Demographic history and genetic differentiation in apes

SummaryComparisons of genetic variation between humans and great apes are hampered by the fact that we still know little about the demographics and evolutionary history of the latter species [1–4]. In addition, characterizing ape genetic variation is important because they are threatened with extinction, and knowledge about genetic differentiation among groups may guide conservation efforts [5]. We sequenced multiple intergenic autosomal regions totaling 22,400 base pairs (bp) in ten individuals each from western, central, and eastern chimpanzee groups and in nine bonobos, and 16,000 bp in ten Bornean and six Sumatran orangutans. These regions are analyzed together with homologous information from three human populations and gorillas. We find that whereas orangutans have the highest diversity, western chimpanzees have the lowest, and that the demographic histories of most groups differ drastically. Special attention should therefore be paid to sampling strategies and the statistics chosen when comparing levels of variation within and among groups. Finally, we find that the extent of genetic differentiation among “subspecies” of chimpanzees and orangutans is comparable to that seen among human populations, calling the validity of the “subspecies” concept in apes into question

Nonverbal communication interface for collaborative virtual environments

Nonverbal communication is an important aspect of real-life face-to-face interaction and one of the most efficient ways to convey emotions, therefore users should be provided the means to replicate it in the virtual world. Because articulated embodiments are well suited to provide body communication in virtual environments, this paper first reviews some of the advantages and disadvantages of complex embodiments. After a brief introduction to nonverbal communication theories, we present our solution, taking into account the practical limitations of input devices and social science aspects. We introduce our sample of actions and implementation using our VLNET (Virtual Life Network) networked virtual environment and discuss the results of an informal evaluation experimen

Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110

Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or outside Alphaproteobacteria and most of them are similar to genes found in transposable elements, in line with their broad distribution. Stabilizing selection was demonstrated for sORFs with proteomic evidence and bll1319_ISGA which is conserved at the nucleotide level in 16 alphaproteobacterial species, 79 species from other taxa and 49 other Proteobacteria. Further we used Northern blot hybridization to validate ten small RNAs (BjsR1 to BjsR10) belonging to new RNA families. We found that BjsR1 and BjsR3 have homologs outside the genus Bradyrhizobium, and BjsR5, BjsR6, BjsR7, and BjsR10 have up to four imperfect copies in Bradyrhizobium genomes. BjsR8, BjsR9, and BjsR10 are present exclusively in nodules, while the other sRNAs are also expressed in liquid cultures. We also found that the level of BjsR4 decreases after exposure to tellurite and iron, and this down-regulation contributes to survival under high iron conditions. Analysis of additional small RNAs overlapping with 3’-UTRs revealed two new repetitive elements named Br-REP1 and Br-REP2. These REP elements may play roles in the genomic plasticity and gene regulation and could be useful for strain identification by PCR-fingerprinting. Furthermore, we studied two potential toxin genes in the symbiotic island and confirmed toxicity of the yhaV homolog bll1687 but not of the newly annotated higB homolog blr0229_ISGA in E. coli. Finally, we revealed transcription interference resulting in an antisense RNA complementary to blr1853, a gene induced in symbiosis. The presented results expand our knowledge on sORFs, non-coding RNAs and repetitive elements in B. japonicum and related bacteria

Magnetic Helicity Estimations in Models and Observations of the Solar Magnetic Field. Part III: Twist Number Method

We study the writhe, twist and magnetic helicity of different magnetic flux ropes, based on models of the solar coronal magnetic field structure. These include an analytical force-free Titov--D\'emoulin equilibrium solution, non force-free magnetohydrodynamic simulations, and nonlinear force-free magnetic field models. The geometrical boundary of the magnetic flux rope is determined by the quasi-separatrix layer and the bottom surface, and the axis curve of the flux rope is determined by its overall orientation. The twist is computed by the Berger--Prior formula that is suitable for arbitrary geometry and both force-free and non-force-free models. The magnetic helicity is estimated by the twist multiplied by the square of the axial magnetic flux. We compare the obtained values with those derived by a finite volume helicity estimation method. We find that the magnetic helicity obtained with the twist method agrees with the helicity carried by the purely current-carrying part of the field within uncertainties for most test cases. It is also found that the current-carrying part of the model field is relatively significant at the very location of the magnetic flux rope. This qualitatively explains the agreement between the magnetic helicity computed by the twist method and the helicity contributed purely by the current-carrying magnetic field.Comment: To be published in Ap

Spatially Rendering Decomposed Recordings - Integrating Score-Informed Source Separation and Semantic Playback Technologies

In this contribution, we present a system for creating novel renderings of a given music recording that aurally highlight certain musical aspects or semantics using spatial localiza-tions. The system decomposes a monaural audio recording into separate events using score-informed source separa-tion techniques and prepares them for an interactive mobile player that renders audio based on semantic information. We demonstrate the capabilities of the system by means of an example using an immersive chroma helix model which the listener can navigate in realtime using mobile sensor controls. 1

Comparison of force-free coronal magnetic field modeling using vector fields from Hinode and Solar Dynamics Observatory

Photospheric magnetic vector maps from two different instruments are used to model the nonlinear force-free coronal magnetic field above an active region. We use vector maps inferred from polarization measurements of the Solar Dynamics Observatory/Helioseismic and Magnetic Imager (HMI) and the Solar Optical Telescope Spectropolarimeter (SP) aboard Hinode. Besides basing our model calculations on HMI data, we use both, SP data of original resolution and scaled down to the resolution of HMI. This allows us to compare the model results based on data from different instruments and to investigate how a binning of high-resolution data effects the model outcome. The resulting 3D magnetic fields are compared in terms of magnetic energy content and magnetic topology. We find stronger magnetic fields in the SP data, translating into a higher total magnetic energy of the SP models. The net Lorentz forces of the HMI and SP lower boundaries verify their force-free compatibility. We find substantial differences in the absolute estimates of the magnetic field energy but similar relative estimates, e.g., the fraction of excess energy and of the flux shared by distinct areas. The location and extension of neighboring connectivity domains differs and the SP model fields tend to be higher and more vertical. Hence, conclusions about the magnetic connectivity based on force-free field models are to be drawn with caution. We find that the deviations of the model solution when based on the lower-resolution SP data are small compared to the differences of the solutions based on data from different instruments.Comment: 8 pages, 10 figures, APJ, accepte

Dissecting the Moth: Discovery of an off-centered ring in the HD 61005 debris disk with high-resolution imaging

The debris disk known as "The Moth" is named after its unusually asymmetric surface brightness distribution. It is located around the ~90 Myr old G8V star HD 61005 at 34.5 pc and has previously been imaged by the HST at 1.1 and 0.6 microns. Polarimetric observations suggested that the circumstellar material consists of two distinct components, a nearly edge-on disk or ring, and a swept-back feature, the result of interaction with the interstellar medium. We resolve both components at unprecedented resolution with VLT/NACO H-band imaging. Using optimized angular differential imaging techniques to remove the light of the star, we reveal the disk component as a distinct narrow ring at inclination i=84.3 \pm 1.0{\deg}. We determine a semi-major axis of a=61.25 \pm 0.85 AU and an eccentricity of e=0.045 \pm 0.015, assuming that periastron is located along the apparent disk major axis. Therefore, the ring center is offset from the star by at least 2.75 \pm 0.85 AU. The offset, together with a relatively steep inner rim, could indicate a planetary companion that perturbs the remnant planetesimal belt. From our imaging data we set upper mass limits for companions that exclude any object above the deuterium-burning limit for separations down to 0.3". The ring shows a strong brightness asymmetry along both the major and minor axis. A brighter front side could indicate forward-scattering grains, while the brightness difference between the NE and SW components can be only partly explained by the ring center offset, suggesting additional density enhancements on one side of the ring. The swept-back component appears as two streamers originating near the NE and SW edges of the debris ring.Comment: 6 pages, 6 figures. Accepted to Astronomy and Astrophysics letter

The Influence of Spatial Resolution on Nonlinear Force-Free Modeling

The nonlinear force-free field (NLFFF) model is often used to describe the solar coronal magnetic field, however a series of earlier studies revealed difficulties in the numerical solution of the model in application to photospheric boundary data. We investigate the sensitivity of the modeling to the spatial resolution of the boundary data, by applying multiple codes that numerically solve the NLFFF model to a sequence of vector magnetogram data at different resolutions, prepared from a single Hinode/SOT-SP scan of NOAA Active Region 10978 on 2007 December 13. We analyze the resulting energies and relative magnetic helicities, employ a Helmholtz decomposition to characterize divergence errors, and quantify changes made by the codes to the vector magnetogram boundary data in order to be compatible with the force-free model. This study shows that NLFFF modeling results depend quantitatively on the spatial resolution of the input boundary data, and that using more highly resolved boundary data yields more self-consistent results. The free energies of the resulting solutions generally trend higher with increasing resolution, while relative magnetic helicity values vary significantly between resolutions for all methods. All methods require changing the horizontal components, and for some methods also the vertical components, of the vector magnetogram boundary field in excess of nominal uncertainties in the data. The solutions produced by the various methods are significantly different at each resolution level. We continue to recommend verifying agreement between the modeled field lines and corresponding coronal loop images before any NLFFF model is used in a scientific setting.Comment: Accepted to ApJ; comments/corrections to this article are welcome via e-mail, even after publicatio

Twisting solar coronal jet launched at the boundary of an active region

A broad jet was observed in a weak magnetic field area at the edge of active region NOAA 11106. The peculiar shape and magnetic environment of the broad jet raised the question of whether it was created by the same physical processes of previously studied jets with reconnection occurring high in the corona. We carried out a multi-wavelength analysis using the EUV images from the Atmospheric Imaging Assembly (AIA) and magnetic fields from the Helioseismic and Magnetic Imager (HMI) both on-board the SDO satellite. The jet consisted of many different threads that expanded in around 10 minutes to about 100 Mm in length, with the bright features in later threads moving faster than in the early ones, reaching a maximum speed of about 200 km s^{-1}. Time-slice analysis revealed a striped pattern of dark and bright strands propagating along the jet, along with apparent damped oscillations across the jet. This is suggestive of a (un)twisting motion in the jet, possibly an Alfven wave. A topological analysis of an extrapolated field was performed. Bald patches in field lines, low-altitude flux ropes, diverging flow patterns, and a null point were identified at the basis of the jet. Unlike classical lambda or Eiffel-tower shaped jets that appear to be caused by reconnection in current sheets containing null points, reconnection in regions containing bald patches seems to be crucial in triggering the present jet. There is no observational evidence that the flux ropes detected in the topological analysis were actually being ejected themselves, as occurs in the violent phase of blowout jets; instead, the jet itself may have gained the twist of the flux rope(s) through reconnection. This event may represent a class of jets different from the classical quiescent or blowout jets, but to reach that conclusion, more observational and theoretical work is necessary.Comment: 12 pages, 9 figures, accepted for publication in A&