1,198 research outputs found
Why my photos look sideways or upside down? Detecting Canonical Orientation of Images using Convolutional Neural Networks
Image orientation detection requires high-level scene understanding. Humans
use object recognition and contextual scene information to correctly orient
images. In literature, the problem of image orientation detection is mostly
confronted by using low-level vision features, while some approaches
incorporate few easily detectable semantic cues to gain minor improvements. The
vast amount of semantic content in images makes orientation detection
challenging, and therefore there is a large semantic gap between existing
methods and human behavior. Also, existing methods in literature report highly
discrepant detection rates, which is mainly due to large differences in
datasets and limited variety of test images used for evaluation. In this work,
for the first time, we leverage the power of deep learning and adapt
pre-trained convolutional neural networks using largest training dataset
to-date for the image orientation detection task. An extensive evaluation of
our model on different public datasets shows that it remarkably generalizes to
correctly orient a large set of unconstrained images; it also significantly
outperforms the state-of-the-art and achieves accuracy very close to that of
humans
Family of solvable generalized random-matrix ensembles with unitary symmetry
We construct a very general family of characteristic functions describing
Random Matrix Ensembles (RME) having a global unitary invariance, and
containing an arbitrary, one-variable probability measure which we characterize
by a `spread function'. Various choices of the spread function lead to a
variety of possible generalized RMEs, which show deviations from the well-known
Gaussian RME originally proposed by Wigner. We obtain the correlation functions
of such generalized ensembles exactly, and show examples of how particular
choices of the spread function can describe ensembles with arbitrary eigenvalue
densities as well as critical ensembles with multifractality.Comment: 4 pages, to be published in Phys. Rev. E, Rapid Com
Scalar Field Quantization Without Divergences In All Spacetime Dimensions
Covariant, self-interacting scalar quantum field theories admit solutions for
low enough spacetime dimensions, but when additional divergences appear in
higher dimensions, the traditional approach leads to results, such as
triviality, that are less than satisfactory. Guided by idealized but soluble
{\it non}renormalizable models, a nontraditional proposal for the quantization
of covariant scalar field theories is advanced, which achieves a term-by-term,
divergence-free, perturbation analysis of interacting models expanded about a
suitable pseudofree theory, which differs from a free theory by an O(\hbar^2)
counterterm. These positive features are realized within a functional integral
formulation by a local, nonclassical, counterterm that effectively transforms
parameter changes in the action from generating mutually singular measures,
which are the basis for divergences, to equivalent measures, thereby removing
all divergences. The use of an alternative model about which to perturb is
already supported by properties of the classical theory, and is allowed by the
inherent ambiguity in the quantization process itself. This procedure not only
provides acceptable solutions for models for which no acceptable, faithful
solution currently exists, e.g., \phi^4_n, for spacetime dimensions n\ge4, but
offers a new, divergence-free solution, for less-singular models as well, e.g.,
\phi^4_n, for n=2,3. Our analysis implies similar properties for multicomponent
scalar models, such as those associated with the Higgs model.Comment: 45 pages, has relevance for the Higgs model, review and updated
analysis, version accepted for publicatio
Ultrafast Structural Dynamics of BlsA, a Photoreceptor from the Pathogenic Bacterium Acinetobacter baumannii
Acinetobacter baumannii is an important human pathogen that can form biofilms and persist under harsh environmental conditions. Biofilm formation and virulence are modulated by blue light, which is thought to be regulated by a BLUF protein, BlsA. To understand the molecular mechanism of light sensing, we have used steady-state and ultrafast vibrational spectroscopy to compare the photoactivation mechanism of BlsA to the BLUF photosensor AppA from Rhodobacter sphaeroides. Although similar photocycles are observed, vibrational data together with homology modeling identify significant differences in the β5 strand in BlsA caused by photoactivation, which are proposed to be directly linked to downstream signaling
BLUF Domain Function Does Not Require a Metastable Radical Intermediate State
BLUF
(blue light using flavin) domain proteins are an important
family of blue light-sensing proteins which control a wide variety
of functions in cells. The primary light-activated step in the BLUF
domain is not yet established. A number of experimental and theoretical
studies points to a role for photoinduced electron transfer (PET)
between a highly conserved tyrosine and the flavin chromophore to
form a radical intermediate state. Here we investigate the role of
PET in three different BLUF proteins, using ultrafast broadband transient
infrared spectroscopy. We characterize and identify infrared active
marker modes for excited and ground state species and use them to
record photochemical dynamics in the proteins. We also generate mutants
which unambiguously show PET and, through isotope labeling of the
protein and the chromophore, are able to assign modes characteristic
of both flavin and protein radical states. We find that these radical
intermediates are not observed in two of the three BLUF domains studied,
casting doubt on the importance of the formation of a population of
radical intermediates in the BLUF photocycle. Further, unnatural amino
acid mutagenesis is used to replace the conserved tyrosine with fluorotyrosines,
thus modifying the driving force for the proposed electron transfer
reaction; the rate changes observed are also not consistent with a
PET mechanism. Thus, while intermediates of PET reactions can be observed
in BLUF proteins they are not correlated with photoactivity, suggesting
that radical intermediates are not central to their operation. Alternative
nonradical pathways including a keto–enol tautomerization induced
by electronic excitation of the flavin ring are considered
A Grassmann integral equation
The present study introduces and investigates a new type of equation which is
called Grassmann integral equation in analogy to integral equations studied in
real analysis. A Grassmann integral equation is an equation which involves
Grassmann integrations and which is to be obeyed by an unknown function over a
(finite-dimensional) Grassmann algebra G_m. A particular type of Grassmann
integral equations is explicitly studied for certain low-dimensional Grassmann
algebras. The choice of the equation under investigation is motivated by the
effective action formalism of (lattice) quantum field theory. In a very general
setting, for the Grassmann algebras G_2n, n = 2,3,4, the finite-dimensional
analogues of the generating functionals of the Green functions are worked out
explicitly by solving a coupled system of nonlinear matrix equations. Finally,
by imposing the condition G[{\bar\Psi},{\Psi}] = G_0[{\lambda\bar\Psi},
{\lambda\Psi}] + const., 0<\lambda\in R (\bar\Psi_k, \Psi_k, k=1,...,n, are the
generators of the Grassmann algebra G_2n), between the finite-dimensional
analogues G_0 and G of the (``classical'') action and effective action
functionals, respectively, a special Grassmann integral equation is being
established and solved which also is equivalent to a coupled system of
nonlinear matrix equations. If \lambda \not= 1, solutions to this Grassmann
integral equation exist for n=2 (and consequently, also for any even value of
n, specifically, for n=4) but not for n=3. If \lambda=1, the considered
Grassmann integral equation has always a solution which corresponds to a
Gaussian integral, but remarkably in the case n=4 a further solution is found
which corresponds to a non-Gaussian integral. The investigation sheds light on
the structures to be met for Grassmann algebras G_2n with arbitrarily chosen n.Comment: 58 pages LaTeX (v2: mainly, minor updates and corrections to the
reference section; v3: references [4], [17]-[21], [39], [46], [49]-[54],
[61], [64], [139] added
Integrated random processes exhibiting long tails, finite moments and 1/f spectra
A dynamical model based on a continuous addition of colored shot noises is
presented. The resulting process is colored and non-Gaussian. A general
expression for the characteristic function of the process is obtained, which,
after a scaling assumption, takes on a form that is the basis of the results
derived in the rest of the paper. One of these is an expansion for the
cumulants, which are all finite, subject to mild conditions on the functions
defining the process. This is in contrast with the Levy distribution -which can
be obtained from our model in certain limits- which has no finite moments. The
evaluation of the power spectrum and the form of the probability density
function in the tails of the distribution shows that the model exhibits a 1/f
spectrum and long tails in a natural way. A careful analysis of the
characteristic function shows that it may be separated into a part representing
a Levy processes together with another part representing the deviation of our
model from the Levy process. This allows our process to be viewed as a
generalization of the Levy process which has finite moments.Comment: Revtex (aps), 15 pages, no figures. Submitted to Phys. Rev.
Modeling Proactive Decisions to Manage Pneumonia Epizootics in Bighorn Sheep
Pneumonia epizootics in bighorn sheep (Ovis canadensis) are a major challenge for wildlife agencies due to the complexity of the disease, long-term impacts, and lack of tools to manage risk. We developed a decision model to facilitate proactive management of pneumonia epizootics in bighorn sheep in Montana. Our decision model integrates a risk model to predict probability of pneumonia epizootics based on identified risk factors. It uses a structured decision making (SDM) approach to analyze potential decisions based on predictions from the risk model, herd-specific management objectives, and predicted consequences and trade-offs. We demonstrated our model’s use with an analysis of representative herds and analyzed the recommended decisions to understand them clearly. We learned that proactive management for each herd was expected to outperform in meeting multiple, competing management objectives compared to ongoing status quo management. Based on sensitivity analyses, we also learned that the recommended decisions were relatively robust with limited sensitivity to variations in model inputs and uncertainties; we expect this to be the case in future analyses as well. Our decision model addressed the challenges of uncertainty, risk tolerance, and the multi-objective nature of management of bighorn sheep while providing a consistent, transparent, and deliberative approach for making decisions for each herd. It is a unique tool for managing pneumonia epizootics using an accessible framework for biologists and managers. Our work also provides a case study for developing similar SDM-based decision models, particularly for other wildlife diseases, to address challenges of making complex decisions
Development and characterization of synthetic antibodies binding to the cystic fibrosis conductance regulator
Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel in the apical surface of epithelial cells in the airway and gastrointestinal tract, and mutation of CFTR is the underlying cause of cystic fibrosis. However, the precise molecular details of the structure and function of CFTR in native and disease states remains elusive and cystic fibrosis researchers are hindered by a lack of high specificity, high affinity binding reagents for use in structural and biological studies. Here, we describe a panel of synthetic antigen-binding fragments (Fabs) isolated from a phage-displayed library that are specific for intracellular domains of CFTR that include the nucleotide-binding domains (NBD1 and NBD2), the R-region, and the regulatory insertion loop of NBD1. Binding assays performed under conditions that promote the native fold of the protein demonstrated that all Fabs recognized full-length CFTR. However, only the NBD1-specific Fab recognized denatured CFTR by western blot, suggesting a conformational epitope requirement for the other Fabs. Surface plasmon resonance experiments showed that the R-region Fab binds with high affinity to both the phosphorylated and unphosphorylated R-region. In addition, NMR analysis of bound versus unbound R-region revealed a distinct conformational effect upon Fab binding. We further defined residues involved with antibody recognition using an overlapping peptide array. In summary, we describe methodology complementary to previous hybridoma-based efforts to develop antibody reagents to CFTR, and introduce a synthetic antibody panel to aid structural and biological studies
Distribution and Abundance of the Kittlitz\u27s Murrelet \u3ci\u3eBrachyramphus brevirostris\u3c/i\u3e in Selected Areas of Southeastern Alaska
We conducted boat-based surveys for the Kittlitz’s Murrelet Brachyramphus brevirostris during the breeding season in southeastern Alaska from 2002 to 2009. We completed a single survey in seven areas and multiple annual surveys in three areas. Although surveys spanned a broad geographic area, from LeConte Bay in the south to the Lost Coast in the north (~655 km linear distance), roughly 79% of the regional population of Kittlitz’s Murrelet was found in and between Icy and Yakutat bays (~95 km linear distance). The congeneric Marbled Murrelet B. marmoratus outnumbered the Kittlitz’s Murrelet in all areas surveyed except Icy Bay; in fact, Kittlitz’s Murrelet abundance constituted a relatively small proportion (7%) of the total Brachyramphus murrelet abundance in our survey areas. In areas for which there are multiple years of survey data, Kittlitz’s Murrelet abundance varied considerably, whereas Marbled Murrelet abundance was comparatively stable during the same time period. Since the southern distribution of this species has likely narrowed over the last 50 years, and the distribution of the Kittlitz’s Murrelet appears to be restricted to glacially influenced marine waters in southeastern Alaska, we expect that any future changes in glacial extent will likely affect this species and its long-term persistence in the region
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