gebhart/patrepeval huggingface dataset:
Glycosylphosphatidylinositol-anchored Glucanosyltransferases Play an Active Role in the Biosynthesis of the Fungal Cell Wall (2000)

A novel 1,3-beta-glucanosyltransferase isolated from the cell wall of Aspergillus fumigatus was recently characterized. This enzyme splits internally a 1,3-beta-glucan molecule and transfers the newly generated reducing end to the non-reducing end of another 1, 3-beta-glucan molecule forming a 1,3-beta linkage, resulting in the elongation of 1,3-beta-glucan chains. The GEL1 gene encoding this enzyme was cloned and sequenced. The predicted amino acid sequence of Gel1p was homologous to several yeast protein families encoded by GAS of Saccharomyces cerevisiae, PHR of Candida albicans, and EPD of Candida maltosa. Although the expression of these genes is required for correct morphogenesis in yeast, the biochemical function of the encoded proteins was unknown. The biochemical assays performed on purified recombinant Gas1p, Phr1p, and Phr2p showed that these proteins have a 1,3-beta-glucanosyltransferase activity similar to that of Gel1p. Biochemical data and sequence analysis have shown that Gel1p is attached to the membrane through a glycosylphosphatidylinositol in a similar manner as the yeast homologous proteins. The activity has been also detected in membrane preparations, showing that this 1,3-beta-glucanosyltransferase is indeed active in vivo. Our results show that transglycosidases anchored to the plasma membrane via glycosylphosphatidylinositols can play an active role in fungal cell wall synthesis.
Meningococcal Factor H Binding Protein Vaccine Antigens with Increased Thermal Stability and Decreased Binding of Human Factor H (2016)

Neisseria meningitidis causes cases of bacterial meningitis and sepsis. Factor H binding protein (FHbp) is a component of two licensed meningococcal serogroup B vaccines. FHbp recruits the complement regulator factor H (FH) to the bacterial surface, which inhibits the complement alternative pathway and promotes immune evasion. Binding of human FH impairs the protective antibody responses to FHbp, and mutation of FHbp to decrease binding of FH can increase the protective responses. In a previous study, we identified two amino acid substitutions in FHbp variant group 2 that increased its thermal stability by 21°C and stabilized epitopes recognized by protective monoclonal antibodies (MAbs). Our hypothesis was that combining substitutions to increase stability and decrease FH binding would increase protective antibody responses in the presence of human FH. In the present study, we generated four new FHbp single mutants that decreased FH binding and retained binding of anti-FHbp MAbs and immunogenicity in wild-type mice. From these mutants, we selected two, K219N and G220S, to combine with the stabilized double-mutant FHbp antigen. The two triple mutants decreased FH binding >200-fold, increased the thermal stability of the N-terminal domain by 21°C, and bound better to an anti-FHbp MAb than the wild-type FHbp. In human-FH-transgenic mice, the FHbp triple mutants elicited 8- to 15-fold-higher protective antibody responses than the wild-type FHbp antigen. Collectively, the data suggest that mutations to eliminate binding of human FH and to promote conformational stability act synergistically to optimize FHbp immunogenicity.
Image-Based Proxy Accumulation for Real-Time Soft Global Illumination (2007)

We present a new, general, and real-time technique for soft global illumination in low-frequency environmental lighting. It accumulates over relatively few spherical proxies which approximate the light blocking and re-radiating effect of dynamic geometry. Soft shadows are computed by accumulating log visibility vectors for each sphere proxy as seen by each receiver point. Inter-reflections are computed by accumulating vectors representing the proxy's unshadowed radiance when illuminated by the environment. Both vectors capture low-frequency directional dependence using the spherical harmonic basis. We also present a new proxy accumulation strategy that splats each proxy to receiver pixels in image space to collect its shadowing and indirect lighting contribution. Our soft GI rendering pipeline unifies direct and indirect soft effects with a simple accumulation strategy that maps entirely to the GPU and outperforms previous vertex-based methods.
Inhibition of Human Sperm Motility by Contraceptive Anti-Eppin Antibodies from Infertile Male Monkeys: Effect on Cyclic Adenosine Monophosphate1 (2008)

Epididymal protease inhibitor (eppin [official symbol, SPINLW1]) is of interest as a male contraceptive target because of its specificity and location on the human sperm surface. We have examined the effect of anti-eppin antibodies from infertile male monkeys and the effect of recombinant human semenogelin on human sperm motility. Anti-eppin antibodies significantly decreased the progressive motility of human spermatozoa as measured by decreased total distance traveled, decreased straight-line distance, and decreased velocity. Anti-eppin treatment of spermatozoa significantly increased the amount of cAMP present in nonprogressive spermatozoa; however, approximately 25% of antibody-treated spermatozoa could be rescued by the addition of cAMP-acetoxymethyl ester, indicating that anti-eppin-treated spermatozoa have a compromised ability to utilize cAMP. Addition of recombinant human semenogelin has a concentration-dependent inhibitory effect on progressive motility (increased tortuosity and decreased velocity). We tested the hypothesis that anti-eppin antibodies bound to eppin would subsequently block semenogelin binding to eppin. Anti-eppin antibodies from infertile monkeys inhibited eppin from binding to semenogelin. Addition of affinity-purified antibodies made to the dominant C-terminal epitope of eppin had an inhibitory effect on progressive motility (increased tortuosity, decreased velocity, and straight distance). Our results suggest that the eppin-semenogelin binding site is critical for the removal of semenogelin in vivo during semen liquefaction and for the initiation of progressive motility. We conclude that the eppin-semenogelin binding site on the surface of human spermatozoa is an ideal target for a nonsteroidal male contraceptive.
Cooperative Relaying in Next-Generation Mobile WiMAX Networks (2012)

Distributed space-time coding (DSTC) is a key physical (PHY) layer technique to enable cooperative relaying in wireless networks. Compared with direct transmission and single-relay cooperation, DSTC exploits spatial diversity gain and achieves a higher end-to-end throughput performance. In particular, a novel variation of DSTC, which is called randomized DSTC (R-DSTC), further enhances the performance of conventional DSTC in a mobile environment due to its decentralized relay recruitment. This paper presents a medium access control (MAC) protocol, which is called CoopMAX, for Worldwide Interoperability for Microwave Access (WiMAX) systems to provide cooperative relaying with DSTC and R-DSTC techniques by the use of fixed and mobile relays. CoopMAX explores a joint PHY layer and MAC layer optimization for rate adaptation. The efficiency of CoopMAX is investigated, showing pronounced advantages, such as a doubling of throughput as compared with conventional WiMAX protocols in some typical scenarios.
Hardware acceleration of FDTD computations for 3-D microwave breast tomography (2009)

Microwave tomography is an area of ongoing research in the University of Wisconsin Computational Electromagnetics Laboratory (UWCEM). We image anatomically realistic, three-dimensional, numerical breast models using electromagnetic inverse scattering methods. The iterative approach requires a set of finite-difference time-domain (FDTD) field solutions at each iteration. The size of the breast model and the spatial sampling density required to simulate UHF-band pulse-widths result in a significant engineering challenge with respect to timely completion of the imaging algorithm. In this paper we report on the performance of UWCEM hardware resources in application to 3-D microwave breast tomography. A sample test domain is selected for quantitative illustration of this practical application of hardware acceleration.
Use of in-fiber chirped Bragg gratings in an all-fiber femtosecond-pulse amplification circuit (1995)

Chirped fiber gratings recently emerged as a new technology for dispersion compensation in communication systems.1 Here we investigate in-fiber chirped Bragg gratings as stretchers and compressors for distortionless amplification of femtosecond pulses in a fiber amplifier. The first all-fiber femtosecond chirped-pulse-amplification (CPA) system is demonstrated. It consists of a mode-locked fiber oscillator, an erbium-doped fiber amplifier, and an in-fiber stretcher and compressor, and it is pumped with a diode laser.
Assessment of targeting accuracy of a low-energy stereotactic radiosurgery treatment for age-related macular degeneration (2010)

Age-related macular degeneration (AMD), a leading cause of blindness in the United States, is a neovascular disease that may be controlled with radiation therapy. Early patient outcomes of external beam radiotherapy, however, have been mixed. Recently, a novel multimodality treatment was developed, comprising external beam radiotherapy and concomitant treatment with a vascular endothelial growth factor inhibitor. The radiotherapy arm is performed by stereotactic radiosurgery, delivering a 16 Gy dose in the macula (clinical target volume, CTV) using three external low-energy x-ray fields while adequately sparing normal tissues. The purpose of our study was to test the sensitivity of the delivery of the prescribed dose in the CTV using this technique and of the adequate sparing of normal tissues to all plausible variations in the position and gaze angle of the eye. Using Monte Carlo simulations of a 16 Gy treatment, we varied the gaze angle by ±5° in the polar and azimuthal directions, the linear displacement of the eye ±1 mm in all orthogonal directions, and observed the union of the three fields on the posterior wall of spheres concentric with the eye that had diameters between 20 and 28 mm. In all cases, the dose in the CTV fluctuated <6%, the maximum dose in the sclera was <20 Gy, the dose in the optic disc, optic nerve, lens and cornea were <0.7 Gy and the three-field junction was adequately preserved. The results of this study provide strong evidence that for plausible variations in the position of the eye during treatment, either by the setup error or intrafraction motion, the prescribed dose will be delivered to the CTV and the dose in structures at risk will be kept far below tolerance doses.
An integrated scratch-pad allocator for affine and non-affine code (2006)

Scratch-pad memory (SPM) allocators that exploit the presence of affine references to arrays are important for scientific benchmarks. On the other hand, such allocators have so far been limited in their general applicability. In this paper we propose an integrated scheme that for the first time combines the specialized solution for affine program allocation with a general framework for other code. We find that our integrated framework does as well or outperforms other allocators for a variety of SPM sizes.
Production of ultra high quantities of <sup>18</sup>F‐fluoride Via <sup>18</sup>O<sub>2</sub> gas target: A progress report (2001)

Abstract There is a real need to develop a superior high yield target system for the production of large quantities of 18 F‐fluoride with the increasing numbers of clinical PET centers worldwide. Therefore we have investigated a route to higher yield target system for 18 F‐fluoride production which relies on gas target designs. (1)
Rapamycin and interleukin-10 treatment induces T regulatory type 1 cells that mediate antigen-specific transplantation tolerance. (2006)

Islet transplantation is a cure for type 1 diabetes, but its potential is limited by the need for constant immunosuppression. One solution to this problem is the induction of transplantation tolerance mediated by T regulatory cells. T regulatory type 1 (Tr1) cells are characterized by their production of high levels of interleukin (IL)-10, which is crucial for their differentiation and suppressive function. We investigated the effects of IL-10 administered in combination with rapamycin on the induction of Tr1 cells that could mediate a state of tolerance in diabetic mice after pancreatic islet transplantation. The efficacy of this treatment was compared with IL-10 alone and standard immunosuppression. Stable long-term tolerance that was not reversible by alloantigen rechallenge was achieved only in mice treated with rapamycin plus IL-10. Tr1 cells that produced high levels of IL-10 and suppressed T-cell proliferation were isolated from splenocytes of rapamycin plus IL-10-treated mice after treatment withdrawal. In rapamycin plus IL-10-treated mice, endogenous IL-10 mediated an active state of tolerance, as was observed when the blockade of IL-10 activity rapidly induced graft rejection >100 days after transplantation. CD4(+) T-cells from rapamycin plus IL-10-treated mice transferred antigen-specific tolerance in mice that received new transplants. Thus rapamycin plus IL-10 not only prevented allograft rejection but also induced Tr1 cells that mediated stable antigen-specific, long-term tolerance in vivo.
Separation and contrast enhancement of overlapping cast shadow components using polarization (2006)

Shadow is an inseparable aspect of all natural scenes. When there are multiple light sources or multiple reflections several different shadows may overlap at the same location and create complicated patterns. Shadows are a potentially good source of information about a scene if the shadow regions can be properly identified and segmented. However, shadow region identification and segmentation is a difficult task and improperly identified shadows often interfere with machine vision tasks like object recognition and tracking. We propose here a new shadow separation and contrast enhancement method based on the polarization of light. Polarization information of the scene captured by our polarization-sensitive camera is shown to separate shadows from different light sources effectively. Such shadow separation is almost impossible to realize with conventional, polarization-insensitive imaging.
OC-060 A clinically applicable three gene signature is independently highly prognostic in oesophageal and junctional adenocarcinoma (2010)

<h3>Introduction</h3> The incidence of oesophageal and junctional adenocarcinoma has increased sixfold in the last 30 years and 5-year survival remains <14%. Most patients present with advanced disease and current staging is limited in its ability to predict survival. We aimed to generate and externally validate a molecular prognostic signature for oesophageal adenocarcinoma. <h3>Methods</h3> Gene expression profiling was performed and the resulting 42 000 gene signatures correlated with clinical features for 91 snap frozen oesophageal and junctional resection specimens. External validation of selected targets was carried out on 371 independent cases using immunohistochemistry to maximise clinical applicability. <h3>Results</h3> Gene expression profiles were obtained from 75/91 of the samples (82%). 119 genes were significantly associated with survival and 270 genes with the number of involved lymph nodes. Ten of these genes were taken forward to external validation at the protein level. Three genes were prognostic in the external validation data set (TRIM44, SIRT2 and PAPSS2). Patients with dysregulation of none of these three genes had a significantly better outcome (5-year survival 48%) than those with dysregulation of one gene (5-year survival 29%), who in turn did better than those with two or more genes dysregulated (5-year survival 15%) (p=0.004). The three gene signature was independently prognostic in a multivariable model together with the existing clinical TNM staging system (p=0.003). <h3>Conclusion</h3> We have generated and externally validated an immunohistochemical prognostic gene signature which is independently highly prognostic in an external validation data set. In addition these three genes are possible therapeutic targets raising the possibility of personalised therapy based on a patient9s molecular prognostic signature. Our three gene signature is suitable for application in routine clinical practice and this study may provide a framework for similar future projects.
Oversampled A/D Conversion using Alternate Projections (1991)

In this paper, it is shown that oversampled A/D conversion methods can be substantially improved by using iterative postprocessing involving linear filtering as well as nonlinear operations. The only condition is that the quantizer produces a so-called convex code, which is the case for the simple and dithered A/D conversion, as well as for n th order single path \\Sigma\\Delta modulation. The iterative algorithm, using alternate projection, searches for the intersection of a subspace (band limited signals) and a convex set (signals with same code). Convergence is guaranteed by convexity. We indicate practical algorithms for simple, dithered, 1 st and 2 nd order (single path) \\Sigma\\Delta oversampled quantization. The improvements in SNR due to oversampling in these schemes which would normally be 3; 3; 9 and 15dB per octave of oversampling respectively, are increased to 6; 6; 12 and 18dB. That is an increase of 3dB per octave. 1 Introduction Oversampled A/D conversion (or ADC) i...
Prediction of Aqueous Solubility of a Diverse Set of Compounds Using Quantitative Structure−Property Relationships (2003)

"Fail early and fail fast" is the current paradigm that the pharmaceutical industry has adopted widely. Removing non-drug-like compounds from the drug discovery lifecycle in the early stages can lead to tremendous savings of resources. Thus, fast screening methods are needed to profile the large collection of synthesized and virtual libraries involved in the early stage. Solubility is one of the filters that are applied extensively to ensure that the compounds are reasonably soluble so that synthesis of the compounds and assay studies of pharmacokinetics and toxicity are feasible. To address this need, we have developed a fast quantitative structure-property relationship (QSPR) model for the prediction of aqueous solubility (at 298 K, unbuffered solution) from the molecular structures. Multiple linear regressions and genetic algorithms were used to develop the models. The model was based on a set of diverse compounds including small organic molecules and drug and drug-like species. The predicted solubility for the training and test sets agrees well with the experimental values. The coefficient of determination is R(2) = 0.84 for the training set of 775 compounds and the RMS error = 0.87. This model was validated on four sets of compounds. The RMS error for the 1665 compounds from the four validation data sets (including compounds from the Physician's Desk References and Comprehensive Medicinal Chemistry databases) is 1 log unit and the unsigned error is 0.77. This model does not require 3-D structure generation which is rather time-consuming. Using 2-D structure as input, this model is able to compute solubility for 90 000-700 000 compounds/h on a SGI Origin 2000 workstation. This kind of fast calculation allows the model to be used in data mining and screening of large synthesized or virtual libraries.
A Beam Search Algorithm for ITG Word Alignment (2012)

Inversion transduction grammar (ITG) provides a syntactically motivated solution to modeling the distortion of words between two languages. Although the Viterbi ITG alignments can be found in polynomial time using a bilingual parsing algorithm, the computational complexity is still too high to handle real-world data, especially for long sentences. Alternatively, we propose a simple and effective beam search algorithm. The algorithm starts with an empty alignment and keeps adding single promising links as early as possible until the model probability does not increase. Experiments on Chinese-English data show that our algorithm is one order of magnitude faster than the bilingual parsing algorithm with bitext cell pruning without loss in alignment and translation quality.
A potent plant virus inhibitor found in Mirabilis jalapa L. (1990)

An inhibitor of plant virus infection was found in the extracts of Mirabilis jalapa L. The inhibitor, a protein designated as MAP (Mirabilis antiviral protein), showed highly potent activity against mechanical transmission of viruses, tobacco mosaic (TMV), cucumber green mottle mosaic, potato Y, turnip mosaic and cucumber mosaic. Almost complete inhibition was achieved when MAP at 0.8μg/ml was applied on the upper surface of leaves of Xanthi nc tobacco 24hr before TMV inoculation, and 50% inhibition when MAP at 10μg/ml was applied on the under surface of leaves. MAP induced systemic resistance to TMV infection in tobacco plants when it was applied on their basal leaves 24hr before TMV inoculation onto the upper ones. MAP showed no inhibition when it was applied 1hr after TMV inoculation. Antiserum against MAP gave positive reaction in the agar gel with leaf extracts of M. jalapa and did not with those of the other Chenopodiales plants such as Basella rubra, Boerhaavia diffusa, Bougainvillea sp., Chenopodium amaranticolor and Phytolacca americana. Concentration of MAP was successfully quantified using enzyme-linked immunosorbent assay. MAP content in the root tissue was exceedingly higher than in the other parts of the plant and that of an yellow-flower trait of M. jalapa was as high as 1.1mg/g fresh weight. M. jalapa seems to be a promising source of antiviral substances for the practical use.
Model reduction for PEEC models including retardation (2002)

Partial element equivalent circuits (PEEC) are applied for modeling of interconnects in packages. These models are suitable for a wide range of three-dimensional problems. When PEEC models are applied to large packages, large equivalent circuits are generated. Model reduction techniques for PEEC models have been proposed by several researchers but typically for problems where retardation is not important or where two-dimensional models suffice. In this paper, we give a new model reduction procedure applicable to full wave PEEC models which include losses and retardation. We include two examples to demonstrate the application of this method.
Deep Ultraviolet Light‐Emitting Hexagonal Boron Nitride Synthesized at Atmospheric Pressure. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
ChemInform Abstract: POTENTIAL CENTRAL NERVOUS SYSTEM ANTITUMOR AGENTS, HYDANTOIN DERIVATIVES (1975)

Abstract Aus den Hydantoinen (I) entstehen mit Brom‐chlor‐äthylen die Substitutionsprodukte (II), die mit Diäthanolamin zu (III) und weiter mit Phosphoroxychlorid zu den Stickstoff‐Lost‐Verbindungen (IV) umgesetzt werden.
A computationally efficient method for identifying network parameter errors (2016)

A recently proposed method that is based on the normalized Lagrange multipliers for identifying network parameter errors has shown to be very effective yet also carries a high computational burden prohibiting its efficient use for large transmission grids. This paper presents an efficient solution that greatly reduces this burden facilitating the method's implementation in large practical power systems. The reduction in the computational cost is achieved by exploiting the sparse structure of the jacobian and gain matrices. The necessary subset of entries of the inverse matrix is determined by a two-step back stepping logic, and they are computed by a modified version of the well-known “sparse inverse” algorithm. Simulation results show that the proposed approach drastically reduces the computational load. Scenarios with different types of parameter errors are simulated to illustrate the application of the proposed implementation for very large size power systems.