gebhart/patrepeval huggingface dataset:
Pediocins: The bacteriocins of Pediococci. Sources, production, properties and applications (2009)

Class IIa bacteriocins from lactic acid bacteria are small, cationic proteins with antilisterial activity. Within this class, the pediocins are those bacteriocins that share a highly conserved hydrophilic and charged N-terminal part harboring the consensus sequence -YGNGV- and a more variable hydrophobic and/or amphiphilic C-terminal part. Several pediocins have been isolated and characterized. Despite the structural similarities, their molecular weight varies, as well as their spectrum of antimicrobial activity. They exhibit important technological properties, e.g. thermostability and retaining of activity at a wide pH range, which along with the bactericidal action against Gram-positive food spoilage and pathogenic bacteria, make them an important class of biopreservatives. Much new information regarding the pediocins has emerged during the last years. In this review, we summarize and discuss all the available information regarding the sources of pediocins, the characteristics of their biosynthesis and production in fermentation systems, the characteristics of the known pediocin molecules, and their antibacterial action. The advances made by genetic engineering in improving the features of pediocins are also discussed, as well as their perspectives for future applications.
Intrahepatic Cholestasis for 15 Years without Cirrhosis (1980)

Whether prolonged cholestasis is followed by hepatic cirrhosis is still controversial. We have studied two unrelated children who have had cholestasis for 15 years, but neither of whom have developed cirrhosis. Both have severe growth retardation, peculiar facies, pulmonic stenosis, transitory renal tubular acidosis, and vitamin D-resistant rickets. The patients presented in infancy with hepatomegaly and direct hyperbilirubinemia; liver biopsy at that time revealed cholestasis and paucity of bile ducts. Subsequent serial liver biopsies have continued to demonstrate cholestasis, but there has been no evidence of cirrhosis. Electron microscopy has revealed swollen and blunted microvilli of the canalicular membrane of the hepatocyte. The patients have had elevated bile acids in the serum as well as a reversed ration of tri- to dihydroxy bile acids. Treatment with cholestyramine and phenobarbital has brought about symptomatic relief from severe pruritus and excoriation and has lowered the level of serum bile acids, although they are still above the normal range. These findings suggest that cholestasis accompanied by an elevated and reversed bile acid ratio does not universally cause hepatic cirrhosis.
High-Throughput Microcoil NMR of Compound Libraries Using Zero-Dispersion Segmented Flow Analysis (2004)

An automated system for loading samples into a microcoil NMR probe has been developed using segmented flow analysis. This approach enhanced 2-fold the throughput of the published direct injection and flow injection methods, improved sample utilization 3-fold, and was applicable to high-field NMR facilities with long transfer lines between the sample handler and NMR magnet. Sample volumes of 2 microL (10-30 mM, approximately 10 microg) were drawn from a 96-well microtiter plate by a sample handler, then pumped to a 0.5-microL microcoil NMR probe as a queue of closely spaced "plugs" separated by an immiscible fluorocarbon fluid. Individual sample plugs were detected by their NMR signal and automatically positioned for stopped-flow data acquisition. The sample in the NMR coil could be changed within 35 s by advancing the queue. The fluorocarbon liquid wetted the wall of the Teflon transfer line, preventing the DMSO samples from contacting the capillary wall and thus reducing sample losses to below 5% after passage through the 3-m transfer line. With a wash plug of solvent between samples, sample-to-sample carryover was <1%. Significantly, the samples did not disperse into the carrier liquid during loading or during acquisitions of several days for trace analysis. For automated high-throughput analysis using a 16-second acquisition time, spectra were recorded at a rate of 1.5 min/sample and total deuterated solvent consumption was <0.5 mL (1 US dollar) per 96-well plate.
Tissue-Specific Expression of as-1 in Transgenic Tobacco. (1994)

When integrated as a transgene in one or a few copies, the -90 35S promoter of cauliflower mosaic virus confers expression in roots with little or no expression in cotyledons and leaves. The responsible cis element, activation sequence-1 (as-1), can bind to the nuclear factor ASF-1 as well as to the transcription factor TGA1a. Here, we show that microinjection of 104 molecules of TGA1a per cotyledon cell activated transgenes containing as-1-linked promoters. Transgenes with promoters linked to the octopine synthase (ocs) element, which also binds TGA1a, responded similarly. The acidic, N-terminal segment of TGA1a is important for transcription activation in vivo because a deletion mutant without the first 80 amino acids was inactive. Finally, we show that the -90 35S-[beta]-glucuronidase (GUS) fusion gene conferred GUS expression in cotyledon cells when injected at 50,000 copies per cell. Collectively, these results provide support for the hypothesis that the undetectable expression of the as-1-linked transgene in cotyledon cells is most likely a result of its inability to compete for a limiting amount of its cognate transcription factor(s), presumably TGA1a or related proteins.
Lack of efficacy of L-759274, a novel neurokinin 1 (substance P) receptor antagonist, for the treatment of generalized anxiety disorder (2012)

Preclinical studies suggest that substance P acting at neurokinin 1 (NK1) receptors may be involved in stress responses and NK1 receptor antagonists show activity in tests of anxiety. These data raise the possibility that NK1 receptor antagonists could be potential anxiolytic treatments in humans. We evaluated this hypothesis clinically using the NK1 antagonist L-759274. This is a randomized, double-blind, placebo- and active-controlled, multicentre, proof-of-concept trial. Patients with generalized anxiety disorder were randomized 1:1:1 to 6 wk of treatment with 40 mg L-759274 (n = 73), 1-6 mg lorazepam (n = 69) or placebo (n = 71). Efficacy was assessed using the Hamilton Anxiety Scale (HAMA). A positron emission tomography (PET) study was also performed in 16 healthy subjects to determine the relationship between NK1 receptor occupancy and plasma levels of L-759274 to verify adequate target engagement by the doses tested during the clinical trial. No statistically significant difference in mean change from baseline HAMA score at 6 wk was seen for L-759274 vs. placebo [difference = 1.0 (95% confidence intervals (CI) -1.2 to 3.2), p = 0.359] whereas the lorazepam group did show a significant improvement vs. placebo (difference = -2.7, 95% CI -5.0 to -0.4, p = 0.020) and L-759274 (difference = 3.7, 95% CI 1.5-6.0, p = 0.001]. Results from the PET study indicated that the L-759274 dosing regimen used in the clinical trial likely provided high levels of NK1 receptor occupancy (>90%), supporting the view that it was an adequate proof-of-concept trial. The NK1 receptor antagonist L-759274 does not appear to be efficacious for the treatment of generalized anxiety disorder.
Temporal invariance and clonal uniformity of brain and cerebrospinal IgG, IgA, and IgM in multiple sclerosis. (1986)

Elevated cerebrospinal fluid (CSF) IgG and oligoclonal IgG bands on electrophoresis are valuable clinical markers for B cell proliferation in the brains of patients with multiple sclerosis (MS). Using two-dimensional electrophoresis, (2DE) we have established that the humoral immune response in MS brain is characterized by finite clonal complexity for the major Ig classes. An important question is whether this immune response is clonally stable or varies with time, related to the development of new lesions and random entry of B cells into the MS brain. To investigate this, we performed serial electrophoretic studies on CSF obtained from 19 patients with MS; the intervals ranged from 7 to 12 yr, with a mean of 8 yr. These analyses included studies of IgG, IgA, and IgM, and revealed that the humoral immune response in MS is clonally stable over long periods. Spontaneous fluctuations or reduction in CSF IgG levels by drugs did not qualitatively affect B cell clonal proliferation in MS brain, in that dominant bands and spots were not obliterated. It has been asserted that IgG synthesis in MS is nonsense antibody because the spectotypes of IgG isolated from different regions of MS brains differ. Factors other than clonal heterogeneity could account for differences found using one-dimensional analysis. B cell clonal products resolve into unique and well-resolved spots by 2DE; the method is uniquely suitable for analysis of restricted immune responses. Therefore, Ig were isolated from 11 regions of three MS brains and the 2DE patterns were compared. The similarity of the 2DE patterns indicate unequivocally that major clones are distributed uniformly although some clones are more prominent in some brain areas. IgA and IgM isolated from the same areas also showed similar patterns. Furthermore, the patterns of light and heavy chains in brain regions differed from serum but were similar to the autologous CSF, providing new evidence that CSF IgG in MS derives from synthesis in situ. Our results indicate that, once initiated, B cell clonal proliferation persists indefinitely and is little altered qualitatively at a clonal level over time, even when CSF IgG levels change or are altered by drugs. Our results are consistent with allotype and idiotype analysis of Ig production in MS and conflict with nonsense antibody proposals of the origin and nature of in situ synthesized Ig in MS.
Fibroblast Growth Factor 23 (FGF23) Predicts Progression of Chronic Kidney Disease (2007)

It has not been firmly established whether disturbed calcium-phosphate metabolism affects progression of chronic kidney disease (CKD) in humans. In this cohort study of 227 nondiabetic patients with CKD, we assessed fibroblast growth factor 23 (FGF23) plasma concentrations in addition to other variables involved in calcium-phosphate metabolism, and we followed 177 of the patients prospectively for a median of 53 months to assess progression of renal disease. In the baseline cohort, we found a significant inverse correlation between glomerular filtration rate and both c-terminal and intact FGF23 levels (both P < 0.001). The 65 patients who experienced a doubling of serum creatinine and/or terminal renal failure were significantly older, had a significantly lower glomerular filtration rate at baseline, and significantly higher levels of intact parathormone, c-terminal and intact FGF23, and serum phosphate (all P < 0.001). Cox regression analysis revealed that both c-terminal and intact FGF23 independently predict progression of CKD after adjustment for age, gender, GFR, proteinuria, and serum levels of calcium, phosphate, and parathyroid hormone. The mean follow-up time to a progression end point was 46.9 (95% CI 40.2 to 53.6) months versus 72.5 (95% CI 67.7 to 77.3) months for patients with c-terminal FGF23 levels above or below the optimal cut-off level of 104 rU/mL (derived by receiver operator curve analysis), respectively. In conclusion, FGF23 is a novel independent predictor of progression of renal disease in patients with nondiabetic CKD. Its pathophysiological significance remains to be elucidated.
Acrylamide Formation from Asparagine under Low-Moisture Maillard Reaction Conditions. 1. Physical and Chemical Aspects in Crystalline Model Systems (2004)

The formation of acrylamide in crystalline model systems based on asparagine and reducing sugars was investigated under low-moisture reaction conditions. The acrylamide amounts were correlated with physical changes occurring during the reaction. Molecular mobility of the precursors turned out to be a critical parameter in solid systems, which is linked to the melting behavior and the release of crystallization water of the reaction sample. Heating binary mixtures of asparagine monohydrate and anhydrous reducing sugars led to higher acrylamide amounts in the presence of fructose compared to glucose. Differential scanning calorimetry measurements performed in open systems indicated melting of fructose at 126 degrees C, whereas glucose and galactose fused at 157 and 172 degrees C, respectively. However, glucose was the most reactive and fructose the least efficient sugar in anhydrous liquid systems, indicating that at given molecular mobility the chemical reactivity of the sugar was the major driver in acrylamide formation. Furthermore, reaction time and temperature were found to be covariant parameters: acrylamide was preferably formed by reacting glucose and asparagine at 120 degrees C for 60 min, whereas 160 degrees C was required at shorter reaction time (5 min). These results suggest that, in addition to the chemical reactivity of ingredients, their physical state as well as reaction temperature and time would influence the formation of acrylamide during food processing.
Optical absorption enhancement in silicon nanowire arrays with a large lattice constant for photovoltaic applications (2009)

In this paper, we use the transfer matrix method to calculate the optical absorptance of vertically-aligned silicon nanowire (SiNW) arrays. For fixed filling ratio, significant optical absorption enhancement occurs when the lattice constant is increased from 100 nm to 600 nm. The enhancement arises from an increase in field concentration within the nanowire as well as excitation of guided resonance modes. We quantify the absorption enhancement in terms of ultimate efficiency. Results show that an optimized SiNW array with lattice constant of 600 nm and wire diameter of 540 nm has a 72.4% higher ultimate efficiency than a Si thin film of equal thickness. The enhancement effect can be maintained over a large range of incidence angles.
Security Label Framework for the Internet (1993)

This memo presents a security labeling framework for the Internet. The
framework is intended to help protocol designers determine what, if
any, security labeling should be supported by their protocols. This
memo provides information for the Internet community. It does not
specify an Internet standard.
ChemInform Abstract: Recent Patents on Oligonucleotide Synthesis and Gene Synthesis (2012)

Abstract Review: 37 refs.
Determination of protein-DNA binding constants and specificities from statistical analyses of single molecules: MutS-DNA interactions (2005)

Atomic force microscopy (AFM) is a powerful technique for examining the conformations of protein-DNA complexes and determining the stoichiometries and affinities of protein-protein complexes. We extend the capabilities of AFM to the determination of protein-DNA binding constants and specificities. The distribution of positions of the protein on the DNA fragments provides a direct measure of specificity and requires no knowledge of the absolute binding constants. The fractional occupancies of the protein at a given position in conjunction with the protein and DNA concentrations permit the determination of the absolute binding constants. We present the theoretical basis for this analysis and demonstrate its utility by characterizing the interaction of MutS with DNA fragments containing either no mismatch or a single mismatch. We show that MutS has significantly higher specificities for mismatches than was previously suggested from bulk studies and that the apparent low specificities are the result of high affinity binding to DNA ends. These results resolve the puzzle of the apparent low binding specificity of MutS with the expected high repair specificities. In conclusion, from a single set of AFM experiments, it is possible to determine the binding affinity, specificity and stoichiometry, as well as the conformational properties of the protein-DNA complexes.
Improvement of periodontal status by green tea catechin using a local delivery system: A clinical pilot study (2002)

The purpose of this study was to determine the usefulness of green tea catechin for the improvement of periodontal disease. The minimum inhibitory concentration (MIC) and bactericidal activity of green tea catechin against black-pigmented, Gram-negative anaerobic rods (BPR) were measured. Hydroxypropylcellulose strips containing green tea catechin as a slow release local delivery system were applied in pockets in patients once a week for 8 weeks. The clinical, enzymatic and microbiological effects of the catechin were determined. Green tea catechin showed a bactericidal effect against Porphyromonas gingivalis and Prevotella spp. in vitro with an MIC of 1.0 mg/ml. In the in vivo experiment, the pocket depth (PD) and the proportion of BPR were markedly decreased in the catechin group with mechanical treatment at week 8 compared with the baseline with significant difference. In contrast, PD and BPR were similar to the baseline and the value at the end of the experimental period in the placebo sites of scaled groups. The peptidase activities in the gingival fluid were maintained at lower levels during the experimental period in the test sites, while it reached 70% of that at baseline in the placebo sites. No morbidity was observed in the placebo and catechin groups without mechanical treatment. Green tea catechin showed a bactericidal effect against BPR and the combined use of mechanical treatment and the application of green tea catechin using a slow release local delivery system was effective in improving periodontal status.
Handbook of Heterogeneous Catalysis (2008)

Preparation of Solid Catalysts. Characterization of Solid Catalysts. Model Systems. Elementary Steps and Mechanisms. Kinetics and Transport Processes. Deactivation and Regeneration. Special Catalytic Systems. Laboratory Reactors. Reaction Engineering. Environmental Catalysis. Inorganic Reactions. Energy-related Catalysis. Organic Reactions.
PAPR Reduction Using Low Complexity PTS to Construct of OFDM Signals Without Side Information (2011)

Partial transmit sequence (PTS) is one of the most well-known peak-to-average power ratio (PAPR) reduction techniques proposed for orthogonal frequency-division multiplexing (OFDM) systems. The main drawbacks of the conventional PTS (C-PTS) are high computational complexity and transmission of several side information bits. A new PTS with simple detector is proposed in this paper to deal with these drawbacks of C-PTS. The candidates can be generated through cyclically shifting each sub-block sequence in time domain and combining them in a recursive manner. At the receiver, by utilizing the natural diversity of phase constellation for different candidates, the detector can successfully recover the original signal without side information. Numerical simulation shows that the proposed scheme performs very well in terms of PAPR. The probability of detection failure of the side information demonstrates that the detector could work without any side information with high reliability. The proposed scheme achieves almost the same bit error rate (BER) performance as the C-PTS with perfect side information, under both additive white Gaussian noise (AWGN) channel and Rayleigh fading channel.
Actin filaments and the growth, movement, and spread of the intracellular bacterial parasite, Listeria monocytogenes. (1989)

Listeria monocytogenes was used as a model intracellular parasite to study stages in the entry, growth, movement, and spread of bacteria in a macrophage cell line. The first step in infection is phagocytosis of the Listeria, followed by the dissolution of the membrane surrounding the phagosome presumably mediated by hemolysin secreted by Listeria as nonhemolytic mutants remain in intact vacuoles. Within 2 h after infection, each now cytoplasmic Listeria becomes encapsulated by actin filaments, identified as such by decoration of the actin filaments with subfragment 1 of myosin. These filaments are very short. The Listeria grow and divide and the actin filaments rearrange to form a long tail (often 5 microns in length) extending from only one end of the bacterium, a "comet's tail," in which the actin filaments appear randomly oriented. The Listeria "comet" moves to the cell surface with its tail oriented towards the cell center and becomes incorporated into a cell extension with the Listeria at the tip of the process and its tail trailing into the cytoplasm behind it. This extension contacts a neighboring macrophage that phagocytoses the extension of the first macrophage. Thus, within the cytoplasm of the second macrophage is a Listeria with its actin tail surrounded by a membrane that in turn is surrounded by the phagosome membrane of the new host. Both these membranes are then solubilized by the Listeria and the cycle is repeated. Thus, once inside a host cell, the infecting Listeria and their progeny can spread from cell to cell by remaining intracellular and thus bypass the humoral immune system of the organism. To establish if actin filaments are essential for the spread of Listeria from cell to cell, we treated infected macrophages with cytochalasin D. The Listeria not only failed to spread, but most were found deep within the cytoplasm, rather than near the periphery of the cell. Thin sections revealed that the net of actin filaments is not formed nor is a "comet" tail produced.
Surface-enhanced Raman scattering on gold and aluminum particle arrays (1982)

The intensity and excitation wavelength dependence of the surface-enhanced Raman effect is measured on microlithographically prepared gold and aluminum particle surfaces. Comparison of enhancement relative to identically fabricated silver surfaces gives good agreement with particle-plasmon theories of surface-enhanced Raman scattering.
Expression of spectral distortion using line spectrum frequencies (1997)

Line spectrum frequencies (LSFs) are commonly used in the domain of speech coding as means of representing prediction filters. Quantization of these parameters needs evaluation of spectral distortion. The exact equation giving distortion is presented here using only LSFs. A simplified equation is also proposed as a good approximation.
Fullerene Pipes (1998)

Single-wall fullerene nanotubes were converted from nearly endless, highly tangled ropes into short, open-ended pipes that behave as individual macromolecules. Raw nanotube material was purified in large batches, and the ropes were cut into 100- to 300-nanometer lengths. The resulting pieces formed a stable colloidal suspension in water with the help of surfactants. These suspensions permit a variety of manipulations, such as sorting by length, derivatization, and tethering to gold surfaces.
Purification and Properties of a New Type of Protease Produced byMicrobacterium liquefaciens (2005)

A bacterium, identified as Microbacterium liquefaciens MIM-CG-9535-I, was isolated from a soil sample taken from the industrial site of a gelatin manufacturer. A new type of protease, which restrictively decomposes gelatin at one or two positions, was purified from the bacterial culture. The molecular mass of the purified enzyme was 21 kDa by SDS-polyacrylamide gel electrophoresis. The purified enzyme specifically degraded the alpha-chain of gelatin with a molecular weight of 100 kDa into two peptides of 60 kDa and 40 kDa. Native collagen was not a substrate for the enzyme.
Highly Z-Selective Metathesis Homocoupling of Terminal Olefins (2009)

Mo and W MonoAryloxide-Pyrrolide (MAP) olefin metathesis catalysts can couple terminal olefins to give as high as >98% Z-products in moderate to high yields with as little as 0.2% catalyst. Results are reported for 1-hexene, 1-octene, allylbenzene, allyltrimethylsilane, methyl-10-undecenoate, methyl-9-decenoate, allylB(pinacolate), allylOBenzyl, allylNHTosyl, and allylNHPh. It is proposed that high Z-selectivity is achieved because a large aryloxide only allows metallacyclobutanes to form that contain adjacent cis substituents and because isomerization of Z-product to E-product can be slow in that same steric environment.