Showing papers by "Agilent Technologies published in 2012"

A cross-platform toolkit for mass spectrometry and proteomics

Abstract: Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and quantify the proteins in biological and clinical samples1, identify pathways affected by endogenous and exogenous perturbations2, and characterize protein complexes3. Despite successes, the interpretation of vast proteomics datasets remains a challenge. There have been several calls for improvements and standardization of proteomics data analysis frameworks, as well as for an application-programming interface for proteomics data access4,5. In response, we have developed the ProteoWizard Toolkit, a robust set of open-source, software libraries and applications designed to facilitate proteomics research. The libraries implement the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats. In addition, diverse software classes enable rapid development of vendor-agnostic proteomics software. Additionally, ProteoWizard projects and applications, building upon the core libraries, are becoming standard tools for enabling significant proteomics inquiries.

Error Vector Magnitude as a Performance Measure for Advanced Modulation Formats

Abstract: We examine the relation between optical signal-to-noise ratio (OSNR), error vector magnitude (EVM), and bit-error ratio (BER). Theoretical results and numerical simulations are compared to measured values of OSNR, EVM, and BER. We conclude that the EVM is an appropriate metric for optical channels limited by additive white Gaussian noise. Results are supported by experiments with six modulation formats at symbol rates of 20 and 25 GBd generated by a software-defined transmitter.

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

Abstract: Despite extensive research, our understanding of the rules according to which cis-regulatory sequences are converted into gene expression is limited. We devised a method for obtaining parallel, highly accurate gene expression measurements from thousands of designed promoters and applied it to measure the effect of systematic changes in the location, number, orientation, affinity and organization of transcription-factor binding sites and nucleosome-disfavoring sequences. Our analyses reveal a clear relationship between expression and binding-site multiplicity, as well as dependencies of expression on the distance between transcription-factor binding sites and gene starts which are transcription-factor specific, including a striking ~10-bp periodic relationship between gene expression and binding-site location. We show how this approach can measure transcription-factor sequence specificities and the sensitivity of transcription-factor sites to the surrounding sequence context, and compare the activity of 75 yeast transcription factors. Our method can be used to study both cis and trans effects of genotype on transcriptional, post-transcriptional and translational control.

A roadmap for the development of alternative (non-animal) methods for systemic toxicity testing.

Abstract: Systemic toxicity testing forms the cornerstone for the safety evaluation of substances. Pressures to move from traditional animal models to novel technologies arise from various concerns, including: the need to evaluate large numbers of previously untested chemicals and new products (such as nanoparticles or cell therapies), the limited predictivity of traditional tests for human health effects, duration and costs of current approaches, and animal welfare considerations. The latter holds especially true in the context of the scheduled 2013 marketing ban on cosmetic ingredients tested for systemic toxicity. Based on a major analysis of the status of alternative methods (Adler et al., 2011) and its independent review (Hartung et al., 2011), the present report proposes a roadmap for how to overcome the acknowledged scientific gaps for the full replacement of systemic toxicity testing using animals. Five whitepapers were commissioned addressing toxicokinetics, skin sensitization, repeated-dose toxicity, carcinogenicity, and reproductive toxicity testing. An expert workshop of 35 participants from Europe and the US discussed and refined these whitepapers, which were subsequently compiled to form the present report. By prioritizing the many options to move the field forward, the expert group hopes to advance regulatory science.

Electropolymerized Polyaniline Stabilized Tungsten Oxide Nanocomposite Films: Electrochromic Behavior and Electrochemical Energy Storage

Abstract: Polyaniline (PANI)/tungsten oxide (WO3) nanocomposite films were fabricated by electropolymerization of aniline monomers onto WO3 coated indium tin oxide (ITO) glass slides, which were prepared by spin coating technique and followed by annealing at 500 °C for 2 h. The morphology and crystalline structure of the composite films were studied using Fourier transform infrared (FT-IR) spectroscopy, atomic force microscopy (AFM), X-ray diffraction (XRD), and transmission electron microscopy (TEM). The results confirm chemical interactions between the polymer matrix and the WO3 particles and reveal a well crystallized PANI/WO3 nanocomposite structure. The optical properties and electrochemical capacitive behaviors of the composite films for electrochromic (EC) and energy storage devices applications were investigated using spectroelectrochemistry (SEC), cyclic voltammetry (CV) and galvanostatic charge–discharge measurements. The composite films show dual electrochromism at both positive and negative potentials a...

Real-time Nyquist pulse generation beyond 100 Gbit/s and its relation to OFDM

Abstract: Nyquist sinc-pulse shaping provides spectral efficiencies close to the theoretical limit. In this paper we discuss the analogy to optical orthogonal frequency division multiplexing and compare both techniques with respect to spectral efficiency and peak to average power ratio. We then show that using appropriate algorithms, Nyquist pulse shaped modulation formats can be encoded on a single wavelength at speeds beyond 100 Gbit/s in real-time. Finally we discuss the proper reception of Nyquist pulses.

Signal-dependent incorporation of MyoD-BAF60c into Brg1-based SWI/SNF chromatin-remodelling complex.

Abstract: Tissue-specific transcriptional activators initiate differentiation towards specialized cell types by inducing chromatin modifications permissive for transcription at target loci, through the recruitment of SWItch/Sucrose NonFermentable (SWI/SNF) chromatin-remodelling complex. However, the molecular mechanism that regulates SWI/SNF nuclear distribution in response to differentiation signals is unknown. We show that the muscle determination factor MyoD and the SWI/SNF subunit BAF60c interact on the regulatory elements of MyoD-target genes in myoblasts, prior to activation of transcription. BAF60c facilitates MyoD binding to target genes and marks the chromatin for signal-dependent recruitment of the SWI/SNF core to muscle genes. BAF60c phosphorylation on a conserved threonine by differentiation-activated p38α kinase is the signal that promotes incorporation of MyoD–BAF60c into a Brg1-based SWI/SNF complex, which remodels the chromatin and activates transcription of MyoD-target genes. Our data support an unprecedented two-step model by which pre-assembled BAF60c–MyoD complex directs recruitment of SWI/SNF to muscle loci in response to differentiation cues.

Global Methylation Patterns in Idiopathic Pulmonary Fibrosis

Abstract: Background Idiopathic Pulmonary Fibrosis (IPF) is characterized by profound changes in the lung phenotype including excessive extracellular matrix deposition, myofibroblast foci, alveolar epithelial cell hyperplasia and extensive remodeling. The role of epigenetic changes in determining the lung phenotype in IPF is unknown. In this study we determine whether IPF lungs exhibit an altered global methylation profile.

Triple Quad ICPMS (ICPQQQ) as a New Tool for Absolute Quantitative Proteomics and Phosphoproteomics

Abstract: It is clear that sensitive and interference-free quantification of ICP-detectable elements naturally present in proteins will boost the role of ICPMS in proteomics. In this study, a completely new way of polyatomic interference removal in ICPMS for detection of sulfur (present in the majority of proteins as methionine or cysteine) and phosphorus (present in phosphorylated proteins) is presented. It is based on the concept of tandem mass spectrometry (QQQ) typically used in molecular MS. Briefly, the first quadrupole can be operated as 1 amu window band-pass mass filter to select target analyte ions (31P, 32S, and their on-mass polyatomic interferences). In this way, only selected ions enter the cell and react with O2, reducing the interferences produced by matrix ions as well as background noise. After optimization of the cell conditions, product ions formed for the targets, 47PO+ and 48SO+, could be detected with enhanced sensitivity and selectivity. The coupling to capillary HPLC allowed analysis of S- ...

Quality metrics for optical signals: Eye diagram, Q-factor, OSNR, EVM and BER

Abstract: Measuring the quality of optical signals is one of the most important tasks in optical communications. A variety of metrics are available, namely the general shape of the eye diagram, the optical signal-to-noise power ratio (OSNR), the Q-factor as a measure of the eye opening, the error vector magnitude (EVM) that is especially suited for quadrature amplitude modulation (QAM) formats, and the bit error ratio (BER). While the BER is the most conclusive quality determinant, it is sometimes difficult to quantify, especially for simulations and off-line processing. We compare various metrics analytically, by simulation, and through experiments. We further discuss BER estimates derived from OSNR, Q-factor and EVM data and compare them to measurements employing six modulation formats at symbol rates of 20 GBd and 25 GBd, which were generated by a software-defined transmitter. We conclude that for optical channels with additive Gaussian noise the EVM metric is a reliable quality measure. For nondata-aided reception, BER below 0.01 can be estimated from measured EVM.

Single-laser 32.5 Tbit/s Nyquist WDM transmission

Abstract: We demonstrate single-laser 32.5 Tbit/s 16QAM Nyquist wavelength division multiplexing transmission over a total length of 227 km of SMF-28 without optical dispersion compensation. A number of 325 optical carriers is derived from a single laser and encoded with dual-polarization 16QAM data using sinc-shaped Nyquist pulses. As we use no guard bands, the carriers have a spacing of 12.5 GHz equal to the symbol rate or Nyquist bandwidth of the data. We achieve a net spectral efficiency of 6.4 bit/s/Hz using a software-defined transmitter, which generates the electric drive signals for the electro-optic modulator in real time.

LTE UE Power Consumption Model: For System Level Energy and Performance Optimization

Abstract: In this work a novel LTE user equipment (UE) power consumption model is presented. It was developed for LTE system level optimization, because it is important to understand how network settings like scheduling of resources and transmit power control affect the UE's battery life. The proposed model is based on a review of the major power consuming parts in an LTE UE radio modem. The model includes functions of UL and DL power and data rate. Measurements on a commercial LTE USB dongle were used to assign realistic power consumption values to each model parameter. Verification measurements on the dongle show that the model results in an average error of 2.6 %. The measurements show that UL transmit power and DL data rate determines the overall power consumption, while UL data rate and DL receive power have smaller impact.

Silencing of a large microRNA cluster on human chromosome 14q32 in melanoma: biological effects of mir-376a and mir-376c on insulin growth factor 1 receptor.

Abstract: Metastatic melanoma is a devastating disease with limited therapeutic options. MicroRNAs (miRNAs) are small non coding RNA molecules with important roles in post-transcriptional gene expression regulation, whose aberrant expression has been implicated in cancer. We show that the expression of miRNAs from a large cluster on human chromosome 14q32 is significantly down-regulated in melanoma cell lines, benign nevi and melanoma samples relative to normal melanocytes. This miRNA cluster resides within a parentally imprinted chromosomal region known to be important in development and differentiation. In some melanoma cell lines, a chromosomal deletion or loss-of-heterozygosity was observed in the cis-acting regulatory region of this cluster. In several cell lines we were able to re-express two maternally-induced genes and several miRNAs from the cluster with a combination of de-methylating agents and histone de-acetylase inhibitors, suggesting that epigenetic modifications take part in their silencing. Stable over-expression of mir-376a and mir-376c, two miRNAs from this cluster that could be re-expressed following epigenetic manipulation, led to modest growth retardation and to a significant decrease in migration in-vitro. Bioinformatic analysis predicted that both miRNAs could potentially target the 3'UTR of IGF1R. Indeed, stable expression of mir-376a and mir-376c in melanoma cells led to a decrease in IGF1R mRNA and protein, and a luciferase reporter assay indicated that the 3'UTR of IGF1R is a target of both mir-376a and mir-376c. Our work is the first to show that the large miRNA cluster on chromosome 14q32 is silenced in melanoma. Our results suggest that down-regulation of mir-376a and mir-376c may contribute to IGF1R over-expression and to aberrant negative regulation of this signaling pathway in melanoma, thus promoting tumorigenesis and metastasis.

Annotation of a Serum N-Glycan Library for Rapid Identification of Structures

Abstract: Glycosylation is one of the most common post-translational modifications of proteins and has been shown to change with various pathological states including cancer Global glycan profiling of human serum based on mass spectrometry has already led to several promising markers for diseases The changes in glycan structure can result in altered monosaccharide composition as well as in the linkages between the monosaccharides High-throughput glycan structural elucidation is not possible due to the lack of a glycan template to expedite identification In an effort toward rapid profiling and identification of glycans, we have constructed a library of structures for the serum glycome to aid in the rapid identification of serum glycans N-Glycans from human serum glycoproteins are used as a standard and compiled into a library with exact structure (composition and linkage), liquid chromatography retention time, and accurate mass Development of the library relies on highly reproducible nanoLC/MS retention times Tandem MS and exoglycosidase digestions were used for structural elucidation The library currently contains over 300 entries with 50 structures completely elucidated and over 60 partially elucidated structures This database is steadily growing and will be used to rapidly identify glycans in unknown biological samples

Stable isotope dilution assay for the accurate determination of mycotoxins in maize by UHPLC-MS/MS.

Abstract: A fast, easy-to-handle and cost-effective analytical method for 11 mycotoxins currently regulated in maize and other cereal-based food products in Europe was developed and validated for maize. The method is based on two extraction steps using different acidified acetonitrile–water mixtures. Separation is achieved using ultrahigh-performance liquid chromatography (UHPLC) by a linear water–methanol gradient. After electrospray ionisation, tandem mass spectrometric detection is performed in dynamic multiple reaction monitoring mode. Since accurate mass spectrometric quantification is hampered by matrix effects, uniformly [13C]-labelled mycotoxins for each of the 11 compounds were added to the sample extracts prior to UHPLC-MS/MS analysis. Method performance parameters were obtained by spiking blank maize samples with mycotoxins before as well as after extraction on six levels in triplicates. The twofold extraction led to total recoveries of the extraction steps between 97% and 111% for all target analytes, including fumonisins. The [13C]-labelled internal standards efficiently compensated all matrix effects in electrospray ionisation, leading to apparent recoveries between 88% and 105% with reasonable additional costs. The relative standard deviations of the whole method were between 4% and 11% for all analytes. The trueness of the method was verified by the measurement of several maize test materials with well-characterized concentrations. In conclusion, the developed method is capable of determining all regulated mycotoxins in maize and presuming similar matrix effects and extraction recovery also in other cereal-based foods.

High-Throughput SISCAPA Quantitation of Peptides from Human Plasma Digests by Ultrafast, Liquid Chromatography-Free Mass Spectrometry

Abstract: We investigated the utility of an SPE-MS/MS platform in combination with a modified SISCAPA workflow for chromatography-free MRM analysis of proteotypic peptides in digested human plasma. This combination of SISCAPA and SPE-MS/MS technology allows sensitive, MRM-based quantification of peptides from plasma digests with a sample cycle time of ∼7 s, a 300-fold improvement over typical MRM analyses with analysis times of 30-40 min that use liquid chromatography upstream of MS. The optimized system includes capture and enrichment to near purity of target proteotypic peptides using rigorously selected, high affinity, antipeptide monoclonal antibodies and reduction of background peptides using a novel treatment of magnetic bead immunoadsorbents. Using this method, we have successfully quantitated LPS-binding protein and mesothelin (concentrations of ∼5000 ng/mL and ∼10 ng/mL, respectively) in human plasma. The method eliminates the need for upstream liquid-chromatography and can be multiplexed, thus facilitating quantitative analysis of proteins, including biomarkers, in large sample sets. The method is ideal for high-throughput biomarker validation after affinity enrichment and has the potential for applications in clinical laboratories.

Magnetic graphene nanocomposites: electron conduction, giant magnetoresistance and tunable negative permittivity

Abstract: Magnetic graphene nanocomposites (MGNCs) with surface-adhered magnetic nanoparticles (NPs) are synthesized by a facile thermal-decomposition method. Two different sized graphenes (Gra-10 and Gra-40) are used. The stacking of a few layers of NPs is revealed by the AFM observation in the nanocomposites, especially with a higher particle loading. The TEM observations show that the average particle size increases from 12.1 to 17.4 nm with increasing particle loading from 2 to 10% on Gra-10 substrate. The NPs exhibit a core@shell structure with an iron core and iron oxide shell, confirmed by high resolution TEM, selected area electron diffraction and X-ray diffraction analysis. The graphene size and particle loading dependent behavior such as dielectric permittivity, electrical conductivity, magnetization and giant magnetoresistance (GMR) are observed. The electrical conductivity has been significantly changed in the different sized graphenes after coating with NPs (conductivity: Gra-10 > NPs/Gra-10; Gra-40 < NPs/Gra-40). The MR is observed to vary from 38 to 64% at 130 K, and even higher MR of about 46–72% is observed at 290 K. More interestingly, the dielectric permittivity can be tuned from negative to positive at high frequency with increasing particle loading. All the results indicate that graphene with smaller size obtains superior properties than the one with larger size.

512QAM Nyquist sinc-pulse transmission at 54 Gbit/s in an optical bandwidth of 3 GHz

Abstract: We demonstrate for the first time transmission of 54 Gbit/s and 48 Gbit/s over 44 km and 150 km, respectively, utilizing an optical bandwidth of only 3 GHz. We used polarization division multiplexed 512QAM and 256QAM modulation formats in combination with Nyquist pulse shaping having virtually zero roll-off. The resulting spectral efficiencies range up to 18 bit/s/Hz and 16 bit/s/Hz, respectively. Taking into account the overhead required for forward error correction, the occupied signal bandwidth corresponds to net spectral efficiencies of 14.4 bit/s/Hz and 15 bit/s/Hz, which could be achieved in a wavelength division multiplexed network without spectral guard bands.

Future Device Modeling Trends

Abstract: Good transistor models are essential for efficient computer-aided-design (CAD) of nonlinear microwave and RF circuits, monolithic microwave integrated circuits (MMICs), power amplifiers (PAs), and nonlinear RF systems. Increasingly complicated demands of the various semiconductor technologies (e.g., GaAs pHEMTs, InP double heterojunction bipolar transistors (DHBTs), silicon on insulator (SOI), LDMOS, GaN HFETs, etc.), and their applications in terms of power and frequency of operation and complexity of applied signals (e.g., modern communication signals with high peak-toaverage ratios) have placed commensurate requirements on the accuracy and generality of the device models used for design. New semiconductor material systems (e.g., GaN) have been developing at such a fast rate that conventional compact modeling approaches may not be able to keep up. These and other challenges have spawned much research into the advanced nonlinear device modeling techniques that are the focus of this article.

New Trends for the Nonlinear Measurement and Modeling of High-Power RF Transistors and Amplifiers With Memory Effects

Abstract: Power amplifier (PA) behavior is inextricably linked to the characteristics of the transistors underlying the PA design. All transistors exhibit some degree of memory effects, which must therefore be taken into account in the modeling and design of these PAs. In this paper, we will present new trends for the characterization, device modeling, and behavioral modeling of power transistors and amplifiers with strong memory effects. First the impact of thermal and electrical memory effects upon the performance of a transistor will be revealed by comparing continuous wave and pulsed RF large-signal measurements. Pulsed-RF load-pull from the proper hot bias condition yields a more realistic representation of the peak power response of transistors excited with modulated signals with high peak-to-average power ratio. Next, an advanced device modeling method based on large-signal data from a modern nonlinear vector network analyzer instrument, coupled with modeling approaches based on advanced artificial neural network technology, will be presented. This approach enables the generation of accurate and robust time-domain nonlinear simulation models of modern transistors that exhibit significant memory effects. Finally an extension of the X-parameter (X-parameter is a trademark of Agilent Technologies Inc.) behavioral model to account for model memory effects of RF and microwave components will be presented. The approach can be used to model hard nonlinear behavior and long-term memory effects and is valid for all possible modulation formats for all possible peak-to-average ratios and for a wide range of modulation bandwidths. Both the device and behavioral models have been validated by measurements and are implemented in a commercial nonlinear circuit simulator.

Deubiquitination of EGFR by Cezanne-1 contributes to cancer progression.

Abstract: Once stimulated, the epidermal growth factor receptor (EGFR) undergoes self-phosphorylation, which, on the one hand, instigates signaling cascades, and on the other hand, recruits CBL ubiquitin ligases, which mark EGFRs for degradation. Using RNA interference screens, we identified a deubiquitinating enzyme, Cezanne-1, that opposes receptor degradation and enhances EGFR signaling. These functions require the catalytic- and ubiquitin-binding domains of Cezanne-1, and they involve physical interactions and transphosphorylation of Cezanne-1 by EGFR. In line with the ability of Cezanne-1 to augment EGF-induced growth and migration signals, the enzyme is overexpressed in breast cancer. Congruently, the corresponding gene is amplified in approximately one third of mammary tumors, and high transcript levels predict an aggressive disease course. In conclusion, deubiquitination by Cezanne-1 curtails degradation of growth factor receptors, thereby promotes oncogenic growth signals.

MIMO Over-The-Air Research, Development, and Testing

Abstract: Multiple-input multiple-output (MIMO) over-the-air (OTA) measurements and simulations for network and terminal performance evaluation and prediction have become very important research topics in recent years. Research into MIMO OTA for standardisation purposes has been ongoing in The Wireless Association (CTIA), the Third Generation Partnership Project (3GPP), and the European Cooperation in Science and Technology (COST) for three years. This is motivated by the urgent need to develop accurate, realistic, and cost-effective test standards for UMTS and LTE systems. Although many MIMO-capable networks are already deployed, there is pressure to finish the test standards by the end of 2012. While the first MIMO devices appeared some years ago and were commercially deployed two years ago, there are not yet any standards for testing MIMO performance OTA. The development of MIMO OTA test standards has proven to be particularly complex compared to single-input single-output (SISO) OTA, and developing a test standard is taking considerable time. Unlike SISO OTA, which was relatively straightforward and purely a function of the device, MIMO OTA is highly dependent on the interaction between the propagation characteristics of the radio channel and the receive antennas of the UE. Consequently, the existing SISO measurement techniques are unable to test the UE’s MIMO properties. Many different MIMO test methods have been proposed, which vary widely in their propagation channel characteristics, size, and cost. Many challenges remain in the areas of identifying the optimal channel models and test method(s), and it is possible that the outcome could be that more than one test methodology will be standardized. Current standards activities are concentrated on showing if the proposed test methodologies provide the same results, with the ultimate goal being to clearly differentiate good from bad MIMO devices. The aim of this special issue, guest edited by a balanced representation from across academia and industry is to provide a valuable source of information for the state of this important research area. Section 2 of this introductory paper provides an introduction to MIMO OTA standardization activities, and Section 3 describes the different test methodologies under consideration by 3GPP/CTIA. A comparison between test methodologies is made in Section 4. A summary of the papers accepted for publication in this special issue is presented in Section 5. These articles discuss important aspects of MIMO OTA testing and the latest advances of all test methodologies. The research represents the latest thinking of well-known experts in industry and academia and will undoubtedly influence future decisions on testing standardization. Some conclusions and future work are provided in Section 6.

Widely tunable midinfrared difference frequency generation in orientation-patterned GaAs pumped with a femtosecond Tm-fiber system

Abstract: We demonstrate a midinfrared source tunable from 6.7 to 12.7 μm via difference frequency generation (DFG) in orientation-patterned GaAs, with 1.3 mW average output power. The input pulses are generated via Raman self-frequency shift of a femtosecond Tm-doped-fiber laser system in a fluoride fiber. We numerically model the DFG process and show good agreement between simulations and experiments. We use this numerical model to show an improved design using longer pump pulses.