Complementary Array Research Articles

Metallic Membranes with Subwavelength Complementary Patterns: Distinct Substrates for Surface-Enhanced Raman Scattering

We present a detailed comparison of surface-enhanced Raman spectroscopy (SERS) signals from metallic nanoparticle arrays and their complementary hole arrays. Using an analytical model for local field enhancement, we show that the SERS enhancements of the hole arrays are closely related to their transmission spectra. This trend is experimentally confirmed and characterized by a cos(4 )θ dependence of the SERS signal on the excitation polarization angle θ. The particle arrays, on the other hand, exhibit quite different behavior because of the existence of considerable evanescent modes in the near field. Their maximal local field gains appear at wavelengths generally much larger than their localized surface plasmonic resonant wavelengths.

Overexpression of Glycogen Synthase Kinase-3 in Ovarian Carcinoma Cells With Acquired Paclitaxel Resistance

Acquired resistance to paclitaxel, including regimens, is one of the most significant reasons for treatment failure and death in patients with ovarian cancer, but the causes of this resistance remain unclear. However, cell cycle regulation is a key mechanism by which most chemotherapeutic agents exert their cytotoxic effects. We created a paclitaxel-resistant ovarian carcinoma cell line from SKOV3 cell line, and the difference of cell cycle distribution was analyzed using flow cytometry. Analysis of human cell cycle pathway complementary DNA array was performed to identify candidate genes associated with paclitaxel resistance. Gene expression changes were validated at the messenger RNA and protein levels by real-time reverse transcriptase polymerase chain reaction and Western analysis, respectively. The ratio of Gap0/Gap1 phase in SKOV3-TR30 was significantly lower than that in SKOV3 (54.8% ± 6.3% vs 72.7% ± 7.6%, P = 0.035), and the ratio of G2/M phase in SKOV3-TR30 was significantly higher than that in SKOV3 (24.9% ± 6.0% vs 10.2% ± 3.5%, P = 0.021). Complementary DNA microarray analysis demonstrated enhanced glycogen synthase kinase-3α (GSK-3α) expression in paclitaxel-resistant ovarian carcinoma cells. Real-time reverse transcriptase polymerase chain reaction analysis revealed that the paclitaxel-resistant subline exhibited a 7.0 ± 1.8-fold increase in GSK-3α messenger RNA expression. There was a 3.34 ± 0.47-fold increase of total GSK-3 protein (GSK-3α/β) in SKOV3-TR30 cells validated by Western analysis. This study demonstrates that enhanced expression of GSK-3 is associated with acquired resistance to paclitaxel in ovarian carcinoma cells. Glycogen synthase kinase-3 overexpression may probably be a significant contributor to chemoresistance.

Hydrogen Bonding Patterns in Trimethoprimium Cinnamate 1.52 Hydrate

In the title compound, [C14H19N4O3 +, C9H5 O2 −, H2O, O0.52] the asymmetric unit contains a protonated trimethoprim cation and a cinnamate anion and two water molecules. The crystal structure was determined by single crystal X-ray diffraction. This compound crystallized in the triclinic system; space group P−1 with the unit cell parameters a = 10.010(2) A, b = 10.339(3) A, c = 13.486(8) A, α = 105.32(3)°, β = 109.88(3)°, γ = 100.89(3)°, V = 1204.6(10) A3, Z = 2. The cinnamate group is disordered. The trimethoprim (TMP) molecule is protonated at one of the pyrimidine nitrogen atoms. The carboxylate group of the cinnamate anion interacts with the protonated pyrimidine atom N1 and the 2-amino group via a pair of N–H···O hydrogen bonds, generating the R 2 2 (8) ring motif. The inversion related TMP cations are paired via N–H···N hydrogen bonds. In addition to the base pairing, the O1W atom bridges the 2-amino and 4-amino groups on either side of the paired bases, resulting in a self complementary DADA array. Two inversion related TMP cations and water molecules (O1W) are linked via N–H···O and O–H···O hydrogen bonds, forming a 22 membered ring with graph-set R 4 4 (22). The protonated trimethoprim cation interacts with the cinnamate anion through a pair of N-H…O hydrogen bonds, generating the R 2 2 (8) ring motif. .

ERRATUM: “DETECTION OF DIFFUSE NEUTRAL INTRAGROUP MEDIUM IN HICKSON COMPACT GROUPS” (2010, ApJ, 710, 385)

We present new Green Bank Telescope (GBT) 21 cm neutral hydrogen (HI) observations of a complete distance limited sample of 22 Hickson Compact Groups (HCGs) with at least four true members. We detected an average HI mass of $8 \times 10^{9} M_{\odot}$ (median= $6\times 10^{9} M_{\odot}$), which is significantly larger than previous single-dish measurements. Consequently, the HI-deficiencies for these HCGs have been reduced, although not completely eliminated. Spectral comparison of the GBT data with complementary Very Large Array (VLA) data shows significant HI excess in the GBT spectra. The observed excess is primarily due to the high surface brightness sensitivity of the GBT detecting diffuse, low column density HI in these groups. The excess gas forms a faint diffused neutral medium which is an intermediate stage in the evolution of high-surface brightness HI tidal debris in the intra-group medium (IGM) before it is fully ionized. The excess gas mass fraction (ratio of excess HI to total HI) for our complete sample varies from 5% to 81% with an average of 36% (median=30%). The excess gas mass fraction is highest in slightly HI deficient groups where the tidal debris has had enough time to evolve. We also find the excess gas content increases with the evolutionary phase of the group described in Verdes-Montenegro et al. 2001. Theoretical calculations indicate that an HI cloud of radius >200 pc would survive in an IGM of 2 million Kelvin for more than the typical dynamical lifetime of a group. However, smaller clouds get evaporated and assimilated into the hot IGM in a much shorter timescale.

MEMS microwell and microcolumn arrays: novel methods for high-throughput cell-based assays

Although the cell-based assay is becoming more popular for high throughput drug screening and the functional characterization of disease-associated genes, most researchers in these areas do not use it because it is a complex and expensive process. We wanted to create a simple method of performing an on-chip cell-based assay. To do this, we used micro-electro-mechanical systems (MEMS) to fabricate a microwell array chip comprised of a glass substrate covered with a photoresist film patterned to form multiple microwells and tested it in two reverse transfection experiments, an exogenous gene expression study and an endogenous gene knockdown study. It was used effectively in both. Then, using the same MEMS technology, we fabricated a complementary microcolumn array to be used as a drug carrier device to topically apply drugs to cells cultured in the microwell array. We tested the effectiveness of microwell-microcolumn on-chip cell-based assay by using it in experiments to identify epidermal growth factor receptor (EGFR) activity inhibitors, for which it was found to provide effective high throughput and high content functional screening. In conclusion, this new method of cell-based screening proved to be a simple and efficient method of characterizing gene function and discovering drug leads.

Nanoreplicated positive and inverted submicrometer polymer pyramid array for surface-enhanced Raman spectroscopy

We demonstrated gold-coated polymer surface enhanced Raman scattering (SERS) substrates with a pair of complementary structures-positive and inverted pyramid array structures fabricated by a multiple-step molding and replication process. The uniform SERS enhancement factors over the entire device surface were measured as 7.2×104 for positive pyramid substrates while 1.6×106 for inverted pyramid substrates with Rhodamine 6G as the target analyte. Based on the optical reflection measurement and finite difference time domain simulation result, the enhancement factor difference is attributable to plasmon resonance matching and to SERS "hot spots" distribution. With this simple, fast, and versatile complementary molding process, we can produce polymer SERS substrates with extremely low cost, high throughput, and high repeatability.

Use of Orthogonal Arrays for Efficient Evaluation of Geometric Designs for Reducing Vibration of a Non-Pneumatic Wheel during High-Speed Rolling

Abstract During high speed rolling of a nonpneumatic wheel, vibration may be produced by the interaction of collapsible spokes with a shear deformable ring as they enter the contact region, buckle, and then snap back into a state of tension. In the present work, a systematic study of the effects of six key geometric design parameters is presented using Orthogonal Arrays. Orthogonal Arrays are part of a design process method developed by Taguchi which provides an efficient way to determine optimal combinations of design variables. In the present work, a two-dimensional planar finite element model with geometric nonlinearity and explicit time-stepping is used to simulate rolling of the nonpneumatic wheel. Vibration characteristics are measured from the FFT frequency spectrum of the time signals of perpendicular distance of marker nodes from the virtual plane of the spoke, and ground reaction forces. Both maximum peak amplitudes and RMS measures are considered. Two complementary Orthogonal Arrays are evaluated. The first is the L8 orthogonal array which considers the six geometric design variables evaluated at lower and higher limiting values for a total of eight experiments defined by statistically efficient variable combinations. Based on the results from the L8 orthogonal array, a second L9 orthogonal array experiment evaluates the nonlinear effects in the four parameters of greatest interest, (a) spoke length, (b) spoke curvature, (c) spoke thickness, and (d) shear beam thickness. The L9 array consists of nine experiments with efficient combinations of low, intermediate, and high value levels. Results from use of the Orthogonal Array experiments were used to find combinations of parameters which significantly reduce peak and RMS amplitudes, and suggest that spoke length has the greatest effect on vibration amplitudes.

Compact Voltage and Current Stimulation Buffer for High-Density Microelectrode Arrays

We report on a compact (0.02 mm(2) ) buffer for both voltage and current stimulation of electrogenic cells on a complementary metal-oxide semiconductor microelectrode array. In voltage mode, the circuit is a high-current class-AB voltage follower, based on a local common-mode feedback (LCMFB) amplifier. In current mode, the circuit is a current conveyor of type II, using the same LCMFB amplifier with cascode stages to increase the gain. The circuit shows good linearity in the 0.5-3.5 V input range and has extensively been used for stimulation of neuronal cultures.

Gene-expression profiles of epithelial cells treated with EMD in vitro: analysis using complementary DNA arrays

During surgical periodontal treatment, EMD is topically applied in order to facilitate regeneration of the periodontal ligament, acellular cementum and alveolar bone. Suppresion of epithelial down-growth is essential for successful periodontal regeneration; however, the underlying mechanisms of how EMD influences epithelial wound healing are poorly understood. In the present study, the effects of EMD on gene-expression profiling in an epithelial cell line (HSC-2) model were investigated. Gene-expression modifications, determined using a comparative genome-wide expression-profiling strategy, were independently validated by quantitative real-time RT-PCR. Additionally, cell cycle, cell growth and in vitro wound-healing assays were conducted. A set of 43 EMD-regulated genes was defined, which may be responsible for the reduced epithelial down-growth upon EMD application. Gene ontology analysis revealed genes that could be attributed to pathways of locomotion, developmental processes and associated processes such as regulation of cell size and cell growth. Additionally, eight regulated genes have previously been reported to take part in the process of epithelial-to-mesenchymal transition. Several independent experimental assays revealed significant inhibition of cell migration, growth and cell cycle by EMD. The set of EMD-regulated genes identified in this study offers the opportunity to clarify mechanisms underlying the effects of EMD on epithelial cells. Reduced epithelial repopulation of the dental root upon periodontal surgery may be the consequence of reduced migration and cell growth, as well as epithelial-to-mesenchymal transition.

Negative refraction in three-dimensional point-dipolelike polaritonic crystals

We propose two practical realizations of the point-dipole crystal, shown previously to be capable of negative refraction and other metamaterial and plasmonic properties. These are: an array of highly polarizable spheres, and the complementary array of spherical cavities in a highly polarizable medium. We study light propagation through these polaritonic crystals and show that they are capable of negative refraction, and can be constructed from available materials for experimental demonstrations at both microwave and optical frequencies.

Bis-(2-amino-5-methyl-pyridinium) fumarate-fumaric acid (1/1).

In the crystal structure of the title compound, C6H9N2 +·0.5C4H2O4 2−·0.5C4H6O4, the fumarate dianion and fumaric acid mol­ecule are located on inversion centres. The 2-amino-5-methyl­pyrimidinium cation inter­acts with the carboxyl­ate group of the fumarate anion through a pair of N—H⋯O hydrogen bonds, forming an R 2 2(8) ring motif. These motifs are centrosymmetrically paired via N—H⋯O hydrogen bonds, forming a complementary DDAA array. The carboxyl groups of the fumaric acid mol­ecules and the carboxyl­ate groups of the fumarate anions are hydrogen bonded through O—H⋯O hydrogen bonds, leading to a supra­molecular chain along [101]. The crystal structure is further stabilized by weak C—H⋯O hydrogen bonds.

CMOS arrays as chemiluminescence detectors on microfluidic devices

A simple, low-cost process to integrate complementary metal oxide semiconductor array detectors (CMOSAD) for chemiluminescence is presented, evaluated, and applied to the determination of nitrite in ground water samples. CMOS arrays of different brands (obtained from commercial image sensors) were adapted as chemiluminescence detectors on microfluidic devices. The performance of the CMOSADs was evaluated in the visible zone of the spectrum using a tungsten halogen lamp as light source. Intrinsic parameters assessed included signal stability, spectral response, dark current, and signal-to-noise ratio. Thereafter, the CMOSADs were integrated on microfluidic devices and their performances in quantitative analysis were assessed with the chemiluminometric reaction of hydrogen peroxide with luminol, catalyzed with hexacyanoferrate (III). The parameters assessed were sensitivity, linear range, detection limit, reproducibility, correlation coefficient of the calibration curves, and baseline drift during measurements. The CMOSAD with the best performance was selected to assess the applicability of the developed microfluidic devices with the integrated detector. The microfluidic system permitted the determination of nitrite with both good precision and good recovery values in the analysis of ground water samples. Integration was easily achieved and enabled the development of a simple, low-cost, and feasible alternative to conventional detectors.

DETECTION OF DIFFUSE NEUTRAL INTRAGROUP MEDIUM IN HICKSON COMPACT GROUPS

We present new Green Bank Telescope (GBT) 21 cm neutral hydrogen (HI) observations of a complete distance limited sample of 22 Hickson Compact Groups (HCGs) with at least four true members. We detected an average HI mass of $8 \times 10^{9} M_{\odot}$ (median= $6\times 10^{9} M_{\odot}$), which is significantly larger than previous single-dish measurements. Consequently, the HI-deficiencies for these HCGs have been reduced, although not completely eliminated. Spectral comparison of the GBT data with complementary Very Large Array (VLA) data shows significant HI excess in the GBT spectra. The observed excess is primarily due to the high surface brightness sensitivity of the GBT detecting diffuse, low column density HI in these groups. The excess gas forms a faint diffused neutral medium which is an intermediate stage in the evolution of high-surface brightness HI tidal debris in the intra-group medium (IGM) before it is fully ionized. The excess gas mass fraction (ratio of excess HI to total HI) for our complete sample varies from 5% to 81% with an average of 36% (median=30%). The excess gas mass fraction is highest in slightly HI deficient groups where the tidal debris has had enough time to evolve. We also find the excess gas content increases with the evolutionary phase of the group described in Verdes-Montenegro et al. 2001. Theoretical calculations indicate that an HI cloud of radius >200 pc would survive in an IGM of 2 million Kelvin for more than the typical dynamical lifetime of a group. However, smaller clouds get evaporated and assimilated into the hot IGM in a much shorter timescale.

Practical prevention of cardiac remodeling and atrial fibrillation with full-spectrum antioxidant therapy and ancillary strategies

A wealth of research data points to increased oxidative stress as a key driver of the cardiac remodeling triggered by chronic pressure overload, loss of functional myocardial tissue, or atrial fibrillation. Oxidative stress is a mediator of the cardiomyocyte hypertrophy and apoptosis, the cardiac fibrosis, and the deficits in cardiac function which typify this syndrome, and may play a role in initiating and sustaining atrial fibrillation. Nox2- and Nox4-dependent NADPH oxidase activity appears to be a major source of this oxidative stress, and oxidants can induce conformational changes in xanthine dehydrogenase, nitric oxide synthase, and the mitochondrial respiratory chain which increase their capacity to generate superoxide as well. Consistent with these insights, various synthetic antioxidants have been shown to suppress cardiac remodeling in rodents subjected to myocardial infarction, aortic constriction, or rapid atrial pacing. It may prove feasible to achieve comparable benefits in humans through use of a "full-spectrum antioxidant therapy" (FSAT) that features a complementary array of natural antioxidants. Spirulina is a rich source of phycocyanobilin, a derivative and homolog of biliverdin that appears to mimic the potent inhibitory impact of biliverdin and free bilirubin on NADPH oxidase activity. Mega-doses of folate can markedly increase intracellular levels of tetrahydrofolates which have potent and versatile radical-scavenging activities - including efficient quenching of peroxynitrite-derived radicals Supplemental coenzyme Q10, already shown to improve heart function in clinical congestive failure, can provide important antioxidant protection to mitochondria. Phase 2 inducer nutraceuticals such as lipoic acid, administered in conjunction with N-acetylcysteine, have the potential to blunt the impact of oxidative stress by boosting myocardial levels of glutathione. While taurine can function as an antioxidant for myeloperoxidase-derived radicals, its positive inotropic effect on the failing heart seems more likely to reflect an effect on intracellular calcium dynamics. These measures could aid control of cardiac modeling less directly by lowering elevated blood pressure, or by aiding the perfusion of ischemic cardiac regions through an improvement in coronary endothelial function. Since nitric oxide functions physiologically to oppose cardiomyocyte hypertrophy and cardiac fibrosis, and is also a key regulator of blood pressure and endothelial function, cocoa flavanols - which provoke endothelial release of nitric oxide - might usefully complement the antioxidant measures recommended here.

Genome-wide expression profiling reveals new candidate genes associated with osteoarthritis

Although the extracellular matrix (ECM) is the functional element in articular cartilage and its degradation is central in the pathogenetic process in osteoarthritis (OA), increasing the knowledge about the cellular OA phenotype is essential. The aim of this study is therefore to provide a more complete picture of the cellular and molecular alterations detected in OA cartilage. Human articular cartilage biopsies were collected from donors with macroscopical and microscopical signs of OA as well as donors with no previous history of OA and with microscopically intact cartilage. RNA was isolated from the biopsies and subjected to whole genome microarray analysis. Important results from the microarray analysis were verified using real-time PCR and immunohistochemistry. Our results reveal several new candidate genes not previously associated with OA to display significantly higher expression in OA cartilage than in normal donor cartilage, including genes involved in bone formation (CLEC3B, CDH11, GPNMB, CLEC3A, CHST11, MSX1, MSX2) and genes encoding collagens (COL13A1, COL14A1, COL15A1, COL8A2). This study is the first to report a comprehensive gene expression analysis of human OA cartilage compared to control cartilage from donors lacking macroscopical and microscopical signs of OA using recently developed microarrays containing the whole human genome. Our results could broadly confirm previously published data on many characteristic features of OA as well as adding a panel of genes to the list of genes known to be differentially expressed in OA. Elucidation of the phenotypical alterations occurring in OA chondrocytes is important for the development of effective treatments for OA.

Construction of Multi-Dimensional Periodic Complementary Array Sets

Multi-dimensional (MD) periodic complementary array sets (CASs) with impulse-like MD periodic autocorrelation function are naturally generalized to (one dimensional) periodic complementary sequence sets, and such array sets are widely applied to communication, radar, sonar, coded aperture imaging, and so forth. In this letter, based on multi-dimensional perfect arrays (MD PAs), a method for constructing MD periodic CASs is presented, which is carried out by sampling MD PAs. It is particularly worth mentioning that the numbers and sizes of sub-arrays in the proposed MD periodic CASs can be freely changed within the range of possibilities. In particular, for arbitrarily given positive integers M and L, two-dimensional periodic polyphase CASs with the number M2 and size L × L of sub-arrays can be produced by the proposed method. And analogously, pseudo-random MD periodic CASs can be given when pseudo-random MD arrays are sampled. Finally, the proposed method's validity is made sure by a given example.

The Nature of the Extraordinary Finish of Stradivari’s Instruments

What is Stradivari's “secret”? The composition of the mythical varnish that coats Stradivari's violins has raised controversial assumptions for the past two centuries. By using a complementary array of analytical tools, the chemical microstratigraphy of these varnishes has been established. The results provide information on the materials and techniques that were used by the Master, with a detailed characterization of the varnish.

Inhibitor of DNA binding/differentiation 2 induced by hypoxia promotes synovial fibroblast–dependent osteoclastogenesis

To map hypoxic areas in arthritic synovium and to establish the relevance of low oxygen levels to the phenotype of synovial fibroblasts, with special focus on bone degradation. To analyze the distribution of hypoxia in arthritic joints, the hypoxia marker EF5 was administered to mice with collagen-induced arthritis (CIA). To evaluate the effect of hypoxia on rheumatoid arthritis synovial fibroblasts (RASFs), reverse suppression subtractive hybridization and complementary DNA array were used. Real-time polymerase chain reaction, Western blotting, and immunohistochemistry were used to evaluate the expression of inhibitor of DNA binding/differentiation 2 (ID-2). To investigate the function of ID-2 in RASFs, cells were transfected either with ID-2 vector or with ID-2-specific small interfering RNA. EF5 staining showed the presence of hypoxia in arthritic joints, particularly at sites of synovial invasion into bone. Differential expression analysis revealed that ID-2 was strongly induced by hypoxia in RASFs. Immunohistochemical analysis of CIA mouse synovium and human RA synovium showed a strong expression of ID-2 by RASFs at sites of synovial invasion into bone. Overexpression of ID-2 in RASFs significantly induced the expression of several factors promoting osteoclastogenesis. The biologic relevance of the potent osteoclastogenesis-promoting effects was shown by coculture assays of ID-2-overexpressing RASFs with bone marrow cells, leading to an increased differentiation of osteoclasts from bone marrow precursors. The data show that hypoxic conditions are present at sites of inflammation and synovial invasion into bone in arthritic synovium. Hypoxia-induced ID-2 may contribute to joint destruction in RA patients by promoting synovial fibroblast-dependent osteoclastogenesis.

DNA hypomethylation in rheumatoid arthritis synovial fibroblasts

Rheumatoid arthritis synovial fibroblasts (RASFs) are phenotypically activated and aggressive. We undertook this study to investigate whether the intrinsic activation of RASFs is due to global genomic hypomethylation, an epigenetic modification. Global genomic hypomethylation was assessed by immunohistochemistry, flow cytometry, and L1 promoter bisulfite sequencing. The levels of Dnmt1 were determined in synovial tissue and cultured SFs by Western blotting before and after treatment with cytokines and growth factors. Normal SFs were treated for 3 months with a nontoxic dose of the DNA hypomethylation drug 5-azacytidine (5-azaC), and changes in gene expression were revealed using complementary DNA arrays. The phenotypic changes were confirmed by flow cytometry. In situ and in vitro, RASF DNA had fewer 5-methylcytosine and methylated CG sites upstream of an L1 open-reading frame than did DNA of osteoarthritis SFs, and proliferating RASFs were deficient in Dnmt1. Using 5-azaC, we reproduced the activated phenotype of RASFs in normal SFs. One hundred eighty-six genes were up-regulated>2-fold by hypomethylation, with enhanced protein expression. These included growth factors and receptors, extracellular matrix proteins, adhesion molecules, and matrix-degrading enzymes. The hypomethylating milieu induced irreversible phenotypic changes in normal SFs, which resembled those of the activated phenotype of RASFs. DNA hypomethylation contributes to the chronicity of RA and could be responsible for the limitation of current therapies.

Annotating non-coding transcription using functional genomics strategies

Non-coding RNA (ncRNA) transcripts are RNA molecules that do not code for proteins, but elicit function by other mechanisms. The vast majority of RNA produced in a cell is non-coding ribosomal RNA, produced from relatively few loci, however more recently complementary DNA (cDNA) cloning, tag sequencing, and genome tiling array studies suggest that ncRNAs also account for the majority of RNA species produced by a cell. ncRNA based regulation has been referred to as a 'hidden layer' of signals or 'dark matter' that control gene expression in cellular processes by poorly described mechanisms. These terms have appeared as ncRNAs until recently have been ignored by expression profiling and cDNA annotation projects and their mode of action is diverse (e.g. influencing chromatin structure and epigenetics, translational silencing, transcriptional silencing). Here, we highlight recent functional genomics strategies toward identifying and assigning function to ncRNA transcription.