Soundings: the Newsletter of the Monterey Bay Chapter of the American Cetacean Society. 2014

Issues January - November/December 2014. (PDF contains 100 pages)

Dog chromosome-specific paints reveal evolutionary inter- and intrachromosomal rearrangements in the American mink and human

Forty chromosome-specific paint probes of the domestic dog (Canis familiaris, 2n = 78) were used to delineate conserved segments on metaphase chromosomes of the American mink (Mustela vison, 2n = 30) by fluorescence in situ hybridisation. Half of the 38 canine autosomal probes each painted one pair of homologous segments in a diploid mink metaphase, whereas the other 19 dog probes each painted from two to five pairs of discrete segments. In total, 38 canine autosomal paints highlighted 71 pairs of conserved segments in the mink. These painting results allow us to establish a complete comparative chromosome map between the American mink and domestic dog. This map demonstrates that extensive chromosome rearrangements differentiate the karyotypes of the dog and American mink. The 38 dog autosomes could be reconstructed from the 14 autosomes of the American mink through at least 47 fissions, 25 chromosome fusions, and six inversions. Furthermore, comparison of the current dog/mink map with the published human/dog map discloses 23 cryptic intrachromosomal rearrangements in 10 regions of conserved synteny in the human and American mink genomes and thus further refined the human/mink comparative genome map. Copyright (C) 2000 S. Karger AG, Basel.

Identification of native American founder mtDNAs through the analysis of complete mtDNA sequences: Some caveats

In this study, a detailed analysis of both previously published and new data was performed to determine whether complete, or almost complete, mtDNA sequences can resolve the long-debated issue of which Asian mtDNAs were founder sequences for the Native American mtDNA pool. Unfortunately, we now know that coding region data and their analysis are not without problems. To obtain and report reasonably correct sequences does not seem to be a trivial task, and to discriminate between Asian-and Native American mtDNA ancestries may be more complex than previously believed. It is essential to take into account the effects of mutational hot spots in both the control and coding regions, so that the number of apparent Native American mtDNA founder sequences is not erroneously inflated. As we report here, a careful analysis of all available data indicates that there is very little evidence that more than five founder mtDNA sequences entered Beringia before the Last Glacial Maximum and left their traces in the current Native American mtDNA pool.

Computation of transient and steady turbulent isothermal flows with an impinging rectangular jet

The computation of both transient and steady turbulent incompressible isothermal flows is studied. The flow is very complex, having streamline curvature, large vortex structures and stagnation resulting from an impinging rectangular jet. For transient computations, the standard k-ε model is adopted. For steady flows, the k-ε, high and low Reynolds number k-l and mixing length models are tried. Zonal approaches combining the above turbulence models are also investigated. None of the models are found to give satisfactory agreement with velocity measurements.

Band alignment between Ta2O5 and metals for resistive random access memory electrodes engineering

Band alignment of resistive random access memory (RRAM) switching material Ta2O5 and different metal electrode materials was examined using high-resolution X-ray photoelectron spectroscopy. Schottky and hole barrier heights at the interface between electrode and Ta2O 5 were obtained, where the electrodes consist of materials with low to high work function (Φ m, v a c from 4.06 to 5.93 eV). Effective metal work functions were extracted to study the Fermi level pinning effect and to discuss the dominant conduction mechanism. An accurate band alignment between electrodes and Ta2O5 is obtained and can be used for RRAM electrode engineering and conduction mechanism study. © 2013 American Institute of Physics.

Neural mechanisms of belief inference during cooperative games.

Humans have the arguably unique ability to understand the mental representations of others. For success in both competitive and cooperative interactions, however, this ability must be extended to include representations of others' belief about our intentions, their model about our belief about their intentions, and so on. We developed a "stag hunt" game in which human subjects interacted with a computerized agent using different degrees of sophistication (recursive inferences) and applied an ecologically valid computational model of dynamic belief inference. We show that rostral medial prefrontal (paracingulate) cortex, a brain region consistently identified in psychological tasks requiring mentalizing, has a specific role in encoding the uncertainty of inference about the other's strategy. In contrast, dorsolateral prefrontal cortex encodes the depth of recursion of the strategy being used, an index of executive sophistication. These findings reveal putative computational representations within prefrontal cortex regions, supporting the maintenance of cooperation in complex social decision making.

The role of damping in steel pan manufacture

Results are presented of systematic studies of vibration damping in steel of a type, and processed by a route, rel-evant to Caribbean steel pans. Damping is likely to be a significant factor in the variation of sound quality be-tween different pans. The main stages in pan manufac-ture are simulated in a controlled manner using sheet steel, cold-rolled to a prescribed level of thickness reduc-tion then annealed at a chosen temperature in a laboratory furnace. Small test strips were cut from the resulting material, and tested in free-free beam bending to deduce the Young’s modulus and its associated loss factor. It is shown that the steel type, the degree of cold working and the annealing temperature all have a significant influence on damping. Furthermore, for each individual specimen damping is found to decrease with rising frequency, ap-proximately following a power law. Comparison with samples cut from a real pan show that there are further influences from the pan’s geometrical details.

Molecular evidence for diphyly of the Asian catfish family Amblycipitidae (Teleostei: Siluriformes) and exclusion of the South American Aspredinidae from Sisoroidea

Amblycipitidae Day, 1873 is an Asian family of catfishes (Siluriformes) usually considered to contain 28 species placed in three genera: Amblyceps (14 spp.), Liobagrus (12 spp.) and Xiurenbagrus (2 spp.). Morphology-based systematics has supported the monophyly of this family, with some authors placing Amblycipitidae within a larger group including Akysidae, Sisoridae and Aspredinidae, termed the Sisoroidea. Here we investigate the phylogenetic relationships among four species of Amblyceps, six species of Liobagrus and the two species of Xiurenbagrus with respect to other sisoroid taxa as well as other catfish groups using 6100 aligned base pairs of DNA sequence data from the rag1 and rag2 genes of the nuclear genome and from three regions (cyt b, COL ND4 plus tRNA-His and tRNA-Ser) of the mitochondrial genome. Parsimony and Bayesian analyses of the data indicate strong support for a diphyletic Amblycipitidae in which the genus Amblyceps is the sister group to the Sisoridae and a clade formed by genera Liobagrus and Xiurenbagrus is the sister group to Akysidae. These taxa together form a well supported monophyletic group that assembles all Asian sisoroid taxa, but excludes the South American Aspredinidae. Results for aspredinids are consistent with previous molecular studies that indicate these catfishes are not sisoroids, but the sister group to the South American doradoid catfishes (Auchenipteridae + Doradidae). The redefined sisoroid clade plus Bagridae, Horabagridae and (Ailia + Laides) make up a larger monophyletic group informally termed "Big Asia." Likelihood-based SH tests and Bayes Factor comparisons of the rag and the mitochondrial data partitions considered separately and combined reject both the hypothesis of amblycipitid monophyly and the hypothesis of aspredinid inclusion within Sisoroidea. This result for amblycipitids conflicts with a number of well documented morphological synapomorphies that we briefly review. Possible nomenclatural changes for amblycipitid taxa are noted.

Effect of InAs quantum dots on the Fermi level pinning of undoped-n(+) type GaAs surface studied by contactless electroreflectance

Self-assembled InAs quantum dots (QDs) have been fabricated by depositing 1.6, 1.8, 2.0 and 2.5 monolayer (ML) InAs on surfaces of the undoped-n(+) (UN+) type GaAs structure. Room temperature contactless electroreflectance (CER) was employed to study the built-in electric field and the surface Fermi level pinning of these QD-covered UN+ GaAs samples. The CER results show that 1.6 ML InAs QDs on GaAs do not modify the Fermi level, whereas for samples with more than 1.6 ML InAs coverage, the surface Fermi level is moved to the valence band maximum of GaAs by about 70 meV (which is independent of the InAs deposition thickness) compared to bare GaAs. It is concluded that the modification of InAs coverage on the Fermi level on the GaAs surface is due to the QDs, rather than to the wetting layer. (C) 2003 American Institute of Physics.

Photoluminescence properties of Eu3+-doped ZnS nanocrystals prepared in a water/methanol solution

Monodispersed ZnS and Eu3+-doped ZnS nanocrystals have been prepared through the co-precipitation reaction of inorganic precursors ZnCl2, EuCl3, and Na2S in a water/methanol binary solution. The mean particle sizes are about 3-5 nm. The structures of the as-prepared ZnS nanoparticles are cubic (zinc blende) as demonstrated by an x-ray powder diffraction. Photoluminescence studies showed a stable room temperature emission in the visible spectrum region for all the samples, with a broadening in the emission band and, in particular, a partially overlapped twin peak in the Eu3+-doped ZnS nanocrystals. The experimental results also indicated that Eu3+-doped ZnS nanocrystals, prepared by controlling synthetic conditions, were stable. (C) 2002 American Institute of Physics.

Photoluminescence properties of a GaN0.015As0.985/GaAs single quantum well under short pulse excitation

Under short pulse laser excitation, we have observed an extra high-energy photoluminescence (PL) emission from GaNAs/GaAs single quantum wells (QWs). It dominates the PL spectra under high excitation and/or at high temperature. By measuring the PL dependence on both temperature and excitation power and by analyzing the time-resolved PL results, we have attributed the PL peak to the recombination of delocalized excitons in QWs. Furthermore, a competition process between localized and delocalized excitons is observed in the temperature-dependent PL spectra under the short pulse excitation. This competition is believed to be responsible for the temperature-induced S-shaped PL shift often observed in the disordered alloy semiconductor system under continuous-wave excitation. (C) 2001 American Institute of Physics.

Hydrostatic pressure effect on photoluminescence from a GaN0.015As0.985/GaAs quantum well

Photoluminescence from a GaN0.015As0.985/GaAs quantum well has been measured at 15 K under hydrostatic pressure up to 9 GPa. Both the emissions from the GaNAs well and GaAs barrier are observed. The GaNAs-related peak shows a much weaker pressure dependence compared to that of the GaAs band gap. A group of new peaks appear in the spectra when the pressure is beyond 2.5 GPa, which is attributed to the emissions from the N isoelectronic traps in GaAs. The pressure dependence of the GaNAs-related peaks was calculated using the two-level model with the measured pressure coefficients of the GaAs band gap and N level as fitting parameters. It is found that the calculated results deviate seriously from the experimental data. An increasing of the emission intensity and the linewidth of the GaNAs-related peaks was also observed and briefly discussed. (C) 2001 American Institute of Physics.

Effects of rapid thermal annealing and SiO2 encapsulation on GaNAs/GaAs single quantum wells grown by plasma-assisted molecular-beam epitaxy

Effects of rapid thermal annealing and SiO2 encapsulation on GaNAs/GaAs single quantum wells grown by plasma-assisted molecular-beam epitaxy were studied. Photoluminescence measurements on a series of samples with different well widths and N compositions were used to evaluate the effects. The intermixing of GaNAs and GaAs layers was clearly enhanced by the presence of a SiO2-cap layer. However, it was strongly dependent on the N composition. After annealing at 900 degreesC for 30 s, a blueshift up to 62 meV was observed for the SiO2-capped region of the sample with N composition of 1.5%, whereas only a small blueshift of 26 meV was exhibited for the bare region. For the sample with the N composition of 3.1%, nearly identical photoluminescence peak energy shift for both the SiO2-capped region and the bare region was observed. It is suggested that the enhanced intermixing is mainly dominated by SiO2-capped layer induced defects-assisted diffusion for the sample with smaller N composition, while with increasing N composition, the diffusion assisted by interior defects become predominant. (C) 2001 American Institute of Physics.

Conduction band offset and electron effective mass in GaInNAs/GaAs quantum-well structures with low nitrogen concentration

We have investigated the optical transitions in Ga1-yInyNxAs1-x/GaAs single and multiple quantum wells using photovoltaic measurements at room temperature. From a theoretical fit to the experimental data, the conduction band offset Q(c), electron effective mass m(e)*, and band gap energy E-g were estimated. It was found that the Q(c) is dependent on the indium concentration, but independent on the nitrogen concentration over the range x=(0-1)%. The m(e)* of GaInNAs is much greater than that of InGaAs with the same concentration of indium, and increases as the nitrogen concentration increases up to 1%. Our experimental results for the m(e)* and E-g of GaInNAs are quantitatively explained by the two-band model based on the strong interaction of the conduction band minimum with the localized N states. (C) 2001 American Institute of Physics.