gebhart/patrepeval huggingface dataset:
Vectors for improved Tet repressor-dependent gradual gene induction or silencing in Staphylococcus aureus (2011)

A set of vectors for improved tetracycline-dependent gene regulation in Staphylococcus aureus is presented. Plasmid pRAB11 was generated from pRMC2 by adding a second tet operator within the TetR-regulated promoter P(xyl/tet). Pronounced repression was observed in the absence of anhydrotetracycline (ATc) combined with high induction in the presence of the drug, as demonstrated for pRAB11 bearing staphylococcal nuclease nuc1, lacZ or gfp. Also, in plasmid pCG261, the pRAB11 tetR-P(xyl/tet) regulatory architecture permitted tight repression and a stepwise increase in transcript amounts of the target gene rny (putative RNase) correlated with rising ATc concentrations. Additionally, pRAB11-derived vectors harbouring semi-rationally designed P(xyl/tet)-like fragments, mutated at up to six defined positions, were constructed. Sixteen mutant sequences with single to quadruple exchanges were analysed for transcriptional strength and ATc-dependent inducibility. A set of promoters with gradually decreased activities and improved repression is presented. Finally, the implementation of reverse TetR revtetR-r2, which exhibits three amino acid exchanges and binds to tetO in the presence of ATc, yielded an efficiently co-repressible vector within the pRAB11 system. Intriguingly, revtetR was found to contain a fourth mutation only after propagation in S. aureus. We predict that the described vectors constitute valuable tools for staphylococcal genetics.
An autoregressive approach to the identification of multipath ray parameters from field measurements (1989)

This study is concerned with using modern spectral analysis techniques to derive estimates of multipath ray parameters (delays and amplitudes) from measurements of selective fading over a wide band at microwave frequencies. The applicability of the general category of autoregressive methods is addressed, and the specific method adopted, the Prony algorithm, is described. An illustrative example in which this is applied to a typical field measurement is followed by an investigation into the capabilities and limitations of the algorithm. A statistical analysis of the method has been carried out using a database of laboratory measurements. The Prony algorithm's ability to resolve delays to better than half the Fourier limit is shown, and its tendency to yield biased estimates is studied.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A one-measurement form of simultaneous perturbation stochastic approximation (1997)

The simultaneous perturbation stochastic approximation (SPSA) algorithm has proven very effective for difficult multivariate optimization problems where it is not possible to obtain direct gradient information. As discussed to date, SPSA is based on a highly efficient gradient approximation requiring only two measurements of the loss function independent of the number of parameters being estimated. This note presents a form of SPSA that requires only one function measurement (for any dimension). Theory is presented that identifies the class of problems for which this one-measurement form will be asymptotically superior to the standard two-measurement form.
Biological Activity of Soluble CD100. I. The Extracellular Region of CD100 Is Released from the Surface of T Lymphocytes by Regulated Proteolysis (2001)

CD100 is the first semaphorin described in lymphoid tissues, where it has been shown to be associated with a serine kinase activity. Semaphorins are molecules involved in axon pathfinding during nerve development and act as repellent guidance cues. In the nervous system semaphorins exist as either membrane-bound or secreted forms. We report here a spontaneous processing of membrane CD100, suggesting that it is also produced as a diffusable semaphorin from lymphoid cells. Monomeric and homodimeric forms of CD100 are expressed by T lymphocytes and CD100-transfected fibroblasts. We demonstrate that CD100 is released through a proteolytic process blocked by metalloprotease inhibitors. In T cells, only soluble CD100 dimers are produced, suggesting that CD100 dimerization is required for proteolysis. In agreement, we observe that increasing membrane dimers strongly favors shedding of the molecule. By expressing a CD100 molecule mutated at cysteine 674 into a COS cell system, we additionally demonstrate that this particular residue in the extracellular domain of the molecule is required for dimerization. Finally, we show that staurosporine, a serine kinase inhibitor, enhances the membrane cleavage of CD100. Together these results demonstrate that membrane CD100 is cleaved by a metalloprotease-dependent process, which is probably regulated by phosphorylation. Mainly, these findings shed light on a possible function for the semaphorin region of CD100 as a long range guidance cue in the immune system.
Preemptive RANSAC for live structure and motion estimation (2003)

A system capable of performing robust live ego-motion estimation for perspective cameras is presented. The system is powered by random sample consensus with preemptive scoring of the motion hypotheses. A general statement of the problem of efficient preemptive scoring is given. Then a theoretical investigation of preemptive scoring under a simple inlier-outlier model is performed. A practical preemption scheme is proposed and it is shown that the preemption is powerful enough to enable robust live structure and motion estimation.
Top‐Down Patterning and Self‐Assembly for Regular Arrays of Semiconducting Single‐Walled Carbon Nanotubes (2014)

Highly pure semiconducting single-walled carbon nanotubes (SWNTs), sorted by density-gradient ultracentrifugation, undergo self-assembly using depletion attraction forces into rafts along lithographically defined patterns of narrow pitch (100 or 200 nm). The arrays demonstrate high pattern fidelity and channel filling, along with large-scale homogeneity. Field-effect transistors made from these arrays exhibit high performance at on/off ratios>1000.
Evanescent Coupling Device Design for Waveguide-Integrated Group IV Photodetectors (2010)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We have fabricated vertical p-i-n silicon photodetectors that are monolithically integrated with compact silicon-oxynitride channel waveguides. By comparing the evanescent coupling from low index-contrast waveguides and compact, high index-contrast waveguides, the dependence of evanescent coupling behavior on the waveguide index and geometry designs was analyzed. The effects of fabrication variations in the coupling structure have been studied and it was found that an offsetting step in the waveguide can help compensate for the mode mismatch at the transition interface from the input bus waveguide to the waveguide on top of the photodetector. Finally, we present a design map, built by drawing the evanescent coupling rate contour lines in the waveguide design space, which well predicts the evanescent coupling trends. </para>
Regulation of human T lymphocyte coactivation with an alpha4 integrin antagonist peptide (1997)

The cyclic hexapeptide CWLDVC (TBC 772) is an antagonist of alpha4 integrins and a potent inhibitor of lymphocyte interactions with fibronectin, vascular cell adhesion molecule-1, and muscosal vascular addressin cell adhesion molecule-1 (MAdCAM-1). As such, peptide TBC 772 effectively inhibits the activation of freshly isolated human T lymphocytes stimulated with purified vascular cell adhesion molecule-1 coimmobilized with anti-CD3 mAb. The influence of peptide binding on distinct sites of the alpha4beta1 complex was determined by flow cytometry and cellular adhesion assays employing a panel of mAbs. Binding of the alpha4-specific mAb L25 and the beta1-specific mAb 33B6 was not altered by the peptide; however, binding of mAb 19H8, which is specific for a combinatorial epitope of alpha4beta1, was dramatically inhibited. Treatment of lymphocytes with the peptide caused an increase in a ligand-induced epitope on beta1 integrin defined by mAb 15/7. In T cell activation studies using coimmobilized anti-CD3 mAb and the anti-integrin mAbs, the peptide had broader inhibitory activity, suppressing costimulation induced by all the integrin mAbs. The peptide was not generally toxic and was integrin selective in its suppressive activity, as coactivation by ligation of CD3 in conjunction with CD28 or CD26 was not affected. These results suggest that the antagonist peptide CWLDVC can effectively neutralize integrin coactivation systems by a mechanism independent of competitive binding.
Foreign affairs: Central American blues (1988)

The apparent collapse of the political hege mony of the Christian Democrats in El Salvador may appear, in the light of glasnost and perestroika, the Soviet withdrawal from Afghanistan and the likely Cuban withdrawal from Angola and Vietnamese withdrawal from Kampuchea, a fairly minor setback for Western interests. And yet it symbolises and is a major part of the substantial failure of United States policy in the Central American isthmus.
Acute Effect of an Incision on Mechanosensitive Afferents in the Plantar Rat Hindpaw (2002)

The purpose of this study was to examine which primary afferent fibers are sensitized to mechanical stimuli after an experimental surgical incision to the glabrous skin of the rat hindpaw. Afferent fibers teased from the L(5) dorsal root or the tibial nerve were recorded in anesthetized rats. The mechanical response properties of each fiber were characterized before and 45 min after an incision (or sham procedure) within the mechanical receptive field. Sensitization is characterized by an expansion of the mechanical receptive field, an increase in background activity, an increase in response magnitude, or a decrease in response threshold. After incision, the background activity and response properties of Abeta-fibers (n = 9) to mechanical stimuli were unchanged. Four of 13 mechanosensitive Adelta-fibers exhibited sensitization after the incision; response threshold decreased, response magnitude increased, or receptive field size increased. Background activity of Adelta-fibers was not increased by the incision. Sensitization was observed in 4 of 18 mechanosensitive C-fibers 45 min after the incision. Background activity of C-fibers was not increased by the incision. In a group of mechanically insensitive afferent fibers (MIAs), 3 of 7 Adelta-fibers and 4 of 10 C-fibers sensitized 45 min after incision. Response threshold was decreased in only 2 of 17 MIAs; receptive field size increased in 7 of 17 MIAs. Abeta-fibers did not sensitize after the incision, and only 8 of 31 (26%) mechanosensitive Adelta- and C-fibers gave evidence of sensitization. In a group of MIA Adelta- and C-fibers, a greater percentage of 17 fibers studied (41%) were sensitized after incision. In this model, the principal effect of an incision, when examined 45 min after the insult, is an increase in receptive field size of the afferents, particularly those characterized as MIAs. To the extent that the mechanical hyperalgesia characterized in the same model is initiated in the periphery, it would appear that spatial summation of modestly increased response magnitude is important to the development of hyperalgesia.
Computing the bivariate Gaussian probability integral (1999)

In signal processing applications, it is often required to compute the integral of the bivariate Gaussian probability density function (PDF) over the four quadrants. When the mean of the random variables are nonzero, computing the closed form solution to these integrals with the usual techniques of integration is infeasible. Many numerical solutions have been proposed; however, the accuracy of these solutions depends on various constraints. In this work, we derive the closed form solution to this problem using the characteristic function method. The solution is derived in terms of the well-known confluent hypergeometric function. When the mean of the random variables is zero, the solution is shown to reduce to a known result for the value of the integral over the first quadrant. The solution is implementable in software packages such as MAPLE.
A List-Priority Rendering Algorithm for Redisplaying Projected Surfaces (1995)

Projected grid surfaces are a particularly interesting subset of bivariate parametric functions. Images generated using three-dimensional computer graphics methods and those resulting from ideal pin-hole cameras fall into this class. Often, a range image is provided in addition to the actual image, this may be in the form of a Z-buffer for synthetic images or stereo-disparity field for acquired images. In this research I report on an algorithm for computing the visible subset of a projected surface from any arbitrary view. This method has several important properties. It determines an occlusion-compatible paint order such that surfaces closest to the desired viewpoint are drawn last, thus overwriting any previously rendered surface. This painting order is determined independent of the range information. Also, facets of the image are drawn sequentially, taking advantage of local spatial coherency. This report also describes a method for the fast rendering of small triangles using a tabl...
Inducible Expression of Lectin-like Oxidized LDL Receptor-1 in Vascular Endothelial Cells (1998)

Endothelial dysfunction, or activation, elicited by oxidized LDL (Ox-LDL) or its lipid constituent, has been implicated in the initiation and progression of atherosclerosis. We have recently identified a C-type lectin-like molecule, designated lectin-like Ox-LDL receptor-1 (LOX-1), which acts as a cell-surface receptor for Ox-LDL in cultured vascular endothelial cells. In this study, we provide evidence that LOX-1 expression can be upregulated by tumor necrosis factor-alpha (TNF-alpha) and phorbol 12-myristate 13-acetate (PMA) in cultured bovine aortic endothelial cells. TNF-alpha and PMA upregulated LOX-1 protein and mRNA in a time- and dose-dependent manner. Nuclear runoff assay revealed that TNF-alpha stimulates transcription of the LOX-1 gene. Chinese hamster ovary K1 cells stably expressing LOX-1 internalized 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI)-labeled Ox-LDL but did not significantly internalize acetylated LDL (Ac-LDL), which was effectively suppressed by excess amounts of unlabeled Ox-LDL but not by Ac-LDL. Upregulated expression of LOX-1 by TNF-alpha and PMA was associated with increased uptake of DiI-Ox-LDL that cannot be blocked by excess amounts of unlabeled Ac-LDL. Taken together, LOX-1 is a receptor specific for Ox-LDL, and enhanced uptake of Ox-LDL via this novel receptor on vascular endothelial cells may play an important role in endothelial activation in atherogenesis.
Molecular Cloning and Biological Activity of a Novel Lysyl Oxidase-related Gene Expressed in Cartilage (2001)

We cloned a cDNA encoding a novel lysyl oxidase-related protein, named LOXC, by suppression subtractive hybridization between differentiated and calcified ATDC5 cells, a clonal mouse chondrogenic EC cell line. The deduced amino acid sequence of mouse LOXC consists of 757 amino acids and shows 50% identity with that of mouse lysyl oxidase. Northern blot analysis showed a distinct hybridization band of 5.4 kilobases, and Western blot analysis showed an immunoreactive band at 82 kilodaltons. Expression of LOXC mRNA was detected in osteoblastic MC3T3-E1 cells and embryonic fibroblast C3H10T1/2 cells, whereas none of NIH3T3 fibroblasts and myoblastic C2C12 cells expressed LOXC mRNA in vitro. Moreover, the LOXC mRNA and protein levels dramatically increased throughout a process of chondrogenic differentiation in ATDC5 cells. In vivo, LOXC gene expression was localized in hypertrophic and calcified chondrocytes of growth plates in adult mice. The conditioned media of COS-7 cells transfected with the full-length LOXC cDNA showed the lysyl oxidase activity in both type I and type II collagens derived from chick embryos, and these activities of LOXC were inhibited by beta-aminopropionitrile, a specific inhibitor of lysyl oxidase. Our data indicate that LOXC is expressed in cartilage in vivo and modulates the formation of a collagenous extracellular matrix.
The 65-kDa subunit of human NF-kappa B functions as a potent transcriptional activator and a target for v-Rel-mediated repression. (1992)

Molecular cloning of the polypeptide component of the Rel-related human p75 nucleoprotein complex has revealed its identity with the 65-kDa (p65) subunit of NF-kappa B. Functional analyses of chimeric proteins composed of NF-kappa B p65 C-terminal sequences linked to the DNA-binding domain of the yeast GAL4 polypeptide have indicated that the final 101 amino acids of NF-kappa B p65 comprise a potent transcriptional activation domain. Transient transfection of human T cells with an expression vector encoding NF-kappa B p65, but not NF-kappa B p50, produced marked transcriptional activation of a basal promoter containing duplicated kappa B enhancer motifs from the long terminal repeat of type 1 human immunodeficiency virus. These stimulatory effects of NF-kappa B p65 were synergistically enhanced by coexpression of NF-kappa B p50 but were completely inhibited by coexpression of the v-rel oncogene product. Together, these functional studies demonstrate that NF-kappa B p65 is a transactivating subunit of the heterodimeric NF-kappa B complex and serves as one cellular target for v-Rel-mediated transcriptional repression.
Electric‐current‐induced detachment of Staphylococcus epidermidis strains from surgical stainless steel (2003)

Infection of percutaneous biomaterials implants, such as fixation frames used for the repair of complicated fractures in orthopedics, is a major complication that almost inevitably leads to replacement of the implant. As antibiotic therapy usually has little impact on biomaterial-associated infections, it is the aim of this article to examine whether implant-associated Staphylococcus epidermidis and Staphylococcus aureus strains could be stimulated to detach from a surgical stainless steel anode during application of an electric current. First, bacteria were allowed to adhere from a flowing suspension of physiological ionic strength in a parallel plate flow chamber to a stainless-steel surface, after which the suspension was replaced by a bacterium-free solution with a specified ionic strength (0.5-150-mM potassium phosphate). DC currents ranging from 15 to 125 microA were applied to induce bacterial detachment. Initial detachment decreased with increasing ionic strength at 100 microA. The percentage detachment achieved by application of an electric current after 2.5 h was highest (95%) in 1-mM potassium phosphate and decreased to 15% when the ionic strength exceeded 40 mM. The electric current did not significantly affect the percentage detachment, but initial detachment rates increased with increasing current from 1000 cm(-2) s(-1) at 15 microA to 7000 cm(-2) s(-1) at 125 microA. Although different isolates of S. epidermidis and S. aureus showed different patterns of current-induced detachment, all strains could be stimulated to detach. The results of this study define ionic-strength conditions and electric currents yielding staphylococcal detachment from surgical stainless steel and therewith point to a pathway for the treatment and prevention of percutaneous metal-implant infection.
Interleukin-6 Treatment Augments Cutaneous Wound Healing in Immunosuppressed Mice (2001)

It has been postulated that the inflammatory response that occurs after cutaneous wounding is a prerequisite for healing and that inflammatory cytokines, such as interleukin-6 (IL-6) are involved in this process. We showed previously that IL-6-deficient mice display delayed wound healing, which could be reversed by administration of a murine IL-6 expression plasmid or recombinant murine IL-6 (rMuIL-6). In the present study, we observed that delayed cutaneous wound healing, which occurs as a result of glucocorticoid-induced immunosuppression, can also be reversed by rMuIL-6, as evidenced by epithelialization, granulation tissue formation, and wound closure. In vehicle control mice, rMuIL-6 did not augment healing but rather delayed the process. Immunochemical studies indicated that the expression of matrix metalloproteinase-10 (MMP-10) was increased in dexamethasone-treated mice and that rMuIL-6 treatment reduced its expression, indicating that IL-6 may influence dermal matrix formation and, specifically, collagen synthesis. These results demonstrate that IL-6 can restore abnormal wound repair that occurs in immunodeficiency and suggest its use as a potential therapy.
The full-field equations for acoustic radiation and scattering (1999)

The source simulation technique or related approaches like the multipole method, the superposition method, etc. are used for calculating the sound field radiated (or scattered) from complex-shaped structures. However, it is known that these techniques can lead to ill-conditioned systems of equations, and their numerical treatment requires extreme care. A new stabilized variant of the source simulation technique—called the full-field method—has been developed by using the exterior instead of the interior Helmholtz integral formulation or, equivalently, by expanding the sound field into special trial and weighting functions. These functions are chosen in such a way that the resulting matrix becomes more diagonally dominant. The full-field method is applied to the acoustic radiation from a pulsating sphere and to the high-frequency scattering from a cylinder and a nonconvex structure. The numerical results are compared with calculations obtained from other methods. It is shown that the improved method leads to better conditioned sets of equations which can be solved directly without singular-value decomposition, since the associated condition numbers are decreased strongly, in some cases by a few orders of magnitude.
The CRISPRs, They Are A-Changin': How Prokaryotes Generate Adaptive Immunity (2012)

All organisms need to continuously adapt to changes in their environment. Through horizontal gene transfer, bacteria and archaea can rapidly acquire new traits that may contribute to their survival. However, because new DNA may also cause damage, removal of imported DNA and protection against selfish invading DNA elements are also important. Hence, there should be a delicate balance between DNA uptake and DNA degradation. Here, we describe prokaryotic antiviral defense systems, such as receptor masking or mutagenesis, blocking of phage DNA injection, restriction/modification, and abortive infection. The main focus of this review is on CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated), a prokaryotic adaptive immune system. Since its recent discovery, our biochemical understanding of this defense system has made a major leap forward. Three highly diverse CRISPR/Cas types exist that display major structural and functional differences in their mode of generating resistance against invading nucleic acids. Because several excellent recent reviews cover all CRISPR subtypes, we mainly focus on a detailed description of the type I-E CRISPR/Cas system of the model bacterium Escherichia coli K12.
The role of electrical stimulation techniques in the management of the male patient with urgency incontinence (2014)

Both sacral neuromodulation and percutaneous tibial nerve stimulation prove to be viable, durable options for treating patients with refractory urge incontinence. Alternative modes of stimulation are also beginning to show promise.
A randomized, double-blind, placebo-controlled, ascending, single-dose study of a human monoclonal anti-FGF23 antibody (KRN23) in X-linked hypophosphatemia (2014)

Searchable abstracts of presentations at key conferences on calcified tissues ISSN 2052-1219 (online)