gebhart/patrepeval huggingface dataset:
Sterilization of bacterial spores by using supercritical carbon dioxide and hydrogen peroxide (2006)

It was hypothesized that supercritical carbon dioxide (SC-CO(2)) treatment could serve as an alternative sterilization method at various temperatures (40-105 degrees C), CO(2) pressures (200-680 atm), and treatment times (25 min to 6 h), and with or without the use of a passive additive (distilled water, dH(2)O) or an active additive (hydrogen peroxide, H(2)O(2)). While previous researchers have shown that SC-CO(2) possesses antimicrobial properties, sterilization effectiveness has not been shown at sufficiently low treatment temperatures and cycle times, using resistant bacterial spores. Experiments were conducted using Geobacillus stearothermophilus and Bacillus atrophaeus spores. Spore strips were exposed to SC-CO(2) in commercially available supercritical fluid extraction and reaction systems, at varying temperatures, pressures, treatment times, and with or without the use of a passive additive, such as dH(2)O, or an active additive, such as H(2)O(2). Treatment parameters were varied from 40 to 105 degrees C, 200-680 atm, and from 25 min to 6 h. At 105 degrees C without H(2)O(2), both spore types were completely deactivated at 300 atm in 25 min, a shorter treatment cycle than is obtained with methods in use today. On the other hand, with added H(2)O(2) (<100 ppm), 6 log populations of both spore types were completely deactivated using SC-CO(2) in 1 h at 40 degrees C. It was concluded from the data that large populations of resistant bacterial spores can be deactivated with SC-CO(2) with added H(2)O(2)at lower temperatures and potentially shorter treatment cycles than in most sterilization methods in use today.
Surfactin variants mediate species‐specific biofilm formation and root colonization in Bacillus (2016)

Cyclic lipopeptides (cLP) and especially surfactins produced by Bacillus spp. trigger biofilm formation and root colonization and are crucial for biocontrol activity and systemic resistance in plants. Bacillus atrophaeus 176s isolated from the moss Tortella tortuosa produces the cLP fengycins, iturins and surfactins, possesses antifungal activities and can protect tomato, lettuce and sugar beet against Rhizoctonia solani infection. In B. atrophaeus we identified for the first time the variant surfactin C, which differs from surfactin A produced by B. subtilis and B. amyloliquefaciens by an isoleucine instead of a leucine at position 7 of the lipopeptide backbone. The analysis of the complete surfactin gene clusters revealed that the dissimilarity is encoded in the adenylation domain of srfC and show that surfactin variations are distributed in a species-specific manner in bacilli. We demonstrate that the surfactin A and C with subtle structural differences have varying signal strengths on biofilm formation and root colonization and act specifically on the respective producing strain. This became evident as biofilm formation and root colonization but not swarming motility in surfactin biosynthesis mutants was restored differentially in the presence of exogenously supplemented cognate and non-cognate surfactin variants.
Targeting calcium cycling proteins in heart failure through gene transfer (2003)

Our understanding of cardiac excitation-contraction coupling has improved significantly over the last 10 years. Furthermore, defects in the various steps of excitation-contraction coupling that characterize cardiac dysfunction have been identified in human and experimental models of heart failure. The various abnormalities in ionic channels, transporters, kinases and various signalling pathways collectively contribute to the 'failing phenotype.' However, deciphering the causative changes continues to be a challenge. An important tool in dissecting the importance of the various changes in heart failure has been the use of cardiac gene transfer. To achieve effective cardiac gene transfer a number of obstacles remain, including appropriate vectors for gene delivery, appropriate delivery systems, and a better understanding of the biology of the disease. In this review, we will examine our current understanding of these various factors. Gene transfer provides not only a potential therapeutic modality but also an approach to identifying and validating molecular targets.
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes (2005)

We developed a new computational algorithm for the accurate identification of ligand binding envelopes rather than surface binding sites. We performed a large scale classification of the identified envelopes according to their shape and physicochemical properties. The predicting algorithm, called PocketFinder, uses a transformation of the Lennard-Jones potential calculated from a three-dimensional protein structure and does not require any knowledge about a potential ligand molecule. We validated this algorithm using two systematically collected data sets of ligand binding pockets from complexed (bound) and uncomplexed (apo) structures from the Protein Data Bank, 5616 and 11,510, respectively. As many as 96.8% of experimental binding sites were predicted at better than 50% overlap level. Furthermore 95.0% of the asserted sites from the apo receptors were predicted at the same level. We demonstrate that conformational differences between the apo and bound pockets do not dramatically affect the prediction results. The algorithm can be used to predict ligand binding pockets of uncharacterized protein structures, suggest new allosteric pockets, evaluate feasibility of protein-protein interaction inhibition, and prioritize molecular targets. Finally the data base of the known and predicted binding pockets for the human proteome structures, the human pocketome, was collected and classified. The pocketome can be used for rapid evaluation of possible binding partners of a given chemical compound.
Cannabinoid Receptor Agonists Inhibit Sensory Nerve Activation in Guinea Pig Airways (2004)

We examined the effects of cannabinoid receptor agonists on various respiratory reactions induced by the activation of capsaicin-sensitive afferent sensory nerves (C-fibers). (R)-(+)-[2,3-dihydro-5-methyl-3-[(4-merpholino)methyl]pyrrolo-[1,2,3-de]-1,4-benzoxazin-6-yl](1-naphthyl)methanone (WIN 55212-2) dose-dependently inhibited electrical field stimulation- and capsaicin-induced guinea pig bronchial smooth muscle contraction, but not the neurokinin A-induced contraction. A cannabinoid CB2 receptor antagonist, [N-[(1S)-endo-1,3,3-trimethylbicyclo[2.2.1]heptan-2-yl]-5-(4-chloro-3-methylphenyl)-1-(4-methylbenzyl)pyrazole-3-carboxamide] (SR 144528), reduced the inhibitory effect of WIN 55212-2, but not a cannabinoid CB1 antagonist, [N-(piperidin-1-yl)-5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamidehydrochloride] (SR 141716A). A cannabinoid CB2 agonist, JWH 133, also inhibited electrical field stimulation-induced guinea pig bronchial smooth muscle contraction and its inhibitory effect was blocked by SR 144528. The inhibitory effect of WIN 55212-2 on electrical field stimulation-induced bronchial contraction was reduced by the pretreatment of large conductance Ca(2+)-activated K+ channel (Maxi-K+ channel) blockers, iberiotoxin and charybdotoxin, but not other K+ channel blockers, dendrotoxin or glibenclamide. A Maxi-K+ channel opener, 1-(2'-hydroxy-5'-trifluoromethylphenyl)-5-trifluoromethyl-2(3H)benzimidazolone (NS1619), inhibited bronchial contraction induced by electrical field stimulation. WIN 55212-2 and JWH 133 blocked the capsaicin-induced release of substance P-like immunoreactivity from guinea pig airway tissues. These findings suggest that WIN 55212-2 inhibit the activation of C-fibers via cannabinoid CB2 receptors and Maxi-K+ channels in guinea pig airways.
A Distinctive Interaction Between Chronic Anxiety and Problem Solving in Asymptomatic APOE e4 Homozygotes (2004)

We correlated measures of problem solving (Wisconsin Card Sorting Test [WCST] categories, total errors, and perseverative errors) and chronic anxiety (Personality Assessment Inventory Anxiety Scale [ANX]) in asymptomatic apolipoprotein E (APOE) e4 homozygotes (HMZs), heterozygotes, and noncarriers (NC) (n = 42 in each group) matched for age, education, and gender. Differences between HMZ and NC in the slope of the regression of WCST scores on ANX reached statistical significance on all three WCST measures. Chronic anxiety adversely affects cognitive skills in all groups, and is associated with significantly greater decline in problem solving skills in cognitively normal APOE e4 HMZ.
45nm high-k + metal gate strain-enhanced CMOS transistors (2008)

At the 45 nm technology node, high-k + metal gate transistors were introduced for the first time on a high-volume manufacturing process [1]. The introduction of a high-k gate dielectric enabled transistors with a 0.7x reduction in Tox (electrical gate oxide thickness) while reducing gate leakage 1000x for the PMOS and 25x for the NMOS transistors. Dual-band edge workfunction metal gates were introduced, eliminating polysilicon gate depletion and providing compatibility with the high-k gate dielectric. High-k + Metal gates have also been shown to have improved variability at the 45 nm node [2]. In addition to the high-k + metal gate, the 35 nm gate length CMOS transistors have been integrated with a third generation of strained silicon and have demonstrated the highest drive currents to date for both NMOS and PMOS. An SRAM cell size of 0.346 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> has been achieved while using 193 nm dry lithography. High yield and reliability has been demonstrated on multiple single, dual-, quad- and six-core microprocessors.
A novel de novo germ‐line V292M mutation in the extracellular region of RET in a patient with phaeochromocytoma and medullary thyroid carcinoma: functional characterization (2009)

Complete characterization and classification of all novel RET mutations are essential for extending genetic analysis in clinical practice. Our findings suggest that: (i) in all MEN-2 patients negative for RET hot-spot mutations, testing should be extended to all coding regions of the gene and (ii) the newly identified V292M/RET mutation is characterized by relatively weak in vitro transforming ability.
DNA-Templated Self-Assembly of Protein and Nanoparticle Linear Arrays (2003)

Self-assembling DNA tiling lattices represent a versatile system for nanoscale construction. Self-assembled DNA arrays provide an excellent template for spatially positioning other molecules with increased relative precision and programmability. Here we report an experiment using a linear array of DNA triple crossover tiles to controllably template the self-assembly of single-layer or double-layer linear arrays of streptavidin molecules and streptavidin-conjugated nanogold particles through biotin-streptavidin interaction. The organization of streptavidin and its conjugated gold nanoparticles into periodic arrays was visualized by atomic force microscopy and scanning electron microscopy.
Kinetics of Collision-induced Dissociation in the Paul Trap: a First-order Model (1996)

A first-order model describing the kinetics of collision-induced dissociation (CID) of polyatomic ions as effected via single-frequency resonance excitation in the Paul ion trap is presented. A mathematical expression for the dissociation rate constant associated with the model is developed from the kinetic theory of ion transport in gases, the forced, damped harmonic oscillator model for ion-trap resonance excitation, and thermal kinetic theory. Ion-trap CID is also simulated using a random walk sequence, corresponding to the processes believed to occur during collisional activation, which allows ion internal energy changes due to inelastic ion/helium collisions to be followed as a function of time; dissociation kinetics are included in the simulation by terminating the random walk when the ion internal energy exceeds the minimum required for fragmentation. Validity of the mathematical analysis and random walk simulation for the model is confirmed by comparison with experimental phenomenology associated with CID kinetics in the Paul trap. The first-order model in its present form, along with refinements resulting from further detailed comparison with experimental data, should therefore be a useful tool in expanding our understanding of polyatomic ion energetics in the Paul trap.
Preparation, Solid-State NMR, and Physicochemical Characterization of Surprisingly Tough Open Cell PolyHIPEs Derived from 1-Vinyl-1,2,4-triazole Oil-in-Water Emulsions (2011)

Interconnected microcellular polymeric monoliths have been prepared from oil-in-water concentrated emulsions of aqueous 1-vinyl-1,2,4-triazole using the high internal phase emulsion methodology. The polyHIPE materials thus obtained present a typical polyHIPE morphology having unexpectedly high mechanical strengths considering their low cross-linking level (3 mol % of N,N′-methylenebis(acrylamide)). 13C, 15N, and 1H solid-state NMR analyses confirm the expected polymer structure and evidenced the presence of polymer chain association by strong hydrogen bonding with water.
Gene Induction in Vessel Wall Injury (1993)

VSMC have been long thought to play a critical role in restenosis by proliferating and migrating from the vessel media to the intima, resulting in intimal hyperplasia. Recently, it has been suggested that the VSMC may play an earlier role in the events leading to restenosis, for example through the production of PDGF. The work described above suggests that the VSMC may mediate both the early inflammatory and thrombotic responses associated with vessel injury. Thus the VSMC may be involved in all phases of vascular injury, including thrombosis, inflammation, and intimal hyperplasia. Additional work will be necessary to fully elucidate the programs activated in VSMC in response to growth and migratory factors. The recent advances in recombinant DNA technology provide the hope that this will lead to novel approaches to attenuate the response of the VSMC to injury.
Development and validation of a new radioimmunoassay for parathyrin (PTH). (1982)

A radioimmunoassay for human parathyrin has been developed and characterized with whole-molecule (residues 1-84) human parathyrin and with the 1-34, 44-68, and 53-84 amino acid residue fragments of it. The antiserum used reacted with the whole molecule and with the 44-68 and 53-84 fragments, but not with the 1-34 fragment. Parathyrin concentrations in the serum of 118 normal subjects and of 112 patients with surgically proved primary hyperparathyroidism were determined with this assay. The mean results were 39 (SD 13) microL-Eq/mL for the normals and 111 (SD 77) microL-Eq/mL for the patients with primary hyperparathyroidism (p less than 0.0005). The upper 95% confidence limit of the normal range was 60 microL-Eq/mL. For 54 patients with primary hyperparathyroidism, the preoperative values for serum parathyrin, calcium, and phosphate--but not creatinine--were statistically different from the postoperative values (paired t-test, p less than 0.0005). Normal subjects showed significant (p less than 0.0005) differences in serum calcium concentrations but not in parathyrin concentrations, compared with concentrations found in cancer patients and patients who had thiazide-induced hypercalcemia. Phosphate concentration in serum, although not a specific indicator of disease, is a valuable clue to the diagnosis of primary hyperparathyroidism.
Statistics of the Stokes parameters (1987)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Richard Barakat, "Statistics of the Stokes parameters," J. Opt. Soc. Am. A 4, 1256-1263 (1987) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Triple-Negative Breast Cancer: Clinical Features and Patterns of Recurrence (2007)

Triple-negative breast cancers have a more aggressive clinical course than other forms of breast cancer, but the adverse effect is transient.
Flexible High-Output Nanogenerator Based on Lateral ZnO Nanowire Array (2010)

We report here a simple and effective approach, named scalable sweeping-printing-method, for fabricating flexible high-output nanogenerator (HONG) that can effectively harvesting mechanical energy for driving a small commercial electronic component. The technique consists of two main steps. In the first step, the vertically aligned ZnO nanowires (NWs) are transferred to a receiving substrate to form horizontally aligned arrays. Then, parallel stripe type of electrodes are deposited to connect all of the NWs together. Using a single layer of HONG structure, an open-circuit voltage of up to 2.03 V and a peak output power density of approximately 11 mW/cm(3) have been achieved. The generated electric energy was effectively stored by utilizing capacitors, and it was successfully used to light up a commercial light-emitting diode (LED), which is a landmark progress toward building self-powered devices by harvesting energy from the environment. This research opens up the path for practical applications of nanowire-based piezoelectric nanogeneragtors for self-powered nanosystems.
Prevention of Stroke and Myocardial Infarction by Amlodipine and Angiotensin Receptor Blockers (2007)

In the present quantitative overview of outcome trials, we investigated the efficacy of amlodipine or angiotensin receptor blockers in the prevention of stroke and myocardial infarction in patients with hypertension, coronary artery disease, or diabetic nephropathy. The analysis included 12 trials of 94 338 patients. The analysis of trials involving an amlodipine group showed that amlodipine provided more protection against stroke and myocardial infarction than other antihypertensive drugs, including angiotensin receptor blockers (-19%, P<0.0001 and -7%, P=0.03) and placebo (-37%, P=0.06 and -29%, P=0.04). The analysis of trials involving an angiotensin receptor blocker group showed contrasting results between trials versus amlodipine and trials versus other antihypertensive drugs for stroke (+19% versus -25%; P<0.0001) and myocardial infarction (+21% versus +1%; P=0.03). The results of 3 trials comparing an angiotensin receptor blocker with placebo were neutral (P> or =0.14). The within-trial between-group difference in achieved systolic pressure ranged from -1.1 to +4.7 mm Hg for trials involving an amlodipine group and from -2.8 to +4.0 mm Hg for trials involving an angiotensin receptor blocker group. The metaregression analysis correlating odds ratios with blood pressure differences showed a negative relationship (regression coefficients: -3% to -8%), which reached statistical significance (regression coefficient: -6%; P=0.01) for stroke in trials involving an amlodipine group. In conclusion, blood pressure differences largely accounted for cardiovascular outcome.
Patterning of Single-Wall Carbon Nanotubes via a Combined Technique (Chemical Anchoring and Photolithography) on Patterned Substrates (2005)

Single-walled carbon nanotubes (SWNTs) have been chemically attached with high density onto a patterned substrate. To form the SWNT pattern, the substrate was treated with acid-labile group protected amine, and an amine prepattern was formed using a photolithographic process with a novel polymeric photoacid generator (PAG). The polymeric PAG contains a triphenylsulfonium salt on its backbone and was synthesized to obtain a PAG with enhanced efficiency and ease of spin-coating onto the amine-modified glass substrate. The SWNT monolayer pattern was then formed through the amidation reaction between the carboxylic acid groups of carboxylated SWNTs (ca-SWNTs) and the prepatterned amino groups. A high-density multilayer was fabricated via further repeated reaction between the carboxylic acid groups of the ca-SWNTs and the amino groups of the linker with the aid of a condensation agent. The formation of covalent amide bonding was confirmed by X-ray photoelectron spectroscopy (XPS) analysis. Scanning electron microscopy and UV-vis-near-IR results show that the patterned SWNT films have uniform coverage with high surface density. Unlike previously reported patterned SWNT arrays, this ca-SWNT patterned layer has high surface density and excellent surface adhesion due to its direct chemical bonding to the substrate.
Assembly of collagen fibrils de novo by cleavage of the type I pC-collagen with procollagen C-proteinase. Assay of critical concentration demonstrates that collagen self-assembly is a classical example of an entropy-driven process. (1987)

Type I procollagen was purified from the medium of cultured human fibroblasts incubated with 14C-labeled amino acids, the NH2-terminal propeptides were cleaved with procollagen N-proteinase, and the resulting pC-collagen was isolated by gel filtration chromatography. pC-collagen did not assemble into fibrils or large aggregates even at concentrations of 0.5 mg.ml-1 at 34 degrees C in a physiological buffer. However, cleavage of pC-collagen to collagen with purified C-proteinase (Hojima, Y., (1985) J. Biol. Chem. 260, 15996-16003) generated fibrils that were visible by eye and that were large enough to be separated from solution by centrifugation at 13,000 x g for 4 min. With high concentrations of enzyme, the pC-collagen was completely cleaved in 1 h, and turbidity was near maximal in 3 h, but collagen continued to be incorporated in fibrils for over 10 h. Because the pC-collagen was uniformly labeled with 14C-aminoacids, the concentration of soluble collagen and, therefore, the critical concentration of polymerization were determined directly. The critical concentration was independent of the initial pC-collagen concentration and of the rate of cleavage. The critical concentration decreased with temperature between 29 and 41 degrees C and was 0.12 +/- 0.06 (S.E.) microgram.ml-1 at 41 degrees C. The thermodynamic parameters of assembly were essentially independent of temperature in the range 29 to 41 degrees C. The process was endothermic with a delta H value of +56 kcal.mol-1, but entropy driven with a delta S value of +220 cal.K-1.mol-1. The Gibbs energy change for polymerization was -13 kcal.mol-1 at 37 degrees C. The data demonstrate, for the first time, that type I collagen fibril formation de novo is a classical example of an entropy-driven self-assembly process similar to the polymerization of actin, flagella, and tobacco mosaic virus protein.