Science.gov

Sample records for mutually unbiased bases

  1. Mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Chaturvedi, S.

    2002-08-01

    After a brief review of the notion of a full set of mutually unbiased bases in an N-dimensional Hilbert space, we summarize the work of Wootters and Fields (W K Wootters and B C Fields, Ann. Phys. 191, 363 (1989)) which gives an explicit construction for such bases for the case N=pr, where p is a prime. Further, we show how, by exploiting certain freedom in the Wootters-Fields construction, the task of explicitly writing down such bases can be simplified for the case when p is an odd prime. In particular, we express the results entirely in terms of the character vectors of the cyclic group G of order p. We also analyse the connection between mutually unbiased bases and the representations of G.

  2. Covariant mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Carmeli, Claudio; Schultz, Jussi; Toigo, Alessandro

    2016-06-01

    The connection between maximal sets of mutually unbiased bases (MUBs) in a prime-power dimensional Hilbert space and finite phase-space geometries is well known. In this article, we classify MUBs according to their degree of covariance with respect to the natural symmetries of a finite phase-space, which are the group of its affine symplectic transformations. We prove that there exist maximal sets of MUBs that are covariant with respect to the full group only in odd prime-power dimensional spaces, and in this case, their equivalence class is actually unique. Despite this limitation, we show that in dimension 2r covariance can still be achieved by restricting to proper subgroups of the symplectic group, that constitute the finite analogues of the oscillator group. For these subgroups, we explicitly construct the unitary operators yielding the covariance.

  3. Entanglement in Mutually Unbiased Bases

    NASA Astrophysics Data System (ADS)

    Wiesniak, Marcin; Paterek, Tomasz; Zeilinger, Anton

    2011-03-01

    Higher-dimensional Hilbert spaces are still not fully explored. One issue concerns mutually unbiased bases (MUBs). For primes and their powers (e.g.), full sets of MUBs are known. The question of existence of all MUBs in composite dimensions is still open. We show that for all full sets of MUBs of a given dimension a certain entanglement measure of the bases is constant. This fact could be an argument either for or against the existence of full sets of MUBs in some dimensions and tells us that almost all MUBs are maximally entangled for high-dimensional composite systems, whereas this is not the case for prime dimensions. We present a new construction of MUBs in squared prime dimensions. We use only one entangling operation, which simplifies possible experiments. The construction gives only product states and maximally entangled states. Research supported by ERC Advanced Grant QIT4QAD and FWF SFB-grant F4007 of the Austrian Science Fund.

  4. Arithmetic, mutually unbiased bases and complementary observables

    NASA Astrophysics Data System (ADS)

    Sheppeard, M. D.

    2010-02-01

    Complementary observables in quantum mechanics may be viewed as Frobenius structures in a dagger monoidal category, such as the category of finite dimensional Hilbert spaces over the complex numbers. On the other hand, their properties crucially depend on the discrete Fourier transform and its associated quantum torus, requiring only the finite fields that underlie mutually unbiased bases. In axiomatic topos theory, the complex numbers are difficult to describe and should not be invoked unnecessarily. This paper surveys some fundamentals of quantum arithmetic using finite field complementary observables, with a view considering more general axiom systems.

  5. Mutually unbiased bases and bound entanglement

    NASA Astrophysics Data System (ADS)

    Hiesmayr, Beatrix C.; Löffler, Wolfgang

    2014-04-01

    In this contribution we relate two different key concepts: mutually unbiased bases (MUBs) and entanglement. We provide a general toolbox for analyzing and comparing entanglement of quantum states for different dimensions and numbers of particles. In particular we focus on bound entanglement, i.e. highly mixed states which cannot be distilled by local operations and classical communications. For a certain class of states—for which the state-space forms a ‘magic’ simplex—we analyze the set of bound entangled states detected by the MUB criterion for different dimensions d and number of particles n. We find that the geometry is similar for different d and n, consequently the MUB criterion opens possibilities to investigate the typicality of positivity under partial transposition (PPT)-bound and multipartite bound entanglement more deeply and provides a simple experimentally feasible tool to detect bound entanglement.

  6. Quantum process reconstruction based on mutually unbiased basis

    NASA Astrophysics Data System (ADS)

    Fernández-Pérez, A.; Klimov, A. B.; Saavedra, C.

    2011-05-01

    We study a quantum process reconstruction based on the use of mutually unbiased projectors (MUB projectors) as input states for a D-dimensional quantum system, with D being a power of a prime number. This approach connects the results of quantum-state tomography using mutually unbiased bases with the coefficients of a quantum process, expanded in terms of MUB projectors. We also study the performance of the reconstruction scheme against random errors when measuring probabilities at the MUB projectors.

  7. Graph-state formalism for mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Spengler, Christoph; Kraus, Barbara

    2013-11-01

    A pair of orthonormal bases is called mutually unbiased if all mutual overlaps between any element of one basis and an arbitrary element of the other basis coincide. In case the dimension, d, of the considered Hilbert space is a power of a prime number, complete sets of d+1 mutually unbiased bases (MUBs) exist. Here we present a method based on the graph-state formalism to construct such sets of MUBs. We show that for n p-level systems, with p being prime, one particular graph suffices to easily construct a set of pn+1 MUBs. In fact, we show that a single n-dimensional vector, which is associated with this graph, can be used to generate a complete set of MUBs and demonstrate that this vector can be easily determined. Finally, we discuss some advantages of our formalism regarding the analysis of entanglement structures in MUBs, as well as experimental realizations.

  8. Detecting entanglement of continuous variables with three mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Paul, E. C.; Tasca, D. S.; Rudnicki, Łukasz; Walborn, S. P.

    2016-07-01

    An uncertainty relation is introduced for a symmetric arrangement of three mutually unbiased bases in continuous-variable phase space, and then used to derive a bipartite entanglement criterion based on the variance of global operators composed of these three phase-space variables. We test this criterion using spatial variables of photon pairs and show that the entangled photons are correlated in three pairs of bases.

  9. An analytic function approach to weak mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Olupitan, T.; Lei, C.; Vourdas, A.

    2016-08-01

    Quantum systems with variables in Z(d) are considered, and three different structures are studied. The first is weak mutually unbiased bases, for which the absolute value of the overlap of any two vectors in two different bases is 1 /√{ k } (where k | d) or 0. The second is maximal lines through the origin in the Z(d) × Z(d) phase space. The third is an analytic representation in the complex plane based on Theta functions, and their zeros. It is shown that there is a correspondence (triality) that links strongly these three apparently different structures. For simplicity, the case where d =p1 ×p2, where p1 ,p2 are odd prime numbers different from each other, is considered.

  10. Galois-unitary operators that cycle mutually-unbiased bases

    NASA Astrophysics Data System (ADS)

    Dang, Hoan; Appleby, Marcus; Bengtsson, Ingemar

    2015-03-01

    Wigner's theorem states that probability-preserving transformations of quantum states must be either unitary or anti-unitary. However, if we restrict ourselves to a subspace of a Hilbert space, it is possible to generalize the notion of anti-unitaries. Such transformations were recently constructed in search of Symmetric Informationally-Complete (SIC) states. They are called Galois-unitaries (g-unitaries for short), as they are unitaries composed with Galois automorphisms of a chosen number field extension. Despite certain bizarre behaviors of theirs, we show that g-unitaries are indeed useful in the theory of Mutually-Unbiased Bases (MUBs), as they help solve the MUB-cycling problem and provide a construction of MUB-balanced states. HD was supported by the Natural Sciences and Engineering Research Council of Canada and the Vanier Canada Graduate Scholarship

  11. Mutually unbiased bases as minimal Clifford covariant 2-designs

    NASA Astrophysics Data System (ADS)

    Zhu, Huangjun

    2015-06-01

    Mutually unbiased bases (MUBs) are interesting for various reasons. The most attractive example of (a complete set of) MUBs is the one constructed by Ivanović as well as Wootters and Fields, which is referred to as the canonical MUB. Nevertheless, little is known about anything that is unique to this MUB. We show that the canonical MUB in any prime power dimension is uniquely determined by an extremal orbit of the (restricted) Clifford group except in dimension 3, in which case the orbit defines a special symmetric informationally complete measurement (SIC), known as the Hesse SIC. Here the extremal orbit is the orbit with the smallest number of pure states. Quite surprisingly, this characterization does not rely on any concept that is related to bases or unbiasedness. As a corollary, the canonical MUB is the unique minimal 2-design covariant with respect to the Clifford group except in dimension 3. In addition, these MUBs provide an infinite family of highly symmetric frames and positive-operator-valued measures (POVMs), which are of independent interest.

  12. Mutually unbiased bases in six dimensions: The four most distant bases

    SciTech Connect

    Raynal, Philippe; Lue Xin; Englert, Berthold-Georg

    2011-06-15

    We consider the average distance between four bases in six dimensions. The distance between two orthonormal bases vanishes when the bases are the same, and the distance reaches its maximal value of unity when the bases are unbiased. We perform a numerical search for the maximum average distance and find it to be strictly smaller than unity. This is strong evidence that no four mutually unbiased bases exist in six dimensions. We also provide a two-parameter family of three bases which, together with the canonical basis, reach the numerically found maximum of the average distance, and we conduct a detailed study of the structure of the extremal set of bases.

  13. Higher-dimensional orbital-angular-momentum-based quantum key distribution with mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Mafu, Mhlambululi; Dudley, Angela; Goyal, Sandeep; Giovannini, Daniel; McLaren, Melanie; Padgett, Miles J.; Konrad, Thomas; Petruccione, Francesco; Lütkenhaus, Norbert; Forbes, Andrew

    2013-09-01

    We present an experimental study of higher-dimensional quantum key distribution protocols based on mutually unbiased bases, implemented by means of photons carrying orbital angular momentum. We perform (d+1) mutually unbiased measurements in a classically simulated prepare-and-measure scheme and on a pair of entangled photons for dimensions ranging from d=2 to 5. In our analysis, we pay attention to the detection efficiency and photon pair creation probability. As security measures, we determine from experimental data the average error rate, the mutual information shared between the sender and receiver, and the secret key generation rate per photon. We demonstrate that increasing the dimension leads to an increased information capacity as well as higher key generation rates per photon. However, we find that the benefit of increasing the dimension is limited by practical implementation considerations, which in our case results in deleterious effects observed beyond a dimension of d=4.

  14. There is no generalization of known formulas for mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Archer, Claude

    2005-02-01

    In a quantum system having a finite number N of orthogonal states, two orthonormal bases {ai} and {bj} are called mutually unbiased if all inner products ⟨ai∣bj⟩ have the same modulus 1/√N . This concept appears in several quantum information problems. The number of pairwise mutually unbiased bases is at most N +1 and various constructions of such N +1 bases have been found when N is a power of a prime number. We study families of formulas that generalize these constructions to arbitrary dimensions using finite rings. We then prove that there exists a set of N +1 mutually unbiased bases described by such formulas, if and only if N is a power of a prime number.

  15. Test of mutually unbiased bases for six-dimensional photonic quantum systems

    PubMed Central

    D'Ambrosio, Vincenzo; Cardano, Filippo; Karimi, Ebrahim; Nagali, Eleonora; Santamato, Enrico; Marrucci, Lorenzo; Sciarrino, Fabio

    2013-01-01

    In quantum information, complementarity of quantum mechanical observables plays a key role. The eigenstates of two complementary observables form a pair of mutually unbiased bases (MUBs). More generally, a set of MUBs consists of bases that are all pairwise unbiased. Except for specific dimensions of the Hilbert space, the maximal sets of MUBs are unknown in general. Even for a dimension as low as six, the identification of a maximal set of MUBs remains an open problem, although there is strong numerical evidence that no more than three simultaneous MUBs do exist. Here, by exploiting a newly developed holographic technique, we implement and test different sets of three MUBs for a single photon six-dimensional quantum state (a “qusix”), encoded exploiting polarization and orbital angular momentum of photons. A close agreement is observed between theory and experiments. Our results can find applications in state tomography, quantitative wave-particle duality, quantum key distribution. PMID:24067548

  16. Discrete phase-space structure of n-qubit mutually unbiased bases

    SciTech Connect

    Klimov, A.B.; Romero, J.L.; Bjoerk, G.; Sanchez-Soto, L.L.

    2009-01-15

    We work out the phase-space structure for a system of n qubits. We replace the field of real numbers that label the axes of the continuous phase space by the finite field GF(2{sup n}) and investigate the geometrical structures compatible with the notion of unbiasedness. These consist of bundles of discrete curves intersecting only at the origin and satisfying certain additional properties. We provide a simple classification of such curves and study in detail the four- and eight-dimensional cases, analyzing also the effect of local transformations. In this way, we provide a comprehensive phase-space approach to the construction of mutually unbiased bases for n qubits.

  17. Temporal steering and security of quantum key distribution with mutually unbiased bases against individual attacks

    NASA Astrophysics Data System (ADS)

    Bartkiewicz, Karol; Černoch, Antonín; Lemr, Karel; Miranowicz, Adam; Nori, Franco

    2016-06-01

    Temporal steering, which is a temporal analog of Einstein-Podolsky-Rosen steering, refers to temporal quantum correlations between the initial and final state of a quantum system. Our analysis of temporal steering inequalities in relation to the average quantum bit error rates reveals the interplay between temporal steering and quantum cloning, which guarantees the security of quantum key distribution based on mutually unbiased bases against individual attacks. The key distributions analyzed here include the Bennett-Brassard 1984 protocol and the six-state 1998 protocol by Bruss. Moreover, we define a temporal steerable weight, which enables us to identify a kind of monogamy of temporal correlation that is essential to quantum cryptography and useful for analyzing various scenarios of quantum causality.

  18. Nonexistence of sharply covariant mutually unbiased bases in odd prime dimensions

    NASA Astrophysics Data System (ADS)

    Zhu, Huangjun

    2015-09-01

    Mutually unbiased bases (MUB) are useful in a number of research areas. The symmetry of MUB is an elusive and interesting subject. A (complete set of) MUB in dimension d is sharply covariant if it can be generated by a group of order d (d +1 ) from a basis state. Such MUB, if they exist, would be most appealing to theoretical studies and practical applications. Unfortunately, they seem to be quite rare. Here we prove that no MUB in odd prime dimensions is sharply covariant, by virtue of clever applications of Mersenne primes, Galois fields, and Frobenius groups. This conclusion provides valuable insight about the symmetry of MUB and the geometry of quantum state space. It complements and strengthens the earlier result of the author that only two stabilizer MUB are sharply covariant. Our study leads to the conjecture that no MUB other than those in dimensions 2 and 4 is sharply covariant.

  19. Bipartite entangled stabilizer mutually unbiased bases as maximum cliques of Cayley graphs

    SciTech Connect

    Dam, Wim van; Howard, Mark

    2011-07-15

    We examine the existence and structure of particular sets of mutually unbiased bases (MUBs) in bipartite qudit systems. In contrast to well-known power-of-prime MUB constructions, we restrict ourselves to using maximally entangled stabilizer states as MUB vectors. Consequently, these bipartite entangled stabilizer MUBs (BES MUBs) provide no local information, but are sufficient and minimal for decomposing a wide variety of interesting operators including (mixtures of) Jamiolkowski states, entanglement witnesses, and more. The problem of finding such BES MUBs can be mapped, in a natural way, to that of finding maximum cliques in a family of Cayley graphs. Some relationships with known power-of-prime MUB constructions are discussed, and observables for BES MUBs are given explicitly in terms of Pauli operators.

  20. Reply to ''Comment on 'Mutually unbiased bases, orthogonal Latin squares, and hidden-variable models'''

    SciTech Connect

    Paterek, Tomasz; Dakic, Borivoje; Brukner, Caslav

    2011-03-15

    In this Reply to the preceding Comment by Hall and Rao [Phys. Rev. A 83, 036101 (2011)], we motivate terminology of our original paper and point out that further research is needed in order to (dis)prove the claimed link between every orthogonal Latin square of order being a power of a prime and a mutually unbiased basis.

  1. Block-circulant matrices with circulant blocks, Weil sums, and mutually unbiased bases. II. The prime power case

    NASA Astrophysics Data System (ADS)

    Combescure, Monique

    2009-03-01

    In our previous paper [Combescure, M., "Circulant matrices, Gauss sums and the mutually unbiased bases. I. The prime number case," Cubo A Mathematical Journal (unpublished)] we have shown that the theory of circulant matrices allows to recover the result that there exists p +1 mutually unbiased bases in dimension p, p being an arbitrary prime number. Two orthonormal bases B, B' of Cd are said mutually unbiased if ∀bɛB, ∀b'ɛB' one has that |b ṡb'|=1/√d (b ṡb' Hermitian scalar product in Cd). In this paper we show that the theory of block-circulant matrices with circulant blocks allows to show very simply the known result that if d =pn (p a prime number and n any integer) there exists d +1 mutually unbiased bases in Cd. Our result relies heavily on an idea of Klimov et al. ["Geometrical approach to the discrete Wigner function," J. Phys. A 39, 14471 (2006)]. As a subproduct we recover properties of quadratic Weil sums for p ≥3, which generalizes the fact that in the prime case the quadratic Gauss sum properties follow from our results.

  2. FAST TRACK COMMUNICATION: Affine constellations without mutually unbiased counterparts

    NASA Astrophysics Data System (ADS)

    Weigert, Stefan; Durt, Thomas

    2010-10-01

    It has been conjectured that a complete set of mutually unbiased bases in a space of dimension d exists if and only if there is an affine plane of order d. We introduce affine constellations and compare their existence properties with those of mutually unbiased constellations. The observed discrepancies make a deeper relation between the two existence problems unlikely.

  3. Separability criteria via sets of mutually unbiased measurements

    PubMed Central

    Liu, Lu; Gao, Ting; Yan, Fengli

    2015-01-01

    Mutually unbiased measurements (MUMs) are generalized from the concept of mutually unbiased bases (MUBs) and include the complete set of MUBs as a special case, but they are superior to MUBs as they do not need to be rank one projectors. We investigate entanglement detection using sets of MUMs and derive separability criteria for multipartite qudit systems, arbitrary high-dimensional bipartite systems of a d1-dimensional subsystem and a d2-dimensional subsystem, and multipartite systems of multi-level subsystems. These criteria are of the advantages of more effective and wider application range than previous criteria. They provide experimental implementation in detecting entanglement of unknown quantum states. PMID:26278628

  4. Entanglement patterns in mutually unbiased basis sets

    SciTech Connect

    Lawrence, Jay

    2011-08-15

    A few simply stated rules govern the entanglement patterns that can occur in mutually unbiased basis sets (MUBs) and constrain the combinations of such patterns that can coexist in full complements of MUBs. We consider Hilbert spaces of prime power dimensions (D=p{sup N}), as realized by systems of N prime-state particles, where full complements of D+1 MUBs are known to exist, and we assume only that MUBs are eigenbases of generalized Pauli operators, without using any particular construction. The general rules include the following: (1) In any MUB, a given particle appears either in a pure state or totally entangled and (2) in any full MUB complement, each particle is pure in (p+1) bases (not necessarily the same ones) and totally entangled in the remaining (p{sup N}-p). It follows that the maximum number of product bases is p+1 and, when this number is realized, all remaining (p{sup N}-p) bases in the complement are characterized by the total entanglement of every particle. This ''standard distribution'' is inescapable for two-particle systems (of any p), where only product and generalized Bell bases are admissible MUB types. This and the following results generalize previous results for qubits [Phys. Rev. A 65. 032320 (2002); Phys. Rev. A 72, 062310 (2005)] and qutrits [Phys. Rev. A 70, 012302 (2004)], drawing particularly upon [Phys. Rev. A 72, 062310 (2005)]. With three particles there are three MUB types, and these may be combined in (p+2) different ways to form full complements. With N=4, there are 6 MUB types for p=2, but new MUB types become possible with larger p, and these are essential to realizing full complements. With this example, we argue that new MUB types that show new entanglement patterns should enter with every step in N and, also, when N is a prime plus 1, at a critical p value, p=N-1. Such MUBs should play critical roles in filling complements.

  5. Partially unbiased entangled bases

    NASA Astrophysics Data System (ADS)

    Kalev, A.; Khanna, F. C.; Revzen, M.

    2009-08-01

    In this contribution we group the operator basis for d2 -dimensional Hilbert space in a way that enables us to relate bases of entangled states with single-particle mutually unbiased state bases (MUB), each in dimensionality d . We utilize these sets of operators to show that an arbitrary density matrix for this d2 -dimensional Hilbert-space system is analyzed via d2+d+1 measurements, d2-d of which involve those entangled states that we associate with MUB of the d -dimensional single-particle constituents. The number d2+d+1 lies in the middle of the number of measurements needed for bipartite state reconstruction with two-particle MUB (d2+1) and those needed by single-particle MUB [(d2+1)2] .

  6. Quantum state tomography via mutually unbiased measurements in driven cavity QED systems

    NASA Astrophysics Data System (ADS)

    Yuan, Hao; Zhou, Zheng-Wei; Guo, Guang-Can

    2016-04-01

    We present a feasible proposal for quantum tomography of qubit and qutrit states via mutually unbiased measurements in dispersively coupled driven cavity QED systems. We first show that measurements in the mutually unbiased bases (MUBs) are practically implemented by projecting the detected states onto the computational basis after performing appropriate unitary transformations. The measurement outcomes can then be determined by detecting the steady-state transmission spectra (SSTS) of the driven cavity. It is found that all the measurement outcomes for each MUB (i.e., all the diagonal elements of the density matrix of each detected state) can be read out directly from only one kind of SSTS. In this way, we numerically demonstrate that the exemplified qubit and qutrit states can be reconstructed with the fidelities 0.952 and 0.961, respectively. Our proposal could be straightforwardly extended to other high-dimensional quantum systems provided that their MUBs exist.

  7. TOPICAL REVIEW: An angular momentum approach to quadratic Fourier transform, Hadamard matrices, Gauss sums, mutually unbiased bases, the unitary group and the Pauli group

    NASA Astrophysics Data System (ADS)

    Kibler, Maurice R.

    2009-09-01

    The construction of unitary operator bases in a finite-dimensional Hilbert space is reviewed through a nonstandard approach combining angular momentum theory and representation theory of SU(2). A single formula for the bases is obtained from a polar decomposition of SU(2) and is analyzed in terms of cyclic groups, quadratic Fourier transforms, Hadamard matrices and generalized Gauss sums. Weyl pairs, generalized Pauli operators and their application to the unitary group and the Pauli group naturally arise in this approach. Dedicated to the memory of Yurii Fedorovich Smirnov.

  8. Personalized recommendation based on unbiased consistence

    NASA Astrophysics Data System (ADS)

    Zhu, Xuzhen; Tian, Hui; Zhang, Ping; Hu, Zheng; Zhou, Tao

    2015-08-01

    Recently, in physical dynamics, mass-diffusion-based recommendation algorithms on bipartite network provide an efficient solution by automatically pushing possible relevant items to users according to their past preferences. However, traditional mass-diffusion-based algorithms just focus on unidirectional mass diffusion from objects having been collected to those which should be recommended, resulting in a biased causal similarity estimation and not-so-good performance. In this letter, we argue that in many cases, a user's interests are stable, and thus bidirectional mass diffusion abilities, no matter originated from objects having been collected or from those which should be recommended, should be consistently powerful, showing unbiased consistence. We further propose a consistence-based mass diffusion algorithm via bidirectional diffusion against biased causality, outperforming the state-of-the-art recommendation algorithms in disparate real data sets, including Netflix, MovieLens, Amazon and Rate Your Music.

  9. Mutual information-based facial expression recognition

    NASA Astrophysics Data System (ADS)

    Hazar, Mliki; Hammami, Mohamed; Hanêne, Ben-Abdallah

    2013-12-01

    This paper introduces a novel low-computation discriminative regions representation for expression analysis task. The proposed approach relies on interesting studies in psychology which show that most of the descriptive and responsible regions for facial expression are located around some face parts. The contributions of this work lie in the proposition of new approach which supports automatic facial expression recognition based on automatic regions selection. The regions selection step aims to select the descriptive regions responsible or facial expression and was performed using Mutual Information (MI) technique. For facial feature extraction, we have applied Local Binary Patterns Pattern (LBP) on Gradient image to encode salient micro-patterns of facial expressions. Experimental studies have shown that using discriminative regions provide better results than using the whole face regions whilst reducing features vector dimension.

  10. Mutually Unbiasedness between Maximally Entangled Bases and Unextendible Maximally Entangled Systems in C2⊗ C^{2k}

    NASA Astrophysics Data System (ADS)

    Zhang, Jun; Nan, Hua; Tao, Yuan-Hong; Fei, Shao-Ming

    2016-02-01

    The mutually unbiasedness between a maximally entangled basis (MEB) and an unextendible maximally entangled system (UMES) in the bipartite system C2⊗ C^{2k} (k>1) are introduced and discussed first in this paper. Then two mutually unbiased pairs of a maximally entangled basis and an unextendible maximally entangled system are constructed; lastly, explicit constructions are obtained for mutually unbiased MEB and UMES in C2⊗ C4 and C2⊗ C8, respectively.

  11. Spatial Mutual Information Based Hyperspectral Band Selection for Classification

    PubMed Central

    2015-01-01

    The amount of information involved in hyperspectral imaging is large. Hyperspectral band selection is a popular method for reducing dimensionality. Several information based measures such as mutual information have been proposed to reduce information redundancy among spectral bands. Unfortunately, mutual information does not take into account the spatial dependency between adjacent pixels in images thus reducing its robustness as a similarity measure. In this paper, we propose a new band selection method based on spatial mutual information. As validation criteria, a supervised classification method using support vector machine (SVM) is used. Experimental results of the classification of hyperspectral datasets show that the proposed method can achieve more accurate results. PMID:25918742

  12. Problem decomposition by mutual information and force-based clustering

    NASA Astrophysics Data System (ADS)

    Otero, Richard Edward

    The scale of engineering problems has sharply increased over the last twenty years. Larger coupled systems, increasing complexity, and limited resources create a need for methods that automatically decompose problems into manageable sub-problems by discovering and leveraging problem structure. The ability to learn the coupling (inter-dependence) structure and reorganize the original problem could lead to large reductions in the time to analyze complex problems. Such decomposition methods could also provide engineering insight on the fundamental physics driving problem solution. This work forwards the current state of the art in engineering decomposition through the application of techniques originally developed within computer science and information theory. The work describes the current state of automatic problem decomposition in engineering and utilizes several promising ideas to advance the state of the practice. Mutual information is a novel metric for data dependence and works on both continuous and discrete data. Mutual information can measure both the linear and non-linear dependence between variables without the limitations of linear dependence measured through covariance. Mutual information is also able to handle data that does not have derivative information, unlike other metrics that require it. The value of mutual information to engineering design work is demonstrated on a planetary entry problem. This study utilizes a novel tool developed in this work for planetary entry system synthesis. A graphical method, force-based clustering, is used to discover related sub-graph structure as a function of problem structure and links ranked by their mutual information. This method does not require the stochastic use of neural networks and could be used with any link ranking method currently utilized in the field. Application of this method is demonstrated on a large, coupled low-thrust trajectory problem. Mutual information also serves as the basis for an

  13. MR images denoising using DCT-based unbiased nonlocal means filter

    NASA Astrophysics Data System (ADS)

    Zheng, Xiuqing; Hu, Jinrong; Zhou, Jiuliu

    2013-03-01

    The non-local means (NLM) filter has been proven to be an efficient feature-preserved denoising method and can be applied to remove noise in the magnetic resonance (MR) images. To suppress noise more efficiently, we present a novel NLM filter by using a low-pass filtered and low dimensional version of neighborhood for calculating the similarity weights. The discrete cosine transform (DCT) is used as a smoothing kernel, allowing both improvements in similarity estimation and computational speed-up. Experimental results show that the proposed filter achieves better denoising performance in MR Images compared to others filters, such as recently proposed NLM filter and unbiased NLM (UNLM) filter.

  14. Networks in financial markets based on the mutual information rate

    NASA Astrophysics Data System (ADS)

    Fiedor, Paweł

    2014-05-01

    In the last few years there have been many efforts in econophysics studying how network theory can facilitate understanding of complex financial markets. These efforts consist mainly of the study of correlation-based hierarchical networks. This is somewhat surprising as the underlying assumptions of research looking at financial markets are that they are complex systems and thus behave in a nonlinear manner, which is confirmed by numerous studies, making the use of correlations which are inherently dealing with linear dependencies only baffling. In this paper we introduce a way to incorporate nonlinear dynamics and dependencies into hierarchical networks to study financial markets using mutual information and its dynamical extension: the mutual information rate. We show that this approach leads to different results than the correlation-based approach used in most studies, on the basis of 91 companies listed on the New York Stock Exchange 100 between 2003 and 2013, using minimal spanning trees and planar maximally filtered graphs.

  15. Autonomous navigation method based on unbiased minimum-variance estimation during Mars entry

    NASA Astrophysics Data System (ADS)

    Fu, Huimin; Yang, Yusong; Xiao, Qiang; Wu, Yunzhang; Zhang, Yongbo

    2015-03-01

    Accurate navigation systems are required for future pinpoint Mars landing missions. A radio ranging augmented inertial measurement unit (IMU) navigation system concept is considered for the guided atmospheric entry phase. The systematic errors associated to the radio ranging and inertial measurements, and the atmospheric mission uncertainties are considered to be unknown. This paper presents the extension of an unbiased minimum-variance (EUMV) filter of a radio beacon/IMU navigation system. In the presence of unknown dynamics inputs, the filter joins the system state and the unknown systematic error estimation of a stochastic nonlinear time-varying discrete system. 3-DOF simulation results show that the performances of the proposed navigation filter algorithm, 100 m estimated altitude error and 8 m/s estimated velocity error, fulfills the need of future pinpoint Mars landing missions.

  16. Least-bias state estimation with incomplete unbiased measurements

    NASA Astrophysics Data System (ADS)

    Řeháček, Jaroslav; Hradil, Zdeněk; Teo, Yong Siah; Sánchez-Soto, Luis L.; Ng, Hui Khoon; Chai, Jing Hao; Englert, Berthold-Georg

    2015-11-01

    Measuring incomplete sets of mutually unbiased bases constitutes a sensible approach to the tomography of high-dimensional quantum systems. The unbiased nature of these bases optimizes the uncertainty hypervolume. However, imposing unbiasedness on the probabilities for the unmeasured bases does not generally yield the estimator with the largest von Neumann entropy, a popular figure of merit in this context. Furthermore, this imposition typically leads to mock density matrices that are not even positive definite. This provides a strong argument against perfunctory applications of linear estimation strategies. We propose to use instead the physical state estimators that maximize the Shannon entropy of the unmeasured outcomes, which quantifies our lack of knowledge fittingly and gives physically meaningful statistical predictions.

  17. Predicting Genetic Values: A Kernel-Based Best Linear Unbiased Prediction With Genomic Data

    PubMed Central

    Ober, Ulrike; Erbe, Malena; Long, Nanye; Porcu, Emilio; Schlather, Martin; Simianer, Henner

    2011-01-01

    Genomic data provide a valuable source of information for modeling covariance structures, allowing a more accurate prediction of total genetic values (GVs). We apply the kriging concept, originally developed in the geostatistical context for predictions in the low-dimensional space, to the high-dimensional space spanned by genomic single nucleotide polymorphism (SNP) vectors and study its properties in different gene-action scenarios. Two different kriging methods [“universal kriging” (UK) and “simple kriging” (SK)] are presented. As a novelty, we suggest use of the family of Matérn covariance functions to model the covariance structure of SNP vectors. A genomic best linear unbiased prediction (GBLUP) is applied as a reference method. The three approaches are compared in a whole-genome simulation study considering additive, additive-dominance, and epistatic gene-action models. Predictive performance is measured in terms of correlation between true and predicted GVs and average true GVs of the individuals ranked best by prediction. We show that UK outperforms GBLUP in the presence of dominance and epistatic effects. In a limiting case, it is shown that the genomic covariance structure proposed by VanRaden (2008) can be considered as a covariance function with corresponding quadratic variogram. We also prove theoretically that if a specific linear relationship exists between covariance matrices for two linear mixed models, the GVs resulting from BLUP are linked by a scaling factor. Finally, the relation of kriging to other models is discussed and further options for modeling the covariance structure, which might be more appropriate in the genomic context, are suggested. PMID:21515573

  18. MIRA: mutual information-based reporter algorithm for metabolic networks

    PubMed Central

    Cicek, A. Ercument; Roeder, Kathryn; Ozsoyoglu, Gultekin

    2014-01-01

    Motivation: Discovering the transcriptional regulatory architecture of the metabolism has been an important topic to understand the implications of transcriptional fluctuations on metabolism. The reporter algorithm (RA) was proposed to determine the hot spots in metabolic networks, around which transcriptional regulation is focused owing to a disease or a genetic perturbation. Using a z-score-based scoring scheme, RA calculates the average statistical change in the expression levels of genes that are neighbors to a target metabolite in the metabolic network. The RA approach has been used in numerous studies to analyze cellular responses to the downstream genetic changes. In this article, we propose a mutual information-based multivariate reporter algorithm (MIRA) with the goal of eliminating the following problems in detecting reporter metabolites: (i) conventional statistical methods suffer from small sample sizes, (ii) as z-score ranges from minus to plus infinity, calculating average scores can lead to canceling out opposite effects and (iii) analyzing genes one by one, then aggregating results can lead to information loss. MIRA is a multivariate and combinatorial algorithm that calculates the aggregate transcriptional response around a metabolite using mutual information. We show that MIRA’s results are biologically sound, empirically significant and more reliable than RA. Results: We apply MIRA to gene expression analysis of six knockout strains of Escherichia coli and show that MIRA captures the underlying metabolic dynamics of the switch from aerobic to anaerobic respiration. We also apply MIRA to an Autism Spectrum Disorder gene expression dataset. Results indicate that MIRA reports metabolites that highly overlap with recently found metabolic biomarkers in the autism literature. Overall, MIRA is a promising algorithm for detecting metabolic drug targets and understanding the relation between gene expression and metabolic activity. Availability and

  19. Mutual information-based LPI optimisation for radar network

    NASA Astrophysics Data System (ADS)

    Shi, Chenguang; Zhou, Jianjiang; Wang, Fei; Chen, Jun

    2015-07-01

    Radar network can offer significant performance improvement for target detection and information extraction employing spatial diversity. For a fixed number of radars, the achievable mutual information (MI) for estimating the target parameters may extend beyond a predefined threshold with full power transmission. In this paper, an effective low probability of intercept (LPI) optimisation algorithm is presented to improve LPI performance for radar network. Based on radar network system model, we first provide Schleher intercept factor for radar network as an optimisation metric for LPI performance. Then, a novel LPI optimisation algorithm is presented, where for a predefined MI threshold, Schleher intercept factor for radar network is minimised by optimising the transmission power allocation among radars in the network such that the enhanced LPI performance for radar network can be achieved. The genetic algorithm based on nonlinear programming (GA-NP) is employed to solve the resulting nonconvex and nonlinear optimisation problem. Some simulations demonstrate that the proposed algorithm is valuable and effective to improve the LPI performance for radar network.

  20. Mutual information-based feature selection for radiomics

    NASA Astrophysics Data System (ADS)

    Oubel, Estanislao; Beaumont, Hubert; Iannessi, Antoine

    2016-03-01

    Background The extraction and analysis of image features (radiomics) is a promising field in the precision medicine era, with applications to prognosis, prediction, and response to treatment quantification. In this work, we present a mutual information - based method for quantifying reproducibility of features, a necessary step for qualification before their inclusion in big data systems. Materials and Methods Ten patients with Non-Small Cell Lung Cancer (NSCLC) lesions were followed over time (7 time points in average) with Computed Tomography (CT). Five observers segmented lesions by using a semi-automatic method and 27 features describing shape and intensity distribution were extracted. Inter-observer reproducibility was assessed by computing the multi-information (MI) of feature changes over time, and the variability of global extrema. Results The highest MI values were obtained for volume-based features (VBF). The lesion mass (M), surface to volume ratio (SVR) and volume (V) presented statistically significant higher values of MI than the rest of features. Within the same VBF group, SVR showed also the lowest variability of extrema. The correlation coefficient (CC) of feature values was unable to make a difference between features. Conclusions MI allowed to discriminate three features (M, SVR, and V) from the rest in a statistically significant manner. This result is consistent with the order obtained when sorting features by increasing values of extrema variability. MI is a promising alternative for selecting features to be considered as surrogate biomarkers in a precision medicine context.

  1. Estimation and classification by sigmoids based on mutual information

    NASA Technical Reports Server (NTRS)

    Baram, Yoram

    1994-01-01

    An estimate of the probability density function of a random vector is obtained by maximizing the mutual information between the input and the output of a feedforward network of sigmoidal units with respect to the input weights. Classification problems can be solved by selecting the class associated with the maximal estimated density. Newton's s method, applied to an estimated density, yields a recursive maximum likelihood estimator, consisting of a single internal layer of sigmoids, for a random variable or a random sequence. Applications to the diamond classification and to the prediction of a sun-spot process are demonstrated.

  2. Certainty relations, mutual entanglement, and nondisplaceable manifolds

    NASA Astrophysics Data System (ADS)

    Puchała, Zbigniew; Rudnicki, Łukasz; Chabuda, Krzysztof; Paraniak, Mikołaj; Życzkowski, Karol

    2015-09-01

    We derive explicit bounds for the average entropy characterizing measurements of a pure quantum state of size N in L orthogonal bases. Lower bounds lead to novel entropic uncertainty relations, while upper bounds allow us to formulate universal certainty relations. For L =2 the maximal average entropy saturates at logN because there exists a mutually coherent state, but certainty relations are shown to be nontrivial for L ≥3 measurements. In the case of a prime power dimension, N =pk , and the number of measurements L =N +1 , the upper bound for the average entropy becomes minimal for a collection of mutually unbiased bases. An analogous approach is used to study entanglement with respect to L different splittings of a composite system linked by bipartite quantum gates. We show that, for any two-qubit unitary gate U ∈U(4 ) there exist states being mutually separable or mutually entangled with respect to both splittings (related by U ) of the composite system. The latter statement follows from the fact that the real projective space R P3⊂C P3 is nondisplaceable by a unitary transformation. For L =3 splittings the maximal sum of L entanglement entropies is conjectured to achieve its minimum for a collection of three mutually entangled bases, formed by two mutually entangling gates.

  3. Building an unbiased sample of quiescent galaxies up to z=2.5 based on the Mg(UV) absorption index

    NASA Astrophysics Data System (ADS)

    Domínguez Sánchez, H.; Eliche-Moral, M. Carmen; Pérez-González, P. G.; Esquej, P.; Alcalde-Pampliega, B.; SHARDS Team

    2015-05-01

    Samples of ``red & dead" galaxies selected through traditional color-based techniques usually suffer from contamination by strongly dust obscured sources. We are using GTC/OSIRIS data from the SHARDS project on the GOODSN field to define unbiased samples of really quiescent massive galaxies at different redshifts up to z=2.5. By measuring the Mg(UV) absorption index in the pseudo-spectra of these galaxies, we intend to determine the redshift evolution of the characteristic age of their stellar populations to shed some light into their assembly epoch.

  4. School-Based Mutual Support Groups for Low-Income Parents.

    ERIC Educational Resources Information Center

    Simoni, Jane M.; Adelman, Howard S.

    1993-01-01

    School-based mutual support groups (MSGs) are proposed to enhance school involvement of parents from lower socioeconomic and ethnic minority backgrounds. A school-based MSG format is presented with results of a survey of interests from 62 parents (36 respondents and 26 nonrespondents) and a discussion of a pilot demonstration in 3 urban elementary…

  5. Managing Mutual Orientation in the Absence of Physical Copresence: Multiparty Voice-Based Chat Room Interaction

    ERIC Educational Resources Information Center

    Jenks, Christopher Joseph; Brandt, Adam

    2013-01-01

    This study investigates the interactional work involved in ratifying mutual participation in online, multiparty, voice-based chat rooms. The purpose of this article is to provide a preliminary sketch of how talk and participation is managed in a spoken communication environment that comprises interactants who are not physically copresent but are…

  6. Study on the technology of mutual alignment based on the four-quadrant photo electric detector

    NASA Astrophysics Data System (ADS)

    Hu, Ya-bin; Wang, Miao

    2015-11-01

    Panoramic stereo cameras and laser radars have their own coordinate system in the dynamic spatial sensing area and they have to determine the position relationship between each other through joint calibration. As using the traditional technology of mutual alignment based on the telescope cross wire is tedious and requires high operating skills, a new method of mutual alignment using lasers and four-quadrant photo electric detectors is provided after analyzing the working principle of four-quadrant photo electric detectors. Firstly make the laser beam irradiate the active area of the four-quadrant photo electric detector through coarse aiming. Then the center of a light spot offset relative to the center of the active area can be obtained according to the output voltage of four quadrants. The pose of two instruments can be adjusted properly to realize mutual alignment. The experimental results indicate that the alignment accuracy of four-quadrant detectors can meet the requirements of mutual alignment, which provides a new idea for joint calibration.

  7. A Secure ECC-based RFID Mutual Authentication Protocol to Enhance Patient Medication Safety.

    PubMed

    Jin, Chunhua; Xu, Chunxiang; Zhang, Xiaojun; Li, Fagen

    2016-01-01

    Patient medication safety is an important issue in patient medication systems. In order to prevent medication errors, integrating Radio Frequency Identification (RFID) technology into automated patient medication systems is required in hospitals. Based on RFID technology, such systems can provide medical evidence for patients' prescriptions and medicine doses, etc. Due to the mutual authentication between the medication server and the tag, RFID authentication scheme is the best choice for automated patient medication systems. In this paper, we present a RFID mutual authentication scheme based on elliptic curve cryptography (ECC) to enhance patient medication safety. Our scheme can achieve security requirements and overcome various attacks existing in other schemes. In addition, our scheme has better performance in terms of computational cost and communication overhead. Therefore, the proposed scheme is well suitable for patient medication systems. PMID:26573649

  8. Comparison of co-expression measures: mutual information, correlation, and model based indices

    PubMed Central

    2012-01-01

    Background Co-expression measures are often used to define networks among genes. Mutual information (MI) is often used as a generalized correlation measure. It is not clear how much MI adds beyond standard (robust) correlation measures or regression model based association measures. Further, it is important to assess what transformations of these and other co-expression measures lead to biologically meaningful modules (clusters of genes). Results We provide a comprehensive comparison between mutual information and several correlation measures in 8 empirical data sets and in simulations. We also study different approaches for transforming an adjacency matrix, e.g. using the topological overlap measure. Overall, we confirm close relationships between MI and correlation in all data sets which reflects the fact that most gene pairs satisfy linear or monotonic relationships. We discuss rare situations when the two measures disagree. We also compare correlation and MI based approaches when it comes to defining co-expression network modules. We show that a robust measure of correlation (the biweight midcorrelation transformed via the topological overlap transformation) leads to modules that are superior to MI based modules and maximal information coefficient (MIC) based modules in terms of gene ontology enrichment. We present a function that relates correlation to mutual information which can be used to approximate the mutual information from the corresponding correlation coefficient. We propose the use of polynomial or spline regression models as an alternative to MI for capturing non-linear relationships between quantitative variables. Conclusion The biweight midcorrelation outperforms MI in terms of elucidating gene pairwise relationships. Coupled with the topological overlap matrix transformation, it often leads to more significantly enriched co-expression modules. Spline and polynomial networks form attractive alternatives to MI in case of non-linear relationships

  9. Feature selection of fMRI data based on normalized mutual information and fisher discriminant ratio.

    PubMed

    Wang, Yanbin; Ji, Junzhong; Liang, Peipeng

    2016-03-17

    Pattern classification has been increasingly used in functional magnetic resonance imaging (fMRI) data analysis. However, the classification performance is restricted by the high dimensional property and noises of the fMRI data. In this paper, a new feature selection method (named as "NMI-F") was proposed by sequentially combining the normalized mutual information (NMI) and fisher discriminant ratio. In NMI-F, the normalized mutual information was firstly used to evaluate the relationships between features, and fisher discriminant ratio was then applied to calculate the importance of each feature involved. Two fMRI datasets (task-related and resting state) were used to test the proposed method. It was found that classification base on the NMI-F method could differentiate the brain cognitive and disease states effectively, and the proposed NMI-F method was prior to the other related methods. The current results also have implications to the future studies. PMID:27257882

  10. Artifact reduction in mutual-information-based CT-MR image registration

    NASA Astrophysics Data System (ADS)

    Wei, Mingxiu; Liu, Jundong; Liu, Junhong

    2004-05-01

    Abstract Mutual information (MI) is currently the most popular match metric in handling the registration problem for multi modality images. However, interpolation artifacts impose deteriorating effects to the accuracy and robustness of MI-based methods. This paper analyzes the generation mechanism of the artifacts inherent in linear partial volume interpolation (PVI) and shows that the mutual information resulted from PVI is a convex function within each voxel grid. We conclude that the generation of the artifacts is due to two facts: 1) linear interpolation causes the histogram bin values to change at a synchronized pace; 2) entropy computation function Σxlgx is convex. As a remedy we propose to use non-uniform interpolation functions as the interpolation kernels in estimating the joint histogram. Cubic B-splin and Gaussian interpolators are compared and we demonstrate the improvements via experiments on misalignments between CT/MR brain scans.

  11. Robust Feature Selection from Microarray Data Based on Cooperative Game Theory and Qualitative Mutual Information

    PubMed Central

    Mortazavi, Atiyeh; Moattar, Mohammad Hossein

    2016-01-01

    High dimensionality of microarray data sets may lead to low efficiency and overfitting. In this paper, a multiphase cooperative game theoretic feature selection approach is proposed for microarray data classification. In the first phase, due to high dimension of microarray data sets, the features are reduced using one of the two filter-based feature selection methods, namely, mutual information and Fisher ratio. In the second phase, Shapley index is used to evaluate the power of each feature. The main innovation of the proposed approach is to employ Qualitative Mutual Information (QMI) for this purpose. The idea of Qualitative Mutual Information causes the selected features to have more stability and this stability helps to deal with the problem of data imbalance and scarcity. In the third phase, a forward selection scheme is applied which uses a scoring function to weight each feature. The performance of the proposed method is compared with other popular feature selection algorithms such as Fisher ratio, minimum redundancy maximum relevance, and previous works on cooperative game based feature selection. The average classification accuracy on eleven microarray data sets shows that the proposed method improves both average accuracy and average stability compared to other approaches. PMID:27127506

  12. An Efficient and Adaptive Mutual Authentication Framework for Heterogeneous Wireless Sensor Network-Based Applications

    PubMed Central

    Kumar, Pardeep; Ylianttila, Mika; Gurtov, Andrei; Lee, Sang-Gon; Lee, Hoon-Jae

    2014-01-01

    Robust security is highly coveted in real wireless sensor network (WSN) applications since wireless sensors' sense critical data from the application environment. This article presents an efficient and adaptive mutual authentication framework that suits real heterogeneous WSN-based applications (such as smart homes, industrial environments, smart grids, and healthcare monitoring). The proposed framework offers: (i) key initialization; (ii) secure network (cluster) formation (i.e., mutual authentication and dynamic key establishment); (iii) key revocation; and (iv) new node addition into the network. The correctness of the proposed scheme is formally verified. An extensive analysis shows the proposed scheme coupled with message confidentiality, mutual authentication and dynamic session key establishment, node privacy, and message freshness. Moreover, the preliminary study also reveals the proposed framework is secure against popular types of attacks, such as impersonation attacks, man-in-the-middle attacks, replay attacks, and information-leakage attacks. As a result, we believe the proposed framework achieves efficiency at reasonable computation and communication costs and it can be a safeguard to real heterogeneous WSN applications. PMID:24521942

  13. An efficient and adaptive mutual authentication framework for heterogeneous wireless sensor network-based applications.

    PubMed

    Kumar, Pardeep; Ylianttila, Mika; Gurtov, Andrei; Lee, Sang-Gon; Lee, Hoon-Jae

    2014-01-01

    Robust security is highly coveted in real wireless sensor network (WSN) applications since wireless sensors' sense critical data from the application environment. This article presents an efficient and adaptive mutual authentication framework that suits real heterogeneous WSN-based applications (such as smart homes, industrial environments, smart grids, and healthcare monitoring). The proposed framework offers: (i) key initialization; (ii) secure network (cluster) formation (i.e., mutual authentication and dynamic key establishment); (iii) key revocation; and (iv) new node addition into the network. The correctness of the proposed scheme is formally verified. An extensive analysis shows the proposed scheme coupled with message confidentiality, mutual authentication and dynamic session key establishment, node privacy, and message freshness. Moreover, the preliminary study also reveals the proposed framework is secure against popular types of attacks, such as impersonation attacks, man-in-the-middle attacks, replay attacks, and information-leakage attacks. As a result, we believe the proposed framework achieves efficiency at reasonable computation and communication costs and it can be a safeguard to real heterogeneous WSN applications. PMID:24521942

  14. Weighted mutual information analysis substantially improves domain-based functional network models

    PubMed Central

    Shim, Jung Eun; Lee, Insuk

    2016-01-01

    Motivation: Functional protein–protein interaction (PPI) networks elucidate molecular pathways underlying complex phenotypes, including those of human diseases. Extrapolation of domain–domain interactions (DDIs) from known PPIs is a major domain-based method for inferring functional PPI networks. However, the protein domain is a functional unit of the protein. Therefore, we should be able to effectively infer functional interactions between proteins based on the co-occurrence of domains. Results: Here, we present a method for inferring accurate functional PPIs based on the similarity of domain composition between proteins by weighted mutual information (MI) that assigned different weights to the domains based on their genome-wide frequencies. Weighted MI outperforms other domain-based network inference methods and is highly predictive for pathways as well as phenotypes. A genome-scale human functional network determined by our method reveals numerous communities that are significantly associated with known pathways and diseases. Domain-based functional networks may, therefore, have potential applications in mapping domain-to-pathway or domain-to-phenotype associations. Availability and Implementation: Source code for calculating weighted mutual information based on the domain profile matrix is available from www.netbiolab.org/w/WMI. Contact: Insuklee@yonsei.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27207946

  15. The (w)hole survey: An unbiased sample study of transition disk candidates based on Spitzer catalogs

    NASA Astrophysics Data System (ADS)

    van der Marel, N.; Verhaar, B. W.; van Terwisga, S.; Merín, B.; Herczeg, G.; Ligterink, N. F. W.; van Dishoeck, E. F.

    2016-08-01

    Understanding disk evolution and dissipation is essential for studies of planet formation. Transition disks, i.e., disks with large dust cavities and gaps, are promising candidates of active evolution. About two dozen candidates, selected by their spectral energy distribution (SED), have been confirmed to have dust cavities through millimeter interferometric imaging, but this sample is biased toward the brightest disks. The Spitzer surveys of nearby low-mass star-forming regions have resulted in more than 4000 young stellar objects. Using color criteria, we selected a sample of ~150 candidates and an additional 40 candidates and known transition disks from the literature. The Spitzer data were complemented by new observations at longer wavelengths, including new JCMT and APEX submillimeter photometry, and WISE and Herschel-PACS mid- and far-infrared photometry. Furthermore, optical spectroscopy was obtained and stellar types were derived for 85% of the sample, including information from the literature. The SEDs were fit to a grid of RADMC-3D disk models with a limited number of parameters: disk mass, inner disk mass, scale height and flaring, and disk cavity radius, where the latter is the main parameter of interest. About 72% of our targets possibly have dust cavities based on the SED. The derived cavity sizes are consistent with imaging/modeling results in the literature, where available. Trends are found with Ldisk over L∗ ratio and stellar mass and a possible connection with exoplanet orbital radii. A comparison with a previous study where color observables are used reveals large overlap between their category of planet-forming disks and our transition disks with cavities. A large number of the new transition disk candidates are suitable for follow-up observations with ALMA. Full Tables 4, 5, A.1-A.3, C.1, and D.1 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc

  16. Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel.

    PubMed

    Graf, Erin H; Simmon, Keith E; Tardif, Keith D; Hymas, Weston; Flygare, Steven; Eilbeck, Karen; Yandell, Mark; Schlaberg, Robert

    2016-04-01

    Current infectious disease molecular tests are largely pathogen specific, requiring test selection based on the patient's symptoms. For many syndromes caused by a large number of viral, bacterial, or fungal pathogens, such as respiratory tract infections, this necessitates large panels of tests and has limited yield. In contrast, next-generation sequencing-based metagenomics can be used for unbiased detection of any expected or unexpected pathogen. However, barriers for its diagnostic implementation include incomplete understanding of analytical performance and complexity of sequence data analysis. We compared detection of known respiratory virus-positive (n= 42) and unselected (n= 67) pediatric nasopharyngeal swabs using an RNA sequencing (RNA-seq)-based metagenomics approach and Taxonomer, an ultrarapid, interactive, web-based metagenomics data analysis tool, with an FDA-cleared respiratory virus panel (RVP; GenMark eSensor). Untargeted metagenomics detected 86% of known respiratory virus infections, and additional PCR testing confirmed RVP results for only 2 (33%) of the discordant samples. In unselected samples, untargeted metagenomics had excellent agreement with the RVP (93%). In addition, untargeted metagenomics detected an additional 12 viruses that were either not targeted by the RVP or missed due to highly divergent genome sequences. Normalized viral read counts for untargeted metagenomics correlated with viral burden determined by quantitative PCR and showed high intrarun and interrun reproducibility. Partial or full-length viral genome sequences were generated in 86% of RNA-seq-positive samples, allowing assessment of antiviral resistance, strain-level typing, and phylogenetic relatedness. Overall, untargeted metagenomics had high agreement with a sensitive RVP, detected viruses not targeted by the RVP, and yielded epidemiologically and clinically valuable sequence information. PMID:26818672

  17. Interpretation of personal genome sequencing data in terms of disease ranks based on mutual information

    PubMed Central

    2015-01-01

    Background The rapid advances in genome sequencing technologies have resulted in an unprecedented number of genome variations being discovered in humans. However, there has been very limited coverage of interpretation of the personal genome sequencing data in terms of diseases. Methods In this paper we present the first computational analysis scheme for interpreting personal genome data by simultaneously considering the functional impact of damaging variants and curated disease-gene association data. This method is based on mutual information as a measure of the relative closeness between the personal genome and diseases. We hypothesize that a higher mutual information score implies that the personal genome is more susceptible to a particular disease than other diseases. Results The method was applied to the sequencing data of 50 acute myeloid leukemia (AML) patients in The Cancer Genome Atlas. The utility of associations between a disease and the personal genome was explored using data of healthy (control) people obtained from the 1000 Genomes Project. The ranks of the disease terms in the AML patient group were compared with those in the healthy control group using "Leukemia, Myeloid, Acute" (C04.557.337.539.550) as the corresponding MeSH disease term. The mutual information rank of the disease term was substantially higher in the AML patient group than in the healthy control group, which demonstrates that the proposed methodology can be successfully applied to infer associations between the personal genome and diseases. Conclusions Overall, the area under the receiver operating characteristics curve was significantly larger for the AML patient data than for the healthy controls. This methodology could contribute to consequential discoveries and explanations for mining personal genome sequencing data in terms of diseases, and have versatility with respect to genomic-based knowledge such as drug-gene and environmental-factor-gene interactions. PMID:26045178

  18. A Semidefinite Programming Based Search Strategy for Feature Selection with Mutual Information Measure.

    PubMed

    Naghibi, Tofigh; Hoffmann, Sarah; Pfister, Beat

    2015-08-01

    Feature subset selection, as a special case of the general subset selection problem, has been the topic of a considerable number of studies due to the growing importance of data-mining applications. In the feature subset selection problem there are two main issues that need to be addressed: (i) Finding an appropriate measure function than can be fairly fast and robustly computed for high-dimensional data. (ii) A search strategy to optimize the measure over the subset space in a reasonable amount of time. In this article mutual information between features and class labels is considered to be the measure function. Two series expansions for mutual information are proposed, and it is shown that most heuristic criteria suggested in the literature are truncated approximations of these expansions. It is well-known that searching the whole subset space is an NP-hard problem. Here, instead of the conventional sequential search algorithms, we suggest a parallel search strategy based on semidefinite programming (SDP) that can search through the subset space in polynomial time. By exploiting the similarities between the proposed algorithm and an instance of the maximum-cut problem in graph theory, the approximation ratio of this algorithm is derived and is compared with the approximation ratio of the backward elimination method. The experiments show that it can be misleading to judge the quality of a measure solely based on the classification accuracy, without taking the effect of the non-optimum search strategy into account. PMID:26352993

  19. Mutual Lewis acid-base interactions of cations and anions in ionic liquids.

    PubMed

    Holzweber, Markus; Lungwitz, Ralf; Doerfler, Denise; Spange, Stefan; Koel, Mihkel; Hutter, Herbert; Linert, Wolfgang

    2013-01-01

    Solute properties are known to be strongly influenced by solvent molecules due to solvation. This is due to mutual interaction as both the properties of the solute and of the solvent strongly depend on each other. The present paper is based on the idea that ionic liquids are cations solvated by anions and anions solvated by cations. To show this (in this system strongly pronounced) interaction the long time established donor-acceptor concept for solvents and ions in solution by Viktor Gutmann is extended to ionic liquids. A number of solvent parameters, such as the Kamlet-Abboud-Taft and the Dimroth-Reichardt E(T) scale for ionic liquids neglect this mutual influence, which, however, seems to be in fact necessary to get a proper description of ionic liquid properties. It is shown how strong such parameters vary when the influence of the counter ion is taken into account. Furthermore, acceptor and donor numbers for ionic liquids are presented. PMID:23180598

  20. A mutual-information-based mining method for marine abnormal association rules

    NASA Astrophysics Data System (ADS)

    Cunjin, Xue; Wanjiao, Song; Lijuan, Qin; Qing, Dong; Xiaoyang, Wen

    2015-03-01

    Long time series of remote sensing images are a key source of data for exploring large-scale marine abnormal association patterns, but pose significant challenges for traditional approaches to spatiotemporal analysis. This paper proposes a mutual-information-based quantitative association rule-mining algorithm (MIQarma) to address these challenges. MIQarma comprises three key steps. First, MIQarma calculates the asymmetrical mutual information between items with one scan of the database, and extracts pair-wise related items according to the user-specified information threshold. Second, a linking-pruning-generating recursive loop generates (k+1)-dimensional candidate association rules from k-dimensional rules on basis of the user-specified minimum support threshold, and this step is repeated until no more candidate association rules are generated. Finally, strong association rules are generated according to the user-specified minimum evaluation indicators. To demonstrate the feasibility and efficiency of MIQarma, we present two case studies: one considers performance analysis and the other identifies marine abnormal association relationships.

  1. An Assessment of Hermite Function Based Approximations of Mutual Information Applied to Independent Component Analysis

    NASA Astrophysics Data System (ADS)

    Sorensen, Julian

    2008-12-01

    At the heart of many ICA techniques is a nonparametric estimate of an information measure, usually via nonparametric density estimation, for example, kernel density estimation. While not as popular as kernel density estimators, orthogonal functions can be used for nonparametric density estimation (via a truncated series expansion whose coefficients are calculated from the observed data). While such estimators do not necessarily yield a valid density, which kernel density estimators do, they are faster to calculate than kernel density estimators, in particular for a modified version of Renyi's entropy of order 2. In this paper, we compare the performance of ICA using Hermite series based estimates of Shannon's and Renyi's mutual information, to that of Gaussian kernel based estimates. The comparisons also include ICA using the RADICAL estimate of Shannon's entropy and a FastICA estimate of neg-entropy.

  2. Power Spectrum and Mutual Information Analyses of DNA Base (Nucleotide) Sequences

    NASA Astrophysics Data System (ADS)

    Isohata, Yasuhiko; Hayashi, Masaki

    2003-03-01

    On the basis of the power spectrum analyses for the base (nucleotide) sequences of various genes, we have studied long-range correlations in total base sequences which are expressed as 1/fα, behaviour of the exponent α for the accumulated base sequences as well as periodicities at short range. In particular from the analysis of content rate distributions of α we have obtained the average value \\barα=0.40± 0.01 and \\barα=0.20± 0.01 for the human genes and S. cerevisiae genes, respectively. We have also performed the analyses using the mutual information function. We show that there exists a clear difference between the content rate distributions of correlation lengths for the sample human genes and the S. cerevisiae genes. We are led to a conjecture that the elongation of the correlation length in the base sequences of genes from the early eukaryote (S. cerevisiae) to the late eukaryote (human) should be the definite reflection of the evolutionary process.

  3. Registration of 2D to 3D joint images using phase-based mutual information

    NASA Astrophysics Data System (ADS)

    Dalvi, Rupin; Abugharbieh, Rafeef; Pickering, Mark; Scarvell, Jennie; Smith, Paul

    2007-03-01

    Registration of two dimensional to three dimensional orthopaedic medical image data has important applications particularly in the area of image guided surgery and sports medicine. Fluoroscopy to computer tomography (CT) registration is an important case, wherein digitally reconstructed radiographs derived from the CT data are registered to the fluoroscopy data. Traditional registration metrics such as intensity-based mutual information (MI) typically work well but often suffer from gross misregistration errors when the image to be registered contains a partial view of the anatomy visible in the target image. Phase-based MI provides a robust alternative similarity measure which, in addition to possessing the general robustness and noise immunity that MI provides, also employs local phase information in the registration process which makes it less susceptible to the aforementioned errors. In this paper, we propose using the complex wavelet transform for computing image phase information and incorporating that into a phase-based MI measure for image registration. Tests on a CT volume and 6 fluoroscopy images of the knee are presented. The femur and the tibia in the CT volume were individually registered to the fluoroscopy images using intensity-based MI, gradient-based MI and phase-based MI. Errors in the coordinates of fiducials present in the bone structures were used to assess the accuracy of the different registration schemes. Quantitative results demonstrate that the performance of intensity-based MI was the worst. Gradient-based MI performed slightly better, while phase-based MI results were the best consistently producing the lowest errors.

  4. Mutual information-based context template modeling for bitplane coding in remote sensing image compression

    NASA Astrophysics Data System (ADS)

    Zhang, Yongfei; Cao, Haiheng; Jiang, Hongxu; Li, Bo

    2016-04-01

    As remote sensing image applications are often characterized with limited bandwidth and high-quality demands, higher coding performance of remote sensing images are desirable. The embedded block coding with optimal truncation (EBCOT) is the fundamental part of JPEG2000 image compression standard. However, EBCOT only considers correlation within a sub-band and utilizes a context template of eight spatially neighboring coefficients in prediction. The existing optimization methods in literature using the current context template prove little performance improvements. To address this problem, this paper presents a new mutual information (MI)-based context template selection and modeling method. By further considering the correlation across the sub-bands, the potential prediction coefficients, including neighbors, far neighbors, parent and parent neighbors, are comprehensively examined and selected in such a manner that achieves a nice trade-off between the MI-based correlation criterion and the prediction complexity. Based on the selected context template, a high-order prediction model, which jointly considers the weight and the significance state of each coefficient, is proposed. Experimental results show that the proposed algorithm consistently outperforms the benchmark JPEG2000 standard and state-of-the-art algorithms in term of coding efficiency at a competitive computational cost, which makes it desirable in real-time compression applications, especially for remote sensing images.

  5. Mutual solubility of water and structural/positional isomers of N-alkylpyridinium-based ionic liquids.

    PubMed

    Freire, Mara G; Neves, Catarina M S S; Shimizu, Karina; Bernardes, Carlos E S; Marrucho, Isabel M; Coutinho, João A P; Canongia Lopes, José N; Rebelo, Luís Paulo N

    2010-12-01

    Despite many previous important contributions to the characterization of the liquid-liquid phase behavior of ionic liquids (ILs) plus water systems, a gap still exists as far as the effect of isomers (of ILs) is concerned. Therefore, in this work, a comprehensive study of the liquid-liquid equilibria between water and isomeric pyridinium-based ionic liquids has been performed. Atmospheric pressure mutual solubilities between water and pyridinium-based ionic liquids combined with the common anion bis[(trifluoromethyl)sulfonyl]imide were experimentally determined between (288.15 and 318.15) K. The main goal of this work is to study the isomeric effects on the pyridinium-based cation, namely, the structural and positional isomerism, as well as the alkyl side chain length. To the best of our knowledge, the influence of both structural and positional isomerism on the liquid-liquid behavior in ionic-liquid-water-containing systems is an unexplored field and is here assessed for the first time. Moreover, from the experimental solubility data, several infinite dilution molar thermodynamic functions of solution, namely, the Gibbs energy, the enthalpy, and the entropy, were estimated and discussed. In addition, aiming at gathering a broader picture of the underlying thermodynamic solvation phenomenon, molecular dynamics simulations were also carried out for the same experimental systems. PMID:21077599

  6. Fully Integrated Passive UHF RFID Tag for Hash-Based Mutual Authentication Protocol.

    PubMed

    Mikami, Shugo; Watanabe, Dai; Li, Yang; Sakiyama, Kazuo

    2015-01-01

    Passive radio-frequency identification (RFID) tag has been used in many applications. While the RFID market is expected to grow, concerns about security and privacy of the RFID tag should be overcome for the future use. To overcome these issues, privacy-preserving authentication protocols based on cryptographic algorithms have been designed. However, to the best of our knowledge, evaluation of the whole tag, which includes an antenna, an analog front end, and a digital processing block, that runs authentication protocols has not been studied. In this paper, we present an implementation and evaluation of a fully integrated passive UHF RFID tag that runs a privacy-preserving mutual authentication protocol based on a hash function. We design a single chip including the analog front end and the digital processing block. We select a lightweight hash function supporting 80-bit security strength and a standard hash function supporting 128-bit security strength. We show that when the lightweight hash function is used, the tag completes the protocol with a reader-tag distance of 10 cm. Similarly, when the standard hash function is used, the tag completes the protocol with the distance of 8.5 cm. We discuss the impact of the peak power consumption of the tag on the distance of the tag due to the hash function. PMID:26491714

  7. Fully Integrated Passive UHF RFID Tag for Hash-Based Mutual Authentication Protocol

    PubMed Central

    Mikami, Shugo; Watanabe, Dai; Li, Yang; Sakiyama, Kazuo

    2015-01-01

    Passive radio-frequency identification (RFID) tag has been used in many applications. While the RFID market is expected to grow, concerns about security and privacy of the RFID tag should be overcome for the future use. To overcome these issues, privacy-preserving authentication protocols based on cryptographic algorithms have been designed. However, to the best of our knowledge, evaluation of the whole tag, which includes an antenna, an analog front end, and a digital processing block, that runs authentication protocols has not been studied. In this paper, we present an implementation and evaluation of a fully integrated passive UHF RFID tag that runs a privacy-preserving mutual authentication protocol based on a hash function. We design a single chip including the analog front end and the digital processing block. We select a lightweight hash function supporting 80-bit security strength and a standard hash function supporting 128-bit security strength. We show that when the lightweight hash function is used, the tag completes the protocol with a reader-tag distance of 10 cm. Similarly, when the standard hash function is used, the tag completes the protocol with the distance of 8.5 cm. We discuss the impact of the peak power consumption of the tag on the distance of the tag due to the hash function. PMID:26491714

  8. An ensemble method based on uninformative variable elimination and mutual information for spectral multivariate calibration

    NASA Astrophysics Data System (ADS)

    Tan, Chao; Wang, Jinyue; Wu, Tong; Qin, Xin; Li, Menglong

    2010-12-01

    Based on the combination of uninformative variable elimination (UVE), bootstrap and mutual information (MI), a simple ensemble algorithm, named ESPLS, is proposed for spectral multivariate calibration (MVC). In ESPLS, those uninformative variables are first removed; and then a preparatory training set is produced by bootstrap, on which a MI spectrum of retained variables is calculated. The variables that exhibit higher MI than a defined threshold form a subspace on which a candidate partial least-squares (PLS) model is constructed. This process is repeated. After a number of candidate models are obtained, a small part of models is picked out to construct an ensemble model by simple/weighted average. Four near/mid-infrared (NIR/MIR) spectral datasets concerning the determination of six components are used to verify the proposed ESPLS. The results indicate that ESPLS is superior to UVEPLS and its combination with MI-based variable selection (SPLS) in terms of both the accuracy and robustness. Besides, from the perspective of end-users, ESPLS does not increase the complexity of a calibration when enhancing its performance.

  9. Comparison and evaluation of joint histogram estimation methods for mutual information based image registration

    NASA Astrophysics Data System (ADS)

    Liang, Yongfang; Chen, Hua-mei

    2005-04-01

    Joint histogram is the only quantity required to calculate the mutual information (MI) between two images. For MI based image registration, joint histograms are often estimated through linear interpolation or partial volume interpolation (PVI). It has been pointed out that both methods may result in a phenomenon known as interpolation induced artifacts. In this paper, we implemented a wide range of interpolation/approximation kernels for joint histogram estimation. Some kernels are nonnegative. In this case, these kernels are applied in two ways as the linear kernel is applied in linear interpolation and PVI. In addition, we implemented two other joint histogram estimation methods devised to overcome the interpolation artifact problem. They are nearest neighbor interpolation with jittered sampling with/without histogram blurring and data resampling. We used the clinical data obtained from Vanderbilt University for all of the experiments. The objective of this study is to perform a comprehensive comparison and evaluation of different joint histogram estimation methods for MI based image registration in terms of artifacts reduction and registration accuracy.

  10. Mutual information image registration based on improved bee evolutionary genetic algorithm

    NASA Astrophysics Data System (ADS)

    Xu, Gang; Tu, Jingzhi

    2009-07-01

    In recent years, the mutual information is regarded as a more efficient similarity metrics in the image registration. According to the features of mutual information image registration, the Bee Evolution Genetic Algorithm (BEGA) is chosen for optimizing parameters, which imitates swarm mating. Besides, we try our best adaptively set the initial parameters to improve the BEGA. The programming result shows the wonderful precision of the algorithm.

  11. Research on non rigid registration algorithm of DCE-MRI based on mutual information and optical flow

    NASA Astrophysics Data System (ADS)

    Yu, Shihua; Wang, Rui; Wang, Kaiyu; Xi, Mengmeng; Zheng, Jiashuo; Liu, Hui

    2015-07-01

    Image matching plays a very important role in the field of medical image, while the two image registration methods based on the mutual information and the optical flow are very effective. The experimental results show that the two methods have their prominent advantages. The method based on mutual information is good for the overall displacement, while the method based on optical flow is very sensitive to small deformation. In the breast DCE-MRI images studied in this paper, there is not only overall deformation caused by the patient, but also non rigid small deformation caused by respiratory deformation. In view of the above situation, the single-image registration algorithms cannot meet the actual needs of complex situations. After a comprehensive analysis to the advantages and disadvantages of these two methods, this paper proposes a registration algorithm of combining mutual information with optical flow field, and applies subtraction images of the reference image and the floating image as the main criterion to evaluate the registration effect, at the same time, applies the mutual information between image sequence values as auxiliary criterion. With the test of the example, this algorithm has obtained a better accuracy and reliability in breast DCE-MRI image sequences.

  12. IR and visual image registration based on mutual information and PSO-Powell algorithm

    NASA Astrophysics Data System (ADS)

    Zhuang, Youwen; Gao, Kun; Miu, Xianghu

    2014-11-01

    Infrared and visual image registration has a wide application in the fields of remote sensing and military. Mutual information (MI) has proved effective and successful in infrared and visual image registration process. To find the most appropriate registration parameters, optimal algorithms, such as Particle Swarm Optimization (PSO) algorithm or Powell search method, are often used. The PSO algorithm has strong global search ability and search speed is fast at the beginning, while the weakness is low search performance in late search stage. In image registration process, it often takes a lot of time to do useless search and solution's precision is low. Powell search method has strong local search ability. However, the search performance and time is more sensitive to initial values. In image registration, it is often obstructed by local maximum and gets wrong results. In this paper, a novel hybrid algorithm, which combined PSO algorithm and Powell search method, is proposed. It combines both advantages that avoiding obstruction caused by local maximum and having higher precision. Firstly, using PSO algorithm gets a registration parameter which is close to global minimum. Based on the result in last stage, the Powell search method is used to find more precision registration parameter. The experimental result shows that the algorithm can effectively correct the scale, rotation and translation additional optimal algorithm. It can be a good solution to register infrared difference of two images and has a greater performance on time and precision than traditional and visible images.

  13. Characteristics analysis of acupuncture electroencephalograph based on mutual information Lempel—Ziv complexity

    NASA Astrophysics Data System (ADS)

    Luo, Xi-Liu; Wang, Jiang; Han, Chun-Xiao; Deng, Bin; Wei, Xi-Le; Bian, Hong-Rui

    2012-02-01

    As a convenient approach to the characterization of cerebral cortex electrical information, electroencephalograph (EEG) has potential clinical application in monitoring the acupuncture effects. In this paper, a method composed of the mutual information method and Lempel—Ziv complexity method (MILZC) is proposed to investigate the effects of acupuncture on the complexity of information exchanges between different brain regions based on EEGs. In the experiments, eight subjects are manually acupunctured at ‘Zusanli’ acupuncture point (ST-36) with different frequencies (i.e., 50, 100, 150, and 200 times/min) and the EEGs are recorded simultaneously. First, MILZC values are compared in general. Then average brain connections are used to quantify the effectiveness of acupuncture under the above four frequencies. Finally, significance index P values are used to study the spatiality of the acupuncture effect on the brain. Three main findings are obtained: (i) MILZC values increase during the acupuncture; (ii) manual acupunctures (MAs) with 100 times/min and 150 times/min are more effective than with 50 times/min and 200 times/min; (iii) contralateral hemisphere activation is more prominent than ipsilateral hemisphere's. All these findings suggest that acupuncture contributes to the increase of brain information exchange complexity and the MILZC method can successfully describe these changes.

  14. A mutual information-based metric for evaluation of fMRI data-processing approaches.

    PubMed

    Afshin-Pour, Babak; Soltanian-Zadeh, Hamid; Hossein-Zadeh, Gholam-Ali; Grady, Cheryl L; Strother, Stephen C

    2011-05-01

    We propose a novel approach for evaluating the performance of activation detection in real (experimental) datasets using a new mutual information (MI)-based metric and compare its sensitivity to several existing performance metrics in both simulated and real datasets. The proposed approach is based on measuring the approximate MI between the fMRI time-series of a validation dataset and a calculated activation map (thresholded label map or continuous map) from an independent training dataset. The MI metric is used to measure the amount of information preserved during the extraction of an activation map from experimentally related fMRI time-series. The processing method that preserves maximal information between the maps and related time-series is proposed to be superior. The results on simulation datasets for multiple analysis models are consistent with the results of ROC curves, but are shown to have lower information content than for real datasets, limiting their generalizability. In real datasets for group analyses using the general linear model (GLM; FSL4 and SPM5), we show that MI values are (1) larger for groups of 15 versus 10 subjects and (2) more sensitive measures than reproducibility (for continuous maps) or Jaccard overlap metrics (for thresholded maps). We also show that (1) for an increasing fraction of nominally active voxels, both MI and false discovery rate (FDR) increase, and (2) at a fixed FDR, GLM using FSL4 tends to extract more voxels and more information than SPM5 using the default processing techniques in each package. PMID:20533565

  15. New direction of arrival estimation of coherent signals based on reconstructing matrix under unknown mutual coupling

    NASA Astrophysics Data System (ADS)

    Guo, Rui; Li, Weixing; Zhang, Yue; Chen, Zengping

    2016-01-01

    A direction of arrival (DOA) estimation algorithm for coherent signals in the presence of unknown mutual coupling is proposed. A group of auxiliary sensors in a uniform linear array are applied to eliminate the effects on the orthogonality of subspaces brought by mutual coupling. Then, a Toeplitz matrix, whose rank is independent of the coherency between impinging signals, is reconstructed to eliminate the rank loss of the spatial covariance matrix. Therefore, the signal and noise subspaces can be estimated properly. This method can estimate the DOAs of coherent signals under unknown mutual coupling accurately without any iteration and calibration sources. It has a low computational burden and high accuracy. Simulation results demonstrate the effectiveness of the algorithm.

  16. School-Based Mutual Support Groups for Parents: An Intervention Guidebook.

    ERIC Educational Resources Information Center

    Simoni, Jane M.

    This handbook focuses on steps and tasks related to establishing mutual support groups for parents in a school setting. A sequential approach is described that involves: working within the school to get started; recruiting members; training parents how to run their own meetings; and offering off-site consultation as requested. The first section…

  17. On the feature selection criterion based on an approximation of multidimensional mutual information.

    PubMed

    Balagani, Kiran S; Phoha, Vir V

    2010-07-01

    We derive the feature selection criterion presented in [CHECK END OF SENTENCE] and [CHECK END OF SENTENCE] from the multidimensional mutual information between features and the class. Our derivation: 1) specifies and validates the lower-order dependency assumptions of the criterion and 2) mathematically justifies the utility of the criterion by relating it to Bayes classification error. PMID:20489237

  18. TELEsarPHONE: Mutual Telexistence Master-Slave Communication System Based on Retroreflective Projection Technology

    NASA Astrophysics Data System (ADS)

    Tachi, Susumu; Kawakami, Naoki; Nii, Hideaki; Watanabe, Kouichi; Minamizawa, Kouta

    TELEsarPHONE is a conceptual prototype of a mutual telexistence system, designed for face-to-face telecommunication via robots. Because of the development of telexistence technology, we can acquire a feeling that we are present in several actual remote places using remote robots as our surrogates and can work and act freely there. However, people in the place where someone telexists using a robot see only the robot, and they cannot feel the existence of the telexisting person. Mutual telexistence aims to solve this problem so that the existence of a telexisting person (visitor) is apparent to the people in the remote environment by providing mutual sensations of presence. On the basis of the concept of mutual telexistence, we have designed and developed a prototype of a telexistence master-slave system for remote communication by applying retroreflective projection technology. In the TELEsarPHONE system, the face and chest of the slave robot TELESAR II are covered by retroreflective material. To provide the feeling of existence, the real-time image of the visitor is projected onto the robot so that people can see the visitor in real time.

  19. School-Based Mutual Support Groups (For Parents, Staff, Older Students). A Technical Aid Packet.

    ERIC Educational Resources Information Center

    Simoni, Jane, Comp.

    Mutual support groups in schools can be developed as part of strategies to provide assistance for parents or other family members, students, or school staff. These groups can also be used to provide support for newcomers and others in periods of transition. This technical aid packet describes the process as used with parents, but the procedures…

  20. Unbiased Cell-based Screening in a Neuronal Cell Model of Batten Disease Highlights an Interaction between Ca2+ Homeostasis, Autophagy, and CLN3 Protein Function*

    PubMed Central

    Chandrachud, Uma; Walker, Mathew W.; Simas, Alexandra M.; Heetveld, Sasja; Petcherski, Anton; Klein, Madeleine; Oh, Hyejin; Wolf, Pavlina; Zhao, Wen-Ning; Norton, Stephanie; Haggarty, Stephen J.; Lloyd-Evans, Emyr; Cotman, Susan L.

    2015-01-01

    Abnormal accumulation of undigested macromolecules, often disease-specific, is a major feature of lysosomal and neurodegenerative disease and is frequently attributed to defective autophagy. The mechanistic underpinnings of the autophagy defects are the subject of intense research, which is aided by genetic disease models. To gain an improved understanding of the pathways regulating defective autophagy specifically in juvenile neuronal ceroid lipofuscinosis (JNCL or Batten disease), a neurodegenerative disease of childhood, we developed and piloted a GFP-microtubule-associated protein 1 light chain 3 (GFP-LC3) screening assay to identify, in an unbiased fashion, genotype-sensitive small molecule autophagy modifiers, employing a JNCL neuronal cell model bearing the most common disease mutation in CLN3. Thapsigargin, a sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) Ca2+ pump inhibitor, reproducibly displayed significantly more activity in the mouse JNCL cells, an effect that was also observed in human-induced pluripotent stem cell-derived JNCL neural progenitor cells. The mechanism of thapsigargin sensitivity was Ca2+-mediated, and autophagosome accumulation in JNCL cells could be reversed by Ca2+ chelation. Interrogation of intracellular Ca2+ handling highlighted alterations in endoplasmic reticulum, mitochondrial, and lysosomal Ca2+ pools and in store-operated Ca2+ uptake in JNCL cells. These results further support an important role for the CLN3 protein in intracellular Ca2+ handling and in autophagic pathway flux and establish a powerful new platform for therapeutic screening. PMID:25878248

  1. Unbiased Cell-based Screening in a Neuronal Cell Model of Batten Disease Highlights an Interaction between Ca2+ Homeostasis, Autophagy, and CLN3 Protein Function.

    PubMed

    Chandrachud, Uma; Walker, Mathew W; Simas, Alexandra M; Heetveld, Sasja; Petcherski, Anton; Klein, Madeleine; Oh, Hyejin; Wolf, Pavlina; Zhao, Wen-Ning; Norton, Stephanie; Haggarty, Stephen J; Lloyd-Evans, Emyr; Cotman, Susan L

    2015-06-01

    Abnormal accumulation of undigested macromolecules, often disease-specific, is a major feature of lysosomal and neurodegenerative disease and is frequently attributed to defective autophagy. The mechanistic underpinnings of the autophagy defects are the subject of intense research, which is aided by genetic disease models. To gain an improved understanding of the pathways regulating defective autophagy specifically in juvenile neuronal ceroid lipofuscinosis (JNCL or Batten disease), a neurodegenerative disease of childhood, we developed and piloted a GFP-microtubule-associated protein 1 light chain 3 (GFP-LC3) screening assay to identify, in an unbiased fashion, genotype-sensitive small molecule autophagy modifiers, employing a JNCL neuronal cell model bearing the most common disease mutation in CLN3. Thapsigargin, a sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA) Ca(2+) pump inhibitor, reproducibly displayed significantly more activity in the mouse JNCL cells, an effect that was also observed in human-induced pluripotent stem cell-derived JNCL neural progenitor cells. The mechanism of thapsigargin sensitivity was Ca(2+)-mediated, and autophagosome accumulation in JNCL cells could be reversed by Ca(2+) chelation. Interrogation of intracellular Ca(2+) handling highlighted alterations in endoplasmic reticulum, mitochondrial, and lysosomal Ca(2+) pools and in store-operated Ca(2+) uptake in JNCL cells. These results further support an important role for the CLN3 protein in intracellular Ca(2+) handling and in autophagic pathway flux and establish a powerful new platform for therapeutic screening. PMID:25878248

  2. Motion Estimation Based on Mutual Information and Adaptive Multi-Scale Thresholding.

    PubMed

    Xu, Rui; Taubman, David; Naman, Aous Thabit

    2016-03-01

    This paper proposes a new method of calculating a matching metric for motion estimation. The proposed method splits the information in the source images into multiple scale and orientation subbands, reduces the subband values to a binary representation via an adaptive thresholding algorithm, and uses mutual information to model the similarity of corresponding square windows in each image. A moving window strategy is applied to recover a dense estimated motion field whose properties are explored. The proposed matching metric is a sum of mutual information scores across space, scale, and orientation. This facilitates the exploitation of information diversity in the source images. Experimental comparisons are performed amongst several related approaches, revealing that the proposed matching metric is better able to exploit information diversity, generating more accurate motion fields. PMID:26742132

  3. Ant colony optimization image registration algorithm based on wavelet transform and mutual information

    NASA Astrophysics Data System (ADS)

    Zhang, Hong; Sun, Yanfeng; Zhai, Bing; Wang, Yiding

    2013-07-01

    This paper studies on the image registration of the medical images. Wavelet transform is adopted to decompose the medical images because the resolution of the medical image is high and the computational amount of the registration is large. Firstly, the low frequency sub-images are matched. Then source images are matched. The image registration was fulfilled by the ant colony optimization algorithm to search the extremum of the mutual information. The experiment result demonstrates the proposed approach can not only reduce calculation amount, but also skip from the local extremum during optimization process, and search the optimization value.

  4. A Method for Evaluating Tuning Functions of Single Neurons based on Mutual Information Maximization

    NASA Astrophysics Data System (ADS)

    Brostek, Lukas; Eggert, Thomas; Ono, Seiji; Mustari, Michael J.; Büttner, Ulrich; Glasauer, Stefan

    2011-03-01

    We introduce a novel approach for evaluation of neuronal tuning functions, which can be expressed by the conditional probability of observing a spike given any combination of independent variables. This probability can be estimated out of experimentally available data. By maximizing the mutual information between the probability distribution of the spike occurrence and that of the variables, the dependence of the spike on the input variables is maximized as well. We used this method to analyze the dependence of neuronal activity in cortical area MSTd on signals related to movement of the eye and retinal image movement.

  5. Mutual Adaptaion in Action

    ERIC Educational Resources Information Center

    Siskin, Leslie Santee

    2016-01-01

    Building on an expanded concept of mutual adaptation, this chapter explores a distinctive and successful aspect of International Baccalaureate's effort to scale up, as they moved to expand their programs and support services in Title I schools. Based on a three-year, mixed-methods study, it offers a case where we see not only local adaptations…

  6. Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel® Xeon Phi™ Coprocessor.

    PubMed

    Misra, Sanchit; Pamnany, Kiran; Aluru, Srinivas

    2015-01-01

    Construction of whole-genome networks from large-scale gene expression data is an important problem in systems biology. While several techniques have been developed, most cannot handle network reconstruction at the whole-genome scale, and the few that can, require large clusters. In this paper, we present a solution on the Intel Xeon Phi coprocessor, taking advantage of its multi-level parallelism including many x86-based cores, multiple threads per core, and vector processing units. We also present a solution on the Intel® Xeon® processor. Our solution is based on TINGe, a fast parallel network reconstruction technique that uses mutual information and permutation testing for assessing statistical significance. We demonstrate the first ever inference of a plant whole genome regulatory network on a single chip by constructing a 15,575 gene network of the plant Arabidopsis thaliana from 3,137 microarray experiments in only 22 minutes. In addition, our optimization for parallelizing mutual information computation on the Intel Xeon Phi coprocessor holds out lessons that are applicable to other domains. PMID:26451815

  7. Unbiased estimators for spatial distribution functions of classical fluids.

    PubMed

    Adib, Artur B; Jarzynski, Christopher

    2005-01-01

    We use a statistical-mechanical identity closely related to the familiar virial theorem, to derive unbiased estimators for spatial distribution functions of classical fluids. In particular, we obtain estimators for both the fluid density rho(r) in the vicinity of a fixed solute and the pair correlation g(r) of a homogeneous classical fluid. We illustrate the utility of our estimators with numerical examples, which reveal advantages over traditional histogram-based methods of computing such distributions. PMID:15638649

  8. An advanced temporal credential-based security scheme with mutual authentication and key agreement for wireless sensor networks.

    PubMed

    Li, Chun-Ta; Weng, Chi-Yao; Lee, Cheng-Chi

    2013-01-01

    Wireless sensor networks (WSNs) can be quickly and randomly deployed in any harsh and unattended environment and only authorized users are allowed to access reliable sensor nodes in WSNs with the aid of gateways (GWNs). Secure authentication models among the users, the sensor nodes and GWN are important research issues for ensuring communication security and data privacy in WSNs. In 2013, Xue et al. proposed a temporal-credential-based mutual authentication and key agreement scheme for WSNs. However, in this paper, we point out that Xue et al.'s scheme cannot resist stolen-verifier, insider, off-line password guessing, smart card lost problem and many logged-in users' attacks and these security weaknesses make the scheme inapplicable to practical WSN applications. To tackle these problems, we suggest a simple countermeasure to prevent proposed attacks while the other merits of Xue et al.'s authentication scheme are left unchanged. PMID:23887085

  9. An Advanced Temporal Credential-Based Security Scheme with Mutual Authentication and Key Agreement for Wireless Sensor Networks

    PubMed Central

    Li, Chun-Ta; Weng, Chi-Yao; Lee, Cheng-Chi

    2013-01-01

    Wireless sensor networks (WSNs) can be quickly and randomly deployed in any harsh and unattended environment and only authorized users are allowed to access reliable sensor nodes in WSNs with the aid of gateways (GWNs). Secure authentication models among the users, the sensor nodes and GWN are important research issues for ensuring communication security and data privacy in WSNs. In 2013, Xue et al. proposed a temporal-credential-based mutual authentication and key agreement scheme for WSNs. However, in this paper, we point out that Xue et al.'s scheme cannot resist stolen-verifier, insider, off-line password guessing, smart card lost problem and many logged-in users' attacks and these security weaknesses make the scheme inapplicable to practical WSN applications. To tackle these problems, we suggest a simple countermeasure to prevent proposed attacks while the other merits of Xue et al.'s authentication scheme are left unchanged. PMID:23887085

  10. Efficient and Unbiased Estimation of Population Size.

    PubMed

    Cruz, Marcos; Gómez, Domingo; Cruz-Orive, Luis M

    2015-01-01

    Population sizing from still aerial pictures is of wide applicability in ecological and social sciences. The problem is long standing because current automatic detection and counting algorithms are known to fail in most cases, and exhaustive manual counting is tedious, slow, difficult to verify and unfeasible for large populations. An alternative is to multiply population density with some reference area but, unfortunately, sampling details, handling of edge effects, etc., are seldom described. For the first time we address the problem using principles of geometric sampling. These principles are old and solid, but largely unknown outside the areas of three dimensional microscopy and stereology. Here we adapt them to estimate the size of any population of individuals lying on an essentially planar area, e.g. people, animals, trees on a savanna, etc. The proposed design is unbiased irrespective of population size, pattern, perspective artifacts, etc. The implementation is very simple-it is based on the random superimposition of coarse quadrat grids. Also, an objective error assessment is often lacking. For the latter purpose the quadrat counts are often assumed to be independent. We demonstrate that this approach can perform very poorly, and we propose (and check via Monte Carlo resampling) a new theoretical error prediction formula. As far as efficiency, counting about 50 (100) individuals in 20 quadrats, can yield relative standard errors of about 8% (5%) in typical cases. This fact effectively breaks the barrier hitherto imposed by the current lack of automatic face detection algorithms, because semiautomatic sampling and manual counting becomes an attractive option. PMID:26535587

  11. Efficient and Unbiased Estimation of Population Size

    PubMed Central

    Cruz, Marcos; Gómez, Domingo; Cruz-Orive, Luis M.

    2015-01-01

    Population sizing from still aerial pictures is of wide applicability in ecological and social sciences. The problem is long standing because current automatic detection and counting algorithms are known to fail in most cases, and exhaustive manual counting is tedious, slow, difficult to verify and unfeasible for large populations. An alternative is to multiply population density with some reference area but, unfortunately, sampling details, handling of edge effects, etc., are seldom described. For the first time we address the problem using principles of geometric sampling. These principles are old and solid, but largely unknown outside the areas of three dimensional microscopy and stereology. Here we adapt them to estimate the size of any population of individuals lying on an essentially planar area, e.g. people, animals, trees on a savanna, etc. The proposed design is unbiased irrespective of population size, pattern, perspective artifacts, etc. The implementation is very simple—it is based on the random superimposition of coarse quadrat grids. Also, an objective error assessment is often lacking. For the latter purpose the quadrat counts are often assumed to be independent. We demonstrate that this approach can perform very poorly, and we propose (and check via Monte Carlo resampling) a new theoretical error prediction formula. As far as efficiency, counting about 50 (100) individuals in 20 quadrats, can yield relative standard errors of about 8% (5%) in typical cases. This fact effectively breaks the barrier hitherto imposed by the current lack of automatic face detection algorithms, because semiautomatic sampling and manual counting becomes an attractive option. PMID:26535587

  12. Unbiased selective isolation of protein N-terminal peptides from complex proteome samples using phospho tagging (PTAG) and TiO(2)-based depletion.

    PubMed

    Mommen, Geert P M; van de Waterbeemd, Bas; Meiring, Hugo D; Kersten, Gideon; Heck, Albert J R; de Jong, Ad P J M

    2012-09-01

    A positional proteomics strategy for global N-proteome analysis is presented based on phospho tagging (PTAG) of internal peptides followed by depletion by titanium dioxide (TiO(2)) affinity chromatography. Therefore, N-terminal and lysine amino groups are initially completely dimethylated with formaldehyde at the protein level, after which the proteins are digested and the newly formed internal peptides modified with the PTAG reagent glyceraldhyde-3-phosphate in nearly perfect yields (> 99%). The resulting phosphopeptides are depleted through binding onto TiO(2), keeping exclusively a set of N-acetylated and/or N-dimethylated terminal peptides for analysis by liquid chromatography-tandem MS. Analysis of peptides derivatized with differentially labeled isotopic analogs of the PTAG reagent revealed a high depletion efficiency (> 95%). The method enabled identification of 753 unique N-terminal peptides (428 proteins) in N. meningitidis and 928 unique N-terminal peptides (572 proteins) in S. cerevisiae. These included verified neo-N termini from subcellular-relocalized membrane and mitochondrial proteins. The presented PTAG approach is therefore a novel, versatile, and robust method for mass spectrometry-based N-proteome analysis and identification of protease-generated cleavage products. PMID:22729381

  13. Mutual information-based template matching scheme for detection of breast masses: from mammography to digital breast tomosynthesis.

    PubMed

    Mazurowski, Maciej A; Lo, Joseph Y; Harrawood, Brian P; Tourassi, Georgia D

    2011-10-01

    Development of a computational decision aid for a new medical imaging modality typically is a long and complicated process. It consists of collecting data in the form of images and annotations, development of image processing and pattern recognition algorithms for analysis of the new images and finally testing of the resulting system. Since new imaging modalities are developed more rapidly than ever before, any effort for decreasing the time and cost of this development process could result in maximizing the benefit of the new imaging modality to patients by making the computer aids quickly available to radiologists that interpret the images. In this paper, we make a step in this direction and investigate the possibility of translating the knowledge about the detection problem from one imaging modality to another. Specifically, we present a computer-aided detection (CAD) system for mammographic masses that uses a mutual information-based template matching scheme with intelligently selected templates. We presented principles of template matching with mutual information for mammography before. In this paper, we present an implementation of those principles in a complete computer-aided detection system. The proposed system, through an automatic optimization process, chooses the most useful templates (mammographic regions of interest) using a large database of previously collected and annotated mammograms. Through this process, the knowledge about the task of detecting masses in mammograms is incorporated in the system. Then, we evaluate whether our system developed for screen-film mammograms can be successfully applied not only to other mammograms but also to digital breast tomosynthesis (DBT) reconstructed slices without adding any DBT cases for training. Our rationale is that since mutual information is known to be a robust inter-modality image similarity measure, it has high potential of transferring knowledge between modalities in the context of the mass detection

  14. Unbiased Categorical Classification of Pediatric Sleep Disordered Breathing

    PubMed Central

    Spruyt, Karen; Verleye, Gino; Gozal, David

    2010-01-01

    Study Objectives: To classify pediatric sleep disordered breathing (SDB) using unbiased approaches. In children, decisions regarding severity and treatment of SDB are conducted solely based on empirical observations. Although recognizable entities clearly exist under the SDB spectrum, neither the number of SDB categories nor their specific criteria have been critically defined. Design: retrospective cohort analysis and random prospective cohort Setting: community and clinical sample Patients or Participants: Urban 5- to 9-year-old community children undergoing overnight sleep study (NPSG), and a comparable prospectively recruited clinical SDB sample. Interventions: n/a Measurements and Results: Principal component analysis was used to identify the uniqueness of the polysomnographically derived measures that are routinely used in clinical settings: apnea-hypopnea index, apnea index, obstructive apnea index, nadir SpO2, spontaneous arousal index and respiratory arousal index. These measures were then incorporated using unbiased data mining approaches to further characterize and discriminate across categorical phenotypes. Of 1,133 subjects, 52.8% were habitual snorers. Six categorical phenotypes clustered without any a priori hypothesis. Secondly, a non-hierarchical model that incorporated 6 NPSG-derived measures enabled unbiased identification of algorithms that predicted these 6 severity-based clusters. Thirdly, a hierarchical model was developed and performed well on all severity-based clusters. Classification and predictive models were subsequently cross-validated statistically as well as clinically, using 2 additional datasets that included 259 subjects. Modeling reached ∼93% accuracy in cluster assignment. Conclusions: Data-driven analysis of conventional NPSG-derived indices identified 6 distinct clusters ranging from a cluster with normal indices toward clusters with more abnormal indices. Categorical assignment of individual cases to any of such clusters

  15. Design of a mutual authentication based on NTRUsign with a perturbation and inherent multipoint control protocol frames in an Ethernet-based passive optical network

    NASA Astrophysics Data System (ADS)

    Yin, Aihan; Ding, Yisheng

    2014-11-01

    Identity-related security issues inherently present in passive optical networks (PON) still exist in the current (1G) and next-generation (10G) Ethernet-based passive optical network (EPON) systems. We propose a mutual authentication scheme that integrates an NTRUsign digital signature algorithm with inherent multipoint control protocol (MPCP) frames over an EPON system between the optical line terminal (OLT) and optical network unit (ONU). Here, a primitive NTRUsign algorithm is significantly modified through the use of a new perturbation so that it can be effectively used for simultaneously completing signature and authentication functions on the OLT and the ONU sides. Also, in order to transmit their individual sensitive messages, which include public key, signature, and random value and so forth, to each other, we redefine three unique frames according to MPCP format frame. These generated messages can be added into the frames and delivered to each other, allowing the OLT and the ONU to go ahead with a mutual identity authentication process to verify their legal identities. Our simulation results show that this proposed scheme performs very well in resisting security attacks and has low influence on the registration efficiency to to-be-registered ONUs. A performance comparison with traditional authentication algorithms is also presented. To the best of our knowledge, no detailed design of mutual authentication in EPON can be found in the literature up to now.

  16. A Support Method with Changeable Training Strategies Based on Mutual Adaptation between a Ubiquitous Pet and a Learner

    NASA Astrophysics Data System (ADS)

    Ye, Xianzhi; Jing, Lei; Kansen, Mizuo; Wang, Junbo; Ota, Kaoru; Cheng, Zixue

    With the progress of ubiquitous technology, ubiquitous learning presents new opportunities to learners. Situations of a learner can be grasped through analyzing the learner's actions collected by sensors, RF-IDs, or cameras in order to provide support at proper time, proper place, and proper situation. Training for acquiring skills and enhancing physical abilities through exercise and experience in the real world is an important domain in u-learning. A training program may last for several days and has one or more training units (exercises) for a day. A learner's performance in a unit is considered as short term state. The performance in a series of units may change with patterns: progress, plateau, and decline. Long term state in a series of units is accumulatively computed based on short term states. In a learning/training program, it is necessary to apply different support strategies to adapt to different states of the learner. Adaptation in learning support is significant, because a learner loses his/her interests easily without adaptation. Systems with the adaptive support usually provide stimulators to a learner, and a learner can have a great motivation in learning at beginning. However, when the stimulators reach some levels, the learner may lose his/her motivation, because the long term state of the learner changes dynamically, which means a progress state may change to a plateau state or a decline state. In different long term learning states, different types of stimulators are needed. However, the stimulators and advice provided by the existing systems are monotonic without changeable support strategies. We propose a mutual adaptive support. The mutual adaptation means each of the system and the learner has their own states. On one hand, the system tries to change its state to adapt to the learner's state for providing adaptive support. On the other hand, the learner can change its performance following the advice given based on the state of the system

  17. Reconstructing input for artificial neural networks based on embedding theory and mutual information to simulate soil pore water salinity in tidal floodplain

    NASA Astrophysics Data System (ADS)

    Zheng, Fawen; Wan, Yongshan; Song, Keunyea; Sun, Detong; Hedgepeth, Marion

    2016-01-01

    Soil pore water salinity plays an important role in the distribution of vegetation and biogeochemical processes in coastal floodplain ecosystems. In this study, artificial neural networks (ANNs) were applied to simulate the pore water salinity of a tidal floodplain in Florida. We present an approach based on embedding theory with mutual information to reconstruct ANN model input time series from one system state variable. Mutual information between system output and input was computed and the local minimum mutual information points were used to determine a time lag vector for time series embedding and reconstruction, with which the mutual information weighted average method was developed to compute the components of reconstructed time series. The optimal embedding dimension was obtained by optimizing model performance. The method was applied to simulate soil pore water salinity dynamics at 12 probe locations in the tidal floodplain influenced by saltwater intrusion using 4 years (2005-2008) data, in which adjacent river water salinity was used to reconstruct model input. The simulated electrical conductivity of the pore water showed close agreement with field observations (RMSE and ), suggesting the reconstructed input by the proposed approach provided adequate input information for ANN modeling. Multiple linear regression model, partial mutual information algorithm for input variable selection, k-NN algorithm, and simple time delay embedding were also used to further verify the merit of the proposed approach.

  18. A hash based mutual RFID tag authentication protocol in telecare medicine information system.

    PubMed

    Srivastava, Keerti; Awasthi, Amit K; Kaul, Sonam D; Mittal, R C

    2015-01-01

    Radio Frequency Identification (RFID) is a technology which has multidimensional applications to reduce the complexity of today life. Everywhere, like access control, transportation, real-time inventory, asset management and automated payment systems etc., RFID has its enormous use. Recently, this technology is opening its wings in healthcare environments, where potential applications include patient monitoring, object traceability and drug administration systems etc. In this paper, we propose a secure RFID-based protocol for the medical sector. This protocol is based on hash operation with synchronized secret. The protocol is safe against active and passive attacks such as forgery, traceability, replay and de-synchronization attack. PMID:25491577

  19. Mutual exclusion

    NASA Technical Reports Server (NTRS)

    Denning, Peter J.

    1991-01-01

    Almost all computers today operate as part of a network, where they assist people in coordinating actions. Sometimes what appears to be a single computer is actually a network of cooperating computers; e.g., some supercomputers consist of many processors operating in parallel and exchanging synchronization signals. One of the most fundamental requirements in all these systems is that certain operations be indivisible: the steps of one must not be interleaved with the steps of another. Two approaches were designed to implement this requirement, one based on central locks and the other on distributed order tickets. Practicing scientists and engineers need to come to be familiar with these methods.

  20. Using a Search Engine-Based Mutually Reinforcing Approach to Assess the Semantic Relatedness of Biomedical Terms

    PubMed Central

    Hsu, Yi-Yu; Chen, Hung-Yu; Kao, Hung-Yu

    2013-01-01

    Background Determining the semantic relatedness of two biomedical terms is an important task for many text-mining applications in the biomedical field. Previous studies, such as those using ontology-based and corpus-based approaches, measured semantic relatedness by using information from the structure of biomedical literature, but these methods are limited by the small size of training resources. To increase the size of training datasets, the outputs of search engines have been used extensively to analyze the lexical patterns of biomedical terms. Methodology/Principal Findings In this work, we propose the Mutually Reinforcing Lexical Pattern Ranking (ReLPR) algorithm for learning and exploring the lexical patterns of synonym pairs in biomedical text. ReLPR employs lexical patterns and their pattern containers to assess the semantic relatedness of biomedical terms. By combining sentence structures and the linking activities between containers and lexical patterns, our algorithm can explore the correlation between two biomedical terms. Conclusions/Significance The average correlation coefficient of the ReLPR algorithm was 0.82 for various datasets. The results of the ReLPR algorithm were significantly superior to those of previous methods. PMID:24348899

  1. MINT: Mutual Information Based Transductive Feature Selection for Genetic Trait Prediction.

    PubMed

    He, Dan; Rish, Irina; Haws, David; Parida, Laxmi

    2016-01-01

    Whole genome prediction of complex phenotypic traits using high-density genotyping arrays has attracted a lot of attention, as it is relevant to the fields of plant and animal breeding and genetic epidemiology. Since the number of genotypes is generally much bigger than the number of samples, predictive models suffer from the curse of dimensionality. The curse of dimensionality problem not only affects the computational efficiency of a particular genomic selection method, but can also lead to a poor performance, mainly due to possible overfitting, or un-informative features. In this work, we propose a novel transductive feature selection method, called MINT, which is based on the MRMR (Max-Relevance and Min-Redundancy) criterion. We apply MINT on genetic trait prediction problems and show that, in general, MINT is a better feature selection method than the state-of-the-art inductive method MRMR. PMID:27295642

  2. Cross-kingdom chemical communication drives a heritable, mutually beneficial prion-based transformations of metabolism

    PubMed Central

    Walker, Gordon A.; Datta, Manoshi S.; Ung, W. Lloyd; Lancaster, Alex K.; Chang, Amelia; Newby, Gregory A.; Weitz, David A.; Bisson, Linda F.; Lindquist, Susan

    2015-01-01

    SUMMARY In experimental science, organisms are usually studied in isolation, but in the wild they compete and cooperate in complex communities. We report a system for cross-kingdom communication by which bacteria heritably transform yeast metabolism. An ancient biological circuit blocks yeast from using other carbon sources in the presence of glucose. [GAR+], a protein-based epigenetic element, allows yeast to circumvent this glucose repression and use multiple carbon sources in the presence of glucose. Some bacteria secrete a chemical factor that induces [GAR+]. [GAR+] is advantageous to bacteria because yeast cells make less ethanol, and is advantageous to yeast because their growth and long-term viability is improved in complex carbon sources. This cross-kingdom communication is broadly conserved, providing a compelling argument for its adaptive value. By heritably transforming growth and survival strategies in response to the selective pressures of life in a biological community, [GAR+] presents a unique example of Lamarckian inheritance. PMID:25171409

  3. Reinforcement-based decision making in corticostriatal circuits: mutual constraints by neurocomputational and diffusion models.

    PubMed

    Ratcliff, Roger; Frank, Michael J

    2012-05-01

    In this letter, we examine the computational mechanisms of reinforce-ment-based decision making. We bridge the gap across multiple levels of analysis, from neural models of corticostriatal circuits-the basal ganglia (BG) model (Frank, 2005 , 2006 ) to simpler but mathematically tractable diffusion models of two-choice decision making. Specifically, we generated simulated data from the BG model and fit the diffusion model (Ratcliff, 1978 ) to it. The standard diffusion model fits underestimated response times under conditions of high response and reinforcement conflict. Follow-up fits showed good fits to the data both by increasing nondecision time and by raising decision thresholds as a function of conflict and by allowing this threshold to collapse with time. This profile captures the role and dynamics of the subthalamic nucleus in BG circuitry, and as such, parametric modulations of projection strengths from this nucleus were associated with parametric increases in decision boundary and its modulation by conflict. We then present data from a human reinforcement learning experiment involving decisions with low- and high-reinforcement conflict. Again, the standard model failed to fit the data, but we found that two variants similar to those that fit the BG model data fit the experimental data, thereby providing a convergence of theoretical accounts of complex interactive decision-making mechanisms consistent with available data. This work also demonstrates how to make modest modifications to diffusion models to summarize core computations of the BG model. The result is a better fit and understanding of reinforcement-based choice data than that which would have occurred with either model alone. PMID:22295983

  4. A web-based care-requiring client and Home Helper mutual support system.

    PubMed

    Ogawa, Hidekuni; Yonezawa, Yoshiharu; Maki, Hiromichi; Hahn, Allen W; Caldwell, W Morton

    2005-01-01

    For the improved efficiency of home care of the elderly, a web-based system has been developed to enable faster communications between care-requiring clients, their Home Helper and the care manager. Changes to care items, such as cooking, bathing, washing, cleaning and shopping are usually requested by the elderly client over the telephone. However, the care central office often requires 24 hours to process and respond to such spoken requests. The system we have developed consists of Internet client computers with liquid crystal input tablets, wireless Internet Java enabled mobile phones and a central office server that yields almost instant communication. The care clients enter requests on the liquid crystal tablet at their home and then their computer sends these requests to the server at the Home Helper central office. The server automatically creates a new file of the requested items, and then immediately transfers them to the care manager and Home Helper's mobile phone. With this non-vocal and paperless system, the care-requiring clients, who can easily operate the liquid crystal tablet, can very quickly communicate their needed care change requests to their Home Helper. PMID:15850098

  5. [Construction and simplification of the calibration model for spectral analysis of fuel oil properties based on mutual information method].

    PubMed

    Hao, Yong; Sun, Xu-dong; Cai, Li-jun; Liu, Yan-de

    2012-01-01

    Near infrared diffuse reflectance (NIRS) and ultraviolet (UV) spectral analysis were adopted for quantitative determination of octane number and monoaromatics in fuel oil. Partial least squares regression (PLSR) was used for construction of vibrational spectral calibration models. Variables selection strategy based on mutual information (MI) theory was introduced to optimize the models for improving the precision and reducing the complexity. The results indicate that MI-PLSR method can effectively improve the predictive ability of the models and simplify them. For octane number models, the root mean square error of prediction (RMSEP) and the number of calibration variables were reduced from 0.288 and 401 to 0.111 and 112, respectively, and correlation coefficient (R) was improved from 0.985 to 0.998. For monoaromatics models, RMSEP and the number of calibration variables were reduced from 0.753 and 572 to 0.478 and 37, respectively, and R was improved from 0.996 to 0.998. Vibrational spectral analysis combined with MI-PLSR method can be used for quantitative analysis of fuel oil properties, and improve the cost-effectiveness. PMID:22497153

  6. Comparison of - and Mutual Informaton Based Calibration of Terrestrial Laser Scanner and Digital Camera for Deformation Monitoring

    NASA Astrophysics Data System (ADS)

    Omidalizarandi, M.; Neumann, I.

    2015-12-01

    In the current state-of-the-art, geodetic deformation analysis of natural and artificial objects (e.g. dams, bridges,...) is an ongoing research in both static and kinematic mode and has received considerable interest by researchers and geodetic engineers. In this work, due to increasing the accuracy of geodetic deformation analysis, a terrestrial laser scanner (TLS; here the Zoller+Fröhlich IMAGER 5006) and a high resolution digital camera (Nikon D750) are integrated to complementarily benefit from each other. In order to optimally combine the acquired data of the hybrid sensor system, a highly accurate estimation of the extrinsic calibration parameters between TLS and digital camera is a vital preliminary step. Thus, the calibration of the aforementioned hybrid sensor system can be separated into three single calibrations: calibration of the camera, calibration of the TLS and extrinsic calibration between TLS and digital camera. In this research, we focus on highly accurate estimating extrinsic parameters between fused sensors and target- and targetless (mutual information) based methods are applied. In target-based calibration, different types of observations (image coordinates, TLS measurements and laser tracker measurements for validation) are utilized and variance component estimation is applied to optimally assign adequate weights to the observations. Space resection bundle adjustment based on the collinearity equations is solved using Gauss-Markov and Gauss-Helmert model. Statistical tests are performed to discard outliers and large residuals in the adjustment procedure. At the end, the two aforementioned approaches are compared and advantages and disadvantages of them are investigated and numerical results are presented and discussed.

  7. SU-E-J-132: Automated Segmentation with Post-Registration Atlas Selection Based On Mutual Information

    SciTech Connect

    Ren, X; Gao, H; Sharp, G

    2015-06-15

    Purpose: The delineation of targets and organs-at-risk is a critical step during image-guided radiation therapy, for which manual contouring is the gold standard. However, it is often time-consuming and may suffer from intra- and inter-rater variability. The purpose of this work is to investigate the automated segmentation. Methods: The automatic segmentation here is based on mutual information (MI), with the atlas from Public Domain Database for Computational Anatomy (PDDCA) with manually drawn contours.Using dice coefficient (DC) as the quantitative measure of segmentation accuracy, we perform leave-one-out cross-validations for all PDDCA images sequentially, during which other images are registered to each chosen image and DC is computed between registered contour and ground truth. Meanwhile, six strategies, including MI, are selected to measure the image similarity, with MI to be the best. Then given a target image to be segmented and an atlas, automatic segmentation consists of: (a) the affine registration step for image positioning; (b) the active demons registration method to register the atlas to the target image; (c) the computation of MI values between the deformed atlas and the target image; (d) the weighted image fusion of three deformed atlas images with highest MI values to form the segmented contour. Results: MI was found to be the best among six studied strategies in the sense that it had the highest positive correlation between similarity measure (e.g., MI values) and DC. For automated segmentation, the weighted image fusion of three deformed atlas images with highest MI values provided the highest DC among four proposed strategies. Conclusion: MI has the highest correlation with DC, and therefore is an appropriate choice for post-registration atlas selection in atlas-based segmentation. Xuhua Ren and Hao Gao were partially supported by the NSFC (#11405105), the 973 Program (#2015CB856000) and the Shanghai Pujiang Talent Program (#14PJ1404500)

  8. Unbiased sampling of lattice Hamilton path ensembles

    NASA Astrophysics Data System (ADS)

    Mansfield, Marc L.

    2006-10-01

    Hamilton paths, or Hamiltonian paths, are walks on a lattice which visit each site exactly once. They have been proposed as models of globular proteins and of compact polymers. A previously published algorithm [Mansfield, Macromolecules 27, 5924 (1994)] for sampling Hamilton paths on simple square and simple cubic lattices is tested for bias and for efficiency. Because the algorithm is a Metropolis Monte Carlo technique obviously satisfying detailed balance, we need only demonstrate ergodicity to ensure unbiased sampling. Two different tests for ergodicity (exact enumeration on small lattices, nonexhaustive enumeration on larger lattices) demonstrate ergodicity unequivocally for small lattices and provide strong support for ergodicity on larger lattices. Two other sampling algorithms [Ramakrishnan et al., J. Chem. Phys. 103, 7592 (1995); Lua et al., Polymer 45, 717 (2004)] are both known to produce biases on both 2×2×2 and 3×3×3 lattices, but it is shown here that the current algorithm gives unbiased sampling on these same lattices. Successive Hamilton paths are strongly correlated, so that many iterations are required between statistically independent samples. Rules for estimating the number of iterations needed to dissipate these correlations are given. However, the iteration time is so fast that the efficiency is still very good except on extremely large lattices. For example, even on lattices of total size 10×10×10 we are able to generate tens of thousands of uncorrelated Hamilton paths per hour of CPU time.

  9. Two Phase Non-Rigid Multi-Modal Image Registration Using Weber Local Descriptor-Based Similarity Metrics and Normalized Mutual Information

    PubMed Central

    Yang, Feng; Ding, Mingyue; Zhang, Xuming; Wu, Yi; Hu, Jiani

    2013-01-01

    Non-rigid multi-modal image registration plays an important role in medical image processing and analysis. Existing image registration methods based on similarity metrics such as mutual information (MI) and sum of squared differences (SSD) cannot achieve either high registration accuracy or high registration efficiency. To address this problem, we propose a novel two phase non-rigid multi-modal image registration method by combining Weber local descriptor (WLD) based similarity metrics with the normalized mutual information (NMI) using the diffeomorphic free-form deformation (FFD) model. The first phase aims at recovering the large deformation component using the WLD based non-local SSD (wldNSSD) or weighted structural similarity (wldWSSIM). Based on the output of the former phase, the second phase is focused on getting accurate transformation parameters related to the small deformation using the NMI. Extensive experiments on T1, T2 and PD weighted MR images demonstrate that the proposed wldNSSD-NMI or wldWSSIM-NMI method outperforms the registration methods based on the NMI, the conditional mutual information (CMI), the SSD on entropy images (ESSD) and the ESSD-NMI in terms of registration accuracy and computation efficiency. PMID:23765270

  10. Obtaining an unbiased redshift distribution for submm galaxies

    NASA Astrophysics Data System (ADS)

    Ivison, Rob; Norris, Ray; Feain, Ilana; Huynh, Minh; Smail, Ian; Thomson, Alasdair

    2009-07-01

    We request 36hr with ATCA to test a new method for determining an unbiased redshift distribution for submm galaxies (SMGs) - a critical parameter capable of breaking degeneracies in galaxy evolution models. Our method is based on the expectation that dusty ULIRGs will exhibit maser activity similar to that observed in other IR-luminous AGN. As well as determining redshifts, detections will allow us to estimate the mass of the central black hole (to compare with X-ray-based estimates), to pinpoint the maser relative to the synchrotron emission, and to explore any correlation between L(FIR) and L(H2O). The key to our project is the largest deep submm survey undertaken thus far - LESS - in the Extended Chandra Deep Field South. We propose to piggyback on the Huynh et al. 5-GHz survey of ECDFS, going 2.3x deeper in two pointings centred on over-densities of bright SMGs.

  11. Unbiased Deep Sequencing of RNA Viruses from Clinical Samples.

    PubMed

    Matranga, Christian B; Gladden-Young, Adrianne; Qu, James; Winnicki, Sarah; Nosamiefan, Dolo; Levin, Joshua Z; Sabeti, Pardis C

    2016-01-01

    Here we outline a next-generation RNA sequencing protocol that enables de novo assemblies and intra-host variant calls of viral genomes collected from clinical and biological sources. The method is unbiased and universal; it uses random primers for cDNA synthesis and requires no prior knowledge of the viral sequence content. Before library construction, selective RNase H-based digestion is used to deplete unwanted RNA - including poly(rA) carrier and ribosomal RNA - from the viral RNA sample. Selective depletion improves both the data quality and the number of unique reads in viral RNA sequencing libraries. Moreover, a transposase-based 'tagmentation' step is used in the protocol as it reduces overall library construction time. The protocol has enabled rapid deep sequencing of over 600 Lassa and Ebola virus samples-including collections from both blood and tissue isolates-and is broadly applicable to other microbial genomics studies. PMID:27403729

  12. Unbiased approaches to biomarker discovery in neurodegenerative diseases

    PubMed Central

    Chen-Plotkin, Alice S.

    2014-01-01

    Neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis, and frontotemporal dementia have several important features in common. They are progressive, they affect a relatively inaccessible organ, and we have no disease-modifying therapies for them. For these brain-based diseases, current diagnosis and evaluation of disease severity rely almost entirely on clinical examination, which may only be a rough approximation of disease state. Thus, the development of biomarkers – objective, relatively easily measured and precise indicators of pathogenic processes – could improve patient care and accelerate therapeutic discovery. Yet existing, rigorously tested neurodegenerative disease biomarkers are few, and even fewer biomarkers have translated into clinical use. To find new biomarkers for these diseases, an unbiased, high-throughput screening approach may be needed. In this review, I will describe the potential utility of such an approach to biomarker discovery, using Parkinson’s disease as a case example. PMID:25442938

  13. Neurostereology protocol for unbiased quantification of neuronal injury and neurodegeneration

    PubMed Central

    Golub, Victoria M.; Brewer, Jonathan; Wu, Xin; Kuruba, Ramkumar; Short, Jenessa; Manchi, Maunica; Swonke, Megan; Younus, Iyan; Reddy, Doodipala Samba

    2015-01-01

    Neuronal injury and neurodegeneration are the hallmark pathologies in a variety of neurological conditions such as epilepsy, stroke, traumatic brain injury, Parkinson’s disease and Alzheimer’s disease. Quantification of absolute neuron and interneuron counts in various brain regions is essential to understand the impact of neurological insults or neurodegenerative disease progression in animal models. However, conventional qualitative scoring-based protocols are superficial and less reliable for use in studies of neuroprotection evaluations. Here, we describe an optimized stereology protocol for quantification of neuronal injury and neurodegeneration by unbiased counting of neurons and interneurons. Every 20th section in each series of 20 sections was processed for NeuN(+) total neuron and parvalbumin(+) interneuron immunostaining. The sections that contain the hippocampus were then delineated into five reliably predefined subregions. Each region was separately analyzed with a microscope driven by the stereology software. Regional tissue volume was determined by using the Cavalieri estimator, as well as cell density and cell number were determined by using the optical disector and optical fractionator. This protocol yielded an estimate of 1.5 million total neurons and 0.05 million PV(+) interneurons within the rat hippocampus. The protocol has greater predictive power for absolute counts as it is based on 3D features rather than 2D images. The total neuron counts were consistent with literature values from sophisticated systems, which are more expensive than our stereology system. This unbiased stereology protocol allows for sensitive, medium-throughput counting of total neurons in any brain region, and thus provides a quantitative tool for studies of neuronal injury and neurodegeneration in a variety of acute brain injury and chronic neurological models. PMID:26582988

  14. Why mutual helping in most natural systems is neither conflict-free nor based on maximal conflict.

    PubMed

    Bshary, Redouan; Zuberbühler, Klaus; van Schaik, Carel P

    2016-02-01

    Mutual helping for direct benefits can be explained by various game theoretical models, which differ mainly in terms of the underlying conflict of interest between two partners. Conflict is minimal if helping is self-serving and the partner benefits as a by-product. In contrast, conflict is maximal if partners are in a prisoner's dilemma with both having the pay-off-dominant option of not returning the other's investment. Here, we provide evolutionary and ecological arguments for why these two extremes are often unstable under natural conditions and propose that interactions with intermediate levels of conflict are frequent evolutionary endpoints. We argue that by-product helping is prone to becoming an asymmetric investment game since even small variation in by-product benefits will lead to the evolution of partner choice, leading to investments by the chosen class. Second, iterated prisoner's dilemmas tend to take place in stable social groups where the fitness of partners is interdependent, with the effect that a certain level of helping is self-serving. In sum, intermediate levels of mutual helping are expected in nature, while efficient partner monitoring may allow reaching higher levels. PMID:26729931

  15. Smooth-Threshold Multivariate Genetic Prediction with Unbiased Model Selection.

    PubMed

    Ueki, Masao; Tamiya, Gen

    2016-04-01

    We develop a new genetic prediction method, smooth-threshold multivariate genetic prediction, using single nucleotide polymorphisms (SNPs) data in genome-wide association studies (GWASs). Our method consists of two stages. At the first stage, unlike the usual discontinuous SNP screening as used in the gene score method, our method continuously screens SNPs based on the output from standard univariate analysis for marginal association of each SNP. At the second stage, the predictive model is built by a generalized ridge regression simultaneously using the screened SNPs with SNP weight determined by the strength of marginal association. Continuous SNP screening by the smooth thresholding not only makes prediction stable but also leads to a closed form expression of generalized degrees of freedom (GDF). The GDF leads to the Stein's unbiased risk estimation (SURE), which enables data-dependent choice of optimal SNP screening cutoff without using cross-validation. Our method is very rapid because computationally expensive genome-wide scan is required only once in contrast to the penalized regression methods including lasso and elastic net. Simulation studies that mimic real GWAS data with quantitative and binary traits demonstrate that the proposed method outperforms the gene score method and genomic best linear unbiased prediction (GBLUP), and also shows comparable or sometimes improved performance with the lasso and elastic net being known to have good predictive ability but with heavy computational cost. Application to whole-genome sequencing (WGS) data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) exhibits that the proposed method shows higher predictive power than the gene score and GBLUP methods. PMID:26947266

  16. Evolution of mutualism between species

    SciTech Connect

    Post, W.M.; Travis, C.C.; DeAngelis, D.L.

    1980-01-01

    Recent theoretical work on mutualism, the interaction between species populations that is mutually beneficial, is reviewed. Several ecological facts that should be addressed in the construction of dynamic models for mutualism are examined. Basic terminology is clarified. (PSB)

  17. Behavioral Ecology: Manipulative Mutualism.

    PubMed

    Hughes, David P

    2015-09-21

    A new study reveals that an apparent mutualism between lycaenid caterpillars and their attendant ants may not be all it seems, as the caterpillars produce secretions that modify the brains and behavior of their attendant ants. PMID:26394105

  18. The joint effect of ethnicity and gender on occupational segregation. An approach based on the Mutual Information Index.

    PubMed

    Guinea-Martin, Daniel; Mora, Ricardo; Ruiz-Castillo, Javier

    2015-01-01

    In this article, we study the effects of ethnicity and gender on occupational segregation. Traditionally, researchers have examined the two sources of segregation separately. In contrast, we measure their joint effect by applying a multigroup segregation index-the Mutual Information or M index-to the product of the seven ethnic groups and two genders distinguished in our 2001 Census data for England and Wales. We exploit M's additive decomposability property to pose the following two questions: (i) Is there an interaction effect? (ii) How much does each source contribute to occupational segregation, controlling for the effect of the other? Although the role of ethnicity is non-negligible in the areas where minorities are concentrated, our findings confirm the greater importance of gender over ethnicity as a source of segregation. Moreover, we find a small "dwindling" interaction effect between the two sources of segregation: ethnicity slightly weakens the segregating power of gender and vice versa. PMID:25432611

  19. Estimating mutual information.

    PubMed

    Kraskov, Alexander; Stögbauer, Harald; Grassberger, Peter

    2004-06-01

    We present two classes of improved estimators for mutual information M(X,Y), from samples of random points distributed according to some joint probability density mu(x,y). In contrast to conventional estimators based on binnings, they are based on entropy estimates from k -nearest neighbor distances. This means that they are data efficient (with k=1 we resolve structures down to the smallest possible scales), adaptive (the resolution is higher where data are more numerous), and have minimal bias. Indeed, the bias of the underlying entropy estimates is mainly due to nonuniformity of the density at the smallest resolved scale, giving typically systematic errors which scale as functions of k/N for N points. Numerically, we find that both families become exact for independent distributions, i.e. the estimator M(X,Y) vanishes (up to statistical fluctuations) if mu(x,y)=mu(x)mu(y). This holds for all tested marginal distributions and for all dimensions of x and y. In addition, we give estimators for redundancies between more than two random variables. We compare our algorithms in detail with existing algorithms. Finally, we demonstrate the usefulness of our estimators for assessing the actual independence of components obtained from independent component analysis (ICA), for improving ICA, and for estimating the reliability of blind source separation. PMID:15244698

  20. A Simplified model of mutually inhibitory sleep-active and wake-active neuronal populations employing a noise-based switching mechanism.

    PubMed

    Patel, Mainak

    2016-04-01

    Infant rats switch randomly between the sleeping and waking states; during early infancy (up to postnatal day 8), sleep and wake bouts are random, brief (with means on the order of several seconds) and exponentially distributed, with the length of a particular bout independent of the length of prior bouts. As the rat ages during this early period, mean sleep and wake bout lengths gradually increase, though sleep and wake bouts remain exponentially distributed. Additionally, sleep and wake bouts are regulated independently of each other - alterations in the development of sleep (wake) bouts has no impact on the regulation wake (sleep) bouts. Sleep and wake bout behavior is associated with the activity of mutually inhibitory sleep-active and wake-active brainstem populations. In this work, I employ a simplified biophysical model of two mutually inhibitory populations consisting of ten integrate-and-fire neurons each and a noise-based switching mechanism. I show that such a noise-based switching mechanism naturally accounts for the experimentally observed features of sleep-wake switching during early infancy - random alternating activity bouts occur as a consequence of noise (provided inhibition is strong relative to excitation), bout durations are exponential (due to a lack of memory within the system), and cross-population inhibition or intrapopulation excitatory coupling provide mechanisms for changing and independently regulated sleep and wake bout means. PMID:26802484

  1. MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation.

    PubMed

    Wang, Luman; Mo, Qiaochu; Wang, Jianxin

    2015-01-01

    Most current gene coexpression databases support the analysis for linear correlation of gene pairs, but not nonlinear correlation of them, which hinders precisely evaluating the gene-gene coexpression strengths. Here, we report a new database, MIrExpress, which takes advantage of the information theory, as well as the Pearson linear correlation method, to measure the linear correlation, nonlinear correlation, and their hybrid of cell-specific gene coexpressions in immune cells. For a given gene pair or probe set pair input by web users, both mutual information (MI) and Pearson correlation coefficient (r) are calculated, and several corresponding values are reported to reflect their coexpression correlation nature, including MI and r values, their respective rank orderings, their rank comparison, and their hybrid correlation value. Furthermore, for a given gene, the top 10 most relevant genes to it are displayed with the MI, r, or their hybrid perspective, respectively. Currently, the database totally includes 16 human cell groups, involving 20,283 human genes. The expression data and the calculated correlation results from the database are interactively accessible on the web page and can be implemented for other related applications and researches. PMID:26881263

  2. MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation

    PubMed Central

    Wang, Luman; Mo, Qiaochu; Wang, Jianxin

    2015-01-01

    Most current gene coexpression databases support the analysis for linear correlation of gene pairs, but not nonlinear correlation of them, which hinders precisely evaluating the gene-gene coexpression strengths. Here, we report a new database, MIrExpress, which takes advantage of the information theory, as well as the Pearson linear correlation method, to measure the linear correlation, nonlinear correlation, and their hybrid of cell-specific gene coexpressions in immune cells. For a given gene pair or probe set pair input by web users, both mutual information (MI) and Pearson correlation coefficient (r) are calculated, and several corresponding values are reported to reflect their coexpression correlation nature, including MI and r values, their respective rank orderings, their rank comparison, and their hybrid correlation value. Furthermore, for a given gene, the top 10 most relevant genes to it are displayed with the MI, r, or their hybrid perspective, respectively. Currently, the database totally includes 16 human cell groups, involving 20,283 human genes. The expression data and the calculated correlation results from the database are interactively accessible on the web page and can be implemented for other related applications and researches. PMID:26881263

  3. General SIC measurement-based entanglement detection

    NASA Astrophysics Data System (ADS)

    Chen, Bin; Li, Tao; Fei, Shao-Ming

    2015-06-01

    We study the quantum separability problem by using general symmetric informationally complete measurements and present separability criteria for both -dimensional bipartite and multipartite systems. The criterion for bipartite quantum states is effective in detecting several well-known classes of quantum states. For isotropic states, it becomes both necessary and sufficient. Furthermore, our criteria can be experimentally implemented, and the criterion for two-qudit states requires less local measurements than the one based on mutually unbiased measurements.

  4. Computational Analysis of an Autophagy/Translation Switch Based on Mutual Inhibition of MTORC1 and ULK1

    PubMed Central

    Szymańska, Paulina; Martin, Katie R.; MacKeigan, Jeffrey P.; Hlavacek, William S.; Lipniacki, Tomasz

    2015-01-01

    We constructed a mechanistic, computational model for regulation of (macro)autophagy and protein synthesis (at the level of translation). The model was formulated to study the system-level consequences of interactions among the following proteins: two key components of MTOR complex 1 (MTORC1), namely the protein kinase MTOR (mechanistic target of rapamycin) and the scaffold protein RPTOR; the autophagy-initiating protein kinase ULK1; and the multimeric energy-sensing AMP-activated protein kinase (AMPK). Inputs of the model include intrinsic AMPK kinase activity, which is taken as an adjustable surrogate parameter for cellular energy level or AMP:ATP ratio, and rapamycin dose, which controls MTORC1 activity. Outputs of the model include the phosphorylation level of the translational repressor EIF4EBP1, a substrate of MTORC1, and the phosphorylation level of AMBRA1 (activating molecule in BECN1-regulated autophagy), a substrate of ULK1 critical for autophagosome formation. The model incorporates reciprocal regulation of mTORC1 and ULK1 by AMPK, mutual inhibition of MTORC1 and ULK1, and ULK1-mediated negative feedback regulation of AMPK. Through analysis of the model, we find that these processes may be responsible, depending on conditions, for graded responses to stress inputs, for bistable switching between autophagy and protein synthesis, or relaxation oscillations, comprising alternating periods of autophagy and protein synthesis. A sensitivity analysis indicates that the prediction of oscillatory behavior is robust to changes of the parameter values of the model. The model provides testable predictions about the behavior of the AMPK-MTORC1-ULK1 network, which plays a central role in maintaining cellular energy and nutrient homeostasis. PMID:25761126

  5. Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1

    DOE PAGESBeta

    Szymańska, Paulina; Martin, Katie R.; MacKeigan, Jeffrey P.; Hlavacek, William S.; Lipniacki, Tomasz

    2015-03-11

    We constructed a mechanistic, computational model for regulation of (macro)autophagy and protein synthesis (at the level of translation). The model was formulated to study the system-level consequences of interactions among the following proteins: two key components of MTOR complex 1 (MTORC1), namely the protein kinase MTOR (mechanistic target of rapamycin) and the scaffold protein RPTOR; the autophagy-initiating protein kinase ULK1; and the multimeric energy-sensing AMP-activated protein kinase (AMPK). Inputs of the model include intrinsic AMPK kinase activity, which is taken as an adjustable surrogate parameter for cellular energy level or AMP:ATP ratio, and rapamycin dose, which controls MTORC1 activity. Outputsmore » of the model include the phosphorylation level of the translational repressor EIF4EBP1, a substrate of MTORC1, and the phosphorylation level of AMBRA1 (activating molecule in BECN1-regulated autophagy), a substrate of ULK1 critical for autophagosome formation. The model incorporates reciprocal regulation of mTORC1 and ULK1 by AMPK, mutual inhibition of MTORC1 and ULK1, and ULK1-mediated negative feedback regulation of AMPK. Through analysis of the model, we find that these processes may be responsible, depending on conditions, for graded responses to stress inputs, for bistable switching between autophagy and protein synthesis, or relaxation oscillations, comprising alternating periods of autophagy and protein synthesis. A sensitivity analysis indicates that the prediction of oscillatory behavior is robust to changes of the parameter values of the model. The model provides testable predictions about the behavior of the AMPK-MTORC1-ULK1 network, which plays a central role in maintaining cellular energy and nutrient homeostasis.« less

  6. Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1

    SciTech Connect

    Szymańska, Paulina; Martin, Katie R.; MacKeigan, Jeffrey P.; Hlavacek, William S.; Lipniacki, Tomasz

    2015-03-11

    We constructed a mechanistic, computational model for regulation of (macro)autophagy and protein synthesis (at the level of translation). The model was formulated to study the system-level consequences of interactions among the following proteins: two key components of MTOR complex 1 (MTORC1), namely the protein kinase MTOR (mechanistic target of rapamycin) and the scaffold protein RPTOR; the autophagy-initiating protein kinase ULK1; and the multimeric energy-sensing AMP-activated protein kinase (AMPK). Inputs of the model include intrinsic AMPK kinase activity, which is taken as an adjustable surrogate parameter for cellular energy level or AMP:ATP ratio, and rapamycin dose, which controls MTORC1 activity. Outputs of the model include the phosphorylation level of the translational repressor EIF4EBP1, a substrate of MTORC1, and the phosphorylation level of AMBRA1 (activating molecule in BECN1-regulated autophagy), a substrate of ULK1 critical for autophagosome formation. The model incorporates reciprocal regulation of mTORC1 and ULK1 by AMPK, mutual inhibition of MTORC1 and ULK1, and ULK1-mediated negative feedback regulation of AMPK. Through analysis of the model, we find that these processes may be responsible, depending on conditions, for graded responses to stress inputs, for bistable switching between autophagy and protein synthesis, or relaxation oscillations, comprising alternating periods of autophagy and protein synthesis. A sensitivity analysis indicates that the prediction of oscillatory behavior is robust to changes of the parameter values of the model. The model provides testable predictions about the behavior of the AMPK-MTORC1-ULK1 network, which plays a central role in maintaining cellular energy and nutrient homeostasis.

  7. Mutually Exclusive, Complementary, or . . .

    ERIC Educational Resources Information Center

    Schloemer, Cathy G.

    2016-01-01

    Whether students are beginning their study of probability or are well into it, distinctions between complementary sets and mutually exclusive sets can be confusing. Cathy Schloemer writes in this article that for years she used typical classroom examples but was not happy with the student engagement or the level of understanding they produced.…

  8. An approximately unbiased test of phylogenetic tree selection.

    PubMed

    Shimodaira, Hidetoshi

    2002-06-01

    An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap technique was developed for general hypothesis testing of regions in an attempt to reduce test bias. It was applied to maximum-likelihood tree selection for obtaining the confidence set of trees. The AU test is based on the theory of Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434; 1996), but the new method provides higher-order accuracy yet simpler implementation. The AU test, like the Shimodaira-Hasegawa (SH) test, adjusts the selection bias overlooked in the standard use of the bootstrap probability and Kishino-Hasegawa tests. The selection bias comes from comparing many trees at the same time and often leads to overconfidence in the wrong trees. The SH test, though safe to use, may exhibit another type of bias such that it appears conservative. Here I show that the AU test is less biased than other methods in typical cases of tree selection. These points are illustrated in a simulation study as well as in the analysis of mammalian mitochondrial protein sequences. The theoretical argument provides a simple formula that covers the bootstrap probability test, the Kishino-Hasegawa test, the AU test, and the Zharkikh-Li test. A practical suggestion is provided as to which test should be used under particular circumstances. PMID:12079646

  9. Within-subject template estimation for unbiased longitudinal image analysis

    PubMed Central

    Reuter, Martin; Schmansky, Nicholas J.; Rosas, H. Diana; Fischl, Bruce

    2012-01-01

    Longitudinal image analysis has become increasingly important in clinical studies of normal aging and neurodegenerative disorders. Furthermore, there is a growing appreciation of the potential utility of longitudinally acquired structural images and reliable image processing to evaluate disease modifying therapies. Challenges have been related to the variability that is inherent in the available cross-sectional processing tools, to the introduction of bias in longitudinal processing and to potential over-regularization. In this paper we introduce a novel longitudinal image processing framework, based on unbiased, robust, within-subject template creation, for automatic surface reconstruction and segmentation of brain MRI of arbitrarily many time points. We demonstrate that it is essential to treat all input images exactly the same as removing only interpolation asymmetries is not sufficient to remove processing bias. We successfully reduce variability and avoid over-regularization by initializing the processing in each time point with common information from the subject template. The presented results show a significant increase in precision and discrimination power while preserving the ability to detect large anatomical deviations; as such they hold great potential in clinical applications, e.g. allowing for smaller sample sizes or shorter trials to establish disease specific biomarkers or to quantify drug effects. PMID:22430496

  10. An Unbiased Oncology Compound Screen to Identify Novel Combination Strategies.

    PubMed

    O'Neil, Jennifer; Benita, Yair; Feldman, Igor; Chenard, Melissa; Roberts, Brian; Liu, Yaping; Li, Jing; Kral, Astrid; Lejnine, Serguei; Loboda, Andrey; Arthur, William; Cristescu, Razvan; Haines, Brian B; Winter, Christopher; Zhang, Theresa; Bloecher, Andrew; Shumway, Stuart D

    2016-06-01

    Combination drug therapy is a widely used paradigm for managing numerous human malignancies. In cancer treatment, additive and/or synergistic drug combinations can convert weakly efficacious monotherapies into regimens that produce robust antitumor activity. This can be explained in part through pathway interdependencies that are critical for cancer cell proliferation and survival. However, identification of the various interdependencies is difficult due to the complex molecular circuitry that underlies tumor development and progression. Here, we present a high-throughput platform that allows for an unbiased identification of synergistic and efficacious drug combinations. In a screen of 22,737 experiments of 583 doublet combinations in 39 diverse cancer cell lines using a 4 by 4 dosing regimen, both well-known and novel synergistic and efficacious combinations were identified. Here, we present an example of one such novel combination, a Wee1 inhibitor (AZD1775) and an mTOR inhibitor (ridaforolimus), and demonstrate that the combination potently and synergistically inhibits cancer cell growth in vitro and in vivo This approach has identified novel combinations that would be difficult to reliably predict based purely on our current understanding of cancer cell biology. Mol Cancer Ther; 15(6); 1155-62. ©2016 AACR. PMID:26983881

  11. All-optical control of ultrafast photocurrents in unbiased graphene

    PubMed Central

    Obraztsov, Petr A.; Kaplas, Tommi; Garnov, Sergey V.; Kuwata-Gonokami, Makoto; Obraztsov, Alexander N.; Svirko, Yuri P.

    2014-01-01

    Graphene has recently become a unique playground for studying light-matter interaction effects in low-dimensional electronic systems. Being of strong fundamental importance, these effects also open a wide range of opportunities in photonics and optoelectronics. In particular, strong and broadband light absorption in graphene allows one to achieve high carrier densities essential for observation of nonlinear optical phenomena. Here, we make use of strong photon-drag effect to generate and optically manipulate ultrafast photocurrents in graphene at room temperature. In contrast to the recent reports on injection of photocurrents in graphene due to external or built-in electric field effects and by quantum interference, we force the massless charge carriers to move via direct transfer of linear momentum from photons of incident laser beam to excited electrons in unbiased sample. Direction and amplitude of the drag-current induced in graphene are determined by polarization, incidence angle and intensity of the obliquely incident laser beam. We also demonstrate that the irradiation of graphene with two laser beams of the same wavelength offers an opportunity to manipulate the photocurrents in time domain. The obtained all-optical control of the photocurrents opens new routes towards graphene based high-speed and broadband optoelectronic devices. PMID:24500084

  12. Unbiased methods for removing systematics from galaxy clustering measurements

    NASA Astrophysics Data System (ADS)

    Elsner, Franz; Leistedt, Boris; Peiris, Hiranya V.

    2016-02-01

    Measuring the angular clustering of galaxies as a function of redshift is a powerful method for extracting information from the three-dimensional galaxy distribution. The precision of such measurements will dramatically increase with ongoing and future wide-field galaxy surveys. However, these are also increasingly sensitive to observational and astrophysical contaminants. Here, we study the statistical properties of three methods proposed for controlling such systematics - template subtraction, basic mode projection, and extended mode projection - all of which make use of externally supplied template maps, designed to characterize and capture the spatial variations of potential systematic effects. Based on a detailed mathematical analysis, and in agreement with simulations, we find that the template subtraction method in its original formulation returns biased estimates of the galaxy angular clustering. We derive closed-form expressions that should be used to correct results for this shortcoming. Turning to the basic mode projection algorithm, we prove it to be free of any bias, whereas we conclude that results computed with extended mode projection are biased. Within a simplified setup, we derive analytical expressions for the bias and discuss the options for correcting it in more realistic configurations. Common to all three methods is an increased estimator variance induced by the cleaning process, albeit at different levels. These results enable unbiased high-precision clustering measurements in the presence of spatially varying systematics, an essential step towards realizing the full potential of current and planned galaxy surveys.

  13. Unbiased diffusion of Brownian particles on disordered correlated potentials

    NASA Astrophysics Data System (ADS)

    Salgado-Garcia, Raúl; Maldonado, Cesar

    2015-06-01

    In this work we study the diffusion of non-interacting overdamped particles, moving on unbiased disordered correlated potentials, subjected to Gaussian white noise. We obtain an exact expression for the diffusion coefficient which allows us to prove that the unbiased diffusion of overdamped particles on a random polymer does not depend on the correlations of the disordered potentials. This universal behavior of the unbiased diffusivity is a direct consequence of the validity of the Einstein relation and the decay of correlations of the random polymer. We test the independence on correlations of the diffusion coefficient for correlated polymers produced by two different stochastic processes, a one-step Markov chain and the expansion-modification system. Within the accuracy of our simulations, we found that the numerically obtained diffusion coefficient for these systems agree with the analytically calculated ones, confirming our predictions.

  14. Estimating unbiased phenological trends by adapting site-occupancy models.

    PubMed

    Roth, Tobias; Strebel, Nicolas; Amrhein, Valentin

    2014-08-01

    As a response to climate warming, many animals and plants have been found to shift phenologies, such as appearance in spring or timing of reproduction. However, traditional measures for shifts in phenology that are based on observational data likely are biased due to a large influence of population size, observational effort, starting date of a survey, or other causes that may affect the probability of detecting a species. Understanding phenological responses of species to climate change, however, requires a robust measure that could be compared among studies and study years. Here, we developed a new method for estimating arrival and departure dates based on site-occupancy models. Using simulated data, we show that our method provided virtually unbiased estimates of phenological events even if detection probability or the number of sites occupied by the species is changing over time. To illustrate the flexibility of our method, we analyzed spring arrival of two long-distance migrant songbirds and the length of the flight period of two butterfly species, using data from a long-term biodiversity monitoring program in Switzerland. In contrast to many birds that migrate short distances, the two long-distance migrant songbirds tended to postpone average spring arrival by -0.5 days per year between 1995 and 2012. Furthermore, the flight period of the short-distance-flying butterfly species apparently became even shorter over the study period, while the flight period of the longer-distance-flying butterfly species remained relatively stable. Our method could be applied to temporally and spatially extensive data from a wide range of monitoring programs and citizen science projects, to help unravel how species and communities respond to global warming. PMID:25230466

  15. Extending unbiased stereology of brain ultrastructure to three-dimensional volumes

    NASA Technical Reports Server (NTRS)

    Fiala, J. C.; Harris, K. M.; Koslow, S. H. (Principal Investigator)

    2001-01-01

    OBJECTIVE: Analysis of brain ultrastructure is needed to reveal how neurons communicate with one another via synapses and how disease processes alter this communication. In the past, such analyses have usually been based on single or paired sections obtained by electron microscopy. Reconstruction from multiple serial sections provides a much needed, richer representation of the three-dimensional organization of the brain. This paper introduces a new reconstruction system and new methods for analyzing in three dimensions the location and ultrastructure of neuronal components, such as synapses, which are distributed non-randomly throughout the brain. DESIGN AND MEASUREMENTS: Volumes are reconstructed by defining transformations that align the entire area of adjacent sections. Whole-field alignment requires rotation, translation, skew, scaling, and second-order nonlinear deformations. Such transformations are implemented by a linear combination of bivariate polynomials. Computer software for generating transformations based on user input is described. Stereological techniques for assessing structural distributions in reconstructed volumes are the unbiased bricking, disector, unbiased ratio, and per-length counting techniques. A new general method, the fractional counter, is also described. This unbiased technique relies on the counting of fractions of objects contained in a test volume. A volume of brain tissue from stratum radiatum of hippocampal area CA1 is reconstructed and analyzed for synaptic density to demonstrate and compare the techniques. RESULTS AND CONCLUSIONS: Reconstruction makes practicable volume-oriented analysis of ultrastructure using such techniques as the unbiased bricking and fractional counter methods. These analysis methods are less sensitive to the section-to-section variations in counts and section thickness, factors that contribute to the inaccuracy of other stereological methods. In addition, volume reconstruction facilitates visualization

  16. Extending Unbiased Stereology of Brain Ultrastructure to Three-dimensional Volumes

    PubMed Central

    Fiala, John C.; Harris, Kristen M.

    2001-01-01

    Objective: Analysis of brain ultrastructure is needed to reveal how neurons communicate with one another via synapses and how disease processes alter this communication. In the past, such analyses have usually been based on single or paired sections obtained by electron microscopy. Reconstruction from multiple serial sections provides a much needed, richer representation of the three-dimensional organization of the brain. This paper introduces a new reconstruction system and new methods for analyzing in three dimensions the location and ultrastructure of neuronal components, such as synapses, which are distributed non-randomly throughout the brain. Design and Measurements: Volumes are reconstructed by defining transformations that align the entire area of adjacent sections. Whole-field alignment requires rotation, translation, skew, scaling, and second-order nonlinear deformations. Such transformations are implemented by a linear combination of bivariate polynomials. Computer software for generating transformations based on user input is described. Stereological techniques for assessing structural distributions in reconstructed volumes are the unbiased bricking, disector, unbiased ratio, and per-length counting techniques. A new general method, the fractional counter, is also described. This unbiased technique relies on the counting of fractions of objects contained in a test volume. A volume of brain tissue from stratum radiatum of hippocampal area CA1 is reconstructed and analyzed for synaptic density to demonstrate and compare the techniques. Results and Conclusion: Reconstruction makes practicable volume-oriented analysis of ultrastructure using such techniques as the unbiased bricking and fractional counter methods. These analysis methods are less sensitive to the section-to-section variations in counts and section thickness, factors that contribute to the inaccuracy of other stereological methods. In addition, volume reconstruction facilitates visualization

  17. Unbiased Estimates of Variance Components with Bootstrap Procedures

    ERIC Educational Resources Information Center

    Brennan, Robert L.

    2007-01-01

    This article provides general procedures for obtaining unbiased estimates of variance components for any random-model balanced design under any bootstrap sampling plan, with the focus on designs of the type typically used in generalizability theory. The results reported here are particularly helpful when the bootstrap is used to estimate standard…

  18. Research on the relationships of the domestic mutual investment of China based on the cross-shareholding networks of the listed companies

    NASA Astrophysics Data System (ADS)

    Ma, Yuan-yuan; Zhuang, Xin-tian; Li, Ling-xuan

    2011-02-01

    Enterprises are the core power and the carriers to promote the country's economy developing sustainably and rapidly; the listed enterprises are the outstanding companies which can represent the economic level at the places where the enterprises are located, so we establish the cross-shareholding networks of the listed companies between 2002 and 2009, and then analyze the mutual investment at company-level, province-level and region-level. We have researched the overall trend of economic development and the overall tendency of capital flow of China in the recent 8 years based on the cross-shareholding networks, the influence of a global economic crisis on the stock markets and the overall economics of China in 2008 and the recovery of the economy after the economic crisis. Moreover, we analyze the variations of the cross-shareholding networks and the influence of the state-owned large and medium enterprises listing frequently on Chinese stock markets. We divide the provinces of China into 3 main categories according to their industrial situations. Though the analysis, we find that the wealth gap between the different areas is not significantly reduced even though the government has carried out strategies such as the Development of the West Regions and the Rejuvenation of Old Industrial Bases in Northeastern China. We analyze the cumulative distribution function of the degree of the vertices and use large amounts of data to do empirical analysis. The methods used include the hierarchical cluster analysis, regression analysis, etc.

  19. Mutual synchronization of nanoconstriction-based spin Hall nano-oscillators through evanescent and propagating spin waves

    NASA Astrophysics Data System (ADS)

    Kendziorczyk, T.; Kuhn, T.

    2016-04-01

    We perform a micromagnetic study of the synchronization dynamics in nanoconstriction-based spin Hall nano-oscillator (SHNO) arrays. The simulation reveals that efficient synchronization in this kind of system is possible, and indicates that the synchronization is mediated by a combination of linear coupling through the overlap of localized modes and parametric coupling through propagating spin waves which are excited by the second harmonic oscillation in the SHNOs. Due to the anisotropic spin wave dispersion in the studied system, the synchronization properties decisively depend on the geometrical alignment of the SHNO array with respect to the external field. We find that, by utilizing the directional spin wave emission and correspondingly optimizing the alignment of the SHNO array, the synchronization is enhanced with a significant increase of the phase-locking bandwidth.

  20. Rhodamine based dual probes for selective detection of mercury and fluoride ions in water using two mutually independent sensing pathways.

    PubMed

    Kumari, Namita; Dey, Nilanjan; Bhattacharya, Santanu

    2014-05-21

    New rhodamine based molecules have been designed as dual probes for the ppb-level selective detection of Hg(2+) and F(-) ions in aqueous medium at physiological pH 7.4. The probes have been designed in such a way to utilize both the properties of the metal ion induced 'turn-on' detection mechanism of the spirolactam ring opening of the rhodamine moiety and the reaction based cleavage of the O-silyl bond in presence of the fluoride ion. The probes have been synthesized conveniently by coupling rhodamine hydrazone with O-silyl protected mono- and di-hydroxybenzaldehydes. Both the probes showed a 'turn-on' detection of the fluoride ion due to the cleavage of the O-silyl bond upon treatment with the added F(-) ion. However, the probes showed selective 'turn-on' detection of Hg(2+) ion by opening of the spirolactam ring. The two detection mechanisms worked in isolation and hence the corresponding spectral responses appeared completely independent of each other. The presence of Hg(2+) in solution induced generation of an intense pink color with bright green fluorescence emission. In contrast a deep yellow color with yellow fluorescence was observed upon addition of the fluoride ion to the probe solution. Two different mechanisms of interactions have been proposed on the basis of (1)H-NMR, IR and mass spectrometric studies. Thus, using a single probe the selective sensing of two different ions could be achieved in aqueous medium well below their permitted limit of detection. PMID:24669370

  1. Unbiased rigid registration using transfer functions

    NASA Astrophysics Data System (ADS)

    Hahn, Dieter A.; Hornegger, Joachim; Bautz, Werner; Kuwert, Torsten; Roemer, Wolfgang

    2005-04-01

    The evaluation of tumor growth as regression under therapy is an important clinical issue. Rigid registration of sequentially acquired 3D-images has proven its value for this purpose. Existing approaches to rigid image registration use the whole volume for the estimation of the rigid transform. Non-rigid soft tissue deformation, however, will imply a bias to the registration result, because local deformations cannot be modeled by rigid transforms. Anatomical substructures, like bones or teeth, are not affected by these deformations, but follow a rigid transform. This important observation is incorporated in the proposed registration algorithm. The selection of anatomical substructure is done by manual interaction of medical experts adjusting the transfer function of the volume rendering software. The parameters of the transfer function are used to identify the voxels that are considered for registration. A rigid transform is estimated by a quaternion gradient descent algorithm based on the intensity values of the specified tissue classes. Commonly used voxel intensity measures are adjusted to the modified registration algorithm. The contribution describes the mathematical framework of the proposed registration method and its implementation in a commercial software package. The experimental evaluation includes the discussion of different similarity measures, the comparison of the proposed method to established rigid registration techniques and the evaluation of the efficiency of the new method. We conclude with the discussion of potential medical applications of the proposed registration algorithm.

  2. The effect of turbulence on entanglement-based free-space quantum key distribution with photonic orbital angular momentum

    NASA Astrophysics Data System (ADS)

    Goyal, Sandeep K.; Hamadou Ibrahim, Alpha; Roux, Filippus S.; Konrad, Thomas; Forbes, Andrew

    2016-06-01

    Using an experimental setup that simulates a turbulent atmosphere, we study the secret key rate for quantum key distribution (QKD) protocols in orbital angular momentum based free space quantum communication. The QKD protocols under consideration include the Ekert 91 protocol for different choices of mutually unbiased bases and the six-state protocol. We find that the secret key rate of these protocols decay to zero, roughly at the same scale where the entanglement of formation decays to zero.

  3. Unbiased quantitative testing of conventional orthodontic beliefs.

    PubMed

    Baumrind, S

    1998-03-01

    This study used a preexisting database to test in hypothesis from the appropriateness of some common orthodontic beliefs concerning upper first molar displacement and changes in facial morphology associated with conventional full bonded/banded treatment in growing subjects. In an initial pass, the author used data from a stratified random sample of 48 subjects drawn retrospectively from the practice of a single, experienced orthodontist. This sample consisted of 4 subgroups of 12 subjects each: Class I nonextraction, Class I extraction, Class II nonextraction, and Class II extraction. The findings indicate that, relative to the facial profile, chin point did not, on average, displace anteriorly during treatment, either overall or in any subgroup. Relative to the facial profile, Point A became significantly less prominent during treatment, both overall and in each subgroup. The best estimate of the mean displacement of the upper molar cusp relative to superimposition on Anterior Cranial Base was in the mesial direction in each of the four subgroups. In only one extraction subject out of 24 did the cusp appear to be displaced distally. Mesial molar cusp displacement was significantly greater in the Class II extraction subgroup than in the Class II nonextraction subgroup. Relative to superimposition on anatomical "best fit" of maxillary structures, the findings for molar cusp displacement were similar, but even more dramatic. Mean mesial migration was highly significant in both the Class II nonextraction and Class II extraction subgroups. In no subject in the entire sample was distal displacement noted relative to this superimposition. Mean increase in anterior Total Face Height was significantly greater in the Class II extraction subgroup than in the Class II nonextraction subgroup. (This finding was contrary to the author's original expectation.) The generalizability of the findings from the initial pass to other treated growing subjects was then assessed by

  4. Mutual information and spontaneous symmetry breaking

    NASA Astrophysics Data System (ADS)

    Hamma, A.; Giampaolo, S. M.; Illuminati, F.

    2016-01-01

    We show that the metastable, symmetry-breaking ground states of quantum many-body Hamiltonians have vanishing quantum mutual information between macroscopically separated regions and are thus the most classical ones among all possible quantum ground states. This statement is obvious only when the symmetry-breaking ground states are simple product states, e.g., at the factorization point. On the other hand, symmetry-breaking states are in general entangled along the entire ordered phase, and to show that they actually feature the least macroscopic correlations compared to their symmetric superpositions is highly nontrivial. We prove this result in general, by considering the quantum mutual information based on the two-Rényi entanglement entropy and using a locality result stemming from quasiadiabatic continuation. Moreover, in the paradigmatic case of the exactly solvable one-dimensional quantum X Y model, we further verify the general result by considering also the quantum mutual information based on the von Neumann entanglement entropy.

  5. Classification of brain signals associated with imagination of hand grasping, opening and reaching by means of wavelet-based common spatial pattern and mutual information.

    PubMed

    Amanpour, Behzad; Erfanian, Abbas

    2013-01-01

    An important issue in designing a practical brain-computer interface (BCI) is the selection of mental tasks to be imagined. Different types of mental tasks have been used in BCI including left, right, foot, and tongue motor imageries. However, the mental tasks are different from the actions to be controlled by the BCI. It is desirable to select a mental task to be consistent with the desired action to be performed by BCI. In this paper, we investigated the detecting the imagination of the hand grasping, hand opening, and hand reaching in one hand using electroencephalographic (EEG) signals. The results show that the ERD/ERS patterns, associated with the imagination of hand grasping, opening, and reaching are different. For classification of brain signals associated with these mental tasks and feature extraction, a method based on wavelet packet, regularized common spatial pattern (CSP), and mutual information is proposed. The results of an offline analysis on five subjects show that the two-class mental tasks can be classified with an average accuracy of 77.6% using proposed method. In addition, we examine the proposed method on datasets IVa from BCI Competition III and IIa from BCI Competition IV. PMID:24110165

  6. Reconstructing palaeotemperatures for the Early and Middle Pleistocene using the mutual climatic range method based on plant fossils

    NASA Astrophysics Data System (ADS)

    Pross, Jörg; Klotz, Stefan; Mosbrugger, Volker

    2000-12-01

    A new approach is proposed to obtain quantitative temperature reconstructions from Early and Middle Pleistocene pollen and megafloral records. Utilizing the indicator species concept pioneered by Iversen (1944, Geologiska Föreningen Förhandlingar Stockholm 66, 463-483), the new methodology overcomes the problem of non-analogue plant communities by only taking into account the presence/absence of taxa rather than their relative abundances. Based on the present day thermal tolerances of the taxa from a fossil assemblage, the temperature interval in which all taxa from this assemblage can coexist is determined. A databank containing the climate tolerances of 85 taxa from European pollen records was established. To increase the temperature resolution of the method, procedures were developed to assess the most likely intervals for the actual temperatures within the calculated common thermospheres and the routine evaluation of the mean temperatures of the warmest and coldest months (MTW and MTC). After calibrating the approach on modern assemblages, it was applied to Tiglian and Holsteinian pollen sequences from Lieth (northern Germany) and Lac du Bourget (northern French Alps). For both records the method yields detailed temperature reconstructions of temperate and cold episodes. During the coldest episode of the Lieth section, the MTC may have been as low as -16°C. Corresponding MTW values range from 14.5 to 21°C, thus testifying to a strong continentality at that time. During the warmest period reconstructed for the Lieth section, the MTC was similar to the value as measured in the area today (1.5°C), whereas the MTW was probably higher than at present (20.1°C). For the coldest interval from the Lac du Bourget pollen sequence, the reconstructed MTC values reach a minimum of -15°C. Corresponding MTW values range from 15 to 22°C, again implying a strong continentality. For the warmest period our approach yields MTC values between -2 and 2°C and MTW values

  7. Mutual information rate and bounds for it.

    PubMed

    Baptista, Murilo S; Rubinger, Rero M; Viana, Emilson R; Sartorelli, José C; Parlitz, Ulrich; Grebogi, Celso

    2012-01-01

    The amount of information exchanged per unit of time between two nodes in a dynamical network or between two data sets is a powerful concept for analysing complex systems. This quantity, known as the mutual information rate (MIR), is calculated from the mutual information, which is rigorously defined only for random systems. Moreover, the definition of mutual information is based on probabilities of significant events. This work offers a simple alternative way to calculate the MIR in dynamical (deterministic) networks or between two time series (not fully deterministic), and to calculate its upper and lower bounds without having to calculate probabilities, but rather in terms of well known and well defined quantities in dynamical systems. As possible applications of our bounds, we study the relationship between synchronisation and the exchange of information in a system of two coupled maps and in experimental networks of coupled oscillators. PMID:23112809

  8. Mutually temporally independent connectivity patterns: a new framework to study the dynamics of brain connectivity at rest with application to explain group difference based on gender.

    PubMed

    Yaesoubi, Maziar; Miller, Robyn L; Calhoun, Vince D

    2015-02-15

    Functional connectivity analysis of the human brain is an active area in fMRI research. It focuses on identifying meaningful brain networks that have coherent activity either during a task or in the resting state. These networks are generally identified either as collections of voxels whose time series correlate strongly with a pre-selected region or voxel, or using data-driven methodologies such as independent component analysis (ICA) that compute sets of maximally spatially independent voxel weightings (component spatial maps (SMs)), each associated with a single time course (TC). Studies have shown that regardless of the way these networks are defined, the activity coherence among them has a dynamic nature which is hard to estimate with global coherence analysis such as correlation or mutual information. Sliding window analyses in which functional network connectivity (FNC) is estimated separately at each time window is one of the more widely employed approaches to studying the dynamic nature of functional network connectivity (dFNC). Observed FNC patterns are summarized and replaced with a smaller set of prototype connectivity patterns ("states" or "components"), and then a dynamical analysis is applied to the resulting sequences of prototype states. In this work we are looking for a small set of connectivity patterns whose weighted contributions to the dynamically changing dFNCs are independent of each other in time. We discuss our motivation for this work and how it differs from existing approaches. Also, in a group analysis based on gender we show that males significantly differ from females by occupying significantly more combinations of these connectivity patterns over the course of the scan. PMID:25485713

  9. Child Temperament Moderates Effects of Parent-Child Mutuality on Self-Regulation: A Relationship-Based Path for Emotionally Negative Infants

    ERIC Educational Resources Information Center

    Kim, Sanghag; Kochanska, Grazyna

    2012-01-01

    This study examined infants' negative emotionality as moderating the effect of parent-child mutually responsive orientation (MRO) on children's self-regulation (n = 102). Negative emotionality was observed in anger-eliciting episodes and in interactions with parents at 7 months. MRO was coded in naturalistic interactions at 15 months.…

  10. The Evolution of Interspecific Mutualisms

    NASA Astrophysics Data System (ADS)

    Doebeli, Michael; Knowlton, Nancy

    1998-07-01

    Interspecific mutualisms are widespread, but how they evolve is not clear. The Iterated Prisoner's Dilemma is the main theoretical tool to study cooperation, but this model ignores ecological differences between partners and assumes that amounts exchanged cannot themselves evolve. A more realistic model incorporating these features shows that strategies that succeed with fixed exchanges (e.g., Tit-for-Tat) cannot explain mutualism when exchanges vary because the amount exchanged evolves to 0. For mutualism to evolve, increased investments in a partner must yield increased returns, and spatial structure in competitive interactions is required. Under these biologically plausible assumptions, mutualism evolves with surprising ease. This suggests that, contrary to the basic premise of past theoretical analyses, overcoming a potential host's initial defenses may be a bigger obstacle for mutualism than the subsequent recurrence and spread of noncooperative mutants.

  11. [Human cerebral image registration using generalized mutual information].

    PubMed

    Zhang, Jingzhou; Li, Ting; Zhang, Jia

    2008-12-01

    Medical image registration is a highlight of actual research on medical image processing. Based onsimilarity measure of Shannon entropy, a new generalized distance measurement based on Rényi entropy applied to image rigid registration is introduced and is called here generalized mutual information (GMI). It is used in three dimensional cerebral image registration experiments. The simulation results show that generalized distance measurement and Shannon entropy measurement apply to different areas; that the registration measure based o n generalized distance is a natural extension of mutual information of Shannon entropy. The results prove that generalized mutual information uses less time than simple mutual information does, and the new similarity measure manifests higher degree of consistency between the two cerebral registration images. Also, the registration results provide the clinical diagnoses with more important references. In conclusion, generalized mutual information has satisfied the demands of clinical application to a wide extent. PMID:19166197

  12. [Biological mutualism, concepts and models].

    PubMed

    Perru, Olivier

    2011-01-01

    Mutualism is a biological association for a mutual benefit between two different species. In this paper, firstly, we examine the history and signification of mutualism in relation to symbiosis. Then, we consider the link between concepts and models of mutualism. Models of mutualism depend on different concepts we use: If mutualism is situated at populations' level, it will be expressed by Lotka-Volterra models, concerning exclusively populations' size. If mutualism is considered as a resources' exchange or a biological market increasing the fitness of these organisms, it will be described at an individual level by a cost-benefit model. Our analysis will be limited to the history and epistemology of Lotka-Volterra models and we hypothesize that these models are adapted at first to translate dynamic evolutions of mutualism. They render stability or variations of size and assume that there are clear distinctions and a state of equilibrium between populations of different species. Italian mathematician Vito Volterra demonstrated that biological associations consist in a constant relation between some species. In 1931 and 1935, Volterra described the general form of antagonistic or mutualistic biological associations by the same differential equations. We recognize that these equations have been more used to model competition or prey-predator interactions, but a simple sign change allows describing mutualism. The epistemological problem is the following: Volterra's equations help us to conceptualize a global phenomenon. However, mutualistic interactions may have stronger effects away from equilibrium and these effects may be better understood at individual level. We conclude that, between 1985 and 2000, some researchers carried on working and converting Lotka-Volterra models but this description appeared as insufficient. So, other researchers adopted an economical viewpoint, considering mutualism as a biological market. PMID:22288336

  13. Unbiased estimation of mutation rates under fluctuating final counts.

    PubMed

    Ycart, Bernard; Veziris, Nicolas

    2014-01-01

    Estimation methods for mutation rates (or probabilities) in Luria-Delbrück fluctuation analysis usually assume that the final number of cells remains constant from one culture to another. We show that this leads to systematically underestimate the mutation rate. Two levels of information on final numbers are considered: either the coefficient of variation has been independently estimated, or the final number of cells in each culture is known. In both cases, unbiased estimation methods are proposed. Their statistical properties are assessed both theoretically and through Monte-Carlo simulation. As an application, the data from two well known fluctuation analysis studies on Mycobacterium tuberculosis are reexamined. PMID:24988217

  14. Mobility of Holstein Polaron at Finite Temperature: An Unbiased Approach

    NASA Astrophysics Data System (ADS)

    Mishchenko, A. S.; Nagaosa, N.; De Filippis, G.; de Candia, A.; Cataudella, V.

    2015-04-01

    We present the first unbiased results for the mobility μ of a one-dimensional Holstein polaron obtained by numerical analytic continuation combined with diagrammatic and worldline Monte Carlo methods in the thermodynamic limit. We have identified for the first time several distinct regimes in the λ -T plane including a band conduction region, incoherent metallic region, an activated hopping region, and a high-temperature saturation region. We observe that although mobilities and mean free paths at different values of λ differ by many orders of magnitude at small temperatures, their values at T larger than the bandwidth become very close to each other.

  15. Grief and Palliative Care: Mutuality

    PubMed Central

    Moon, Paul J

    2013-01-01

    Grief and palliative care are interrelated and perhaps mutually inclusive. Conceptually and practically, grief intimately relates to palliative care, as both domains regard the phenomena of loss, suffering, and a desire for abatement of pain burden. Moreover, the notions of palliative care and grief may be construed as being mutually inclusive in terms of one cueing the other. As such, the discussions in this article will center on the conceptualizations of the mutuality between grief and palliative care related to end-of-life circumstances. Specifically, the complementarity of grief and palliative care, as well as a controvertible view thereof, will be considered. PMID:25278758

  16. Improving Agricultural Drought Monitoring in East Africa with Unbiased Rainfall Fields and Detailed Land Surface Physics

    NASA Astrophysics Data System (ADS)

    McNally, A.; Yatheendradas, S.; Peters-Lidard, C. D.; Michaelsen, J.

    2010-12-01

    Monitoring drought is particularly challenging within rainfed agricultural and pastoral systems, where it can serve the greatest need. Such locations often have sparse or non-existent ground based measurements of precipitation, evapotranspiration (ET), and soil moisture. For more effective drought monitoring with limited hydroclimate observations, we simulate land surface states using the Community Noah Land Surface Model forced with different merged rainfall products inside a Land Information System (LIS). Using model outputs we will answer the questions: How sensitive are soil moisture and ET fields to differences in rainfall forcing and model physics? What are acceptable drought-specific tradeoffs between near-real time availability and skill of rainfall data? Preliminary results with the African Rainfall Estimation Algorithm Version 2 (RFE2.0) outperformed global products, suggesting that sub-global rainfall estimates are the way forward for regional drought monitoring. Specifically, the Noah model forced with RFE2.0 better resolved the heterogeneous patterns in crop stress than the Famine Early Warning System Network (FEWS NET) operational Water Requirement Satisfaction Index (WRSI) model. To further investigate the improvement in drought monitoring while maintaining timeliness, we unbias (using Africa specific climatology) the precipitation products from CPC Merged Analysis of Precipitation (CMAP), Tropical Rainfall Measurement Mission (TRMM), and RFE2.0. The skill (relative accuracy) and reliability (average agreement) of the unbiased rainfall are calculated against an unbiased precipitation product augmented with station data from Ethiopia and Kenya. Soil moisture and ET fields from Noah are compared to the operational FEWS NET WRSI, soil water anomaly index, and the World Food Program’s Crop and Food Security Assessment Mission reports. We anticipate that the unbiased rainfall fields will improve the accuracy, spatio-temporal resolution, and

  17. Far-infrared observations of an unbiased sample of gamma-ray burst host galaxies

    NASA Astrophysics Data System (ADS)

    Kohn, S. A.; Michałowski, M. J.; Bourne, N.; Baes, M.; Fritz, J.; Cooray, A.; De Looze, I.; De Zotti, G.; Dannerbauer, H.; Dunne, L.; Dye, S.; Eales, S.; Furlanetto, C.; Gonzalez-Nuevo, J.; Ibar, E.; Ivison, R. J.; Maddox, S. J.; Scott, D.; Smith, D. J. B.; Smith, M. W. L.; Symeonidis, M.; Valiante, E.

    2015-04-01

    Gamma-ray bursts (GRBs) are the most energetic phenomena in the Universe; believed to result from the collapse and subsequent explosion of massive stars. Even though it has profound consequences for our understanding of their nature and selection biases, little is known about the dust properties of the galaxies hosting GRBs. We present analysis of the far-infrared properties of an unbiased sample of 20 BeppoSAX and Swift GRB host galaxies (at an average redshift of z = 3.1) located in the Herschel Astrophysical Terahertz Large Area Survey, the Herschel Virgo Cluster Survey, the Herschel Fornax Cluster Survey, the Herschel Stripe 82 Survey and the Herschel Multi-tiered Extragalactic Survey, totalling 880 deg2, or ˜3 per cent of the sky in total. Our sample selection is serendipitous, based only on whether the X-ray position of a GRB lies within a large-scale Herschel survey - therefore our sample can be considered completely unbiased. Using deep data at wavelengths of 100-500 μm, we tentatively detected 1 out of 20 GRB hosts located in these fields. We constrain their dust masses and star formation rates (SFRs), and discuss these in the context of recent measurements of submillimetre galaxies and ultraluminous infrared galaxies. The average far-infrared flux of our sample gives an upper limit on SFR of <114 M⊙ yr-1. The detection rate of GRB hosts is consistent with that predicted assuming that GRBs trace the cosmic SFR density in an unbiased way, i.e. that the fraction of GRB hosts with SFR > 500 M⊙ yr-1 is consistent with the contribution of such luminous galaxies to the cosmic star formation density.

  18. Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination.

    PubMed

    Bolland, Daniel J; Koohy, Hashem; Wood, Andrew L; Matheson, Louise S; Krueger, Felix; Stubbington, Michael J T; Baizan-Edge, Amanda; Chovanec, Peter; Stubbs, Bryony A; Tabbada, Kristina; Andrews, Simon R; Spivakov, Mikhail; Corcoran, Anne E

    2016-06-14

    Variable (V), diversity (D), and joining (J) (V(D)J) recombination is the first determinant of antigen receptor diversity. Understanding how recombination is regulated requires a comprehensive, unbiased readout of V gene usage. We have developed VDJ sequencing (VDJ-seq), a DNA-based next-generation-sequencing technique that quantitatively profiles recombination products. We reveal a 200-fold range of recombination efficiency among recombining V genes in the primary mouse Igh repertoire. We used machine learning to integrate these data with local chromatin profiles to identify combinatorial patterns of epigenetic features that associate with active VH gene recombination. These features localize downstream of VH genes and are excised by recombination, revealing a class of cis-regulatory element that governs recombination, distinct from expression. We detect two mutually exclusive chromatin signatures at these elements, characterized by CTCF/RAD21 and PAX5/IRF4, which segregate with the evolutionary history of associated VH genes. Thus, local chromatin signatures downstream of VH genes provide an essential layer of regulation that determines recombination efficiency. PMID:27264181

  19. Toward automated quantification of biological microstructures using unbiased stereology

    NASA Astrophysics Data System (ADS)

    Bonam, Om P.; Elozory, Daniel; Kramer, Kurt; Goldgof, Dmitry; Hall, Lawrence O.; Mangual, Osvaldo; Mouton, Peter R.

    2011-03-01

    Quantitative analysis of biological microstructures using unbiased stereology plays a large and growing role in bioscience research. Our aim is to add a fully automatic, high-throughput mode to a commercially available, computerized stereology device (Stereologer). The current method for estimation of first- and second order parameters of biological microstructures, requires a trained user to manually select objects of interest (cells, fibers etc.,) while stepping through the depth of a stained tissue section in fixed intervals. The proposed approach uses a combination of color and gray-level processing. Color processing is used to identify the objects of interest, by training on the images to obtain the threshold range for objects of interest. In gray-level processing, a region-growing approach was used to assign a unique identity to the objects of interest and enumerate them. This automatic approach achieved an overall object detection rate of 93.27%. Thus, these results support the view that automatic color and gray-level processing combined with unbiased sampling and assumption and model-free geometric probes can provide accurate and efficient quantification of biological objects.

  20. Reveal quantum correlation in complementary bases

    PubMed Central

    Wu, Shengjun; Ma, Zhihao; Chen, Zhihua; Yu, Sixia

    2014-01-01

    An essential feature of genuine quantum correlation is the simultaneous existence of correlation in complementary bases. We reveal this feature of quantum correlation by defining measures based on invariance under a basis change. For a bipartite quantum state, the classical correlation is the maximal correlation present in a certain optimum basis, while the quantum correlation is characterized as a series of residual correlations in the mutually unbiased bases. Compared with other approaches to quantify quantum correlation, our approach gives information-theoretical measures that directly reflect the essential feature of quantum correlation. PMID:24503595

  1. Construction of an Unbiased Spatio-temporal Atlas of the Tongue During Speech

    PubMed Central

    Woo, Jonghye; Xing, Fangxu; Lee, Junghoon; Stone, Maureen; Prince, Jerry L.

    2016-01-01

    Quantitative characterization and comparison of tongue motion during speech and swallowing present fundamental challenges because of striking variations in tongue structure and motion across subjects. A reliable and objective description of the dynamics tongue motion requires the consistent integration of inter-subject variability to detect the subtle changes in populations. To this end, in this work, we present an approach to constructing an unbiased spatio-temporal atlas of the tongue during speech for the first time, based on cine-MRI from twenty two normal subjects. First, we create a common spatial space using images from the reference time frame, a neutral position, in which the unbiased spatio-temporal atlas can be created. Second, we transport images from all time frames of all subjects into this common space via the single transformation. Third, we construct atlases for each time frame via groupwise diffeomorphic registration, which serves as the initial spatio-temporal atlas. Fourth, we update the spatio-temporal atlas by realigning each time sequence based on the Lipschitz norm on diffeomorphisms between each subject and the initial atlas. We evaluate and compare different configurations such as similarity measures to build the atlas. Our proposed method permits to accurately and objectively explain the main pattern of tongue surface motion. PMID:26221715

  2. Unbiased water and methanol maser surveys of NGC 1333

    SciTech Connect

    Lyo, A-Ran; Kim, Jongsoo; Byun, Do-Young; Lee, Ho-Gyu

    2014-11-01

    We present the results of unbiased 22 GHz H{sub 2}O water and 44 GHz class I CH{sub 3}OH methanol maser surveys in the central 7' × 10' area of NGC 1333 and two additional mapping observations of a 22 GHz water maser in a ∼3' × 3' area of the IRAS4A region. In the 22 GHz water maser survey of NGC 1333 with a sensitivity of σ ∼ 0.3 Jy, we confirmed the detection of masers toward H{sub 2}O(B) in the region of HH 7-11 and IRAS4B. We also detected new water masers located ∼20'' away in the western direction of IRAS4B or ∼25'' away in the southern direction of IRAS4A. We could not, however, find young stellar objects or molecular outflows associated with them. They showed two different velocity components of ∼0 and ∼16 km s{sup –1}, which are blue- and redshifted relative to the adopted systemic velocity of ∼7 km s{sup –1} for NGC 1333. They also showed time variabilities in both intensity and velocity from multi-epoch observations and an anti-correlation between the intensities of the blue- and redshifted velocity components. We suggest that the unidentified power source of these masers might be found in the earliest evolutionary stage of star formation, before the onset of molecular outflows. Finding this kind of water maser is only possible through an unbiased blind survey. In the 44 GHz methanol maser survey with a sensitivity of σ ∼ 0.5 Jy, we confirmed masers toward IRAS4A2 and the eastern shock region of IRAS2A. Both sources are also detected in 95 and 132 GHz methanol maser lines. In addition, we had new detections of methanol masers at 95 and 132 GHz toward IRAS4B. In terms of the isotropic luminosity, we detected methanol maser sources brighter than ∼5 × 10{sup 25} erg s{sup –1} from our unbiased survey.

  3. 26 CFR 1.831-3 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 26 Internal Revenue 8 2010-04-01 2010-04-01 false Tax on insurance companies (other than life or...-3 Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual... insurance companies, other than life or mutual or foreign insurance companies not carrying on an...

  4. An Example of an Improvable Rao–Blackwell Improvement, Inefficient Maximum Likelihood Estimator, and Unbiased Generalized Bayes Estimator

    PubMed Central

    Galili, Tal; Meilijson, Isaac

    2016-01-01

    The Rao–Blackwell theorem offers a procedure for converting a crude unbiased estimator of a parameter θ into a “better” one, in fact unique and optimal if the improvement is based on a minimal sufficient statistic that is complete. In contrast, behind every minimal sufficient statistic that is not complete, there is an improvable Rao–Blackwell improvement. This is illustrated via a simple example based on the uniform distribution, in which a rather natural Rao–Blackwell improvement is uniformly improvable. Furthermore, in this example the maximum likelihood estimator is inefficient, and an unbiased generalized Bayes estimator performs exceptionally well. Counterexamples of this sort can be useful didactic tools for explaining the true nature of a methodology and possible consequences when some of the assumptions are violated. [Received December 2014. Revised September 2015.

  5. 31 CFR 1024.220 - Customer identification programs for mutual funds.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... information available, and the mutual fund's customer base. At a minimum, these procedures must contain the... mutual fund must retain the information in paragraph (a)(3)(i)(A) of this section for five years after the date the account is closed. The mutual fund must retain the information in paragraphs...

  6. 31 CFR 1024.220 - Customer identification programs for mutual funds.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... information available, and the mutual fund's customer base. At a minimum, these procedures must contain the... mutual fund must retain the information in paragraph (a)(3)(i)(A) of this section for five years after the date the account is closed. The mutual fund must retain the information in paragraphs...

  7. 31 CFR 1024.220 - Customer identification programs for mutual funds.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... information available, and the mutual fund's customer base. At a minimum, these procedures must contain the... mutual fund must retain the information in paragraph (a)(3)(i)(A) of this section for five years after the date the account is closed. The mutual fund must retain the information in paragraphs...

  8. 31 CFR 1024.220 - Customer identification programs for mutual funds.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... information available, and the mutual fund's customer base. At a minimum, these procedures must contain the... mutual fund must retain the information in paragraph (a)(3)(i)(A) of this section for five years after the date the account is closed. The mutual fund must retain the information in paragraphs...

  9. Maximum likelihood: Extracting unbiased information from complex networks

    NASA Astrophysics Data System (ADS)

    Garlaschelli, Diego; Loffredo, Maria I.

    2008-07-01

    The choice of free parameters in network models is subjective, since it depends on what topological properties are being monitored. However, we show that the maximum likelihood (ML) principle indicates a unique, statistically rigorous parameter choice, associated with a well-defined topological feature. We then find that, if the ML condition is incompatible with the built-in parameter choice, network models turn out to be intrinsically ill defined or biased. To overcome this problem, we construct a class of safely unbiased models. We also propose an extension of these results that leads to the fascinating possibility to extract, only from topological data, the “hidden variables” underlying network organization, making them “no longer hidden.” We test our method on World Trade Web data, where we recover the empirical gross domestic product using only topological information.

  10. Biased and unbiased strategies to identify biologically active small molecules.

    PubMed

    Abet, Valentina; Mariani, Angelica; Truscott, Fiona R; Britton, Sébastien; Rodriguez, Raphaël

    2014-08-15

    Small molecules are central players in chemical biology studies. They promote the perturbation of cellular processes underlying diseases and enable the identification of biological targets that can be validated for therapeutic intervention. Small molecules have been shown to accurately tune a single function of pluripotent proteins in a reversible manner with exceptional temporal resolution. The identification of molecular probes and drugs remains a worthy challenge that can be addressed by the use of biased and unbiased strategies. Hypothesis-driven methodologies employs a known biological target to synthesize complementary hits while discovery-driven strategies offer the additional means of identifying previously unanticipated biological targets. This review article provides a general overview of recent synthetic frameworks that gave rise to an impressive arsenal of biologically active small molecules with unprecedented cellular mechanisms. PMID:24811300

  11. Unbiased sampling of globular lattice proteins in three dimensions.

    PubMed

    Jacobsen, Jesper Lykke

    2008-03-21

    We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular proteins, upon adding suitable local interactions. Our algorithm can easily be equipped with such interactions, but we study here mainly the flexible homopolymer case where each conformation is generated with uniform probability. We argue that the algorithm is ergodic and has dynamical exponent z=0. We then use it to study polymers of size up to 64(3)=262 144 monomers. Results are presented for the effective interaction between end points, and the interaction with the boundaries of the system. PMID:18517831

  12. Viscosity and mutual diffusion in strongly asymmetric plasma mixtures

    SciTech Connect

    Bastea, S

    2004-09-07

    The authors present molecular dynamics simulation results for the viscosity and mutual diffusion constant of a strongly asymmetric two-component plasma (TCP). They compare the results with available theoretical models previously tested for much smaller asymmetries. for the case of viscosity they propose a new predictive framework based on the linear mixing rule, while for mutual diffusion they point out some consistency problems of widely used Boltzmann equation based models.

  13. Automotive radar - investigation of mutual interference mechanisms

    NASA Astrophysics Data System (ADS)

    Goppelt, M.; Blöcher, H.-L.; Menzel, W.

    2010-09-01

    In the past mutual interference between automotive radar sensors has not been regarded as a major problem. With an increasing number of such systems, however, this topic is receiving more and more attention. The investigation of mutual interference and countermeasures is therefore one topic of the joint project "Radar on Chip for Cars" (RoCC) funded by the German Federal Ministry of Education and Research (BMBF). RoCC's goal is to pave the way for the development of high-performance, low-cost 79 GHz radar sensors based on Silicon-Germanium (SiGe) Monolithic Microwave Integrated Circuits (MMICs). This paper will present some generic interference scenarios and report on the current status of the analysis of interference mechanisms.

  14. Hierarchical clustering using mutual information

    NASA Astrophysics Data System (ADS)

    Kraskov, A.; Stögbauer, H.; Andrzejak, R. G.; Grassberger, P.

    2005-04-01

    We present a conceptually simple method for hierarchical clustering of data called mutual information clustering (MIC) algorithm. It uses mutual information (MI) as a similarity measure and exploits its grouping property: The MI between three objects X, Y, and Z is equal to the sum of the MI between X and Y, plus the MI between Z and the combined object (XY). We use this both in the Shannon (probabilistic) version of information theory and in the Kolmogorov (algorithmic) version. We apply our method to the construction of phylogenetic trees from mitochondrial DNA sequences and to the output of independent components analysis (ICA) as illustrated with the ECG of a pregnant woman.

  15. Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures

    SciTech Connect

    Procacci, Piero

    2015-04-21

    In this paper, we present an improved method for obtaining unbiased estimates of the free energy difference between two thermodynamic states using the work distribution measured in nonequilibrium driven experiments connecting these states. The method is based on the assumption that any observed work distribution is given by a mixture of Gaussian distributions, whose normal components are identical in either direction of the nonequilibrium process, with weights regulated by the Crooks theorem. Using the prototypical example for the driven unfolding/folding of deca-alanine, we show that the predicted behavior of the forward and reverse work distributions, assuming a combination of only two Gaussian components with Crooks derived weights, explains surprisingly well the striking asymmetry in the observed distributions at fast pulling speeds. The proposed methodology opens the way for a perfectly parallel implementation of Jarzynski-based free energy calculations in complex systems.

  16. Mutual information analysis of JPEG2000 contexts

    NASA Astrophysics Data System (ADS)

    Liu, Zhen; Karam, Lina J.

    2003-05-01

    Context-based arithmetic coding has been widely adopted in image and video compression and is a key component of the new JPEG2000 image compression standard. In this paper, the contexts used in JPEG2000 are analyzed using the mutual information, which has a direct link with the compression performance. We first show that, when combining the contexts, the mutual information between the contexts and the encoded data will decrease unless the conditional probability distributions of the combined contexts are the same. Given I, the initial number of contexts, and F, the final desired number of contexts, there are S(I, F) possible context classification schemes where S(I, F) is called the Stirling number of the second kind. The optimal classification scheme is the one that gives the maximum mutual information. Instead of exhaustive search, the optimal classification scheme can be obtained through a modified Generalized Lloyd algorithm with the relative entropy as the distortion metric. For binary arithmetic coding, the search complexity can be reduced by using the dynamic programming. Our experimental results show that the JPEG2000 contexts capture very well the correlations among the wavelet coefficients. At the same time, the number of contexts used as part of the standard can be reduced without loss in the coding performance.

  17. Mutual Gains Means Everyone Wins.

    ERIC Educational Resources Information Center

    Flaherty, Bernard L.

    1997-01-01

    Mutual gains negotiation is an innovative system that emphasizes interests instead of positions and problem solving instead of preconceived solutions. The process can reverse social disintegration, reverse worker alienation, and address a shifting educational environment. It can resolve difficult labor-management problems such as contracting out,…

  18. Mutual Respect and Civic Education

    ERIC Educational Resources Information Center

    Bird, Colin

    2010-01-01

    Contemporary theories of civic education frequently appeal to an ideal of mutual respect in the context of ethical, ethical and religious disagreement. This paper critically examines two recently popular criticisms of this ideal. The first, coming from a postmodern direction, charges that the ideal is hypocritical in its effort to be maximally…

  19. FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data

    PubMed Central

    Min, Junhong; Vonesch, Cédric; Kirshner, Hagai; Carlini, Lina; Olivier, Nicolas; Holden, Seamus; Manley, Suliana; Ye, Jong Chul; Unser, Michael

    2014-01-01

    Super resolution microscopy such as STORM and (F)PALM is now a well known method for biological studies at the nanometer scale. However, conventional imaging schemes based on sparse activation of photo-switchable fluorescent probes have inherently slow temporal resolution which is a serious limitation when investigating live-cell dynamics. Here, we present an algorithm for high-density super-resolution microscopy which combines a sparsity-promoting formulation with a Taylor series approximation of the PSF. Our algorithm is designed to provide unbiased localization on continuous space and high recall rates for high-density imaging, and to have orders-of-magnitude shorter run times compared to previous high-density algorithms. We validated our algorithm on both simulated and experimental data, and demonstrated live-cell imaging with temporal resolution of 2.5 seconds by recovering fast ER dynamics. PMID:24694686

  20. Cluster-span threshold: An unbiased threshold for binarising weighted complete networks in functional connectivity analysis.

    PubMed

    Smith, Keith; Azami, Hamed; Parra, Mario A; Starr, John M; Escudero, Javier

    2015-08-01

    We propose a new unbiased threshold for network analysis named the Cluster-Span Threshold (CST). This is based on the clustering coefficient, C, following logic that a balance of `clustering' to `spanning' triples results in a useful topology for network analysis and that the product of complementing properties has a unique value only when perfectly balanced. We threshold networks by fixing C at this balanced value, rather than fixing connection density at an arbitrary value, as has been the trend. We compare results from an electroencephalogram data set of volunteers performing visual short term memory tasks of the CST alongside other thresholds, including maximum spanning trees. We find that the CST holds as a sensitive threshold for distinguishing differences in the functional connectivity between tasks. This provides a sensitive and objective method for setting a threshold on weighted complete networks which may prove influential on the future of functional connectivity research. PMID:26736883

  1. Unbiased contaminant removal for 3D galaxy power spectrum measurements

    NASA Astrophysics Data System (ADS)

    Kalus, B.; Percival, W. J.; Bacon, D. J.; Samushia, L.

    2016-08-01

    We assess and develop techniques to remove contaminants when calculating the 3D galaxy power spectrum. We separate the process into three separate stages: (i) removing the contaminant signal, (ii) estimating the uncontaminated cosmological power spectrum, (iii) debiasing the resulting estimates. For (i), we show that removing the best-fit contaminant (mode subtraction), and setting the contaminated components of the covariance to be infinite (mode deprojection) are mathematically equivalent. For (ii), performing a Quadratic Maximum Likelihood (QML) estimate after mode deprojection gives an optimal unbiased solution, although it requires the manipulation of large N_mode^2 matrices (Nmode being the total number of modes), which is unfeasible for recent 3D galaxy surveys. Measuring a binned average of the modes for (ii) as proposed by Feldman, Kaiser & Peacock (1994, FKP) is faster and simpler, but is sub-optimal and gives rise to a biased solution. We present a method to debias the resulting FKP measurements that does not require any large matrix calculations. We argue that the sub-optimality of the FKP estimator compared with the QML estimator, caused by contaminants is less severe than that commonly ignored due to the survey window.

  2. 26 CFR 1.831-3 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual...

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 26 Internal Revenue 8 2012-04-01 2012-04-01 false Tax on insurance companies (other than life or... Companies § 1.831-3 Tax on insurance companies (other than life or mutual), mutual marine insurance...) All insurance companies, other than life or mutual or foreign insurance companies not carrying on...

  3. 26 CFR 1.831-3 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 26 Internal Revenue 8 2011-04-01 2011-04-01 false Tax on insurance companies (other than life or... Companies § 1.831-3 Tax on insurance companies (other than life or mutual), mutual marine insurance...) All insurance companies, other than life or mutual or foreign insurance companies not carrying on...

  4. 26 CFR 1.831-3 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual...

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 26 Internal Revenue 8 2013-04-01 2013-04-01 false Tax on insurance companies (other than life or... Companies § 1.831-3 Tax on insurance companies (other than life or mutual), mutual marine insurance...) All insurance companies, other than life or mutual or foreign insurance companies not carrying on...

  5. 26 CFR 1.831-3 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual...

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 26 Internal Revenue 8 2014-04-01 2014-04-01 false Tax on insurance companies (other than life or... Companies § 1.831-3 Tax on insurance companies (other than life or mutual), mutual marine insurance...) All insurance companies, other than life or mutual or foreign insurance companies not carrying on...

  6. Mutual impedance computation between printed dipoles

    NASA Astrophysics Data System (ADS)

    Alexopoulos, N. G.; Rana, I. E.

    1981-01-01

    The mutual impedance between microstrip dipoles printed on a grounded substrate is computed. Results for the microstrip dipoles in broadside, collinear, and echelon arrangements are presented. The significance of surface wave to mutual coupling is discussed.

  7. Pluto-charon mutual events

    SciTech Connect

    Binzel, R.P. )

    1989-11-01

    Since 1985, planetary astronomers have been working to take advantage of a once-per-century apparent alignment between Pluto and its satellite, Charon, which has allowed mutual occultation and transit events to be observed. There events, which will cease in 1990, have permitted the first precise determinations of their individual radii, densities, and surface compositions. In addition, information on their surface albedo distributions can be obtained.

  8. UNBIASED INCLINATION DISTRIBUTIONS FOR OBJECTS IN THE KUIPER BELT

    SciTech Connect

    Gulbis, A. A. S.; Elliot, J. L.; Adams, E. R.; Benecchi, S. D.; Buie, M. W.; Trilling, D. E.; Wasserman, L. H. E-mail: jle@mit.ed E-mail: lhw@lowell.ed E-mail: buie@boulder.swri.ed

    2010-08-15

    Using data from the Deep Ecliptic Survey (DES), we investigate the inclination distributions of objects in the Kuiper Belt. We present a derivation for observational bias removal and use this procedure to generate unbiased inclination distributions for Kuiper Belt objects (KBOs) of different DES dynamical classes, with respect to the Kuiper Belt plane. Consistent with previous results, we find that the inclination distribution for all DES KBOs is well fit by the sum of two Gaussians, or a Gaussian plus a generalized Lorentzian, multiplied by sin i. Approximately 80% of KBOs are in the high-inclination grouping. We find that Classical object inclinations are well fit by sin i multiplied by the sum of two Gaussians, with roughly even distribution between Gaussians of widths 2.0{sup +0.6}{sub -0.5}{sup 0} and 8.1{sup +2.6}{sub -2.1}{sup 0}. Objects in different resonances exhibit different inclination distributions. The inclinations of Scattered objects are best matched by sin i multiplied by a single Gaussian that is centered at 19.1{sup +3.9}{sub -3.6}{sup 0} with a width of 6.9{sup +4.1}{sub -2.7}{sup 0}. Centaur inclinations peak just below 20{sup 0}, with one exceptionally high-inclination object near 80{sup 0}. The currently observed inclination distribution of the Centaurs is not dissimilar to that of the Scattered Extended KBOs and Jupiter-family comets, but is significantly different from the Classical and Resonant KBOs. While the sample sizes of some dynamical classes are still small, these results should begin to serve as a critical diagnostic for models of solar system evolution.

  9. Highly sensitive and unbiased approach for elucidating antibody repertoires.

    PubMed

    Lin, Sherry G; Ba, Zhaoqing; Du, Zhou; Zhang, Yu; Hu, Jiazhi; Alt, Frederick W

    2016-07-12

    Developing B lymphocytes undergo V(D)J recombination to assemble germ-line V, D, and J gene segments into exons that encode the antigen-binding variable region of Ig heavy (H) and light (L) chains. IgH and IgL chains associate to form the B-cell receptor (BCR), which, upon antigen binding, activates B cells to secrete BCR as an antibody. Each of the huge number of clonally independent B cells expresses a unique set of IgH and IgL variable regions. The ability of V(D)J recombination to generate vast primary B-cell repertoires results from a combinatorial assortment of large numbers of different V, D, and J segments, coupled with diversification of the junctions between them to generate the complementary determining region 3 (CDR3) for antigen contact. Approaches to evaluate in depth the content of primary antibody repertoires and, ultimately, to study how they are further molded by secondary mutation and affinity maturation processes are of great importance to the B-cell development, vaccine, and antibody fields. We now describe an unbiased, sensitive, and readily accessible assay, referred to as high-throughput genome-wide translocation sequencing-adapted repertoire sequencing (HTGTS-Rep-seq), to quantify antibody repertoires. HTGTS-Rep-seq quantitatively identifies the vast majority of IgH and IgL V(D)J exons, including their unique CDR3 sequences, from progenitor and mature mouse B lineage cells via the use of specific J primers. HTGTS-Rep-seq also accurately quantifies DJH intermediates and V(D)J exons in either productive or nonproductive configurations. HTGTS-Rep-seq should be useful for studies of human samples, including clonal B-cell expansions, and also for following antibody affinity maturation processes. PMID:27354528

  10. Rethinking mutualism stability: cheaters and the evolution of sanctions.

    PubMed

    Frederickson, Megan E

    2013-12-01

    How cooperation originates and persists in diverse species, from bacteria to multicellular organisms to human societies, is a major question in evolutionary biology. A large literature asks: what prevents selection for cheating within cooperative lineages? In mutualisms, or cooperative interactions between species, feedback between partners often aligns their fitness interests, such that cooperative symbionts receive more benefits from their hosts than uncooperative symbionts. But how do these feedbacks evolve? Cheaters might invade symbiont populations and select for hosts that preferentially reward or associate with cooperators (often termed sanctions or partner choice); hosts might adapt to variation in symbiont quality that does not amount to cheating (e.g., environmental variation); or conditional host responses might exist before cheaters do, making mutualisms stable from the outset. I review evidence from yucca-yucca moth, fig-fig wasp, and legume-rhizobium mutualisms, which are commonly cited as mutualisms stabilized by sanctions. Based on the empirical evidence, it is doubtful that cheaters select for host sanctions in these systems; cheaters are too uncommon. Recognizing that sanctions likely evolved for functions other than retaliation against cheaters offers many insights about mutualism coevolution, and about why mutualism evolves in only some lineages of potential hosts. PMID:24552098

  11. Spectral image analysis of mutual illumination between florescent objects.

    PubMed

    Tominaga, Shoji; Kato, Keiji; Hirai, Keita; Horiuchi, Takahiko

    2016-08-01

    This paper proposes a method for modeling and component estimation of the spectral images of the mutual illumination phenomenon between two fluorescent objects. First, we briefly describe the bispectral characteristics of a single fluorescent object, which are summarized as a Donaldson matrix. We suppose that two fluorescent objects with different bispectral characteristics are located close together under a uniform illumination. Second, we model the mutual illumination between two objects. It is shown that the spectral composition of the mutual illumination is summarized with four components: (1) diffuse reflection, (2) diffuse-diffuse interreflection, (3) fluorescent self-luminescence, and (4) interreflection by mutual fluorescent illumination. Third, we develop algorithms for estimating the spectral image components from the observed images influenced by the mutual illumination. When the exact Donaldson matrices caused by the mutual illumination influence are unknown, we have to solve a non-linear estimation problem to estimate both the spectral functions and the location weights. An iterative algorithm is then proposed to solve the problem based on the alternate estimation of the spectral functions and the location weights. In our experiments, the feasibility of the proposed method is shown in three cases: the known Donaldson matrices, weak interreflection, and strong interreflection. PMID:27505645

  12. 76 FR 20458 - Mutual Holding Company

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-12

    ... Office of Thrift Supervision Mutual Holding Company AGENCY: Office of Thrift Supervision (OTS), Treasury... collection. Title of Proposal: Mutual Holding Company. OMB Number: 1550-0072. Form Numbers: MHC-1 (OTS Form... whether the applicant meets the statutory and regulatory criteria to form a mutual holding company...

  13. Parents Helping Parents: Mutual Parenting Network Handbook.

    ERIC Educational Resources Information Center

    Simkinson, Charles H.; Redmond, Robert F.

    Guidelines for mutual parenting are provided in this handbook. "Mutual parenting" means that everyone in the community shares the responsibility for the safety and well-being of the community's youngsters. Several topics are discussed in the 15 brief chapters of the handbook. Chapters 1 through 3 focus on the formation of a mutual parenting…

  14. Generalized mutual information of quantum critical chains

    NASA Astrophysics Data System (ADS)

    Alcaraz, F. C.; Rajabpour, M. A.

    2015-04-01

    We study the generalized mutual information I˜n of the ground state of different critical quantum chains. The generalized mutual information definition that we use is based on the well established concept of the Rényi divergence. We calculate this quantity numerically for several distinct quantum chains having either discrete Z (Q ) symmetries (Q -state Potts model with Q =2 ,3 ,4 and Z (Q ) parafermionic models with Q =5 ,6 ,7 ,8 and also Ashkin-Teller model with different anisotropies) or the U (1 ) continuous symmetries (Klein-Gordon field theory, X X Z and spin-1 Fateev-Zamolodchikov quantum chains with different anisotropies). For the spin chains these calculations were done by expressing the ground-state wave functions in two special bases. Our results indicate some general behavior for particular ranges of values of the parameter n that defines I˜n. For a system, with total size L and subsystem sizes ℓ and L -ℓ , the I˜n has a logarithmic leading behavior given by c/˜n4 log[L/π sin(π/ℓ L ) ] where the coefficient c˜n is linearly dependent on the central charge c of the underlying conformal field theory describing the system's critical properties.

  15. Propagating Resource Constraints Using Mutual Exclusion Reasoning

    NASA Technical Reports Server (NTRS)

    Frank, Jeremy; Sanchez, Romeo; Do, Minh B.; Clancy, Daniel (Technical Monitor)

    2001-01-01

    One of the most recent techniques for propagating resource constraints in Constraint Based scheduling is Energy Constraint. This technique focuses in precedence based scheduling, where precedence relations are taken into account rather than the absolute position of activities. Although, this particular technique proved to be efficient on discrete unary resources, it provides only loose bounds for jobs using discrete multi-capacity resources. In this paper we show how mutual exclusion reasoning can be used to propagate time bounds for activities using discrete resources. We show that our technique based on critical path analysis and mutex reasoning is just as effective on unary resources, and also shows that it is more effective on multi-capacity resources, through both examples and empirical study.

  16. Defense mutualisms enhance plant diversification.

    PubMed

    Weber, Marjorie G; Agrawal, Anurag A

    2014-11-18

    The ability of plants to form mutualistic relationships with animal defenders has long been suspected to influence their evolutionary success, both by decreasing extinction risk and by increasing opportunity for speciation through an expanded realized niche. Nonetheless, the hypothesis that defense mutualisms consistently enhance plant diversification across lineages has not been well tested due to a lack of phenotypic and phylogenetic information. Using a global analysis, we show that the >100 vascular plant families in which species have evolved extrafloral nectaries (EFNs), sugar-secreting organs that recruit arthropod mutualists, have twofold higher diversification rates than families that lack species with EFNs. Zooming in on six distantly related plant clades, trait-dependent diversification models confirmed the tendency for lineages with EFNs to display increased rates of diversification. These results were consistent across methodological approaches. Inference using reversible-jump Markov chain Monte Carlo (MCMC) to model the placement and number of rate shifts revealed that high net diversification rates in EFN clades were driven by an increased number of positive rate shifts following EFN evolution compared with sister clades, suggesting that EFNs may be indirect facilitators of diversification. Our replicated analysis indicates that defense mutualisms put lineages on a path toward increased diversification rates within and between clades, and is concordant with the hypothesis that mutualistic interactions with animals can have an impact on deep macroevolutionary patterns and enhance plant diversity. PMID:25349406

  17. Defense mutualisms enhance plant diversification

    PubMed Central

    Weber, Marjorie G.; Agrawal, Anurag A.

    2014-01-01

    The ability of plants to form mutualistic relationships with animal defenders has long been suspected to influence their evolutionary success, both by decreasing extinction risk and by increasing opportunity for speciation through an expanded realized niche. Nonetheless, the hypothesis that defense mutualisms consistently enhance plant diversification across lineages has not been well tested due to a lack of phenotypic and phylogenetic information. Using a global analysis, we show that the >100 vascular plant families in which species have evolved extrafloral nectaries (EFNs), sugar-secreting organs that recruit arthropod mutualists, have twofold higher diversification rates than families that lack species with EFNs. Zooming in on six distantly related plant clades, trait-dependent diversification models confirmed the tendency for lineages with EFNs to display increased rates of diversification. These results were consistent across methodological approaches. Inference using reversible-jump Markov chain Monte Carlo (MCMC) to model the placement and number of rate shifts revealed that high net diversification rates in EFN clades were driven by an increased number of positive rate shifts following EFN evolution compared with sister clades, suggesting that EFNs may be indirect facilitators of diversification. Our replicated analysis indicates that defense mutualisms put lineages on a path toward increased diversification rates within and between clades, and is concordant with the hypothesis that mutualistic interactions with animals can have an impact on deep macroevolutionary patterns and enhance plant diversity. PMID:25349406

  18. Population dynamics and mutualism: Functional responses of benefits and costs

    USGS Publications Warehouse

    Holland, J. Nathaniel; DeAngelis, Donald L.; Bronstein, Judith L.

    2002-01-01

    We develop an approach for studying population dynamics resulting from mutualism by employing functional responses based on density‐dependent benefits and costs. These functional responses express how the population growth rate of a mutualist is modified by the density of its partner. We present several possible dependencies of gross benefits and costs, and hence net effects, to a mutualist as functions of the density of its partner. Net effects to mutualists are likely a monotonically saturating or unimodal function of the density of their partner. We show that fundamental differences in the growth, limitation, and dynamics of a population can occur when net effects to that population change linearly, unimodally, or in a saturating fashion. We use the mutualism between senita cactus and its pollinating seed‐eating moth as an example to show the influence of different benefit and cost functional responses on population dynamics and stability of mutualisms. We investigated two mechanisms that may alter this mutualism's functional responses: distribution of eggs among flowers and fruit abortion. Differences in how benefits and costs vary with density can alter the stability of this mutualism. In particular, fruit abortion may allow for a stable equilibrium where none could otherwise exist.

  19. Mutual information in classical spin models

    NASA Astrophysics Data System (ADS)

    Wilms, Johannes; Troyer, Matthias; Verstraete, Frank

    2011-10-01

    The total many-body correlations present in finite temperature classical spin systems are studied using the concept of mutual information. As opposed to zero-temperature quantum phase transitions, the total correlations are not maximal at the phase transition, but reach a maximum in the high-temperature paramagnetic phase. The Shannon mutual information and the Renyi mutual information in both Ising and Potts models in two dimensions are calculated numerically by combining matrix product state algorithms and Monte Carlo sampling techniques.

  20. Mutual enhancement of diverse terminologies

    PubMed Central

    Hardiker, Nicholas R.; Casey, Anne; Coenen, Amy; Konicek, Debra

    2006-01-01

    The purpose of this study was to map the North American Nursing Diagnosis Association (NANDA) nursing diagnoses to the International Classification for Nursing Practice Version 1.0 (ICNP®) and to compare the resulting representations and relationships to those within SNOMED® Clinical Terms (CT). Independent reviewers reached agreement on 25 (i.e. 64%) of the 39 parent-child relationships identified via the mappings between NANDA entities. Other parent-child relationships were more questionable and are in need of further discussion. This work does not seek to promote one terminology over any other. Rather, this collaborative effort has the potential to mutually enhance all three terminologies involved in the study: ICNP®, SNOMED® CT and NANDA. In doing so it provides an example of the type of collaborative effort that is needed to facilitate the development of tools to support interoperability at a global level. PMID:17238355

  1. High levels of absorption in orientation-unbiased, radio-selected 3CR Active Galaxies

    NASA Astrophysics Data System (ADS)

    Wilkes, Belinda J.; Haas, Martin; Barthel, Peter; Leipski, Christian; Kuraszkiewicz, Joanna; Worrall, Diana; Birkinshaw, Mark; Willner, Steven P.

    2014-08-01

    A critical problem in understanding active galaxies (AGN) is the separation of intrinsic physical differences from observed differences that are due to orientation. Obscuration of the active nucleus is anisotropic and strongly frequency dependent leading to complex selection effects for observations in most wavebands. These can only be quantified using a sample that is sufficiently unbiased to test orientation effects. Low-frequency radio emission is one way to select a close-to orientation-unbiased sample, albeit limited to the minority of AGN with strong radio emission.Recent Chandra, Spitzer and Herschel observations combined with multi-wavelength data for a complete sample of high-redshift (1 24.2) = 2.5:1.4:1 in these high-luminosity (log L(0.3-8keV) ~ 44-46) sources. These ratios are consistent with current expectations based on modelingthe Cosmic X-ray Background. A strong correlation with radio orientation constrains the geometry of the obscuring disk/torus to have a ~60 degree opening angle and ~12 degree Compton-thick cross-section. The deduced ~50% obscured fraction of the population contrasts with typical estimates of ~20% obscured in optically- and X-ray-selected high-luminosity samples. Once the primary nuclear emission is obscured, AGN X-ray spectra are frequently dominated by unobscured non-nuclear or scattered nuclear emission which cannot be distinguished from direct nuclear emission with a lower obscuration level unless high quality data is available. As a result, both the level of obscuration and the estimated instrinsic luminosities of highly-obscured AGN are likely to be significantly (*10-1000) underestimated for 25-50% of the population. This may explain the lower obscured fractions reported for optical and X-ray samples which have no independent measure of the AGN

  2. Empirical study of the tails of mutual fund size

    NASA Astrophysics Data System (ADS)

    Schwarzkopf, Yonathan; Farmer, J. Doyne

    2010-06-01

    The mutual fund industry manages about a quarter of the assets in the U.S. stock market and thus plays an important role in the U.S. economy. The question of how much control is concentrated in the hands of the largest players is best quantitatively discussed in terms of the tail behavior of the mutual fund size distribution. We study the distribution empirically and show that the tail is much better described by a log-normal than a power law, indicating less concentration than, for example, personal income. The results are highly statistically significant and are consistent across fifteen years. This contradicts a recent theory concerning the origin of the power law tails of the trading volume distribution. Based on the analysis in a companion paper, the log-normality is to be expected, and indicates that the distribution of mutual funds remains perpetually out of equilibrium.

  3. Lessons learned from two peer-led mutual support groups.

    PubMed

    Viverito, Kristen M; Cardin, Scott A; Johnson, Leigh Ann; Owen, Richard R

    2013-10-01

    This case report and analysis describe the formation of two peer-led mutual support groups conducted within the context of a Veterans Administration Medical Center. Based on our assessment of the success of one of these groups and the failure of the other, we offer several recommendations and suggestions to help promote this modality. More specifically, we hypothesize that such groups are more likely to be successful (1) if participants are transferred en masse from another group, (2) that, at least initially, housing the group in the same context as formal clinician-led groups or overlapping clinician-led and peer-led groups may help smooth the transition from authority-led treatment to a mutual peer support format, and finally, (3) that prior experiences in interpersonal process groups may promote the skills and cohesion to promote successful transition to mutual support. PMID:24004015

  4. The Environment of Classification: The Concept of Mutual Exclusivity

    ERIC Educational Resources Information Center

    Jones, Kevin P.

    1973-01-01

    Classification is interpreted so as to incorporate all attempts at the imposition of order upon our observations of the universe. In this article, the fundamental bases of classification are examined: in particular the alien notions of mutual exclusivity and the use of inflexible structures to mirror a dynamic universe. (26 references) (Author/KE)

  5. Institutionalized Mutuality in Canada-China Management Education Collaboration

    ERIC Educational Resources Information Center

    Wei, Shuguang; Liu, Xianjun

    2015-01-01

    This paper examines the Canada-China Management Education Program (CCMEP, 1983-1996) between the University of Toronto (UT) and Huazhong University of Science and Technology (HUST). In this paper, we create a "Three Levels/Four Parameters" analytical framework, based on the concept of mutuality from Johan Galtung (1980) and the concept…

  6. A Grand Challenge: Unbiased Phenotypic Function of Metabolites from Jaspis splendens against Parkinson's Disease.

    PubMed

    Wang, Dongdong; Feng, Yunjiang; Murtaza, Mariyam; Wood, Stephen; Mellick, George; Hooper, John N A; Quinn, Ronald J

    2016-02-26

    A grand challenge in natural product chemistry is to determine the biological effects of all natural products. A phenotypic approach is frequently used for determining the activity of a compound and its potential impact on a disease state. Chemical investigation of a specimen of Jaspis splendens collected from the Great Barrier Reef resulted in the isolation of a new pterin derivative, jaspterin (1), a new bisindole alkaloid, splendamide (2), and a new imidazole alkaloid, jaspnin A (3) TFA salt. Jaspamycin (8) and 6-bromo-1H-indole-3-carboximidamide (16) are reported for the first time as naturally occurring metabolites. Known nucleosides (4-7, 9, 10), aglycones (11-13), indole alkaloids (14, 15, 17), and jaspamide peptides (18-22) were also isolated. The structures of the three new compounds 1-3 were unambiguously elucidated based on NMR and mass spectroscopic data. Jaspnin A (3) contained a rare thiomethylated imidazolinium unit. Coupling an unbiased phenotypic assay using a human olfactory neurosphere-derived cell model of Parkinson's disease to all of the natural products from the species J. splendens allowed the phenotypic profiles of the metabolites to be investigated. PMID:26883470

  7. Unbiased Feature Selection in Learning Random Forests for High-Dimensional Data

    PubMed Central

    Nguyen, Thanh-Tung; Huang, Joshua Zhexue; Nguyen, Thuy Thi

    2015-01-01

    Random forests (RFs) have been widely used as a powerful classification method. However, with the randomization in both bagging samples and feature selection, the trees in the forest tend to select uninformative features for node splitting. This makes RFs have poor accuracy when working with high-dimensional data. Besides that, RFs have bias in the feature selection process where multivalued features are favored. Aiming at debiasing feature selection in RFs, we propose a new RF algorithm, called xRF, to select good features in learning RFs for high-dimensional data. We first remove the uninformative features using p-value assessment, and the subset of unbiased features is then selected based on some statistical measures. This feature subset is then partitioned into two subsets. A feature weighting sampling technique is used to sample features from these two subsets for building trees. This approach enables one to generate more accurate trees, while allowing one to reduce dimensionality and the amount of data needed for learning RFs. An extensive set of experiments has been conducted on 47 high-dimensional real-world datasets including image datasets. The experimental results have shown that RFs with the proposed approach outperformed the existing random forests in increasing the accuracy and the AUC measures. PMID:25879059

  8. Automated and unbiased classification of chemical profiles from fungi using high performance liquid chromatography.

    PubMed

    Hansen, Michael Edberg; Andersen, Birgitte; Smedsgaard, Jørn

    2005-06-01

    In this paper we present a method for unbiased/unsupervised classification and identification of closely related fungi, using chemical analysis of secondary metabolite profiles created by HPLC with UV diode array detection. For two chromatographic data matrices a vector of locally aligned full spectral similarities is calculated along the retention time axis. The vector depicts the evaluating of the alikeness between two fungal extracts based upon eluted compounds and corresponding UV-absorbance spectra. For assessment of the chemotaxonomic grouping the vector is condensed to one similarity describing the overall degree of similarity between the profiles. Two sets of data were used in this study: One set was used in the method development and a second dataset used for method validation. First we developed a method for evaluating the secondary metabolite production from closely related Penicillium species. Then the algorithm was validated on fungal isolates belonging to the genus Alternaria. The results showed that the species may be segregated into taxa in full accordance with published taxonomy. PMID:15767006

  9. Unraveling cognitive traits using the Morris water maze unbiased strategy classification (MUST-C) algorithm.

    PubMed

    Illouz, Tomer; Madar, Ravit; Louzon, Yoram; Griffioen, Kathleen J; Okun, Eitan

    2016-02-01

    The assessment of spatial cognitive learning in rodents is a central approach in neuroscience, as it enables one to assess and quantify the effects of treatments and genetic manipulations from a broad perspective. Although the Morris water maze (MWM) is a well-validated paradigm for testing spatial learning abilities, manual categorization of performance in the MWM into behavioral strategies is subject to individual interpretation, and thus to biases. Here we offer a support vector machine (SVM) - based, automated, MWM unbiased strategy classification (MUST-C) algorithm, as well as a cognitive score scale. This model was examined and validated by analyzing data obtained from five MWM experiments with changing platform sizes, revealing a limitation in the spatial capacity of the hippocampus. We have further employed this algorithm to extract novel mechanistic insights on the impact of members of the Toll-like receptor pathway on cognitive spatial learning and memory. The MUST-C algorithm can greatly benefit MWM users as it provides a standardized method of strategy classification as well as a cognitive scoring scale, which cannot be derived from typical analysis of MWM data. PMID:26522398

  10. Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

    PubMed Central

    Donovan, Rory M.; Tapia, Jose-Juan; Sullivan, Devin P.; Faeder, James R.; Murphy, Robert F.; Dittrich, Markus; Zuckerman, Daniel M.

    2016-01-01

    The long-term goal of connecting scales in biological simulation can be facilitated by scale-agnostic methods. We demonstrate that the weighted ensemble (WE) strategy, initially developed for molecular simulations, applies effectively to spatially resolved cell-scale simulations. The WE approach runs an ensemble of parallel trajectories with assigned weights and uses a statistical resampling strategy of replicating and pruning trajectories to focus computational effort on difficult-to-sample regions. The method can also generate unbiased estimates of non-equilibrium and equilibrium observables, sometimes with significantly less aggregate computing time than would be possible using standard parallelization. Here, we use WE to orchestrate particle-based kinetic Monte Carlo simulations, which include spatial geometry (e.g., of organelles, plasma membrane) and biochemical interactions among mobile molecular species. We study a series of models exhibiting spatial, temporal and biochemical complexity and show that although WE has important limitations, it can achieve performance significantly exceeding standard parallel simulation—by orders of magnitude for some observables. PMID:26845334

  11. The Competitive Strategy of Mutual Learning.

    ERIC Educational Resources Information Center

    Kelner, Stephen P.; Slavin, Lois

    1998-01-01

    Defines and discusses mutual learning in organizations. Suggests that the idea of people and companies sharing knowledge is becoming a competitive strategy because mutual learning enables executives and employees to increase their capacity to work together, accelerate organizational learning, and avoid mistakes. (JOW)

  12. Victimization within Mutually Antipathetic Peer Relationships

    ERIC Educational Resources Information Center

    Card, Noel A.; Hodges, Ernest V. E.

    2007-01-01

    Children's victimization experiences within relationships characterized by mutual animosity were examined among 210 6th- and 7th-grade boys and girls. Participants reported that a greater proportion of mutual antipathies, relative to other peers, victimized them. Moreover, the receipt of victimization within antipathetic relationships was greater…

  13. Quadratic mutual information for dimensionality reduction and classification

    NASA Astrophysics Data System (ADS)

    Gray, David M.; Principe, José C.

    2010-04-01

    A research area based on the application of information theory to machine learning has attracted considerable interest in the last few years. This research area has been coined information-theoretic learning within the community. In this paper we apply elements of information-theoretic learning to the problem of automatic target recognition (ATR). A number of researchers have previously shown the benefits of designing classifiers based on maximizing the mutual information between the class data and the class labels. Following prior research in information-theoretic learning, in the current results we show that quadratic mutual information, derived using a special case of the more general Renyi's entropy, can be used for classifier design. In this implementation, a simple subspace projection classifier is formulated to find the optimal projection weights such that the quadratic mutual information between the class data and the class labels is maximized. This subspace projection accomplishes a dimensionality reduction of the raw data set wherein information about the class membership is retained while irrelevant information is discarded. A subspace projection based on this criterion preserves as much class discriminability as possible within the subspace. For this paper, laser radar images are used to demonstrate the results. Classification performance against this data set is compared for a gradient descent MLP classifier and a quadratic mutual information MLP classifier.

  14. [Maintaining solidarity: is mutuality the solution?].

    PubMed

    Gevers, J K M; Ploem, M C

    2013-01-01

    Solidarity is essentially the willingness to contribute to the community and its demands, which may even involve contributing more than one is expecting to receive. Another principle is mutuality: this refers to a balance between rights and obligations or between mutual obligations. In its advisory document 'The importance of mutuality......solidarity takes work!', The Dutch Council for Public Health and Health Care underlines the importance of ensuring solidarity within the Dutch health care system, e.g. by encouraging patients to take responsibility for their own health, possibly by introducing elements of mutuality. In our contribution, we comment on the Council's advice. Although we fully agree with the overall conclusion that solidarity should be maintained within the system, we do not see how the introduction of increased mutuality will contribute to this goal. PMID:23945438

  15. Two-Level Document Ranking Using Mutual Information in Natural Language Information Retrieval.

    ERIC Educational Resources Information Center

    Kang, Hyun-Kyu; Choi, Key-Sun

    1997-01-01

    Discussion of information retrieval and relevance focuses on mutual information, a measure which represents the relation between two words. A model of a natural-language information-retrieval system that is based on a two-level document-ranking method using mutual information is presented, and a Korean encyclopedia test collection is explained.…

  16. Mutual Orbits of Transneptunian Binaries

    NASA Astrophysics Data System (ADS)

    Grundy, William M.; Noll, K. S.; Roe, H. G.; Porter, S. B.; Trujillo, C. A.; Benecchi, S. D.; Buie, M. W.

    2012-10-01

    We report the latest results from a program of high spatial resolution imaging to resolve the individual components of binary transneptunian objects. These observations use Hubble Space Telescope and also laser guide star adaptive optics systems on Keck and Gemini telescopes on Mauna Kea. From relative astrometry over multiple epochs, we determine the mutual orbits of the components, and thus the total masses of the systems. Accurate masses anchor subsequent detailed investigations into the physical characteristics of these systems. For instance, dynamical masses enable computation of bulk densities for systems where the component sizes can be estimated from other measurements. Additionally, patterns in the ensemble characteristics of binary orbits offer clues to circumstances in the protoplanetary nebula when these systems formed, as well as carrying imprints of various subsequent dynamical evolution processes. The growing ensemble of known orbits shows intriguing patterns that can shed light on the evolution of this population of distant objects. This work has been supported by an NSF Planetary Astronomy grant and by several Hubble Space Telescope and NASA Keck data analysis grants. The research makes use of data from the Gemini Observatory obtained through NOAO survey program 11A-0017, from a large number of Hubble Space Telescope programs, and from several NASA Keck programs.

  17. 12 CFR 575.3 - Mutual holding company reorganizations.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Mutual holding company reorganizations. 575.3... COMPANIES § 575.3 Mutual holding company reorganizations. A mutual savings association may reorganize to become a mutual holding company, or join in a mutual holding company reorganization as an...

  18. Mutual coupling, channel model, and BER for curvilinear antenna arrays

    NASA Astrophysics Data System (ADS)

    Huang, Zhiyong

    interferers, Doppler spread and convergence are investigated. The tracking mode is introduced to the adaptive array system, and it further improves the BER. The benefit of using faster data rate (wider bandwidth) is discussed. In order to have better performance in a 3D space, the geometries of uniform spherical array (USAs) are presented and different configurations of USAs are discussed. The LMS algorithm based on temporal a priori information is applied to UCAs and USAs to beamform the patterns. Their performances are compared based on simulation results. Based on the analytical and simulation results, it can be concluded that mutual coupling slightly influences the performance of the adaptive array in communication systems. In addition, arrays with curvilinear geometries perform well in AWGN and fading channels.

  19. Generalized mutual information and Tsirelson's bound

    SciTech Connect

    Wakakuwa, Eyuri; Murao, Mio

    2014-12-04

    We introduce a generalization of the quantum mutual information between a classical system and a quantum system into the mutual information between a classical system and a system described by general probabilistic theories. We apply this generalized mutual information (GMI) to a derivation of Tsirelson's bound from information causality, and prove that Tsirelson's bound can be derived from the chain rule of the GMI. By using the GMI, we formulate the 'no-supersignalling condition' (NSS), that the assistance of correlations does not enhance the capability of classical communication. We prove that NSS is never violated in any no-signalling theory.

  20. Inhibitory impact of 3'-terminal 2'-O-methylated small silencing RNA on target-primed polymerization and unbiased amplified quantification of the RNA in Arabidopsis thaliana.

    PubMed

    Chen, Feng; Fan, Chunhai; Zhao, Yongxi

    2015-09-01

    3'-terminal 2'-O-methylation has been found in several kinds of small silencing RNA, regarded as a protective mechanism against enzymatic 3' → 5' degradation and 3'-end uridylation. The influence of this modification on enzymatic polymerization, however, remains unknown. Herein, a systematic investigation is performed to explore this issue. We found these methylated small RNAs exhibited a suppression behavior in target-primed polymerization, revealing biased result for the manipulation of these small RNAs by conventional polymerization-based methodology. The related potential mechanism is investigated and discussed, which is probably ascribed to the big size of modified group and its close location to 3'-OH. Furthermore, two novel solutions each utilizing base-stacking hybridization and three-way junction structure have been proposed to realize unbiased recognition of small RNAs. On the basis of phosphorothioate against nicking, a creative amplified strategy, phosphorothioate-protected polymerization/binicking amplification, has also been developed for the unbiased quantification of methylated small RNA in Arabidopsis thaliana, demonstrating its promising potential for real sample analysis. Collectively, our studies uncover the polymerization inhibition by 3'-terminal 2'-O-methylated small RNAs with mechanistic discussion, and propose novel unbiased solutions for amplified quantification of small RNAs in real sample. PMID:26244621

  1. Quantum correlation in degenerate optical parametric oscillators with mutual injections

    NASA Astrophysics Data System (ADS)

    Takata, Kenta; Marandi, Alireza; Yamamoto, Yoshihisa

    2015-10-01

    We theoretically and numerically study the quantum dynamics of two degenerate optical parametric oscillators with mutual injections. The cavity mode in the optical coupling path between the two oscillator facets is explicitly considered. Stochastic equations for the oscillators and mutual injection path based on the positive P representation are derived. The system of two gradually pumped oscillators with out-of-phase mutual injections is simulated, and its quantum state is investigated. When the incoherent loss of the oscillators other than the mutual injections is small, the squeezed quadratic amplitudes p ̂ in the oscillators are positively correlated near the oscillation threshold. It indicates finite quantum correlation, estimated via Gaussian quantum discord, and the entanglement between the intracavity subharmonic fields. When the loss in the injection path is low, each oscillator around the phase transition point forms macroscopic superposition even under a small pump noise. It suggests that the squeezed field stored in the low-loss injection path weakens the decoherence in the oscillators.

  2. Measurement reduction for mutual coupling calibration in DOA estimation

    NASA Astrophysics Data System (ADS)

    Aksoy, Taylan; Tuncer, T. Engin

    2012-01-01

    Mutual coupling is an important source of error in antenna arrays that should be compensated for super resolution direction-of-arrival (DOA) algorithms, such as Multiple Signal Classification (MUSIC) algorithm. A crucial step in array calibration is the determination of the mutual coupling coefficients for the antenna array. In this paper, a system theoretic approach is presented for the mutual coupling characterization of antenna arrays. The comprehension and implementation of this approach is simple leading to further advantages in calibration measurement reduction. In this context, a measurement reduction method for antenna arrays with omni-directional and identical elements is proposed which is based on the symmetry planes in the array geometry. The proposed method significantly decreases the number of measurements during the calibration process. This method is evaluated using different array types whose responses and the mutual coupling characteristics are obtained through numerical electromagnetic simulations. It is shown that a single calibration measurement is sufficient for uniform circular arrays. Certain important and interesting characteristics observed during the experiments are outlined.

  3. Estimating Unbiased Treatment Effects in Education Using a Regression Discontinuity Design

    ERIC Educational Resources Information Center

    Smith, William C.

    2014-01-01

    The ability of regression discontinuity (RD) designs to provide an unbiased treatment effect while overcoming the ethical concerns plagued by Random Control Trials (RCTs) make it a valuable and useful approach in education evaluation. RD is the only explicitly recognized quasi-experimental approach identified by the Institute of Education…

  4. A Derivation of the Unbiased Standard Error of Estimate: The General Case.

    ERIC Educational Resources Information Center

    O'Brien, Francis J., Jr.

    This paper is part of a series of applied statistics monographs intended to provide supplementary reading for applied statistics students. In the present paper, derivations of the unbiased standard error of estimate for both the raw score and standard score linear models are presented. The derivations for raw score linear models are presented in…

  5. 76 FR 71437 - Mutual Savings Association Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-17

    ... Office of the Comptroller of the Currency Mutual Savings Association Advisory Committee AGENCY... Mutual Savings Association Advisory Committee (MSAAC or Committee) formerly administered by the Office of... of and challenges facing mutual savings associations. The OCC is seeking nominations of...

  6. Unbiased estimation of chloroplast number in mesophyll cells: advantage of a genuine three-dimensional approach

    PubMed Central

    Kubínová, Zuzana

    2014-01-01

    Chloroplast number per cell is a frequently examined quantitative anatomical parameter, often estimated by counting chloroplast profiles in two-dimensional (2D) sections of mesophyll cells. However, a mesophyll cell is a three-dimensional (3D) structure and this has to be taken into account when quantifying its internal structure. We compared 2D and 3D approaches to chloroplast counting from different points of view: (i) in practical measurements of mesophyll cells of Norway spruce needles, (ii) in a 3D model of a mesophyll cell with chloroplasts, and (iii) using a theoretical analysis. We applied, for the first time, the stereological method of an optical disector based on counting chloroplasts in stacks of spruce needle optical cross-sections acquired by confocal laser-scanning microscopy. This estimate was compared with counting chloroplast profiles in 2D sections from the same stacks of sections. Comparing practical measurements of mesophyll cells, calculations performed in a 3D model of a cell with chloroplasts as well as a theoretical analysis showed that the 2D approach yielded biased results, while the underestimation could be up to 10-fold. We proved that the frequently used method for counting chloroplasts in a mesophyll cell by counting their profiles in 2D sections did not give correct results. We concluded that the present disector method can be efficiently used for unbiased estimation of chloroplast number per mesophyll cell. This should be the method of choice, especially in coniferous needles and leaves with mesophyll cells with lignified cell walls where maceration methods are difficult or impossible to use. PMID:24336344

  7. Onset of immune senescence defined by unbiased pyrosequencing of human immunoglobulin mRNA repertoires.

    PubMed

    Rubelt, Florian; Sievert, Volker; Knaust, Florian; Diener, Christian; Lim, Theam Soon; Skriner, Karl; Klipp, Edda; Reinhardt, Richard; Lehrach, Hans; Konthur, Zoltán

    2012-01-01

    The immune system protects us from foreign substances or pathogens by generating specific antibodies. The variety of immunoglobulin (Ig) paratopes for antigen recognition is a result of the V(D)J rearrangement mechanism, while a fast and efficient immune response is mediated by specific immunoglobulin isotypes obtained through class switch recombination (CSR). To get a better understanding on how antibody-based immune protection works and how it changes with age, the interdependency between these two parameters need to be addressed. Here, we have performed an in depth analysis of antibody repertoires of 14 healthy donors representing different gender and age groups. For this task, we developed a unique pyrosequencing approach, which is able to monitor the expression levels of all immunoglobulin V(D)J recombinations of all isotypes including subtypes in an unbiased and quantitative manner. Our results show that donors have individual immunoglobulin repertoires and cannot be clustered according to V(D)J recombination patterns, neither by age nor gender. However, after incorporating isotype-specific analysis and considering CSR information into hierarchical clustering the situation changes. For the first time the donors cluster according to age and separate into young adults and elderly donors (>50). As a direct consequence, this clustering defines the onset of immune senescence at the age of fifty and beyond. The observed age-dependent reduction of CSR ability proposes a feasible explanation why reduced efficacy of vaccination is seen in the elderly and implies that novel vaccine strategies for the elderly should include the "Golden Agers". PMID:23226220

  8. A/T/N: An unbiased descriptive classification scheme for Alzheimer disease biomarkers.

    PubMed

    Jack, Clifford R; Bennett, David A; Blennow, Kaj; Carrillo, Maria C; Feldman, Howard H; Frisoni, Giovanni B; Hampel, Harald; Jagust, William J; Johnson, Keith A; Knopman, David S; Petersen, Ronald C; Scheltens, Philip; Sperling, Reisa A; Dubois, Bruno

    2016-08-01

    Biomarkers have become an essential component of Alzheimer disease (AD) research and because of the pervasiveness of AD pathology in the elderly, the same biomarkers are used in cognitive aging research. A number of current issues suggest that an unbiased descriptive classification scheme for these biomarkers would be useful. We propose the "A/T/N" system in which 7 major AD biomarkers are divided into 3 binary categories based on the nature of the pathophysiology that each measures. "A" refers to the value of a β-amyloid biomarker (amyloid PET or CSF Aβ42); "T," the value of a tau biomarker (CSF phospho tau, or tau PET); and "N," biomarkers of neurodegeneration or neuronal injury ([(18)F]-fluorodeoxyglucose-PET, structural MRI, or CSF total tau). Each biomarker category is rated as positive or negative. An individual score might appear as A+/T+/N-, or A+/T-/N-, etc. The A/T/N system includes the new modality tau PET. It is agnostic to the temporal ordering of mechanisms underlying AD pathogenesis. It includes all individuals in any population regardless of the mix of biomarker findings and therefore is suited to population studies of cognitive aging. It does not specify disease labels and thus is not a diagnostic classification system. It is a descriptive system for categorizing multidomain biomarker findings at the individual person level in a format that is easy to understand and use. Given the present lack of consensus among AD specialists on terminology across the clinically normal to dementia spectrum, a biomarker classification scheme will have broadest acceptance if it is independent from any one clinically defined diagnostic scheme. PMID:27371494

  9. A/T/N: An unbiased descriptive classification scheme for Alzheimer disease biomarkers

    PubMed Central

    Bennett, David A.; Blennow, Kaj; Carrillo, Maria C.; Feldman, Howard H.; Frisoni, Giovanni B.; Hampel, Harald; Jagust, William J.; Johnson, Keith A.; Knopman, David S.; Petersen, Ronald C.; Scheltens, Philip; Sperling, Reisa A.; Dubois, Bruno

    2016-01-01

    Biomarkers have become an essential component of Alzheimer disease (AD) research and because of the pervasiveness of AD pathology in the elderly, the same biomarkers are used in cognitive aging research. A number of current issues suggest that an unbiased descriptive classification scheme for these biomarkers would be useful. We propose the “A/T/N” system in which 7 major AD biomarkers are divided into 3 binary categories based on the nature of the pathophysiology that each measures. “A” refers to the value of a β-amyloid biomarker (amyloid PET or CSF Aβ42); “T,” the value of a tau biomarker (CSF phospho tau, or tau PET); and “N,” biomarkers of neurodegeneration or neuronal injury ([18F]-fluorodeoxyglucose–PET, structural MRI, or CSF total tau). Each biomarker category is rated as positive or negative. An individual score might appear as A+/T+/N−, or A+/T−/N−, etc. The A/T/N system includes the new modality tau PET. It is agnostic to the temporal ordering of mechanisms underlying AD pathogenesis. It includes all individuals in any population regardless of the mix of biomarker findings and therefore is suited to population studies of cognitive aging. It does not specify disease labels and thus is not a diagnostic classification system. It is a descriptive system for categorizing multidomain biomarker findings at the individual person level in a format that is easy to understand and use. Given the present lack of consensus among AD specialists on terminology across the clinically normal to dementia spectrum, a biomarker classification scheme will have broadest acceptance if it is independent from any one clinically defined diagnostic scheme. PMID:27371494

  10. Mycorrhiza: A Common Form of Mutualism.

    ERIC Educational Resources Information Center

    Medve, Richard J.

    1978-01-01

    Mycorrhizae are among the most common examples of mutualism. This article discusses their structure, symbolic relationship, factors affecting formation and applying research. Questions are posed and answers suggested. (MA)

  11. Phenological shifts and the fate of mutualisms

    PubMed Central

    Rafferty, Nicole E.; CaraDonna, Paul J.; Bronstein, Judith L.

    2014-01-01

    Climate change is altering the timing of life history events in a wide array of species, many of which are involved in mutualistic interactions. Because many mutualisms can form only if partner species are able to locate each other in time, differential phenological shifts are likely to influence their strength, duration and outcome. At the extreme, climate change-driven shifts in phenology may result in phenological mismatch: the partial or complete loss of temporal overlap of mutualistic species. We have a growing understanding of how, when, and why phenological change can alter one type of mutualism–pollination. However, as we show here, there has been a surprising lack of attention to other types of mutualism. We generate a set of predictions about the characteristics that may predispose mutualisms in general to phenological mismatches. We focus not on the consequences of such mismatches but rather on the likelihood that mismatches will develop. We explore the influence of three key characteristics of mutualism: 1) intimacy, 2) seasonality and duration, and 3) obligacy and specificity. We predict that the following characteristics of mutualism may increase the likelihood of phenological mismatch: 1) a non-symbiotic life history in which co-dispersal is absent; 2) brief, seasonal interactions; and 3) facultative, generalized interactions. We then review the limited available data in light of our a priori predictions and point to mutualisms that are more and less likely to be at risk of becoming phenologically mismatched, emphasizing the need for research on mutualisms other than plant–pollinator interactions. Future studies should explicitly focus on mutualism characteristics to determine whether and how changing phenologies will affect mutualistic interactions. PMID:25883391

  12. Unbiased polarized PDFs upgraded with new inclusive DIS data

    NASA Astrophysics Data System (ADS)

    Nocera, Emanuele R.

    2016-02-01

    I present a determination of longitudinally-polarized parton distribution functions of the proton from inclusive deep-inelastic scattering data: NNPDFpol1.0+. This determination, based on the NNPDF methodology, upgrades a previous analysis, NNPDFpol1.0, in two respects: first, it includes all new data sets which have recently become available from the COMPASS experiment at CERN and from the E93-009, EG1-DVCS and E06-014 experiments at JLAB; second, it uses the state-of-the-art unpolarized parton set NNPDF3.0 as a baseline for the reconstruction of fitted observables and for the determination of positivity constraints. I discuss the impact of both these new inputs on the uncertainty of parton distribution functions.

  13. Unbiased degree-preserving randomization of directed binary networks

    NASA Astrophysics Data System (ADS)

    Roberts, E. S.; Coolen, A. C. C.

    2012-04-01

    Randomizing networks using a naive “accept-all” edge-swap algorithm is generally biased. Building on recent results for nondirected graphs, we construct an ergodic detailed balance Markov chain with nontrivial acceptance probabilities for directed graphs, which converges to a strictly uniform measure and is based on edge swaps that conserve all in and out degrees. The acceptance probabilities can also be generalized to define Markov chains that target any alternative desired measure on the space of directed graphs in order to generate graphs with more sophisticated topological features. This is demonstrated by defining a process tailored to the production of directed graphs with specified degree-degree correlation functions. The theory is implemented numerically and tested on synthetic and biological network examples.

  14. Unbiased dynamical and physical characteristics of the near-Earth-object population

    NASA Astrophysics Data System (ADS)

    Granvik, M.; Morbidelli, A.; Jedicke, R.; Bottke, W.; Bolin, B.; Beshore, E.; Delbo, M.; Vokrouhlicky, D.; Penttilä, A.; Nesvorny, D.; Michel, P.

    2014-07-01

    Recent years have witnessed a renewed interest in the population-level characteristics of near-Earth objects (NEOs) in terms of their unbiased orbital and absolute-magnitude distributions. The interest has been driven by the realization that the Bottke et al.NEO model [1,2] has started fraying at the edges after a decade of success. The number of known NEOs is currently about two orders of magnitude larger than the number of calibration targets used for the Bottke model and a new population model is needed to explain the discrepancy between the observed and predicted NEO distributions. The recent update [3] of the Bottke model improved the statistics of the orbital distributions and made some new predictions such as the existence of near-Earth asteroids on retrograde orbits, but did not attempt a full re-calibration of the model. Our new NEO model is an improvement on the approach originally developed by Bottke et al. [1,2]. The orbital distributions for NEOs originating in different regions of the main asteroid belt have been re-computed from scratch. We start with a forward integration of an unbiased sample of known main-belt objects (MBOs) to locate all possible NEO source regions in the main asteroid belt. We then record the orbital evolution of particles that enter the NEO region until they are ejected from the solar system or collide with the Sun or the planets in order to build up the so-called NEO residence-time distributions. We calibrate the model with some 4,550 NEOs detected by the Catalina Sky Survey's (CSS) Mt.Lemmon (G96) and Catalina (703) stations in 2005--2012 during untargeted observations. The nightly detection efficiencies measured by CSS are turned into likelihoods that an NEO with a given semimajor axis 0.6 au < a < 3.5 au, eccentricity 0 < e < 1, inclination 0° < i < 180° and absolute magnitude 15 < H < 25 would have been detected by CSS in the above timeframe. We use a novel, computationally efficient approach to numerically estimate the

  15. An automated hydrodynamic process for controlled, unbiased DNA shearing.

    PubMed

    Thorstenson, Y R; Hunicke-Smith, S P; Oefner, P J; Davis, R W

    1998-08-01

    An automated, inexpensive, easy-to-use, and reproducible technique for controlled, random DNA fragmentation has been developed. The technique is based on point-sink hydrodynamics that result when a DNA sample is forced through a small hole by a syringe pump. Commercially available components are used to reduce the cost and complexity of the instrument. The design is optimized to reduce the volume of sample required and to speed processing time. Shearing of the samples can be completely automated by computer control. Ninety percent of sheared DNA fragments fall within a twofold size distribution that is highly reproducible. Three parameters are critical: the flow geometry, the flow rate, and a minimum number of iterations. Shearing is reproducible over a wide range of temperatures, DNA concentrations, and initial DNA size. The cloning efficiency of the sheared DNA is very good even without end repair, the distribution of assembled sequences is random, and there is no sequence bias at the ends of sheared fragments that have been cloned. The instrument, called the Point-sink Shearer (PtS), has already been exported successfully to many other laboratories. PMID:9724331

  16. Separability conditions based on local fine-grained uncertainty relations

    NASA Astrophysics Data System (ADS)

    Rastegin, Alexey E.

    2016-03-01

    Many protocols of quantum information processing use entangled states. Hence, separability criteria are of great importance. We propose new separability conditions for a bipartite finite-dimensional system. They are derived by using fine-grained uncertainty relations. Fine-grained uncertainty relations can be obtained by consideration of the spectral norms of certain positive matrices. One of possible approaches to separability conditions is connected with upper bounds on the sum of maximal probabilities. Separability conditions are often formulated for measurements that have a special structure. For instance, mutually unbiased bases and mutually unbiased measurements can be utilized for such purposes. Using resolution of the identity for each subsystem of a bipartite system, we construct some resolution of the identity in the product of Hilbert spaces. Separability conditions are then formulated in terms of maximal probabilities for a collection of specific outcomes. The presented conditions are compared with some previous formulations. Our results are exemplified with entangled states of a two-qutrit system.

  17. Separability conditions based on local fine-grained uncertainty relations

    NASA Astrophysics Data System (ADS)

    Rastegin, Alexey E.

    2016-06-01

    Many protocols of quantum information processing use entangled states. Hence, separability criteria are of great importance. We propose new separability conditions for a bipartite finite-dimensional system. They are derived by using fine-grained uncertainty relations. Fine-grained uncertainty relations can be obtained by consideration of the spectral norms of certain positive matrices. One of possible approaches to separability conditions is connected with upper bounds on the sum of maximal probabilities. Separability conditions are often formulated for measurements that have a special structure. For instance, mutually unbiased bases and mutually unbiased measurements can be utilized for such purposes. Using resolution of the identity for each subsystem of a bipartite system, we construct some resolution of the identity in the product of Hilbert spaces. Separability conditions are then formulated in terms of maximal probabilities for a collection of specific outcomes. The presented conditions are compared with some previous formulations. Our results are exemplified with entangled states of a two-qutrit system.

  18. Unbiased Identification of Patients with Disorders of Sex Development

    PubMed Central

    Hanauer, David A.; Gardner, Melissa; Sandberg, David E.

    2014-01-01

    Disorders of sex development (DSD) represent a collection of rare diseases that generate substantial controversy regarding best practices for diagnosis and treatment. A significant barrier preventing a better understanding of how patients with these conditions should be evaluated and treated, especially from a psychological standpoint, is the lack of systematic and standardized approaches to identify cases for study inclusion. Common approaches include “hand-picked” subjects already known to the practice, which could introduce bias. We implemented an informatics-based approach to identify patients with DSD from electronic health records (EHRs) at three large, academic children’s hospitals. The informatics approach involved comprehensively searching EHRs at each hospital using a combination of structured billing codes as an initial filtering strategy followed by keywords applied to the free text clinical documentation. The informatics approach was implemented to replicate the functionality of an EHR search engine (EMERSE) available at one of the hospitals. At the two hospitals that did not have EMERSE, we compared case ascertainment using the informatics method to traditional approaches employed for identifying subjects. Potential cases identified using all approaches were manually reviewed by experts in DSD to verify eligibility criteria. At the two institutions where both the informatics and traditional approaches were applied, the informatics approach identified substantially higher numbers of potential study subjects. The traditional approaches yielded 14 and 28 patients with DSD, respectively; the informatics approach yielded 226 and 77 patients, respectively. The informatics approach missed only a few cases that the traditional approaches identified, largely because those cases were known to the study team, but patient data were not in the particular children’s hospital EHR. The use of informatics approaches to search electronic documentation can

  19. Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

    PubMed Central

    2014-01-01

    Background Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas. Results We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy. Conclusions The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle

  20. Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism.

    PubMed

    Kosina, Suzanne M; Danielewicz, Megan A; Mohammed, Mujahid; Ray, Jayashree; Suh, Yumi; Yilmaz, Suzan; Singh, Anup K; Arkin, Adam P; Deutschbauer, Adam M; Northen, Trent R

    2016-07-15

    Synthetic microbial ecology has the potential to enhance the productivity and resiliency of biotechnology processes compared to approaches using single isolates. Engineering microbial consortia is challenging; however, one approach that has attracted significant attention is the creation of synthetic obligate mutualism using auxotrophic mutants that depend on each other for exchange or cross-feeding of metabolites. Here, we describe the integration of mutant library fitness profiling with mass spectrometry based exometabolomics as a method for constructing synthetic mutualism based on cross-feeding. Two industrially important species lacking known ecological interactions, Zymomonas mobilis and Escherichia coli, were selected as the test species. Amino acid exometabolites identified in the spent medium of Z. mobilis were used to select three corresponding E. coli auxotrophs (proA, pheA and IlvA), as potential E. coli counterparts for the coculture. A pooled mutant fitness assay with a Z. mobilis transposon mutant library was used to identify mutants with improved growth in the presence of E. coli. An auxotroph mutant in a gene (ZMO0748) with sequence similarity to cysteine synthase A (cysK), was selected as the Z. mobilis counterpart for the coculture. Exometabolomic analysis of spent E. coli medium identified glutathione related metabolites as potentially available for rescue of the Z. mobilis cysteine synthase mutant. Three sets of cocultures between the Z. mobilis auxotroph and each of the three E. coli auxotrophs were monitored by optical density for growth and analyzed by flow cytometry to confirm high cell counts for each species. Taken together, our methods provide a technological framework for creating synthetic mutualisms combining existing screening based methods and exometabolomics for both the selection of obligate mutualism partners and elucidation of metabolites involved in auxotroph rescue. PMID:26885935

  1. Contextual classification of multispectral image data - An unbiased estimator for the context distribution

    NASA Technical Reports Server (NTRS)

    Tilton, J. C.; Swain, P. H.; Vardeman, S. B.

    1981-01-01

    Recent investigations have demonstrated the effectiveness of a contextual classifier that combines spatial and spectral information employing a general statistical approach. This statistical classification algorithm exploits the tendency of certain ground-cover classes to occur more frequently in some spatial contexts than in others. Indeed, a key input to this algorithm is a statistical characterization of the context: the context distribution. Here a discussion is given of an unbiased estimator of the context distribution which, besides having the advantage of statistical unbiasedness, has the additional advantage over other estimation techniques of being amenable to an adaptive implementation in which the context distribution estimate varies according to local contextual information. Results from applying the unbiased estimator to the contextual classification of three real Landsat data sets are presented and contrasted with results from noncontextual classifications and from contextual classifications utilizing other context distribution estimation techniques.

  2. Unbiased reconstruction of a mammalian transcriptional network mediating the differential response to pathogens

    PubMed Central

    Amit, Ido; Garber, Manuel; Chevrier, Nicolas; Leite, Ana Paula; Donner, Yoni; Eisenhaure, Thomas; Guttman, Mitchell; Grenier, Jennifer K.; Li, Weibo; Zuk, Or; Schubert, Lisa A.; Birditt, Brian; Shay, Tal; Goren, Alon; Zhang, Xiaolan; Smith, Zachary; Deering, Raquel; McDonald, Rebecca C.; Cabili, Moran; Bernstein, Bradley E; Rinn, John L.; Meissner, Alex; Root, David E.; Hacohen, Nir; Regev, Aviv

    2010-01-01

    Models of mammalian regulatory networks controlling gene expression have been inferred from genomic data, yet have largely not been validated. We present an unbiased strategy to systematically perturb candidate regulators and monitor cellular transcriptional responses. We apply this approach to derive regulatory networks that control the transcriptional response of mouse primary dendritic cells (DCs) to pathogens. Our approach revealed the regulatory functions of 125 transcription factors, chromatin modifiers, and RNA binding proteins and constructed a network model consisting of two dozen core regulators and 76 fine-tuners that help explain how pathogen-sensing pathways achieve specificity. This study establishes a broadly-applicable, comprehensive and unbiased approach to reveal the wiring and functions of a regulatory network controlling a major transcriptional response in primary mammalian cells. PMID:19729616

  3. 12 CFR 575.3 - Mutual holding company reorganizations.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Mutual holding company reorganizations. 575.3 Section 575.3 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY MUTUAL HOLDING COMPANIES § 575.3 Mutual holding company reorganizations. A mutual savings association may reorganize...

  4. 12 CFR 575.3 - Mutual holding company reorganizations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 6 2014-01-01 2012-01-01 true Mutual holding company reorganizations. 575.3 Section 575.3 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY MUTUAL HOLDING COMPANIES § 575.3 Mutual holding company reorganizations. A mutual savings association may reorganize...

  5. 78 FR 64600 - Mutual Savings Association Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-29

    ... Office of the Comptroller of the Currency Mutual Savings Association Advisory Committee AGENCY... Mutual Savings Association Advisory Committee (MSAAC). DATES: A public meeting of the MSAAC will be held... mutual savings associations and other issues of concern to the existing mutual savings...

  6. 75 FR 77048 - Mutual Savings Association Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-10

    ... Office of Thrift Supervision Mutual Savings Association Advisory Committee AGENCY: Department of the... Thrift Supervision has determined that the renewal of the ] Charter of the OTS Mutual Savings Association... facing mutual savings associations. DATES: The Charter of the OTS Mutual Savings Association...

  7. Group Differences in the Mutual Gaze of Chimpanzees (Pan Troglodytes)

    ERIC Educational Resources Information Center

    Bard, Kim A.; Myowa-Yamakoshi, Masako; Tomonaga, Masaki; Tanaka, Masayuki; Costall, Alan; Matsuzawa, Tetsuro

    2005-01-01

    A comparative developmental framework was used to determine whether mutual gaze is unique to humans and, if not, whether common mechanisms support the development of mutual gaze in chimpanzees and humans. Mother-infant chimpanzees engaged in approximately 17 instances of mutual gaze per hour. Mutual gaze occurred in positive, nonagonistic…

  8. 12 CFR 544.5 - Federal mutual savings association bylaws.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Federal mutual savings association bylaws. 544.5 Section 544.5 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY FEDERAL MUTUAL SAVINGS ASSOCIATIONS-CHARTER AND BYLAWS Bylaws § 544.5 Federal mutual savings association bylaws. (a) General. A Federal mutual...

  9. 12 CFR 144.1 - Federal mutual charter.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 1 2012-01-01 2012-01-01 false Federal mutual charter. 144.1 Section 144.1 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY FEDERAL MUTUAL SAVINGS ASSOCIATIONS-CHARTER AND BYLAWS Charter § 144.1 Federal mutual charter. A Federal mutual savings association shall have a charter in the following...

  10. 12 CFR 544.1 - Federal mutual charter.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Federal mutual charter. 544.1 Section 544.1 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY FEDERAL MUTUAL SAVINGS ASSOCIATIONS-CHARTER AND BYLAWS Charter § 544.1 Federal mutual charter. A Federal mutual savings association shall have a charter in the following...