977 research outputs found
Aspects of Discrete Breathers and New Directions
We describe results concerning the existence proofs of Discrete Breathers
(DBs) in the two classes of dynamical systems with optical linear phonons and
with acoustic linear phonons. A standard approach is by continuation of DBs
from an anticontinuous limit. A new approach, which is purely variational, is
presented. We also review some numerical results on intraband DBs in random
nonlinear systems. Some non-conventional physical applications of DBs are
suggested. One of them is understanding slow relaxation properties of glassy
materials. Another one concerns energy focusing and transport in biomolecules
by targeted energy transfer of DBs. A similar theory could be used for
describing targeted charge transfer of nonlinear electrons (polarons) and, more
generally, for targeted transfer of several excitations (e.g. Davydov soliton).Comment: to appear in the Proceedings of NATO Advanced Research Workshop
"Nonlinearity and Disorder: Theory and Applications",
Tashkent,Uzbekistan,October 1-6, 200
The origin of defects induced in ultra-pure germanium by Electron Beam Deposition
The creation of point defects in the crystal lattices of various
semiconductors by subthreshold events has been reported on by a number of
groups. These observations have been made in great detail using sensitive
electrical techniques but there is still much that needs to be clarified.
Experiments using Ge and Si were performed that demonstrate that energetic
particles, the products of collisions in the electron beam, were responsible
for the majority of electron-beam deposition (EBD) induced defects in a
two-step energy transfer process. Lowering the number of collisions of these
energetic particles with the semiconductor during metal deposition was
accomplished using a combination of static shields and superior vacuum
resulting in devices with defect concentrations lower than cm, the measurement limit of our deep level transient
spectroscopy (DLTS) system. High energy electrons and photons that samples are
typically exposed to were not influenced by the shields as most of these
particles originate at the metal target thus eliminating these particles as
possible damage causing agents. It remains unclear how packets of energy that
can sometimes be as small of 2eV travel up to a m into the material while
still retaining enough energy, that is, in the order of 1eV, to cause changes
in the crystal. The manipulation of this defect causing phenomenon may hold the
key to developing defect free material for future applications.Comment: 18 pages, 9 figure
Reinforcement learning or active inference?
This paper questions the need for reinforcement learning or control theory when optimising behaviour. We show that it is fairly simple to teach an agent complicated and adaptive behaviours using a free-energy formulation of perception. In this formulation, agents adjust their internal states and sampling of the environment to minimize their free-energy. Such agents learn causal structure in the environment and sample it in an adaptive and self-supervised fashion. This results in behavioural policies that reproduce those optimised by reinforcement learning and dynamic programming. Critically, we do not need to invoke the notion of reward, value or utility. We illustrate these points by solving a benchmark problem in dynamic programming; namely the mountain-car problem, using active perception or inference under the free-energy principle. The ensuing proof-of-concept may be important because the free-energy formulation furnishes a unified account of both action and perception and may speak to a reappraisal of the role of dopamine in the brain
Mapping transcription mechanisms from multimodal genomic data
Background
Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene expression data, raising a new computational challenge due to the tremendous size of data.
Results
We develop a method to identify eQTLs. The method represents eQTLs as information flux between genetic variants and transcripts. We use information theory to simultaneously interrogate SNP and gene expression data, resulting in a Transcriptional Information Map (TIM) which captures the network of transcriptional information that links genetic variations, gene expression and regulatory mechanisms. These maps are able to identify both cis- and trans- regulating eQTLs. The application on a dataset of leukemia patients identifies eQTLs in the regions of the GART, PCP4, DSCAM, and RIPK4 genes that regulate ADAMTS1, a known leukemia correlate.
Conclusions
The information theory approach presented in this paper is able to infer the dependence networks between SNPs and transcripts, which in turn can identify cis- and trans-eQTLs. The application of our method to the leukemia study explains how genetic variants and gene expression are linked to leukemia.National Human Genome Research Institute (U.S.) (R01HG003354)National Institute of Allergy and Infectious Diseases (U.S.) (U19 AI067854-05)National Heart, Lung, and Blood Institute (grant T32 HL007427-28)National Institutes of Health (U.S.) (grant K99 LM009826
Nonlinear Localization in Metamaterials
Metamaterials, i.e., artificially structured ("synthetic") media comprising
weakly coupled discrete elements, exhibit extraordinary properties and they
hold a great promise for novel applications including super-resolution imaging,
cloaking, hyperlensing, and optical transformation. Nonlinearity adds a new
degree of freedom for metamaterial design that allows for tuneability and
multistability, properties that may offer altogether new functionalities and
electromagnetic characteristics. The combination of discreteness and
nonlinearity may lead to intrinsic localization of the type of discrete
breather in metallic, SQUID-based, and symmetric metamaterials. We
review recent results demonstrating the generic appearance of breather
excitations in these systems resulting from power-balance between intrinsic
losses and input power, either by proper initialization or by purely dynamical
procedures. Breather properties peculiar to each particular system are
identified and discussed. Recent progress in the fabrication of low-loss,
active and superconducting metamaterials, makes the experimental observation of
breathers in principle possible with the proposed dynamical procedures.Comment: 19 pages, 14 figures, Invited (Review) Chapte
The Old Ladies of the Seed Harvester ant Pogonomyrmex Rugosus: Foraging Performed by Two Groups of Workers
We examined temporal polyethism in Pogonomyrmex rugosus, predicting a pattern of decreasing age from foragers to nest maintenance workers to individuals that were recruited to harvest a temporary food source. Nest maintenance workers were younger than foragers, as indicated by their heavier mass and lower mandibular wear. In contrast, recruited foragers were similar in mass to foragers but they displayed higher mandibular wear, suggesting that they were at least as old as foragers. Longevity estimates for marked individuals of these two latter task groups showed mixed results. Higher mandibular wear of recruited foragers suggests that they did not follow the normal sequence for temporal polyethism, but rather that they functioned as seed-millers, which should more quickly abrade their dentition. This would be the first demonstration of specialist milling individuals in a monomorphic seed-harvester ant
Phenotypic Plasticity of the Drosophila Transcriptome
Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to changing environments. We assessed variation in genome-wide gene expression and four fitness-related phenotypes of an outbred Drosophila melanogaster population under 20 different physiological, social, nutritional, chemical, and physical environments; and we compared the phenotypically plastic transcripts to genetically variable transcripts in a single environment. The environmentally sensitive transcriptome consists of two transcript categories, which comprise ∼15% of expressed transcripts. Class I transcripts are genetically variable and associated with detoxification, metabolism, proteolysis, heat shock proteins, and transcriptional regulation. Class II transcripts have low genetic variance and show sexually dimorphic expression enriched for reproductive functions. Clustering analysis of Class I transcripts reveals a fragmented modular organization and distinct environmentally responsive transcriptional signatures for the four fitness-related traits. Our analysis suggests that a restricted environmentally responsive segment of the transcriptome preserves the balance between phenotypic plasticity and environmental canalization
Olfactory discrimination predicts cognitive decline among community-dwelling older adults
The presence of olfactory dysfunction in individuals at higher risk of Alzheimer's disease has significant diagnostic and screening implications for preventive and ameliorative drug trials. Olfactory threshold, discrimination and identification can be reliably recorded in the early stages of neurodegenerative diseases. The current study has examined the ability of various olfactory functions in predicting cognitive decline in a community-dwelling sample. A group of 308 participants, aged 46–86 years old, were recruited for this study. After 3 years of follow-up, participants were divided into cognitively declined and non-declined groups based on their performance on a neuropsychological battery. Assessment of olfactory functions using the Sniffin' Sticks battery indicated that, contrary to previous findings, olfactory discrimination, but not olfactory identification, significantly predicted subsequent cognitive decline (odds ratio=0.869; P<0.05; 95% confidence interval=0.764−0.988). The current study findings confirm previously reported associations between olfactory and cognitive functions, and indicate that impairment in olfactory discrimination can predict future cognitive decline. These findings further our current understanding of the association between cognition and olfaction, and support olfactory assessment in screening those at higher risk of dementia
BAFF Mediates Splenic B Cell Response and Antibody Production in Experimental Chagas Disease
Chagas disease, caused by the protozoan Trypanosoma cruzi, is endemic in Central and South America. It affects 20 million people and about 100 million people are at risk of infection in endemic areas. Some cases have been identified in non-endemic countries as a consequence of blood transfusion and organ transplantation. Chagas disease presents three stages of infection. The acute phase appears one to two weeks after infection and includes fever, swelling around the bite site, enlarged lymph glands and spleen, and fatigue. This stage is characterized by circulating parasites and many immunological disturbances including a massive B cell response. In general, the acute episode self-resolves in about 2 months and is followed by a clinically silent indeterminate phase characterized by absence of circulating parasites. In about one-third of the cases, the indeterminate phase evolves into a chronic phase with clinically defined cardiac or digestive disturbances. Current knowledge suggests that the persistence of parasites coupled with an unbalanced immune response sustain inflammatory response in the chronic stage. We believe that an effective treatment for chronic Chagas disease should combine antiparasitic drugs with immunomodulators aimed at reducing inflammation and autoreactive response. Our findings enlighten a new role of BAFF-BAFF-R signaling in parasite infection that partially controls polyclonal B cell response but not parasitespecific class-switched primary effectors B cells
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
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