人类基因中同义密码子的偏好与密码子-反密码子间的结合强度密切相关吗?

统计了人类基因组中各种密码子的使用频率,各种二核苷酸在密码子2、3位和3、4位(即密码子的第3位和后接密码子的第1位)出现的频率,发现同义密码子的选择除了取决于基因组的结构(isochore和DNA signature)外,与密码子-反密码子间的结合强弱也可能密切相关。

Different protein tyrosine phosphatase superfamilies resulting from different gene reading frames

Protein tyrosine phosphatases (PTPs) are comprised of two superfamilies, the phosphatase I superfamily containing a single low-molecular-weight PTP (lmwPTP) family and the phosphatase II superfamily including both the higher-molecular-weight PTP (hmwPTP) and the dual-specificity phosphatase (DSP) families. The phosphatase I and H superfamilies are often considered to be the result of convergent evolution. The PTP sequence and structure analyses indicate that lmwPTPs, hmwPTPs, and DSPs share similar structures, functions, and a common signature motif, although they have low sequence identities and a different order of active sites in sequence or a circular permutation. The results of this work suggest that lmwPTPs and hmwPTPs/DSPs are remotely related in evolution. The earliest ancestral gene of PTPs could be from a short fragment containing about 90similar to120 nucleotides or 30similar to40 residues; however, a probable full PTP ancestral gene contained one transcript unit with two lmwPTP genes. All three PTP families may have resulted from a common ancestral gene by a series of duplications, fusions, and circular permutations. The circular permutation in PTPs is caused by a reading frame difference, which is similar to that in DNA methyltransferases. Nevertheless, the evolutionary mechanism of circular permutation in PTP genes seems to be more complicated than that in DNA methyltransferase genes. Both mechanisms in PTPs and DNA methyltransferases can be used to explain how some protein families and superfamilies came to be formed by circular permutations during molecular evolution.

High velocity vortex channeling in vicinal YBCO thin films

We report on electrical transport measurements at high current densities on optimally doped YBa 2Cu 3O 7-δ thin films grown on vicinal SrTiO 3 substrates. Data were collected by using a pulsed-current technique in a four-probe arrangement, allowing to extend the current-voltage characteristics to high supercritical current densities (up to 24 MA cm -2) and high electric fields (more than 20 V/cm), in the superconducting state at temperatures between 30 and 80 K. The electric measurements were performed on tracks perpendicular to the vicinal step direction, such that the current crossed between ab planes, under magnetic field rotated in the plane defined by the crystallographic c axis and the current density. At magnetic field orientation parallel to the cuprate layers, evidence for the sliding motion along the ab planes (vortex channeling) was found. The signature of vortex channeling appeared to get enhanced with increasing electric field, due to the peculiar depinning features in the kinked vortex range. They give rise to a current-voltage characteristics steeper than in the more off-plane rectilinear vortex orientations, in the electric field range below approximately 1 V/cm. Roughly above this value, the high vortex channeling velocities (up to 8.6 km/s) could be ascribed to the flux flow, although the signature of ohmic transport appeared to be altered by unavoidable macroscopic self-heating and hot-electron-like effects. © 2012 Elsevier B.V. All rights reserved.

Detection of potential positive regulatory motifs of transcription in yeast introns by comparative analysis of oligonucleotide frequencies

We conducted a comparative statistical analysis of tetra- through hexanucleotide frequencies in two sets of introns of yeast genes. The first set consisted of introns of genes that have transcription rates higher than 30 mRNAs/h while the second set contained introns of genes whose transcription rates were lower than or equal to 10 mRNAs/h. Some oligonucleotides whose occurrence frequencies in the first set of introns are significantly higher than those in the second set of introns were detected. The frequencies of occurrence of most of these detected oligonucleotides are also significantly higher than those in the exons flanking the introns of the first set. Interestingly some of these detected oligonucleotides are the same as well known "signature" sequences of transcriptional regulatory elements. This could imply the existence of potential positive regulatory motifs of transcription in yeast introns. (C) 2003 Elsevier Ltd. All rights reserved.

Improving Pothole Recognition through Vision Tracking for Automated Pavement Assessment

Pavement condition assessment is essential when developing road network maintenance programs. In practice, pavement sensing is to a large extent automated when regarding highway networks. Municipal roads, however, are predominantly surveyed manually due to the limited amount of expensive inspection vehicles. As part of a research project that proposes an omnipresent passenger vehicle network for comprehensive and cheap condition surveying of municipal road networks this paper deals with pothole recognition. Existing methods either rely on expensive and high-maintenance range sensors, or make use of acceleration data, which can only provide preliminary and rough condition surveys. In our previous work we created a pothole detection method for pavement images. In this paper we present an improved recognition method for pavement videos that incrementally updates the texture signature for intact pavement regions and uses vision tracking to track detected potholes. The method is tested and results demonstrate its reasonable efficiency.

Vibration response of a wind-turbine planetary gear set in the presence of a localized planet bearing defect

In a wind-turbine gearbox, planet bearings exhibit a high failure rate and are considered as one of the most critical components. Development of efficient vibration based fault detection methods for these bearings requires a thorough understanding of their vibration signature. Much work has been done to study the vibration properties of healthy planetary gear sets and to identify fault frequencies in fixed-axis bearings. However, vibration characteristics of planetary gear sets containing localized planet bearing defects (spalls or pits) have not been studied so far. In this paper, we propose a novel analytical model of a planetary gear set with ring gear flexibility and localized bearing defects as two key features. The model is used to simulate the vibration response of a planetary system in the presence of a defective planet bearing with faults on inner or outer raceway. The characteristic fault signature of a planetary bearing defect is determined and sources of modulation sidebands are identified. The findings from this work will be useful to improve existing sensor placement strategies and to develop more sophisticated fault detection algorithms. Copyright © 2011 by ASME.

A body force-based method for prediction of multiple-pure-tone noise: Validation

Emissions, fuel burn, and noise are the main drivers for innovative aircraft design. Embedded propulsion systems, such as for example used in hybrid-wing body aircraft, can offer fuel burn and noise reduction benefits but the impact of inlet flow distortion on the generation and propagation of turbomachinery noise has yet to be assessed. A novel approach is used to quantify the effects of non-uniform flow on the creation and propagation of multiple pure tone (MPT) noise. The ultimate goal is to conduct a parametric study of S-duct inlets to quantify the effects of inlet design parameters on the acoustic signature. The key challenge is that the effects of distortion transfer, noise source generation and propagation through the non-uniform flow field are inherently coupled such that a simultaneous computation of the aerodynamics and acoustics is required to capture the mechanisms at play. The technical approach is based on a body force description of the fan blade row that is able to capture the distortion transfer and the blade-to-blade flow variations that cause the MPT noise while reducing computational cost. A single, 3-D full-wheel CFD simulation, in which the Euler equations are solved to second-order spatial and temporal accuracy, simultaneously computes the MPT noise generation and its propagation in distorted inlet flow. A new method of producing the blade-to-blade variations in the body force field for MPT noise generation has been developed and validated. The numerical dissipation inherent to the solver is quantified and used to correct for non-physical attenuation in the far-field noise spectra. Source generation, acoustic propagation and acoustic energy transfer between modes is examined in detail. The new method is validated on NASA's Source Diagnostic Test fan and inlet, showing good agreement with experimental data for aerodynamic performance, acoustic source generation, and far-field noise spectra. The next steps involve the assessment of MPT noise in serpentine inlet ducts and the development of a reduced order formulation suitable for incorporation into NASA's ANOPP framework. © 2010 by Jeff Defoe, Alex Narkaj & Zoltan Spakovszky.

A novel MPT noise prediction methodology for highly-integrated propulsion systems with inlet flow distortion

Embedded propulsion systems, such as for example used in advanced hybrid-wing body aircraft, can potentially offer major fuel burn and noise reduction benefits but introduce challenges in the aerodynamic and acoustic integration of the high-bypass ratio fan system. A novel approach is proposed to quantify the effects of non-uniform flow on the generation and propagation of multiple pure tone noise (MPTs). The new method is validated on a conventional inlet geometry first. The ultimate goal is to conduct a parametric study of S-duct inlets in order to quantify the effects of inlet design parameters on the acoustic signature. The key challenge is that the mechanism underlying the distortion transfer, noise source generation and propagation through the non-uniform flow field are inherently coupled such that a simultaneous computation of the aerodynamics and acoustics is required. The technical approach is based on a body force description of the fan blade row that is able to capture the distortion transfer and the MPT noise generation mechanisms while greatly reducing computational cost. A single, 3-D full-wheel unsteady CFD simulation, in which the Euler equations are solved to second-order spatial and temporal accuracy, simultaneously computes the MPT noise generation and its propagation in distorted mean flow. Several numerical tools were developed to enable the implementation of this new approach. Parametric studies were conducted to determine appropriate grid and time step sizes for the propagation of acoustic waves. The Ffowcs-Williams and Hawkings integral method is used to propagate the noise to far field receivers. Non-reflecting boundary conditions are implemented through the use of acoustic buffer zones. The body force modeling approach is validated and proof-of-concept studies demonstrate the generation of disturbances at both blade-passing and shaft-order frequencies using the perturbed body force method. The full methodology is currently being validated using NASA's Source Diagnostic Test (SDT) fan and inlet geometry. Copyright © 2009 by Jeff Defoe, Alex Narkaj & Zoltan Spakovszky.

Studying adsorbent dynamics on a quartz crystal resonator using its nonlinear electrical response

The quartz crystal resonator has been traditionally employed in studying surface-confined physisorbed films and particles by measuring dissipation and frequency shifts. However, theoretical interpretation of the experimental observations is often challenged due to limited understanding of physical interaction mechanisms at the interfaces involved. Here we model a physisorbed interaction between particles and gold electrode surface of a quartz crystal and demonstrate how the nonlinear modulation of the electric response of the crystal due to the nonlinear interaction forces may be used to study the dynamics of the particles. In particular, we show that the graphs of the deviation in the third Fourier harmonic response versus oscillation amplitude provide important information about the onset, progress and nature of sliding of the particles. The graphs also present a signature of the surface-particle interaction and could be used to estimate the interaction energy profile. Interestingly, the insights gained from the model help to explain some of the experimental observations with physisorbed streptavidin-coated polystyrene microbeads on quartz resonators. © 2012 Elsevier B.V. All rights reserved.

Identifying cancer subtypes in glioblastoma by combining genomic, transcriptomic and epigenomic data

We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likely number of disease subtypes, given the data. We apply the method to 277 glioblastoma samples from The Cancer Genome Atlas, for which there are gene expression, copy number variation, methylation and microRNA data. We identify 8 distinct consensus subtypes and study their prognostic value for death, new tumour events, progression and recurrence. The consensus subtypes are prognostic of tumour recurrence (log-rank p-value of $3.6 \times 10^{-4}$ after correction for multiple hypothesis tests). This is driven principally by the methylation data (log-rank p-value of $2.0 \times 10^{-3}$) but the effect is strengthened by the other 3 data types, demonstrating the value of integrating multiple data types. Of particular note is a subtype of 47 patients characterised by very low levels of methylation. This subtype has very low rates of tumour recurrence and no new events in 10 years of follow up. We also identify a small gene expression subtype of 6 patients that shows particularly poor survival outcomes. Additionally, we note a consensus subtype that showly a highly distinctive data signature and suggest that it is therefore a biologically distinct subtype of glioblastoma. The code is available from https://sites.google.com/site/multipledatafusion/

Magnetotransport of La0.5Ba0.5MnO3

Physical properties of polycrystalline La0.5Ba 0.5MnO3 are reported from low temperature (10 K) up to above room temperature. An aim has been to obtain microscopic parameters and to search for the characteristic lengths in terms of which one can discuss the interplay between magnetic, electric, and phonon excitations. The structural and magnetotransport measurements reveal a set of relatively high transition temperatures (near 300 K) between ferromagnetic/metallic and paramagnetic/semiconducting phases. It is found, in particular, that the so-called localization length increases from 0.085 to 0.24 nm when the magnetic field varies from 0 to 8 T. Moreover a "special field value" ∼0.03 T is observed in the description of the electrical resistance. It cannot be presently distinguished whether it is the signature of a spin reorientation transition in the canted phase or a mere saturation field for aligning magnetic domains. The relatively high magnetoresistance effect (≃55% at 8 T and 10 K) makes the La0.5Ba0.5MnO3 a very interesting material for among others sensor applications. © 2009 American Institute of Physics.

Extreme sensitivity of graphene photoconductivity to environmental gases.

Graphene is a single layer of covalently bonded carbon atoms, which was discovered only 8 years ago and yet has already attracted intense research and commercial interest. Initial research focused on its remarkable electronic properties, such as the observation of massless Dirac fermions and the half-integer quantum Hall effect. Now graphene is finding application in touch-screen displays, as channels in high-frequency transistors and in graphene-based integrated circuits. The potential for using the unique properties of graphene in terahertz-frequency electronics is particularly exciting; however, initial experiments probing the terahertz-frequency response of graphene are only just emerging. Here we show that the photoconductivity of graphene at terahertz frequencies is dramatically altered by the adsorption of atmospheric gases, such as nitrogen and oxygen. Furthermore, we observe the signature of terahertz stimulated emission from gas-adsorbed graphene. Our findings highlight the importance of environmental conditions on the design and fabrication of high-speed, graphene-based devices.

Enhanced grass carp reovirus resistance of Mx-transgenic rare minnow (Gobiocypris rarus)

In the interferon-induced antiviral mechanisms, the Mx pathway is one of the most powerful. Mx proteins have direct antiviral activity and inhibit a wide range of viruses by blocking an early stage of the viral genome replication cycle. However, antiviral activity of piscine Mx remains unclear in vivo. In the present study, an Mx-like gene was cloned, characterized and gene-transferred in rare minnow Gobiocypris rarus, and its antiviral activity was confirmed in vivo. The full length of the rare minnow Mx-like cDNA is 2241 bp in length and encodes a polypeptide of 625 amino acids with an estimated molecular mass of 70.928 kDa and a predicted isoelectric point of 7.33. Analysis of the deduced amino acid sequence indicated that the mature peptide contains an amino-terminal tripartite GTP-binding motif, a dynamin family signature sequence, a GTPase effector domain and two carboxy-terminal leucine zipper motifs, and is the most similar to the crucian carp (Carassius auratus) Mx3 sequence with an identity of 89%. Both P0 and F1 generations of Mx-transgenic rare minnow demonstrated very significantly high survival rate to GCRV infection (P < 0.01). The mRNA expression of Mx gene was consistent with survival rate in F1 generation. The virus yield was also concurrent with survival time using electron microscope technology. Rare minnow has Mx gene(s) of its own but introducing more Mx gene improves their resistance to GCRV. Mx-transgenic rare minnow might contribute to control the GCRV diseases. (C) 2008 Published by Elsevier Ltd.

Acoustic Observation of the Spawning Aggregation of Megalobrama hoffmanni in the Pearl River

Using the Simrad EY60 split-beam echosounder, the spawning aggregation of Megalobrama hoffmanni was observed at the Luopang spawning grounds in the Pearl River, China, from April 19 to 22 2006. With the boat anchored, the transducer was stationary and was aimed horizontally to monitor the migration of the fish. Using fishery information, the echoes of M. hoffmanni were identified. The results showed that the spawning aggregation of M. hoffmanni at Luopang was obvious and easy to discriminate. The target strength of M hoffmanni in situ ranged from -33.8 dB to -52.3 dB (average 42.2dB). The aggregation of M. hoffmanni was obviously affected by light. With a speed of -0.31 m/s, 88.9% of the spawning stocks migrated upstream. Most M hoffmanni were recorded moving near the bottom. Their distinctive acoustic signature demonstrated the suitability of the stationary acoustic observation for M. hoffmanni identification and discrimination.

Isolation and characterization of Argonaute 2: A key gene of the RNA interference pathway in the rare minnow, Gobiocypris rarus

Argonaute 2 gene plays a pivotal role in RNAi in many species. Herein is the first report of the cloning and characterization of Argonaute 2 gene in fish. The full-length cDNA of Gobiocypris rarus Argonaute 2 (GrAgo2) consisted of 3073 nucleotides encoding 869 amino acid residues with a calculated molecular weight of 98.499 kDa and an estimated isoelectric point of 9.18. Analysis of the deduced amino acid sequence showed the presence of two signature domains, PAZ and Piwi. RT-PCR analysis indicated that GrAgo2 mRNA expression could be detected in widespread tissues. After infection with grass carp reovirus, GrAgo2 expression was up-regulated from 12 h post-injection (p < 0.05) and returned to control levels at 48 h post-injection (p > 0.05). These data imply that GrAgo2 is involved in antiviral defense in rare minnow. (C) 2008 Published by Elsevier Ltd.