gebhart/patrepeval huggingface dataset:
Strain-specific parallel evolution drives short-term diversification during <i>Pseudomonas aeruginosa</i> biofilm formation (2014)

Generation of genetic diversity is a prerequisite for bacterial evolution and adaptation. Short-term diversification and selection within populations is, however, largely uncharacterised, as existing studies typically focus on fixed substitutions. Here, we use whole-genome deep-sequencing to capture the spectrum of mutations arising during biofilm development for two Pseudomonas aeruginosa strains. This approach identified single nucleotide variants with frequencies from 0.5% to 98.0% and showed that the clinical strain 18A exhibits greater genetic diversification than the type strain PA01, despite its lower per base mutation rate. Mutations were found to be strain specific: the mucoid strain 18A experienced mutations in alginate production genes and a c-di-GMP regulator gene; while PA01 acquired mutations in PilT and PilY1, possibly in response to a rapid expansion of a lytic Pf4 bacteriophage, which may use type IV pili for infection. The Pf4 population diversified with an evolutionary rate of 2.43 × 10(-3) substitutions per site per day, which is comparable to single-stranded RNA viruses. Extensive within-strain parallel evolution, often involving identical nucleotides, was also observed indicating that mutation supply is not limiting, which was contrasted by an almost complete lack of noncoding and synonymous mutations. Taken together, these results suggest that the majority of the P. aeruginosa genome is constrained by negative selection, with strong positive selection acting on an accessory subset of genes that facilitate adaptation to the biofilm lifecycle. Long-term bacterial evolution is known to proceed via few, nonsynonymous, positively selected mutations, and here we show that similar dynamics govern short-term, within-population bacterial diversification.
Evaluation of TcpF-A2-CTB Chimera and Evidence of Additive Protective Efficacy of Immunizing with TcpF and CTB in the Suckling Mouse Model of Cholera (2012)

The secreted colonization factor, TcpF, which is produced by Vibrio cholerae 01 and 0139, has generated interest as a potential protective antigen in the development of a subunit vaccine against cholera. This study evaluated immunogenicity/protective efficacy of a TcpF holotoxin-like chimera (TcpF-A2-CTB) following intraperitoneal immunization compared to TcpF alone, a TcpF+CTB mixture, or CTB alone. Immunization with the TcpF-A2-CTB chimera elicited significantly greater amounts of anti-TcpF IgG than immunization with the other antigens (P<0.05). Protective efficacy was measured using 6-day-old pups reared from immunized dams and orogastrically challenged with a lethal dose of El Tor V. cholerae 01 Inaba strain N16961. Protection from death, and weight loss analysis at 24 and 48 hours post-infection demonstrated that immunization with TcpF alone was poorly protective. However, immunization with TcpF+CTB was highly protective and showed a trend toward greater protection than immunization with CTB alone (82% vs 64% survival). Immunization with the TcpF-A2-CTB chimera demonstrated less protection (50% survival) than immunization with the TcpF+CTB mixture. The TcpF-A2-CTB chimera used for this study contained the heterologous classical CTB variant whereas the El Tor CTB variant (expressed by the challenge strain) was used in the other immunization groups. For all immunization groups that received CTB, quantitative ELISA data demonstrated that the amounts of serum IgG directed against the homologous immunizing CTB antigen was statistically greater than the amount to the heterologous CTB antigen (P≤0.003). This finding provides a likely explanation for the poorer protection observed following immunization with the TcpF-A2-CTB chimera and the relatively high level of protection seen after immunization with homologous CTB alone. Though immunization with TcpF alone provided no protection, the additive protective effect when TcpF was combined with CTB demonstrates its possible value as a component of a multivalent subunit vaccine against Vibrio cholerae 01 and 0139.
Fast Mode and Partition Decision Using Machine Learning for Intra-Frame Coding in HEVC Screen Content Coding Extension (2016)

This paper presents a fast mode and partition decision framework for screen content coding (SCC) based on machine learning. Extensive statistical studies and complexity evaluations are conducted to explore the distribution of different coding modes and their complexities. The proposed encoder scheme is designed based on the results from these studies. Firstly, a CU is classified as either a natural image block (NIB) or a screen content block (SCB). An SCB only goes through SCC modes at the current CU level. An NIB is further classified as “ partitioned” or “ non-partitioned”. The partitioned block will bypass current level intra modes. The non-partitioned block is classified as “ directional” or “ non-directional” and only goes through a subset of intra candidates. Decision tree classifiers are designed with chosen features that can distinguish different types of blocks. Furthermore, additional mode/partition checking is terminated once the current mode coding rate is lower than a statistics-based threshold. Compared with HEVC-SCC reference software, our proposed fast encoder can balance the encoding efficiency and complexity by adjusting decision confidence thresholds and rate thresholds. Under all-intra configurations, our “ rate-distortion preserving” setting can achieve 40% complexity reduction with only 1.46% BD-loss. Our “ complexity-reduction boosting” setting can achieve 52% complexity reduction with 3.65% BD-loss.
The Thermal Limit of an HMX Perforating System for Through-Tubing Gas Well Operations (2016)

Abstract For through-tubing perforating operations, it is important to consider jobs with temperatures above 360°F (182°C) at depths of approximately 15,000 ft. In this instance, the wireline conveyance time approaches 1.5 hours, which begins nearing the HMX thermal limit. This may require a switch to a higher-rated explosive, such as HNS, but unfortunately, this comes with an accompanying 20% loss of charge performance. To guide perforating operations for these conditions, an experimental test-firing program was conducted to determine the performance of a 2.0-in. diameter HMX perforating system using 7.0-g shaped charges as a function of well temperature from 360–440°F (182–227°C). A novel two-step heating ramp was used to "thermally equate" perforating gun tests with shooting fixture tests. This experimental technique was necessary because of the large difference in thermal mass between the gun, which had a relatively small thermal mass, versus a shooting fixture whose mass was much larger for safety reasons. The two-step heating-ramp tests showed that the temperature inside the perforating gun was still climbing toward the external well temperature even after the simulated 1.5-hr conveyance time. Temperature differences between the external gun surface and a charge located inside the gun ranged from 12–25°F (7–14°C). This thermal delay experienced by the gun worked to the advantage of HMX exposure, as the decomposition reaction for the explosive was also delayed. Taking the thermal delay into account, an upper temperature limit was established when perforating gas wells with the 7.0-g HMX-shaped charges inside 2.0-in. OD perforating guns. In addition, penetration performance for the HMX charge at various temperature levels was generated and then compared to baseline performance data that had been generated at ambient temperature. The outcome of the test program provided guidelines for: (1) how far 2.0-in. HMX charges can be thermally pushed when perforating gas wells and still undergo proper ballistic functioning, (2) performance degradation of the 7.0-g charge as a function of temperature, and (3) recommendations for when to switch to higher thermally rated systems.
IPR: An Integrated Placement and Routing Algorithm (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
The Safety and Efficacy of Salicylic Acid Chemical Peels in Darker Racial-ethnic Groups (1999)

The results of this study suggest that superficial salicylic acid peels are both safe and efficacious for treatment of acne vulgaris, oily skin, textural changes, melasma, and post-inflammatory hyperpigmentation in patients with skin types V and VI.
Constructions and families of covering codes and saturated sets of points in projective geometry (1995)

In Davydov (1990), constructions of linear binary covering codes were considered. In the present paper, constructions and techniques of the earlier paper are developed and modified for q-ary linear nonbinary covering codes, q/spl ges/3, and new constructions are proposed. The described constructions design an infinite family of codes with covering radius R based on a starting code of the same covering radius. For arbitrary R/spl ges/2, q/spl ges/3, new infinite families of nonbinary covering codes with "good" parameters are obtained with the help of an iterative process when constructed codes are the starting codes for the following steps. The table of upper bounds on the length function for codes with q=3, R=2, 3, and codimension up to 24 is given. The author proposes to use saturated sets of points in projective geometries over finite fields as parity check matrices of starting codes. New saturated sets are obtained.
ChemInform Abstract: The Classic Concept of Solid Support (2009)

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 of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The Potential Role of Dendritic Cells in the Therapy of Type 1 Diabetes (2013)

Type 1 diabetes (T1D) is the result of T-cell mediated autoimmune destruction of pancreatic islet β-cells. The two current treatments for T1D are based on insulin or islet-cell replacement rather than the pathogenesis of T1D and remain problematic. Islet/pancreas transplantation does not cater for the majority of sufferers due to the lack of supply of organs and the need for continuous immunosuppression regimens. The mainstay treatment is insulin replacement, but this is disruptive to lifestyle and does not protect against severe long-term complications. An early vaccination and long-term restoration of immune tolerance to self-antigens in T1D patients (reversing the immunopathogenesis of the disease) would be preferable. Dendritic cells (DCs) are potent APCs and play an important role in inducing and maintaining immune tolerance. Targeting DCs through different DC surface molecules shows effective modulation of immune responses. Their feasibility for immunotherapy to prolong transplant survival and cancer immunotherapy has been demonstrated. Therefore, DCs could potentially be used in the treatment of autoimmune diseases. This review summarizes new insights into DCs as a potential therapeutic target for the treatment of T1D.
Thiourea-Catalyzed Enantioselective Hydrophosphonylation of Imines:  Practical Access to Enantiomerically Enriched α-Amino Phosphonic Acids (2004)

Chiral thiourea 1b catalyzes the highly enantioselective hydrophosphonylation of a wide range of N-benzyl imines. The hydrophosphonylation products are readily deprotected by hydrogenolysis, providing access to free alpha-amino phosphonic acids in highly enantioenriched form.
Antimicrobial activity of propolis agents on some pathogenic microbes (2010)

The study aims to investigate the antimicrobial activity of propolis obtained from different regions of Iraq compared with that of propolis obtained from Iran. Samples were investigated for their antimicrobial activity against Staphylococcus aureus, Pseudomonas aeruginosa, Eschericha coli, Klebsiella pneumoniae, Bacillus cereus , Staphylococcus epidermidis and Candida albicans using standard antimicrobial assays. Marked variations in the antimicrobial activity of the different propolis samples were observed, the method of extraction selected gives the highest antimicrobial activity and the best alcohol concentration using in the extraction of propolis , then the crude extract of propolis showed synergistic effect with some antibiotics in inhibition of pathogenic microorganisms.
Occupational endotoxin‐exposure and possible health effects on humans (review) (2006)

The adverse health effects of endotoxins are known, standardization of measurements is a necessary goal and protection measures should be established immediately.
Applications of smart metering and home appliances' power signatures (2014)

Over the last decade, significant changes have occurred in area of both power systems and computing systems. Furthermore, we are witnessing the fast spreading of smart grid technology deployments, which combines applications and solutions from both these domains. Therefore with our work we aim to propose and develop applications on top of smart grid power infrastructures that monitor, analyze, classify and characterize various electronic equipment connected to this infrastructure. The present paper aims at discussing the future applications of Advanced Metering Infrastructure (AMI) and how they can make use of consumer electronic equipment power signatures. Power signature of an electronic device is defined as the power consumption response to a specific workload or program executed by the device.
A reactive continuous chromatographic process for protein PEGylation (2016)

A multicolumn process in the form of a twin-column MCSGP unit is fitted with an additional column to perform a on-column protein PEGylation reaction. Thanks to this rMCSGP process, the conjugation reaction is obtained simultaneously with the purification of the products at high yield and high conversion of the protein.
Efficient Production of Casoxin D, a Bradykinin Agonist Peptide Derived from Human Casein, by<i>Bacillus brevis</i> (1995)

We efficiently produced a small peptide by the host-vector system using Bacillus brevis as a host. DNA encoding the physiologically functional casoxin D, composed of seven amino acids, was ligated in tandem. An expression-secretion vector containing DNA, which codes for a fusion protein of epidermal growth factor-casoxin D pentamer, was constructed. B. brevis transformed with this plasmid produced about 0.5 g/liter of the fusion protein in the culture supernatant. The fusion protein was purified with ammonium sulfate fractionation from the supernatant and digested with two kinds of proteinases. A peptide well separated by high pressure liquid chromatography was identified as biologically active casoxin D.
In vitro photosensitization I. Cellular uptake and subcellular localization of mono‐L‐aspartyl chlorin e<sub>6</sub>, chloro‐aluminum sulfonated phthalocyanine, and photofrin II (1989)

The mechanisms of cellular uptake, subcellular localization, and cellular retention kinetics of the photosensitizers photofrin II (PfII), mono-L-aspartyl chlorin e6 (MACE), and chloro-aluminum sulfonated phthalocyanine (CASPc) are reported in this paper. Each photosensitizer's cellular uptake mechanism was determined by preferentially inhibiting endocytosis by chilling cells to 2 degrees C, while allowing diffusion across the membrane. Subcellular localization was studied by computer-enhanced low-light level video fluorescence microscopy, while flow cytometry was used to determine uptake and retention kinetics. The results indicate that PfII enters the cell primarily by diffusion across the membrane, whereas MACE and CASPc enter the cell through endocytosis.
Decoder-driven switching matrices in multicontext FPGAs: area reduction and their effect on routability (2003)

Modern FPGAs use SRAM-cells to store the programming bits that drive the switching matrices. The area of these SRAM cells can be as large as 40% of the total area. This figure dramatically increases in the case of multicontext FPGAs, where the programming configuration has to be repeated as many times as contexts. This problem is alleviated if the switches that connect an input line to several output lines in each switching block are driven by a decoder. In this case, the number of SRAM cells decreases in O(log), at the cost of routability. This paper shows with experimental results obtained from 175 benchmark circuits that, for usual FPGA parameters, routability losses are small, making the decoder-driven switch (DDS) approach an excellent method for reducing FPGA area by as much as 20%, while preserving routability.
A method for soluble overexpression of the α7 nicotinic acetylcholine receptor extracellular domain (2001)

We describe the construction of a soluble protein carrying the N-terminal extracellular domain (ECD) of the alpha7 subunit of the nicotinic acetylcholine receptor. The approach was to fuse the alpha7 ECD at the C and N termini of several monomeric and pentameric soluble carrier proteins and to investigate the soluble expression of the product in Escherichia coli. An initial screening of six carrier proteins resulted in the selection of a fusion protein comprising, from the N to the C terminus, the maltose binding protein, a 17-aa linker containing an enterokinase binding site, and the alpha7 ECD. This protein is soluble upon expression in bacteria and is purified by affinity chromatography. It binds the competitive nicotinic antagonist alpha-bungarotoxin with 2.5 microM affinity and displays a CD spectrum corresponding to a folded protein. The method might be suitable to produce large quantities of protein for crystallization and immunochemical experiments.
Pure Translational Tomography – a Non- Rotational Approach for Tomographic Reconstruction (2006)

Abstract. We report the first preliminary simulated experiments of an algebraic iterative tomographic reconstruction algorithm having excellent materials identification accuracy, based on linear stepping scans of 3D objects. The new algorithm, mainly intended for luggage control CT implementation, could substantially reduce the equipment cost, size and the scanning time, offering also good materials identification accuracy.
Phototherapy for Neonatal Jaundice (2008)

A newborn male infant is brought to the pediatrician's office with pronounced jaundice and a total serum bilirubin level of 19.5 mg per deciliter. Phototherapy is considered. In term and late-preterm infants, phototherapy is typically used according to guidelines that take into account the total serum bilirubin level, gestational age, postpartum age, and the presence or absence of specific risk factors.
Electrocatalytic upgrading of model lignin monomers with earth abundant metal electrodes (2014)

Electrocatalytic hydrogenation (ECH) of guaiacol for production of chemical and fuel in a divided cell using earth abundant metal electrodes. Specific energies shown below the organics are their higher heating values (HHV).
Cardiac responses to induced lactate oxidation: NMR analysis of metabolic equilibria (1995)

The role of lactate as a source of pyruvate oxidation in supporting cardiac work, energetics, and formation of oxidative metabolites was examined in normal myocardium. 13C- and 31P-nuclear magnetic resonance (NMR) spectra were acquired from isolated rabbit hearts supplied 2.5 mM [3-13C]lactate or [3-13C]pyruvate with or without stimulation of pyruvate dehydrogenase (PDH) by dichloroacetate (DCA). Similar workloads determined by rate-pressure products were noted with pyruvate (21,700 +/- 2,400; mean +/- SE) and lactate (18,970 +/- 1,510). Oxygen consumption was similar in all four groups with means between 19.0 and 22.2 mumol.min-1.g dry weight-1 (SE = 1.6-2.0) as was the ratio of phosphocreatine to ATP with means between 1.8 and 2.1 (SE = 0.1-0.6). Intracellular pH, determined from 31P-NMR spectra, was essentially the same with pyruvate (7.06 +/- 0.02) and lactate (7.05 +/- 0.04). 13C enrichment of glutamate was higher with lactate (92%) than with pyruvate (70%). Pyruvate plus DCA induced no change in glutamate content at 9-10 mumol/g, but 13C enrichment increased to 83%, while lactate plus DCA maintained enrichment at 90%. Levels of alpha-ketoglutarate were lower with lactate (1.81 mumol/g) than with pyruvate (2.36 mumol/g). Lactate plus DCA elevated glutamate by 60% with a proportional increase in alpha-ketoglutarate. Thus the balance between glutamate and alpha-ketoglutarate was affected by substrate supply only and not by PDH activation. The results suggest that the equilibrium between alpha-ketoglutarate and glutamate is sensitive to cytosolic redox state, an important consideration for 13C-NMR analyses that rely on glutamate.(ABSTRACT TRUNCATED AT 250 WORDS)
Yeast Influence on Volatile Composition of Wines (1999)

Nine Saccharomyces cerevisiae and four Saccharomyces bayanus strains used in the production of Trebbiano wine were examined. The aim of this study is to evaluate the different abilities of various yeast strains in wine-making. The possibility of yeast discrimination on the basis of their volatile production is another possibility. Wine chemical analyses showed statistically significant differences depending on the yeast strain used. Some compounds such as 2-phenylethanol, 2-phenethyl acetate, ethyl lactate, 3-ethoxypropanol, and, to a lesser extent, diethyl succinate and propionic acid characterized examined Saccharomyces bayanus yeasts. Moreover, these strains did not produce any undesirable compounds, such as acetic acid and sulfur anhydride. For these reasons and because they synthesized malic acid, they could be more suitable for white wine production. The other yeasts showed great differences, which are difficult to correlate with the strain. However, some strains had peculiar characteristics, such as an uncommonly high concentration of n-propanol and 3-ethoxypropanol.
Properties of Whey Protein Isolates Extruded under Acidic and Alkaline Conditions (2006)

Whey proteins have wide acceptance and use in many products due to their beneficial nutritional properties. To further increase the amount of whey protein isolates (WPI) that may be added to products such as extruded snacks and meats, texturization of WPI is necessary. Texturization changes the folding of globular proteins to improve interaction with other ingredients and create new functional ingredients. In this study, WPI pastes (60% solids) were extruded in a twin-screw extruder at 100 degrees C with 4 pH-adjusted water streams: acidic (pH 2.0 +/- 0.2) and alkaline (pH 12.4 +/- 0.4) streams from 2 N HCl and 2 N NaOH, respectively, and acidic (pH 2.5 +/- 0.2) and alkaline (pH 11.5 +/- 0.4) electrolyzed water streams; these were compared with WPI extruded with deionized water. The effects of water acidity on WPI solubility at pH 7, color, microstructure, Rapid Visco Analyzer pasting properties, and physical structure were determined. Alkaline conditions increased insolubility caused yellowing and increased pasting properties significantly. Acidic conditions increased solubility and decreased WPI pasting properties. Subtle structural changes occurred under acidic conditions, but were more pronounced under alkaline conditions. Overall, alkaline conditions increased denaturation in the extruded WPI resulting in stringy texturized WPI products, which could be used in meat applications.