1,731 research outputs found
Pattern Recognition Software and Techniques for Biological Image Analysis
The increasing prevalence of automated image acquisition systems is enabling new types of microscopy experiments that generate large image datasets. However, there is a perceived lack of robust image analysis systems required to process these diverse datasets. Most automated image analysis systems are tailored for specific types of microscopy, contrast methods, probes, and even cell types. This imposes significant constraints on experimental design, limiting their application to the narrow set of imaging methods for which they were designed. One of the approaches to address these limitations is pattern recognition, which was originally developed for remote sensing, and is increasingly being applied to the biology domain. This approach relies on training a computer to recognize patterns in images rather than developing algorithms or tuning parameters for specific image processing tasks. The generality of this approach promises to enable data mining in extensive image repositories, and provide objective and quantitative imaging assays for routine use. Here, we provide a brief overview of the technologies behind pattern recognition and its use in computer vision for biological and biomedical imaging. We list available software tools that can be used by biologists and suggest practical experimental considerations to make the best use of pattern recognition techniques for imaging assays
Pedestrian, Crowd, and Evacuation Dynamics
This contribution describes efforts to model the behavior of individual
pedestrians and their interactions in crowds, which generate certain kinds of
self-organized patterns of motion. Moreover, this article focusses on the
dynamics of crowds in panic or evacuation situations, methods to optimize
building designs for egress, and factors potentially causing the breakdown of
orderly motion.Comment: This is a review paper. For related work see http://www.soms.ethz.c
Microwave studies of the fractional Josephson effect in HgTe-based Josephson junctions
The rise of topological phases of matter is strongly connected to their
potential to host Majorana bound states, a powerful ingredient in the search
for a robust, topologically protected, quantum information processing. In order
to produce such states, a method of choice is to induce superconductivity in
topological insulators. The engineering of the interplay between
superconductivity and the electronic properties of a topological insulator is a
challenging task and it is consequently very important to understand the
physics of simple superconducting devices such as Josephson junctions, in which
new topological properties are expected to emerge. In this article, we review
recent experiments investigating topological superconductivity in topological
insulators, using microwave excitation and detection techniques. More
precisely, we have fabricated and studied topological Josephson junctions made
of HgTe weak links in contact with two Al or Nb contacts. In such devices, we
have observed two signatures of the fractional Josephson effect, which is
expected to emerge from topologically-protected gapless Andreev bound states.
We first recall the theoretical background on topological Josephson junctions,
then move to the experimental observations. Then, we assess the topological
origin of the observed features and conclude with an outlook towards more
advanced microwave spectroscopy experiments, currently under development.Comment: Lectures given at the San Sebastian Topological Matter School 2017,
published in "Topological Matter. Springer Series in Solid-State Sciences,
vol 190. Springer
Anti-tumor effect of adenovirus-mediated gene transfer of pigment epithelium-derived factor on mouse B16-F10 melanoma
<p>Abstract</p> <p>Background</p> <p>Angiogenesis plays an important role in tumor growth, invasion, and eventually metastasis. Antiangiogenic strategies have been proven to be a promising approach for clinical therapy for a variety of tumors. As a potent inhibitor of tumor angiogenesis, pigment epithelium-derived factor (PEDF) has recently been studied and used as an anticancer agent in several tumor models.</p> <p>Methods</p> <p>A recombined adenovirus carrying PEDF gene (Ad-PEDF) was prepared, and its expression by infected cells and in treated animals was confirmed with Western blotting and ELISA, respectively. Its activity for inhibiting human umbilical vein endothelial cell (HUVEC) proliferation was tested using the MTT assay. C57BL/6 mice bearing B16-F10 melanoma were treated with i.v. administration of 5 × 10<sup>8 </sup>IU/mouse Ad-PEDF, or 5 × 10<sup>8 </sup>IU/mouse Ad-Null, or normal saline (NS), every 3 days for a total of 4 times. Tumor volume and survival time were recorded. TUNEL, CD31 and H&E stainings of tumor tissue were conducted to examine apoptosis, microvessel density and histological morphology changes. Antiangiogenesis was determined by the alginate-encapsulated tumor cell assay.</p> <p>Results</p> <p>The recombinant PEDF adenovirus is able to transfer the PEDF gene to infected cells and successfully produce secretory PEDF protein, which exhibits potent inhibitory effects on HUVEC proliferation. Through inhibiting angiogenesis, reducing MVD and increasing apoptosis, Ad-PEDF treatment reduced tumor volume and prolonged survival times of mouse bearing B16-F10 melanoma.</p> <p>Conclusion</p> <p>Our data indicate that Ad-PEDF may provide an effective approach to inhibit mouse B16-F10 melanoma growth.</p
Transcription of toll-like receptors 2, 3, 4 and 9, FoxP3 and Th17 cytokines in a susceptible experimental model of canine Leishmania infantum infection
Canine leishmaniosis (CanL) due to Leishmania infantum is a chronic zoonotic systemic disease resulting from complex interactions between protozoa and the canine immune system. Toll-like receptors (TLRs) are essential components of the innate immune system and facilitate the early detection of many infections. However, the role of TLRs in CanL remains unknown and information describing TLR transcription during infection is extremely scarce. The aim of this research project was to investigate the impact of L. infantum infection on canine TLR transcription using a susceptible model. The objectives of this study were to evaluate transcription of TLRs 2, 3, 4 and 9 by means of quantitative reverse transcription polymerase chain reaction (qRT-PCR) in skin, spleen, lymph node and liver in the presence or absence of experimental L. infantum infection in Beagle dogs. These findings were compared with clinical and serological data, parasite densities in infected tissues and transcription of IL-17, IL-22 and FoxP3 in different tissues in non-infected dogs (n = 10), and at six months (n = 24) and 15 months (n = 7) post infection. Results revealed significant down regulation of transcription with disease progression in lymph node samples for TLR3, TLR4, TLR9, IL-17, IL-22 and FoxP3. In spleen samples, significant down regulation of transcription was seen in TLR4 and IL-22 when both infected groups were compared with controls. In liver samples, down regulation of transcription was evident with disease progression for IL-22. In the skin, upregulation was seen only for TLR9 and FoxP3 in the early stages of infection. Subtle changes or down regulation in TLR transcription, Th17 cytokines and FoxP3 are indicative of the silent establishment of infection that Leishmania is renowned for. These observations provide new insights about TLR transcription, Th17 cytokines and Foxp3 in the liver, spleen, lymph node and skin in CanL and highlight possible markers of disease susceptibility in this model
Hopf bifurcation of an SEIRS epidemic model with delays and vertical transmission in the network
Solitary waves in the Nonlinear Dirac Equation
In the present work, we consider the existence, stability, and dynamics of
solitary waves in the nonlinear Dirac equation. We start by introducing the
Soler model of self-interacting spinors, and discuss its localized waveforms in
one, two, and three spatial dimensions and the equations they satisfy. We
present the associated explicit solutions in one dimension and numerically
obtain their analogues in higher dimensions. The stability is subsequently
discussed from a theoretical perspective and then complemented with numerical
computations. Finally, the dynamics of the solutions is explored and compared
to its non-relativistic analogue, which is the nonlinear Schr{\"o}dinger
equation. A few special topics are also explored, including the discrete
variant of the nonlinear Dirac equation and its solitary wave properties, as
well as the PT-symmetric variant of the model
Cluster Lenses
Clusters of galaxies are the most recently assembled, massive, bound
structures in the Universe. As predicted by General Relativity, given their
masses, clusters strongly deform space-time in their vicinity. Clusters act as
some of the most powerful gravitational lenses in the Universe. Light rays
traversing through clusters from distant sources are hence deflected, and the
resulting images of these distant objects therefore appear distorted and
magnified. Lensing by clusters occurs in two regimes, each with unique
observational signatures. The strong lensing regime is characterized by effects
readily seen by eye, namely, the production of giant arcs, multiple-images, and
arclets. The weak lensing regime is characterized by small deformations in the
shapes of background galaxies only detectable statistically. Cluster lenses
have been exploited successfully to address several important current questions
in cosmology: (i) the study of the lens(es) - understanding cluster mass
distributions and issues pertaining to cluster formation and evolution, as well
as constraining the nature of dark matter; (ii) the study of the lensed objects
- probing the properties of the background lensed galaxy population - which is
statistically at higher redshifts and of lower intrinsic luminosity thus
enabling the probing of galaxy formation at the earliest times right up to the
Dark Ages; and (iii) the study of the geometry of the Universe - as the
strength of lensing depends on the ratios of angular diameter distances between
the lens, source and observer, lens deflections are sensitive to the value of
cosmological parameters and offer a powerful geometric tool to probe Dark
Energy. In this review, we present the basics of cluster lensing and provide a
current status report of the field.Comment: About 120 pages - Published in Open Access at:
http://www.springerlink.com/content/j183018170485723/ . arXiv admin note:
text overlap with arXiv:astro-ph/0504478 and arXiv:1003.3674 by other author
Differential Conservation and Divergence of Fertility Genes boule and dazl in the Rainbow Trout
10.1371/journal.pone.0015910PLoS ONE61
Tutorial : applying machine learning in behavioral research
Machine-learning algorithms hold promise for revolutionizing how educators and clinicians make decisions. However, researchers in behavior analysis have been slow to adopt this methodology to further develop their understanding of human behavior and improve the application of the science to problems of applied significance. One potential explanation for the scarcity of research is that machine learning is not typically taught as part of training programs in behavior analysis. This tutorial aims to address this barrier by promoting increased research using machine learning in behavior analysis. We present how to apply the random forest, support vector machine, stochastic gradient descent, and k-nearest neighbors algorithms on a small dataset to better identify parents of children with autism who would benefit from a behavior analytic interactive web training. These step-by-step applications should allow researchers to implement machine-learning algorithms with novel research questions and datasets
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