Near-perfect Match Research Articles

Food Poisoning Investigation in an Under-resourced Environment: A Case Report

Food borne diseases are of public health importance. A food poisoning incident occurred on 24th October 2010 amongst 22 mourners who had consumed porridge one day after the funeral rites of a child in Mubachi Sub-Location of Suba West Division in Migori District, south western . An investigation of the incident was conducted with only two objectives in mind, i.e. (1) to document the poisoning incident for learning and for future reference and (2) to determine the causative factors so as to recommend appropriate public health interventions. Both patient and clinician interviews were conducted. A total of seven patients were interviewed. Patients denied any knowledge of environmental contamination within or without the homestead. They also denied care-less handling of tobacco farming pesticides. The investigation established that the water used in preparing the porridge had been left uncovered on the verandah overnight and it had developed a brownish discoloration. The porridge was prepared from a mixture of cassava and sorghum flour in the ordinary way and mourners had consumed between 250ml-500ml in clean plastic cups. The victims developed signs and symptoms about 30ГўВҖВ“60 minutes after consumption. Children were affected first. They collapsed, vomited, complained of abdominal pains and had diarrhea. Other signs and symptoms occurring in both adults and children were fever, generalized body weakness, and profuse sweating. The frequency distribution of signs and symp-toms showed 63% generalized body weakness, 50% vomiting, 27% nausea, 23% abdominal pain, 14% diarrhea, 9% cough and 5% restlessness. The attack rate was 100%. The suspected cause of poisoning was either hydrocyanic acid in cassava flour or pesticide contamination of the water used in preparing the porridge. In order to arrive at a differential diagnosis, an internet-based literature search was con-ducted to provide an overview of the signs and symptoms associated with the suspected toxicological agents. On this basis, hydrocyanic acid, organochlorine and pyrethroid pesticides were ruled out. There was a near-perfect match between the signs and symptoms of the poisoning to classical signs and symptoms of organophosphate poisoning in the literature. We conclude that the poisoning agent was an organophosphate. Though the victims denied any knowledge of environmental contamination, we strongly believe that the water used in preparing the porridge had been chemically contaminated either by careless handling of pesticides or foul play. We recommend that since the affected area and indeed the rest of Migori district are tobacco growing areas, there is need for mass health education on the safe handling and disposal of pesticide products as these are widely used. Pesticide dispensing outlets should provide also pesticide safety education to customers on each pesticide sold to encourage safe use and handling.

Single-/dual-band metamaterial absorber based on cross-circular-loop resonator with shorted stubs

A single-/dual-band metamaterial absorber (MMA) based on cross-circular-loop resonator (CCLR) with shorted stubs is discussed at microwave frequencies in this paper. The single-/dual-band characteristics are realized by adjusting the positions of the shorted stubs. We briefly analyze the equivalent circuit model of the MMA unit cell and then numerically and experimentally investigate the near-perfect absorptions in such two conditions (single- and dual-band). The results indicate that the proposed MMA exhibits near-perfect impedance matching with free space and high absorptivity of 99.74 % at 8.65 GHz for single-band condition, and absorptivities of 99.75 % and 97.35 % at 8.525 and 9.1 GHz, respectively, for dual-band condition. It also exhibits a wide range of angles of incidence for both transverse electric (TE) and transverse magnetic (TM) radiation. The two operating frequency bands, in dual-band condition, can be further controlled by adjusting the positions of shorted stubs or adding other shorted stubs. So it opens the way to fabricate controllable MMAs, and so controllable perfectly matched layers and bolometers.

MysiRNA-Designer: A Workflow for Efficient siRNA Design

The design of small interfering RNA (siRNA) is a multi factorial problem that has gained the attention of many researchers in the area of therapeutic and functional genomics. MysiRNA score was previously introduced that improves the correlation of siRNA activity prediction considering state of the art algorithms. In this paper, a new program, MysiRNA-Designer, is described which integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. It also features the MysiRNA score, a highly ranked correlated siRNA efficacy prediction score for ranking the designed siRNAs, in addition to top scoring models Biopredsi, DISR, Thermocomposition21 and i-Score, and integrates them in a unique siRNA score-filtration technique. This multi-score filtration layer filters siRNA that passes the 90% thresholds calculated from experimental dataset features. MysiRNA-Designer takes an accession, finds conserved regions among its transcript space, finds accessible regions within the mRNA, designs all possible siRNAs for these regions, filters them based on multi-scores thresholds, and then performs SNP and off-target filtration. These strict selection criteria were tested against human genes in which at least one active siRNA was designed from 95.7% of total genes. In addition, when tested against an experimental dataset, MysiRNA-Designer was found capable of rejecting 98% of the false positive siRNAs, showing superiority over three state of the art siRNA design programs. MysiRNA is a freely accessible (Microsoft Windows based) desktop application that can be used to design siRNA with a high accuracy and specificity. We believe that MysiRNA-Designer has the potential to play an important role in this area.

Efficient fitting of conductance-based model neurons from somatic current clamp

Estimating biologically realistic model neurons from electrophysiological data is a key issue in neuroscience that is central to understanding neuronal function and network behavior. However, directly fitting detailed Hodgkin-Huxley type model neurons to somatic membrane potential data is a notoriously difficult optimization problem that can require hours/days of supercomputing time. Here we extend an efficient technique that indirectly matches neuronal currents derived from somatic membrane potential data to two-compartment model neurons with passive dendrites. In consequence, this approach can fit semi-realistic detailed model neurons in a few minutes. For validation, fits are obtained to model-derived data for various thalamo-cortical neuron types, including fast/regular spiking and bursting neurons. A key aspect of the validation is sensitivity testing to perturbations arising in experimental data, including sampling rates, inadequately estimated membrane dynamics/channel kinetics and intrinsic noise. We find that maximal conductance estimates and the resulting membrane potential fits diverge smoothly and monotonically from near-perfect matches when unperturbed. Curiously, some perturbations have little effect on the error because they are compensated by the fitted maximal conductances. Therefore, the extended current-based technique applies well under moderately inaccurate model assumptions, as required for application to experimental data. Furthermore, the accompanying perturbation analysis gives insights into neuronal homeostasis, whereby tuning intrinsic neuronal properties can compensate changes from development or neurodegeneration.

Intrinsic complexity of the melt-quenched amorphous Ge2Sb2Te5memory alloy

Through the use of first-principles Ge $K$-edge XANES simulations we demonstrate that the structure of melt-quenched amorphous Ge-Sb-Te is intrinsically complex and is a mixture of Ge(3):Te(3) and Ge(4):Te(2) configurations in comparable concentrations, in contrast to the as-deposited amorphous phase that is dominated by the Ge(4):Te(2) configurations. The reasons for Ge-Te polyvalency are discussed and it is argued that both configurations are compatible with the Mott 8--N rule and the definition of an ideal amorphous solid. The near-perfect Te-Te distance match between the two major configurations accounts for the high cyclability of phase-change materials. Stable compositions in the Ge-Sb-Te system are suggested.

Stability of lifted flames in centerbody burner

The centerbody burner was designed with the objective of understanding the coupled processes of formation, growth, and burn-off of soot through decoupling them using recirculation zones (RZs). Experimentally it was found that the sooting characteristics of the centerbody burner could be altered dramatically via simple changes in the operating conditions. One of the interesting operating regimes in which a flame lifts off and forms a column of soot was identified when oxygen in the annulus air jet was reduced sufficiently. This paper describes the numerical studies performed to aid the understanding of lifted flames in the centerbody burner. A time-dependent, axisymmetric, detailed-chemistry CFD model is used. Combustion and PAH formation are modeled using the Wang–Frenklach (99 species and 1066 reactions) mechanism, and soot is simulated using a two-equation model of Lindstedt. Calculations have predicted the structure of the lifted flame very well. Two RZs [outer (ORZ) and inner (IRZ)] are formed between the fuel and air jets. A diffusion flame that is lifted-off the centerbody plate anchors steadily to the outer periphery of the ORZ. A near-perfect match between the computed and measured flame lift-off heights is achieved. RZs transport soot that is formed in the flame toward the face of the centerbody and create the soot column. Ethylene and its lighter fuel fragments that are formed in the RZs diffuse toward the annulus air jet and establish a mixing layer with the inwardly diffusing oxygen. Heat diffusing away from the RZs initiates autoignition reactions in the mixing layer. A flame with a triple-flame-base structure becomes established at a location where the ignition-delay time matches the residence time. Soot that is transported into the RZs is found to have a significant effect on the flame lift-off height. Numerical experiments are performed to aid the understanding of the relationship between soot and flame lift-off. Radiation from the soot decreases the temperature, slows the autoignition process, and increases the lift-off height. Soot oxidation consumes O and OH radicals, slows the autoignition reactions, and increases the lift-off height.

Hamiltonian formulation of nonlinear spin-wave dynamics: Theory and applications

A systematic step-by-step development of nonlinear spin-wave theory within the framework of a Hamiltonian formalism is given. The expansion coefficients in the spin-wave Hamiltonian up to the fourth order in the canonical spin-wave amplitudes for a uniformly magnetized ellipsoidal sample are given in general form. This is done for a general orientation of the external field and for a general wave vector. Applications are given for (A) the second-order Suhl spin-wave instability coupling coefficients, (B) the spin-wave wave-vector-dependent nonlinear frequency shift for an in-plane magnetized thin film, and (C) the uniform magnetization mode (ferromagnetic resonance) nonlinear frequency shift for an obliquely magnetized thin film. The analytical results for (C) are compared with results obtained from a time forward numerical analysis of the torque equation of motion and show a near-perfect match.

Integrative model of genomic factors for determining binding site selection by estrogen receptor‐α

A major question in transcription factor (TF) biology is why a TF binds to only a small fraction of motif eligible binding sites in the genome. Using the estrogen receptor-α as a model system, we sought to explicitly define parameters that determine TF-binding site selection. By examining 12 genetic and epigenetic parameters, we find that an energetically favorable estrogen response element (ERE) motif sequence, co-occupancy by the TF FOXA1, the presence of the H3K4me1 mark and an open chromatin configuration in the pre-ligand state provide specificity for ER binding. These factors can model estrogen-induced ER binding with high accuracy (ROC-AUC=0.95 and 0.88 using different genomic backgrounds). Moreover, when assessed in another estrogen-responsive cell line, this model was highly predictive for ERα binding (ROC-AUC=0.86). Variance in binding site selection between MCF-7 and T47D resides in sites with suboptimal ERE motifs, but modulated by the chromatin configuration. These results suggest a definable interplay between sequence motifs and local chromatin in selecting TF binding.

Cut-and-paste of quadriculated disks and arithmetic properties of the adjacency matrix

We define cut-and-paste, a construction which, given a quadriculated disk obtains a disjoint union of quadriculated disks of smaller total area. We provide two examples of the use of this procedure as a recursive step. Tilings of a disk Δ receive a parity: we construct a perfect or near-perfect matching of tilings of opposite parities. Let B Δ be the black-to-white adjacency matrix: we factor B Δ = L D ∼ U , where L and U are lower and upper triangular matrices, D ∼ is obtained from a larger identity matrix by removing rows and columns and all entries of L , D ∼ and U are equal to 0 , 1 or - 1 .

Nanoscale radiofrequency impedance sensors with unconditionally stable tuning

Impedance sensors perform an important role in a number of biosensing applications, including particle counting, sizing, and velocimetry. Detection of nanoparticles, or changes in, e.g., the interfacial Debye-Hückel layer, can also be performed using nanoscale impedance sensors. One method for monitoring changes in the local impedance is to use radiofrequency reflectometry, which when combined with an impedance-matched sensor can afford very high sensitivity with very large detection bandwidth. Maintaining sensitivity and dynamic range, however, requires continuous tuning of the impedance matching network. Here we demonstrate a dual feedback tuning circuit, which allows us to maintain near-perfect impedance matching, even in the presence of long-term drifts in sensor impedance. We apply this tuning technique to a nanoscale interdigitated impedance sensor, designed to allow the direct detection of nanoparticles or real-time monitoring of molecular surface binding. We demonstrate optimal performance of the nanoscale sensor and tuned impedance network both when modulating the concentration of saline to which the sensor is exposed and when electronically switching between sensors configured in a two-element differential array, achieving a stabilization response time of <20 ms.

Fe 2O 3-doped forsterite ceramics as a joining partner for ZrO 2 in a laser brazing process

Gastight, high-temperature stable sealing between yttria-doped zirconia (ZrO 2) and an electrically insulating ceramic joining partner is necessary for a wide range of applications in oxygen sensing and energy conversion. To accomplish this, laser brazing with glass solders is an attractive alternative to existing joining processes. Due to a near-perfect match of its thermal expansion with the one of ZrO 2 up to high temperatures (∼800 °C) and good thermal and electrical insulation properties, forsterite (Mg 2SiO 4) is chosen as a candidate joining partner. As the absorptivity of pure forsterite at the used diode laser wavelengths of 808 and 940 nm is quite low, increasing the energy absorption by doping forsterite with Fe 2O 3 appears to be a promising refinement of this technique. The optical properties of the resulting olivine ceramics are evaluated. The results show that Fe 2O 3-doped forsterite is both suitable as a joining partner for ZrO 2 and for tuning its absorptivity.

Matchings in 3-vertex-critical graphs: The odd case

A subset of vertices D of a graph G is a dominating set for G if every vertex of G not in D is adjacent to one in D. The cardinality of any smallest dominating set in G is denoted by γ ( G ) and called the domination number of G. Graph G is said to be γ -vertex-critical if γ ( G - v ) < γ ( G ) , for every vertex v in G. A graph G is said to be factor-critical if G - v has a perfect matching for every choice of v ∈ V ( G ) . In this paper, we present two main results about 3-vertex-critical graphs of odd order. First we show that any such graph with positive minimum degree and at least 11 vertices which has no induced subgraph isomorphic to the bipartite graph K 1 , 5 must contain a near-perfect matching. Secondly, we show that any such graph with minimum degree at least three which has no induced subgraph isomorphic to the bipartite graph K 1 , 4 must be factor-critical. We then show that these results are best possible in several senses and close with a conjecture.

MicroRNA Regulates the Expression of Human Cytochrome P450 1B1

MicroRNAs (miRNA) are small noncoding RNAs that regulate gene expression through translational repression or mRNA cleavage. Here, we found that cytochrome P450 (CYP), a superfamily of drug-metabolizing enzymes, is a target of miRNA. Human CYP1B1, which is highly expressed in estrogen target tissues, catalyzes the metabolic activation of various procarcinogens and the 4-hydroxylation of 17beta-estradiol. CYP1B1 protein is abundant in cancerous tissues. We identified a near-perfect matching sequence with miR-27b in the 3'-untranslated region of human CYP1B1. Luciferase assays revealed that the reporter activity of the plasmid containing the miR-27b recognition element was decreased in MCF-7 cells (miR-27 positive) but not in Jurkat cells (miR-27b negative). Exogenously expressed miR-27b could decrease the luciferase activity in Jurkat cells. In MCF-7 cells, the antisense oligoribonucleotide for miR-27b restored the luciferase activity and increased the protein level and enzymatic activity of endogenous CYP1B1. These results suggested that human CYP1B1 is post-transcriptionally regulated by miR-27b. The expression levels of miR-27b and CYP1B1 protein in breast cancerous and adjacent noncancerous tissues from 24 patients were evaluated. In most patients, the expression level of miR-27b was decreased in cancerous tissues, accompanied by a high level of CYP1B1 protein. A significant inverse association was observed between the expression levels of miR-27b and CYP1B1 protein. Thus, the decreased expression of miR-27b would be one of causes of the high expression of CYP1B1 protein in cancerous tissues. This is the first study to show that miRNAs regulate not only essential genes for physiologic events but also drug-metabolizing enzymes.

3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets

Off-target gene silencing can present a notable challenge in the interpretation of data from large-scale RNA interference (RNAi) screens. We performed a detailed analysis of off-targeted genes identified by expression profiling of human cells transfected with small interfering RNA (siRNA). Contrary to common assumption, analysis of the subsequent off-target gene database showed that overall identity makes little or no contribution to determining whether the expression of a particular gene will be affected by a given siRNA, except for near-perfect matches. Instead, off-targeting is associated with the presence of one or more perfect 3' untranslated region (UTR) matches with the hexamer or heptamer seed region (positions 2-7 or 2-8) of the antisense strand of the siRNA. These findings have strong implications for future siRNA design and the application of RNAi in high-throughput screening and therapeutic development.

Mitochondrial Transcription Factor A Induction by Redox Activation of Nuclear Respiratory Factor 1

The nuclear expression of mitochondrial transcription factor A (Tfam), which is required for mitochondrial DNA (mtDNA) transcription and replication, must be linked to cellular energy needs. Because respiration generates reactive oxygen species as a side-product, we tested the idea that reactive oxygen species regulate Tfam expression through phosphorylation of nuclear respiratory factor (NRF-1) and binding to the Tfam promoter. In mitochondria-rich rat hepatoma cells that overexpress NRF-1, basal and oxidant-induced increases were found in Tfam expression and mtDNA content. Specific binding of NRF-1 to Tfam promoter was demonstrated by electrophoretic mobility shift assay and chromatin immunoprecipitation. NRF-1-Tfam binding was augmented under pro-oxidant conditions. NRF-1 gene silencing produced 1:1 knockdown of Tfam expression and decreased mtDNA content. To evaluate oxidation-reduction (redox) regulation of NRF-1 in Tfam expression, blockade of upstream phosphatidylinositol 3-kinase was used to demonstrate loss of oxidant stimulation of NRF-1 phosphorylation and Tfam expression. The oxidant response was also abrogated by specific inhibition of Akt/protein kinase B. Examination of the NRF-1 amino acid sequence revealed an Akt phosphorylation consensus at which site-directed mutagenesis abolished NRF-1 phosphorylation by Akt. Finally, Akt phosphorylation and NRF-1 translocation predictably lacked oxidant regulation in a cancer line having no PTEN tumor suppressor (HCC1937 cells). This study discloses novel redox regulation of NRF-1 phosphorylation and nuclear translocation by phosphatidylinositol 3,4,5-triphosphate kinase/Akt signaling in controlling Tfam induction by an anti-oxidant pro-survival network.

Validation of Diurnal Cycle and Intra-seasonal Variability of TRMM Satellite Rainfall

The version 6 TRMM rainfall products showed signiflcant improvements on satellite rain retrievals as compared to rain gauge observations. The difierences between TRMM TMI rain products and gauge observations are less than 10% over Florida, Texas, Kwajalein, and Darwin ground validation sites for the 8-year period from January 1998 to December 2005. The rain difierences between Version 6 TMI and PR data are also within 10% over these GV sites except the Darwin area. The diurnal cycle from 8-years TRMM TMI and PR rain data showed peaks in the early morning over ocean and in the early afternoon over land. These results are accurate as compared to the gauge statistics over TRMM ground validation sites and other ground observations. TRMM TMI rain products indicate that variances of diurnal cycle are less than 5% of intra-seasonal variances over tropical oceans. Parallel spectrum analyses on TMI and Global Precipitation Climatology Project (GPCP) rain products indicate a near-perfect match of intra-seasonal spectral distributions over tropical oceans. DOI: 10.2529/PIERS060831112605

A pair of forbidden subgraphs and perfect matchings

In this paper, we study the relationship between forbidden subgraphs and the existence of a matching. Let H be a set of connected graphs, each of which has three or more vertices. A graph G is said to be H -free if no graph in H is an induced subgraph of G. We completely characterize the set H such that every connected H -free graph of sufficiently large even order has a perfect matching in the following cases. (1) Every graph in H is triangle-free. (2) H consists of two graphs (i.e. a pair of forbidden subgraphs). A matching M in a graph of odd order is said to be a near-perfect matching if every vertex of G but one is incident with an edge of M. We also characterize H such that every H -free graph of sufficiently large odd order has a near-perfect matching in the above cases.

Epitaxial DySi2 nanowire formation on stepped Si(111)

We report the growth of epitaxial DySi2 nanowires (NW) with a single orientation on miscut Si(111). Using high-resolution electron microscopy, we determine that the islands are hexagonal DySi2 with orientation DySi2(0001)‖Si(111), corresponding to a near-perfect lattice match. The NW islands develop extended defects that correlate perfectly with individual step bunches at the buried interface, produced during growth. By contrast, islands grown on step-free substrates develop a broad, two-dimensional shape with no defects. We suggest that the NW shape results from the energy cost of extended defects, which inhibits growth across step edges.

Evaluation of a plasmid-based 16S–23S rDNA intergenic spacer region array for analysis of microbial diversity in industrial wastewater

A plasmid-based 16S–23S rDNA intergenic spacer region (ISR) array was developed and optimized for analysis of microbial diversity within complex environmental samples. Plasmid probes with 16S–23S rDNA ISR inserts (800–1500 bp) from industrial wastewater treatment plant (WWTP) microorganisms were arrayed onto glass slides. Hybridization of fluorescently labeled target sequences from two clones from the ISR WWTP library to arrayed probes showed that there was a good linear relationship between hybridization intensity and ISR similarity ( r 2=0.82). Hybridization was highly specific (average background from arrayed probes with less than 80% similarity in ISR sequence was less than 7%). Strong fluorescence intensity corresponded to near-perfect match clones (99% or greater similarity in ISR sequence). A majority of probes (79%) showed no background hybridization. However, weak background (less than 50% for arrayed probes with 90% and 95% similarity in the 16S rRNA genes) was observed from closely related microorganisms. Background fluorescence from the negative control (plasmid vector with no insert) was similar to water and dimethyl sulfoxide (DMSO)-negative controls. Hybridization using fluorescently labeled ISR sequences from a mixed community sample produced strong fluorescent signals with no background from negative controls. A Cy5-labeled reference standard, part of the vector and present in every spotted probe, was used to normalize hybridization values. These results indicate that arrayed plasmid containing ISR probe insert sequences provides specificity and sensitivity for microbial community analysis in a high-throughput array format.

High-average-power, high-duty-cycle (λ∼6 μm) quantum cascade lasers

High-power quantum cascade lasers emitting at λ=6.1 μm are demonstrated. Accurate control of growth parameters and strain balancing results in a near-perfect lattice match, which leads to excellent material quality. Excellent peak power for uncoated lasers, up to 1.5 W per facet for a 21 μm emitter width, is obtained at 300 K for 30 period structures. The threshold current density at 300 K is only 2.4 kA/cm2. From 300 to 425 K, the laser exhibits a characteristic temperature T0 of 167 K. Next, Y2O3/Ti/Au mirror coatings were deposited on 1.5 mm cavities and mounted epilayer down. These lasers show an average output power of up to 225 mW at 17% duty cycle, and still show 8 mW average power at 45% duty cycle.