Efficient capacitance computation for structures with non-uniform adaptive surface meshes

We have studied the spatial distribution of IS1 elements in the genomes of natural isolates comprising the ECOR reference collection of Escherichia coli. We find evidence for nonrandomness at three levels. Many pairs of IS1 elements are in much closer proximity (< 10 kb) than can be accounted for by chance. IS1 elements in close proximity were identified by long-range PCR amplification of the genomic sequence between them. Each amplified region was sequenced and its map location determined by database screening of DNA hybridization. Among the ECOR strains with at least two IS1 elements, 54% had one or more pairs of elements separated by < 10 kb. We propose that this type of clustering is a result of "local hopping," in which we assume that a significant proportion of tranposition events leads to the insertion of a daughter IS element in the vicinity of the parental element. A second level of nonrandomness is found in strains with a modest number of IS1 elements that are mapped through the use of inverse PCR to amplify flanking genomic sequences: in these strains, the insertion sites tend to be clustered over a smaller region of chromosome than would be expected by chance. A third level of nonrandomness is observed in the composite distribution of IS elements across strains: among 20 mapped IS1 elements, none were found in the region of 48-77 minutes, a significant gap. One region of the E. coli chromosome, at 98 min, had a cluster of IS1 elements in seven ECOR strains of diverse phylogenetic origin. We deduce from sequence analysis that this pattern of distribution is a result of initial insertion in the most recent common ancestor of these strains and therefore not a hot spot of insertion. Analysis using long-range PCR with primers for IS2 and IS3 also yielded pairs of elements in close proximity, suggesting that these elements may also occasionally transpose by local hopping.

The perturbation of a turbulent boundary layer by two cylindrical roughness elements in close proximity was experimentally investigated in a water channel using planar particle image velocimetry. The two cylinders were arranged in tandem with center-to-center streamwise spacings of 2d, 4d, and 6d, where d is the diameter of the cylinders. The downstream cylinder had a fixed height 0.2δ, where δ is the incoming boundary layer thickness; the height of the upstream cylinder was varied to achieve upstream to downstream cylinder height ratios of 1, 0.75, and 0.5. The flow measurements were made at Reδ = 56 800 and included measurements over an isolated cylinder as a baseline case. The results highlight the effects of sheltering by an upstream cylinder on the wake of the downstream cylinder. Flow features in the wake, including the downwash, upwash, recirculation zone, velocity deficit, Reynolds shear stress, and turbulent kinetic energy (TKE), are dependent on the degree of sheltering, which is reliant on both the streamwise spacing and height ratio. Overall, sheltering results in a reduction in the downwash and size of the recirculation zone past the downstream cylinder. The magnitude and spatial distribution of the Reynolds shear stress and TKE varied significantly from those past the isolated cylinder. Depending on the streamwise spacing and height ratio, the presence of an upstream cylinder has the potential to enhance or reduce the Reynolds shear stress past the downstream cylinder. For example, the maximum Reynolds shear stress in the near wake was approximately doubled for a spacing of 2d and a height ratio of 0.5 and nearly halved for a spacing of 2d and a height ratio of 1 (relative to that past the isolated cylinder). The variations in these flow features across the 9 considered arrangements suggest changes to the wake and its vortical structures due to the presence of an upstream cylinder. The results highlight the potential of flow control through a pair of roughness elements in close proximity to achieve desired outcomes such as reduced or redistributed Reynolds shear stress and TKE, relative to the isolated cylinder.

: This paper summarizes recent MITRE efforts to validate the NEC-3, NEC-GS, and NEC-3I versions of the Numerical Electromagnetics Code (NEC) developed by Lawrence Livermore National Laboratory for predicting the performance of antenna wire elements in close proximity to flat earth. In an early version (NEC-1), the effect of the air-ground interface was included by applying a plane-wave Fresnel reflection coefficient approximation to the field of a point source. The NEC-2 version, while still retaining the Fresnel reflection coefficient model as an option, provides a more accurate ground model by numerically evaluating Sommerfeld integrals. The version NEC-3 extends the NEC-2 version to cases for bare wire segments below the air-earth interface. Version NEC-GS utilizes rotational symmetry to provide a more efficient version of NEC-3 for the case of a monopole element with a uniform radial wire groundscreen (GS). Version NEC-3I extends NEC-3 to include the case of insulated (I) wires.

A binding site model for the opioid family of G-protein coupled receptors (GPCRs) is proposed based on the message-address concept of ligand recognition. Using ligand docking studies of the universal opioid antagonist, naltrexone, the structural basis for "message' recognition is explored across all three receptor types, mu, delta, and kappa. The binding mode proposed and basis for selectivity are also rationalized using the naltrexone-derived ligands, naltrindole (NTI) and norbinaltorphimine (nor BNI). These ligands are docked to the receptor according to the common naltrexone core or message. The resulting orientation places key "address' elements in close proximity to amino acid residues critical to selectivity among receptors types. Selectivity is explained by sequence differences in the mu, delta, and kappa receptors at these recognition points. Support for the model is derived from site directed mutagenesis studies and ligand binding data for the opioid receptors and other related GPCRs.

Network Functions Virtualization (NFV) has enabled operators to dynamically place and allocate resources for network services to match workload requirements. However, unbounded end-to-end (e2e) latency of Service Function Chains (SFCs) resulting from distributed Virtualized Network Function (VNF) deployments can severely degrade performance. In particular, SFC instantiations with inter-data center links can incur high e2e latencies and Service Level Agreement (SLA) violations. These latencies can trigger timeouts and protocol errors with latency-sensitive operations.Traditional solutions to reduce e2e latency involve physical deployment of service elements in close proximity. These solutions are, however, no longer viable in the NFV era. In this paper, we present our solution that bounds the e2e latency in SFCs and inter-VNF control message exchanges by creating micro-service aggregates based on the affinity between VNFs. Our system, Contain-ed, dynamically creates and manages affinity aggregates using light-weight virtualization technologies like containers, allowing them to be placed in close proximity and hence bounding the e2e latency. We have applied Contain-ed to the Clearwater IP Multimedia System and built a proof-of-concept. Our results demonstrate that, by utilizing application and protocol specific knowledge, affinity aggregates can effectively bound SFC delays and significantly reduce protocol errors and service disruptions.

Network Functions Virtualization (NFV) has enabled operators to dynamically place and allocate resources for network services to match workload requirements. However, unbounded end-to-end (e2e) latency of Service Function Chains (SFCs) resulting from distributed Virtualized Network Function (VNF) deployments can severely degrade performance. In particular, SFC instantiations with inter-data center links can incur high e2e latencies and Service Level Agreement (SLA) violations. These latencies can trigger timeouts and protocol errors with latency-sensitive operations. Traditional solutions to reduce e2e latency involve physical deployment of service elements in close proximity. These solutions are, however, no longer viable in the NFV era. In this paper, we present our solution that bounds the e2e latency in SFCs and inter-VNF control message exchanges by creating micro-service aggregates based on the affinity between VNFs. Our system, Contain-ed, dynamically creates and manages affinity aggregates using light-weight virtualization technologies like containers, allowing them to be placed in close proximity and hence bounding the e2e latency. We have applied Contain-ed to the Clearwater IP Multimedia Subsystem and built a proof-of-concept. Our results demonstrate that, by utilizing application and protocol specific knowledge, affinity aggregates can effectively bound SFC delays and significantly reduce protocol errors and service disruptions.

Sensitivity for structure gradient in texture discrimination tasks

Vibration-insensitive fiber optic electric field sensor is created by fabricating two sensing elements in close proximity onto the same optical fiber and subtracting the two signals. The device is used to measure an electric field of 10 kV/m, while the sensor is being bent and impacted.

SummaryThe development of advanced numerical techniques such as eXtended/Generalized Finite Elements Methods (XFEM/GFEM) has provided means for accurate prediction of material failure. However, the present theories mostly rely on a global formulation, where the system of equations is subject to progressive dimension increase with crack evolution. In this regard, an independent multilayered enrichment is proposed for the XFEM/GFEM family of methods where a few elements in close proximity are assigned to an enrichment layer independent of the remaining ones. The enhanced degrees of freedom can be condensed out at the layer level, which leads to system dimensions, sparsity, and bandness identical to those of the underlying finite elements. Nodal and elemental enrichment methods are shown to be particular limit cases of present approach. The robustness of the proposed approach is first demonstrated in element‐level examples. The use of only few adjacent elements in a group enrichment is shown to suffice for acceptable results while the order of the condition number of the final stiffness matrix resembles the underlying uncracked finite element counterpart. Finally, using several structural examples, the accuracy and robustness of the method is shown in terms of force–displacement response, stress fields, and traction continuity in nonlinear problems.

To elucidate the mechanisms underlying the tissue-restricted expression of GATA factor transcription, we have isolated and analyzed the genomic chicken GATA-3 (cGATA-3) locus. Structural analysis of the clones showed that the cGATA-3 gene consists of six exons which span more than 19 kb. Two trans-activating domains and two Zn finger domains of cGATA-3 were found to be encoded separately by exons 2/3 and 4/5, respectively, indicating that each functional domain of GATA-3 is encoded by a discrete exon. We have determined 1.7 kb of upstream promoter sequence and found a number of sequence motifs which match those of known transcription factor binding sites. Activities of presumptive regulatory regions of this gene were assessed by transfecting chimeric constructs into a chicken T cell line MSB-1. The results showed three features of cGATA-3 gene regulation. The basal promoter activity of the cGATA-3 gene is determined by sequences lying between -104 and -29 bp of the promoter region. The upstream region containing the GATA and CACCC elements in close proximity (-1280 to -1152) appeared to act as a negative transcriptional regulator, whereas the region -1151 to -850 acts as a positive regulator. Thus, the expression of cGATA-3 gene is under complex regulation and the mode of regulation of cGATA-3 gene expression is suggested to be different from that of GATA-1 genes.

Cells are physiologically ready to accumulate lipids such as triacylglycerides in the cytoplasm. Five classes of perilipin (PLIN) family proteins are known to be involved in the process of intracellular lipid accumulation. PLIN2 is expressed ubiquitously including adipocytes, hepatocytes and macrophages. Over-expression of PLIN2 is demonstrated in the lesions of fatty liver diseases and atherosclerosis. Suppression of PLIN2 expression prevents from developing these pathological conditions in animal models, suggesting that PLIN2 could be a therapeutic target molecule for excessive intracellular lipid accumulation which leads to various metabolic derangements. The PLIN2 gene promoter has two important cis-acting elements in close proximity:AP-1 element which mediates inflammatory signals and PPRE which mediates free fatty acid effect. In NMuLi mouse liver cells, FFA such as oleic acid requires both functional AP-1 and PPRE simultaneously to stimulate the promoter activity, indicating the presence of intimate interaction of inflammatory and metabolic signals on this gene. PycnogenolR, French maritime pine bark extracts, suppressed the oleic acid-induced PLIN2 expression and lipid accumulation in NMuLi cells. We found that PycnogenolR did not suppress the PLIN2 promoter activity or AP-1 binding to DNA. Instead, PycnogenolR facilitates the PLIN2 mRNA degradation, leading to suppression of lipid accumulation. This effect seems to be independent of antioxidant effect of PycnogenolR. We raise the idea that PLIN2 is a putative target molecule for prevention of pathological condition induced by excessive lipid accumulation, and this class of natural compounds could be putative therapeutic modalities.Key words: PycnogenolR, lipid droplet, perilipin, fatty liver disease

Set-size and chromatic uncertainty in an accuracy visual search task

Summary form only given, as follows. Slot bowtie antennas have been previously utilized as array elements in both microwave electron cyclotron emission imaging (ECEI) and microwave imaging reflectometer (MIR) diagnostics for imaging electron temperature (T/sub e/) profiles and fluctuations, and density (n/sub e/) fluctuations, respectively, in tokamak magnetic fusion plasmas. Recently, planar dual dipole antennas have been successfully developed to replace slot bowtie antennas. These antennas offer a number of advantages over the slot bowtie antennas, including increased sensitivity, reduced sidelobe levels, and reduced interchannel spacings which allow for higher resolution imaging. Antenna development activities have proceeded in four stages. First, detailed computer simulations were made using IE3D, a full wave method of moments electromagnetic simulation code. Here, the effects of antenna lead lengths, widths and spacing were studied with and without insitu RF filters. Successful designs were then fabricated on hybrid printed circuit boards employing millimeter-wave beamlead diodes. Here, subarrays consisting of four array elements in close proximity were characterized over a large RF bandwidth to determine antenna patterns and crosstalk levels between adjacent channels. In this paper, details regarding the simulations and laboratory characterization are presented. Full 16 channel arrays optimized for MIR at 88 GHz and ECEI at 120-130 GHz have been designed, fabricated and installed on the TEXTOR tokamak. Photographs of these arrays together with focal plane patterns measured both in the laboratory and on site on TEXTOR, will also be presented.

Lung cancer is the most common cause of cancer mortality in male and female patients in the US. Non-small cell lung cancer (NSCLC) accounts for more than 85% of lung cancers. Standard initial chemotherapy for patients with advanced NSCLC is a platinum-based regimen, with data showing that these therapies elicit a modest improvement in patient survival. However, a major limitation to cisplatin therapy is development of drug resistance, leading to cancer progression and reduced patient survival. Cisplatin acts by interacting with DNA to form adducts that, in turn, activate signaling pathways for cell death (apoptosis). DNA damage-mediated apoptotic signals, however, can be blocked, and the resistance that ensues is a major drawback of cisplatin therapy. Resistance mechanisms, such as increased DNA adduct repair, may be modulated by interactions with other signaling pathways for cell survival, and emerging data suggest that estrogens may play a role in this process. To understand how estrogens modulate cisplatin resistance in vitro, we used two models of human NSCLC, A549 and H23 cells, that proliferate in response to estradiol-17β (E2) and express estrogen receptors and aromatase (enzyme that produces estrogens locally). Cisplatin markedly reduces tumor cell growth and enhances apoptosis in both models. However, the antitumor action of cisplatin is significantly blocked when cells are treated with estrogen in vitro. Using qRT-PCR and Western immunoblot analysis of excision repair cross-complementing-1 (ERCC1) protein (repairs cisplatin-induced DNA damage), we find that ERCC1 mRNA and protein levels are significantly increased in the presence of estrogen, thereby suggesting a potential mechanism for estrogen-induced cisplatin resistance. Analyses of the 5’-regulatory region of the human ERCC1 gene revealed putative half-estrogen responsive elements in close proximity with sp1 and AP1 sites. Chromatin immunoprecipitation assays showed binding of estrogen receptors to these promoter sites. Furthermore, treatment of human NSCLC xenografts in vivo with an aromatase inhibitor (exemestane) alone or combined with standard cisplatin chemotherapy elicits a significant reduction in tumor progression as compared to paired controls. A new strategy to block NSCLC progression may be use of cisplatin with simultaneous suppression of estrogen signaling (such as use of aromatase inhibitors). [Supported by NIH Lung Cancer SPORE, National Lung Cancer Partnership and Stiles Program funds]. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2923.

Of great interest in the many fields of communication is the requirement to place numerous small antenna elements in close proximity or even inside one another for diversity or mutiband usage. This letter aims to describe the effects of such adjacency in terms of physical distance and operating frequencies as a function of the volume overlap of circumscribing Wheeler-Chu spheres. We investigate any potential bandwidth advantage or in shared near-field space and define tradeoffs between space minimization and acceptable degradation for electrically small antennas. We find that contrary to popular belief among many antenna designers, it is not possible for two antennas having similar modes to reuse volume without suffering degradation in performance, particularly bandwidth.