gebhart/patrepeval huggingface dataset:
Expression and Properties of the Highly Alkalophilic Phenylalanine Ammonia-Lyase of Thermophilic Rubrobacter xylanophilus (2014)

The sequence of a phenylalanine ammonia-lyase (PAL; EC: 4.3.1.24) of the thermophilic and radiotolerant bacterium Rubrobacter xylanophilus (RxPAL) was identified by screening the genomes of bacteria for members of the phenylalanine ammonia-lyase family. A synthetic gene encoding the RxPAL protein was cloned and overexpressed in Escherichia coli TOP 10 in a soluble form with an N-terminal His6-tag and the recombinant RxPAL protein was purified by Ni-NTA affinity chromatography. The activity assay of RxPAL with l-phenylalanine at various pH values exhibited a local maximum at pH 8.5 and a global maximum at pH 11.5. Circular dichroism (CD) studies showed that RxPAL is associated with an extensive α-helical character (far UV CD) and two distinctive near-UV CD peaks. These structural characteristics were well preserved up to pH 11.0. The extremely high pH optimum of RxPAL can be rationalized by a three-dimensional homology model indicating possible disulfide bridges, extensive salt-bridge formation and an excess of negative electrostatic potential on the surface. Due to these properties, RxPAL may be a candidate as biocatalyst in synthetic biotransformations leading to unnatural l- or d-amino acids or as therapeutic enzyme in treatment of phenylketonuria or leukemia.
Automatic Correction for Window Fouling of near Infrared Probes in Fluidised Systems (2014)

Near infrared (NIR) spectroscopy is a versatile, non-invasive and non-destructive tool that is often used for process monitoring in the pharmaceutical industry. Often, equipment window fouling or probe fouling of in-situ NIR probes occurs, leading to biased spectra and wrong interpretations (e.g. process-state estimation). Physical counter measures, including self-cleaning probes and geometrical considerations, are called for. This paper presents a mathematical solution to the problem of window fouling for an NIR-monitored process: by determining the distance to the particles, we established which part of the signal was missing owing to the coating accumulation on the probe window. The proposed approach is illustrated with the example of hot-melt coating in a fluidised bed, during which coating buildup on substrate particles was monitored despite window fouling.
Universal Primer Applications for Pyrosequencing<sup>®</sup> (2007)

Pyrosequencing is a high-throughput technique for single-nucleotide polymorphism (SNP) genotyping, DNA sequencing, and SNP allele frequency and DNA methylation assays. The Pyrosequencing assay involves initially purifying PCR-generated single-strand DNA labeled with biotin as a sequencing template. The disadvantage of the synthesis of a biotinylated sequence-specific primer to assay each DNA variant lies in costs and time consumption. To overcome this problem, methodology has been developed to generate biotinylated Pyrosequencing DNA templates using a universal biotinylated primer. Using this methodology, biotinylated DNA fragments can be generated without the use of sequence-specific biotinylated primers for each DNA variant.
A micrographic and gravimetric study of intercalation and deintercalation of graphite fibers (1985)

Intercalation and deintercalation of Union Carbide P-100 graphite fibers with liquid and vaporous bromine was studied gravimetrically and microscopically. The mass of the bromine intercalated fibers was found to be 17 to 20 percent greater than their pristine counterpart. This variation decreased to 17 to 18 percent after heating in air for 3 days at 200 C and to 14.5 to 18 percent after 6 days of 260 C heating. The fiber length did not change throughout the experiment. The fiber diameter increased during intercalation and decreased slightly upon deintercalation but was not affected by heating to 260 C for 3 days in air. Comparing the mass and volume data to those with highly oriented pyrolitic graphite or natural single crystal graphite suggested the possibility that the intercalated P-100 fibers could be mostly stage 4.
Application of polarization for optical motion-registered SPECT functional imaging of tumors in mice (2005)

The use of small animal models to investigate human diseases is an integral part of the development of new diagnostic and treatment regimens. Consequently, functional imaging modalities such as single photon emission computed tomography (SPECT) are increasingly being utilized to streamline the screening of animal phenotypes and to monitor disease states, progressions, and therapies. This paper focuses on the utilization of polarization filtering to minimize specular reflection from a glass tube used for holding live human-tumor-mice during functional imaging in a dedicated small animal SPECT system. The system presented is potentially useful for the real-time non-invasive investigation of diseases, such as cancer, and drug therapies in small animals because it utilizes optical motion-registered functional imaging that minimizes the effects of motion artifacts.
Detection of antibodies to human herpesvirus-6 using immunofluorescence assay. (1991)

A serological study of human herpesvirus-6 (HHV-6) infection was performed by means of immunofluorescence assay on fixed HHV-6-infected cells. Comparison between indirect immunofluorescence assay (IFA) and anticomplement immunofluorescence assay (ACIF) showed that the latter test was the most appropriate for HHV-6 serology, although both methods exhibited identical sensitivity. ACIF, which was performed on HSB2 cells infected with the HBLV strain (provided by S.Z. Salahuddin), was then used to determine the titre of HHV-6 antibodies in serum by end-point dilution. The sera from 115 healthy subjects and 99 patients with presumed viral infection were tested. A similar distribution of HHV-6 titres was evidenced in both cases and the rate of individuals exhibiting a positive titre of 20 and above was about 30% of the whole population studied. No serological cross-reactivity was observed between HHV-6 and other herpesviruses, suggesting that the HHV-6 ACIF test was quite specific.
Microwave CI <sub>2</sub> /H <sub>2</sub> discharges for high rate etching of InP (1992)

Microwave (2.45GHz) Cl2/H2 discharges operated in the electron cyclotron resonance condition at low pressure (0.5 mtorr) are shown to yield high-rate (1.5 μm min−1) plasma etching of InP at 150°C with low additional DC bias (−150V) on the sample. The etched surface morphology and optical quality, and anisotropy of the resultant features are all strong functions of the Cl2-to-H2 ratio in the discharge.
블록별 부지분류 적용 해안시설 영역에서의 HAZUS 기반 지진피해 추정 (2014)

HAZUS-MH는 지진, 홍수 및 허리케인의 세 가지 다중 재해현상에 대한 잠정적 손실을 추정하기 위한 GIS 기반의 컴퓨터 프로그램이다. 지진 재난에 대해서는 HAZUS에 설정한 가상이나 실제 지진 특성에 따라 지진동의 세기가 평가되고 이에 따라 손실을 계산하게 된다. 본 연구에서는 해안 플랜트시설 영역의 향후 지진에 대한 대비의 일환으로 HAZUS를 활용하였다. 대상 시설영역의 특성 평가를 위해 기존 지반조사 보고서를 토대로 지반특성 자료들을 취합하였다. 또한, 시설구조물들의 재료 및 구조 특성에 따라서도 분류하였다. 연구 영역은 부지 조성 및 시설 분포 상황을 고려하여 17개 블록으로 나누고 지반 조건을 내진설계기준의 부지분류 체계에 따라 구분하였다. 뿐만 아니라, 수치 모델링을 통해 주요 시설물들의 지진취약도 곡선들을 도출하고 HAZUS 데이터베이스에 적용하였다. 이 연구 영역에 대한 HAZUS 활용 추정 결과는 부지 조건 및 구조물 종류에 따라 다양한 지진 피해와 손실 정도를 보였다. 본 사례 연구를 통해 해안시설 영역의 지진 피해 평가를 위한 HAZUS의 적용 가능성을 확인하였다.
Experimental investigation of the nonlinear optical loop mirror with twisted fiber and birefringence bias (2005)

We examine the transmission characteristics of a NOLM device using a symmetrical coupler, highly twisted fiber, and a quarter-wave (QW) retarder plate introducing a polarization asymmetry in the loop. We demonstrate high dynamic range with controllable transmissivity, and good stability over long times. We experimentally study the transmission behavior for different input polarization states and distinguish between different polarization components of the output beam. Experiments are in good agreement with our theoretical approach previously published. Appropriate choice of the input and output polarizations allows a very high dynamic range. The adjustment of the QW retarder and input polarization enables tuning the critical power over a wide range.
ChemInform Abstract: BECKMANN REARRANGEMENT OF ALDOXIMES CATALYZED BY TRANSITION METAL SALTS‐ A DEHYDRATION‐HYDRATION REACTION (1976)

Abstract Die NMR‐spektroskopische Verfolgung der Reaktion von Acetaldoxim (I) mit Phenylacetonitril (II) zeigt, daß, katalysiert durch Ni‐ oder Pd‐acetylacetonat, Ni‐acetat oder Acetylacetonato‐nitromethan‐triphenylphosphinpalladium, das Oxim (I) unter Bildung des Nitrils (III) dehydratisiert und das Nitril (II) unter Bildung des Amids (IV) hydratisiert wird.
Receptor of Activated Protein C Promotes Metastasis and Correlates with Clinical Outcome in Lung Adenocarcinoma (2012)

EPCR and its ligand APC promote cell survival that contributes to tumor cell endurance to stress favoring prometastatic activity of lung adenocarcinoma. EPCR/APC is a novel target of relevance in the clinical outcome of early-stage lung cancer.
Efficient Stereoselective Syntheses of Cyclic Amino Acids via Michael-Induced Ring-Closing Reactions (2003)

[reaction: see text] Zn-chelated glycine ester enolates are highly efficient nucleophiles for the synthesis of trans-methoxycarbonylcyclopropyl- and cyclobutylglycines by domino sequences of Michael additions and subsequent ring closures. They react to give the anti isomers with high yields and excellent diastereoselectivities.
A monoclonal antibody to the beta subunit of the skeletal muscle dihydropyridine receptor immunoprecipitates the brain omega-conotoxin GVIA receptor. (1991)

Antibodies against the subunits of the dihydropyridine-sensitive L-type calcium channel of skeletal muscle were tested for their ability to immunoprecipitate the high affinity (Kd = 0.13 nM) 125I-omega-conotoxin GVIA receptor from rabbit brain membranes. Monoclonal antibody VD2(1) against the beta subunit of the dihydropyridine receptor from skeletal muscle specifically immunoprecipitated up to 86% of the 125I-omega-conotoxin receptor solubilized from brain membranes whereas specific antibodies against the alpha 1, alpha 2, and gamma subunits did not precipitate the brain receptor. Purified skeletal muscle dihydropyridine receptor inhibited the immunoprecipitation of the brain omega-conotoxin receptor by monoclonal antibody VD2(1). The dihydropyridine receptor from rabbit brain membranes was also precipitated by monoclonal antibody VD2(1). However, neither the neuronal ryanodine receptor nor the sodium channel was precipitated by monoclonal antibody VD2(1). The omega-conotoxin receptor immunoprecipitated by monoclonal antibody VD2(1) showed high affinity 125I-omega-conotoxin binding, which was inhibited by unlabeled omega-contoxin and by CaCl2 but not by nitrendipine or by diltiazem. An antibody against the beta subunit of the skeletal muscle dihydropyridine receptor stained 58- and 78-kDa proteins on immunoblot of the omega-conotoxin receptor, partially purified through heparin-agarose chromatography and VD2(1)-Sepharose chromatography. These results suggest that the brain omega-conotoxin-sensitive calcium channel contains a component homologous to the beta subunit of the dihydropyridine-sensitive calcium channel of skeletal muscle and brain.
Improving file system performance with predictive caching (1996)

Despite impressive advances in file system throughput resulting from technologies such as high-bandwidth networks and hard disk arrays, file system latency has not improved and in many cases has become worse. To complicate matters, emerging technologies such as wireless computing, widely distributed telecomputing environments, and wide area file systems are growing in use but often offer higher latency and lower performance than standard file systems. Consequently, file system I/O remains one of the major bottlenecks to computer system performance (Ous90) and is expected to remain a major bottleneck for the foreseeable future.
This dissertation describes the design, implementation and evaluation of an automated predictive approach towards reducing file latency. Automatic Prefetching uses past file accesses to predict future file system requests. The objective is to copy the data into the local cache in advance of the request for the data, effectively masking access latencies. We turn the file cache from a repository of recently used data into a staging area for data about to be used.
Our algorithms are able to use the recent history of file accesses to make heuristic predictions of future requirements while forgetting less useful history from the distant past. Our algorithms predict which files will be needed soon, which portions of the predicted files are required and when that data will be needed. The algorithms are computationally inexpensive and require little storage.
We have developed and tested a simulator to tune the algorithms and developed a working prototype to test its real world performance. Further, we compare our results to both standard nonprefetching file systems and a prefetching file system that makes near optimal predictions. Results from the prototype show that prefetching can reduce the time needed by realistic applications to read a set of files by over 50%.
Useful approximations for converted-wave AVO (2001)

Abstract Converted-wave amplitude versus offset (AVO) behavior may be fit with a cubic relationship between reflection coefficient and ray parameter. Attributes extracted using this form can be directly related to elastic parameters with low-contrast or high-contrast approximations to the Zoeppritz equations. The high-contrast approximation has the advantage of greater accuracy; the low-contrast approximation is analytically simpler. The two coefficients of the low-contrast approximation are a function of the average ratio of compressional-to-shear-wave velocity (α/β) and the fractional changes in S-wave velocity and density (Δβ/β and Δρ/ρ). Because of its simplicity, the low-contrast approximation is subject to errors, particularly for large positive contrasts in P-wave velocity associated with negative contrasts in S-wave velocity. However, for incidence angles up to 40° and models confined to |Δβ/β| &lt; 0.25, the errors in both coefficients are relatively small. Converted-wave AVO crossplotting of the coefficients of the low-contrast approximation is a useful interpretation technique. The background trend in this case has a negative slope and an intercept proportional to the α/β ratio and the fractional change in S-wave velocity. For constant α/β ratio, an attribute trace formed by the weighted sum of the coefficients of the low-contrast approximation provides useful estimates of the fractional change in S-wave velocity and density. Using synthetic examples, we investigate the sensitivity of these parameters to random noise. Integrated P-wave and converted-wave analysis may improve estimation of rock properties by combining extracted attributes to yield fractional contrasts in P-wave and S-wave velocities and density. Together, these parameters may provide improved direct hydrocarbon indication and can potentially be used to identify anomalies caused by low gas saturations.
Vortex-Based Aero- and Hydrodynamic Estimation (2013)

Flow control strategies often require knowledge of unmeasurable quantities, thus presenting a need to reconstruct flow states from measurable ones. In this thesis, the modeling, simulation, and estimator design aspects of flow reconstruction are considered. First, a vortex-based aero- and hydrodynamic estimation paradigm is developed to design a wake sensing algorithm for aircraft formation flight missions. The method assimilates wing distributed pressure measurements with a vortex-based wake model to better predict the state of the flow. The study compares Kalman-type algorithms with particle filtering algorithms, demonstrating that the vortex nonlinearities require particle filters to yield adequate performance. Furthermore, the observability structure of the wake is shown to have a negative impact on filter performance regardless of the algorithm applied. It is demonstrated that relative motions can alleviate the filter divergence issues associated with this observability structure.In addition to estimator development, the dissertation addresses the need for an efficient unsteady multi-body aerodynamics testbed for estimator and controller validation studies. A pure vortex particle implementation of a vortex panel-particle method is developed to satisfy this need. The numerical method is demonstrated on the impulsive startup of a flat plate as well as the impulsive startup of a multi-wing formation. It is clear, from these validation studies, that the method is able to accommodate the unsteady wake effects that arise in formation flight missions.Lastly, successful vortex-based estimation is highly dependent on the reliability of the low-order vortex model used in representing the flow of interest. The present treatise establishes a systematic framework for vortex model improvement, grounded in optimal control theory and the calculus of variations. By minimizing model predicted errors with respect to empirical data, the shortcomings of the baseline vortex model can be revealed and reconciled. Here, the method is demonstrated on an impulse matching model for canonical unsteady wing maneuvers and reveals the shortcomings of the Kutta condition in such flows. The resulting analysis sheds light on the governing physical processes and provides guidance for model improvement for the unsteady aerodynamics associated with these canonical wing maneuvers.
Functionalizing Polymer Surfaces by Field-Induced Migration of Copolymer Additives. 1. Role of Surface Energy Gradients (2001)

Field-induced migration of low surface tension polystyrene-b-poly(dimethyl siloxane) (PS-b-PDMS) block copolymer additives in a polystyrene (PS) host was investigated using a series of narrow molecular weight distribution polystyrenes (5 × 103 < Mw,PS < 2 × 107 g/mol). Dynamic contact angle analysis (DCA) and attenuated total reflection Fourier transform infrared (ATR−FTIR) spectroscopy measurements were used to characterize the surface chemical make-up of polymer/additive blends created by solvent casting, precipitation, and melt annealing processes. For all host PS molecular weights investigated, selective dimethyl siloxane (DMS) enrichment of the air/polymer interface was observed. Near saturation levels of DMS surface coverage were found in PS/PS-b-PDMS blends with bulk copolymer additive compositions as low as 2 wt %. The surface excess concentration of DMS groups ΔφDMS in these blends could be manipulated, however, by careful selection of the host PS and PS-b-PDMS additive molecular weight, annealing conditions, and physicochemical properties of materials comprising the bounding interfaces. The effect of the first two factors on ΔφDMS can be summarized by an approximate scaling relation, ΔφDMS ∼ MwPSα, where the scaling exponent α is a function of annealing conditions. For unannealed PS/PS-b-PDMS blend samples, α ≈ −0.5, whereas for samples annealed for prolonged periods at elevated temperatures α values in the range 0.1−0.15 were found. Surprisingly, PS/PS-b-PDMS blend samples annealed at elevated temperatures near high-energy aluminum substrates also manifested enhanced DMS concentration at the polymer/metal interface. These observations are discussed in terms of the molecular weight dependence of diffusivity, surface tension, and configurational entropy of the host polystyrene.
The spectrum of anionic oligosaccharides released by endo-beta-N-acetylglucosaminidase H from glycoproteins. Structural studies and interactions with the phosphomannosyl receptor. (1983)

We have performed a detailed analysis of all the anionic oligosaccharides released by endo-beta-N-acetylglucosaminidase H from the whole cell glycoproteins of P388D1 mouse macrophage-like cells labeled for 14 h with [2-3H]mannose. The major anionic species consisted of phosphorylated high mannose-type oligosaccharides containing one or two phosphomonoesters or phosphodiesters in several different positions. In addition we identified hybrid-type molecules containing one, two, or three sialic acid residues. A subset of the latter molecules also contained phosphodiesters or phosphomonoesters on another branch of the same oligosaccharide. Unlike previously reported hybrid-type molecules, these do not have a "bisecting" N-acetylglucosamine residue on the beta-linked mannose. Some of these oligosaccharides contained an unidentified acid-labile group on the core N-acetylglucosamine or the beta-linked mannose. The glycoproteins secreted by these cells were greatly enriched in hybrid oligosaccharides containing one sialic acid and one phosphomonoester. The interaction of the isolated oligosaccharides with bovine liver phosphomannosyl receptor immobilized on Affigel was analyzed. Oligosaccharides with phosphomonoesters were the only species that interacted with high affinity with the receptor, and molecules with two phosphomonoesters showed the best binding. The location of the phosphomonoester on the oligosaccharide influenced the degree of interaction with the receptor. Removal of accessible nonphosphorylated mannose residues improved the binding in some cases. These findings indicate that the generation of the physiological phosphomannosyl ligand on lysosomal enzymes involves removal of the blocking N-acetylglucosamine residues, trimming of certain mannose residues, and correct positioning of the phosphate esters.
Excavations at Sparta, 1924—28: § 1.—Introductory (1928)

As was stated in the Annual Report for the Session 1927–28, the excavations at Sparta in 1928 were on quite a small scale, lasting only three weeks, and were restricted to the following pieces of work :—at the Theatre we cleared up some fallen material, undertook some necessary conservation and tested a few points for the purpose of the plan; and at the Orthia Sanctuary we tidied up some fallen rubble-masonry, during which process we uncovered a small portion of the early votive deposit underlying the foundations of the Roman amphitheatre to the south of the limits reached in the excavations of 1906–10. Apart from the discovery of another columnar statue-base of a βωμονίκης , which I have since published elsewhere, the finds from the site need not be further discussed.
Planar wire-type inverted-F RFID tag antenna mountable on metallic objects (2004)

In this paper we present and discuss the development and performance of planar wire-type inverted-F antenna (IFA) for passive RFID tag applications. This antenna design is mountable on metallic objects and can be used in RFID applications. Studies in different fields of RFID and its applications and antenna performance have been carried out at Tampere University of Technology and MIT Auto-ID Lab (P. Raumonen et al., IEEE Int. Antennas and Propag. Symp., 2003; L. Ukkonen et al., Fourth Finnish Wireless Comm. Workshop, 2003; J. Waldrop et al., IEEE Int. Conf. on Comm., 2003; S. Sarma et al, Micro, IEEE, volume 21, issue 6, 2001) and other universities recently. The IFA represents the first low-profile antenna designed for passive RFID applications on metalized objects.
Electrophysiological biomarkers in spinal muscular atrophy: proof of concept (2013)

These studies confirm features of preserved neuromuscular function in the early postnatal period and subsequent motor unit loss in SMNΔ7 mice. SMN restoring therapies result in preserved MUNE and gradual repair of CMAP responses. This provides preclinical evidence for the utilization of CMAP and MUNE as biomarkers in future SMA clinical trials.
The precipitation of metals by means of 8-hydroxyquinoline (oxine). Part II. The effect of pH on the precipitation of cadmium, tungsten, and uranium from acetate solutions (1937)

H. R. Fleck, Analyst, 1937, 62, 378 DOI: 10.1039/AN9376200378