the four counties. Emphasis was given to the richness of endangered species and the rarity of endemic species. Based on the spatial analyses of habitat, fauna, and flora data, four to six areas were selected from each county and ranked according to their biodiversity importance. Overlap between areas important for richness and those important for rarity was highest for data on flora (65.5%) and lowest for data on fauna (16.7%). When different data sets were compared, the lowest overlap was between flora and fauna (17.1%) and largest between fauna and habitats (23.9%). Simultaneous overlap among all three data sets was found in just 6.5% of the overall selected areas. These results suggest that less specific data, with respect to taxa threat status, could better serve as surrogate data in estimating overall biodiversity. In summary, this analysis has demonstrated that Dalmatia is a region with a high overall biodiversity that is important in a broader European context.

Terrestrial Biodiversity Analyses in Dalmatia (Croatia): A Complementary Approach Using Diversity and Rarity

NASA Astrophysics Data System (ADS)

Jelaska, Sven D.; Nikolić, Toni; Šerić Jelaska, Lucija; Kušan, Vladimir; Peternel, Hrvoje; Gužvica, Goran; Major, Zoran

2010-03-01

Here we present the methodology used for terrestrial biodiversity analysis and site selection in Phase B of the UNDP/GEF COAST project. The analysis was focused on the problem of biodiversity evaluation in four Croatian counties stretching from sea level to the highest mountain in Croatia. Data on habitats, vascular flora, and fauna (mammals, birds, reptiles, amphibians, butterflies, ground beetles, and underground invertebrates) were collected and analyzed for each of the four counties. Emphasis was given to the richness of endangered species and the rarity of endemic species. Based on the spatial analyses of habitat, fauna, and flora data, four to six areas were selected from each county and ranked according to their biodiversity importance. Overlap between areas important for richness and those important for rarity was highest for data on flora (65.5%) and lowest for data on fauna (16.7%). When different data sets were compared, the lowest overlap was between flora and fauna (17.1%) and largest between fauna and habitats (23.9%). Simultaneous overlap among all three data sets was found in just 6.5% of the overall selected areas. These results suggest that less specific data, with respect to taxa threat status, could better serve as surrogate data in estimating overall biodiversity. In summary, this analysis has demonstrated that Dalmatia is a region with a high overall biodiversity that is important in a broader European context.

Response to formal comment on Myhrvold (2016) submitted by Griebeler and Werner (2017)

PubMed Central

2018-01-01

Griebeler and Werner offer a formal comment on Myhrvold, 2016 defending the conclusions of Werner and Griebeler, 2014. Although the comment criticizes several aspects of methodology in Myhrvold, 2016, all three papers concur on a key conclusion: the metabolism of extant endotherms and ectotherms cannot be reliably classified using growth-rate allometry, because the growth rates of extant endotherms and ectotherms overlap. A key point of disagreement is that the 2014 paper concluded that despite this general case, one can nevertheless classify dinosaurs as ectotherms from their growth rate allometry. The 2014 conclusion is based on two factors: the assertion (made without any supporting arguments) that the comparison with dinosaurs must be restricted only to extant sauropsids, ignoring other vertebrate groups, and that extant sauropsid endotherm and ectotherm growth rates in a data set studied in the 2014 work do not overlap. The Griebeler and Werner formal comment presents their first arguments in support of the restriction proposition. In this response I show that this restriction is unsupported by established principles of phylogenetic comparison. In addition, I show that the data set studied in their 2014 work does show overlap, and that this is visible in one of its figures. I explain how either point effectively invalidates the conclusion of their 2014 paper. I also address the other methodological criticisms of Myhrvold 2016, and find them unsupported. PMID:29489880

Response to formal comment on Myhrvold (2016) submitted by Griebeler and Werner (2017).

PubMed

Myhrvold, Nathan P

2018-01-01

Griebeler and Werner offer a formal comment on Myhrvold, 2016 defending the conclusions of Werner and Griebeler, 2014. Although the comment criticizes several aspects of methodology in Myhrvold, 2016, all three papers concur on a key conclusion: the metabolism of extant endotherms and ectotherms cannot be reliably classified using growth-rate allometry, because the growth rates of extant endotherms and ectotherms overlap. A key point of disagreement is that the 2014 paper concluded that despite this general case, one can nevertheless classify dinosaurs as ectotherms from their growth rate allometry. The 2014 conclusion is based on two factors: the assertion (made without any supporting arguments) that the comparison with dinosaurs must be restricted only to extant sauropsids, ignoring other vertebrate groups, and that extant sauropsid endotherm and ectotherm growth rates in a data set studied in the 2014 work do not overlap. The Griebeler and Werner formal comment presents their first arguments in support of the restriction proposition. In this response I show that this restriction is unsupported by established principles of phylogenetic comparison. In addition, I show that the data set studied in their 2014 work does show overlap, and that this is visible in one of its figures. I explain how either point effectively invalidates the conclusion of their 2014 paper. I also address the other methodological criticisms of Myhrvold 2016, and find them unsupported.

Using multiple calibration sets to improve the quantitative accuracy of partial least squares (PLS) regression on open-path fourier transform infrared (OP/FT-IR) spectra of ammonia over wide concentration ranges

USDA-ARS?s Scientific Manuscript database

A technique of using multiple calibration sets in partial least squares regression (PLS) was proposed to improve the quantitative determination of ammonia from open-path Fourier transform infrared spectra. The spectra were measured near animal farms, and the path-integrated concentration of ammonia...

Perfectionism Group Treatment for Eating Disorders in an Inpatient, Partial Hospitalization, and Outpatient Setting.

PubMed

Levinson, Cheri A; Brosof, Leigh C; Vanzhula, Irina A; Bumberry, Laura; Zerwas, Stephanie; Bulik, Cynthia M

2017-11-01

Perfectionism is elevated in individuals with eating disorders and is posited to be a risk factor, maintaining factor, and treatment barrier. However, there has been little literature testing the feasibility and effectiveness of perfectionism interventions in individuals specifically with eating disorders in an open group format. In the current study, we tested the feasibility of (a) a short cognitive behavioural therapy for perfectionism intervention delivered in an inpatient, partial hospitalization, and outpatient for eating disorders setting (combined N = 28; inpatient n = 15; partial hospital n = 9; outpatient n = 4), as well as (b) a training for disseminating the treatment in these settings (N = 9). Overall, we found that it was feasible to implement a perfectionism group in each treatment setting, with both an open and closed group format. This research adds additional support for the implementation of perfectionism group treatment for eating disorders and provides information on the feasibility of implementing such interventions across multiple settings. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association.

Working memory component processes: isolating BOLD signal changes.

PubMed

Motes, Michael A; Rypma, Bart

2010-01-15

The chronology of the component processes subserving working memory (WM) and hemodynamic response lags has hindered the use of fMRI for exploring neural substrates of WM. In the present study, however, participants completed full trials that involved encoding two or six letters, maintaining the memory set over a delay, and then deciding whether a probe was in the memory set or not. Additionally, they completed encode-only, encode-and-maintain, and encode-and-decide partial trials intermixed with the full trials. The inclusion of partial trials allowed for the isolation of BOLD signal changes to the different trial periods. The results showed that only lateral and medial prefrontal cortex regions differentially responded to the 2- and 6-letter memory sets over the trial periods, showing greater activation to 6-letter sets during the encode and maintain trial periods. Thus, the data showed the differential involvement of PFC in the encoding and maintenance of supra- and sub-capacity memory sets and show the efficacy of using fMRI partial trial methods to study WM component processes.

Working Memory Component Processes: Isolating BOLD Signal-Changes

PubMed Central

Motes, Michael A.; Rypma, Bart

2009-01-01

The chronology of the component processes subserving working memory (WM) and hemodynamic response lags have hindered the use of fMRI for exploring neural substrates of WM. In the present study, however, participants completed full trials that involved encoding two or six letters, maintaining the memory-set over a delay, and then deciding whether a probe was in the memory-set or not. Additionally, they completed encode only, encode and maintain, and encode and decide partial-trials intermixed with the full-trials. The inclusion of partial-trials allowed for the isolation of BOLD signal-changes to the different trial-periods. The results showed that only lateral and medial prefrontal cortex regions differentially responded to the 2- and 6-letter memory-sets over the trial-periods, showing greater activation to 6-letter sets during the encode and maintain trial-periods. Thus, the data showed the differential involvement of PFC in the encoding and maintenance of supra- and sub-capacity memory-sets and show the efficacy of using fMRI partial-trial methods to study WM component processes. PMID:19732840

MIMO: an efficient tool for molecular interaction maps overlap

PubMed Central

2013-01-01

Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways. PMID:23672344

The auditory and non-auditory brain areas involved in tinnitus. An emergent property of multiple parallel overlapping subnetworks

PubMed Central

Vanneste, Sven; De Ridder, Dirk

2012-01-01

Tinnitus is the perception of a sound in the absence of an external sound source. It is characterized by sensory components such as the perceived loudness, the lateralization, the tinnitus type (pure tone, noise-like) and associated emotional components, such as distress and mood changes. Source localization of quantitative electroencephalography (qEEG) data demonstrate the involvement of auditory brain areas as well as several non-auditory brain areas such as the anterior cingulate cortex (dorsal and subgenual), auditory cortex (primary and secondary), dorsal lateral prefrontal cortex, insula, supplementary motor area, orbitofrontal cortex (including the inferior frontal gyrus), parahippocampus, posterior cingulate cortex and the precuneus, in different aspects of tinnitus. Explaining these non-auditory brain areas as constituents of separable subnetworks, each reflecting a specific aspect of the tinnitus percept increases the explanatory power of the non-auditory brain areas involvement in tinnitus. Thus, the unified percept of tinnitus can be considered an emergent property of multiple parallel dynamically changing and partially overlapping subnetworks, each with a specific spontaneous oscillatory pattern and functional connectivity signature. PMID:22586375

Structural basis of death domain signaling in the p75 neurotrophin receptor

PubMed Central

Lin, Zhi; Tann, Jason Y; Goh, Eddy TH; Kelly, Claire; Lim, Kim Buay; Gao, Jian Fang; Ibanez, Carlos F

2015-01-01

Death domains (DDs) mediate assembly of oligomeric complexes for activation of downstream signaling pathways through incompletely understood mechanisms. Here we report structures of complexes formed by the DD of p75 neurotrophin receptor (p75NTR) with RhoGDI, for activation of the RhoA pathway, with caspase recruitment domain (CARD) of RIP2 kinase, for activation of the NF-kB pathway, and with itself, revealing how DD dimerization controls access of intracellular effectors to the receptor. RIP2 CARD and RhoGDI bind to p75NTR DD at partially overlapping epitopes with over 100-fold difference in affinity, revealing the mechanism by which RIP2 recruitment displaces RhoGDI upon ligand binding. The p75NTR DD forms non-covalent, low-affinity symmetric dimers in solution. The dimer interface overlaps with RIP2 CARD but not RhoGDI binding sites, supporting a model of receptor activation triggered by separation of DDs. These structures reveal how competitive protein-protein interactions orchestrate the hierarchical activation of downstream pathways in non-catalytic receptors. DOI: http://dx.doi.org/10.7554/eLife.11692.001 PMID:26646181

Genetic Relationships Between Schizophrenia, Bipolar Disorder, and Schizoaffective Disorder

PubMed Central

Cardno, Alastair G.

2014-01-01

There is substantial evidence for partial overlap of genetic influences on schizophrenia and bipolar disorder, with family, twin, and adoption studies showing a genetic correlation between the disorders of around 0.6. Results of genome-wide association studies are consistent with commonly occurring genetic risk variants, contributing to both the shared and nonshared aspects, while studies of large, rare chromosomal structural variants, particularly copy number variants, show a stronger influence on schizophrenia than bipolar disorder to date. Schizoaffective disorder has been less investigated but shows substantial familial overlap with both schizophrenia and bipolar disorder. A twin analysis is consistent with genetic influences on schizoaffective episodes being entirely shared with genetic influences on schizophrenic and manic episodes, while association studies suggest the possibility of some relatively specific genetic influences on broadly defined schizoaffective disorder, bipolar subtype. Further insights into genetic relationships between these disorders are expected as studies continue to increase in sample size and in technical and analytical sophistication, information on phenotypes beyond clinical diagnoses are increasingly incorporated, and approaches such as next-generation sequencing identify additional types of genetic risk variant. PMID:24567502

Three-dimensional laser velocimeter simultaneity detector

NASA Technical Reports Server (NTRS)

Brown, James L. (Inventor)

1990-01-01

A three-dimensional laser Doppler velocimeter has laser optics for a first channel positioned to create a probe volume in space, and laser optics and for second and third channels, respectively, positioned to create entirely overlapping probe volumes in space. The probe volumes and overlap partially in space. The photodetector is positioned to receive light scattered by a particle present in the probe volume, while photodetectors and are positioned to receive light scattered by a particle present in the probe volume. The photodetector for the first channel is directly connected to provide a first channel analog signal to frequency measuring circuits. The first channel is therefore a primary channel for the system. Photodetectors and are respectively connected through a second channel analog signal attenuator to frequency measuring circuits and through a third channel analog signal attenuator to frequency measuring circuits. The second and third channels are secondary channels, with the second and third channels analog signal attenuators and controlled by the first channel measurement burst signal on line. The second and third channels analog signal attenuators and attenuate the second and third channels analog signals only when the measurement burst signal is false.

Quantitative Analysis of Single and Mix Food Antiseptics Basing on SERS Spectra with PLSR Method

NASA Astrophysics Data System (ADS)

Hou, Mengjing; Huang, Yu; Ma, Lingwei; Zhang, Zhengjun

2016-06-01

Usage and dosage of food antiseptics are very concerned due to their decisive influence in food safety. Surface-enhanced Raman scattering (SERS) effect was employed in this research to realize trace potassium sorbate (PS) and sodium benzoate (SB) detection. HfO2 ultrathin film-coated Ag NR array was fabricated as SERS substrate. Protected by HfO2 film, the SERS substrate possesses good acid resistance, which enables it to be applicable in acidic environment where PS and SB work. Regression relationship between SERS spectra of 0.3~10 mg/L PS solution and their concentration was calibrated by partial least squares regression (PLSR) method, and the concentration prediction performance was quite satisfactory. Furthermore, mixture solution of PS and SB was also quantitatively analyzed by PLSR method. Spectrum data of characteristic peak sections corresponding to PS and SB was used to establish the regression models of these two solutes, respectively, and their concentrations were determined accurately despite their characteristic peak sections overlapping. It is possible that the unique modeling process of PLSR method prevented the overlapped Raman signal from reducing the model accuracy.

Time-stable overset grid method for hyperbolic problems using summation-by-parts operators

NASA Astrophysics Data System (ADS)

Sharan, Nek; Pantano, Carlos; Bodony, Daniel J.

2018-05-01

A provably time-stable method for solving hyperbolic partial differential equations arising in fluid dynamics on overset grids is presented in this paper. The method uses interface treatments based on the simultaneous approximation term (SAT) penalty method and derivative approximations that satisfy the summation-by-parts (SBP) property. Time-stability is proven using energy arguments in a norm that naturally relaxes to the standard diagonal norm when the overlap reduces to a traditional multiblock arrangement. The proposed overset interface closures are time-stable for arbitrary overlap arrangements. The information between grids is transferred using Lagrangian interpolation applied to the incoming characteristics, although other interpolation schemes could also be used. The conservation properties of the method are analyzed. Several one-, two-, and three-dimensional, linear and non-linear numerical examples are presented to confirm the stability and accuracy of the method. A performance comparison between the proposed SAT-based interface treatment and the commonly-used approach of injecting the interpolated data onto each grid is performed to highlight the efficacy of the SAT method.

Morphological-transformation-based technique of edge detection and skeletonization of an image using a single spatial light modulator

NASA Astrophysics Data System (ADS)

Munshi, Soumika; Datta, A. K.

2003-03-01

A technique of optically detecting the edge and skeleton of an image by defining shift operations for morphological transformation is described. A (2 × 2) source array, which acts as the structuring element of morphological operations, casts four angularly shifted optical projections of the input image. The resulting dilated image, when superimposed with the complementary input image, produces the edge image. For skeletonization, the source array casts four partially overlapped output images of the inverted input image, which is negated, and the resultant image is recorded in a CCD camera. This overlapped eroded image is again eroded and then dilated, producing an opened image. The difference between the eroded and opened image is then computed, resulting in a thinner image. This procedure of obtaining a thinned image is iterated until the difference image becomes zero, maintaining the connectivity conditions. The technique has been optically implemented using a single spatial modulator and has the advantage of single-instruction parallel processing of the image. The techniques have been tested both for binary and grey images.

Point-based and model-based geolocation analysis of airborne laser scanning data

NASA Astrophysics Data System (ADS)

Sefercik, Umut Gunes; Buyuksalih, Gurcan; Jacobsen, Karsten; Alkan, Mehmet

2017-01-01

Airborne laser scanning (ALS) is one of the most effective remote sensing technologies providing precise three-dimensional (3-D) dense point clouds. A large-size ALS digital surface model (DSM) covering the whole Istanbul province was analyzed by point-based and model-based comprehensive statistical approaches. Point-based analysis was performed using checkpoints on flat areas. Model-based approaches were implemented in two steps as strip to strip comparing overlapping ALS DSMs individually in three subareas and comparing the merged ALS DSMs with terrestrial laser scanning (TLS) DSMs in four other subareas. In the model-based approach, the standard deviation of height and normalized median absolute deviation were used as the accuracy indicators combined with the dependency of terrain inclination. The results demonstrate that terrain roughness has a strong impact on the vertical accuracy of ALS DSMs. From the relative horizontal shifts determined and partially improved by merging the overlapping strips and comparison of the ALS, and the TLS, data were found not to be negligible. The analysis of ALS DSM in relation to TLS DSM allowed us to determine the characteristics of the DSM in detail.

Trust-Guided Behavior Adaptation Using Case-Based Reasoning

DTIC Science & Technology

2015-08-01

the same behaviors were evaluated in each set. To account for this, the similarity function looks at the overlap between the two sets and ignores...interruptions would reduce the cost of case genera- tion. 6 Related Work Existing approaches for measuring inverse trust differ from our own in that...where a case- based reasoning system considers the reliability of a case’s source, also takes trust into account . Our work also has sim- ilarities

Uncertainty representation of grey numbers and grey sets.

PubMed

Yang, Yingjie; Liu, Sifeng; John, Robert

2014-09-01

In the literature, there is a presumption that a grey set and an interval-valued fuzzy set are equivalent. This presumption ignores the existence of discrete components in a grey number. In this paper, new measurements of uncertainties of grey numbers and grey sets, consisting of both absolute and relative uncertainties, are defined to give a comprehensive representation of uncertainties in a grey number and a grey set. Some simple examples are provided to illustrate that the proposed uncertainty measurement can give an effective representation of both absolute and relative uncertainties in a grey number and a grey set. The relationships between grey sets and interval-valued fuzzy sets are also analyzed from the point of view of the proposed uncertainty representation. The analysis demonstrates that grey sets and interval-valued fuzzy sets provide different but overlapping models for uncertainty representation in sets.

Digital tomosynthesis mammography using a parallel maximum-likelihood reconstruction method

NASA Astrophysics Data System (ADS)

Wu, Tao; Zhang, Juemin; Moore, Richard; Rafferty, Elizabeth; Kopans, Daniel; Meleis, Waleed; Kaeli, David

2004-05-01

A parallel reconstruction method, based on an iterative maximum likelihood (ML) algorithm, is developed to provide fast reconstruction for digital tomosynthesis mammography. Tomosynthesis mammography acquires 11 low-dose projections of a breast by moving an x-ray tube over a 50° angular range. In parallel reconstruction, each projection is divided into multiple segments along the chest-to-nipple direction. Using the 11 projections, segments located at the same distance from the chest wall are combined to compute a partial reconstruction of the total breast volume. The shape of the partial reconstruction forms a thin slab, angled toward the x-ray source at a projection angle 0°. The reconstruction of the total breast volume is obtained by merging the partial reconstructions. The overlap region between neighboring partial reconstructions and neighboring projection segments is utilized to compensate for the incomplete data at the boundary locations present in the partial reconstructions. A serial execution of the reconstruction is compared to a parallel implementation, using clinical data. The serial code was run on a PC with a single PentiumIV 2.2GHz CPU. The parallel implementation was developed using MPI and run on a 64-node Linux cluster using 800MHz Itanium CPUs. The serial reconstruction for a medium-sized breast (5cm thickness, 11cm chest-to-nipple distance) takes 115 minutes, while a parallel implementation takes only 3.5 minutes. The reconstruction time for a larger breast using a serial implementation takes 187 minutes, while a parallel implementation takes 6.5 minutes. No significant differences were observed between the reconstructions produced by the serial and parallel implementations.

Improving speech perception in noise with current focusing in cochlear implant users.

PubMed

Srinivasan, Arthi G; Padilla, Monica; Shannon, Robert V; Landsberger, David M

2013-05-01

Cochlear implant (CI) users typically have excellent speech recognition in quiet but struggle with understanding speech in noise. It is thought that broad current spread from stimulating electrodes causes adjacent electrodes to activate overlapping populations of neurons which results in interactions across adjacent channels. Current focusing has been studied as a way to reduce spread of excitation, and therefore, reduce channel interactions. In particular, partial tripolar stimulation has been shown to reduce spread of excitation relative to monopolar stimulation. However, the crucial question is whether this benefit translates to improvements in speech perception. In this study, we compared speech perception in noise with experimental monopolar and partial tripolar speech processing strategies. The two strategies were matched in terms of number of active electrodes, microphone, filterbanks, stimulation rate and loudness (although both strategies used a lower stimulation rate than typical clinical strategies). The results of this study showed a significant improvement in speech perception in noise with partial tripolar stimulation. All subjects benefited from the current focused speech processing strategy. There was a mean improvement in speech recognition threshold of 2.7 dB in a digits in noise task and a mean improvement of 3 dB in a sentences in noise task with partial tripolar stimulation relative to monopolar stimulation. Although the experimental monopolar strategy was worse than the clinical, presumably due to different microphones, frequency allocations and stimulation rates, the experimental partial-tripolar strategy, which had the same changes, showed no acute deficit relative to the clinical. Copyright © 2013 Elsevier B.V. All rights reserved.

Effects of partial circadian adjustments on sleep and vigilance quality during simulated night work.

PubMed

Chapdelaine, Simon; Paquet, Jean; Dumont, Marie

2012-08-01

In most situations, complete circadian adjustment is not recommended for night workers. With complete adjustment, workers experience circadian misalignment when returning on a day-active schedule, causing repeated circadian phase shifts and internal desynchrony. For this reason, partial circadian realignment was proposed as a good compromise to stabilize internal circadian rhythms in night shift workers. However, the extent of partial circadian adjustment necessary to improve sleep and vigilance quality is still a matter of debate. In this study, the effects of small but statistically significant partial circadian adjustments on sleep and vigilance quality were assessed in a laboratory simulation of night work to determine whether they were also of clinical significance. Partial adjustments obtained by phase delay or by phase advance were quantified not only by the phase shift of dim light salivary melatonin onset, but also by the overlap of the episode of melatonin production with the sleep-wake cycle adopted during simulated night work. The effects on daytime sleep and night-time vigilance quality were modest. However, they suggest that even small adjustments by phase delay may decrease the accumulation of sleep debt, whereas the advance strategy improves subjective alertness and mood during night work. Furthermore, absolute phase shifts, by advance or by delay, were associated with improved subjective alertness and mood during the night shift. These strategies need to be tested in the field, to determine whether they can be adapted to real-life situations and provide effective support to night workers. © 2012 European Sleep Research Society.

Feasibility of reusing time-matched controls in an overlapping cohort.

PubMed

Delcoigne, Bénédicte; Hagenbuch, Niels; Schelin, Maria Ec; Salim, Agus; Lindström, Linda S; Bergh, Jonas; Czene, Kamila; Reilly, Marie

2018-06-01

The methods developed for secondary analysis of nested case-control data have been illustrated only in simplified settings in a common cohort and have not found their way into biostatistical practice. This paper demonstrates the feasibility of reusing prior nested case-control data in a realistic setting where a new outcome is available in an overlapping cohort where no new controls were gathered and where all data have been anonymised. Using basic information about the background cohort and sampling criteria, the new cases and prior data are "aligned" to identify the common underlying study base. With this study base, a Kaplan-Meier table of the prior outcome extracts the risk sets required to calculate the weights to assign to the controls to remove the sampling bias. A weighted Cox regression, implemented in standard statistical software, provides unbiased hazard ratios. Using the method to compare cases of contralateral breast cancer to available controls from a prior study of metastases, we identified a multifocal tumor as a risk factor that has not been reported previously. We examine the sensitivity of the method to an imperfect weighting scheme and discuss its merits and pitfalls to provide guidance for its use in medical research studies.

Measures of Partial Knowledge and Unexpected Responses in Multiple-Choice Tests

ERIC Educational Resources Information Center

Chang, Shao-Hua; Lin, Pei-Chun; Lin, Zih-Chuan

2007-01-01

This study investigates differences in the partial scoring performance of examinees in elimination testing and conventional dichotomous scoring of multiple-choice tests implemented on a computer-based system. Elimination testing that uses the same set of multiple-choice items rewards examinees with partial knowledge over those who are simply…

Investigations of student understanding of entropy and of mixed second-order partial derivatives in upper-level thermodynamics

NASA Astrophysics Data System (ADS)

Bucy, Brandon R.

While much of physics education research (PER) has traditionally been conducted in introductory undergraduate courses, researchers have begun to study student understanding of physics concepts at the upper-level. In this dissertation, we describe investigations conducted in advanced undergraduate thermodynamics courses. We present and discuss results pertaining to student understanding of two topics: entropy and the role of mixed second-order partial derivatives in thermodynamics. Our investigations into student understanding of entropy consisted of an analysis of written student responses to researcher-designed diagnostic questions. Data gathered in clinical interviews is employed to illustrate and extend results gathered from written responses. The question sets provided students with several ideal gas processes, and asked students to determine and compare the entropy changes of these processes. We administered the question sets to students from six distinct populations, including students enrolled in classical thermodynamics, statistical mechanics, thermal physics, physical chemistry, and chemical engineering courses, as well as a sample of physics graduate students. Data was gathered both before and after instruction in several samples. Several noteworthy features of student reasoning are identified and discussed. These features include student ideas about entropy prior to instruction, as well as specific difficulties and other aspects of student reasoning evident after instruction. As an example, students from various populations tended to emphasize either the thermodynamic or the statistical definition of entropy. Both approaches present students with a unique set of benefits as well as challenges. We additionally studied student understanding of partial derivatives in a thermodynamics context. We identified specific difficulties related to the mixed second partial derivatives of a thermodynamic state function, based on an analysis of student responses to homework and exam problems. Students tended to set these partial derivatives identically equal to zero. Students also displayed difficulties in relating the physical description of a material property to a corresponding mathematical statement involving partial derivatives. We describe the development of a guided-inquiry tutorial activity designed to address these specific difficulties. This tutorial focused on the graphical interpretation of partial derivatives. Preliminary results suggest that the tutorial was effective in addressing several student difficulties related to partial derivatives.

Precise orbit determination of BeiDou constellation based on BETS and MGEX network.

PubMed

Lou, Yidong; Liu, Yang; Shi, Chuang; Yao, Xiuguang; Zheng, Fu

2014-04-15

Chinese BeiDou Navigation Satellite System is officially operational as a regional constellation with five Geostationary Earth Orbit (GEO) satellites, five Inclined Geosynchronous Satellite Orbit (IGSO) satellites and four Medium Earth Orbit (MEO) satellites. Observations from the BeiDou Experimental Tracking Stations (BETS) and the IGS Multi-GNSS Experiment (MGEX) network from 1 January to 31 March 2013 are processed for orbit determination of the BeiDou constellation. Various arc lengths and solar radiation pressure parameters are investigated. The reduced set of ECOM five-parameter model produces better performance than the full set of ECOM nine-parameter model for BeiDou IGSO and MEO. The orbit overlap for the middle days of 3-day arc solutions is better than 20 cm and 14 cm for IGSO and MEO in RMS, respectively. Satellite laser ranging residuals are better than 10 cm for both IGSO and MEO. For BeiDou GEO, the orbit overlap of several meters and satellite laser ranging residuals of several decimetres can be achieved.

An experimentally validated model for geometrically nonlinear plucking-based frequency up-conversion in energy harvesting

NASA Astrophysics Data System (ADS)

Kathpalia, B.; Tan, D.; Stern, I.; Erturk, A.

2018-01-01

It is well known that plucking-based frequency up-conversion can enhance the power output in piezoelectric energy harvesting by enabling cyclic free vibration at the fundamental bending mode of the harvester even for very low excitation frequencies. In this work, we present a geometrically nonlinear plucking-based framework for frequency up-conversion in piezoelectric energy harvesting under quasistatic excitations associated with low-frequency stimuli such as walking and similar rigid body motions. Axial shortening of the plectrum is essential to enable plucking excitation, which requires a nonlinear framework relating the plectrum parameters (e.g. overlap length between the plectrum and harvester) to the overall electrical power output. Von Kármán-type geometrically nonlinear deformation of the flexible plectrum cantilever is employed to relate the overlap length between the flexible (nonlinear) plectrum and the stiff (linear) harvester to the transverse quasistatic tip displacement of the plectrum, and thereby the tip load on the linear harvester in each plucking cycle. By combining the nonlinear plectrum mechanics and linear harvester dynamics with two-way electromechanical coupling, the electrical power output is obtained directly in terms of the overlap length. Experimental case studies and validations are presented for various overlap lengths and a set of electrical load resistance values. Further analysis results are reported regarding the combined effects of plectrum thickness and overlap length on the plucking force and harvested power output. The experimentally validated nonlinear plectrum-linear harvester framework proposed herein can be employed to design and optimize frequency up-conversion by properly choosing the plectrum parameters (geometry, material, overlap length, etc) as well as the harvester parameters.

Salmonella Persistence in Tomatoes Requires a Distinct Set of Metabolic Functions Identified by Transposon Insertion Sequencing.

PubMed

de Moraes, Marcos H; Desai, Prerak; Porwollik, Steffen; Canals, Rocio; Perez, Daniel R; Chu, Weiping; McClelland, Michael; Teplitski, Max

2017-03-01

Human enteric pathogens, such as Salmonella spp. and verotoxigenic Escherichia coli , are increasingly recognized as causes of gastroenteritis outbreaks associated with the consumption of fruits and vegetables. Persistence in plants represents an important part of the life cycle of these pathogens. The identification of the full complement of Salmonella genes involved in the colonization of the model plant (tomato) was carried out using transposon insertion sequencing analysis. With this approach, 230,000 transposon insertions were screened in tomato pericarps to identify loci with reduction in fitness, followed by validation of the screen results using competition assays of the isogenic mutants against the wild type. A comparison with studies in animals revealed a distinct plant-associated set of genes, which only partially overlaps with the genes required to elicit disease in animals. De novo biosynthesis of amino acids was critical to persistence within tomatoes, while amino acid scavenging was prevalent in animal infections. Fitness reduction of the Salmonella amino acid synthesis mutants was generally more severe in the tomato rin mutant, which hyperaccumulates certain amino acids, suggesting that these nutrients remain unavailable to Salmonella spp. within plants. Salmonella lipopolysaccharide (LPS) was required for persistence in both animals and plants, exemplifying some shared pathogenesis-related mechanisms in animal and plant hosts. Similarly to phytopathogens, Salmonella spp. required biosynthesis of amino acids, LPS, and nucleotides to colonize tomatoes. Overall, however, it appears that while Salmonella shares some strategies with phytopathogens and taps into its animal virulence-related functions, colonization of tomatoes represents a distinct strategy, highlighting this pathogen's flexible metabolism. IMPORTANCE Outbreaks of gastroenteritis caused by human pathogens have been increasingly associated with foods of plant origin, with tomatoes being one of the common culprits. Recent studies also suggest that these human pathogens can use plants as alternate hosts as a part of their life cycle. While dual (animal/plant) lifestyles of other members of the Enterobacteriaceae family are well known, the strategies with which Salmonella colonizes plants are only partially understood. Therefore, we undertook a high-throughput characterization of the functions required for Salmonella persistence within tomatoes. The results of this study were compared with what is known about genes required for Salmonella virulence in animals and interactions of plant pathogens with their hosts to determine whether Salmonella repurposes its virulence repertoire inside plants or whether it behaves more as a phytopathogen during plant colonization. Even though Salmonella utilized some of its virulence-related genes in tomatoes, plant colonization required a distinct set of functions. Copyright © 2017 American Society for Microbiology.

Salmonella Persistence in Tomatoes Requires a Distinct Set of Metabolic Functions Identified by Transposon Insertion Sequencing

PubMed Central

Desai, Prerak; Porwollik, Steffen; Canals, Rocio; Perez, Daniel R.; Chu, Weiping; McClelland, Michael; Teplitski, Max

2016-01-01

ABSTRACT Human enteric pathogens, such as Salmonella spp. and verotoxigenic Escherichia coli, are increasingly recognized as causes of gastroenteritis outbreaks associated with the consumption of fruits and vegetables. Persistence in plants represents an important part of the life cycle of these pathogens. The identification of the full complement of Salmonella genes involved in the colonization of the model plant (tomato) was carried out using transposon insertion sequencing analysis. With this approach, 230,000 transposon insertions were screened in tomato pericarps to identify loci with reduction in fitness, followed by validation of the screen results using competition assays of the isogenic mutants against the wild type. A comparison with studies in animals revealed a distinct plant-associated set of genes, which only partially overlaps with the genes required to elicit disease in animals. De novo biosynthesis of amino acids was critical to persistence within tomatoes, while amino acid scavenging was prevalent in animal infections. Fitness reduction of the Salmonella amino acid synthesis mutants was generally more severe in the tomato rin mutant, which hyperaccumulates certain amino acids, suggesting that these nutrients remain unavailable to Salmonella spp. within plants. Salmonella lipopolysaccharide (LPS) was required for persistence in both animals and plants, exemplifying some shared pathogenesis-related mechanisms in animal and plant hosts. Similarly to phytopathogens, Salmonella spp. required biosynthesis of amino acids, LPS, and nucleotides to colonize tomatoes. Overall, however, it appears that while Salmonella shares some strategies with phytopathogens and taps into its animal virulence-related functions, colonization of tomatoes represents a distinct strategy, highlighting this pathogen's flexible metabolism. IMPORTANCE Outbreaks of gastroenteritis caused by human pathogens have been increasingly associated with foods of plant origin, with tomatoes being one of the common culprits. Recent studies also suggest that these human pathogens can use plants as alternate hosts as a part of their life cycle. While dual (animal/plant) lifestyles of other members of the Enterobacteriaceae family are well known, the strategies with which Salmonella colonizes plants are only partially understood. Therefore, we undertook a high-throughput characterization of the functions required for Salmonella persistence within tomatoes. The results of this study were compared with what is known about genes required for Salmonella virulence in animals and interactions of plant pathogens with their hosts to determine whether Salmonella repurposes its virulence repertoire inside plants or whether it behaves more as a phytopathogen during plant colonization. Even though Salmonella utilized some of its virulence-related genes in tomatoes, plant colonization required a distinct set of functions. PMID:28039131

Radial force measurement of endovascular stents: Influence of stent design and diameter.

PubMed

Matsumoto, Takuya; Matsubara, Yutaka; Aoyagi, Yukihiko; Matsuda, Daisuke; Okadome, Jun; Morisaki, Koichi; Inoue, Kentarou; Tanaka, Shinichi; Ohkusa, Tomoko; Maehara, Yoshihiko

2016-04-01

Angioplasty and endovascular stent placement is used in case to rescue the coverage of main branches to supply blood to brain from aortic arch in thoracic endovascular aortic repair. This study assessed mechanical properties, especially differences in radial force, of different endovascular and thoracic stents. We analyzed the radial force of three stent models (Epic, E-Luminexx and SMART) stents using radial force-tester method in single or overlapping conditions. We also analyzed radial force in three thoracic stents using Mylar film testing method: conformable Gore-TAG, Relay, and Valiant Thoracic Stent Graft. Overlapping SMART stents had greater radial force than overlapping Epic or Luminexx stents (P < 0.01). The radial force of the thoracic stents was greater than that of all three endovascular stents (P < 0.01). Differences in radial force depend on types of stents, site of deployment, and layer characteristics. In clinical settings, an understanding of the mechanical characteristics, including radial force, is important in choosing a stent for each patient. © The Author(s) 2015.

Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric

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

Andonov, Rumen; Djidjev, Hristo Nikolov; Klau, Gunnar W.

In this paper, we propose a new distance measure for comparing two protein structures based on their contact map representations. We show that our novel measure, which we refer to as the maximum contact map overlap (max-CMO) metric, satisfies all properties of a metric on the space of protein representations. Having a metric in that space allows one to avoid pairwise comparisons on the entire database and, thus, to significantly accelerate exploring the protein space compared to no-metric spaces. We show on a gold standard superfamily classification benchmark set of 6759 proteins that our exact k-nearest neighbor (k-NN) scheme classifiesmore » up to 224 out of 236 queries correctly and on a larger, extended version of the benchmark with 60; 850 additional structures, up to 1361 out of 1369 queries. Finally, our k-NN classification thus provides a promising approach for the automatic classification of protein structures based on flexible contact map overlap alignments.« less

Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric

DOE PAGES

Andonov, Rumen; Djidjev, Hristo Nikolov; Klau, Gunnar W.; ...

2015-10-09

In this paper, we propose a new distance measure for comparing two protein structures based on their contact map representations. We show that our novel measure, which we refer to as the maximum contact map overlap (max-CMO) metric, satisfies all properties of a metric on the space of protein representations. Having a metric in that space allows one to avoid pairwise comparisons on the entire database and, thus, to significantly accelerate exploring the protein space compared to no-metric spaces. We show on a gold standard superfamily classification benchmark set of 6759 proteins that our exact k-nearest neighbor (k-NN) scheme classifiesmore » up to 224 out of 236 queries correctly and on a larger, extended version of the benchmark with 60; 850 additional structures, up to 1361 out of 1369 queries. Finally, our k-NN classification thus provides a promising approach for the automatic classification of protein structures based on flexible contact map overlap alignments.« less

Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration.

PubMed

Sim, Jaehyun; Sim, Jun; Park, Eunsung; Lee, Julian

2015-06-01

Many proteins undergo large-scale motions where relatively rigid domains move against each other. The identification of rigid domains, as well as the hinge residues important for their relative movements, is important for various applications including flexible docking simulations. In this work, we develop a method for protein rigid domain identification based on an exhaustive enumeration of maximal rigid domains, the rigid domains not fully contained within other domains. The computation is performed by mapping the problem to that of finding maximal cliques in a graph. A minimal set of rigid domains are then selected, which cover most of the protein with minimal overlap. In contrast to the results of existing methods that partition a protein into non-overlapping domains using approximate algorithms, the rigid domains obtained from exact enumeration naturally contain overlapping regions, which correspond to the hinges of the inter-domain bending motion. The performance of the algorithm is demonstrated on several proteins. © 2015 Wiley Periodicals, Inc.

Adverse Event Incidences following Facial Plastic Surgery Procedures: Incorporating FACE-Q Data to Improve Patient Preparation.

PubMed

Fleury, Christopher M; Schwitzer, Jonathan A; Hung, Rex W; Baker, Stephen B

2018-01-01

Before creation and validation of the FACE-Q by Pusic et al., adverse event types and incidences following facial cosmetic procedures were objectively measured and reported by physicians, potentially leading to misrepresentation of the true patient experience. This article analyzes and compares adverse event data from both FACE-Q and recent review articles, incorporating patient-reported adverse event data to improve patient preparation for facial cosmetic procedures. FACE-Q adverse event data were extracted from peer-reviewed validation articles for face lift, rhinoplasty, and blepharoplasty, and these data were compared against adverse effect risk data published in recent Continuing Medical Education/Maintenance of Certification and other articles regarding the same procedures. The patient-reported adverse event data sets and the physician-reported adverse event data sets do contain overlapping elements, but each data set also contains unique elements. The data sets represent differing viewpoints. Furthermore, patient-reported outcomes from the FACE-Q provided incidence data that were otherwise previously not reported. In the growing facial cosmetic surgery industry, patient perspective is critical as a determinant of success; therefore, incorporation of evidence-based patient-reported outcome data will not only improve patient expectations and overall experience, but will also reveal adverse event incidences that were previously unknown. Given that there is incomplete overlap between patient-reported and physician-reported adverse events, presentation of both data sets in the consultation setting will improve patient preparation. Furthermore, use of validated tools such as the FACE-Q will allow surgeons to audit themselves critically.

Informing the Structure of Executive Function in Children: A Meta-Analysis of Functional Neuroimaging Data

PubMed Central

McKenna, Róisín; Rushe, T.; Woodcock, Kate A.

2017-01-01

The structure of executive function (EF) has been the focus of much debate for decades. What is more, the complexity and diversity provided by the developmental period only adds to this contention. The development of executive function plays an integral part in the expression of children's behavioral, cognitive, social, and emotional capabilities. Understanding how these processes are constructed during development allows for effective measurement of EF in this population. This meta-analysis aims to contribute to a better understanding of the structure of executive function in children. A coordinate-based meta-analysis was conducted (using BrainMap GingerALE 2.3), which incorporated studies administering functional magnetic resonance imaging (fMRI) during inhibition, switching, and working memory updating tasks in typical children (aged 6–18 years). The neural activation common across all executive tasks was compared to that shared by tasks pertaining only to inhibition, switching or updating, which are commonly considered to be fundamental executive processes. Results support the existence of partially separable but partially overlapping inhibition, switching, and updating executive processes at a neural level, in children over 6 years. Further, the shared neural activation across all tasks (associated with a proposed “unitary” component of executive function) overlapped to different degrees with the activation associated with each individual executive process. These findings provide evidence to support the suggestion that one of the most influential structural models of executive functioning in adults can also be applied to children of this age. However, the findings also call for careful consideration and measurement of both specific executive processes, and unitary executive function in this population. Furthermore, a need is highlighted for a new systematic developmental model, which captures the integrative nature of executive function in children. PMID:28439231

Ultrasensitive Quantification of Hepatitis B Virus A1762T/G1764A Mutant by a SimpleProbe PCR Using a Wild-Type-Selective PCR Blocker and a Primer-Blocker-Probe Partial-Overlap Approach ▿

PubMed Central

Nie, Hui; Evans, Alison A.; London, W. Thomas; Block, Timothy M.; Ren, Xiangdong David

2011-01-01

Hepatitis B virus (HBV) carrying the A1762T/G1764A double mutation in the basal core promoter (BCP) region is associated with HBe antigen seroconversion and increased risk of liver cirrhosis and hepatocellular carcinoma (HCC). Quantification of the mutant viruses may help in predicting the risk of HCC. However, the viral genome tends to have nucleotide polymorphism, which makes it difficult to design hybridization-based assays including real-time PCR. Ultrasensitive quantification of the mutant viruses at the early developmental stage is even more challenging, as the mutant is masked by excessive amounts of the wild-type (WT) viruses. In this study, we developed a selective inhibitory PCR (siPCR) using a locked nucleic acid-based PCR blocker to selectively inhibit the amplification of the WT viral DNA but not the mutant DNA. At the end of siPCR, the proportion of the mutant could be increased by about 10,000-fold, making the mutant more readily detectable by downstream applications such as real-time PCR and DNA sequencing. We also describe a primer-probe partial overlap approach which significantly simplified the melting curve patterns and minimized the influence of viral genome polymorphism on assay accuracy. Analysis of 62 patient samples showed a complete match of the melting curve patterns with the sequencing results. More than 97% of HBV BCP sequences in the GenBank database can be correctly identified by the melting curve analysis. The combination of siPCR and the SimpleProbe real-time PCR enabled mutant quantification in the presence of a 100,000-fold excess of the WT DNA. PMID:21562108

Nonlinear force-length relationship in the ADP-induced contraction of skeletal myofibrils.

PubMed

Shimamoto, Yuta; Kono, Fumiaki; Suzuki, Madoka; Ishiwata, Shin'ichi

2007-12-15

The regulatory mechanism of sarcomeric activity has not been fully clarified yet because of its complex and cooperative nature, which involves both Ca(2+) and cross-bridge binding to the thin filament. To reveal the mechanism of regulation mediated by the cross-bridges, separately from the effect of Ca(2+), we investigated the force-sarcomere length (SL) relationship in rabbit skeletal myofibrils (a single myofibril or a thin bundle) at SL > 2.2 microm in the absence of Ca(2+) at various levels of activation by exogenous MgADP (4-20 mM) in the presence of 1 mM MgATP. The individual SLs were measured by phase-contrast microscopy to confirm the homogeneity of the striation pattern of sarcomeres during activation. We found that at partial activation with 4-8 mM MgADP, the developed force nonlinearly depended on the length of overlap between the thick and the thin filaments; that is, contrary to the maximal activation, the maximal active force was generated at shorter overlap. Besides, the active force became larger, whereas this nonlinearity tended to weaken, with either an increase in [MgADP] or the lateral osmotic compression of the myofilament lattice induced by the addition of a macromolecular compound, dextran T-500. The model analysis, which takes into account the [MgADP]- and the lattice-spacing-dependent probability of cross-bridge formation, was successfully applied to account for the force-SL relationship observed at partial activation. These results strongly suggest that the cross-bridge works as a cooperative activator, the function of which is highly sensitive to as little as

Anxiety Disorders Interview Schedule – Autism Addendum: Reliability and Validity in Children with Autism Spectrum Disorder

PubMed Central

Kerns, Connor Morrow; Renno, Patricia; Kendall, Philip C.; Wood, Jeffrey J.; Storch, Eric A.

2017-01-01

Objective Assessing anxiety in autism spectrum disorder (ASD) is inherently challenging due to overlapping (e.g., social avoidance) and ambiguous symptoms (e.g., fears of change). An ASD addendum to the Anxiety Disorders Interview Schedule–Child/Parent, Parent Version (ADIS/ASA) was developed to provide a systematic approach for differentiating traditional anxiety disorders from symptoms of ASD and more ambiguous, ASD-related anxiety symptoms. Method Inter-rater reliability and convergent and discriminant validity were examined in a sample of 69 youth with ASD (8–13 years, 75% male, IQ:68–143) seeking treatment for anxiety. The parents of participants completed the ADIS/ASA and a battery of behavioral measures. A second rater independently observed and scored recordings of the original interviews. Results Findings suggest reliable measurement of comorbid (ICC=0.85–0.98; κ =0.67–0.91) as well as ambiguous anxiety-like symptoms (ICC=0.87–95, κ=0.77–0.90) in children with ASD. Convergent and discriminant validity were supported for the traditional anxiety symptoms on the ADIS/ASA, whereas convergent and discriminant validity were partially supported for the ambiguous anxiety-like symptoms. Conclusions Results provide evidence for the reliability and validity of the ADIS/ASA as a measure of traditional anxiety categories in youth with ASD, with partial support for the validity of the ambiguous anxiety-like categories. Unlike other measures, the ADIS/ASA differentiates comorbid anxiety disorders from overlapping and ambiguous anxiety-like symptoms in ASD, allowing for more precise measurement and clinical conceptualization. Ambiguous anxiety-like symptoms appear phenomenologically distinct from comorbid anxiety disorders and may reflect either symptoms of ASD or a novel variant of anxiety in ASD. PMID:27925775

The Behavioural Ecology of Indo-Pacific Humpback Dolphins in Hong Kong.

PubMed

Würsig, Bernd; Parsons, E C M; Piwetz, Sarah; Porter, Lindsay

2016-01-01

Fewer than 200 Indo-Pacific humpback dolphins (Sousa chinensis) occur in Hong Kong waters (though these are part of a much larger population in the Pearl River Estuary), with a decrease in the past about 10 years. They have partially overlapping individual ranges (mean=100km(2)), and two partially overlapping communities. Seasonal occurrence is higher in June-November than December-May, approximate wet and dry monsoon seasons, respectively. Group sizes tend to average three dolphins, a decrease from the past decade. Feeding often occurs in abruptly changing water depths and off rocky natural shores. The area immediately north of Hong Kong International Airport is largely used for travelling between locations to the west, east and further north. The area around Lung Kwu Chau Island in northwest Hong Kong is a "hot spot" for foraging and socializing. The area off Fan Lau, southwest Lantau Island, is largely used for foraging. A former foraging "hot spot" was located around the Brothers Islands east of the airport, now reduced, possibly due to increases in high-speed ferries (HSFs) and other activities. Sound recordings of dolphins from bottom-mounted hydrophones suggest that northwestern Hong Kong waters are used more at night than in daytime. Sexual activity and calving occur throughout the year, with a peak in late spring to autumn (wet monsoon season). Humpback dolphins communicate acoustically with each other and probably passively listen to prey in murky waters, and anthropogenic noises may be masking communication and affecting prey location. Increasing sounds of shipping, HSFs and industrial activities are likely to alter dolphin habitat use patterns and overall behaviours beyond the present already affected status. © 2016 Elsevier Ltd. All rights reserved.

Protecting DNA from errors and damage: an overview of DNA repair mechanisms in plants compared to mammals.

PubMed

Spampinato, Claudia P

2017-05-01

The genome integrity of all organisms is constantly threatened by replication errors and DNA damage arising from endogenous and exogenous sources. Such base pair anomalies must be accurately repaired to prevent mutagenesis and/or lethality. Thus, it is not surprising that cells have evolved multiple and partially overlapping DNA repair pathways to correct specific types of DNA errors and lesions. Great progress in unraveling these repair mechanisms at the molecular level has been made by several talented researchers, among them Tomas Lindahl, Aziz Sancar, and Paul Modrich, all three Nobel laureates in Chemistry for 2015. Much of this knowledge comes from studies performed in bacteria, yeast, and mammals and has impacted research in plant systems. Two plant features should be mentioned. Plants differ from higher eukaryotes in that they lack a reserve germline and cannot avoid environmental stresses. Therefore, plants have evolved different strategies to sustain genome fidelity through generations and continuous exposure to genotoxic stresses. These strategies include the presence of unique or multiple paralogous genes with partially overlapping DNA repair activities. Yet, in spite (or because) of these differences, plants, especially Arabidopsis thaliana, can be used as a model organism for functional studies. Some advantages of this model system are worth mentioning: short life cycle, availability of both homozygous and heterozygous lines for many genes, plant transformation techniques, tissue culture methods and reporter systems for gene expression and function studies. Here, I provide a current understanding of DNA repair genes in plants, with a special focus on A. thaliana. It is expected that this review will be a valuable resource for future functional studies in the DNA repair field, both in plants and animals.

The performance of different classification criteria sets for spondyloarthritis in the worldwide ASAS-COMOSPA study.

PubMed

Bakker, Pauline; Moltó, Anna; Etcheto, Adrien; Van den Bosch, Filip; Landewé, Robert; van Gaalen, Floris; Dougados, Maxime; van der Heijde, Désirée

2017-05-16

In this study, we sought to compare the performance of spondyloarthritis (SpA) classification criteria sets in an international SpA cohort with patients included from five continents around the world. Data from the (ASAS) COMOrbidities in SPondyloArthritis (ASAS-COMOSPA) study were used. ASAS-COMOSPA is a multinational, cross-sectional study with consecutive patients diagnosed with SpA by rheumatologists worldwide. Patients were classified according to the European Spondyloarthropathy Study Group (ESSG), modified European Spondyloarthropathy Study Group (mESSG), Amor, modified Amor, Assessment of SpondyloArthritis international Society (ASAS) axial Spondyloarthritis (axSpA), ASAS peripheral spondyloarthritis (pSpA) and ClASsification criteria for Psoriatic Arthritis (CASPAR) criteria. Overlap between the classification criteria sets was assessed for patients with and without back pain. Furthermore, patients fulfilling different arms of the ASAS axSpA criteria (imaging arm, clinical arm, both arms) were compared on the presence of SpA features. A total of 3942 patients (5 continents, 26 countries) were included. The mean age was 43.6 years, 65.0% were male, 56.2% were human leucocyte antigen B27-positive and 64.4% had radiographic sacroiliitis (based on modified New York criteria). Of the patients, 85.5% were classified by the ASAS SpA criteria (87.7% ASAS axSpA, 12.3% ASAS pSpA). Fulfilment of the Amor, ESSG and CASPAR criteria was present in 83.3%, 88.4% and 21.6% of patients, respectively. Of the patients with back pain (n = 3227), most were classified by all three of Amor, ESSG and ASAS axSpA criteria (71.4%). Patients fulfilling the imaging arm and the clinical arm of the ASAS axSpA criteria had similar presentations of SpA features. In patients without back pain, overlap between classification criteria sets was seen, although to a lesser extent. Most patients with a clinical diagnosis of axial SpA in the worldwide ASAS-COMOSPA study fulfil several classification criteria sets, and a substantial overlap between different criteria sets is seen, which suggests a high level of credibility of the criteria. Large inter-regional differences in the fulfilment of classification criteria were not found. Patients fulfilling the clinical arm were remarkably similar to patients fulfilling the imaging arm with respect to the presence of most SpA features.

Using partially labeled data for normal mixture identification with application to class definition

NASA Technical Reports Server (NTRS)

Shahshahani, Behzad M.; Landgrebe, David A.

1992-01-01

The problem of estimating the parameters of a normal mixture density when, in addition to the unlabeled samples, sets of partially labeled samples are available is addressed. The density of the multidimensional feature space is modeled with a normal mixture. It is assumed that the set of components of the mixture can be partitioned into several classes and that training samples are available from each class. Since for any training sample the class of origin is known but the exact component of origin within the corresponding class is unknown, the training samples as considered to be partially labeled. The EM iterative equations are derived for estimating the parameters of the normal mixture in the presence of partially labeled samples. These equations can be used to combine the supervised and nonsupervised learning processes.

Communication: Electron ionization of DNA bases.

PubMed

Rahman, M A; Krishnakumar, E

2016-04-28

No reliable experimental data exist for the partial and total electron ionization cross sections for DNA bases, which are very crucial for modeling radiation damage in genetic material of living cell. We have measured a complete set of absolute partial electron ionization cross sections up to 500 eV for DNA bases for the first time by using the relative flow technique. These partial cross sections are summed to obtain total ion cross sections for all the four bases and are compared with the existing theoretical calculations and the only set of measured absolute cross sections. Our measurements clearly resolve the existing discrepancy between the theoretical and experimental results, thereby providing for the first time reliable numbers for partial and total ion cross sections for these molecules. The results on fragmentation analysis of adenine supports the theory of its formation in space.

Parenting style as a mediator between children's negative emotionality and problematic behavior in early childhood.

PubMed

Paulussen-Hoogeboom, Marja C; Stams, Geert Jan J M; Hermanns, Jo M A; Peetsma, Thea T D; van den Wittenboer, Godfried L H

2008-09-01

Negative emotionality is considered to be the core of the difficult temperament concept (J. E. Bates, 1989; R. L. Shiner, 1998). In this correlational study, the authors examined whether the relations between children's negative emotionality and problematic behavior (internalizing and externalizing) were partially mediated by parenting style (authoritative and authoritarian) in a community sample of 196 3-year-old children and their mothers. The authors assessed maternal perception of child negative emotionality using the Children's Behavior Questionnaire (M. K. Rothbart, S. A. Ahadi, K. L. Hershey, & P. Fisher, 2001) and assessed problematic child behavior by means of maternal report using the Child Behavior Checklist (T. M. Achenbach, 1992). The results showed that the relations between child negative emotionality and internalizing and externalizing behaviors were partially mediated by mothers' authoritative parenting style. Moreover, when the authors used confirmatory factor analysis to decontaminate possible overlap in item content between measures assessing temperament and problematic behavior, the association between negative emotionality and internalizing behavior was fully mediated by authoritative parenting.

The oculo-dento-digital syndrome: male-to-male transmission and variable expression in a family.

PubMed

Ioan, D M; Dumitriu, L; Belengeariu, V; Fryns, J P

1997-01-01

We report two siblings--a 5 1/2 year old female and her 4 1/2 year old brother, both presenting the classical clinical findings of oculo-dento-digital dysplasia (ODD). 1. Digital anomalies: bilateral complete cutaneous syndactyly of fingers IV-V (III-IV-V at the left hand of the boy) and camptodactyly IV. 2. Facial and ocular anomalies: microphtalamos-epicanthal folds, small midfacies, thin nose with hypoplastic alae nasi and small nares. 3. Dental anomalies with partial dental agenesis and enamel hypoplasia. Examination of the parents showed a bilateral cutaneous syndactyly IV-V in the father as the sole partial manifestation of ODD. The findings in the present family confirm the autosomal dominant inheritance of ODD with great variability in clinical expression. Moreover, the facial morphology (thin, hypoplastic nose) observed in several ODD patients suggests nosological overlap with the Hallerman-Streiff syndrome and could indicate that both syndromes are variable expressions of a contiguous gene deletion syndrome.

Contextual memory and skill transfer in category search.

PubMed

Kole, James A; Healy, Alice F; Fierman, Deanna M; Bourne, Lyle E

2010-01-01

In three experiments, we examined transfer and contextual memory in a category search task. Each experiment included two phases (training and test), during which participants searched through category and exemplar menus for targets. In Experiment 1, the targets were from one of two domains during training (grocery store or department store); the domain was either the same or changed at test. Also, the categories were organized in one of two ways (alphabetically or semantically); the organization either remained the same or changed at test. In Experiments 2 and 3, domain and organization were held constant; however, categories or exemplars were the same, partially replaced, or entirely replaced across phases in order to simulate the dynamic nature of category search in everyday situations. Transfer occurred at test when the category organization or domain was maintained and when the categories or exemplars matched (partially or entirely) those at training. These results demonstrate that transfer is facilitated by overlap in training and testing contexts.

Polarization effects on quantum levels in InN/GaN quantum wells.

PubMed

Lin, Wei; Li, Shuping; Kang, Junyong

2009-12-02

Polarization effects on quantum states in InN/GaN quantum wells have been investigated by means of ab initio calculation and spectroscopic ellipsometry. Through the position-dependent partial densities of states, our results show that the polarization modified by the strain with different well thickness leads to an asymmetry band bending of the quantum well. The quantum levels are identified via the band structures and their square wave function distributions are analyzed by the partial charge densities. Further theoretical and experimental comparison of the imaginary part of the dielectric function show that the overall transition probability increases under larger polarization fields, which can be attributable to the fact that the excited quantum states of 2h have a greater overlap with 1e states and enhance other hole quantum states in the well by a hybridization. These results would provide a new approach to improve the transition probability and light emission by enhancing the polarization fields in a proper way.

The Way Ahead for Human Terrain Teams

DTIC Science & Technology

2013-01-01

achievements without ignoring shortcomings. That history can be summarized as a set of sometimes overlap- ping developmental periods. The first period...and Technology Commit- tee , U.S. House of Representatives, 110th Cong., 2nd sess., Hearings on Role of the Social and Behavioral Sciences in National

Greening Montessori School Grounds by Design

ERIC Educational Resources Information Center

Moore, Robin; Cosco, Nilda

2013-01-01

Robin Moore and Nilda Cosco view the Montessori approach to the prepared environment as overlapping their understanding of the naturalization of school grounds. As they present the possibilities for a naturalized setting to overcome sedentary lifestyles and maximize learning in the outdoors, they establish necessary components for success:…

The Economics of Has-Beens

ERIC Educational Resources Information Center

MacDonald, Glenn; Weisbach, Michael S.

2004-01-01

The evolution of technology causes human capital to become obsolete. We study this phenomenon in an overlapping generations setting, assuming that technology evolves stochastically and that older workers find updating uneconomic. Experience and learning by doing may offer the old some income protection, but technology advance always turns them…

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison.

PubMed

Hahn, Lars; Leimeister, Chris-André; Ounit, Rachid; Lonardi, Stefano; Morgenstern, Burkhard

2016-10-01

Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de/.

Poster - Thur Eve - 57: Craniospinal irradiation with jagged-junction IMRT approach without beam edge matching for field junctions.

PubMed

Cao, F; Ramaseshan, R; Corns, R; Harrop, S; Nuraney, N; Steiner, P; Aldridge, S; Liu, M; Carolan, H; Agranovich, A; Karva, A

2012-07-01

Craniospinal irradiation were traditionally treated the central nervous system using two or three adjacent field sets. A intensity-modulated radiotherapy (IMRT) plan (Jagged-Junction IMRT) which overcomes problems associated with field junctions and beam edge matching, improves planning and treatment setup efficiencies with homogenous target dose distribution was developed. Jagged-Junction IMRT was retrospectively planned on three patients with prescription of 36 Gy in 20 fractions and compared to conventional treatment plans. Planning target volume (PTV) included the whole brain and spinal canal to the S3 vertebral level. The plan employed three field sets, each with a unique isocentre. One field set with seven fields treated the cranium. Two field sets treated the spine, each set using three fields. Fields from adjacent sets were overlapped and the optimization process smoothly integrated the dose inside the overlapped junction. For the Jagged-Junction IMRT plans vs conventional technique, average homogeneity index equaled 0.08±0.01 vs 0.12±0.02, and conformity number equaled 0.79±0.01 vs 0.47±0.12. The 95% isodose surface covered (99.5±0.3)% of the PTV vs (98.1±2.0)%. Both Jagged-Junction IMRT plans and the conventional plans had good sparing of the organs at risk. Jagged-Junction IMRT planning provided good dose homogeneity and conformity to the target while maintaining a low dose to the organs at risk. Jagged-Junction IMRT optimization smoothly distributed dose in the junction between field sets. Since there was no beam matching, this treatment technique is less likely to produce hot or cold spots at the junction in contrast to conventional techniques. © 2012 American Association of Physicists in Medicine.

Task representation in individual and joint settings

PubMed Central

Prinz, Wolfgang

2015-01-01

This paper outlines a framework for task representation and discusses applications to interference tasks in individual and joint settings. The framework is derived from the Theory of Event Coding (TEC). This theory regards task sets as transient assemblies of event codes in which stimulus and response codes interact and shape each other in particular ways. On the one hand, stimulus and response codes compete with each other within their respective subsets (horizontal interactions). On the other hand, stimulus and response code cooperate with each other (vertical interactions). Code interactions instantiating competition and cooperation apply to two time scales: on-line performance (i.e., doing the task) and off-line implementation (i.e., setting the task). Interference arises when stimulus and response codes overlap in features that are irrelevant for stimulus identification, but relevant for response selection. To resolve this dilemma, the feature profiles of event codes may become restructured in various ways. The framework is applied to three kinds of interference paradigms. Special emphasis is given to joint settings where tasks are shared between two participants. Major conclusions derived from these applications include: (1) Response competition is the chief driver of interference. Likewise, different modes of response competition give rise to different patterns of interference; (2) The type of features in which stimulus and response codes overlap is also a crucial factor. Different types of such features give likewise rise to different patterns of interference; and (3) Task sets for joint settings conflate intraindividual conflicts between responses (what), with interindividual conflicts between responding agents (whom). Features of response codes may, therefore, not only address responses, but also responding agents (both physically and socially). PMID:26029085

Assessment of Uncertainties Related to Seismic Hazard Using Fuzzy Analysis

NASA Astrophysics Data System (ADS)

Jorjiashvili, N.; Yokoi, T.; Javakhishvili, Z.

2013-05-01

Seismic hazard analysis in last few decades has been become very important issue. Recently, new technologies and available data have been improved that helped many scientists to understand where and why earthquakes happen, physics of earthquakes, etc. They have begun to understand the role of uncertainty in Seismic hazard analysis. However, there is still significant problem how to handle existing uncertainty. The same lack of information causes difficulties to quantify uncertainty accurately. Usually attenuation curves are obtained in statistical way: regression analysis. Statistical and probabilistic analysis show overlapped results for the site coefficients. This overlapping takes place not only at the border between two neighboring classes, but also among more than three classes. Although the analysis starts from classifying sites using the geological terms, these site coefficients are not classified at all. In the present study, this problem is solved using Fuzzy set theory. Using membership functions the ambiguities at the border between neighboring classes can be avoided. Fuzzy set theory is performed for southern California by conventional way. In this study standard deviations that show variations between each site class obtained by Fuzzy set theory and classical way are compared. Results on this analysis show that when we have insufficient data for hazard assessment site classification based on Fuzzy set theory shows values of standard deviations less than obtained by classical way which is direct proof of less uncertainty.

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

Springer, H K; Miller, W O; Levatin, J L

Satellite collision debris poses risks to existing space assets and future space missions. Predictive models of debris generated from these hypervelocity collisions are critical for developing accurate space situational awareness tools and effective mitigation strategies. Hypervelocity collisions involve complex phenomenon that spans several time- and length-scales. We have developed a satellite collision debris modeling approach consisting of a Lagrangian hydrocode enriched with smooth particle hydrodynamics (SPH), advanced material failure models, detailed satellite mesh models, and massively parallel computers. These computational studies enable us to investigate the influence of satellite center-of-mass (CM) overlap and orientation, relative velocity, and material composition onmore » the size, velocity, and material type distributions of collision debris. We have applied our debris modeling capability to the recent Iridium 33-Cosmos 2251 collision event. While the relative velocity was well understood in this event, the degree of satellite CM overlap and orientation was ill-defined. In our simulations, we varied the collision CM overlap and orientation of the satellites from nearly maximum overlap to partial overlap on the outermost extents of the satellites (i.e, solar panels and gravity boom). As expected, we found that with increased satellite overlap, the overall debris cloud mass and momentum (transfer) increases, the average debris size decreases, and the debris velocity increases. The largest predicted debris can also provide insight into which satellite components were further removed from the impact location. A significant fraction of the momentum transfer is imparted to the smallest debris (< 1-5mm, dependent on mesh resolution), especially in large CM overlap simulations. While the inclusion of the smallest debris is critical to enforcing mass and momentum conservation in hydrocode simulations, there seems to be relatively little interest in their disposition. Based on comparing our results to observations, it is unlikely that the Iridium 33-Cosmos 2251 collision event was a large mass-overlap collision. We also performed separate simulations studying the debris generated by the collision of 5 and 10 cm spherical projectiles on the Iridium 33 satellite at closing velocities of 5, 10, and 15 km/s. It is important to understand the vulnerability of satellites to small debris threats, given their pervasiveness in orbit. These studies can also be merged with probabilistic conjunction analysis to better understand the risk to space assets. In these computational studies, we found that momentum transfer, kinetic energy losses due to dissipative mechanisms (e.g., fracture), fragment number, and fragment velocity increases with increasing velocity for a fixed projectile size. For a fixed velocity, we found that the smaller projectile size more efficiently transfers momentum to the satellite. This latter point has an important implication: Eight (spaced) 5 cm debris objects can impart more momentum to the satellite, and likely cause more damage, than a single 10 cm debris object at the same velocity. Further studies are required to assess the satellite damage induced by 1-5 cm sized debris objects, as well as multiple debris objects, in this velocity range.« less

A polyphonic acoustic vortex and its complementary chords

NASA Astrophysics Data System (ADS)

Wilson, C.; Padgett, M. J.

2010-02-01

Using an annular phased array of eight loudspeakers, we generate sound beams that simultaneously contain phase singularities at a number of different frequencies. These frequencies correspond to different musical notes and the singularities can be set to overlap along the beam axis, creating a polyphonic acoustic vortex. Perturbing the drive amplitudes of the speakers means that the singularities no longer overlap, each note being nulled at a slightly different lateral position, where the volume of the other notes is now nonzero. The remaining notes form a tri-note chord. We contrast this acoustic phenomenon to the optical case where the perturbation of a white light vortex leads to a spectral spatial distribution.

Determination of Patterson group symmetry from sparse multi-crystal data sets in the presence of an indexing ambiguity.

PubMed

Gildea, Richard J; Winter, Graeme

2018-05-01

Combining X-ray diffraction data from multiple samples requires determination of the symmetry and resolution of any indexing ambiguity. For the partial data sets typical of in situ room-temperature experiments, determination of the correct symmetry is often not straightforward. The potential for indexing ambiguity in polar space groups is also an issue, although methods to resolve this are available if the true symmetry is known. Here, a method is presented to simultaneously resolve the determination of the Patterson symmetry and the indexing ambiguity for partial data sets. open access.

Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications.

PubMed

Leung, Tiffany I; Dumontier, Michel

2016-06-08

Clinical practice guidelines (CPGs) recommend pharmacologic treatments for clinical conditions, and drug structured product labels (SPLs) summarize approved treatment indications. Both resources are intended to promote evidence-based medical practices and guide clinicians' prescribing decisions. However, it is unclear how well CPG recommendations about pharmacologic therapies match SPL indications for recommended drugs. In this study, we perform text mining of CPG summaries to examine drug-disease associations in CPG recommendations and in SPL treatment indications for 15 common chronic conditions. We constructed an initial text corpus of guideline summaries from the National Guideline Clearinghouse (NGC) from a set of manually selected ICD-9 codes for each of the 15 conditions. We obtained 377 relevant guideline summaries and their Major Recommendations section, which excludes guidelines for pediatric patients, pregnant or breastfeeding women, or for medical diagnoses not meeting inclusion criteria. A vocabulary of drug terms was derived from five medical taxonomies. We used named entity recognition, in combination with dictionary-based and ontology-based methods, to identify drug term occurrences in the text corpus and construct drug-disease associations. The ATC (Anatomical Therapeutic Chemical Classification) was utilized to perform drug name and drug class matching to construct the drug-disease associations from CPGs. We then obtained drug-disease associations from SPLs using conditions mentioned in their Indications section in SIDER. The primary outcomes were the frequency of drug-disease associations in CPGs and SPLs, and the frequency of overlap between the two sets of drug-disease associations, with and without using taxonomic information from ATC. Without taxonomic information, we identified 1444 drug-disease associations across CPGs and SPLs for 15 common chronic conditions. Of these, 195 drug-disease associations overlapped between CPGs and SPLs, 917 associations occurred in CPGs only and 332 associations occurred in SPLs only. With taxonomic information, 859 unique drug-disease associations were identified, of which 152 of these drug-disease associations overlapped between CPGs and SPLs, 541 associations occurred in CPGs only, and 166 associations occurred in SPLs only. Our results suggest that CPG-recommended pharmacologic therapies and SPL indications do not overlap frequently when identifying drug-disease associations using named entity recognition, although incorporating taxonomic relationships between drug names and drug classes into the approach improves the overlap. This has important implications in practice because conflicting or inconsistent evidence may complicate clinical decision making and implementation or measurement of best practices.

Creating a sampling frame for population-based veteran research: representativeness and overlap of VA and Department of Defense databases.

PubMed

Washington, Donna L; Sun, Su; Canning, Mark

2010-01-01

Most veteran research is conducted in Department of Veterans Affairs (VA) healthcare settings, although most veterans obtain healthcare outside the VA. Our objective was to determine the adequacy and relative contributions of Veterans Health Administration (VHA), Veterans Benefits Administration (VBA), and Department of Defense (DOD) administrative databases for representing the U.S. veteran population, using as an example the creation of a sampling frame for the National Survey of Women Veterans. In 2008, we merged the VHA, VBA, and DOD databases. We identified the number of unique records both overall and from each database. The combined databases yielded 925,946 unique records, representing 51% of the 1,802,000 U.S. women veteran population. The DOD database included 30% of the population (with 8% overlap with other databases). The VHA enrollment database contributed an additional 20% unique women veterans (with 6% overlap with VBA databases). VBA databases contributed an additional 2% unique women veterans (beyond 10% overlap with other databases). Use of VBA and DOD databases substantially expands access to the population of veterans beyond those in VHA databases, regardless of VA use. Adoption of these additional databases would enhance the value and generalizability of a wide range of studies of both male and female veterans.

Adaptive handling of Rayleigh and Raman scatter of fluorescence data based on evaluation of the degree of spectral overlap

NASA Astrophysics Data System (ADS)

Hu, Yingtian; Liu, Chao; Wang, Xiaoping; Zhao, Dongdong

2018-06-01

At present the general scatter handling methods are unsatisfactory when scatter and fluorescence seriously overlap in excitation emission matrix. In this study, an adaptive method for scatter handling of fluorescence data is proposed. Firstly, the Raman scatter was corrected by subtracting the baseline of deionized water which was collected in each experiment to adapt to the intensity fluctuations. Then, the degrees of spectral overlap between Rayleigh scatter and fluorescence were classified into three categories based on the distance between the spectral peaks. The corresponding algorithms, including setting to zero, fitting on single or both sides, were implemented after the evaluation of the degree of overlap for individual emission spectra. The proposed method minimized the number of fitting and interpolation processes, which reduced complexity, saved time, avoided overfitting, and most importantly assured the authenticity of data. Furthermore, the effectiveness of this procedure on the subsequent PARAFAC analysis was assessed and compared to Delaunay interpolation by conducting experiments with four typical organic chemicals and real water samples. Using this method, we conducted long-term monitoring of tap water and river water near a dyeing and printing plant. This method can be used for improving adaptability and accuracy in the scatter handling of fluorescence data.

Genetics, Cognition, and Neurobiology of Schizotypal Personality: A Review of the Overlap with Schizophrenia

PubMed Central

Ettinger, Ulrich; Meyhöfer, Inga; Steffens, Maria; Wagner, Michael; Koutsouleris, Nikolaos

2013-01-01

Schizotypy refers to a set of temporally stable traits that are observed in the general population and that resemble the signs and symptoms of schizophrenia. Here, we review evidence from studies on genetics, cognition, perception, motor and oculomotor control, brain structure, brain function, and psychopharmacology in schizotypy. We specifically focused on identifying areas of overlap between schizotypy and schizophrenia. Evidence was corroborated that significant overlap exists between the two, covering the behavioral brain structural and functional as well molecular levels. In particular, several studies showed that individuals with high levels of schizotypal traits exhibit alterations in neurocognitive task performance and underlying brain function similar to the deficits seen in patients with schizophrenia. Studies of brain structure have shown both volume reductions and increase in schizotypy, pointing to schizophrenia-like deficits as well as possible protective or compensatory mechanisms. Experimental pharmacological studies have shown that high levels of schizotypy are associated with (i) enhanced dopaminergic response in striatum following administration of amphetamine and (ii) improvement of cognitive performance following administration of antipsychotic compounds. Together, this body of work suggests that schizotypy shows overlap with schizophrenia across multiple behavioral and neurobiological domains, suggesting that the study of schizotypal traits may be useful in improving our understanding of the etiology of schizophrenia. PMID:24600411

Motorcycle helmet effectiveness in reducing head, face and brain injuries by state and helmet law.

PubMed

Olsen, Cody S; Thomas, Andrea M; Singleton, Michael; Gaichas, Anna M; Smith, Tracy J; Smith, Gary A; Peng, Justin; Bauer, Michael J; Qu, Ming; Yeager, Denise; Kerns, Timothy; Burch, Cynthia; Cook, Lawrence J

2016-12-01

Despite evidence that motorcycle helmets reduce morbidity and mortality, helmet laws and rates of helmet use vary by state in the U.S. We pooled data from eleven states: five with universal laws requiring all motorcyclists to wear a helmet, and six with partial laws requiring only a subset of motorcyclists to wear a helmet. Data were combined in the Crash Outcome Data Evaluation System's General Use Model and included motorcycle crash records probabilistically linked to emergency department and inpatient discharges for years 2005-2008. Medical outcomes were compared between partial and universal helmet law settings. We estimated adjusted relative risks (RR) and 95 % confidence intervals (CIs) for head, facial, traumatic brain, and moderate to severe head/facial injuries associated with helmet use within each helmet law setting using generalized log-binomial regression. Reported helmet use was higher in universal law states (88 % vs. 42 %). Median charges, adjusted for inflation and differences in state-incomes, were higher in partial law states (emergency department $1987 vs. $1443; inpatient $31,506 vs. $25,949). Injuries to the head and face, including traumatic brain injuries, were more common in partial law states. Effectiveness estimates of helmet use were higher in partial law states (adjusted-RR (CI) of head injury: 2.1 (1.9-2.2) partial law single vehicle; 1.4 (1.2, 1.6) universal law single vehicle; 1.8 (1.6-2.0) partial law multi-vehicle; 1.2 (1.1-1.4) universal law multi-vehicle). Medical charges and rates of head, facial, and brain injuries among motorcyclists were lower in universal law states. Helmets were effective in reducing injury in both helmet law settings; lower effectiveness estimates were observed in universal law states.