Quantum noise induced entanglement and chaos in the dissipative quantum model of brain

We discuss some features of the dissipative quantum model of brain in the frame of the formalism of quantum dissipation. Such a formalism is based on the doubling of the system degrees of freedom. We show that the doubled modes account for the quantum noise in the fluctuating random force in the system-environment coupling. Remarkably, such a noise manifests itself through the coherent structure of the system ground state. The entanglement of the system modes with the doubled modes is shown to be permanent in the infinite volume limit. In such a limit the trajectories in the memory space are classical chaotic trajectories.Comment: 14 page

Multistability and metastability: understanding dynamic coordination in the brain

Multistable coordination dynamics exists at many levels, from multifunctional neural circuits in vertebrates and invertebrates to large-scale neural circuitry in humans. Moreover, multistability spans (at least) the domains of action and perception, and has been found to place constraints upon, even dictating the nature of, intentional change and the skill-learning process. This paper reviews some of the key evidence for multistability in the aforementioned areas, and illustrates how it has been measured, modelled and theoretically understood. It then suggests how multistability—when combined with essential aspects of coordination dynamics such as instability, transitions and (especially) metastability—provides a platform for understanding coupling and the creative dynamics of complex goal-directed systems, including the brain and the brain–behaviour relation

ABAEnrichment: An R package to test for gene set expression enrichment in the adult and developing human brain

Summary: We present ABAEnrichment, an R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas. We validate ABAEnrichment by successfully recovering the origin of gene sets identified in specific brain cell-types and developmental stages. Availability and Implementation: ABAEnrichment was implemented as an R package and is available under GPL (≥ 2) from the Bioconductor website (http://bioconductor.org/packages/3.3/bioc/html/ABAEnrichment.html). Contacts: [email protected], [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Computational challenges in the analysis of ancient DNA

High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering

Products, coproducts and singular value decomposition

Products and coproducts may be recognized as morphisms in a monoidal tensor category of vector spaces. To gain invariant data of these morphisms, we can use singular value decomposition which attaches singular values, ie generalized eigenvalues, to these maps. We show, for the case of Grassmann and Clifford products, that twist maps significantly alter these data reducing degeneracies. Since non group like coproducts give rise to non classical behavior of the algebra of functions, ie make them noncommutative, we hope to be able to learn more about such geometries. Remarkably the coproduct for positive singular values of eigenvectors in $A$ yields directly corresponding eigenvectors in A\otimes A.Comment: 17 pages, three eps-figure

Beam profile reflectometry: a new technique for thin film measurements

In the manufacture of semiconductor devices, it is of critical importance to know the thickness and material properties of various dielectric and semiconducting thin films. Although there are many techniques for measuring these films, the most commonly used are reflection spectrophotometry [1,2] and ellipsometry [3]. In the former method, the normal- incidence reflectivity is measured as a function of wavelength. The shape of the reflectivity spectrum is then analyzed using the Fresnel equations to determine the thickness of the film. In some cases, the refractive index can also be determined provided that the dispersion of the optical constants are well known. The latter method consists of reflecting a beam of known polarization off the sample surface at an oblique angle. The film thickness, and in some cases the refractive index, can be determined from the change in polarization experienced upon reflection

Cephalosporin-3’-diazeniumdiolate NO-donor prodrug PYRRO-C3D enhances azithromycin susceptibility of non-typeable Haemophilus influenzae biofilms

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Objectives: PYRRO-C3D is a cephalosporin-3-diazeniumdiolate nitric oxide (NO)-donor prodrug designed to selectively deliver NO to bacterial infection sites. The objective of this study was to assess the activity of PYRRO-C3D against non-typeable Haemophilus influenzae (NTHi) biofilms and examine the role of NO in reducing biofilm-associated antibiotic tolerance. Methods: The activity of PYRRO-C3D on in vitro NTHi biofilms was assessed through CFU enumeration and confocal microscopy. NO release measurements were performed using an ISO-NO probe. NTHi biofilms grown on primary ciliated respiratory epithelia at an air-liquid interface were used to investigate the effects of PYRRO-C3D in the presence of host tissue. Label-free LC/MS proteomic analyses were performed to identify differentially expressed proteins following NO treatment. Results: PYRRO-C3D specifically released NO in the presence of NTHi, while no evidence of spontaneous NO release was observed when the compound was exposed to primary epithelial cells. NTHi lacking β-lactamase activity failed to trigger NO release. Treatment significantly increased the susceptibility of in vitro NTHi biofilms to azithromycin, causing a log-fold reduction in viability (p<0.05) relative to azithromycin alone. The response was more pronounced for biofilms grown on primary respiratory epithelia, where a 2-log reduction was observed (p<0.01). Label-free proteomics showed that NO increased expression of sixteen proteins involved in metabolic and transcriptional/translational functions. Conclusions: NO release from PYRRO-C3D enhances the efficacy of azithromycin against NTHi biofilms, putatively via modulation of NTHi metabolic activity. Adjunctive therapy with NO mediated through PYRRO-C3D represents a promising approach for reducing biofilm associated antibiotic tolerance

Direct Determination of Sizes of Excitations from Optical Measurements on Ion-Implanted GaAs

Using a simple model that describes the decrease of the amplitudes of optical structures in ion-implanted crystals, projected areas of several valence and core excitons in GaAs are determined. The last remnant of crystal-related optical structure vanishes for crystallite areas less than (16Å)2

Medical applications of artificial olfactometry

The present invention provides methods for detecting the presence of an analyte indicative of various medical conditions, including halitosis, periodontal disease and other diseases are also disclosed

Nuclear and mitochondrial DNA sequences from two Denisovan individuals

Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans