bluuebunny/crossref_metadata_2025 huggingface dataset:
Enzymatic Production of Cocoa Butter Equivalents High in 1‐Palmitoyl‐2‐oleoyl‐3‐stearin in Continuous Packed Bed Reactors
Authors: Kim Sohee , Kim In‐Hwan , Akoh Casimir C. , Kim Byung Hee
Published: January 2014

This study aimed to optimize the lipase‐catalyzed transesterification of high oleic sunflower oil (A) with a mixture of ethyl palmitate and ethyl stearate (B) to produce cocoa butter equivalents with a weight ratio of 1‐palmitoyl‐2‐oleoyl‐3‐stearoyl‐rac‐glycerol (POS) to total symmetric monounsaturated triacylglycerols (SMUT) that is similar to that of cocoa butter by response surface methodology. The reaction was performed in a continuous packed bed reactor, using 0.45 g of Lipozyme RM IM as the biocatalyst. The effects of temperature (Te), residence time (RT), substrate molar ratio (SR, B/A), and water content (WC) of the substrates on the composition of reaction products were elucidated using the models established. Optimal reaction conditions for maximizing total SMUT and POS contents while minimizing the levels of diacylglycerol formation and acyl migration were: Te, 60 °C; RT, 28.5 min; SR, 8.5; WC, 300 mg/kg. The contents of total SMUT, POS, and diacylglycerol in the reaction products and the content of palmitoyl and stearoyl residues at the sn‐2 position of triacylglycerols in the products were 52.0, 25.1, 9.4, and 4.8 %, respectively, under these conditions. Successful scale‐up of the reaction was achieved under the optimal conditions, using 5 g of the lipase. A silver‐ion high performance liquid chromatography analysis showed that the products obtained by the larger scale reaction contained 49.1 % total SMUT and 6.1 % of their positional isomers.
The role of chemical policy in improving supply chain knowledge and product safety
Authors: Scruggs Caroline E. , Ortolano Leonard , Schwarzman Megan R. , Wilson Michael P.
Published: January 2014

Although the US government has made important improvements in chemical management since the 1970s, these advances have not kept pace with scientific knowledge about chemical hazards. While US federal chemical policy reform is being debated for the first time since 1976, some US businesses have voluntarily sought to improve their knowledge of chemical hazards in their supply chains, and several US states, the European Union, China, and other countries have moved forward with chemical policy reforms. Until policy reforms occur in the USA, the US chemical market will continue to experience problems associated with poor information on hazardous chemicals in supply chains. These market conditions make it difficult for consumer product companies to identify hazards and create safer products. Results from interviews with consumer product company representatives demonstrate that challenges in obtaining chemical-related information exist across sectors, and information on chemical hazards and uses can be conflicting, protected by trade secrets, lost in supply chains, or nonexistent. Interview results illustrate how some consumer product companies are exceeding regulatory requirements by voluntarily restricting from their products chemicals that could harm human health or the environment. Understanding the motivations behind—and barriers to—these actions could inform efforts to modernize US chemicals policies in ways that promote effective chemical management in supply chains. Using examples from the European Union and some US states, we introduce policy suggestions that would increase knowledge, market transparency, and information flows regarding hazardous chemicals and their uses; these would support the efforts of companies to develop and market safer products.
Identification of BP16 as a non-toxic cell-penetrating peptide with highly efficient drug delivery properties
Authors: Soler Marta , González-Bártulos Marta , Soriano-Castell David , Ribas Xavi , Costas Miquel , Tebar Francesc , Massaguer Anna , Feliu Lidia , Planas Marta
Published: January 2014

BP16is a non-toxic cell-penetrating peptide with high cellular uptakein vitro. This peptide is an efficient vector for the delivery of therapeutic agents into cells, as has been shown for the anticancer drug chlorambucil.
A new fluorescent and colorimetric sensor for hydrazine and its application in biological systems
Authors: Sun Mingda , Guo Jing , Yang Qingbiao , Xiao Ning , Li Yaoxian
Published: January 2014

A highly selective and sensitive fluorescent sensor for the detection of hydrazine has been developed. It can trace hydrazine changes in live cells and live fish. The sensing mechanism is well rationalized with the aid of TD-DFT calculations.
Design and implementation of compact WPT system using printed spiral resonators
Authors: Mohammadi Falavarjani M. , Shahabadi M. , Rashed‐Mohassel J.
Published: January 2014

A planar wireless power transfer (WPT) system with printed square spiral resonators is reported. To facilitate its fabrication, both the spiral resonator and its coupling loop are printed on the top and bottom layer of a single FR4 substrate, such that the spiral resonator is driven by the magnetic field of the coupling loop. The utilised coupling loop along with the appropriate matching circuit will improve the overall efficiency. The proposed WPT system which features a measured efficiency of more than 40% is not only compact but also low cost.
2D SAR imaging scheme based on compressive sensing
Authors: Zhang Xin , Huang Puming , Li Xiaohui
Published: January 2014

Synthetic aperture radar (SAR) processing is assumed to start with a demodulated baseband signal and attempt to solve ground reflectivity. An expression of two‐dimensional SAR echo data in the discrete domain is presented. To meet the requirements of the processing power and reduce the storage, a compressive sensing framework is adopted to solve the ground reflectivity. By a small number of signal samplings, the imaging is constructed efficiently and has a higher resolution. Promising results were obtained by several experiments.
0.5 V inverter‐based ultra‐low‐power, low‐noise VGA for medical ultrasound probes
Authors: Wang P. , Halvorsrød T.M. , Ytterdal T.
Published: January 2014

An inverter‐based ultra‐low‐power, low‐noise, single‐ended to differential continuous‐time variable gain amplifier is presented for 2–6 MHz second harmonic cardiac imaging ultrasound probes in a 65 nm CMOS technology. The proposed variable gain amplifier (VGA) consists of three equal inverters and resistor arrays which form a feedback loop. To improve both the power and noise performances, the inverters operate in the sub‐threshold region by adopting a 0.5 V supply voltage. By doubling the input transconductance of the VGA, the noise figure (NF) is enhanced further. The 6‐b thermometer resistor arrays achieve a gain range of the VGA from 0 to 22 dB. The total power consumption is 55 μW, NF is 2.7 dB referred to an 8 kΩ source resistor at a centre frequency of 4 MHz. 8‐b thermometer calibration codes are added into the inverters to force the static operating point of the inverters to half of the supply voltage, which could increase the immunity of the second harmonic distortion (HD2) to the process variation. The HD2 of the proposed VGA is −60.6 dB at the 330 mV peak‐to‐peak output swing. The active size is 154 × 102 μm.
Coded subcarrier intensity modulated free‐space optical links over generalised turbulence channels
Authors: Samimi Hossein
Published: January 2014

In this study, the authors investigate the error rate performance for a convolutionally coded subcarrier intensity modulated free‐space optical communication system. The analysis is conducted for the M‐distributed turbulence channels. M distribution is a newly developed model that unifies most of the irradiance statistical models proposed in the literature. In the authors derivations, they first express the probability density function of M distribution in terms of a series expansion. By relying on these results, a novel, highly accurate series solution is developed for the pairwise error probability (PEP). The derived PEP expression is in the form of a generalised infinite power series and can be used for different turbulence conditions. Then, this solution is used to formulate a generalised upper bound on the average bit‐error rate. Simulation results are further demonstrated to confirm the analytical results.
Performance analysis for downlink massive multiple‐input multiple‐output system with channel state information delay under maximum ratio transmission precoding
Authors: Zhao Long , Zheng Kan , Long Hang , Zhao Hui , Wang Wenbo
Published: January 2014

This study comprehensively investigates the performance of the downlink massive multiple‐input multiple‐output (MIMO) system with channel state information (CSI) delay, when the base station serves multiple user terminals (UTs) taking advantage of maximum ratio transmission precoding. Through the characteristic analysis of the received signal‐to‐interference‐plus‐noise ratio at UT, the tight lower bound of average area spectrum efficiency (SE) and its asymptotic bound with the infinite number of UTs are deduced, respectively. Based on the asymptotic bound and the realistic power consumption model consisting of both radiated power and circuit power, the trade‐off between SE and energy efficiency (EE) is developed, and the optimal EE with respect to SE is attained concisely. Moreover, the approximate expressions of both outage probability and bit error ratio (BER) are derived when the massive MIMO system works at its interference limited region. All theoretical results coincide to numerical results, and they show that deploying more transmission antennas will be helpful to improve SE, EE and reliability simultaneously; SE will be enhanced; however, the reliability, including both outage probability and BER, will be worsened by multiplexing more UTs; enlarging CSI delay can extensively deteriorate SE, EE and reliability.
Third‐order complex amplitudes tracking loop for slow flat fading channel online estimation
Authors: Shu Huaqiang , Ros Laurent , Simon Eric Pierre
Published: January 2014

This study deals with channel estimation in tracking mode over a flat Rayleigh fading channel with Jakes’ Doppler spectrum. Many estimation algorithms exploit the time‐domain correlation of the channel by employing a Kalman filter based on a first‐order (or sometimes second‐order) approximation model of the time‐varying channel. However, the nature of the approximation model itself degrades the estimation performance for slow to moderate varying channel scenarios. Furthermore, the Kalman‐based algorithms exhibit a certain complexity. Hence, a different model and approach has been investigated in this study to tackle all of these issues. A novel phase‐locked‐loop‐structured third‐order tracking loop estimator with a low complexity is proposed. The connection between a steady‐state Kalman filter based on a random walk approximation model and the proposed estimator is first established. Then, a suboptimal mean‐squared‐error (MSE) is given in a closed‐form expression as a function of the tracking loop parameters. The parameters that minimise this suboptimal MSE are also given in a closed‐form expression. The asymptotic MSE and bit‐error‐ratio simulation results demonstrate that the proposed estimator outperforms the first‐ and second‐order Kalman‐based filters reported in literature. The robustness of the proposed estimator is also verified by a mismatch simulation.
Support vector regression ‐based robust frequency estimation algorithm by instantaneous phase
Authors: Liu Xueqian , Yu Hongyi
Published: January 2014

There are two important factors which impact the performance of phase‐based frequency estimation algorithms remarkably: the approximations of noise phase model and imperfections in phase unwrapping process. Support vector regression (SVR) exits excellent capabilities for learning unknown data and forecasting the future ones, especially under the small sample condition. Therefore, the authors introduce it to predict the variation trend of instantaneous phase and unwrap phases efficiently. Even though with that being the case, errors still exist in phase unwrapping process because of its ambiguous phase characteristic. Furthermore, a SVR‐based frequency estimation algorithm is proposed and makes it immune to these error phases by means of setting the SVR's parameters properly. The results show that, compared with other phased‐based algorithms, not only does the proposed one maintain a wide estimation range and quality capabilities at low frequencies, but also improves accuracy at high frequencies and decreases the impact with the initial phase. The proposed algorithm is fit for not only linear phase signal but also polynomial phase signal, under both the Gaussian and non‐Gaussian condition.
Dual active bridge synchronous chopper control strategy in electronic power transformer
Authors: Zhang Rui , Wang Dan , Mao Chengxiong , Lu Jiming , Yang Jiawei , Yi Yang , Chen Xun , Zhang Junfeng
Published: January 2014

The electronic power transformer (EPT) is a novel transmission and transformation device, which consists of a series connection of two voltage‐source H‐bridge converters and a DC–DC converter with high‐frequency isolation transformer. When applied to microgrids, EPT will not only deliver energy to loads from the utility grid but also inject some amount of excess power into the utility grid. Hence, the capability of bidirectional power flow is important for EPT, which depends on the DC‐link stage. The traditional synchronous chopper control for a dual active bridge (DAB) converter has some limitations in the application of bidirectional power flow area. This study proposes a novel synchronous chopper control strategy for the DAB converter to implement bi‐direction power flow, details the basic principle and steady‐state operation and presents the mathematical derivations. A three‐phase three‐stage circuit configuration of 10 kV/400 V bi‐direction EPT system based on the novel control DAB converter is designed, and corresponding control schemes for the system are discussed. The performance of this EPT system is validated by the MATLAB/Simulink‐based simulations and the laboratory prototype experiments.
Multiobjective multistage distribution system planning using tabu search
Authors: Pereira Junior Benvindo Rodrigues , Cossi Antonio Marcos , Contreras Javier , Mantovani José Roberto Sanches
Published: January 2014

This study presents a multiobjective tabu search algorithm to solve the multistage planning problem of a distribution system formulated as a multiobjective dynamic mixed integer non‐linear programming problem. Multiobjective problems do not have a specific solution, but a set of solutions that allows us to observe the trade‐off among the analysed objectives. Taking into account this concept, the objective functions of the model proposed in this study are: costs (investment and operational) and reliability. The actions deemed in this model for each period of the planning horizon are: increase in the capacity of existing substations (or construction of new ones), exchange of cables in existing lines (and construction of new feeders), reconfiguration of the network, allocation of sectionalising switches and construction of tie lines. The system's reliability is evaluated by means of the non‐supplied energy under contingencies using the n − 1 criterion. By line switching and the use of tie lines, part of the loads affected by a contingency can be restored, thus, the non‐supplied energy can be evaluated by solving a distribution network restoration problem. Numerical results are presented for a 54‐bus system.
Real time adaptive non‐linear estimator/predictor design for traffic systems with inadequate detectors
Authors: Barimani Nasim , Rahimi Kian Ashkan , Moshiri Behzad
Published: January 2014

Traffic control and management needs accurate estimation and prediction of traffic variables such as flow, speed, volume, travel time etc. Linear stochastic time series methods are powerful analytical tools. The capability of state space reconstruction makes them popular in traffic prediction and estimation. In this study, to overcome the linearity assumption of these methods, a non‐linear kernel‐based stochastic time series method with state space reconstruction capability is proposed. To minimise the prediction error of the method, adaptive time variant transformation from primary space to reproducing kernel Hilbert space is proposed by employing extended Kalman filter. Owing to high costs of traffic detectors, not all the metropolitan areas are equipped with these sensors; therefore in this study, an extended Kalman observer based on the new dynamic‐adaptive‐non‐linear predictor is designed and applied for traffic flow estimation and prediction in the areas that suffer from lack of detectors. Practical data simulations and evaluations justify the high strength and accuracy of the proposed method in prediction of traffic speed with incomplete data sources.
High performance integrated terahertz sensor for detection of biomolecular processes in solution
Authors: Matvejev Vladimir , Zhang Yuchen , Stiens Johan
Published: January 2014

Biomolecular processes occurring within a physiological buffer induce changes in the dielectric permittivity of the solution at terahertz frequencies (0.1–10 THz). Therefore novel high sensitivity THz sensors could potentially satisfy the need for a label‐free, immobilisation‐free, real‐time and in‐solution biosensor technology. However, the application is hindered by insufficient performance of current measurement techniques resulting in low sensitivity, low resolution, high detection limit and excessive sample volume. This work presents an integrated THz sensor topology designed to overcome the aforementioned challenges, performance evaluation with a number of typical biomolecule processes, and analysis of possible applications. The state‐of‐the‐art performance is demonstrated with room‐temperature operated solid‐state active components operating at f ≃ 0.25 THz: the sample volume is V = 4 nl, detection limit is DL <9 mg/l, sensitivity to biomolecule concentration, conformation and binding. The technology could become a versatile tool for hydration shell study, protein conformation and function analysis, concentration measurements including nucleic acid amplification by polymerase chain reaction, protein and nucleic acid binding assay.
System design of series Z‐source inverter with feedforward and space vector pulse‐width modulation control strategy
Authors: Tang Yu , Xie Shaojun
Published: January 2014

For Z‐source inverter (ZSI), the peak DC‐link voltage is the actual voltage fed to the inversion stage. Controlling the peak DC‐link voltage at the constant level can effectively decrease the voltage stress and simplify the design process of the inversion stage. By adopting input feedforward control, the constant peak DC‐link voltage can be achieved. The feedback control of the peak output voltage is utilised to obtain the constant output without steady‐stage error under load variation. Both the peak DC‐link voltage and ac output is controlled to a desired level under different input and load condition. A prototype is built in the lab, and detailed design procedure of the ZSI with space vector pulse‐width modulation scheme is given. Simulation and experimental results are presented to demonstrate the feasibility of the proposed control strategy and parameters design method.
Torque controller of a doubly‐fed induction generator impelled by a DC motor for wind system applications
Authors: Morfin Onofre A. , Ruiz‐Cruz Riemann , Loukianov Alexander G. , Sánchez Edgar N. , Castellanos M.I. , Valenzuela Fredy A.
Published: January 2014

The authors propose robust non‐linear controllers for a wind system. The proposed controllers are based on a combination of the block control linearisation and super‐twisting algorithm, as a second‐order sliding mode technique. The main control loop is designed to regulate the electromagnetic torque and stator power factor of a doubly‐fed induction generator which is connected to the grid. The generator is mechanically coupled with a DC motor, which can emulate the wind turbine operation. Therefore, an auxiliary control loop is designed to control the DC motor velocity. Additionally, a grid‐side converter controller is proposed to regulate the DC‐link voltage into AC/DC/AC converter, and displacement factor of the energy flow between the rotor and the grid. A robust stability analysis of the complete closed‐loop system under external disturbances is presented. The robustness of the proposed control schemes is validated in real time using a workbench, which consists of a motor–generator group, AC/DC/AC electronic drive and dSPACE DS 1104 controller boards.
Quantitative assessment and comparison of fault responses for synchronous generator and wind turbine generators based on modified transient energy function
Authors: Chowdhury Md Ayaz , Shen Weixiang , Hosseinzadeh Nasser , Pota Hemanshu Roy
Published: January 2014

This study presents the quantitative transient stability assessment and comparison for conventional synchronous generator (SG) and wind turbine generators (WTGs) by studying the impact of the fault clearing time, the grid coupling, the inertia constant, the generator terminal voltage sag and the slip on fault responses. The assessment and comparison is performed by evaluating the transient stability index through the modified transient energy function. Simulation results show WTGs exhibit different transient responses on the occurrence of faults as compared with conventional SG. This justifies the necessity of study in greater depth for reliable operation of conventional power systems with the integration of large wind power.
Fault diagnosis of wind turbine based on multi‐sensors information fusion technology
Authors: Hang Jun , Zhang Jianzhong , Cheng Ming
Published: January 2014

Faults occurring in wind turbine (WT) degrade the performance and efficiency of wind power generation system, which result in large operation and maintenance cost of the WT. Therefore effective fault diagnosis schemes are greatly required for WT. This study presents a multi‐sensors information fusion technology for fault diagnosis of the WT, where vibration sensors are adopted. Firstly, to deal with the non‐stationary nature of the vibration signals of the WT, empirical mode decomposition method is utilised to extract fault features from the signals. Secondly, different classifiers are trained separately to classify fault types based on independent feature vectors from different sensors. Finally, three fusion approaches, named ordered weighted averaging, D‐S evidential reasoning and fuzzy integral, are, respectively, used for fusing the diagnosis results of individual classifiers. To validate the proposed method, a direct‐drive WT test rig is constructed and the related experiments are carried out. The experimental results validate the assumption that the proposed approach is effective for fault diagnosis of the WT, which has a higher diagnostic accuracy than that of individual sensor.
Motion compensation algorithm based on the designing structured gram matrices method
Authors: Xiang Yu , Dai‐yin Zhu , Jing‐dong Zhang , Rui Jiang
Published: January 2014

Motion compensation is a key procedure in inverse synthetic aperture radar (ISAR) imaging. The authors regard the motion compensation as a multi‐parameter estimation problem. Based on the designing structured Gram matrices optimisation method, a novel motion compensation method is presented. This method consists of two parts: the range alignment algorithm and the phase compensation algorithm. The former estimates the offset of each range profile by using a criterion, which makes correlations among all of the range profiles approaching to maximum values simultaneously. Also, the latter can extract phase errors by using the optimisation method to approach the ideal optimal matrix which is derived from analysis on the signal model. The measured data processing results show that the novel motion compensation method has strong robustness and high estimation accuracy.
Improving passive radio‐frequency identification localisation precision with moving direction estimation‐based feature improvement
Authors: Yang Po
Published: January 2014

To achieve high localisation accuracy and precision is a fundamental requirement of passive radio‐frequency identification (RFID) location systems. Current passive RFID location systems mostly deploy a dense RFID tag distribution to give initial localisation accuracy and use advanced localisation algorithms to extract the reliable features for enhancing localisation precision. High quality features are capable of significantly improving precision of passive RFID localisation systems, but it is hardly achieved in practice because of the environmental noise interference and the variety of tag behaviours. A localisation approach by using moving direction estimation to improve the quality of extracted features is proposed for enhancing localisation precision of passive RFID location systems. This approach relies on a general distribution of false‐reading occurring probability function derived from experimental measurements. A feature adjustment scheme is introduced to correct these features regarding the estimation of moving direction of object. The experimental results demonstrate that the proposed localisation approach with feature improvement achieves higher precision for the state‐of‐the art deterministic localisation algorithm (Han et al. 2007) in passive RFID location systems.
Network lifetime enhanced tri‐level clustering and routing protocol for monitoring of offshore wind farms
Authors: Agarwal Deepshikha , Kishor Nand
Published: January 2014

The reliable operation of offshore located wind farms is utmost important to ensure consistent power supply to grid. However, this depends on turbine‐generator availability. The health monitoring of wind system has proven as one of the most efficient methods to improve the availability of turbine‐generator set. This has emerged as one of the many possible applications of wireless sensor networks. This study discusses a novel algorithm for routing protocol of sensor data transmission to the base station. The algorithm is based on three‐level hierarchy, spatial distribution of sensor nodes and use of the current energy level of the node for clustering and information routing. This protocol utilises the best of all methods and provides better energy‐efficiency and a greater network lifetime compared with the low‐energy adaptive clustering hierarchy protocol protocol.
Cost‐effective design and evaluation of wireless sensor networks using topology‐planning methods in small‐world context
Authors: Tadayon Navid , Zonouz Amir Ehsani , Aïssa Sonia , Xing Liudong
Published: January 2014

Low‐power consumption and network resiliency are among the vital qualities for having a seamless, quality‐oriented wireless communication. Networks with small‐world property are known to possess both these favourable qualities. However, wireless networks are not inherently small‐world, neither is easy and cost‐effective to artificially create networks with this property by using the existing techniques. In other words, the traditional blind rewiring techniques that aimed at enhancing the network with such features, suffer from inefficiency and saturation behaviour. In this study, the authors propose topology‐planning methods that efficiently exploit the expensive long‐reach transmission facilities to add the small‐world property to the network. The authors show that these methods are practical, cost‐effective and efficient since they are appropriately tailored based upon the network realities, such as topology and channel fading. The proposed methods are tested for networks with diverse ranges of ‘clustering coefficient’ and ‘diameter’ in order to prove their aptitudes in dealing with real situations. The results illustrate that the incorporation of these techniques altogether decreases the network ‘diameter’ by almost 50% and the ‘average path length’ by 47%. This corresponds to 67% less facilities compared with blind rewiring techniques.
Static contact angle algorithm selection for superhydrophobic surface hydrophobicity detection
Authors: Xu Zhiniu
Published: January 2014

The static contact angle calculation for superhydrophobic surfaces is systematically investigated. The water drop profiles with different volumes, contact angles, rotational angles and apex coordinates are numerically generated based on the Laplace equation. Thereafter, the goniometry, θ/2 method, circle and ellipse fitting algorithms and an improved axisymmetric drop shape analysis‐profile (ADSA‐P) algorithm are used to calculate the static contact angle. The results reveal that the contact angle errors by the θ/2 method, circle and ellipse fitting algorithms increase with the drop volume/contact angle. The goniometry will introduce significant error. The ADSA‐P algorithm can accurately obtain the contact angles (error < 0.3°) for the drop profiles regardless of the water drop volume, contact angle, rotational angle and apex coordinate. The ADSA‐P algorithm should be selected to calculate the static contact angles for the superhydrophobic surfaces. Static contact angle measurements of the superhydrophobic surfaces validate the aforementioned analysis.
SnS nanostructures prepared by simple film technique: catalyst‐free vacuum thermal evaporation
Authors: Li Jin , Wang Shengfeng , Jian Jikang , Sun Yanfei , Xu Jinbao
Published: January 2014

SnS nanostructures were synthesised by simple vacuum thermal evaporation without any catalysts using tin chips and sulphur as the starting materials. The morphology was characterised by scanning electron microscopy and transmission electron microscopy (TEM) equipped with a high‐resolution TEM. It was found that the as‐prepared products were mostly tube shaped with a uniform geometry. The length of the nanostructures was several μm, the outer diameter and the thickness of the tubes was about 40–70 and 10–20 nm, respectively. The phase was analysed by X‐ray diffraction and confirmed that the as‐prepared products were of the orthorhombic phase. The photoluminescence spectra showed two emission bandcentres at 555.4 nm (2.24 eV) and at 785.0 nm (1.58 eV), which indicates that the SnS nanostructures could be used to prepare visible or an infrared light emitter or other optical devices.
Electrospinning system with tunable collector for fabricating three‐dimensional nanofibrous structures
Authors: Wang Feilong , Zhang Wenbo , Shao Zhushuai , Sun Yu , Ru Changhai
Published: January 2014

Electrospinning is a simple and efficient method for creating continuous nanofibres that present unique physical, chemical, electrical, magnetic and optical properties. However, its wide applications in various fields are restricted by the limitation that conventional electrospinning typically produces two‐dimensional (2D) nanofibrous membranes with limited thickness. To address this issue, an electrospinning system is developed to construct 3D nanofibrous structures by using a tunable collector on which a diameter‐adjustable cage rotor was mounted. The thickness of the nanofibrous structures is greatly increased by reducing the cage rotor diameter in certain time intervals during electrospinning. For comparison, different poly(lactic‐co‐glycolic acid) nanofibrous structures were manufactured by using the conventional and the proposed methods, respectively. The results indicated that the improved system is able to construct 3D nanofibrous structures with high porosity, stable geometrical morphology and good mechanical property. The work is expected to be useful for fabricating functional nanofibrous materials for a variety of applications.
Monitoring of small mammal populations in the Brindabella Ranges after fire
Authors: Davies Micah J. , Drew Alex
Published: January 2014

We live-trapped small mammals in the Brindabella Ranges west of Canberra, Australian Capital Territory from April 2009 until October 2011 to assess population recovery after an intense and widespread fire that occurred across the region in 2003. Three native mammals (agile antechinus, Antechinus agilis; dusky antechinus, Antechinus swainsonii; bush rat, Rattus fuscipes) were encountered. Trapping records and spool-and-line movement patterns suggested a strong association of these small mammals with moist gully vegetation that had survived the fire.
myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos
Authors: Montiel Ivan , Konikoff Charlotte , Braun Bremen , Packard Mary , Gramates Sian L. , Sun Qian , Ye Jieping , Kumar Sudhir
Published: January 2014

Summary: Spatial patterns of gene expression are of key importance in understanding developmental networks. Using in situ hybridization, many laboratories are generating images to describe these spatial patterns and to test biological hypotheses. To facilitate such analyses, we have developed biologist-centric software (myFX) that contains computational methods to automatically process and analyze images depicting embryonic gene expression in the fruit fly Drosophila melanogaster. It facilitates creating digital descriptions of spatial patterns in images and enables measurements of pattern similarity and visualization of expression across genes and developmental stages. myFX interacts directly with the online FlyExpress database, which allows users to search thousands of existing patterns to find co-expressed genes by image comparison.

Availability and implementation:  myFX is freely available at http://www.flyexpress.net.

Contact:  s.kumar@asu.edu
Ontodog: a web-based ontology community view generation tool
Authors: Zheng Jie , Xiang Zuoshuang , Stoeckert Christian J. , He Yongqun
Published: January 2014

Summary: Biomedical ontologies are often very large and complex. Only a subset of the ontology may be needed for a specified application or community. For ontology end users, it is desirable to have community-based labels rather than the labels generated by ontology developers. Ontodog is a web-based system that can generate an ontology subset based on Excel input, and support generation of an ontology community view, which is defined as the whole or a subset of the source ontology with user-specified annotations including user-preferred labels. Ontodog allows users to easily generate community views with minimal ontology knowledge and no programming skills or installation required. Currently >100 ontologies including all OBO Foundry ontologies are available to generate the views based on user needs. We demonstrate the application of Ontodog for the generation of community views using the Ontology for Biomedical Investigations as the source ontology.

Availability:  http://ontodog.hegroup.org/

Contact:  yongqunh@umich.edu
Identification of short terminal motifs enriched by antibodies using peptide mass fingerprinting
Authors: Planatscher Hannes , Weiß Frederik , Eisen David , van den Berg B.H.J. , Zell Andreas , Joos Thomas , Poetz Oliver
Published: January 2014

Motivation: Mass spectrometry-based protein profiling has become a key technology in biomedical research and biomarker discovery. Sample preparation strategies that reduce the complexity of tryptic digests by immunoaffinity substantially increase throughput and sensitivity in proteomic mass spectrometry. The scarce availability of peptide-specific capture antibodies limits these approaches. Recently antibodies directed against short terminal motifs were found to enrich subsets of peptides with identical terminal sequences. This approach holds the promise of a significant gain in efficiency. TXP (Triple X Proteomics) and context-independent motif specific/global proteome survey binders are variants of this concept. Principally the binding motifs of such antibodies have to be elucidated after generating these antibodies. This entails a substantial effort in the lab, as it requires synthetic peptide libraries and numerous mass spectrometry experiments.

Results: We present an algorithm for predicting the antibody-binding motif in a mass spectrum obtained from a tryptic digest of a common cell line after immunoprecipitation. The epitope prediction, based on peptide mass fingerprinting, reveals the most enriched terminal epitopes. The tool provides a P-value for each potential epitope, estimated by sampling random spectra from a peptide database. The second algorithm combines the predicted sequences to more complex binding motifs. A comparison with library screenings shows that the predictions made by the novel methods are reliable and reproducible indicators of the binding properties of an antibody.

Availability: Mass spectrum data, predictions, sampling tables, consensus peptide databases and the applied protocols are available as Supplementary Material. TXP-Terminus Enrichment Analysis (TEA) and MATERICS (Mass-spectrometric Analysis of Terminal Epitope Enrichment in Complex Samples) are available as web services at http://webservices.nmi.de/materics.

Contact:  hannes.planatscher@nmi.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
CGARS: cancer genome analysis by rank sums
Authors: Lu Xin , Thomas Roman K. , Peifer Martin
Published: January 2014

Motivation: Cancer genomes are characterized by the accumulation of point mutations and structural alterations such as copy-number alterations and genomic rearrangements. Among structural changes, systematic analyses of copy-number alterations have provided deeper insight into the architecture of cancer genomes and had led to new potential treatment opportunities. During the course of cancer genome evolution, selection mechanisms are leading to a non-random pattern of mutational events contributing to fitness benefits of the cancer cells. We therefore developed a new method to dissect random from non-random patterns in copy-number data and thereby to assess significantly enriched somatic copy-number aberrations across a set of tumor specimens or cell lines. In contrast to existing approaches, the method is invariant to any strictly monotonous transformation of the input data which results to an insensitivity of differences in tumor purity, array saturation effects and copy-number baseline levels.

Results: We applied our approach to recently published datasets of small-cell lung cancer and squamous cell lung cancer and validated its performance by comparing the results to an orthogonal approach. In addition, we found a new deletion peak containing the HLA-A gene in squamous cell lung cancer.

Availability: The CGARS program package is available for download at http://www.translational-genomics.uni-koeln.de/scientific-resources/ Documentation and examples are available together with the package.

Contact:  mpeifer@uni-koeln.de

Supplementary Information:  Supplementary information is available at Bioinformatics online.
Prediction of nuclear export signals using weighted regular expressions (Wregex)
Authors: Prieto Gorka , Fullaondo Asier , Rodriguez Jose A.
Published: January 2014

Motivation: Leucine-rich nuclear export signals (NESs) are short amino acid motifs that mediate binding of cargo proteins to the nuclear export receptor CRM1, and thus contribute to regulate the localization and function of many cellular proteins. Computational prediction of NES motifs is of great interest, but remains a significant challenge.

Results: We have developed a novel approach for amino acid motif searching that can be used for NES prediction. This approach, termed Wregex (weighted regular expression), combines regular expressions with a position-specific scoring matrix (PSSM), and has been implemented in a web-based, freely available, software tool. By making use of a PSSM, Wregex provides a score to prioritize candidates for experimental testing. Key features of Wregex include its flexibility, which makes it useful for searching other types of protein motifs, and its fast execution time, which makes it suitable for large-scale analysis. In comparative tests with previously available prediction tools, Wregex is shown to offer a good rate of true-positive motifs, while keeping a smaller number of potential candidates.

Availability: Wregex is free, open-source software available from http://wregex.ehubio.es

Contact:  gorka.prieto@ehu.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Random effect estimation of time-varying factors in Stock Synthesis
Authors: Thorson James T. , Hicks Allan C. , Methot Richard D.
Published: January 2014

Biological processes such as fishery selectivity, natural mortality, and somatic growth can vary over time, but it is challenging to estimate the magnitude of time-variation of demographic parameters in population dynamics models, particularly when using penalized-likelihood estimation approaches. Random-effect approaches can estimate the variance, but are computationally infeasible or not implemented for many models and software packages. We show that existing models and software based on penalized-likelihood can be used to calculate the Laplace approximation to the marginal likelihood of parameters representing variability over time, and specifically demonstrate this approach via application to Stock Synthesis. Using North Sea cod and Pacific hake models as case studies, we show that this method has little bias in estimating variances for simulated data. It also provides a similar estimate of variability in hake recruitment (log-SD = 1.43) to that obtained from Markov chain Monte Carlo (MCMC) methods (log-SD = 1.68), and the method estimates a non-trivial magnitude (log-SD = 0.07) of variation in growth for North Sea cod. We conclude by discussing the generality of the proposed method and by recommending future research regarding its performance relative to MCMC, particularly when estimating multiple variances simultaneously.
Organization of the human mitochondrial transcription initiation complex
Authors: Yakubovskaya Elena , Guja Kip E. , Eng Edward T. , Choi Woo Suk , Mejia Edison , Beglov Dmitri , Lukin Mark , Kozakov Dima , Garcia-Diaz Miguel
Published: January 2014

Initiation of transcription in human mitochondria involves two factors, TFAM and TFB2M, in addition to the mitochondrial RNA polymerase, POLRMT. We have investigated the organization of the human mitochondrial transcription initiation complex on the light-strand promoter (LSP) through solution X-ray scattering, electron microscopy (EM) and biochemical studies. Our EM results demonstrate a compact organization of the initiation complex, suggesting that protein–protein interactions might help mediate initiation. We demonstrate that, in the absence of DNA, only POLRMT and TFAM form a stable interaction, albeit one with low affinity. This is consistent with the expected transient nature of the interactions necessary for initiation and implies that the promoter DNA acts as a scaffold that enables formation of the full initiation complex. Docking of known crystal structures into our EM maps results in a model for transcriptional initiation that strongly correlates with new and existing biochemical observations. Our results reveal the organization of TFAM, POLRMT and TFB2M around the LSP and represent the first structural characterization of the entire mitochondrial transcriptional initiation complex.
Binary recombinase systems for high-resolution conditional mutagenesis
Authors: Hermann Mario , Stillhard Patrick , Wildner Hendrik , Seruggia Davide , Kapp Viktor , Sánchez-Iranzo Héctor , Mercader Nadia , Montoliu Lluís , Zeilhofer Hanns Ulrich , Pelczar Pawel
Published: January 2014

Conditional mutagenesis using Cre recombinase expressed from tissue specific promoters facilitates analyses of gene function and cell lineage tracing. Here, we describe two novel dual-promoter-driven conditional mutagenesis systems designed for greater accuracy and optimal efficiency of recombination. Co-Driver employs a recombinase cascade of Dre and Dre-respondent Cre, which processes loxP-flanked alleles only when both recombinases are expressed in a predetermined temporal sequence. This unique property makes Co-Driver ideal for sequential lineage tracing studies aimed at unraveling the relationships between cellular precursors and mature cell types. Co-InCre was designed for highly efficient intersectional conditional transgenesis. It relies on highly active trans-splicing inteins and promoters with simultaneous transcriptional activity to reconstitute Cre recombinase from two inactive precursor fragments. By generating native Cre, Co-InCre attains recombination rates that exceed all other binary SSR systems evaluated in this study. Both Co-Driver and Co-InCre significantly extend the utility of existing Cre-responsive alleles.
Differential induction of CCL5 by pathogenic and non-pathogenic strains of West Nile virus in brain endothelial cells and astrocytes
Authors: Hussmann Katherine L. , Fredericksen Brenda L.
Published: January 2014

The neuroinflammatory response to West Nile virus (WNV) infection can be either protective or pathological depending on the context. Although several studies have examined chemokine profiles within brains of WNV-infected mice, little is known about how various cell types within the central nervous system (CNS) contribute to chemokine expression. Here, we assessed chemokine expression in brain microvascular endothelial cells and astrocytes, which comprise the major components of the blood–brain barrier (BBB), in response to a non-pathogenic (WNV-MAD78) and a highly pathogenic (WNV-NY) strain of WNV. Higher levels of the chemokine CCL5 were detected in WNV-MAD78-infected brain endothelial monolayers compared with WNV-NY-infected cells. However, the opposite profile was observed in WNV-infected astrocytes, indicating that pathogenic and non-pathogenic strains of WNV provoke different CCL5 profiles at the BBB. Thus, cells comprising the BBB may contribute to a dynamic pro-inflammatory response within the CNS that evolves as WNV infection progresses.
SIANN: Strain Identification by Alignment to Near Neighbors
Authors: Minot Samuel S. , Turner Stephen D. , Ternus Krista L. , Kadavy Dana R.
Published: January 2014

Next-generation sequencing is increasingly being used to study samples composed of mixtures of organisms, such as in clinical applications where the presence of a pathogen at very low abundance may be highly important. We present an analytical method (SIANN: Strain Identification by Alignment to Near Neighbors) specifically designed to rapidly detect a set of target organisms in mixed samples that achieves a high degree of species- and strain-specificity by aligning short sequence reads to the genomes of near neighbor organisms, as well as that of the target. Empirical benchmarking alongside the current state-of-the-art methods shows an extremely high Positive Predictive Value, even at very low abundances of the target organism in a mixed sample. SIANN is available as an Illumina BaseSpace app, as well as through Signature Science, LLC. SIANN results are presented in a streamlined report designed to be comprehensible to the non-specialist user, providing a powerful tool for rapid species detection in a mixed sample. By focusing on a set of (customizable) target organisms and their near neighbors, SIANN can operate quickly and with low computational requirements while delivering highly accurate results.