gebhart/patrepeval huggingface dataset:
Penicillin Kills Chlamydia following the Fusion of Bacteria with Lysosomes and Prevents Genital Inflammatory Lesions in C. muridarum-Infected Mice (2013)

The obligate intracellular bacterium Chlamydia exists as two distinct forms. Elementary bodies (EBs) are infectious and extra-cellular, whereas reticulate bodies (RBs) replicate within a specialized intracellular compartment termed an 'inclusion'. Alternative persistent intra-cellular forms can be induced in culture by diverse stimuli such as IFNγ or adenosine/EHNA. They do not grow or divide but revive upon withdrawal of the stimulus and are implicated in several widespread human diseases through ill-defined in vivo mechanisms. β-Lactam antibiotics have also been claimed to induce persistence in vitro. The present report shows that upon penicillin G (pG) treatment, inclusions grow as fast as those in infected control cells. After removal of pG, Chlamydia do not revert to RBs. These effects are independent of host cell type, serovar, biovar and species of Chlamydia. Time-course experiments demonstrated that only RBs were susceptible to pG. pG-treated bacteria lost their control over host cell apoptotic pathways and no longer expressed pre-16S rRNA, in contrast to persistent bacteria induced with adenosine/EHNA. Confocal and live-video microscopy showed that bacteria within the inclusion fused with lysosomal compartments in pG-treated cells. That leads to recruitment of cathepsin D as early as 3 h post pG treatment, an event preceding bacterial death by several hours. These data demonstrate that pG treatment of cultured cells infected with Chlamydia results in the degradation of the bacteria. In addition we show that pG is significantly more efficient than doxycycline at preventing genital inflammatory lesions in C. muridarum-C57Bl/6 infected mice. These in vivo results support the physiological relevance of our findings and their potential therapeutic applications.
The Epithelial Sodium Channel (ENaC) Traffics to Apical Membrane in Lipid Rafts in Mouse Cortical Collecting Duct Cells (2007)

We previously showed that ENaC is present in lipid rafts in A6 cells, a Xenopus kidney cell line. We now demonstrate that ENaC can be detected in lipid rafts in mouse cortical collecting duct ((MPK)CCD(14)) cells by detergent insolubility, buoyancy on density gradients using two distinct approaches, and colocalization with caveolin 1. Less than 30% of ENaC subunits were found in raft fractions. The channel subunits also colocalized on sucrose gradients with known vesicle targeting and fusion proteins syntaxin 1A, Vamp 2, and SNAP23. Hormonal stimulation of ENaC activity by either forskolin or aldosterone, short or long term, did not alter the lipid raft distribution of ENaC. Methyl-beta-cyclodextrin added apically to (MPK)CCD(14) cells resulted in a slow decline in amiloride-sensitive sodium transport with short circuit current reductions of 38.1 +/- 9.6% after 60 min. The slow decline in ENaC activity in response to apical cyclodextrin was identical to the rate of decline seen when protein synthesis was inhibited by cycloheximide. Apical biotinylation of (MPK)CCD(14) cells confirmed the loss of ENaC at the cell surface following cyclodextrin treatment. Acute stimulation of the recycling pool of ENaC was unaffected by apical cyclodextrin application. Expression of dominant negative caveolin isoforms (CAV1-eGFP and CAV3-DGV) which disrupt caveolae, reduced basal ENaC currents by 72.3 and 78.2%, respectively; but, as with cyclodextrin, the acute response to forskolin was unaffected. We conclude that ENaC is present in and regulated by lipid rafts. The data are consistent with a model in which rafts mediate the constitutive apical delivery of ENaC.
New Selectivity and Turnover in Peptide Hydrolysis by Metal Complexes. A Palladium(II) Aqua Complex Catalyzes Cleavage of Peptides Next to the Histidine Residue (1996)

This seems to be the first report that a transition-metal complex bonded to a histidine residue effects hydrolytic cleavage of a peptide next to this residue. Dipeptides AcHis-Aa in which the C-terminal amino acid designated Aa is Gly, Ala, Ser, Thr, Leu, Phe, and Tyr are completely hydrolyzed at 60 °C and 1.46 ≤ pD ≤ 2.61 in the presence of cis-[Pd(en)(H2O)2]2+. The reaction is conveniently monitored by 1H NMR spectroscopy, and we report the kinetics. The reaction is unimolecular with respect to the palladium(II)−peptide complex. The cleavage is regioselective. In all the aforementioned dipeptides and in the tripeptide AcGly-His-Gly only the amide bond involving the carboxylic group of histidine is cleaved; the amide bond involving the amino group of histidine is not cleaved. When the carboxylic group of histidine is free, as in AcGly-His, cis-[Pd(en)(H2O)2]2+ does not effect hydrolysis. Lability of palladium(II) complexes and the acidic solution make possible a modest turnover in hydrolysis; the catalyst can cleave several equivalents of the dipeptide. The dipeptides AcHis-Aa, and also one product of their cleavage, AcHis, exist free and bound to the catalyst. They form similar palladium(II) complexes, five types of which are distinguishable by 1H NMR spectroscopy. The other products of cleavage, the amino acids Aa, exist free and in chelate complexes cis-[Pd(en)(N,O-Aa)]+. Partial binding of the catalyst to the peptide and to its cleavage products gives rise to an extended and complex equilibrium. Increase in pH favors catalytically-inactive palladium(II)−peptide complexes, inhibits their conversion into catalytically-active complexes, and lowers the observed rate constant for hydrolysis. Because the equilibria are reversible, even the peptide bound in inactive complexes eventually becomes hydrolyzed. When palladium is removed as a diethyldithiocarbamate complex, the equilibria are abolished and only ethylenediamine, AcHis, and Aa remain. The rate constant for cleavage decreases as the steric bulk of the amino acid Aa increases and as intrapeptide hydrogen bonds mediated by water restrict the access of the palladium(II) catalyst to the His-Aa bond. This hydrogen bonding is possible only when the amino acid Aa contains a hydroxyl group in a flexible side chain, as in Ser and Thr. The intrapeptide hydrogen bonding is impossible when a hydroxyl group is held relatively rigidly, as in Tyr, and, of course, when the hydroxyl group is absent, as in the other four amino acids. The kinetic effects of steric bulk and of specific hydrogen bonding may allow sequence selectivity in cleavage of peptides with palladium(II) complexes. This study points the way toward artificial metallopeptidases, coordination complexes with enzyme-like properties.
Single molecule detector for mass spectrometry with mass independent detection efficiency (2001)

Experimental results from equimolar PEG and protein standards samples are presented from a MALDI-TOF mass spectrometer equipped with both ionizing detectors and the novel single molecule sensitive cryodetectors. The data are consistent with a model hypothesis suggesting that the observed decrease in signal strength in conventional ionizing detector MALDI-TOF mass spectrometers can be explained by the exponentially decreasing quantum efficiency of ionizing detectors. Cryodetectors, in contrast, have a mass independent detection efficiency of 100% on impact and provide additional information on the molecule state owing to the calorimetric nature of the detection mechanism.
Multi-objective test prioritization in software product line testing (2014)

Test prioritization is crucial for testing products in a product line considering limited budget in terms of available time and resources. In general, it is not practically feasible to execute all the possible test cases and so, ordering test case execution permits test engineers to discover faults earlier in the testing process. An efficient prioritization of test cases for one or more products requires a clear consideration of the tradeoff among various costs (e.g., time, required resources) and effectiveness (e.g., feature coverage) objectives. As an integral part of the future Cisco's test scheduling system for validating video conferencing products, we introduce a search-based multi-objective test prioritization technique, considering multiple cost and effectiveness measures. In particular, our multi-objective optimization setup includes the minimization of execution cost (e.g., time), and the maximization of number of prioritized test cases, feature pairwise coverage and fault detection capability. Based on cost-effectiveness measures, a novel fitness function is defined for such test prioritization problem. The fitness function is empirically evaluated together with three commonly used search algorithms (e.g., (1+1) Evolutionary algorithm (EA)) and Random Search as a comparison baseline based on the Cisco's industrial case study and 500 artificial designed problems. The results show that (1+1) EA achieves the best performance for solving the test prioritization problem and it scales up to solve the problems of varying complexity.
THERMAL DENATURATION OF SOLUBLE CALF-SKIN COLLAGEN (1965)

1. Soluble calf-skin collagen has been denatured thermally between 37 degrees and 60 degrees and the component proteins have been separated on carboxymethylcellulose. 2. Four main fractions have been separated; alpha and beta (in the nomenclature in common usage) and two other fractions. (The alpha and beta components are complex owing to the presence of alpha(1), alpha(2), beta(1) and beta(2) parts). 3. Fractions 3 and 4 undergo rapid denaturation between 39 degrees and 40 degrees whereafter fraction 4 remains virtually unchanged even at 60 degrees . 4. That portion of fraction 4 which remains at 60 degrees is thought to be identical with the fraction designated gamma by other workers, this fraction being composed of three alpha-chains in covalent linkage (such bonds are alkali-labile). 5. The equilibrium between alpha, beta and fractions 3 and 4 is apparently reversible since acid-soluble collagen after denaturation at 45 degrees or 60 degrees followed by cooling to 0 degrees for 30min. was found to contain only fraction 4 when chromatographed at 37 degrees .
Electrochemistry at the Edge of a Single Graphene Layer in a Nanopore (2012)

We study the electrochemistry of single layer graphene edges using a nanopore-based structure consisting of stacked graphene and Al(2)O(3) dielectric layers. Nanopores, with diameters ranging from 5 to 20 nm, are formed by an electron beam sculpting process on the stacked layers. This leads to a unique edge structure which, along with the atomically thin nature of the embedded graphene electrode, demonstrates electrochemical current densities as high as 1.2 × 10(4) A/cm(2). The graphene edge embedded structure offers a unique capability to study the electrochemical exchange at an individual graphene edge, isolated from the basal plane electrochemical activity. We also report ionic current modulation in the nanopore by biasing the embedded graphene terminal with respect to the electrodes in the fluid. The high electrochemical specific current density for a graphene nanopore-based device can have many applications in sensitive chemical and biological sensing, and energy storage devices.
Growth Structure of Thin Films for Perpendicular Magnetic Recording Media (2000)

Thin film systems composed of Co-Cr-Nb-Pt, Ti, Co-Zr-Nb, Co-Cr and permalloy layers have been deposited onto glass substrates in order to investigate the correlation between the magnetic behaviour and microstructure. The grains of the Co-Cr-Nb-Pt films show oriented growth on the permalloy grains, whereas their growth is started by the formation of an amorphous layer on a Ti layer. A better magnetic performance was observed when Ti or Zr containing intermadiate layers were applied between the permalloy and Co-Cr-Nb-Pt film.
<title>Optimization of properties of ion-sensitive amorphous silicon (a-Si:H) based transistors</title> (1997)

In this work the application of a-Si:H thin film transistor technology in the field of chemical sensors is presented. In particularly, the optimization of magnetron deposition process for obtaining various silicon nitride films and TFT structures are described as well as adequate structures of Ion Sensitive Field Effect Transistor with respect to the ion sensitive hydrogen properties are studied. The device shows a good Nernst response and high reproducibility but not acceptable stability yet.
IP3R2 levels dictate the apoptotic sensitivity of diffuse large B-cell lymphoma cells to an IP3R-derived peptide targeting the BH4 domain of Bcl-2 (2013)

Disrupting inositol 1,4,5-trisphosphate (IP3) receptor (IP3R)/B-cell lymphoma 2 (Bcl-2) complexes using a cell-permeable peptide (stabilized TAT-fused IP3R-derived peptide (TAT-IDP(S))) that selectively targets the BH4 domain of Bcl-2 but not that of B-cell lymphoma 2-extra large (Bcl-Xl) potentiated pro-apoptotic Ca(2+) signaling in chronic lymphocytic leukemia cells. However, the molecular mechanisms rendering cancer cells but not normal cells particularly sensitive to disrupting IP3R/Bcl-2 complexes are poorly understood. Therefore, we studied the effect of TAT-IDP(S) in a more heterogeneous Bcl-2-dependent cancer model using a set of 'primed to death' diffuse large B-cell lymphoma (DL-BCL) cell lines containing elevated Bcl-2 levels. We discovered a large heterogeneity in the apoptotic responses of these cells to TAT-IDP(S) with SU-DHL-4 being most sensitive and OCI-LY-1 being most resistant. This sensitivity strongly correlated with the ability of TAT-IDP(S) to promote IP3R-mediated Ca(2+) release. Although total IP3R-expression levels were very similar among SU-DHL-4 and OCI-LY-1, we discovered that the IP3R2-protein level was the highest for SU-DHL-4 and the lowest for OCI-LY-1. Strikingly, TAT-IDP(S)-induced Ca(2+) rise and apoptosis in the different DL-BCL cell lines strongly correlated with their IP3R2-protein level, but not with IP3R1-, IP3R3- or total IP3R-expression levels. Inhibiting or knocking down IP3R2 activity in SU-DHL-4-reduced TAT-IDP(S)-induced apoptosis, which is compatible with its ability to dissociate Bcl-2 from IP3R2 and to promote IP3-induced pro-apoptotic Ca(2+) signaling. Thus, certain chronically activated B-cell lymphoma cells are addicted to high Bcl-2 levels for their survival not only to neutralize pro-apoptotic Bcl-2-family members but also to suppress IP3R hyperactivity. In particular, cancer cells expressing high levels of IP3R2 are addicted to IP3R/Bcl-2 complex formation and disruption of these complexes using peptide tools results in pro-apoptotic Ca(2+) signaling and cell death.
An Implement of Virtual Campus System Base on the X3D Technology (2011)

For searching a balance between networked virtual campus real-time rendering scene and precise modeling, this paper proposed a method of constructing virtual campus system. The method based on the latest X3D technology, using AutoCAD and 3DS MAX as the development and optimization tools, realizing interactive browse in the Web. Software developed using this method has been actually used for the display of a university campus.
Implementation of a general real-time visual anomaly detection system via soft computing (2004)

An intelligent visual system prototype was built to detect anomalies or defects in real time under normal lighting operating conditions. The application is basically a learning machine that integrates fuzzy logic (FL), artificial neural network (ANN), and genetic algorithm (GA) schemes to process the image, run the learning process, and finally detect the anomalies or defects. The system acquires the image, performs segmentation to separate the object being tested from the background, preprocesses the image using fuzzy reasoning, performs the final segmentation using fuzzy reasoning techniques to retrieve regions with potential anomalies or defects, and finally retrieves them using a learning model built via ANN and GA techniques. FL provides a powerful framework for knowledge representation and overcomes uncertainty and vagueness typically found in image analysis. ANN provides learning capabilities, and GA leads to robust learning results. An application prototype currently runs on a regular PC under Windows NT, and preliminary work has been performed to build an embedded version with multiple image processors. The application prototype is being tested at the Kennedy Space Center (KSC), Florida, to visually detect anomalies along slide basket cables utilized by the astronauts to evacuate the NASA Shuttle launch pad in an emergency. The potential applications of this anomaly detection system in an open environment are quite wide. Another current, potentially viable application at NASA is in detecting anomalies of the NASA Space Shuttle Orbiter's radiator panels.
Mechanisms of Stress Relief in Polycrystalline Films (1969)

The stress required to operate dislocation sources within a grain, at a grain boundary, and at surfaces is found to be larger than the intrinsic stresses observed in polycrystalline films. It is therefore unlikely that a dislocation flow mechanism can relieve stresses in films. Grain boundary sliding and diffusional creep can, however, relieve stresses in films and equations describing the kinetics of stress relaxation are derived. It is suggested that stress relief occurs primarily by a diffusion-creep mechanism. Growth of hillocks during annealing of a film is briefly discussed in terms of the diffusion-creep mechanism.
Isolation from Sewage Influent and Characterization of Novel <i>Staphylococcus aureus</i> Bacteriophages with Wide Host Ranges and Potent Lytic Capabilities (2009)

Staphylococcus aureus is a gram-positive pathogen that causes a variety of diseases, including bovine mastitis, which has severe economic consequences. Standard antibiotic treatment results in selection of resistant strains, leading to a need for alternative treatments, such as bacteriophage therapy. Forty-nine S. aureus isolates were obtained from the milk of mastitic cows for use in screening of staphylococcal phages. Fifteen isolates which were positive for both coagulase and hemolysin were assayed by PCR for variation in the X region and the immunoglobulin G-binding region of the protein A gene (spa) and in the carboxy terminus of the coagulase gene (coa) and for the presence of enterotoxin C, G, H, and I genes. The host ranges of 52 phages isolated from sewage influent were determined by performing spot tests with the 15 S. aureus isolates, and two phages were subsequently chosen for further analysis. PhiSA039 had the widest host range, producing clear plaques on 13 of the 15 isolates (87%), while PhiSA012 produced clear plaques on 8 isolates (53%) and was the only phage that produced a clear plaque on a nonmastitic S. aureus strain. Transmission electron microscopy revealed that the phages were similar sizes and belonged to the Myoviridae family. Measurement of optical densities during coculture with S. aureus isolates confirmed the breadth of the PhiSA039 host range and showed that PhiSA012 had potent lytic capability. PhiSA012-resistant bacteria did not appear for three of seven isolates tested (43%) after 65 h of incubation. These two phages are proposed as candidates for phage therapy of bovine mastitis.
Atheroprotective effects of methotrexate on reverse cholesterol transport proteins and foam cell transformation in human THP‐1 monocyte/macrophages (2008)

This study provides evidence supporting the notion of an atheroprotective effect of MTX. Through adenosine A2A receptor activation, MTX promotes reverse cholesterol transport and limits foam cell formation in THP-1 macrophages. This is the first reported evidence that any commonly used medication can increase expression of antiatherogenic reverse cholesterol transport proteins and can counteract the effects of COX-2 inhibition. Our results suggest that one mechanism by which MTX protects against cardiovascular disease in rheumatoid arthritis patients is through facilitation of cholesterol outflow from cells of the artery wall.
Transition in cardiac contractile sensitivity to calcium during the in vitro differentiation of mouse embryonic stem cells. (1994)

Mouse embryonic stem (ES) cells differentiate in vitro into a variety of cell types including spontaneously contracting cardiac myocytes. We have utilized the ES cell differentiation culture system to study the development of the cardiac contractile apparatus in vitro. Difficulties associated with the cellular and developmental heterogeneity of this system have been overcome by establishing attached cultures of differentiating ES cells, and by the micro-dissection of the contracting cardiac myocytes from culture. The time of onset and duration of continuous contractile activity of the individual contracting myocytes was determined by daily visual inspection of the cultures. A functional assay was used to directly measure force production in ES cell-derived cardiac myocyte preparations. The forces produced during spontaneous contractions in the membrane intact preparation, and during activation by Ca2+ subsequent to chemical permeabilization of the surface membranes were determined in the same preparation. Results showed a transition in contractile sensitivity to Ca2+ in ES cell-derived cardiac myocytes during development in vitro. Cardiac preparations isolated from culture following the initiation of spontaneous contractile activity showed marked sensitivity of the contractile apparatus to activation by Ca2+. However, the Ca2+ sensitivity of tension development was significantly decreased in preparations isolated from culture following prolonged continuous contractile activity in vitro. The alteration in Ca2+ sensitivity obtained in vitro paralleled that observed during murine cardiac myocyte development in vivo. This provides functional evidence that ES cell-derived cardiac myocytes recapitulate cardiogenesis in vitro. Alterations in Ca2+ sensitivity could be important in optimizing the cardiac contractile response to variations in the myoplasmic Ca2+ transient during embryogenesis. The potential to stably transfect ES cells with cardiac regulatory genes, together with the availability of a functional assay using control and genetically modified ES cell-derived cardiac myocytes, will permit determination of the functional significance of altered cardiac gene expression during cardiogenesis in vitro.
The Generative Force of Memory: Early Christian Traditions as Processes of Remembering (2006)

This article seeks to carry forward recent work on social or cultural memory in relation to the early Christian tradition. It develops the concept of a memorially empowered tradition which operates less as transmission of traditions, and more precisely as a functioning social memory, e.g., as a dynamic driven by the desire to keep Jesus' words alive by making them communicate to the present. Memory understood as a continual process of commemorating activities, intent on remembering the past while simultaneously addressing social identity in the present, is seen as the grand motivating force of tradition.