gebhart/patrepeval huggingface dataset:
Identification and Molecular Analysis of Rough-Colony-Specific Outer Membrane Proteins of <i>Actinobacillus actinomycetemcomitans</i> (1999)

Actinobacillus actinomycetemcomitans, a gram-negative bacterium isolated from the human mouth, has been implicated in the pathogenesis of early-onset periodontitis. Primary isolates cultured from subgingival plaque exhibit an adherent, rough colony phenotype which spontaneously converts to a nonadherent, smooth phenotype upon in vitro subculture. The rough colony variant produces abundant fimbriae and autoaggregates, while the smooth colony variant is planktonic and produces scant fimbriae. To begin to understand the significance of colony variation in biofilm formation by A. actinomycetemcomitans, outer membrane protein profiles of four isogenic rough and smooth colony variants were compared by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Two proteins with relative molecular masses of 43 and 20 kDa were expressed by the rough colony variants exclusively. Expression of these proteins was not found to be dependent on growth phase, oxygen tension, or type of complex medium. N-terminal amino acid sequences of these proteins obtained by Edman degradation were compared with sequences from the University of Oklahoma A. actinomycetemcomitans genome database. Two contiguous open reading frames (ORFs) encoding proteins having sequence homology with these proteins were identified. The 43-kDa protein (RcpA [rough colony protein A]) was similar to precursor protein D of the general secretion pathway of gram-negative bacilli, while the 20-kDa protein (RcpB [rough colony protein B]) appeared to be unique. The genes encoding these proteins have been cloned from A. actinomycetemcomitans 283 and sequenced. A BLASTX (gapped BLAST) search of the surrounding ORFs revealed homology with other fimbria-related proteins. These data suggest that the genes encoding the 43-kDa (rcpA) and 20-kDa (rcpB) proteins may be functionally related to each other and to genes that may encode fimbria-associated proteins.
Secondary purification of islets by the use of immunomagnetic separation techniques (1995)

Type I diabetes 1.1% of the population in the UK affects. Whilst insulin injections can control diabetes it has been shown that the frequency of secondary complications are only reduced by strict glycemic control. Pancreas transplants have been carried out to reverse diabetes. However, due to the severity, the morbidity and mortality of the procedure, only patients who have already received a kidney transplant and therefore have secondary complications have undergone such a procedure. Pancreatic islet transplantation is a less invasive procedure. Since the 1980's, reports of clinical islet transplantation using purified and unpurified islets have been made. Studies in the animal model, recent reports from clinical studies, and work carried out in this thesis, have emphasised the need to purify islets prior to transplantation. Islets are purified by the use of density gradients. However, due to the overlapping densities of the islet and exocrine tissue, complete separation cannot be achieved. Therefore a more specific method is needed to increase the yield of islets obtained from a cadaver donor pancreas. This thesis describes the development of a system using immunomagnetic techniques for the purification of islets. Using a quadripolar magnetic field into which the digest is released from a vibrating pipette with the addition of BSA prior to release, islets can be successfully purified with a loss of only 25%. The system can be used as a secondary purification following density dependent purification to increase the yield of islets from a single pancreas, making one donor to one recipient transplants a realistic option.
Antireflection coated, wedged, single-crystal silicon aircraft window for the far-infrared (1999)

Operating far-infrared remote-sensing instruments from inside a pressurized cabin of an aircraft requires a window with high transmittance. Furthermore, the radiometric properties of the window, such as the transmittance and the emitted radiation (i.e., temperature distribution), have to be known. The design of a wedged, antireflection coated single-crystal silicon aircraft window, its modeled transmittance spectrum, and the applied coating technique are presented. Measurements of the window transmittance with the 2.5 THz heterodyne spectrometer TeraHertz OH-Measurement Airborne Sounder (THOMAS) and a Fourier-transform spectrometer are presented, showing a transmittance of about 90% around 84 cm/sup -1/. The window was designed and built for the 2.5 THz OH-Sensor THOMAS, operated on the DLR research aircraft FALCON. The transmittance of 90% means a substantial improvement compared to the window used previously. With this new window, systematic errors in the measured atmospheric radiance could be lowered, making the retrieval of atmospheric parameters easier. Several successful flights with the new window up to an altitude of 43000 ft have already been performed.
Study on the laser irradiation effects on coating reinforced glass fiber/resin composite material (2016)

Two kinds of anti-laser coating made of reflective / ablative resin, called reinforcement schemes of A and B, are applied to the glass fiber reinforced resin matrix composite plate. The anti-laser performance of these samples to the laser operated at the wavelength of 976nm is tested, under the case of a 0.3 Mach tangential airflow pass over the surface of the sample. The experimental results show that the laser damage threshold of the coating reinforced samples have increased more than 50% compared to the original sample, the reinforcement scheme B is better than A. The laser power density damage threshold of the coating reinforced samples to the near infrared laser is higher than 100W/cm<sup>2</sup>, under the irradiation time is 60 seconds. For the resin reinforced fiber samples, the removal process of the ablation residues has important effects on the perforation time of samples, when there is a strong airflow pass over the surface. The larger laser spot corresponding to the removal of the ablation residues is easier.
STUDY OF PARAMETERS WHICH AFFECT CORROSION BETWEEN SOLID FILM LUBRICANTS AND AIRCRAFT ALLOYS (1977)

This paper summarizes the findings of a program demonstrating how parameters such as humidity, surface pretreatment, inhibitors, SO2/salt ratio, environment, etc., affect corrosion between solid film lubricants and various aircraft alloys. It was found that burnishing the surface of a solid film lubricant causes rapid loss of corrosion protection. The reason for this could be that the MoS2 particles are pressed closer together and become more of the conductor. If this is true, it would mean that a lubricant does not have to contain graphite to cause galvanic corrosion when involved in a dissimilar metal couple. Pretreatments were found to have less effect than expected on corrosion prevention. Humidity was found to have no effect on wear life or corrosion rate.
Vaccine to prevent AIDS overstated. (1999)

The effectiveness of AIDSVAX is challenged because the vaccine's principal component is designed to induce immune responses against the envelope protein gp120, which mutates easily. The vaccine cannot cause AIDS, and trials have shown it to be safe. However, those who take the vaccine will test positive on HIV antibody tests. Other issues challenging the effectiveness of AIDSVAX are discussed.
Receptor-stimulated death pathway is opened by antigen in mature T cells. (1991)

Clonal deletion provides an important mechanism for the elimination of autoreactive T cells. Deletion is accomplished by programmed cell death directed by interaction of the T-cell receptor (TCR) of the developing thymocyte with major histocompatibility complex elements in the thymic environment. In this report we present evidence to support the hypothesis that the activation and the maturation state of the T cell may be important in coupling the TCR to the "death program." We show that coupling of the TCR to the death program is open during maturation but closed in naive mature T cells. However, during primary antigenic stimulation, coupling between the TCR and the death program is reopened, as demonstrated by the stimulation of the death of these cells by immobilized anti-TCR. Our results suggest that further examination of mature cells that are either resistant or sensitive to receptor-stimulated death may lead to the identification of the components of the death pathway and may provide clues to the regulation of their coupling to TCR signals.
Human serum procarboxypeptidase A (1983)

Zymogen activation is an important biochemical control process and has important physiological and pathological implications. We have simultaneously measured both procarboxypeptidase A, the enzyme precursor, and carboxypeptidase A, its active product, in serum by using an affinity resin and the synthetic peptide substrate N-(2-furanacryloyl)-L-phenylalanyl-L-phenylalanine. Serum procarboxypeptidase A is activated by trypsin, chymotrypsin, plasmin, subtilisin, or urokinase but not by thrombin or enteropeptidase. The molecular weight of the precursor is approximately 5000-10 000 greater than that of the active product. Both enzyme and precursor increase in serum in the course of pancreatic inflammation, but the degree of activation can vary up to 2000-fold, independent of the amount of precursor present. The existence of this pancreatic proteolytic precursor in serum opens new avenues for the investigation of zymogen activation and its regulation.
Competitive Analysis of Minimum-Cut Maximum Flow Algorithms in Vision Problems (2010)

Rapid advances in image acquisition and storage technology underline the need for algorithms that are capable of solving large scale image processing and computer-vision problems. The minimum cut problem plays an important role in processing many of these imaging problems such as, image and video segmentation, stereo vision, multi-view reconstruction and surface fitting. While several min-cut/max-flow algorithms can be found in the literature, their performance in practice has been studied primarily outside the scope of computer vision. We present here the results of a comprehensive computational study, in terms of execution times and memory utilization, of four recently published algorithms, which optimally solve the {\em s-t} cut and maximum flow problems: (i) Goldberg's and Tarjan's {\em Push-Relabel}; (ii) Hochbaum's {\em pseudoflow}; (iii) Boykov's and Kolmogorov's {\em augmenting paths}; and (iv) Goldberg's {\em partial augment-relabel}. Our results demonstrate that the {\em Hochbaum's pseudoflow} algorithm, is faster and utilizes less memory than the other algorithms on all problem instances investigated.
Phospholipase A2 gene expression and activity in histologically normal ileal mucosa and in Crohn's ileitis. (1995)

Increased activity of phospholipase A2 (PLA2) in the ileal mucosa may contribute to the inflammation in Crohn's disease. The results of this study showed that (a) three months after ileocolonic resection for Crohn's disease the neoterminal ileal mucosa showed endoscopically new inflammation and had higher PLA2 activity than at the time of the operation (n = 8); no such findings were seen in controls (n = 7), (b) histologically normal ileal mucosa (n = 3) contained mRNA for three isoforms of PLA2 (PLA2-I, PLA2-II, and cPLA2), but the amounts of PLA2-II mRNA clearly exceeded the amounts of mRNA for PLA2-I and cPLA2, (c) ileal mucosa from Crohn's patients (n = 2) contained higher values of PLA2-II mRNA than ileal mucosa from two controls, (d) ileal mucosa from Crohn's patients (n = 4) showed increased PLA2-II mRNA three months after ileocolonic resection. In conclusion, these results show that the predominating PLA2 mRNA in the human ileal mucosa is type II PLA2, and the increased synthesis of PLA2-II might be responsible for the increased PLA2 activity found in the ileal mucosa accompanying recurrent ileal inflammation in Crohn's disease.
UDPgalactose 4‐epimerase from <i>Saccharomyces cerevisiae</i> (2004)

UDPgalactose 4-epimerase (epimerase) catalyzes the reversible conversion between UDPgalactose and UDPglucose and is an important enzyme of the galactose metabolic pathway. The Saccharomyces cerevisiae epimerase encoded by the GAL10 gene is about twice the size of either the bacterial or human protein. Sequence analysis indicates that the yeast epimerase has an N-terminal domain (residues 1-377) that shows significant similarity with Escherichia coli and human UDPgalactose 4-epimerase, and a C-terminal domain (residues 378-699), which shows extensive identity to either the bacterial or human aldose 1-epimerase (mutarotase). The S. cerevisiae epimerase was purified to > 95% homogeneity by sequential chromatography on DEAE-Sephacel and Resource-Q columns. Purified epimerase preparations showed mutarotase activity and could convert either alpha-d-glucose or alpha-d-galactose to their beta-anomers. Induction of cells with galactose led to simultaneous enhancement of both epimerase and mutarotase activities. Size exclusion chromatography experiments confirmed that the mutarotase activity is an intrinsic property of the yeast epimerase and not due to a copurifying endogenous mutarotase. When the purified protein was treated with 5'-UMP and l-arabinose, epimerase activity was completely lost but the mutarotase activity remained unaffected. These results demonstrate that the S. cerevisiae UDPgalactose 4-epimerase is a bifunctional enzyme with aldose 1-epimerase activity. The active sites for these two enzymatic activities are located in different regions of the epimerase holoenzyme.
Analysis of spatial-temporal regularization methods for linear inverse problems from a common statistical framework (2005)

In some medical imaging problems, the quantity to image is time-varying but related to the measurements by spatial dynamics only. Traditional methods solve the associated inverse problem separately at each time instant. Several recent reports take advantage of prior knowledge and/or measurement temporal behavior to solve jointly in space and time. In this paper we discuss three such approaches, which have been introduced in distinct mathematical contexts, from a common statistical regularization framework, and illuminate their relationships, advantages and disadvantages.
Theoretical Properties for Neural Networks with Weight Matrices of Low Displacement Rank (2017)

Recently low displacement rank (LDR) matrices, or so-called structured matrices, have been proposed to compress large-scale neural networks. Empirical results have shown that neural networks with weight matrices of LDR matrices, referred as LDR neural networks, can achieve significant reduction in space and computational complexity while retaining high accuracy. We formally study LDR matrices in deep learning. First, we prove the universal approximation property of LDR neural networks with a mild condition on the displacement operators. We then show that the error bounds of LDR neural networks are as efficient as general neural networks with both single-layer and multiple-layer structure. Finally, we propose back-propagation based training algorithm for general LDR neural networks.
POSITRON ANNIHILATION AS A METHOD TO CHARACTERIZE POROUS MATERIALS (2006)

▪ Abstract Beam-based positron annihilation spectroscopy (PAS) is a powerful porosimetry technique with broad applicability in the characterization of nanoporous thin films, especially insulators. Pore sizes and distributions in the 0.3–30 nm range are nondestructively determined with only the implantation of low-energy positrons from a table-top beam. Depth-profiling with PAS has proven to be an ideal way to measure the interconnection length of pores, search for depth-dependent inhomogeneities or damage in the pore structure, and explore porosity hidden beneath dense layers or diffusion barriers. The capability of PAS is rapidly maturing as new intense positron beams around the globe spawn more accessible PAS facilities. After a short primer on the physics of positrons in insulators, the various probe techniques of PAS are briefly summarized, followed by a more detailed discussion of the wide range of nanoporous film parameters that PAS can characterize.
Timing synchronization of low power wireless sensor nodes with largely differing clock frequencies and variable synchronization intervals (2015)

In this paper a novel synchronization method for wireless sensor networks with star topology is presented. We address timing synchronization using low frequency real-time clocks in all nodes. A beacon-driven TDMA-protocol for bidirectional node/base communication is used. Between the beacons, which are sent by the base station, lie the superframe time intervals to handle data transmission from node to base. We discuss the protocol and its energy saving advantages including the challenges of synchronization. We reduce the required communication for synchronization based on long term synchronicity of the node to save energy. Due to the individual node clock, the accurate superframe time interval usually will consist of a rational number of clock ticks. We propose to use a ΔΣ-converter to generate a sequence of superframes with different time durations, but each consisting of integer multiples of clock ticks, which - on average - achieve the accurate superframe duration for any rational number of clock ticks. We show by theory and measurements that our novel approach leads to a variance of the synchronization error which is constant at a value of 0.25 clock cycles. The variance is independent of the rate at which the nodes listen to the beacon of the base station.
Regulation of nuclear binding of the avian oviduct progesterone receptor. Changes during estrogen-induced oviduct development, withdrawal, and secondary stimulation. (1984)

The progesterone receptors from various stages of estrogen induced oviduct development, estrogen withdrawal, and secondary stimulation with estrogen were examined. The progesterone receptors were characterized for their biological function (i.e. capacity for nuclear translocation, nuclear binding, and effects on RNA polymerase II activity) as well as certain physical properties. The progesterone receptors from the undeveloped or partially developed oviducts (0 to 8 days of estrogen treatment) displayed little or no nuclear translocation and binding in vivo or in vitro. Similarly, progesterone showed little or no effect in vivo on RNA polymerase II activity at the early stages of development. As development progressed from 8 to 12 days of estrogen treatment, the above parameters rapidly increased to maximal levels and plateaued through day 23 of estrogen treatment. A marked decrease in these parameters occurred within 1 day of estrogen withdrawal. The reverse series of events occurred during secondary estrogen stimulation of 10-day-old withdrawn chicks. While the receptor concentrations increased rapidly to maximum values by 2 days of restimulation, receptor function did not return until day 4. Similarly, the effects of progesterone on RNA polymerase II activity reached maximal values by day 4. The progesterone receptor isolated from oviducts during development, estrogen withdrawal, and restimulation, displayed similar patterns of cell-free binding to chromatin and nucleoacidic protein as that observed in vivo supporting the nativeness of the in vitro binding assay. In contrast, the cell-free binding of these same progesterone receptor to pure DNA were not similar to the in vivo binding, i.e. no patterns (differences) in progesterone receptor binding were observed. These data support that protein DNA complexes and not pure DNA represent the native acceptor sites for oviduct progesterone receptor. Comparison of the progesterone receptor between the functional and nonfunctional states revealed no differences in the steroid affinity for the receptor, in the apparent pI of the species, or in the sedimentation of the receptor under high salt conditions. However, the nonfunctional receptors consistently displayed a deficiency in one of the two monomer molecular species (the B species) as determined by isoelectric focusing. These results suggest that both monomer species of progesterone receptor are required for biological activity. Interestingly, the 7S "aggregate" species of the progesterone receptor was constantly detected even when only one of the monomer species was present.(ABSTRACT TRUNCATED AT 400 WORDS)
Dispersion of Asphaltenes in Petroleum with Ionic Liquids: Evaluation of Molecular Interactions in the Binary Mixture (2014)

Ionic liquids containing imidazolium cations 1-butyl-3-methylimidazolium chloride, 1-butyl-3-methylimidazolium nitrate, and 1-methyl-1H-imidazol-3-ium-2-carboxybenzoate were successfully synthesized and employed for the dispersion of asphaltenes in heavy oil, which is becoming a necessity during oil recovery and transportation. Molecular interaction studies indicated that 1-butyl-3-methylimidazolium chloride displayed a small HOMO–LUMO energy gap, which best explains its higher polarizability and reactivity as compared with 1-butyl-3-methylimidazolium nitrate and 1-methyl-1H-imidazol-3-ium-2-carboxybenzoate. Dispersion indices obtained from the experiments were in agreement with the modeling studies. Maximum asphaltene dispersion indices (%) of 78, 70, and 53 were obtained for 1-butyl-3-methylimidazolium chloride,1-butyl-3-methylimidazolium nitrate, and 1-methyl-1H-imidazol-3-ium-2-carboxybenzoate, respectively, when using an ionic liquid-to-asphaltenes molarity ratio of 9:1. The excellent performance displayed by 1-butyl-3-methylimidazolium chloride is based on the thermodynamic interaction energy and HOMO–LUMO energy it holds.
Antioxidant for fats and oils from canary seed: Sterol and triterpene alcohol esters of caffeic acid (1980)

Abstract Several kinds of seeds used as bird feed were extracted successively with hexane, ether and methanol. In the antioxidant test with extracts, the ether extract from canary seeds showed the highest activity. The antioxidant fraction separated from it by thin layer chromatography showed excellent activity for lard and sardine oil. The effective components were identified by gas chromatography and gas chromatography‐mass spectrometry of the hydrolyzed products as the esters of caffeic acid with cycloartenol, gramisterol, sitosterol and campesterol with the minor amounts of 24‐methylenecycloartanol, obtusifoliol, brassicasterol and Δ7‐stigmastenol.
Telomere erosion varies during in vitro aging of normal human fibroblasts from young and adult donors. (2000)

The life span of normal fibroblasts in vitro (Hayflick limit) depends on donor age, and telomere shortening has been proposed as a potential mechanism. By quantitative fluorescence in situ hybridization and Southern blot analysis, we show progressive telomere loss to about 5 kb mean telomere restriction fragment length in fibroblasts from two adult donors within 40 population doublings, whereas in fibroblasts from two infant donors, telomere erosion is reduced, leaving a mean telomere restriction fragment length of approximately 7 kb at senescence (after approximately 60 population doublings). Aging of fibroblasts from both infant and adult donors was not accompanied by chromosomal abnormalities but was correlated with increased telomere repeat-binding factor 2 expression at both the protein and transcriptional level.