bluuebunny/crossref_metadata_2025 huggingface dataset:
Triple‐band USB dongle antenna using fractal and shorted loops for WiFi and WiMAX applications
Authors: Chaimool S. , Chokchai C. , Akkaraekthalin P.
Published: February 2013

By coupling a fractal loop resonator onto the back of a loaded‐fractal loop monopole and a shorted loop, a new triple‐band USB dongle antenna has been achieved and presented. The proposed antenna supports WiFi (2.4–2.5 GHz and 5.15–5.875 GHz) and WiMAX (3.4–3.6 GHz) applications. The proposed triple‐band planar antenna consists of a loaded‐fractal loop monopole for the 2.4 GHz band, a shorted loop for the 5.5 GHz band, and a coupled fractal loop resonator for 3.5 GHz band. The antenna has a small size of 10 × 42 × 0.8 mm3, which is suitable for USB dongle. Good return loss and omnidirectional radiation pattern characteristics have been obtained in the all three bands. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:863–866, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27421
Compact wideband harmonic suppressed antenna using non‐uniform cascaded defected ground structure
Authors: Damaj Lana , Lepage Anne Claire , Begaud Xavier
Published: February 2013

This article presents a coplanar waveguide‐fed wideband bowtie antenna with harmonic suppression using non‐uniform cascaded defected ground structure units.The antenna operates between 2 GHz and 5.4 GHz and harmonics are effectively reduced. Its size is only 0.44×0.48 λ02, λ0 being the free‐space wavelength at 2 GHz. Simulation and measurement agree very well. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:829–835, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27422
Low cross‐polarization array antenna with suspended probe‐feed
Authors: Lee Dong‐Jin , Lee Soo‐Ji , Oh Kyoung‐Sub , Yu Jong‐Won
Published: February 2013

This paper describes the development and performance of a 2 by 4 element suspended microstrip patch antenna array with linear polarization. The proposed structure with a new geometrical composition of entire array possesses the advantages of being wide bandwidth, high gain, precise side lobe level control and low cross‐polarization level. The measured antenna has the peak gain 14.12 dBi and the cross‐polarization is lower than −16 dBi within the impedance bandwidth. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:825–829, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27423
Improving the bandwidth of a microstrip antenna with a circular‐shaped fractal slot
Authors: Dholakiya Hitesh L. , Pujara Dhaval A.
Published: February 2013

This article presents the design of a microstrip‐line fed printed antenna with a circular‐shaped fractal slot. It is experimentally verified that such a design results in bandwidth (better than −10 dB return‐loss) enhancement of up to 52.8%. The results of parametric study for different iteration factors (IF) and iteration orders (IO) are also presented. For the proposed design, better than 4 dB gain was practically achieved over a frequency band of 2–6 GHz. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:786–789, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27424
Wavelength self‐initialization technique using allocated light paths of WDM‐PON
Authors: Jung Eui‐Suk , Lee Eun‐Gu , Mun Sil‐Gu , Lee Sang‐Soo , Won Yong‐Yuk , Han Sang‐Kook
Published: February 2013

A new wavelength initialization technique for WDM‐PON (wavelength division multiplexed‐passive optical network) system is proposed, where it uses allocated light path over optical link. Compared with other techniques, it is expected that the smallest size and the lowest cost for implementing this will be achieved in the real network. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:753–755, 2013; View this article online at wileyonlinelibrary.com. DOI 10.1002/mop.27426
Modeling for opto‐electronic oscillator considering the nonlinearity of microwave amplifier
Authors: Hong Jun , Yang Chun
Published: February 2013

A new model is proposed to analyze the oscillation power and phase noise characteristics of oscillation signal in the single‐loop opto‐electronic oscillator (OEO), and then verified by experiments. Compared with previous models, in our model, the nonlinearity of not only the E/O modulator but also the microwave amplifier is included in calculating systematic nonlinearities, so this model can describe OEO more accurately than previous models. Experiments verify the correctness of our model and results show that, compared with previous models, the oscillation power is about 10 dB lower and the minimum single‐sideband phase noise after optimization is ∼3 dB higher in our experiments. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:715–719, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27428
A fully‐integrated CMOS quadrature VCO implemented with balanced VCOs
Authors: Jang Sheng‐Lyang , Chang Chia‐Wei , Lin Yu‐Sheng , Juang Miin‐Horng
Published: February 2013

A new CMOS quadrature voltage‐controlled oscillator (QVCO) is proposed. The LC‐tank QVCO consists of two balanced complementary Colpitts VCOs with differential outputs. The tail inductor output of the first balanced VCO is injected to the gate of the tail transistor in the second balanced VCO and vice versa to ensure the two balanced VCOs operate in quadrature. At the supply voltage of 1.2 V, the total power consumption is 4.32 mW. The free‐running frequency tuning range is 13.4%, tunable from 5.92 to 6.77 GHz as the tuning voltage is varied from 0 to 2 V. The QVCO has been implemented with the TSMC 0.18 μm CMOS technology and the die area is 0.843 × 1.024 mm2. The measured phase noise at 1 MHz offset is −121.67 dBc/Hz at the oscillation frequency of 6.74 GHz and the figure of merit of the proposed QVCO is about −191.89 dBc/Hz. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:700–703, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27433
A Compact planar diversity antenna for ultra‐wideband application with band‐notched function
Authors: Natarajamani S. , Behera Santanu Kumar , Patra Sarat Kumar
Published: February 2013

A compact two‐element diversity planar antenna for ultra‐wideband (UWB) application with band‐notch function is proposed. By adapting two symmetrical rectangular patches with three bevels cutting in the edge of the radiators, the antenna provides wideband impedance matching characteristics over the desired frequency range. The wideband isolation can be achieved through uniform branch length ratio used in the ground plane. Measured S‐parameters show that the antenna is able to cover the entire UWB band from 3.1–10.6 GHz and good isolation of less than ‐25 dB. Also it has a band‐notch function to avoid overlap with the 3.5 GHz WiMAX band. The radiation pattern, realized gain, envelope correlation, and pulse handling capacity are measured. From the results, it is observed that the proposed diversity antenna can be suitable for UWB application. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:758–762, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27435
Design of a miniaturized patch antenna for easy deployment on metal surfaces
Authors: Hinnemo Malkolm , Grudén Mathias , Rydberg Anders
Published: February 2013

A small dual‐layer patch antenna designed for placement on a large conducting surface is presented. It uses the surrounding metal as a ground plane in order to reduce its size. The result is a small patch antenna with good radiation qualities in metallic surroundings. It can also be used in applications where shielding sensitive equipment from radiated fields is necessary, by using the shielding as the metal surface. It is constructed for use with the IEEE 802.15.4 standard at the 2.45 GHz ISM band. The lower layer is made in Fr‐4 with standard height and width. This makes eventual serial production cheaper. The antenna has a measured total efficiency between −1.5 dB and −3.6 dB in the frequency range it is designed for. The longest side is 18.35 mm, equaling 14.9% of the wavelength © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:723–727, 2013; View this article online at wileyonlinelibrary.com. DOI 10.1002/mop.27437
Design of a band‐notched broadband series‐fed two dipole array antenna
Authors: Yeo Junho , Lee Jong‐Ig
Published: February 2013

In this article, a band‐notched broadband series‐fed two dipole array (STDA) antenna is proposed. A design method to obtain a band rejection in the 2.4–2.484 GHz WLAN band is investigated for an STDA antenna consisting of two dipoles and a ground reflector operating in the frequency range between 1.7 and 2.7 GHz for mobile communication applications. The notch band is achieved by inserting U‐shaped slots on the coplanar strip line connecting the two dipole elements. The effects of the location and dimension of the slots on the notch band characteristics are investigated. A prototype of the proposed antenna is fabricated on an FR4 substrate. Experimental results show that the proposed antenna presents a broad bandwidth of 1.65–2.78 GHz (51.02%) for a voltage standing wave ratio < 2 and a rejection band of 2.39–2.54 GHz, which covers the desired notch band. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:911–915, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27439
Dispersive optical fiber for measuring frequency response of electro‐optical phase modulators
Authors: Zhang Shangjian , Bao Xiaobin , Zhang Yali , Zhang Xiaoxia , Liu Yong
Published: February 2013

A simple method based on the use of a fold‐loop dispersive fiber path is proposed for measuring high‐frequency modulation response of electro‐optical phase modulators.The method requires only a length of single‐mode fiber and allows high resolution swept frequency measurement with a vector network analyzer. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:909–911, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27440
A novel TRI‐band planar inverted‐F antenna for GSM/DCS/PCS operation in mobile handsets
Authors: Seko Murilo Hiroaki , Correra Fatima Salete
Published: February 2013

In this article, a novel mobile handset planar inverted‐F antenna (PIFA) for tri‐band operation in GSM, DCS, and PCS bands is presented. This PIFA comprises a rectangular folded planar radiator, which has a J‐shaped slot, suspended above a partially grounded substrate. In this antenna, two resonant modes are excited and originate a lower band for GSM and an upper band for DCS and PCS. The influence of several geometrical parameters of the antenna on its performance was investigated to achieve an optimal design. The fabricated prototype of the proposed PIFA has overall dimensions of 45 × 90 × 6.6 mm3. The measured 10 dB return loss bands of the antenna are 880–892 MHz and 1658–2079 MHz. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:821–825, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27441
Design of branch line coupler loaded capacitively with interdigitated fingers by using microstrip fed coplanar structures (L‐shaped conductor backed asymmetric CPS and U‐shaped conductor backed CPW)
Authors: Karpuz Ceyhun , Ozturk Pinar
Published: February 2013

In this letter, L‐shaped conductor backed asymmetric coplanar stripline (LSCBACPS) and U‐shaped conductor backed coplanar waveguide (USCBCPW) branch line coupler fed by microstrip transmission line have been investigated for the miniaturization. The number of interdigital finger unit cells located at the branch and through lines of the conventional branch line coupler is used to provide a desired miniaturization. The proposed branch line couplers in which all ports are formed by microstrip line have been constructed in two different configurations depending on the placement of the capacitively loaded fingers. The effects of the change of the cell number located at the branch and through lines on the center frequency and the propagation velocity are investigated. These effects are expressed by a simple formula depends on the cell number to use in the theoretical model obtained from the even‐odd mode analysis of LSCBACPS and USCBCPW configurations. Proposed couplers are designed, fabricated, and tested for the experimental verification to compare with the simulation and theoretical results. Measured, theoretical, and simulation results are in a very good agreement. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:816–820, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27442
A novel compact configuration for dual‐mode microstrip resonators and dual‐band bandpass filter applications
Authors: Karpuz Ceyhun , Gorur Ali Kursad
Published: February 2013

In this article, a novel compact dual‐mode resonator formed by a square loop having folded arms and mitered bends is proposed.Degenerate modes can be excited by shifting the gaps between the folds. Thus, the center frequency can be arranged at a fixed value because the total electrical length of the proposed configuration is not changed. A novel compact dual‐mode dual‐band bandpass filter is also designed by locating the one resonator within the other. Additionally, to suppress the harmonic of the first passband, open‐circuited stubs are connected to the end of the feedlines. Two dual‐mode dual‐band bandpass filters with the elliptical and linear phase filtering characteristics for both passbands have been designed, fabricated, and tested. Calculated, simulated, and measured results are in a good agreement. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:775–779, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27444
DC‐20 GHz 5‐BIT CMOS digital step attenuator with low insertion loss and phase error
Authors: Cho Moon‐Kyu , Baek Donghyun , Kim Jeong‐Geun
Published: February 2013

This article presents a 5‐bit broadband digital step attenuator with low insertion loss and phase error using a standard 0.13 μm CMOS process for the phased array antenna.The maximum attenuation of 31 dB with the LSB of 1 dB is achieved at DC‐20 GHz. The measured insertion loss of the reference state is <11 dB and the input and output return losses are <−10 dB at DC‐20 GHz. The root mean square (RMS) phase and amplitude errors are <2.5° and <0.7 dB, respectively. The current consumption is near zero with 1.2 V supply. The chip size is 1.04 × 0.48 mm2including pads. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:762–764, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27448
Enhanced wideband performance of coupled frequency selective surfaces using metaheuristics
Authors: Lins H. W. C. , Barreto E. L. F. , d'Assunção A. G.
Published: February 2013

This article presents a bandwidth optimization study of two coupled frequency selective surfaces (FSS).The optimization is performed in two steps. In the first step, a genetic algorithm is developed to synthesize two single FSS crossed dipoles with resonant frequencies equal to 9.5 and 10.5 GHz, to be used in a broadside coupled geometry, separated by an air gap. In the second step, a particle swarm optimization algorithm is developed to determine the optimal value for the air gap length to optimize the geometry bandwidth. Prototypes are fabricated and measured to validate the optimization study results for the two coupled FSS structure. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:711–715, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27451
Broadband four‐element multi‐layer multi‐permittivity cylindrical dielectric resonator antenna
Authors: Chaudhary Raghvendra Kumar , Srivastava Kumar Vaibhav , Biswas Animesh
Published: February 2013

In this article, a four‐element multi‐layer multi‐permittivity (MLMP) cylindrical dielectric resonator antenna (CDRA) for broadband application is proposed. The proposed antenna provides the measured input impedance bandwidth of 58.1% (at resonance frequency 4.03 GHz) from 3.48 GHz to 5.82 GHz for input reflection coefficient (S11) less than −10 dB. The measured average gain is 4.82 dB in the frequency range of 3.48 to 5.82 GHz. The design provides consistent omnidirectional characteristics and low cross polarization within the operating band. Design details of the proposed antenna and the results of both simulation and experiment are presented and discussed. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:932–937, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27452
Transverse magnetic wave reflection from a metamaterial
Authors: Southall Hugh L. , Wu Bae‐Ian , Allen Jeffery W.
Published: February 2013

It has been shown that transverse electric plane waves reflect from certain types of metamaterials with a unit magnitude reflection coefficient (Smith and Schurig, Phys Rev Lett 90 &899;2003), 077405‐1–077405‐4).Here we investigate the reflection of transverse magnetic plane waves using a Hertzian dipole over a semi‐infinite slab of metamaterial, which is used as a ground plane. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:899–903, 2013; View this article online at wileyonlinelibrary.com. DOI 10.1002/mop.27454
Mutual information in weak‐coherent‐state detection using a homodyne optical costas loop with different phase errors
Authors: López Josue A. , Garcia Edith , Arvizu Arturo , Mendieta Francisco J. , Gallion Phillipe , Conte Roberto
Published: February 2013

A free‐space experimental set‐up for measuring the quadrature components of weak‐coherent‐state laser signals, based on a homodyne Costas loop configuration is presented. Loop parameters are optimized as a trade‐off between quantum and phase noises. Using binary phase‐shift‐keying modulation, measurements on the mutual information are presented for different photon numbers and phase errors. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:769–772, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27459
Printed planar UWB antenna with rejection of WLAN and WiMAX bands
Authors: Subbarao Akkala , Raghavan Singaravelu
Published: February 2013

A novel ultra‐wide band planar antenna with dual band‐notched characteristics is presented in this article.The antenna has compact size of 23 × 28 × 0.8 mm3 and it consists of novel patch. The measured antenna has impedance bandwidth of 3–10.7 GHz with dual notched bands of 3.3–3.7 GHz and 5.1–5.9 GHz to avoid interference from WiMAX and WLAN bands, respectively. A set of spiral slots and novel pulse‐shaped slots are etched in ground plane to obtain the dual notched bands. The effects of different geometrical parameters on various characteristics of antenna are investigated. The proposed antenna has consistent gain and stable radiation pattern. The measured group delay indicates that the antenna has good time domain response.© 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:740–744, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27461
Tunable narrow dispersion compensation for independent CWDM channels using the acousto‐optic modulation
Authors: Marques Carlos A.F. , Oliveira Roberson A. , Nogueira Rogério N.
Published: February 2013

A new method for dynamic control of the group delay of a fiber Bragg grating (FBG) is presented. It is based on an acoustic wave applied to the fiber. Tunability is obtained through adjustment of the intensity and/or frequency of the acoustic wave. The experimental results were verified by theoretical simulation. Application as a tunable narrow dispersion compensator for independent coarse wavelength division multiplexing (CWDM) channels is discussed. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:929–932, 2013; View this article online at wileyonlinelibrary.com. DOI: 10.1002/mop.27463
A highly attenuative CMOS LNA at 5–6 GHz using negative GM circuit for UWB applications
Authors: Koirala Nischal , Anand A. , Pokharel Ramesh K. , Kanaya H. , Yoshida K.
Published: February 2013

This paper presents a UWB low noise amplifier (LNA) for 3.1–10.6 GHz applications, with an excellent attenuation at 5–6 GHz for rejecting the wireless local area network (WLAN) interference. A method of canceling the on‐chip inductive resistance has been employed in this work to make the inductor an extremely low loss inductor with a very high quality factor. The fully integrated UWB LNA is designed in the CMOS 0.18 μm Taiwan Semiconductor Manufacturing Company (TSMC) technology. Measurement results show that the LNA achieves attenuation of up to 39 dB at 5.4 GHz, while the 1 dB power gain is 10 dB. The measured return losses (S11 and S22) are better than −7.4 dB while the noise figure is 5–6.1 dB in the range of operation. The measured input P1dB and IIP3 measured at 6.5 GHz are −12.2 and 2 dBm, respectively. The designed LNA occupies an area of 1.105 × 0.68 mm2. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:894–899, 2013; View this article online at wileyonlinelibrary.com. DOI 10.1002/mop.27464
Formulation of a three‐dimensional constitutive model for unsaturated soils incorporating mechanical–water retention couplings
Authors: Lloret‐Cabot Martí , Sánchez Marcelo , Wheeler Simon J.
Published: February 2013

Wheeler, Sharma and Buisson proposed an elasto‐plastic constitutive model for unsaturated soils that couples the mechanical and water retention behaviours. The model was formulated for isotropic stress states and adopts the mean Bishop's stress and modified suction as stress state variables. This paper deals with the extension of this constitutive model to general three‐dimensional stress conditions, proposing the generalized stress–strain relationships required for the numerical integration of the constitutive model. A characteristic of the original model is the consideration of a number of elasto‐plastic mechanisms to describe the complex behaviour of unsaturated soils. This work presents the three‐dimensional formulation of these coupled irreversible mechanisms in a generalized way including anisotropic loading. The paper also compares the results from the model with published experiments performed under different loading conditions. The response of the model is very satisfactory in terms of both mechanical and water retention behaviours. Copyright © 2013 John Wiley & Sons, Ltd.
Germline and somatic polymerase ϵ and δ mutations define a new class of hypermutated colorectal and endometrial cancers
Authors: Briggs Sarah , Tomlinson Ian
Published: February 2013

Polymerases ϵ and δ are the main enzymes that replicate eukaryotic DNA. Accurate replication occurs through Watson–Crick base pairing and also through the action of the polymerases' exonuclease (proofreading) domains. We have recently shown that germline exonuclease domain mutations (EDMs) of POLE and POLD1 confer a high risk of multiple colorectal adenomas and carcinoma (CRC). POLD1 mutations also predispose to endometrial cancer (EC). These mutations are associated with high penetrance and dominant inheritance, although the phenotype can be variable. We have named the condition polymerase proofreading‐associated polyposis (PPAP). Somatic POLE EDMs have also been found in sporadic CRCs and ECs, although very few somatic POLD1 EDMs have been detected. Both the germline and the somatic DNA polymerase EDMs cause an ‘ultramutated’, apparently microsatellite‐stable, type of cancer, sometimes leading to over a million base substitutions per tumour. Here, we present the evidence for POLE and POLD1 as important contributors to the pathogenesis of CRC and EC, and highlight some of the key questions in this emerging field. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Nucleotide resolution analysis of TMPRSS2 and ERG rearrangements in prostate cancer
Authors: Weier Christopher , Haffner Michael C , Mosbruger Timothy , Esopi David M , Hicks Jessica , Zheng Qizhi , Fedor Helen , Isaacs William B , De Marzo Angelo M. , Nelson William G , Yegnasubramanian Srinivasan
Published: February 2013

TMPRSS2–ERG rearrangements occur in approximately 50% of prostate cancers and therefore represent one of the most frequently observed structural rearrangements in all cancers. However, little is known about the genomic architecture of such rearrangements. We therefore designed and optimized a pipeline involving target capture of TMPRSS2 and ERG genomic sequences coupled with paired‐end next‐generation sequencing to resolve genomic rearrangement breakpoints in TMPRSS2 and ERG at nucleotide resolution in a large series of primary prostate cancer specimens (n = 83). This strategy showed > 90% sensitivity and specificity in identifying TMPRSS2–ERG rearrangements, and allowed identification of intra‐ and inter‐chromosomal rearrangements involving TMPRSS2 and ERG with known and novel fusion partners. Our results indicate that rearrangement breakpoints show strong clustering in specific intronic regions of TMPRSS2 and ERG. The observed TMPRSS2–ERG rearrangements often exhibited complex chromosomal architecture associated with several intra‐ and inter‐chromosomal rearrangements. Nucleotide resolution analysis of breakpoint junctions revealed that the majority of TMPRSS2 and ERG rearrangements (∼88%) occurred at or near regions of microhomology or involved insertions of one or more base pairs. This architecture implicates non‐homologous end joining (NHEJ) and microhomology‐mediated end joining (MMEJ) pathways in the generation of such rearrangements. These analyses have provided important insights into the molecular mechanisms involved in generating prostate cancer‐specific recurrent rearrangements. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Complexity from Simplicity: Unique Polymer Capsules, Rods, Monoliths, and Liquid Marbles Prepared via HIPE in Microfluidics
Authors: Gokmen M. Talha , Dereli Busra , De Geest Bruno G. , Du Prez Filip E.
Published: February 2013

Existing methods for preparing complex particles, i.e., hollow porous, depend on either multiple steps or a complex reactor design. Here, a straightforward method to prepare unique polymer particles with complex shapes via the use of simple equipment and readily available chemicals is reported. Beads, capsules, and rods with uniform size and interconnected pores are obtained through the formation of high internal phase emulsion (HIPE) droplets in a microfluidic channel. The method is applicable to a broad range of (meth)acralates. Controlling physical properties, such as viscosity and emulsion stability, is key to control the shape of the resulting particles. Post‐modification of the particles via click chemistry, their application in liquid marble formation, and their use as droplet reactors are also demonstrated.
Coarse‐ and fine‐grained models for proteins: Evaluation by decoy discrimination
Authors: Kauffman Chris , Karypis George
Published: February 2013

Coarse‐grained models for protein structure are increasingly used in simulations and structural bioinformatics. In this study, we evaluated the effectiveness of three granularities of protein representation based on their ability to discriminate between correctly folded native structures and incorrectly folded decoy structures. The three levels of representation used one bead per amino acid (coarse), two beads per amino acid (medium), and all atoms (fine). Multiple structure features were compared at each representation level including two‐body interactions, three‐body interactions, solvent exposure, contact numbers, and angle bending. In most cases, the all‐atom level was most successful at discriminating decoys, but the two‐bead level provided a good compromise between the number of model parameters which must be estimated and the accuracy achieved. The most effective feature type appeared to be two‐body interactions. Considering three‐body interactions increased accuracy only marginally when all atoms were used and not at all in medium and coarse representations. Though two‐body interactions were most effective for the coarse representations, the accuracy loss for using only solvent exposure or contact number was proportionally less at these levels than in the all‐atom representation. We propose an optimization method capable of selecting bead types of different granularities to create a mixed representation of the protein. We illustrate its behavior on decoy discrimination and discuss implications for data‐driven protein model selection. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Disorder and order in unfolded and disordered peptides and proteins: A view derived from tripeptide conformational analysis. I. Tripeptides with long and predominantly hydrophobic side chains
Authors: Schweitzer‐Stenner Reinhard , Hagarman Andrew , Toal Siobhan , Mathieu Daniel , Schwalbe Harald
Published: February 2013

We performed a conformational analysis of the central residues of three tripeptides glycyl‐L‐isoleucyl‐glycine (GIG), glycyl‐L‐tyrosyl‐glycine (GYG) and glycyl‐L‐arginyl‐glycine (GRG) in aqueous solution, based on a global analysis of amide I′ band profiles and NMR J‐coupling constants. The results are compared with recently reported distributions of GVG, GFG and GEG. For GIG and GYG, we found that even though the polyproline II (pPII) fraction is below 0.5, it is still the most populated conformation, whereas GVG and GFG show both a larger β‐strand fraction. For GRG, we observed a clear dominance of pPII over β‐strand, reminiscent of observations for GEG and GKG. This finding indicates that terminal charges on otherwise hydrophobic residue side chains stabilize pPII over β‐strand conformations. For all peptides investigated we found that a variety of compact and turn‐like conformations constitute nearly 20 percent of their conformational distributions. Attempts to analyze our data with a simple two‐state pPII⇔︁β model therefore do not yield any satisfactory reproduction of experimental results. A comparison of the obtained GxG ensembles with conformational distributions of GxG segments in truncated coil libraries (helices and sheets omitted) revealed a much larger fraction of type II βi+2 and type III β like conformations for the latter. Thus, a comparison of conformational distributions of unfolded peptide segments in solution and in coil libraries reveal interesting information on how the interplay between intrinsic propensities of amino acid residues and non‐local interactions in polypeptide chains determine the conformations of loop segments in proteins. Proteins 2013; © 2012 Wiley Periodicals, Inc.
A probabilistic model for secondary structure prediction from protein chemical shifts
Authors: Mechelke Martin , Habeck Michael
Published: February 2013

Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first‐ and second‐order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence‐based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts. Proteins 2013; © 2012 Wiley Periodicals, Inc.
Probing the role of interfacial waters in protein–DNA recognition using a hybrid implicit/explicit solvation model
Authors: Li Shen , Bradley Philip
Published: February 2013

When proteins bind to their DNA target sites, ordered water molecules are often present at the protein–DNA interface bridging protein and DNA through hydrogen bonds. What is the role of these ordered interfacial waters? Are they important determinants of the specificity of DNA sequence recognition, or do they act in binding in a primarily nonspecific manner, by improving packing of the interface, shielding unfavorable electrostatic interactions, and solvating unsatisfied polar groups that are inaccessible to bulk solvent? When modeling details of structure and binding preferences, can fully implicit solvent models be fruitfully applied to protein–DNA interfaces, or must the individualistic properties of these interfacial waters be accounted for? To address these questions, we have developed a hybrid implicit/explicit solvation model that specifically accounts for the locations and orientations of small numbers of DNA‐bound water molecules, while treating the majority of the solvent implicitly. Comparing the performance of this model with that of its fully implicit counterpart, we find that explicit treatment of interfacial waters results in a modest but significant improvement in protein side‐chain placement and DNA sequence recovery. Base‐by‐base comparison of the performance of the two models highlights DNA sequence positions whose recognition may be dependent on interfacial water. Our study offers large‐scale statistical evidence for the role of ordered water for protein–DNA recognition, together with detailed examination of several well‐characterized systems. In addition, our approach provides a template for modeling explicit water molecules at interfaces that should be extensible to other systems. Proteins 2013; 81:1318–1329. © 2013 Wiley Periodicals, Inc.
Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA
Authors: Nakagawa Hirofumi , Kuratani Mitsuo , Goto‐Ito Sakurako , Ito Takuhiro , Katsura Kazushige , Terada Takaho , Shirouzu Mikako , Sekine Shun‐ichi , Shigi Naoki , Yokoyama Shigeyuki
Published: February 2013

In thermophilic bacteria, specific 2‐thiolation occurs on the conserved ribothymidine at position 54 (T54) in tRNAs, which is necessary for survival at high temperatures. T54 2‐thiolation is achieved by the tRNA thiouridine synthetase TtuA and sulfur‐carrier proteins. TtuA has five conserved CXXC/H motifs and the signature PP motif, and belongs to the TtcA family of tRNA 2‐thiolation enzymes, for which there is currently no structural information. In this study, we determined the crystal structure of a TtuA homolog from the hyperthermophilic archeon Pyrococcus horikoshii at 2.1 Å resolution. The P. horikoshii TtuA forms a homodimer, and each subunit contains a catalytic domain and unique N‐ and C‐terminal zinc fingers. The catalytic domain has much higher structural similarity to that of another tRNA modification enzyme, TilS (tRNAIle2 lysidine synthetase), than to the other type of tRNA 2‐thiolation enzyme, MnmA. Three conserved cysteine residues are clustered in the putative catalytic site, which is not present in TilS. An in vivo mutational analysis in the bacterium Thermus thermophilus demonstrated that the three conserved cysteine residues and the putative ATP‐binding residues in the catalytic domain are important for the TtuA activity. A positively charged surface that includes the catalytic site and the two zinc fingers is likely to provide the tRNA‐binding site. Proteins 2013; 81:1232–1244. © 2013 Wiley Periodicals, Inc.
New insights into the half‐of‐the‐sites reactivity of human aldehyde dehydrogenase 1A1
Authors: Yoval‐Sánchez Belem , Pardo Juan Pablo , Rodríguez‐Zavala Jose S.
Published: February 2013

Aldehyde dehydrogenases (ALDHs) couple the oxidation of aldehydes to the reduction of NAD(P)+. These enzymes have gained importance as they have been related to the detoxification of aldehydes generated in several diseases involving oxidative stress. It has been determined that tetrameric ALDHs work only with two of their four active sites (half‐of‐the‐sites reactivity), but the mechanistic reason for this feature remains unknown. In this study, tetrameric human aldehyde dehydrogenase class 1A1 (ALDH1A1) was dimerized to study the correlation of the oligomeric structure with the presence of half‐of‐the‐sites reactivity. Stable dimers from ALDH1A1 were generated by combining the mutation of two residues of the dimer–dimer interface in the tetramer (previously shown to render a low‐active and unstable enzyme) and the fusion of green fluorescent protein (GFP) in the C‐terminus of the mutant. Some kinetic properties of the GFP‐fusion mutant resembled those of human aldehyde dehydrogenase class 3A1, a native dimer, in that the fusion dimer did not show burst in the generation of nicotinamide adenine dinucleotide (NADH) and was less sensitive to the action of specific modulators. The presence of primary isotope effect indicated that the rate‐limiting step changed from NADH release to hydride transfer. The mutant showed higher activity with malondialdehyde and acrolein and was more resistant to inactivation by acrolein compared with the wild type. The mutant kinetic profile showed two hyperbolic components when the substrates were varied, suggesting the presence of two active sites with different affinities and catalytic capacities. In conclusion, the ALDH1A1–GFP dimeric mutant exhibits full site reactivity, suggesting that only the tetrameric structure induces the half‐of‐the‐sites reactivity. Proteins 2013; 81:1330–1339. © 2013 Wiley Periodicals, Inc.
Surface quality and biocompatibility of porous hydroxyapatite scaffolds for bone tissue engineering
Authors: Wu Bin , Braun Anne , Ediger Simon , Huang Wei , Lilischkis Rainer , Schäfer Karl‐Herbert , Wu Quan , Zhang Xianglin , Saumer Monika
Published: February 2013

Surface quality and biocompatibility were critical properties of bone scaffolds. Fabrication and biological properties of porous hydroxyapatite (HA) scaffolds made by extrusion deposition method (EDM) and microwave sintering were investigated in this paper. The scaffolds with side length of 3.61 mm, height of 0.51 mm, pore size of 139 µm, Ra of 1.67 µm, and Rmax of 10.5 µm were used as substrates for osteosarcoma cells (SAOS 2) culturing to investigate the scaffolds' biological properties. Surface metrology and morphology before and after cell culture were measured to approach the interaction of cell culture with the scaffolds. The results showed that the HA scaffolds made by EDM had good biocompatibility and the surface metrology of scaffolds does not have an obvious change under cell culture even for 21 days. SAOS‐2 could attach to and grew well on scaffolds even after culturing for 21 days. And Ra and Rmax of scaffolds surfaces were 1.67 ± 0.59 µm and 10.5 ± 3.9 µm before cell culture and 1.64 ± 0.62 µm and 10.6 ± 4.5 µm after cell culture. EDTA have significant influences upon the HA grains, and the cells themselves also seem to lead to subtle scaffold degradation.
A Novel On‐Package Sticker Sensor Based on Methyl Red for Real‐Time Monitoring of Broiler Chicken Cut Freshness
Authors: Kuswandi Bambang , Jayus  , Oktaviana Revi , Abdullah Aminah , Heng Lee Yook
Published: February 2013

A novel sticker sensor has been fabricated based on methyl red, and tests have been conducted to detect the freshness of broiler chicken cuts. Methyl red was immobilized onto a bacterial cellulose membrane via absorption method. The methyl red/cellulose membrane as a freshness sensor worked based on pH increase as the basic spoilage volatile amines produced gradually in the package headspace, and subsequently, the colour of the sensor will change from red to yellow for spoilage indication, which is easily visible to the naked eye. The results show that the sticker sensor could be used to determine the degree of chicken cut freshness, as the relationship between the colour change of methyl red as a sensor response and the chicken cut freshness follows a similar trend. Therefore, the spoilage of the chicken cut could be detected visually. A sticker sensor indicates the chicken cut freshness by its colour change in real time. Thus, the sticker sensor can be used as an effective tool for monitoring the microbial quality of packaged fresh poultry meat. Finally, the methyl red/cellulose membrane was successfully used as a sticker sensor for the real‐time monitoring of chicken cut freshness in ambient and chiller conditions. Copyright © 2013 John Wiley & Sons, Ltd.
Connectivity of inhomogeneous random graphs
Authors: Devroye Luc , Fraiman Nicolas
Published: February 2013

We find conditions for the connectivity of inhomogeneous random graphs with intermediate density. Our results generalize the classical result for G(n, p), when . We draw n independent points Xi from a general distribution on a separable metric space, and let their indices form the vertex set of a graph. An edge (i, j) is added with probability , where is a fixed kernel. We show that, under reasonably weak assumptions, the connectivity threshold of the model can be determined. © 2013 Wiley Periodicals, Inc. Random Struct. Alg., 45, 408‐420, 2014
Mixed modeling and sample size calculations for identifying housekeeping genes
Authors: Dai Hongying , Charnigo Richard , Vyhlidal Carrie A. , Jones Bridgette L. , Bhandary Madhusudan
Published: February 2013

Normalization of gene expression data using internal control genes that have biologically stable expression levels is an important process for analyzing reverse transcription polymerase chain reaction data. We propose a three‐way linear mixed‐effects model to select optimal housekeeping genes. The mixed‐effects model can accommodate multiple continuous and/or categorical variables with sample random effects, gene fixed effects, systematic effects, and gene by systematic effect interactions. We propose using the intraclass correlation coefficient among gene expression levels as the stability measure to select housekeeping genes that have low within‐sample variation. Global hypothesis testing is proposed to ensure that selected housekeeping genes are free of systematic effects or gene by systematic effect interactions. A gene combination with the highest lower bound of 95% confidence interval for intraclass correlation coefficient and no significant systematic effects is selected for normalization. Sample size calculation based on the estimation accuracy of the stability measure is offered to help practitioners design experiments to identify housekeeping genes. We compare our methods with geNorm and NormFinder by using three case studies. A free software package written in SAS (Cary, NC, U.S.A.) is available at http://d.web.umkc.edu/daih under software tab. Copyright © 2013 John Wiley & Sons, Ltd.
A simulation model of the Devils Hole pupfish population using monthly length‐frequency distributions
Authors: Dzul Maria Christina , Dinsmore Stephen James , Quist Michael Carl , Gaines Daniel Bailey , Wilson Kevin Patrick , Bower Michael Roy , Dixon Philip Michael
Published: February 2013

The Devils Hole pupfish, Cyprinodon diabolis, is a federally‐endangered fish that is endemic to Devils Hole, a discontiguous part of Death Valley National Park in Nye County, Nevada. Due to its status, Devils Hole pupfish monitoring must be non‐obtrusive and thereby exclude techniques that require handling fish. Due to a recent decline in pupfish abundance, Devils Hole pupfish managers have expressed a need for a model that describes population dynamics. This population model would be used to identify vulnerable life history stage(s) and inform management actions. We constructed a set of individual‐based simulation models designed to explore effects of population processes and evaluate assumptions. We developed a baseline model, whose output best resembled both observed length‐frequency data and predicted intra‐annual abundance patterns. We then ran simulations with 5 % increases in egg‐larval, juvenile, and adult survival rates to better understand Devils Hole pupfish life history, thereby helping identify vulnerable life history stages that should become the target of management actions. Simulation models with temporally constant adult, juvenile, and egg‐larval survival rates were able to reproduce observed length‐frequency distributions and predicted intra‐annual population patterns. In particular, models with monthly adult and juvenile survival rates of 80 % and an egg‐larval survival rate of 4.7 % replicated patterns in observed data. Population growth was most affected by 5 % increases in egg‐larval survival, whereas adult and juvenile survival rates had similar but lesser effects on population growth. Outputs from the model were used to assess factors suspected of influencing Devils Hole pupfish population decline.
The effect of tranexamic acid in blood loss and transfusion volume in adolescent idiopathic scoliosis surgery: A single-surgeon experience
Authors: Lykissas Marios G. , Crawford Alvin H. , Chan Gilbert , Aronson Lori A. , Al-Sayyad Mohammed J.
Published: February 2013

Purpose

Intraoperative blood loss in scoliosis surgery often requires transfusions. Autogenous blood decreases but does not eliminate risks typically associated with allogenic blood transfusion. Costs associated with transfusions are significant. Tranexamic acid (TXA) has been shown to decrease blood loss in cardiac and joint surgery. Few studies have examined its use in pediatric spine surgery, and the results are inconsistent. The aim of this study was to determine whether TXA decreases intraoperative blood loss and transfusion requirements in adolescent idiopathic scoliosis patients undergoing posterior spinal fusion by a single surgeon.

Methods

The medical records and operative reports of surgically treated patients with adolescent idiopathic scoliosis between 2000 and 2009 were retrospectively reviewed. The inclusion criteria were: (1) patients who underwent instrumented posterior spinal fusion, (2) had complete medical records, and (3) were treated by the same surgeon. Forty-nine patients who met the inclusion criteria were divided into two groups: Group A (25 patients) received TXA, while Group B (24 patients) did not receive TXA.

Results

After controlling for age at the time of surgery, gender, and number of vertebral levels fused, the mean intraoperative blood loss was significantly lower in Group A (537 ml) than in Group B (1,245 ml) ( p = 0.027). The mean volume of blood transfused intraoperatively was 426 and 740 ml for Group A and Group B, respectively. The difference was not statistically significant after controlling for age, gender, and number of levels fused ( p = 0.078).

Conclusion

TXA significantly decreased intraoperative blood loss in posterior spinal fusions performed for adolescent idiopathic scoliosis.
Systematic analysis of genomic organization and structure of long non‐coding RNAs in the human genome
Authors: Sun Jie , Zhou Meng , Mao Zhi-Tao , Hao Da-Peng , Wang Zhen-zhen , Li Chuan-Xing
Published: February 2013

The genomic architecture of several functional elements in animals and plants, such as microRNAs and tRNA, has been better characterized. As yet, there is very little known about genomic organization and structure of lncRNA in animals and plants. Here, we conducted a genome‐wide systematic computational analysis of genomic architecture of lncRNAs, and further provided a more comprehensive comparative view of genomic organization between lncRNAs and several other functional elements in the human genome. Our study not only provides comprehensive knowledge for further studies into the correlations between the genomic architecture of lncRNAs and their important functional roles in diverse cellular processes and in disease, but also will be valuable for understanding the origin and evolution of lncRNAs.