gebhart/patrepeval huggingface dataset:
HaCaT keratinocytes in co‐culture with <i>Staphylococcus aureus</i> can be protected from bacterial damage by polihexanide (2009)

ABSTRACT Wound healing is compromised by critical colonization and infection with bacteria. Hence, antimicrobial agents are used clinically to decrease the bacterial load and promote wound healing. Polihexanide (PHMB) has been found to be effective against a broad spectrum of micro‐organisms and is increasingly utilized in rinsing solutions or in combination with wound dressings because of its good biocompatibility. In the present study, a co‐culture of human keratinocytes and Staphylococcus aureus was established to serve as an in vitro model for infected wounds. Incubation of keratinocytes with increasing concentrations of S. aureus led to a dose‐dependent decline of cell viability and proliferation. Lactate dehydrogenase release and interleukin‐8 liberation were found to be elevated under these conditions. Polihexanide dose‐dependently was able to protect keratinocytes from bacterial damage and re‐establish normal human cell proliferation in vitro. Furthermore, a dressing consisting of biocellulose derived from Acetobacter xylinum with the addition of polihexanide was adept to safeguard keratinocytes against S. aureus . In conclusion, the co‐culture system presented embodies a valuable tool as a model system for infected cells in a non‐healing wound. Furthermore, the results obtained support the favorable function of polihexanide in the treatment of infected chronic wounds.
Synthesis and structure of a one-dimensional cobalt(ii) coordination polymer with 1,3-bis(1,2,4-triazol-1-yl)propane (2002)

A novel 1D-coordination polymeric Co(II) complex [Co(btp)2(NCS)2]n [1, btp = 1,3-bis(1,2,4-triazol-1-yl)propane] was synthesized and characterized. The coordination geometry of the cobalt ions is distorted octahedral, with the equatorial plane formed by the four nitrogen atoms of the four triazole groups and the axial sites occupied by two terminal trans thiocyanato ligands. The Co(II) ions are linked by the btp ligands, building up coordination polymers of infinite 1D-neutral chains.
Interrelation of Creep and Relaxation: A Modeling Approach for Ligaments (1999)

Experimental data (Thornton et al., 1997) show that relaxation proceeds more rapidly (a greater slope on a log-log scale) than creep in ligament, a fact not explained by linear viscoelasticity. An interrelation between creep and relaxation is therefore developed for ligaments based on a single-integral nonlinear superposition model. This interrelation differs from the convolution relation obtained by Laplace transforms for linear materials. We demonstrate via continuum concepts of nonlinear viscoelasticity that such a difference in rate between creep and relaxation phenomenologically occurs when the nonlinearity is of a strain-stiffening type, i.e., the stress-strain curve is concave up as observed in ligament. We also show that it is inconsistent to assume a Fung-type constitutive law (Fung, 1972) for both creep and relaxation. Using the published data of Thornton et al. (1997), the nonlinear interrelation developed herein predicts creep behavior from relaxation data well (R > or = 0.998). Although data are limited and the causal mechanisms associated with viscoelastic tissue behavior are complex, continuum concepts demonstrated here appear capable of interrelating creep and relaxation with fidelity.
APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure (2013)

Apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like 3G (i.e., APOBEC3G or A3G) is an evolutionarily conserved cytosine deaminase that potently restricts human immunodeficiency virus type 1 (HIV-1), retrotransposons and other viruses. A3G has a nucleotide target site specificity for cytosine dinucleotides, though only certain cytosine dinucleotides are 'hotspots' for cytosine deamination, and others experience little or no editing by A3G. The factors that define these critical A3G hotspots are not fully understood. To investigate how A3G hotspots are defined, we used an in vitro fluorescence resonance energy transfer-based oligonucleotide assay to probe the site specificity of A3G. Our findings strongly suggest that the target single-stranded DNA (ssDNA) secondary structure as well as the bases directly 3' and 5' of the cytosine dinucleotide are critically important A3G recognition. For instance, A3G cannot readily deaminate a cytosine dinucleotide in ssDNA stem structures or in nucleotide base loops composed of three bases. Single-stranded nucleotide loops up to seven bases in length were poor targets for A3G activity unless cytosine residues flanked the cytosine dinucleotide. Furthermore, we observed that A3G favors adenines, cytosines and thymines flanking the cytosine dinucleotide target in unstructured regions of ssDNA. Low cytosine deaminase activity was detected when guanines flanked the cytosine dinucleotide. Taken together, our findings provide the first demonstration that A3G cytosine deamination hotspots are defined by both the sequence context of the cytosine dinucleotide target as well as the ssDNA secondary structure. This knowledge can be used to better trace the origins of mutations to A3G activity, and illuminate its impact on processes such as HIV-1 genetic variation.
Proximal Tubule-Specific Deletion of the NHE3 (Na <sup>+</sup> /H <sup>+</sup> Exchanger 3) in the Kidney Attenuates Ang II (Angiotensin II)-Induced Hypertension in Mice (2019)

The present study directly tested the hypothesis that the NHE3 (Na<sup>+</sup>/H<sup>+</sup> exchanger 3) in the proximal tubules of the kidney is required for the development of Ang II (angiotensin II)-induced hypertension using PT-Nhe3<sup>-/-</sup> (proximal tubule-specific NHE3 knockout) mice. Specifically, PT-Nhe3<sup>-/-</sup> mice were generated using the SGLT2-Cre/Nhe3<sup>loxlox</sup> approach, whereas Ang II-induced hypertension was studied in 12 groups (n=5-12 per group) of adult male and female wild-type (WT) and PT-Nhe3<sup>-/-</sup> mice. Under basal conditions, systolic blood pressure, diastolic blood pressure, and mean arterial blood pressure were significantly lower in male and female PT-Nhe3<sup>-/-</sup> than WT mice (P<0.01). A high pressor, 1.5 mg/kg per day, intraperitoneal or a slow pressor dose of Ang II, 0.5 mg/kg per day, intraperitoneal for 2 weeks significantly increased systolic blood pressure, diastolic blood pressure, and mean arterial blood pressure in male and female WT mice (P<0.01), but the hypertensive response to Ang II was markedly attenuated in male and female PT-Nhe3<sup>-/-</sup> mice (P<0.01). Ang II impaired the pressure-natriuresis response in WT mice, whereas proximal tubule-specific deletion of NHE3 improved the pressure-natriuresis response in Ang II-infused PT-Nhe3<sup>-/-</sup> mice (P<0.01). AT<sub>1</sub> receptor blocker losartan completely blocked Ang II-induced hypertension in both WT and PT-Nhe3<sup>-/-</sup> mice (P<0.01). However, inhibition of nitric oxide synthase with L-N<sup>G</sup>-Nitroarginine methyl ester had no effect on Ang II-induced hypertension in WT or PT-Nhe3<sup>-/-</sup> mice (not significant). Furthermore, Ang II-induced hypertension was significantly attenuated by an orally absorbable NHE3 inhibitor AVE0657. In conclusion, NHE3 in the proximal tubules of the kidney may be a therapeutical target in hypertension induced by Ang II or with increased NHE3 expression in the proximal tubules.
Highly Efficient Small Interfering RNA Delivery to Primary Mammalian Neurons Induces MicroRNA-Like Effects before mRNA Degradation (2004)

The study of protein function in neurons has been hindered by the lack of highly efficient, nontoxic methods of inducing RNA interference in such cells. Here we show that application of synthetic small interfering RNA (siRNA) linked to the vector peptide Penetratin1 results in rapid, highly efficient uptake of siRNA by entire populations of cultured primary mammalian hippocampal and sympathetic neurons. This treatment leads to specific knock-down of targeted proteins within hours without the toxicity associated with transfection. In contrast to current methods, our technique permits study of protein function across entire populations with minimal disturbance of complex cellular networks. Using this technique, we found that protein knock-down (evident after 6 hr) precedes any decrease in targeted message (evident after 24 hr), suggesting an early, translational repression by perfectly targeted siRNAs.
New Mechanisms for Ozone-Based ALD Growth of High-k Dielectrics via Nitrogen-Oxygen Species (2010)

Optimization of the O2/N2 feed gas flow during O3 generation by dielectric barrier discharge was found to improve the growth rate and uniformity of HfO2 and La2O3 films by atomic layer deposition (ALD) in a hot wall cross-flow thermal ALD reactor. Discharge products from the O3 generator and from the exhaust of the ALD reactor were analyzed by FTIR spectrometry. N2O, N2O5, NO2 and NO species were detected, as well as unreacted O3. Alternate models which could explain the behavior of various ozone-based ALD processes utilizing N2 doped O3 generation are presented.
Quality Control in Eukaryotic Membrane Protein Overproduction (2014)

The overexpression of authentically folded eukaryotic membrane proteins in milligramme quantities is a fundamental prerequisite for structural studies. One of the most commonly used expression systems for the production of mammalian membrane proteins is the baculovirus expression system in insect cells. However, a detailed analysis by radioligand binding and comparative Western blotting of G protein-coupled receptors and a transporter produced in insect cells showed that a considerable proportion of the expressed protein was misfolded and incapable of ligand binding. In contrast, production of the same membrane proteins in stable inducible mammalian cell lines suggested that the majority was folded correctly. It was noted that detergent solubilisation of the misfolded membrane proteins using either digitonin or dodecylmaltoside was considerablyless efficient than using sodium dodecyl sulfate or foscholine-12, whilst these detergents were equally efficient at solubilising correctly folded membrane proteins. This provides a simple and rapid test to suggest whether heterologously expressed mammalian membrane proteins are indeed correctly folded, without requiring radioligand binding assays. This will greatly facilitate the high-throughput production of fully functional membrane proteins for structural studies.
An open-label evaluation of rifaximin in the treatment of active Crohn's disease (2005)

These data, which are consistent with the possibility that rifaximin may be useful for active Crohn's disease, warrant confirmation in a randomized, double-blind, placebo-controlled trial.
Antagonism of lactic acid bacteria towards Staphylococcus aureus and Escherichia coli on agar plates and in milk. (1996)

The antagonistic effect of lactic acid bacteria (LAB, including Lactobacillus acidophilus, L. bulgaricus, L. casei and Streptococcus thermophilus) on Staphylococcus aureus and Escherichia coli was evaluated on MRS agar with the deferred and cross-streaking techniques, and in milk with the plate counting method. All LAB were repressive to S aureus and E coli on the agar medium. However, their suppressive activity was significantly reduced when the agar medium was buffered to pH 7.2. In normal milk, L acidophilus strains A and B, S thermophilus and its combinations with L acidophilus A and L bulgaricus 6032 were inhibitory to S aureus, while in mastitic milk, only S thermophilus and its combinations showed inhibition. L acidophilus A and L bulgaricus 34104 were repressive to E coli growth in normal milk. S thermophilus and its combinations were inhibitory to E coli in both the normal and mastitic milk samples. These results indicate that the antagonistic activity of LAB on pathogenic bacteria varied with the type of media in which the tests were done, and that testing of in vitro antagonism in milk would be more informative than that in artificial media for in vivo tests concerning the possible roles of competitive microbiological ecology in mastitis control.
HIV-1 Tat Alters Normal Organization of Neurons and Astrocytes in Primary Rodent Brain Cell Cultures: RGD Sequence Dependence (1993)

The HIV-1 trans-activator protein Tat has been implicated as a mediator of neuronal dysfunction in several model systems. To explore the possibility that Tat can affect primary brain cells, we examined the effect of recombinant Tat protein on rat cortical brain cell cultures. Tat induced marked aggregation of neurons and astrocytes in developing cultures and caused the neuritic processes to coalesce into fascicles. Cell death was not seen and brain macrophages were not affected. These effects mapped to a different region from the trans-activation domain of Tat, as mutating the RGD (arginine-glycine-aspartic acid) sequence within the second exon abrogated aggregation and fascicle formation without affecting trans-activation capacity. Such effects on primary neurons and astrocytes may reflect specific interactions of Tat with uninfected cells within the CNS in vivo.
An improved staining method for rat microglial cells using the lectin from Griffonia simplicifolia (GSA I-B4). (1990)

A simple method for the lectin histochemical visualization of rat microglial cells is described. Advantages include ease of fixation of brain tissue using paraformaldehyde, and rapidity of tissue processing by vibratome sectioning. Furthermore, in addition to providing good structural preservation, the method achieves improved lectin binding, resulting in complete labeling of all microglial cells and in superior visualization of cellular processes. The lectin histochemical technique for rat microglia has the potential to be adapted to any mammalian species, and should prove valuable for neuroscientists interested in studying this glial cell type.
CRC handbook of thermophysical and thermochemical data (1995)

Symbols, Units, and Terminology Recommended Symbols for Thermodynamic and Transport Properties SI Units and Conversion Factors International Temperature Scale of 1990 Thermodynamic Properties of Pure Substances Physical Constants and Phase Behavior Volumetric Properties Calorimetric Properties Associated with Chemical Reactions Heat Capacity Phase Transition Properties Surface Tension Thermodynamic Properties of Mixtures Vapor-Liquid Equilibrium Volumetric Properties Calorimetric Properties Transport Properties Viscosity Thermal Conductivity Diffusion Coefficients Properties of Individual Substances Thermophysical Properties of Some Common Fluids Thermodynamic Properties of Air Properties of Liquid Water Density of Water Steam Tables Indexes Substance List Index
Time-resolved characterization of InAs/InGaAs quantum dot gain material for 1.3 /spl mu/m lasers on gallium arsenide (2000)

Summary form only given. Recent progress in wavelength tuning of InAs/InGaAs/GaAs self-assembled quantum dots (QDs) has shown that this system represents an adequate active material for 1.3 /spl mu/m lasers on gallium arsenide. Integration of 1.3 /spl mu/m QDs in a GaAs/AlGaAs vertical-cavity surface-emitting laser structure would allow the development of a low-cost laser module for 1.3 /spl mu/m fiber links. Embedding the QDs in a InGaAs quantum well (QW) has been proposed as an effective way to red-shift the emission wavelength to the 1.3 /spl mu/m region. In-plane lasers with low threshold current densities <100A/cm/sup 2/ were demonstrated using embedded QDs. We have investigated the carrier dynamics in embedded QDs by time-resolved photoluminescence (PL). The sample consists in a single layer of QDs formed by growing 2.6 monolayers of InAs at the center of a 20 nm In/sub 0.15/Ga/sub 0.85/As QW. The dot density is 10/sup 11/ cm/sup -2/. The room temperature (RT) PL signal is peaked at 1305 nm.
Metabolomic applications of electrochemistry/Mass spectrometry (2004)

Analytical techniques used for multivariate analysis of endogenous metabolites in biological systems (e.g., metabolomics, metabonomics) must be capable of accurately and selectively monitoring many known and unknown molecules that span a diverse chemical spectrum and over extremely large dynamic concentration ranges. Mass spectrometric (MS) and electrochemical array (EC-Array) detection have been widely used for multi-component analysis with applicability to low-level (fmol) metabolites. Described here are practical considerations and results obtained with the combined use of EC-Array and MS for HPLC-based multivariate metabolomic analysis. Data presented include the study of changes in rat urinary metabolite profiles associated with xenobiotic toxin exposure analyzed by HPLC using water:acetonitrile binary gradient conditions and post-column flow splitting between EC-Array and MS detectors. Results show complementary quantitative and qualitative analysis and the ability to differentiate sample groups consistent with xenobiotic-induced histopathological changes. The potential applicability of this hyphenated technique for biomarker elucidation through measurement of redox active compounds that are commonly associated with disease pathology and xenobiotic toxicity is discussed. The use of EC reactor cells in series with MS is also presented as a means of producing likely metabolites to facilitate structural elucidation and confirmation.
Investigating the Effect of the Multiple Comparisons Problem in Visual Analysis (2018)

The goal of a visualization system is to facilitate dataset-driven insight discovery. But what if the insights are spurious? Features or patterns in visualizations can be perceived as relevant insights, even though they may arise from noise. We often compare visualizations to a mental image of what we are interested in: a particular trend, distribution or an unusual pattern. As more visualizations are examined and more comparisons are made, the probability of discovering spurious insights increases. This problem is well-known in Statistics as the multiple comparisons problem (MCP) but overlooked in visual analysis. We present a way to evaluate MCP in visualization tools by measuring the accuracy of user reported insights on synthetic datasets with known ground truth labels. In our experiment, over 60% of user insights were false. We show how a confirmatory analysis approach that accounts for all visual comparisons, insights and non-insights, can achieve similar results as one that requires a validation dataset.
Curvature estimation for multilayer hinged structures with initial strains (2003)

Closed-form estimate of curvature for hinged multilayer structures with initial strains is developed. The finite element method is used for modeling of self-positioning microstructures. The geometrically nonlinear problem with large rotations and large displacements is solved using step procedure with node coordinate update. Finite element results for curvature of the hinged micromirror with variable width is compared to closed-form estimates.
Structural Characterizations of Glycerol Kinase: Unraveling Phosphorylation-Induced Long-Range Activation (2008)

Glycerol metabolism provides a central link between sugar and fatty acid catabolism. In most bacteria, glycerol kinase plays a crucial role in regulating channel/facilitator-dependent uptake of glycerol into the cell. In the firmicute Enterococcus casseliflavus, this enzyme's activity is enhanced by phosphorylation of the histidine residue (His232) located in its activation loop, approximately 25 A from its catalytic cleft. We reported earlier that some mutations of His232 altered enzyme activities; we present here the crystal structures of these mutant GlpK enzymes. The structure of a mutant enzyme with enhanced enzymatic activity, His232Arg, reveals that residues at the catalytic cleft are more optimally aligned to bind ATP and mediate phosphoryl transfer. Specifically, the position of Arg18 in His232Arg shifts by approximately 1 A when compared to its position in wild-type (WT), His232Ala, and His232Glu enzymes. This new conformation of Arg18 is more optimally positioned at the presumed gamma-phosphate location of ATP, close to the glycerol substrate. In addition to structural changes exhibited at the active site, the conformational stability of the activation loop is decreased, as reflected by an approximately 35% increase in B factors ("thermal factors") in a mutant enzyme displaying diminished activity, His232Glu. Correlating conformational changes to alteration of enzymatic activities in the mutant enzymes identifies distinct localized regions that can have profound effects on intramolecular signal transduction. Alterations in pairwise interactions across the dimer interface can communicate phosphorylation states over 25 A from the activation loop to the catalytic cleft, positioning Arg18 to form favorable interactions at the beta,gamma-bridging position with ATP. This would offset loss of the hydrogen bonds at the gamma-phosphate of ATP during phosphoryl transfer to glycerol, suggesting that appropriate alignment of the second substrate of glycerol kinase, the ATP molecule, may largely determine the rate of glycerol 3-phosphate production.
Autophagy (2013)

Autophagy is an evolutionarily conserved cellular process through which long-lived proteins and damaged organelles are recycled to maintain energy homeostasis. These proteins and organelles are sequestered into a double-membrane structure, or autophagosome, which subsequently fuses with a lysosome in order to degrade the cargo. Although originally classified as a type of programmed cell death, autophagy is more widely viewed as a basic cell survival mechanism to combat environmental stressors. Autophagy genes were initially identified in yeast and were found to be necessary to circumvent nutrient stress and starvation. Subsequent elucidation of mammalian gene counterparts has highlighted the importance of this process to normal development. This review provides an overview of autophagy, the types of autophagy, its regulation and its known impact on development gleaned primarily from murine models.
Design of a Multifrequency FMCW Radar (1998)

This paper pertains to the design aspects of a multifrequency FMCW radar with emphasis on the engineerig problems involved in its implementation. This radar generates 8 separate FMCW signals which are then additively mixed and radiated. The target return also comprises returns at these frequencies. The signals are then split into their constituents and processed collectively to obtain an extremely high resolution synthetic image of the target. The ultimate objectives of the radar are multiple: 1. to study waveforms of variable and flexible transmitted power spectra. 2. to study ultra-wide band processing techniques, without the need to have an ultra-wide instantaneous bandwidth. 3. to study coherent, non-coherent and mixed processing concepts. The radar itself will belong to the class of LPI radars. The high resolutions obtained by this technique are comparable to those that can be achieved by ultra-wide band radar. The additional advantage here is that this radar can be built using essentially "bought - out" items i.e. it does not require any radically new technology. The paper discusses the problems involved in the implementation of this radar with special emphasis on the critical items viz. the design of the power combiner and the power resolver. It finally analyses the results achieved in the implementation of these critical units.