gebhart/patrepeval huggingface dataset:
Flow Sorting of Marine Bacterioplankton after Fluorescence In Situ Hybridization (2004)

We describe an approach to sort cells from coastal North Sea bacterioplankton by flow cytometry after in situ hybridization with rRNA-targeted horseradish peroxidase-labeled oligonucleotide probes and catalyzed fluorescent reporter deposition (CARD-FISH). In a sample from spring 2003 >90% of the cells were detected by CARD-FISH with a bacterial probe (EUB338). Approximately 30% of the microbial assemblage was affiliated with the Cytophaga-Flavobacterium lineage of the Bacteroidetes (CFB group) (probe CF319a), and almost 10% was targeted by a probe for the beta-proteobacteria (probe BET42a). A protocol was optimized to detach cells hybridized with EUB338, BET42a, and CF319a from membrane filters (recovery rate, 70%) and to sort the cells by flow cytometry. The purity of sorted cells was >95%. 16S rRNA gene clone libraries were constructed from hybridized and sorted cells (S-EUB, S-BET, and S-CF libraries) and from unhybridized and unsorted cells (UNHYB library). Sequences related to the CFB group were significantly more frequent in the S-CF library (66%) than in the UNHYB library (13%). No enrichment of beta-proteobacterial sequence types was found in the S-BET library, but novel sequences related to Nitrosospira were found exclusively in this library. These bacteria, together with members of marine clade OM43, represented >90% of the beta-proteobacteria in the water sample, as determined by CARD-FISH with specific probes. This illustrates that a combination of CARD-FISH and flow sorting might be a powerful approach to study the diversity and potentially the activity and the genomes of different bacterial populations in aquatic habitats.
Homogeneous temperature- and substrate-resolved technology for a chemiluminescence multianalyte immunoassay (2009)

A novel dual-resolution chemiluminescence (CL) immunoassay platform for the homogeneous determination of four proteins is proposed. The immunoassay is based on temperature- and substrate-resolved technologies. As a proof-of-concept, we evaluated our method for the simultaneous determination of four model proteins (i.e. immunoglobulin A (IgA), IgG, IgM and PEGylated recombinant growth hormone (GH, protein drug)) by using two homogeneous carriers (thermo-sensitive poly-N-isopropylacrylamide (PNIP) and magnetic beads (MB)), and two different CL substrates for alkaline phosphatase (ALP) and horseradish peroxidase (HRP). Briefly, one pair of capture antibodies was immobilized on the PNIP and another pair of capture antibodies was bound to the MB. The four carrier-antibody conjugates were mixed and reacted with the four proteins in a single vessel, and the mixture of two ALP- and two HRP-labeled tracer antibodies was subsequently added to form the four sandwich immunocomplexes. After washing, the two MB conjugates could be easily separated from the two PNIP conjugates by magnetic force while ensuring that the temperature was lower than the lower critical solution temperature (LCST). The CL substrates for ALP and HRP were delivered sequentially into the resultant MB and PNIP solutions. A simple CL setup was employed to perform our novel multiplexed protein assays in the measurement order of ALP and HRP. No obvious cross-reaction was observed. IgA, IgG, IgM and GH were found to be suitably assayed in the ranges of 1.0-50, 0.50-50, 0.50-50 and 0.50-50 ng/mL with limits of detection of 0.50, 0.25, 0.25 and 0.25 ng/mL, respectively. Overall, this simple and homogeneous technique will find applications in areas such as genomics, combinatorial chemistry, drug screening and clinical diagnosis.
A metal-oxide nanofiber-decorated three-dimensional graphene hybrid nanostructured flexible electrode for high-capacity electrochemical capacitors (2014)

Carbonized polypyrrole-coated SnO2/Co3O4 nanofiber-decorated three-dimensional graphene (CPSC-3rGO) was fabricated using single-nozzle co-electrospinning, freeze-drying, and thermal reduction. Polypyrrole-coated SnO2/Co3O4 nanofibers (PSCNFs) were fabricated using vapor deposition polymerization (VDP) of SnO2/Co3O4 nanofibers. The PSCNFs were then mixed with an aqueous graphene oxide (GO) solution and freeze dried to form a PSCNF-decorated 3D GO (CPSC-3GO) structure. The CPSC-3rGO was produced via thermal reduction to form a hybrid nanomaterial for use as the electrodes of electrochemical capacitors (ECs). The specific capacitance of the CPSC-3rGO was 446 F g−1, which is larger than that of the other 3D nanomaterials investigated (the specific capacitance of PSCNFs was 270 F g−1, that of PSC-3GO was 285 F g−1, and that of 3D rGO was 150 F g−1). In addition, ECs with two symmetrical CPSC-3rGO electrodes were fabricated from two layers of CPSC-3rGO separated by a polymer electrolyte gel and encapsulated in polyethylene terephthalate (PET) membranes. These devices exhibited excellent electrical performance, which was preserved following repeated mechanical deformation.
Efficiency and computability of MCMC with Langevin, Hamiltonian, and other matrix-splitting proposals (2015)

We analyse computational efficiency of Metropolis-Hastings algorithms with AR(1) process proposals. These proposals include, as a subclass, discretized Langevin diffusion (e.g. MALA) and discretized Hamiltonian dynamics (e.g. HMC). By including the effect of Metropolis-Hastings we extend earlier work by Fox and Parker, who used matrix splitting techniques to analyse the performance and improve efficiency of AR(1) processes for targeting Gaussian distributions. Our research enables analysis of MCMC methods that draw samples from non-Gaussian target distributions by using AR(1) process proposals in Metropolis-Hastings algorithms, by analysing the matrix splitting of the precision matrix for a local Gaussian approximation of the non-Gaussian target.
T-cell growth factor P40 promotes the proliferation of myeloid cell lines and enhances erythroid burst formation by normal murine bone marrow cells in vitro (1990)

T-cell growth factor P40 was examined for possible effects on murine interleukin-3 (IL-3)-dependent myeloid cell lines and freshly isolated murine bone marrow cells. The results showed that P40 stimulated the proliferation of some IL-3-dependent myeloid cell lines of both early myeloid and mast cell phenotype and synergized with IL-3. P40 did not promote proliferation of fresh bone marrow cells, bone marrow enriched for early myeloid cells by 5-fluorouracil treatment, or bone marrow derived mast cells as assessed in 3H-TdR incorporation assays. P40 did not influence the growth of murine colony-forming unit granulocyte-macrophage in agar cultures, either alone or in the presence of optimal or sub-optimal concentrations of CSF-1, GM-colony-stimulating factor, or IL-3. P40 did potentiate burst-forming unit-erythroid (BFU-E) formation in the presence of erythropoietin; however, this was dependent on the cell plating density, suggesting an indirect stimulation of BFU-E by P40. The indirect nature of P40 action on BFU-E was further demonstrated in cell separation experiments and indicated that the effect was mediated by T cells. These data expand the repertoire of cells that P40 influences.
Cavitation in an orifice flow (2007)

The purpose of this study is to identify the potential locations for cavitation induced by total stress on the flow of a liquid through an orifice of an atomizer. A numerical simulation of two-phase incompressible flow is conducted in an axisymmetric geometry of the orifice for Reynolds numbers between 100 and 2000. The orifice has a rounded upstream corner and a sharp downstream corner with length-to-diameter ratio between 0.1 and 5. The total stress including viscous stress and pressure has been calculated in the flow field and, from there, the maximum principal stress is found. The total-stress criterion for cavitation is applied to find the regions where cavitation is likely to occur and compared with those of the traditional pressure criterion. Results show that the viscous stress has significant effects on cavitation. The effect of geometry and occurrence of hydraulic flip in the orifice on the total stress are studied. The Navier-Stokes equations are solved numerically using a finite-volume method and a boundary-fitted orthogonal grid that comes from the streamlines and potential lines of an axisymmetric equipotential flow in the same geometry. A level-set formulation is used to track the interface and model the surface tension.
Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations (2006)

Multiple targeting is not only prevalent, but also significant. The ability of probesets to hybridize to more than one gene product can lead to false positives when analysing gene expression. Comprehensive annotation describing multiple targeting is required when interpreting array data.
Algorithms for coding scanned halftone pictures (2003)

A method for coding scanned documents containing halftone pictures, e.g. newspapers and magazines, for transmission purposes is proposed. The halftone screen is estimated and the grey value of each dot is found, thus giving a compact description. At the receiver the picture is rescreened. A novel data structure and related algorithms for handling the digital screen without restrictions on the screen parameters is presented. Data compression rates above 20 are obtained for the halftone pictures. The algorithms are suited for implementation with fast dedicated hardware. The rescreening can also be used as digital halftoning with arbitrary screens, using lookup tables.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Serum sialic acid concentration in patients with hypertriglyceridaemia showing the Frederickson's IIB phenotype (1992)

1. Serum total sialic acid concentration, recently shown to be a cardiovascular risk factor, and also serum lipid-associated sialic acid concentration were measured in 15 patients with hypertriglyceridaemia (fasting serum triacyglycerol concentration > 2.3 mmol/l) showing a Frederickson's type IIB phenotype, 15 patients with hypercholesterolaemia showing a IIA phenotype and 15 age- and sex-matched normal control subjects. 2. Total serum sialic acid concentration was significantly raised in the hypertriglyceridaemic group (84.9 +/- 21.5 versus 64.9 +/- 20.8 mg/dl, P < 0.03, Mann-Whitney U-test) compared with the normal control group, as was serum lipid-associated sialic acid concentration (23.0 +/- 4.3 versus 12.0 +/- 3.2 mg/dl, respectively, P < 0.001, Mann-Whitney U-test). 3. Serum total sialic acid concentration was also significantly elevated in the hypertriglyceridaemic group as compared with the IIA phenotype hypercholesterolaemic group (84.9 +/- 21.5 versus 58.4 +/- 11.7 mg/dl, P < 0.03, Mann-Whitney U-test), as was serum lipid-associated sialic acid concentration (23.0 +/- 4.3 versus 14.9 +/- 4.7 mg/dl, P < 0.001, Mann-Whitney U-test). 4. We suggest that serum concentrations of both total sialic acid and lipid-associated sialic acid may be useful markers of cardiovascular risk which could, in part, be related to hypertriglyceridaemia.
Validation of Uromodulin as a Candidate Gene for Human Essential Hypertension (2013)

A recent genome-wide association study identified a locus on chromosome 16 in the promoter region of the uromodulin (UMOD) gene that is associated with hypertension. Here, we examined the hypertension signal with functional studies in Umod knockout (KO) mice. Systolic blood pressure was significantly lower in KO versus wild-type (WT) mice under basal conditions (KO: 116.6±0.3 mm Hg versus WT: 136.2±0.4 mm Hg; P<0.0001). Administration of 2% NaCl did not alter systolic blood pressure in KO mice, whereas it increased in WT mice by ≈33%, P<0.001. The average 24-hour urinary sodium excretion in the KO was greater than that of WT mice (P<0.001). Chronic renal function curves demonstrate a leftward shift in KO mice, suggesting that the relationship between UMOD and blood pressure is affected by sodium. Creatinine clearance was increased during salt loading with 2% NaCl in the KO mice, leading to augmented filtered Na(+) excretion and further Na(+) loss. The difference in sodium uptake that exists between WT and KO strains was explored at the molecular level. Urinary tumor necrosis factor-α levels were significantly higher in KO mice compared with WT mice (P<0.0001). Stimulation of primary thick ascending limb of the loop of Henle cells with exogenous tumor necrosis factor-α caused a reduction in NKCC2A expression (P<0.001) with a concurrent rise in the levels of UMOD mRNA (P<0.001). Collectively, we demonstrate that UMOD regulates sodium uptake in the thick ascending limb of the loop of Henle by modulating the effect of tumor necrosis factor-α on NKCC2A expression, making UMOD an important determinant of blood pressure control.
Simple Synthetic Equivalents for the β-(N,N-Disubstituted)ethylamino Acyl Cation Synthon and their Applications (2001)

Various N,N-disubstituted-β-amino-N-methoxy-N-methylpropanamides 3a-i were prepared which served as an excellent β-aminoacyl cation equivalents. These were used to prepare β-amino ketones 1, pharmacologically active tertiary 1-(3,3-diarylpropyl)amines 7a-c, and the interesting C-glycoside 8.
Activity of methylated forms of selenium in cancer prevention. (1990)

The anticarcinogenic activity of selenium in animal models is well established. The active forms of selenium involved have not been identified to date, but conversion of selenium via hydrogen selenide (H2Se) to methylated forms such as dimethylselenide and trimethylselenonium ion is an important metabolic fate. By controlling the entry of selenium into various points within this pathway through selection of appropriate starting compounds, it is possible to pinpoint more closely the form(s) of selenium responsible for its anticarcinogenic activity. Selenobetaine in the chloride form [(CH3)2Se+CH2COOH] and its methyl ester are extensively metabolized in the rat to mono-, di-, and trimethylated selenides, largely bypassing the inorganic H2Se intermediary pool. The chemopreventive efficacy of these selenobetaines was determined at 1 and 2 ppm selenium supplemented in the diet throughout the duration of the experiment using the dimethylbenz(a)anthracene induced mammary tumor model in rats. There was a dose-dependent inhibitory response to both compounds, and they appeared to be slightly more active than selenite. These doses were without any adverse effects on the animals. Coadministration of selenobetaine with arsenite (5 ppm arsenic) enhanced the tumor-suppressive effect of selenobetaine, although arsenic by itself was totally inactive. Arsenite is known to inhibit certain steps in selenium methylation. The substantial prophylactic efficacy of methylated selenides and the enhancement by arsenite suggest that partially methylated forms of selenium may be directly involved in the anticarcinogenic action of selenium.
ISPD placement contest updates and ISPD 2007 global routing contest (2007)

In 2005 and 2006, ISPD successfully hosted two placement contests and released a total of 16 benchmark circuits. These benchmarks are all derived from real industrial circuits and present modern physical design challenges such as scalability, variety of floorplans, movable macro handling, and congestion mitigation. Since their release, the ISPD placement benchmarks have been extensively used by the physical design community. Indeed, we have observed significant progress in placement and floorplanning in the last few years. Much of this success can be credited to the fact that the placement community finally has large, well-defined benchmark circuits available that allow for fair comparisons among different algorithms. In this presentation, we report the most recent results on ISPD placement benchmarks and review how much progress each placement tool has achieved.
Agmatine acts as an antagonist of neuronal nicotinic receptors (1990)

1. Tritiated agmatine has been used by others in ion flux methods to measure nicotinic receptor function in neurones. However, as shown here, agmatine blocks nicotinic receptor function in both the chick retina and the rat superior cervical ganglion at high concentrations. 2. In intact chick retina, agmatine 1 mM decreases dimethylphenylpiperazinium (DMPP)-induced depolarizations measured in the optic nerve by approximately 70%, while having little effect on responses induced by glutamate analogues. DMPP dose-response curves are reduced in a manner consistent with a non-competitive effect of agmatine, and agmatine at 1 mM does not prevent binding of 125I-labelled neuronal bungarotoxin, a snake venom neurotoxin that competitively binds and blocks functional nicotinic receptors in chick retinal homogenates. 3. Agmatine (10 mM) substantially blocks both DMPP-induced depolarizations of rat superior cervical ganglion and synaptic transmission through the ganglion. Others have established that [3H]-agmatine will pass through nicotinic receptor channels in the rat ganglion. These data suggest that agmatine acts both as a cation and as a weak channel blocker at neuronal nicotinic receptors.
The role of neuron death in the development of the gender difference in the number of neurons in the rat superior cervical ganglion (1987)

Adult male rats have more neurons in their superior cervical ganglia than do adult females. This difference arises over the first two postnatal weeks, and is apparently related to perinatal levels of circulating testosterone. Exposure of neonatal rats to testosterone or estradiol during the first postnatal weeks results in an increase in the number of neurons in the superior cervical ganglion seen at 15, 30 or 60 days postnatally. The present studies were undertaken to determine whether this observed increase in neurons is due to an increase in neuronal proliferation or to a decrease in neuronal death. Results of autoradiographic studies show no evidence of enhanced neuronal proliferation following postnatal exposure to estradiol, but do show an increased survival of a prenatally labeled population of cells. Counts of degenerating cells in the superior cervical ganglion show that during the peak period of normal neuronal degeneration, on postnatal day 5, 17-beta-estradiol or testosterone propionate treated animals have significantly fewer degenerating superior cervical ganglion cells than do vehicle-injected littermate controls. In addition, vehicle-injected females have more degenerating cells on day 5 than do vehicle-injected males. Taken together these results provide strong evidence that the increase in superior cervical ganglion neurons seen after neonatal exposure to estradiol results from a reduction in developmental neuron death.
Heteroepitaxial ridge-overgrown distributed feedback laser at 1.5 μm (1984)

A new distributed feedback laser, the heteroepitaxial ridge-overgrown distributed feedback (HRO DFB) laser, is proposed and demonstrated. The HRO DFB lasers operated in stable single longitudinal mode with no observable mode partition events under 2-Gb/s pseudo-random pulse modulation with dynamic spectral widths typically 0.5–2 Å even with both facets cleaved. Other characteristics of these 1.5-μm GaInAsP HRO DFB lasers include ∼10 mW/facet (no antireflection coating) of stable beam, single longitudinal mode output power, and narrow lateral beam divergence of ∼12° (half-power full width). Actual transmission experiments with dispersive fibers (17 ps/km nm) at ∼1.55 μm confirmed that the HRO DFB laser is an excellent ‘‘single-frequency’’ optical source.
Flexible Touch Sensors Made of Two Layers of Printed Conductive Flexible Adhesives (2016)

Touch sensors are crucial in controlling robotic manipulation when a robot interacts with environmental objects. In this study, multilayer flexible touch sensors in the form of an array were developed. The sensors use ink-type conductive flexible adhesives as electrodes which were printed on polyethylene terephthalate (PET) films in a parallel equidistance stripe pattern. Between the two printed layers, a double-sided adhesive film was used to combine each layer and was perforated at the junctions of the top and bottom electrodes with different-sized circles. These holes represent switching mechanisms between the top and bottom electrodes, and their sizes make the sensor respond to different levels of external pressure. We showed the durability of the fabricated sensor with 1 mm diameter holes by repeated experiments of exerting normal pressure ranging from 0 to 159.15 kPa for 1000 cycles. In case of 1 mm diameter holes, the state of each sensor node was reliably determined by the threshold pressures of 127.3 kPa for increasing pressure and 111.4 kPa for decreasing pressure. On the other hand, decreasing the hole size from 3 to 0.5 mm caused an increase in the threshold pressure from 1.41 to 214 kPa. The relation between the hole size and the threshold pressure was analyzed by a mechanical model. The sensor performance was also verified on curved surfaces up to 60 mm radius of curvatures. Additionally, we fabricated a sensor with three levels of sensitivity with a conventional method which was a thermal evaporation to show the extendibility of the idea.
The length of a tetranucleotide repeat tract in <i>Haemophilus influenzae</i> determines the phase variation rate of a gene with homology to type III DNA methyltransferases (2000)

Haemophilus influenzae is an obligate commensal of the upper respiratory tract of humans that uses simple repeats (microsatellites) to alter gene expression. The mod gene of H. influenzae strain Rd has homology to DNA methyltransferases of type III restriction/modification systems and has 40 tetranucleotide (5'-AGTC) repeats within its open reading frame. This gene was found in 21 out of 23 genetically distinct H. influenzae strains, and in 13 of these strains the locus contained repeats. H. influenzae strains were constructed in which a lacZ reporter was fused to a chromosomal copy of mod downstream of the repeats. Phase variation occurred at a high frequency in strains with the wild-type number of repeats. Mutation rates were derived for similarly engineered strains, containing different numbers of repeats. Rates increased linearly with tract length over the range 17-38 repeat units. The majority of tract alterations were insertions or deletions of one repeat unit with a 2:1 bias towards contractions of the tract. These results demonstrate the number of repeats to be an important determinant of phase variation rate in H. influenzae for a gene containing a microsatellite.
Fast QR Code Detection in Arbitrarily Acquired Images (2011)

The detection of QR codes, a type of 2D barcode, as described in the literature consists merely in the determination of the boundaries of the symbol region in images obtained with the specific intent of highlighting the symbol. However, many important applications such as those related with accessibility technologies or robotics, depends on first detecting the presence of a barcode in an environment. We employ Viola-Jones rapid object detection framework to address the problem of finding QR codes in arbitrarily acquired images. This framework provides an efficient way to focus the detection process in promising regions of the image and a very fast feature calculation approach for pattern classification. An extensive study of variations in the parameters of the framework for detecting finder patterns, present in three corners of every QR code, was carried out. Detection accuracy superior to 90%, with controlled number of false positives, is achieved. We also propose a post-processing algorithm that aggregates the results of the first step and decides if the detected finder patterns are part of QR code symbols. This two-step processing is done in real time.
Fractionation of lignocellulosic biomass using the OrganoCat process (2015)

The fractionation of lignocellulose in its three main components, hemicellulose, lignin and cellulose pulp can be achieved in a biphasic system comprising water and bio-based 2-methyltetrahydrofuran (2-MeTHF) as solvents and oxalic acid as catalyst at temperatures up to 140 °C.