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- Earlier timbre processing of instrumental tones compared to equally complex spectrally rotated sounds as revealed by the mismatch negativity. [JOURNAL ARTICLE]
- Neurosci Lett 2014 Aug 27.
Harmonically rich sounds have been shown to be processed more efficiently by the human brain compared to single sinusoidal tones. To control for stimulus complexity as a potentially confounding factor, tones and equally complex spectrally rotated sounds, have been used in the present study to investigate the role of the overtone series in sensory auditory processing in non-musicians. Timbre differences in instrumental tones with equal pitch elicited a MMN which was earlier compared to that elicited by the spectrally rotated sounds, indicating that harmonically rich tones are processed faster compared to non-musical sounds without an overtone series, even when pitch is not the relevant information.
- Environmental Research Translation: Enhancing interactions with communities at contaminated sites. [REVIEW]
- Sci Total Environ 2014 Aug 26.:651-664.
The characterization and remediation of contaminated sites are complex endeavors fraught with numerous challenges. One particular challenge that is receiving increased attention is the development and encouragement of full participation by communities and community members affected by a given site in all facets of decision-making. Many disciplines have been grappling with the challenges associated with environmental and risk communication, public participation in environmental data generation, and decision-making and increasing community capacity. The concepts and methods developed by these disciplines are reviewed, with a focus on their relevance to the specific dynamics associated with environmental contamination sites. The contributions of these disciplines are then synthesized and integrated to help develop Environmental Research Translation (ERT), a proposed framework for environmental scientists to promote interaction and communication among involved parties at contaminated sites. This holistic approach is rooted in public participation approaches to science, which includes: a transdisciplinary team, effective collaboration, information transfer, public participation in environmental projects, and a cultural model of risk communication. Although there are challenges associated with the implementation of ERT, it is anticipated that application of this proposed translational science method could promote more robust community participation at contaminated sites.
- Functional lysophosphatidic acid receptors expressed in Oryzias latipes. [JOURNAL ARTICLE]
- Gene 2014 Aug 27.
Lysophosphatidic acid (LPA) signaling is known to play biological and pathophysiological roles in many types of animals. Medaka (Oryzias latipes) is an experimental fish that can be easily maintained, propagated, and analyzed, and whose genome has been completely sequenced. However, there is limited information available regarding medaka LPA receptors. Here, using information from the medaka genome database, we examine the genomic structures, expression, and functions of six LPA receptor genes, Lpar1-Lpar6. Our analyses reveal that the genomic structures of Lpar1 and Lpar4 are different from those deduced from the database. Functional analyses using a heterologous expression system demonstrate that all medaka LPA receptors except for LPA5b respond to LPA treatment with cytoskeletal changes. These findings provide useful information on the structure and function of medaka LPA receptor genes, and identify medaka as a useful experimental model for exploration of the biological significance of LPA signaling.
- In silico identification of potential virulence genes in 1,3-propanediol producer Klebsiella pneumonia. [JOURNAL ARTICLE]
- J Biotechnol 2014 Aug 27.
The pathogenic characteristics of Klebsiella pneumoniae could pose security risks for industrial applications. In this study, the existence and distribution of 2457 known virulence genes (VFs) in 9 strains of K. pneumoniae were systematically analyzed by high-throughput in silico methods. We found different numbers and types of VFs in 9K. pneumoniae strains using database sequences. Some VFs in the database were highly homologous with the corresponding genes in K. pneumoniae genomes. Four large fragments with contiguous potential virulence genes named VF1, VF2, VF3 and VF4 were identified. VF1 and VF2 were found in all 9 sequenced strains and the 1,3-propanediol-producing strain KG1. When the VF2 fragment was knocked out in KG1, cell growth and 1,3-propanediol production in the mutant were nearly the same as in KG1. Consequently the resulting information by in silico methods is useful for identifying potential virulence genes of K. pneumoniae used for 1,3-propanediol production.
- Fluorescent sensors reveal subcellular thermal changes. [REVIEW]
- Curr Opin Biotechnol 2014 Aug 28.:57-64.
In mammals and birds, thermoregulation to conserve body temperature is vital to life. Multiple mechanisms of thermogeneration have been proposed, localized in different subcellular organelles. However, studying thermogenesis directly in intact organelles has been challenging. Visualizing patterns of thermal changes at subcellular resolution would reveal physiologically relevant spatio-temporal information, especially if this could be done in the native cellular configuration of the cell. Here we review and compare the wide variety of intracellular thermosensors currently identified. This review focuses particularly on genetically encoded sensors. It also explores the notable physiological discoveries made using these imaging methods, which are rapidly becoming indispensible to the study of thermal biology.
- Field emission scanning electron microscopy (FE-SEM) as an approach for nanoparticle detection inside cells. [JOURNAL ARTICLE]
- Micron 2014 Aug 13.:149-154.
When developing new nanoparticles for bio-applications, it is important to fully characterize the nanoparticle's behavior in biological systems. The most common techniques employed for mapping nanoparticles inside cells include transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM). These techniques entail passing an electron beam through a thin specimen. STEM or TEM imaging is often used for the detection of nanoparticles inside cellular organelles. However, lengthy sample preparation is required (i.e., fixation, dehydration, drying, resin embedding, and cutting). In the present work, a new matrix (FTO glass) for biological samples was used and characterized by field emission scanning electron microscopy (FE-SEM) to generate images comparable to those obtained by TEM. Using FE-SEM, nanoparticle images were acquired inside endo/lysosomes without disruption of the cellular shape. Furthermore, the initial steps of nanoparticle incorporation into the cells were captured. In addition, the conductive FTO glass endowed the sample with high stability under the required accelerating voltage. Owing to these features of the sample, further analyses could be performed (material contrast and energy-dispersive X-ray spectroscopy (EDS)), which confirmed the presence of nanoparticles inside the cells. The results showed that FE-SEM can enable detailed characterization of nanoparticles in endosomes without the need for contrast staining or metal coating of the sample. Images showing the intracellular distribution of nanoparticles together with cellular morphology can give important information on the biocompatibility and demonstrate the potential of nanoparticle utilization in medicine.
- poRe: an R package for the visualization and analysis of nanopore sequencing data. [JOURNAL ARTICLE]
- Bioinformatics 2014 Aug 29.
The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.Here we present poRe, a package for R that enables users to manipulate, organize, summarise and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/. A tutorial and further information is available at https://sourceforge.net/p/rpore/wiki/Home/ CONTACT: firstname.lastname@example.org SUPPLEMENTARY DATA: Further figures and information on the FAST5 data format are available in the supplementary data.
- Optical fiber-based system for continuous measurement of in-bore projectile velocity. [JOURNAL ARTICLE]
- Rev Sci Instrum 2014 Aug; 85(8):085003.
This paper reports the design of an optical fiber-based velocity measurement system and its application in measuring the in-bore projectile velocity. The measurement principle of the implemented system is based on Doppler effect and heterodyne detection technique. The analysis of the velocity measurement principle deduces the relationship between the projectile velocity and the instantaneous frequency (IF) of the optical fiber-based system output signal. To extract the IF of the fast-changing signal carrying the velocity information, an IF extraction algorithm based on the continuous wavelet transforms is detailed. Besides, the performance of the algorithm is analyzed by performing corresponding simulation. At last, an in-bore projectile velocity measurement experiment with a sniper rifle having a 720 m/s muzzle velocity is performed to verify the feasibility of the optical fiber-based velocity measurement system. Experiment results show that the measured muzzle velocity is 718.61 m/s, and the relative uncertainty of the measured muzzle velocity is approximately 0.021%.
- Combination of grazing incidence x-ray fluorescence with x-ray reflectivity in one table-top spectrometer for improved characterization of thin layer and implants on/in silicon wafers. [JOURNAL ARTICLE]
- Rev Sci Instrum 2014 Aug; 85(8):083110.
As Grazing Incidence X-ray Fluorescence (GIXRF) analysis does not provide unambiguous results for the characterization of nanometre layers as well as nanometre depth profiles of implants in silicon wafers by its own, the approach of providing additional information using the signal from X-ray Reflectivity (XRR) was tested. As GIXRF already uses an X-ray beam impinging under grazing incidence and the variation of the angle of incidence, a GIXRF spectrometer was adapted with an XRR unit to obtain data from the angle dependent fluorescence radiation as well as data from the reflected beam. A θ-2θ goniometer was simulated by combining a translation and tilt movement of a Silicon Drift detector, which allows detecting the reflected beam over 5 orders of magnitude. HfO2 layers as well as As implants in Silicon wafers in the nanometre range were characterized using this new setup. A just recently published combined evaluation approach was used for data evaluation.
- Design and construction of an Offner spectrometer based on geometrical analysis of ring fields. [JOURNAL ARTICLE]
- Rev Sci Instrum 2014 Aug; 85(8):083108.
A method to obtain an aberration-corrected Offner spectrometer without ray obstruction is proposed. A new, more efficient spectrometer optics design is suggested in order to increase its spectral resolution. The derivation of a new ring equation to eliminate ray obstruction is based on geometrical analysis of the ring fields for various numerical apertures. The analytical design applying this equation was demonstrated using the optical design software Code V in order to manufacture a spectrometer working in wavelengths of 900-1700 nm. The simulation results show that the new concept offers an analytical initial design taking the least time of calculation. The simulated spectrometer exhibited a modulation transfer function over 80% at Nyquist frequency, root-mean-square spot diameters under 8.6 μm, and a spectral resolution of 3.2 nm. The final design and its realization of a high resolution Offner spectrometer was demonstrated based on the simulation result. The equation and analytical design procedure shown here can be applied to most Offner systems regardless of the wavelength range.