gebhart/patrepeval huggingface dataset:
Enterococcus faecium NCIMB 10415 does not protect interleukin-10 knock-out mice from chronic gut inflammation (2012)

Enterococcus faecium NCIMB 10415 reduces diarrhoea incidence and duration in animals and human study subjects. We tested whether the strain is also capable of reducing chronic gut inflammation and aimed to identify mechanisms that are involved in possible probiotic effects. To identify health-promoting mechanisms of the strain, we used interleukin-10-deficient mice that spontaneously develop gut inflammation and fed these mice a diet containing NCIMB 10415 for 3, 8 and 24 weeks, respectively. Control mice were fed a diet which was identically composed but did not contain the strain. After 3 weeks of intervention the experimental animals were less inflamed in the caecum than the control animals. This effect was not observed in the colon and there were no differences between experimental and control mice at any other time point. The application of the strain was associated with higher expression levels of interferon gamma and interferon gamma-induced protein 10 after 3 and 24 but not after 8 weeks of feeding. No differences between the animals were observed in intestinal barrier function or intestinal microbiota composition. However, we observed a low abundance of the mucin-degrading bacterium Akkermansia muciniphila in the mice that were fed NCIMB 10415 for 8 weeks. These low cell numbers were associated with a significantly lower caecal inflammation score and improved paracellular permeability as compared to the NCIMB-treated mice that were killed after 3 and 24 weeks of intervention. In conclusion, NCIMB 10415 is not capable of reducing gut inflammation in the IL-10-/- mouse model. The exact role of A. muciniphila and of a possible interaction between this bacterium, NCIMB 10415 and the host in gut inflammation requires further investigation.
Polyfluoroalkyl compounds of silicon. Part IX. Silanes containing the bis(trifluoromethyl)amino-group (1970)

The silanes (CF3)2N·CH2·SiX3(X3= Me3, Cl3, or MeCl2) have been prepared by free-radical addition of the corresponding silanes to NN-bis(trifluoromethyl)vinylamine. The polymer [(CF3)2N·CH2CH2·Si·O1·5]n and cyclic and linear siloxane polymers [(CF3)2N·CH2·CH2·SiMe·O]n have been prepared and their thermal and hydrolytic stabilities compared with those of the model compounds (CF3)2N·CH2·CH2·SiMe3 and (CF3)2N·CH2·CH2·SiF3. NN-Bis (trifluoromethyl)-2-bromoethane did not react with magnesium or lithium to give the corresponding metal derivatives. The reaction between mercury(II) bis(trifluoromethyl)amide and iodomethyltrimethylsilane gave perfluoro-(2-azapropene), its dimer perfluoro-(4-methyl-2,4-diazapent-2-ene) and, unexpectedly, fluoromethyl-trimethylsilane, and ethylfluorodimethylsilane.
Chemically defined medium for Legionella pneumophila growth (1981)

A chemically defined medium containing 18 amino acids, inorganic salts, rhamnose, choline, and ferric pyrophosphate has been developed. The final concentrations of salts and amino acids were modeled after yeast extract. This medium supported the growth of four serogroups of Legionella pneumophila. Growth in shake cultures at 37 degrees C produced a lag time of approximately 5 h and a generation time of 4 h with a maximum growth yield of 10 9 colony-forming units per ml. A soluble brown pigment was observed in the stationary phase of growth. The optimal pH was 6.3. Rhamnose and choline were stimulatory; arginine, serine, threonine, cysteine, valine, and methionine were essential. Supplemental iron was not required to attain maximum growth, but iron deprivation caused an extended lag phase.
Idiopathic pulmonary fibrosis: immunohistochemical analysis provides fresh insights into lung tissue remodelling with implications for novel prognostic markers. (2012)

The pathogenesis of IPF is complex and involves multiple factors, possibly including EMT. Histological analysis suggests TGF-β-stimulated myofib rob lasts initiate a contractile response within established fibroblastic foci while proliferating ATII cells attempt to instigate alveolar epithelium repair. Marker expression (N-cadherin and Ki-67) correlation with histological disease activity (as reflected by fibroblastic foci extent) may emerge as future prognostic indicators for IPF.
Diagnosis with Limited Failure Information (2006)

This paper discusses the challenges associated with diagnosing chain integrity and system logic failures in the production test environment with limited failure information. The following three methods were proposed to enhance diagnosis resolution in this scenario: (1) static pattern re-ordering (2) dynamic pattern re-ordering (3) per-pin based diagnosis. Experimental results illustrate that per-pin based failure logging and diagnosis algorithms enable scan chain diagnosis in volume production environment. Successful application of per-pin based chain diagnosis is demonstrated with an industrial case
Agonist‐dependent cannabinoid receptor signalling in human trabecular meshwork cells (2007)

This study demonstrates that endogenous CB1 couples to both Gq/11 and Gi/o in hTM cells in an agonist-dependent manner. Cannabinoid activation of multiple CB1 signalling pathways in TM tissue could lead to differential changes in aqueous humour outflow and IOP.
Interaction of ADP-ribosylation factor with Escherichia coli enterotoxin that contains an inactivating lysine 112 substitution. (1993)

Cholera toxin and Escherichia coli heat-labile enterotoxin (LT) exert their effects on cells through ADP-ribosylation of guanine nucleotide-binding proteins. Both toxins consist of one A subunit, which is an ADP-ribosyltransferase, and five B (or binding) subunits. Their enzymatic activities are latent; activation requires reduction and proteolysis, resulting in a catalytically active A1 protein and a much smaller A2 protein. These ADP-ribosyltransferases are activated by GTP-dependent 20-kDa ADP-ribosylation factors or ARFs. To determine if proteolysis plus reduction is required for appearance of the ARF allosteric site as well as for catalytic activity, an inactive mutant of LT, LT(E112K), with replacement of glutamate by lysine at position 112 of its A subunit, was utilized as a competitor in cholera toxin ADP-ribosyltransferase assays containing limiting amounts of ARF. LT(E112K) required trypsinization and reduction to become a potent, concentration-dependent inhibitor. Inhibition was reversed by increasing concentrations of ARF. Reduction or trypsinization alone did not generate an inhibitory form of LT(E112K). These studies are consistent with the conclusion that the ARF site is not expressed in the latent toxin. Both trypsinization and reduction are required for expression of a functional ARF binding site as well as for catalytic activity.
Dual Time-Interleaved Successive Approximation Register ADCs for an Ultra-Wideband Receiver (2007)

Ultra-wideband radio requires Nyquist sampling rates of at least 500 MS/s with low resolutions. While flash is the traditional choice for these specifications, a comparative energy model is used to show the potential energy savings of the time-interleaved successive approximation register architecture, which requires only a linear number of comparisons versus exponential for flash. A dual 500-MS/s, 5-bit ADC chip is implemented in a 0.18-mum CMOS process, with both ADCs synchronized for use in an I/Q UWB receiver. Each ADC uses a 6-way time-interleaved SAR topology with full custom logic, self-timed bit-cycling, and duty cycling of the comparator preamplifiers to enable 500-MS/s operation with 7.8 mW power consumption. The output resolution is adjustable down to the 1-bit level for additional power savings
Mixed-domain Galerkin expansions in scattering problems (1988)

Entire-domain Galerkin expansions provide a computationally efficient representation in method-of-moments (MM) solutions for electrically extended surfaces forming part of a separable coordinate geometry. For surfaces not conforming to such geometries, such as those with discontinuities, subdomain representations have been used. For many classes of scattering problems involving electrically large two-dimensional scatterers with localized discontinuities, a mixed-domain Galerkin expansion is shown to lead to a computationally efficient formulation. Electromagnetic-scattering solutions are developed for such configurations. Convergence of these solutions is illustrated with choices of mixed-domain expansions as a function of surface discontinuity. The computed results are given for both transverse magnetic (TM) and transverse electric (TE) polarization and are compared with published results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Projector-guided painting (2006)

This paper presents a novel interactive system for guiding artists to paint using traditional media and tools. The enabling technology is a multi-projector display capable of controlling the appearance of an artist's canvas. This display-on-canvas guides the artist to construct the painting as a series of layers. Our process model for painting is based on classical techniques and was designed to address three main issues which are challenging to novices: (1) positioning and sizing elements on the canvas, (2) executing the brushstrokes to achieve a desired texture and (3) mixing pigments to make a target color. These challenges are addressed through a set of interaction modes. Preview and color selection modes enable the artist to focus on the current target layer by highlighting the areas of the canvas to be painted. Orientation mode displays brushstroke guidelines for the creation of desired brush texture. Color mixing mode guides the artist through the color mixing process with a user interface similar to a color wheel. These interaction modes allow a novice artist to focus on a series of manageable subtasks in executing a complex painting. Our system covers the gamut of the painting process from overall composition down to detailed brushwork. We present the results from a user study which quantify the benefit that our system can provide to a novice painter.
In vitro chamber specification during embryonic stem cell cardiogenesis. Expression of the ventricular myosin light chain-2 gene is independent of heart tube formation. (1993)

The molecular cues that control patterning of the heart tube during early cardiogenesis are largely unknown. The present study has explored the embryonic stem (ES) cell differentiation system to determine if this in vitro model could be useful in studying the process of regional specification of cardiac muscle cells at the earliest possible stages. As assessed by polymerase chain reaction, ribonuclease protection, in situ hybridization, and immunohistochemical analyses, ES cell differentiation into embryoid bodies is characterized by the transcriptional and translational activation of the ventricular regulatory (phosphorylatable) myosin light chain gene, demonstrating that ventricular specification occurs during ES cell cardiogenesis. The finding of a ventricular-specific marker in an in vitro system in the absence of an intact heart tube provides evidence for cardiac regional specification independent of positional cues or physiologic stimuli. The temporal expression of the myogenic regulatory factors, myogenin and MyoD, suggests activation of the skeletal muscle program following cardiac myogenesis in vitro, indicating temporal fidelity to the progression of in vivo myogenesis. These data establish the mouse embryonic stem cell system as a model for cardiac chamber specification and suggest a promising approach in the study of regional specification in genetically engineered cardiac muscle cells.
Method for Quantification of a Prostate Cancer Biomarker in Urine without Sample Preparation (2007)

We describe a macrocantilever-based method for detecting a prostate cancer biomarker (alpha-methylacyl-CoA racemase; AMACR) directly in patient urine without a sample preparation step and without the use of labeled reagents. Clean catch voided urine specimens were prospectively collected from five confirmed prostate cancer patients 3 weeks postbiopsy. The presence of AMACR was measured in a blinded manner by exposing 3 mL of urine to the anti-AMACR-immobilized piezoelectric-excited millimeter-sized (PEMC) sensor. The resonance frequency of PEMC decreases as AMACR from sample binds to the antibody on the sensor. The resonance frequency changes for the five patients tested were 4,314 +/- 35 (n = 2), 269 +/- 17 (n = 2), 977 +/- 64 (n = 3), 600 +/- 31 (n = 2), and 801 +/- 81 (n = 2) Hz, respectively. Positive detection was observed within approximately 15 min. The responses to positive, negative, and buffer controls were -9 +/- 13, -34 +/- 18, and -6 +/- 18 Hz, respectively. Positive verification of AMACR attachment was confirmed by low-pH buffer release. The sensor response was quantitatively related to AMACR concentration in control urine, and the relationship was used in developing an in situ calibration method for quantifying AMACR in patient urine. Estimated concentrations of 42, 2, and 3 fg/mL AMACR were calculated for the three patients' urine, while absence of AMACR was confirmed in control urine (n = 13). Because of simplicity of measurement combined with high sensitivity and specificity, the method may be a useful adjunct in a point-of-care setting to identify men at increased risk for prostate cancer.
Base Metal Catalysts for Photochemical C–H Borylation That Utilize Metal–Metal Cooperativity (2013)

Heterobimetallic Cu-Fe and Zn-Fe complexes catalyze C-H borylation, a transformation that previously required noble metal catalysts. The optimal catalyst, (IPr)Cu-FeCp(CO)2, exhibits efficient activity at 5 mol% loading under photochemical conditions, shows only minimal decrease in activity upon reuse, and is able to catalyze borylation of a variety of arene substrates. Stoichiometric reactivity studies are consistent with a proposed mechanism that exploits metal-metal cooperativity and showcases bimetallic versions of the classical organometallic processes, oxidative addition and reductive elimination.
A Survey of Methods for Searching the Conformational Space of Small and Medium‐Sized Molecules (1991)

This chapter contains sections titled: Introduction Systematic Search Methods Model Building Approaches and Symbolic Representations of Conformation Random Search Methods Distance Geometry and Related Methods Molecular Dynamics Summary and Conclusions
L-Tyrosine Production by Analog-resistant Mutants Derived from a Phenylalanine Auxotroph of Corynebacterium glutamicum (1973)

Mutants resistant to various phenylalanine- or tyrosine-analogs were isolated from a phenylalanine auxotroph of Corynebacterium glutamicum KY 10233 by treatment with N- methyl-N′-nitro-N-nitrose guanidine (NTG) and screened for L-tyrosine production. A mutant, 98–Tx–71, which is resistant to 3-aminotyrosine, p-aminophenylalanine, p-fluoro-phenylalanine, and tyrosine hydroxamate was found to produce L-tyrosine at a concentration of 13.5 mg/ml in the cane molasses medium containing 10% of sugar calculated as glucose. A tyrosine-sensitive mutant, pr–20 which was derived from 98–Tx–71 produced L-tyrosine at a concentration of 17.6 mg/ml. L-Tyrosine formation in the strain pr–20 was found to be still inhibited by L-phenylalanine though it was not inhibited by L-tyrosine. The L-tyrosine formation in the mutant was repressed neither by L-phenylalanine nor by L-tyrosine.
Analysis of the interaction between charged side chains and the .alpha.-helix dipole using designed thermostable mutants of phage T4 lysozyme (1991)

It was shown previously that the introduction of a negatively charged amino acid at the N-terminus of an alpha-helix could increase the thermostability of phage T4 lysozyme via an electrostatic interaction with the "helix dipole" [Nicholson, H., Becktel, W. J., & Matthews, B. W. (1988) Nature 336, 651-656]. The prior report focused on the two stabilizing substitutions Ser 38----Asp (S38D) and Asn 144----Asp (N144D). Two additional examples of stabilizing mutants, T109D and N116D, are presented here. Both show the pH-dependent increase in thermal stability expected for the interaction of an aspartic acid with an alpha-helix dipole. Control mutants were also constructed to further characterize the nature of the interaction with the alpha-helix dipole. High-resolution crystal structure analysis was used to determine the nature of the interaction of the substituted amino acids with the end of the alpha-helix in both the primary and the control mutants. Control mutant S38N has stability essentially the same as that of wild-type lysozyme but hydrogen bonding similar to that of the stabilizing mutant S38D. This confirms that it is the electrostatic interaction between Asp 38 and the helix dipole, rather than a change in hydrogen-bonding geometry, that gives enhanced stability. Structural and thermodynamic analysis of mutant T109N provide a similar control for the stabilizing replacement T109D. In the case of mutant N116D, there was concern that the enhanced stability might be due to a favorable salt-bridge interaction between the introduced aspartate and Arg 119, rather than an interaction with the alpha-helix dipole. The additivity of the stabilities of N116D and R119M seen in the double mutant N116D/R119M indicates that favorable interactions are largely independent of residue 119. As a further control, Asp 92, a presumed helix-stabilizing residue in wild-type lysozyme, was replaced with Asn. This decreased the stability of the protein in the manner expected for the loss of a favorable helix dipole interaction. In total, five mutations have been identified that increase the thermostability of T4 lysozyme and appear to do so by favorable interactions with alpha-helix dipoles. As measured by the pH dependence of stability, the strength of the electrostatic interaction between the charged groups studied here and the helix dipole ranges from 0.6 to 1.3 kcal/mol in 150 mM KCl. In the case of mutants S38D and N144H, NMR titration was used to measure the pKa's of Asp 38 and His 144 in the folded structures.(ABSTRACT TRUNCATED AT 400 WORDS)
Effect of Counterion Structure on Ionomer Properties: Quaternary Phosphonium Counterions in Sulfonated EPDM (1980)

The effect of the structure of quaternary phosphonium counterions on the physical properties of an ethylene-propylene-diene monomer elastomer containing about 1 mol % sulfonation was studied. These quaternary counterions have an essentially full positive charge on the heteroatom so covalent interactions with anions are minimal, and the substituents can be varied over a wide range so that systematic studies of the effect of counterion structure can be made. Tensile strength decreased and melt-flow rate increased with increasing length of n-alkyl substituents. Substituent atoms near the central charged atom had a greater effect on physical properties than atoms farther out on a chain. Some ionomers containing divalent quarternary counterions were stronger and some were weaker than those containing corresponding monovalent quaternary ions. The sensitivity of some of these polymers to water uptake also was studied briefly.
Scheduling Tasks with Resource Requirements in Hard Real-Time Systems (1987)

This paper describes a heuristic approach for solving the problem of dynamically scheduling tasks in a real-time system where tasks have deadlines and general resource requirements. The crux of our approach lies in the heuristic function used to select the task to be scheduled next. The heuristic function is composed of three weighted factors. These factors explicitly consider information about real-time constraints of tasks and their utilization of resources. Simulation studies show that the weights for the various factors in the heuristic function have to be fine-tuned in order to obtain a degree of success in the range of 75-88 percent of that obtained via exhaustive search. However, modifying the approach to use limited backtracking improves the degree of success substantially to as high as 99.5 percent. This improvement is observed even when the initial set of weights are not tailored for a particular set of tasks. Simulation studies also show that in most cases the schedule determined by the heuristic algorithm is optimal or close to optimal.
Nitric oxide scavenging by red cell microparticles and cell free hemoglobin as a mechanism for hemolytic diseases and the red blood cell storage lesion (2011)

Intravascular red cell hemolysis impairs NO-redox homeostasis, producing endothelial dysfunction, platelet activation and vasculopathy. A central mechanism is that cell-free plasma hemoglobin reacts with the vasodilator nitric oxide (NO) in a 1:1 stoichiometric reaction that occurs at high rate of 6-8x107 mol/L/s. This consumption of NO by cell free plasma hemoglobin has been shown to cause changes in vascular function in subjects with sickle cell anaemia who had plasma heme concentrations as low as 6 µM. Approximately half of the observed “hemolysis” in stored blood is also encapsulated in microparticles, and, in theory, based on their small molecular size, microparticles may also exhibit accelerated NO scavenging rates compared with intact erythrocytes. The effect of microparticles on NO scavenging could be especially important, particularly in the microvasculature where their clearance may not be reflected by systemic clearance rates. Red blood cell storage under standard blood banking conditions results in reduced integrity of the erythrocyte membrane, with formation of exocytic microvesicles or “microparticles” and hemolysis, which we hypothesized could impair vascular function and contribute to the putative “storage lesion” of banked blood. We now find that storage of human red blood cells under standard blood banking conditions results in the accumulation of cell free and microparticle-encapsulated hemoglobin which, despite 39 days of storage, remains in the reduced ferrous oxyhemoglobin redox state and stoichiometrically reacts with and scavenges the vasodilator NO. Using stopped-flow spectroscopy and laser triggered NO release from a caged NO compound we found that both free hemoglobin and microparticles react with NO about 1000 times faster than with intact erythrocytes. In complementary in vivo studies we show that hemoglobin, even at concentrations below 10 µM (in heme), produces potent vasoconstriction when infused into the rat circulation, while controlled infusions of methemoglobin and cyanomethemoglobin, which do not consume NO, have substantially reduced vasoconstrictor effects. Infusion of the plasma from stored human red cell units into the rat circulation produces significant vasoconstriction related to the magnitude of storage related hemolysis. Finally, we explored new therapies that have the potential to bypass NO scavenging via direct pharmacological activation of soluble guanylyl cyclase (sGC). These sGC activators or stimulators show promise in the reversal of free-hemoglobin mediated vasoconstriction. The results of these studies suggest new mechanisms for endothelial injury and impaired vascular function associated with the most fundamental of red blood cell storage lesions, hemolysis, as well as suggest a new approach to therapeutic restoration of cGMP levels in the setting of NO scavenging reactions.