Multiple maternal origins of chickens: Out of the Asian jungles

Domestic chickens have long been important to human societies for food, religion, entertainment, and decorative uses, yet the origins and phylogeography of chickens through Eurasia remain uncertain. Here, we assessed their origins and phylogeographic hist

Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Self-induced transmission on intersubband resonance in multiple quantum wells

We investigate the nonlinear propagation of ultrashort pulses on resonant intersubband transitions in multiple semiconductor quantum wells. It is shown that the nonlinearity rooted from electron-electron interactions destroys the condition giving rise to self-induced transparency. However, by adjusting the area of input pulse, we find the signatures of self-induced transmission due to a full Rabi flopping of the electron density, and this phenomenon can be approximately interpreted by the traditional standard area theorem via defining the effective area of input pulse.

Multiple in-to-Africa dispersals of labeonin fishes (Teleostei: Cyprinidae) revealed by molecular phylogenetic analysis

An out-of-Africa dispersal route has been proposed for many organisms, including modern man. However, counter examples of in-to-Africa dispersal routes are less common. In the present article, the phylogenetic relationships within the Labeoninae, a subfamily of cyprinid fishes distributed in Asia and Africa, were analyzed to investigate the biogeographic processes governing the modern distribution of these Asian and African cyprinids. The mitochondrial DNA cytochrome b gene was used as a molecular marker. The phylogenetic analysis indicated that the subfamily Labeoninae is a monophyletic group, with some Asian labeonins located at the basal position. Two subclades were found that contained both African and Asian species, which highlighted a need for further biogeographic analysis. Based on this analysis, it is proposed that the centre of origin of the Labeoninae was in East Asia. Molecular clock estimation suggests that the Labeoninae arose by the Early Miocene (similar to 23 MYA) during the period of the second Tibetan uplift. Subsequently, two dispersal events of labeonins from Asia into Africa occured in the Early Miocene (similar to 20 MYA) and Late Miocene (similar to 9 MYA) and serve as examples counter to out-of-Africa dispersal.

Ultracompact triplexer by coupling and decoupling of multiple photonic crystal waveguides

We investigate numerically the self-imaging effect in a system of multiple coupled photonic crystal waveguides (M-CPCWs) with asymmetric coupling. Then two couplers of 2-CPCWs and 3-CPCWs are cascaded to form an ultracompact triplexer by employing coupling and decoupling of M-CPCWs. The wavelength of 1310 nm propagates along the input direction because the M-CPCWs are decoupled at the same decoupling frequency. The other two wavelengths (1490 and 1550 nm) are separated by combining multimode interference and the dual mode coupling effect. Only by introducing a single defect near the crossing point between two output photonic crystal waveguides (PCWs) are the high extinction ratios for the three wavelengths achieved simultaneously.

High-field cyclotron resonance and electron-phonon interaction in modulation-doped multiple quantum well structures

A systematic study of electron cyclotron resonance (CR) in two sets of GaAs/Al0.3Ga0.7As modulation-doped quantum-well samples (well widths between 12 and 24 nm) has been carried out in magnetic fields up to 30 T. Polaron CR is the dominant transition in the region of GaAs optical phonons for the set of lightly doped samples, and the results are in good agreement with calculations that include the interaction with interface optical phonons. The results from the heavily doped set are markedly different. At low magnetic fields (below the GaAs reststrahlen region), all three samples exhibit almost identical CR which shows little effect of the polaron interaction due to screening and Pauli-principle effects. Above the GaAs LO-phonon region (B > similar to 23 T), the three samples behave very differently. For the most lightly doped sample (3 x 10(11) cm(-2)) only one transition minimum is observed, which can be explained as screened polaron CR. A sample of intermediate density (6 x 10(11) cm(-2)) shows two lines above 23 T; the higher frequency branch is indistinguishable from the positions of the single line of the low density sample. For the most heavily, doped sample (1.2 x 10(12) cm(-2)) there is no evidence of high frequency resonance, and the strong, single line observed is indistinguishable from the lower branch observed from sample with intermediate doping density. We suggest that the low frequency branch in our experiment is a magnetoplasmon resonance red-shifted by disorder, and the upper branch is single-particle-like screened polaron CR. (C) 1998 Elsevier Science B.V. All rights reserved.

Resonant magnetopolaron effects in GaAs/AlGaAs multiple quantum well structures

A detailed experimental study of electron cyclotron resonance (CR) has been carried out at 4.2 K in three modulation-doped GaAs/Al0.3Ga0.7As multiple quantum well samples in fields up to 30 T. A strong avoided-level-crossing splitting of the CR energies due to resonant magnetopolaron effects is observed for all samples near the GaAs reststrahlen region. Resonant splittings in the region of AlAs-like interface phonon modes of the barriers are observed in two samples with narrower well width and smaller doping concentration. The interaction between electrons and the AlAs interface optical phonon modes has been calculated for our specific sample structures in the framework of the memory-function formalism. The calculated results are in good agreement with the experimental results, which confirms our assignment of the observed splitting near the AlAs-like phonon region is due to the resonant magnetopolaron interaction of electrons in the wells with AlAs-like interface phonons. (C) 1998 Elsevier Science B.V. All rights reserved.

Photoluminescence investigation of GaInP/GaAs multiple quantum wells grown on (001) and (311) B GaAs surfaces by gas source molecular beam epitaxy

Photoluminescence (PL) investigation was carried out on GaInP/GaAs multiple quantum wells structures grown on (001) and (311) B surfaces of GaAs by gas source molecular beam epitaxy. Superlattice structures of GaAs/GaInP grown on (001) GaAs substrate were also studied in comparison. Deep-level luminescence was seen to dominate the PL spectra from the quantum wells and superlattice structures that were grown on (001) GaAs substrate. In contrast, superior optical properties were exhibited in the same structures grown on (311) B GaAs surfaces. The results suggested that GaAs/GaInP quantum well structures on (311) B oriented substrates could efficiently suppress the deep-level emissions, result in narrower PL peaks indicating smooth interfaces. (C) 1998 American Institute of Physics.

Intrasubband and intersubband transitions in lightly and heavily doped GaAs/AlGa1-xAs multiple quantum wells

We use a polarizer to investigate quantum-well infrared absorption, and report experimental results as follows. The intrasubband transition was observed in GaAs/AlxGa1-xAs multiple quantum wells (MQWs) when the incident infrared radiation (IR) is polarized parallel to the MQW plane. According to the selection rule, an intrasubband transition is forbidden. Up to now, most studies have only observed the intersubband transition between two states with opposite parity. However, our experiment shows not only the intersubband transitions, but also the intrasubband transitions. In our study, we also found that for light doping in the well (4x10(18) cm(-3)), the intrasubband transition occurs only in the lowest subband, while for the heavy doping (8x10(18) cm(-3)), such a transition occurs not only in the lowest subband, but also in the first excited one, because of the electron subband filling. Further experimental results show a linear dependence of the intrasubband transition frequency on the root of the well doping density. These data are in good agreement with our numerical results. Thus we strongly suggest that such a transition can be attributed to plasma oscillation. Conversely, when the incident IR is polarized perpendicular to the MQW plane, intersubband-transition-induced signals appear, while the intrasubband-transition-induced spectra disappear for both light and heavy well dopings. A depolarization blueshift was also taken into account to evaluate the intersubband transition spectra at different well dopings. Furthermore, we performed a deep-level transient spectroscopy (DLTS) measurement to determine the subband energies at different well dopings. A good agreement between DLTS, infrared absorption, and numerical calculation was obtained. In our experiment, two important phenomena are noteworthy: (1) The polarized absorbance is one order of magnitude higher than the unpolarized spectra. This puzzling result is well explained in detail. (2) When the IR, polarized perpendicular to the well plane, normally irradiates the 45 degrees-beveled edge of the samples, we only observed intersubband transition spectra. However, the intrasubband transition signals caused by the in-plane electric-field component are significantly absent. The reason is that such in-plane electric-field components can cancel each other out everywhere during the light propagating in the samples. The spectral widths of bound-to-bound and bound-to-continuum transitions were also discussed, and quantitatively compared to the relaxation time tau, which is deduced from the electron mobility. The relaxation times deduced from spectral widths of bound-to-bound and bound-to-continuum transitions are also discussed, and quantitatively compared to the relaxation time deduced from electron mobility. [S0163-1829(98)01912-2].

High-field cyclotron resonance and electron-phonon interaction in modulation-doped multiple quantum well structures

A systematic study of electron cyclotron resonance (CR) in two sets of GaAs/Al0.3Ga0.7As modulation-doped quantum-well samples (well widths between 12 and 24 nm) has been carried out in magnetic fields up to 30 T. Polaron CR is the dominant transition in the region of GaAs optical phonons for the set of lightly doped samples, and the results are in good agreement with calculations that include the interaction with interface optical phonons. The results from the heavily doped set are markedly different. At low magnetic fields (below the GaAs reststrahlen region), all three samples exhibit almost identical CR which shows little effect of the polaron interaction due to screening and Pauli-principle effects. Above the GaAs LO-phonon region (B > similar to 23 T), the three samples behave very differently. For the most lightly doped sample (3 x 10(11) cm(-2)) only one transition minimum is observed, which can be explained as screened polaron CR. A sample of intermediate density (6 x 10(11) cm(-2)) shows two lines above 23 T; the higher frequency branch is indistinguishable from the positions of the single line of the low density sample. For the most heavily, doped sample (1.2 x 10(12) cm(-2)) there is no evidence of high frequency resonance, and the strong, single line observed is indistinguishable from the lower branch observed from sample with intermediate doping density. We suggest that the low frequency branch in our experiment is a magnetoplasmon resonance red-shifted by disorder, and the upper branch is single-particle-like screened polaron CR. (C) 1998 Elsevier Science B.V. All rights reserved.

Resonant magnetopolaron effects in GaAs/AlGaAs multiple quantum well structures

A detailed experimental study of electron cyclotron resonance (CR) has been carried out at 4.2 K in three modulation-doped GaAs/Al0.3Ga0.7As multiple quantum well samples in fields up to 30 T. A strong avoided-level-crossing splitting of the CR energies due to resonant magnetopolaron effects is observed for all samples near the GaAs reststrahlen region. Resonant splittings in the region of AlAs-like interface phonon modes of the barriers are observed in two samples with narrower well width and smaller doping concentration. The interaction between electrons and the AlAs interface optical phonon modes has been calculated for our specific sample structures in the framework of the memory-function formalism. The calculated results are in good agreement with the experimental results, which confirms our assignment of the observed splitting near the AlAs-like phonon region is due to the resonant magnetopolaron interaction of electrons in the wells with AlAs-like interface phonons. (C) 1998 Elsevier Science B.V. All rights reserved.

Study on the multiple sites binding of human serum albumin and porphyrin by affinity capillary electrophoresis

Equations to describe the two sites binding between proteins and ligands were deduced. According to these equations, not only the binding constants, but also the mole fraction of proteins in different forms could be obtained. Using the published data on the interaction between human serum albumin (HSA) and three kinds of porphyrin (coproporphyrin (CP), uroporphyrin I (UP) and protoporphyrin (PP)), a further study on their binding was carried out. It was concluded that there may exist two binding sites with the binding constants at the first site. proved to be the preferential one, being 6.50 x 10(5) 1.94 x 10(6) and 8.94 x 10(5). respectively. In addition. it was also demonstrated that the two binding sites of HSA with CP and UP might be of different kinds, though those of HSA and PP were of the same kind but at different positions. (C) 2002 Elsevier Science B.V. All rights reserved.

Determination of multiple trace elements in seawater using chelation ion chromatography and ICP-MS

An off-line chelation system combined with ICP-MS technique was developed for the quantitative determination of trace elements in seawater, namely V, Co, Ni, Cu, Zn, Mo, Cd, Pb, U and rare earth elements(REEs). The system was built based on an ion chromatography equipped with MetPac((R)) CC-I chelation columns which had a strong selective chelation to these target elements within a pH range 5.2-5.6. Acidified seawater samples and NH4Ac(2 mol/L) were blended to meet suitable pH before being injected into the chelation column, thus target elements were retained while alkali and alkaline metals were excluded. Then chelated elements were eluted by HNO3 (1 mol/L) and samples were collected for ICP-MS analysis. Varying the ratio of input( gen. 200 mL) to output( gen. 5 mL), the target elements which were concentrated as 40 times as their concentrations were far beyond instrumental quantification limits. At last, a certificated seawater CASS-4 was introduced and our detected values were in good agreement with those certified values.

Multiple Axial Cracks in A Coated Hollow Cylinder due to Thermal Shock

The transient thermal stress problem of an inner-surface-coated hollow cylinder with multiple pre-existing surface cracks contained in the coating is considered. The transient temperature, induced thermal stress, and the crack tip stress intensity factor (SIF) are calculated for the cylinder via finite element method (FEM), which is exposed to convective cooling from the inner surface. As an example, the material pair of a chromium coating and an underlying steel substrate 30CrNi2MoVA is particularly evaluated. Numerical results are obtained for the stress intensity factors as a function of normalized quantities such as time, crack length, convection severity, material constants and crack spacing. (c) 2005 Elsevier Ltd. All rights reserved.