Tracing pathway activities with kinase inhibitors and reverse phase protein arrays

Controlling aberrant protein kinase activity is a promising strategy for a variety of diseases, particularly cancer. Hence, the development of kinase inhibitors is currently a focal point for pharmaceutical research. In this study we utilize a chip-based reverse phase protein array (RPA) platform for profiling of kinase inhibitors in cell-based assays. In combination with the planar wave-guide technology the assay system has an absolute LOD down to the low zeptomole range. A431 cell lysates were analyzed for the activation state of key effectors in the epidermal growth factor (EGF) and insulin signaling pathways to validate this model for compound screening. A microtiter-plate format for growing, treating, and lysing cells was shown to be suitable for this approach, establishing the value of the technology as a screening tool for characterization of large numbers of kinase inhibitors against a wide variety of cellular signaling pathways. Moreover, the reverse array format allows rapid development of site-specific phosphorylation assays, since in contrast to ELISA type systems only a single antigen-specific antibody is required.     

Altered signaling associated with chronic arsenic exposure in human skin keratinocytes

Modulation of signaling pathways upon chronic arsenic exposure remains poorly studied. Here, we carried out SILAC‐based quantitative phosphoproteomics analysis to dissect the signaling induced upon chronic arsenic exposure in human skin keratinocyte cell line, HaCaT. We identified 4171 unique phosphosites derived from 2000 proteins. We observed differential phosphorylation of 406 phosphosites (twofold) corresponding to 305 proteins. Several pathways involved in cytoskeleton maintenance and organization were found to be significantly enriched (p<0.05). Our data revealed altered phosphorylation of proteins associated with adherens junction remodeling and actin polymerization. Kinases such as protein kinase C iota type (PRKCI), mitogen‐activated protein kinase kinase kinase 1 (MAP3K1), tyrosine‐protein kinase BAZ1B (BAZ1B) and STE20 like kinase (SLK) were found to be hyperphosphorylated. Our study provides novel insights into signaling perturbations associated with chronic arsenic exposure in human skin keratinocytes. All MS/MS data have been deposited to the ProteomeXchange with identifier PXD004868.     

Quantification of Biomarker Proteins Using Reverse‐Phase Protein Arrays

It is expected that antibody‐based proteomics will soon occupy a pivotal position in the discovery and validation of biomarkers and therapeutic targets. The reverse‐phase protein array (RPPA) is an antibody‐based proteomic method that can quantify the expression of multiple posttranslationally modified proteins (such as those that have been phosphorylated) across a large number of protein samples. RPPA is highly sensitive and requires only very small protein samples. This feature, in combination with large antibody libraries, makes RPPA ideal for clinical proteomics, as well as the fact that it is an expandable multiplex assay. In Volume 14, Issue 1 of Proteomics Clinical Applications, Suzuki and colleagues report for the first time a study comparing RPPA and immunohistochemistry for quantification of seven biomarker proteins used for subtyping of diffuse large B‐cell lymphoma. Such combination of multiple biomarkers is likely to increase diagnostic accuracy and can be used for precise classification of this heterogeneous disease.     

Nanorod‐form ZnO‐homojunction ultraviolet light‐emitting diodes

Abstract— Ultraviolet (UV) light‐emitting diodes based on ZnO‐homojunction nanorods is reported. p‐type doping can be obtained from intrinsic (or close to) ZnO by introducing acceptors, such as P or As, using ion implantation followed by appropriate thermal annealing and dopant activation. Our approach provides a possible solution to p‐type doping of ZnO and ZnO‐homojunction light‐emitting diodes. It is interesting to note that this solution is offered in the form of nanorods.     

Double‐viewing‐zone integral imaging 3D display without crosstalk based on a tilted barrier array

We propose an integral imaging (II) three‐dimensional (3D) display using a tilted barrier array and a stagger microlens array. The tilted barrier array consists of two orthogonally polarized sheets. In the stagger microlens array, the center of the microlens has p/2 shift with the elemental image along the horizontal direction, where p is the pitch of the microlens. The proposed II 3D display produces two different viewing zones and each of them is almost equal to that of the conventional II 3D display, and it has no crosstalk. We verify the feasibility of the proposed II 3D display in the simulation results.     

Broadband planar dipole array Antenna with double C‐shaped slit elements for digital TV broadcasting transmission

This research has proposed a planar rectangular dipole antenna enclosed in double C‐shaped parasitically slit elements (i.e., radiator element) on a double‐cornered reflector for bandwidth enhancement. In the study, simulations were first carried out to determine the optimal parameters of the radiator element and then a radiator element prototype was fabricated and mounted onto a double‐cornered aluminum reflector. The simulated and measured |S₁₁|<–10 dB of the antenna element covered the frequency ranges of 451–901 MHz (66.6%) and 455–886 MHz (64.3%), respectively. The gain was enhanced by the subsequent deployment of multiple radiator elements to fabricate a four‐element vertically array antenna on an elongated double‐cornered reflector. The simulated and measured |S₁₁|20 and 相似文献   

Evaluation of human antibody responses to keyhole limpet hemocyanin on a carbohydrate microarray

Purpose : Keyhole limpet hemocyanin (KLH) is used as a vaccine adjuvant, as a carrier protein for small haptens, and as a treatment for bladder cancer. Immunization with KLH produces antibodies to tumor‐associated carbohydrate antigens (TACAs) in animals, and these antibodies have been postulated as the basis of efficacy for bladder cancer treatment. The purpose of this study was to evaluate antibody responses to KLH in humans. Experimental design : A carbohydrate microarray was used to profile antibody responses in 14 individuals immunized with KLH plus alum adjuvant. Results : Eight out of fourteen individuals produced antibodies to at least one TACA. Increases to Lewis X, Lewis Y, GA1di, GM3, and sialyl Lewis A were observed in certain individuals, but, in general, antibody profiles were highly variable. Pre‐immunization antibody levels to a subset of array antigens had a statistically significant correlation with the magnitude of the antibody response to KLH. Conclusions and clinical relevance : Antibodies to TACAs can be produced in humans, but antibody profiles differ considerably from person to person, which may contribute to variable clinical responses with KLH. Pre‐treatment antibody levels to certain antigens may be useful for predicting which patients will respond favorably to KLH.     

Broadband T‐bar fed slot antenna array with stable horizontally polarized omnidirectional radiation

A broadband horizontally polarized omnidirectional antenna array is proposed, which consists of a circular array of four identical broadband T‐bar fed cavity‐backed slot antenna elements and a 1‐to‐4 power divider. The proposed omnidirectional antenna array has a compact diameter of only 0.44λ₀, a broad bandwidth of 75.9% (450‐1000 MHz) and a favorable omnidirectional radiation pattern in the azimuth plane with a gain variation below 3 dB in the operating band. Moreover, the cavity‐backed structure makes the proposed antenna array hardly affected by metal environment and the all metal construction allows for high‐power applications, and the reserved cable channel behind the cavities of the antenna elements ensures the extensionality and stability of the proposed array when longitudinal array expansion is needed. Design procedures of the proposed antenna array have been described in detail, simulations and measurements of the proposed antenna array have also been carried out to validate its performance in this article.     

Proteomics integrated with Escherichia coli vector-based vaccines and antigen microarrays reveals the immunogenicity of a surface sialidase-like protein of Propionibacterium acnes

Proteomics is a powerful tool for the identification of proteins, which provides a basis for rational vaccine design. However, it is still a highly technical and time‐consuming task to examine a protein's immunogenicity utilizing traditional approaches. Here, we present a platform for effectively evaluating protein immunogenicity and antibody detection. A tetanus toxin C fragment (Tet‐c) was used as a representative antigen to establish this platform. A cell wall‐anchoring sialidase‐like protein (SLP) of Propionibacterium acnes was utilized to assess the efficacy of this platform. We constructed an Escherichia coli vector‐based vaccine by overexpressing Tet‐c or SLP in E. coli and utilized an intact particle of E. coli itself as a vaccine (E. coli Tet‐c or SLP vector). After ultraviolet (UV) irradiation, the E. coli vector‐based vaccines were administered intranasally into imprinting control region mice without adding exogenous adjuvants. For antibody detection, we fabricated antigen microarrays by printing with purified recombinant proteins including Tet‐c and SLP. Our results demonstrated that detectable antibodies were elicited in mice 6 weeks after intranasal administration of UV‐irradiated E. coli vector‐based vaccines. The antibody production of Tet‐c and SLP was significantly elevated after boosting. Notably, the platform with main benefits of using E. coli itself as a vaccine carrier provides a critical template for applied proteomics aimed at screening novel vaccine targets. In addition, the novel immunogenic SLP potentially serves as an antigen candidate for the development of vaccines targeting P. acnes‐associated diseases.     

MultiArray: a C++ library for generic programming with arrays

In C++, multi‐dimensional arrays are often used but the language provides limited native support for them. The language, in its Standard Library, supplies sophisticated interfaces for manipulating sequential data, but relies on its bare‐bones C heritage for arrays. The MultiArray library, a part of the Boost library collection, enhances a C++ programmer's tool set with versatile multi‐dimensional array abstractions. It includes a general array class template and native array adaptors that support idiomatic array operations and interoperate with C++ Standard Library containers and algorithms. The arrays share a common interface, expressed as a generic programming concept, in terms of which generic array algorithms can be implemented. We present the library design, introduce a generic interface for array programming, demonstrate how the arrays integrate with the C++ Standard Library, and discuss the essential aspects of their implementation. Copyright © 2004 John Wiley & Sons, Ltd.     

Two‐dimensional gel electrophoresis of apolipoprotein C‐III and other serum glycoproteins for the combined screening of human congenital disorders of O‐ and N‐glycosylation

Congenital disorders of glycosylation (CDG) are inherited diseases that can affect not only the N‐glycan (e.g. CDG type I and II) but also the O‐glycan biosynthesis pathway. In the absence of specific clinical symptoms, there is a need for a reliable biological screening of these two groups of CDG. Using a few microlitres of human serum, 2‐DE and immunoblotting were applied to the separation and simultaneous detection of the isoforms of the O‐glycosylated protein apolipoprotein C‐III (apoC‐III) and of four N‐glycosylated proteins, namely alpha‐antitrypsin, alpha‐1 acid glycoprotein, haptoglobin and transferrin. For the study of O‐glycosylation, this technique allowed the reliable separation of the three fractions of apoC‐III and the determination of normal percentage values in an adult population. Concerning N‐glycosylation, the study of serum samples from patients with CDG type Ia revealed marked abnormalities systematically affecting the four 2‐DE separated N‐linked glycoproteins. 2‐DE coupled to immunoblotting using a mixture of specific antibodies could be easily and reliably employed for the combined screening of both N‐ and O‐glycosylation disorders in humans.     

Wide‐angle scanning circular polarization phased array based on polarization rotation technology

A wide‐beam circular polarization (CP) antenna and a wide‐angle scanning phased array based on novel polarization rotation reflective surface (PRRS) are proposed. The CP wide‐beam pattern is obtained by the combination of the radiation wave from the patch antenna and the orthogonal reflected wave from the PRRS with a 90° phase difference. The proposed CP wide‐beam antenna obtains the patterns with the 3‐dB beamwidth more than 136° and the axial ratio (AR) beamwidth more than 132° in the xoz‐plane. Furthermore, an eight‐element phased array based on the wide‐beam CP antenna element is also developed. The measured results show that the main beam of the array can scan from ?65° to 65° with a gain fluctuation less than 3 dB and the ARs at every scanning angle less than 3 dB.     

Practically efficient array initialization

Initialization of an array, out of which only a small initially unknown portion will eventually be used, is a frequent need in programming. A folklore solution for initializing an array of n entries in constant time uses 2n?log2n? extra bits to realize a stack of back pointers to the actually used entries of the array. Navarro has given a succinct version of this technique, which requires only n + o(n) bits of auxiliary storage. We describe, analyze, and experimentally compare these solutions and their space‐efficient but theoretically suboptimal alternatives based on a simple bitmap for keeping track of the array entries which have been assigned a value. Experimental results suggest that each of the methods has its niche of excellence, which are roughly as follows: the theoretically optimal solutions based on a stack of back pointers perform in general best on sparse arrays, whose access frequency is less than 1% of the number of their entries. Brute‐force initialization of the entire array seems generally to give the best overall performance for dense arrays whose access frequency is over 10% of their size. For the remaining cases of arrays with 1–10% access frequency, the methods which use a simple bitmap appear to give the best performance. The experiments show that the choice of a suitable implementation may yield substantial, up to hundreds of times speed‐ups in the performance of initializable array operations. Copyright © 2015 John Wiley & Sons Ltd.     

Millimeter‐wave planar high gain SIW antenna using half elliptic radiation slots

This article reports a high gain millimeter‐wave substrate integrated waveguide (SIW) antenna using low cost printed circuit board technology. The half elliptic slots which can provide small shunt admittance, low cross polarization level and low mutual coupling are etched on the board surface of SIW as radiation slots for large array application. Design procedure for analyzing the characteristics of proposed radiation slot, the beam‐forming structure and the array antenna are presented. As examples, an 8 × 8 and a 32 × 32 SIW slot array antennas are designed and verified by experiments. Good agreements between simulation and measured results are achieved, which shows the 8 × 8 SIW slot array antenna has a gain of 20.8 dBi at 42.5 GHz, the maximum sidelobe level of 42.5 GHz E‐plane and H‐plane radiation patterns are 22.3 dB and 22.1 dB, respectively. The 32 × 32 SIW slot array antenna has a maximum measured gain of 30.05 dBi at 42.5 GHz. At 42.3 GHz, the measured antenna has a gain of 29.6 dBi and a maximum sidelobe level of 19.89 dB and 15.0 dB for the E‐plane and H‐plane radiation patterns. © 2015 Wiley Periodicals, Inc. Int J RF and Microwave CAE 25:709–718, 2015.     

Novel ultra‐compact two‐dimensional waveguide‐based metasurface for electromagnetic coupling reduction of microstrip antenna array

A novel ultracompact two‐dimensional (2D) waveguide‐based metasurface is proposed herein and applied for the first time to reduce mutual coupling in antenna array for multiple‐input multiple‐output applications. The unit cell of the proposed 2D waveguide‐based metasurface is ultracompact (8.6 mm × 4.8 mm, equal to λ₀/14.2 × λ₀/25.5) mainly due to the symmetrical spiral lines etched on the ground. The metasurface exhibits a bandgap with two transmission zeros attributing to the negative permeability in the vicinity of magnetic resonance and the negative permittivity in the vicinity of electric resonance. Taking advantage of these two features, a microstrip antenna array is then designed, fabricated, and measured by embedding an 8 × 1 array of the well‐engineered 2D waveguide‐based metasurface elements between two closely spaced (9.2 mm, equal to λ₀/13.3) H‐plane coupled rectangular patches. There is good agreement between the simulated and measured results, indicating that the metasurface effectively reduces antenna mutual coupling by more than 11.18 dB and improves forward gain. The proposed compact structure has one of the highest reported decoupling efficiencies among similar periodic structures with comparable dimensions. © 2015 Wiley Periodicals, Inc. Int J RF and Microwave CAE 25:789–794, 2015.     

Design,analysis, and modeling of miniaturized multi‐band patch arrays using mushroom‐type electromagnetic band gap structures

Novel designs of miniaturized multi‐band 1 × 2 patch antenna array with electromagnetic band gap (EBG) for wideband operation are presented in this article. The proposed patch array is composed of three unequal arms fed by CPW‐to‐slotline transitions to widen the impedance bandwidth with multiple resonances. By adding two conventional mushroom‐type EBG (CMT‐EBG) structures on both sides of 100 Ω slotline transitions, the compact wideband patch array (first design) is obtained. This proposed design with CMT‐EBG includes two bands with the measured ranges (S₁₁ ≤ ?10 dB) of 6.65‐6.95 GHz (C‐band) and 8.57‐11.53 GHz (X‐band). Moreover, the proposed 1 × 2 patch array with the 3 × 3 CMT‐EBG array on the one side of the structure (second design) operates at multi‐bands with the measured ?10 dB impedance bandwidths of 5.80‐5.98 GHz, 6.25‐6.47 GHz, and 8.48‐11.52 GHz. The second design compared to the first design introduces a considerable size reduction with more resonance tuning capability. The performance of the proposed designs is analyzed based on the EBG band gap properties near the slotline transitions. These designs with the EBGs indicate prominent features like resonance tuning capability, acceptable miniaturization, and enhanced impedance bandwidth with low‐fabrication cost. In this study, an equivalent circuit model of the proposed first design with EBG is also offered to describe the properties of multi‐band operation.     

Design of a subarray with special radiation pattern for low profile wide‐angle scanning phased array

A low profile subarray with a special radiation pattern for the wide‐angle H‐plane scanning phased array is presented. Five parallel dipoles located above a metal ground serve as the radiator. The differential evolution (DE) algorithm is used to obtain the weights for a special radiation pattern, which is realized by a corresponding feed network. The overall dimension of the proposed subarray is only 0.55λ₀ × 0.55λ₀ × 0.14λ₀. The prototype is fabricated and measured, and the measurement results are consistent with the simulation results. Because of the special radiation pattern and compact size, this subarray is suitable as an element in the wide‐angle scanning phased array. A uniform linear array consisting of five proposed subarrays is built in high frequency structural simulator, and the simulated results show that the main beam can scan nearly from ?70° to +70° in the H‐plane with a gain fluctuation less than 3 dB.     

Two dimensional gel electrophoresis of apolipoprotein C‐III and MALDI‐TOF MS are complementary techniques for the study of combined defects in N‐ and mucin type O‐glycan biosynthesis

In the field of diseases related to glycosylation disorders, congenital defects associated with abnormalities in both O‐ and N‐glycosylation of proteins constitute arising novel entities. Defects in subunits of the conserved oligomeric Golgi protein complex have been shown to be involved in an important part of previously unsolved CDG type II combining abnormalities in both mucin type core1 O‐ and N‐glycans; furthermore, recent studies revealed that autosomal recessive cutis laxa type II could also be associated with such combined glycosylation defects. Based on the studies of serum samples from three patients including a case of cutis laxa, we present here evidence that 2‐DE of apolipoprotein C‐III in combination with MALDI‐TOF‐MS analysis of serum O‐ and N‐glycans allow the detection and the biochemical characterization of these newly recognized glycosylation disorders.     

Ka‐band phased patch array antenna integrated with a PET‐controlled phase shifter

In this article, a 4 × 4 linear‐phased patch array antenna, consisting of four 1 × 4 patch subarrays and a true time‐delay multiline phase shifter, is proposed on a thin film liquid crystal polymer substrate at Ka‐band. The patch antenna is designed with a gain of 6 dBi at 35 GHz and a bandwidth of 23% centered at 35 GHz. To enhance the gain and symmetrize the beam patterns of the 4 × 4 array, a 1 × 4 patch subarray in the E‐plane was designed and characterized. The subarray produces an enhanced gain of 11 dBi and a wide beamwidth of ±38° in the H‐plane for beam steering. The proposed phase shifter comprises a 1 × 4 microstrip line power splitter and a piezoelectric transducer‐controlled phase perturber. A large phase variation of up to 370° and a low insertion loss of less than 2 dB were demonstrated for the phase shifter at Ka‐band. The integrated phased array attains a gain of 15.6 dBi, and a continuous true‐time delay beam steering of up to 33 ± 1° from 31 to 39 GHz. © 2015 Wiley Periodicals, Inc. Int J RF and Microwave CAE 26:199–208, 2016.     

Sampled suffix array with minimizers

Sampling (evenly) the suffixes from the suffix array is an old idea trading the pattern search time for reduced index space. A few years ago Claude et al. showed an alphabet sampling scheme allowing for more efficient pattern searches compared with the sparse suffix array, for long enough patterns. A drawback of their approach is the requirement that sought patterns need to contain at least one character from the chosen subalphabet. In this work, we propose an alternative suffix sampling approach with only a minimum pattern length as a requirement, which is more convenient in practice. Experiments show that our algorithm (in a few variants) achieves competitive time‐space tradeoffs on most standard benchmark data. Copyright © 2017 John Wiley & Sons, Ltd.