The contribution of Neanderthals to phenotypic variation in modern humans

Assessing the genetic contribution of Neanderthals to non-disease phenotypes in modern humans has been difficult because of the absence of large cohorts for which common phenotype information is available. Using baseline phenotypes collected for 112,000 individuals by the UK Biobank, we can now elaborate on previous findings that identified associations between signatures of positive selection on Neanderthal DNA and various modern human traits but not any specific phenotypic consequences. Here, we show that Neanderthal DNA affects skin tone and hair color, height, sleeping patterns, mood, and smoking status in present-day Europeans. Interestingly, multiple Neanderthal alleles at different loci contribute to skin and hair color in present-day Europeans, and these Neanderthal alleles contribute to both lighter and darker skin tones and hair color, suggesting that Neanderthals themselves were most likely variable in these traits

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

A Consistent Dark Matter Interpretation For CoGeNT and DAMA/LIBRA

In this paper, we study the recent excess of low energy events observed by the CoGeNT collaboration and the annual modulation reported by the DAMA/LIBRA collaboration, and discuss whether these signals could both be the result of the same elastically scattering dark matter particle. We find that, without channeling but when taking into account uncertainties in the relevant quenching factors, a dark matter candidate with a mass of approximately ~7.0 GeV and a cross section with nucleons of sigma_{DM-N} ~2x10^-4 pb (2x10^-40 cm^2) could account for both of these observations. We also comment on the events recently observed in the oxygen band of the CRESST experiment and point out that these could potentially be explained by such a particle. Lastly, we compare the region of parameter space favored by DAMA/LIBRA and CoGeNT to the constraints from XENON 10, XENON 100, and CDMS (Si) and find that these experiments cannot at this time rule out a dark matter interpretation of these signals.Comment: 8 pages, 6 figure

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

freeIbis: An efficient basecaller with calibrated quality scores for Illumina sequencers

Motivation: The conversion of the raw intensities obtained from next-generation sequencing platforms into nucleotide sequences with well-calibrated quality scores is a critical step in the generation of good sequence data. While recent model-based approaches can yield highly accurate calls, they require a substantial amount of processing time and/or computational resources. We previously introduced Ibis, a fast and accurate basecaller for the Illumina platform. We have continued active development of Ibis to take into account developments in the Illumina technology, as well as to make Ibis fully open source. Results: We introduce here freeIbis, which offers significant improvements in sequence accuracy owing to the use of a novel multiclass support vector machine (SVM) algorithm. Sequence quality scores are now calibrated based on empirically observed scores, thus providing a high correlation to their respective error rates. These improvements result in downstream advantages including improved genotyping accuracy. Availability and implementation: FreeIbis is freely available for use under the GPL (http://bioinf.eva.mpg.de/freeibis/). It requires a Python interpreter and a C++ compiler. Tailored versions of LIBOCAS and LIBLINEAR are distributed along with the package. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

PIV as a Complement to LDA in the Study of an Unsteady Oscillating Turbulent Flow

Chong Y. Wong, Graham J. Nathan, Richard M Kels

Drosophila Kelch regulates actin organization via Src64-dependent tyrosine phosphorylation

The Drosophila kelch gene encodes a member of a protein superfamily defined by the presence of kelch repeats. In Drosophila, Kelch is required to maintain actin organization in ovarian ring canals. We set out to study the actin cross-linking activity of Kelch and how Kelch function is regulated. Biochemical studies using purified, recombinant Kelch protein showed that full-length Kelch bundles actin filaments, and kelch repeat 5 contains the actin binding site. Two-dimensional electrophoresis demonstrated that Kelch is tyrosine phosphorylated in a src64-dependent pathway. Site-directed mutagenesis determined that tyrosine residue 627 is phosphorylated. A Kelch mutant with tyrosine 627 changed to alanine (KelY627A) rescued the actin disorganization phenotype of kelch mutant ring canals, but failed to produce wild-type ring canals. Electron microscopy demonstrated that phosphorylation of Kelch is critical for the proper morphogenesis of actin during ring canal growth, and presence of the nonphosphorylatable KelY627A protein phenocopied src64 ring canals. KelY627A protein in ring canals also dramatically reduced the rate of actin monomer exchange. The phenotypes caused by src64 mutants and KelY627A expression suggest that a major function of Src64 signaling in the ring canal is the negative regulation of actin cross-linking by Kelch

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

Evidence Concerning Instabilities of the Distant Geomagnetic Field: Pioneer I

The search-coil magnetometer carried on Pioneer I has yielded evidence of complex geomagnetic behavior at great distances from the earth. This paper is intended to report only some preliminary observations; in particular, what appears to be directional instability in the field. A comprehensive statistical analysis, to be reported later, is still in progress