gebhart/patrepeval huggingface dataset:
Transcriptional regulation of the proton translocating NADH dehydrogenase (nuoA‐N) of Escherichia coli by electron acceptors, electron donors and gene regulators (1995)

The promoter region and transcriptional regulation of the nuoA-N gene locus encoding the proton-translocating NADH:quinone oxidoreductase was analysed. A 560 bp intergenic region upstream of the nuo locus was followed by a gene (designated lrhA for LysR homologue A) coding for a gene regulator similar to those of the LysR family. Disruption of lrhA did not affect growth (respiratory or non-respiratory) or expression of nuo significantly. Transcriptional regulation of nuo by electron acceptors, electron donors and the transcriptional regulators ArcA, FNR, NarL and NarP, and by IHF (integration host factor) was studied with protein and operon fusions containing the promoter region up to base pair -277 ('nuo277') or up to base pair -89 ('nuo899'). The expression of the nuo277-lacZ fusions was subject to ArcA-mediated anaerobic repression and NarL(+ nitrate)-mediated anaerobic activation. FNR and IHF acted as weak repressors under anaerobic conditions. Expression of nuo899-lacZ was stimulated during anaerobic fumarate respiration and aerobically by C4 dicarboxylates. Therefore, expression of nuo is regulated by O2 and nitrate via ArcA, NarL, FNR and IHF at sites within the -277 region, and by other factors including C4 dicarboxylates at a site between -277 and -899. A physiological role for the transcriptional stimulation by O2 and nitrate is suggested.
Engineering a Rigid Protein Tunnel for Biomolecular Detection (2012)

One intimidating challenge in protein nanopore-based technologies is designing robust protein scaffolds that remain functionally intact under a broad spectrum of detection conditions. Here, we show that an extensively engineered bacterial ferric hydroxamate uptake component A (FhuA), a β-barrel membrane protein, functions as a robust protein tunnel for the sampling of biomolecular events. The key implementation in this work was the coupling of direct genetic engineering with a refolding approach to produce an unusually stable protein nanopore. More importantly, this nanostructure maintained its stability under many experimental circumstances, some of which, including low ion concentration and highly acidic aqueous phase, are normally employed to gate, destabilize, or unfold β-barrel membrane proteins. To demonstrate these advantageous traits, we show that the engineered FhuA-based protein nanopore functioned as a sensing element for examining the proteolytic activity of an enzyme at highly acidic pH and for determining the kinetics of protein-DNA aptamer interactions at physiological salt concentration.
Effects of melatonin in a rat model of splanchnic artery occlusion and reperfusion (1999)

Cuzzocrea, S.1; Costantino, G.1; Mazzon, E.2,*; De Sarro, A.1,*; Caputi, A. P.1 Author Information
Deposition of in-plane textured MgO on amorphous Si3N4 substrates by ion-beam-assisted deposition and comparisons with ion-beam-assisted deposited yttria-stabilized-zirconia (1997)

We report the growth of in-plane textured (100) MgO on amorphous Si3N4 substrates by ion beam assisted deposition (IBAD). The textured MgO can be used as a structural template for subsequent epitaxial thin film deposition. The results are compared with IBAD of (100) and (111) yttria-stabilized-zirconia (YSZ). Based on transmission electron microscopy (TEM) and in situ reflection high energy-electron diffraction (RHEED), we find that MgO texturing is a nucleation-controlled process and the alignment is a function of nuclei size and density. This differs greatly from the evolutionary-type texturing process observed for IBAD (100) YSZ. Consequently, we are able to make 100 Å thick MgO films with 7° in-plane alignment, whereas IBAD (100) YSZ films need to be thicker than 5000 Å to achieve in-plane alignment better than 13°. This has important implications for the economical application of IBAD induced alignment in real manufacturing processes, including high Tc superconductor (i.e., YBCO) coated tapes, photovoltaics, magnetic thin films, and semiconductor devices.
The role of London forces in defining noncentrosymmetric order of high dipole moment–high hyperpolarizability chromophores in electrically poled polymeric thin films (1997)

Graphs of second harmonic generation coefficients and electro-optic coefficients (measured by ellipsometry, attenuated total reflection, and two-slit interference modulation) as a function of chromophore number density (chromophore loading) are experimentally observed to exhibit maxima for polymers containing chromophores characterized by large dipole moments and polarizabilities. Modified London theory is used to demonstrated that this behavior can be attributed to the competition of chromophore-applied electric field and chromophore-chromophore electrostatic interactions. The comparison of theoretical and experimental data explains why the promise of exceptional macroscopic second-order optical nonlinearity predicted for organic materials has not been realized and suggests routes for circumventing current limitations to large optical nonlinearity. The results also suggest extensions of measurement and theoretical methods to achieve an improved understanding of intermolecular interactions in condensed phase materials including materials prepared by sequential synthesis and block copolymer methods.
Adaptive channel queue routing on k-ary n-cubes (2004)

This paper introduces a new adaptive method, Channel Queue Routing (CQR), for load-balanced routing on k-ary n-cube interconnection networks. CQR estimates global congestion in the network from its channel queues while relying on the implicit network backpressure to transfer congestion information to these queues. It uses this estimate to decide the directions to route in each dimension. It further load balances the network by routing in the selected directions adaptively. The only other algorithm that uses global congestion in its routing decision is the Globally Adaptive Load-Balance (GAL) algorithm introduced in [13]. GAL performs better than any other known routing algorithm on a wide variety of throughput and latency metrics. However, there are four serious issues with GAL. First, it has very high latency once it starts routing traffic non-minimally. Second, it is slow to adapt to changes in traffic. Third, it requires a complex method to achieve stability. Finally, it is complex to implement. These issues are all related to GAL's use of injection queue length to infer global congestion. CQR uses channel queues rather than injection queues to estimate global congestion. In doing so, it overcomes the limitations of GAL described above while matching its high performance on all the performance metrics described in [13]. CQR gives much lower latency than GAL at loads where non-minimal routing is required. It adapts rapidly to changes in traffic, is unconditionally stable, and is simple to implement.
Quantitative determination of native proteins in individual human erythrocytes by capillary zone electrophoresis with laser-induced fluorescence detection (1992)

Intracellular fluid within single human erythrocytes is analyzed by capillary electrophoresis with laser-excited native protein fluorescence. Good signal-to-noise is achieved, allowing even minor components to be quantified. Non-Gaussian distributions were found for total protein, fraction carbonic anhydrase, fraction hemoglobin A0, and an unidentified component. Variations among a group of 29 cells for each quantity are as much as 1 order of magnitude, even though erythrocytes are known to be fairly homogeneous in size distribution. Variations in fraction hemoglobin A0 reflect differences in in vitro oxidation rates to methemoglobin. A positive correlation was observed between carbonic anhydrase and hemoglobin A0 for individual cells. This is consistent with the presence of erythrocytes of different ages within the population, with the older cells being less capable of maintaining enzyme activity and preventing oxidative damage.
Hydrogen sulfide accelerates wound healing in diabetic rats. (2015)

The findings in present study suggested that hydrogen sulfide accelerates the wound healing in rats with diabetes. The beneficial effect of H2S may be associated with formation of granulation, anti-inflammation, antioxidant, and the increased level of vascular endothelial growth factor (VEGF).
Analogs of methotrexate (1979)

Analogues of methotrexate (MTX) were prepared by alkylation of side-chain precursors with 6-(bromomethyl)-2,4-pteridinediamine followed, where necessary, by saponification of the intermediate esters and, in two cases, by electrophilic substitution reactions in the pyridine ring portion of 3-deazamethotrexate. Effects of the various modifications on their ability to inhibit dihydrofolate reductase, cytotoxicity, and activity against L1210 leukemia in mice were examined in light of recent findings concerning active transport of MTX and related compounds and the binding features of the MTX-dihydrofolate reductase complex.
Phase Transformations and Phase Stability in Epitaxial β‐GaN Films (1997)

The production of single-phase GaN, which is important for the realization of optoelectronic devices, is intricated by the existence of two polytypes (α-GaN hexagonal, β-GaN cubic, metastable). Both the orientation of the interface between teh cubic matrix and the polytypic hexagonal inclusion and the influence of the specific nature of the interface on the stability of the transformed polytype are of fundamental importance for the phase transformation of β-to α;-GaN.
Frequency Response Enhancement of Optical Injection-Locked Lasers (2007)

The modulation response of injection-locked lasers has been carefully analyzed, theoretically and experimentally, with a focus on the strong optical injection regime. We derive closed-form solutions to the relaxation oscillation (resonance) frequency and damping term, as well as the low-frequency damping term, and discuss design rules for maximizing resonance frequency and broadband performance. A phasor model is described in order to better explain the enhancement of the resonance frequency. Experimental curves match closely to theory. Record resonance frequency of 72 GHz and broadband results are shown.
Heat shock-induced interactions of heat shock transcription factor and the human hsp70 promoter examined by in vivo footprinting. (1991)

Genomic footprinting of the human hsp70 promoter reveals that heat shock induces a rapid binding of a factor, presumably heat shock transcription factor, to a region encompassing five contiguous NGAAN sequences, three perfect and two imperfect matches to the consensus sequence. Arrays of inverted NGAAN sequences have been defined as the heat shock element. No protein is bound to the heat shock element prior to or after recovery from heat shock. Heat shock does not perturb the binding of factors to other regulatory elements in the promoter which contribute to basal expression of the hsp70 gene.
Crystal Structures of the p21-Activated Kinases PAK4, PAK5, and PAK6 Reveal Catalytic Domain Plasticity of Active Group II PAKs (2007)

p21-activated kinases have been classified into two groups based on their domain architecture. Group II PAKs (PAK4-6) regulate a wide variety of cellular functions, and PAK deregulation has been linked to tumor development. Structural comparison of five high-resolution structures comprising all active, monophosphorylated group II catalytic domains revealed a surprising degree of domain plasticity, including a number of catalytically productive and nonproductive conformers. Rearrangements of helix alphaC, a key regulatory element of kinase function, resulted in an additional helical turn at the alphaC N terminus and a distortion of its C terminus, a movement hitherto unseen in protein kinases. The observed structural changes led to the formation of interactions between conserved residues that structurally link the glycine-rich loop, alphaC, and the activation segment and firmly anchor alphaC in an active conformation. Inhibitor screening identified six potent PAK inhibitors from which a tri-substituted purine inhibitor was cocrystallized with PAK4 and PAK5.
MicroRNA-145 regulates oncolytic herpes simplex virus-1 for selective killing of human non-small cell lung cancer cells (2013)

miRNA-145-regulated oncolytic HSV-1 is a promising agent for the treatment of NSCLC.
Proteins in Solution and at Interfaces (2013)

PREFACE ix CONTRIBUTORS xiii PART I 1 X-Ray Crystallography of Biological Macromolecules: Fundamentals and Applications 3 Antonio L. Llamas-Saiz and Mark J. van Raaij 2 Nuclear Magnetic Resonance Methods for Studying Soluble, Fibrous, and Membrane-Embedded Proteins 23 Victoria A. Higman 3 Small-Angle X-Ray Scattering Applied to Proteins in Solution 49 Leandro Ramos Souza Barbosa, Francesco Spinozzi, Paolo Mariani, and Rosangela Itri 4 Analyzing the Solution State of Protein Structure, Interactions, and Ligands by Spectroscopic Methods 73 Veronica I. Dodero and Paula V. Messina 5 Resolving Membrane-Bound Protein Orientation and Conformation by Neutron Reflectivity 99 Hirsh Nanda 6 Investigating Protein Interactions at Solid Surfaces In Situ, Nonlabeling Techniques 113 Olof Svensson, Javier Sotres, and Alejandro Barrantes 7 Calorimetric Methods to Characterize the Forces Driving Macromolecular Association and Folding Processes 139 Conceic, ao A.S.A. Minetti, Peter L. Privalov, and David P. Remeta 8 Virtual Ligand Screening Against Comparative Models of Proteins 179 Hao Fan 9 Atomistic and Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins 193 Thomas J. Piggot, Peter J. Bond, and Syma Khalid PART II 10 Preparation of Nanomaterials Based on Peptides and Proteins 209 Yujing Sun and Zhuang Li 11 Natural Fibrous Proteins: Structural Analysis, Assembly, and Applications 219 Mark J. van Raaij and Anna Mitraki 12 Amyloid-Like Fibrils: Origin, Structure, Properties, and Potential Technological Applications 233 Pablo Taboada, Silvia Barbosa, Josue Juarez, Manuel-Alatorre Meda, and Vyctor Mosquera 13 Proteins and Peptides in Biomimetic Polymeric Membranes 283 Alfredo Gonzalez-Perez 14 Study of Proteins and Peptides at Interfaces By Molecular Dynamics Simulation Techniques 291 David Poger and Alan E. Mark 15 A Single-Molecule Approach to Explore the Role of the Solvent Environment in Protein Folding 315 Katarzyna Tych and Lorna Dougan 16 Enhanced Functionality of Peroxidases By Its Immobilization at The Solid Liquid Interface of Mesoporous Materials and Nanoparticles 335 Jose Campos-Teran, Iker Inarritu, Jorge Aburto, and Eduardo Torres 17 Superactivity of Enzymes in Supramolecular Hydrogels 353 Ye Zhang and Bing Xu 18 Surfactant Proteins and Natural Biofoams 365 Malcolm W. Kennedy and Alan Cooper 19 Promiscuous Enzymes 379 Luis F. Olguin 20 Thermodynamics and Kinetics of Mixed Protein/Surfactant Adsorption Layers at Liquid Interfaces 389 Reinhard Miller, E.V. Aksenenko, V.S. Alahverdjieva, V.B. Fainerman, C.S. Kotsmar, J. Kragel, M.E. Leser, J. Maldonado-Valderrama, V. Pradines, C. Stefaniu, A. Stocco, and R. Wustneck 21 Application of Force Spectroscopy Methods to the Study of Biomaterials 429 Chuan Xu and Erika F. Merschrod S. 22 Protein Gel Rheology 437 Katie Weigandt and Danilo Pozzo 23 Exploring Biomolecular Thermodynamics in Aqueous and Nonaqueous Environments using Time-Resolved Photothermal Methods 449 Randy W. Larsen, Carissa M. Vetromile, William A. Maza, Khoa Pham, Jaroslava Miksovska INDEX 473
Markov modeling of minimally invasive surgery based on tool/tissue interaction and force/torque signatures for evaluating surgical skills (2001)

The best method of training for laparoscopic surgical skills is controversial. Some advocate observation in the operating room, while others promote animal and simulated models or a combination of surgery-related tasks. A crucial process in surgical education is to evaluate the level of surgical skills. For laparoscopic surgery, skill evaluation is traditionally performed subjectively by experts grading a video of a procedure performed by a student. By its nature, this process uses fuzzy criteria. The objective of the current study was to develop and assess a skill scale using Markov models (MMs). Ten surgeons [five novice surgeons (NS); five expert surgeons (ES)] performed a cholecystectomy and Nissen fundoplication in a porcine model. An instrumented laparoscopic grasper equipped with a three-axis force/torque (F/T) sensor was used to measure the forces/torques at the hand/tool interface synchronized with a video of the tool operative maneuvers. A synthesis of frame-by-frame video analysis and a vector quantization algorithm, allowed to define F/T signatures associated with 14 different types of tool/tissue interactions. The magnitude of F/T applied by NS and ES were significantly different (p < 0.05) and varied based on the task being performed. High F/T magnitudes were applied by NS compared with ES while performing tissue manipulation and vise versa in tasks involved tissue dissection. From each step of the surgical procedures, two MMs were developed representing the performance of three surgeons out of the five in the ES and NS groups. The data obtained by the remaining two surgeons in each group were used for evaluating the performance scale. The final result was a surgical performance index which represented a ratio of statistical similarity between the examined surgeon's MM and the MM of NS and ES. The difference between the performance index value, for a surgeon under study, and the NS/ES boundary, indicated the level of expertise in the surgeon's own group. Using this index, 87.5% of the surgical procedures were correctly classified into the NS and ES groups. The 12.5% of the procedures that were misclassified were performed by the ES and classified as NS. However in these cases the performance index values were very close to the NS/ES boundary. Preliminary data suggest that a performance index based on MM and F/T signatures provides an objective means of distinguishing NS from ES. In addition, this methodology can be further applied to evaluate haptic virtual reality surgical simulators for improving realism in surgical education.
M6P/IGFII-receptor complexes urokinase receptor and plasminogen for activation of transforming growth factor-β1 (1999)

Transforming growth factor-beta1 (TGF-beta1) is a critical cytokine for cell proliferation and differentiation. It is secreted by many cells in a latent pro-form (LTGF-beta1) from which biologically active TGF-beta1 is released by an in vivo mechanism that is not known. Here we show that the mannose-6-phosphate/insulin-like growth factor II-receptor (M6P/IGFII-R), which binds LTGF-beta1, complexes with urokinase (plasminogen activator)-receptor (uPA-R) on the surface of human monocytes and directly binds plasminogen (Plg). Plasmin generated from Plg in the complex mediates release of TGF-beta1 when M6P/IGFII-R is associated with uPA-R. Thus, this interaction of M6P/IGFII-R and uPA-R suggests a potential mechanism for the generation of TGF-beta1 by cells.
Clinical Evaluation of a Prototype Motion Artifact Resistant Pulse Oximeter in the Recovery Room (1996)

The frequency and nature of spurious pulse oximetry readings were compared using both a conventional pulse oximeter (CPO) and a prototype Masimo signal extraction technology pulse oximeter (Masimo SET Trademark).At a university hospital, 50 ASA physical status I-IV adult patients who underwent general or spinalepidural anesthesia were selected from a group of 250 patients on the basis of high-alarm generation with routine postoperative pulse oximetry. Pulse oximetry data were recorded simultaneously from both devices with a computer. Overall, the CPO alarm frequency (i.e., oxygen saturation < 90%, or complete signal loss) was once every 13 min, and 87% of these alarms were considered false. Alarms were considered false based on reference electrocardiographs (16 patients), arterial blood gases (7 patients), and clinical assessment. The prototype Masimo SET Trademark device alarm frequency was once every 30 min, and 59% of these were considered false. During arm motion with 15 patients, the CPO device produced spurious signals on 54 occasions compared with five for the prototype Masimo SET Trademark. The incidence of artifactual pulse oximetry events during patient motion appear to be substantially reduced with the prototype Masimo SET Trademark device, relative to a CPO device. (Anesth Analg 1996;83:269-72)
Infrared spectra of tetraphosphorous decasulfide and its decomposition products in solid argon (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfrared spectra of tetraphosphorous decasulfide and its decomposition products in solid argonLester Andrews, Gregg G. Reynolds, Zofia Mielke, and Matthew McCluskeyCite this: Inorg. Chem. 1990, 29, 26, 5222–5225Publication Date (Print):December 1, 1990Publication History Published online1 May 2002Published inissue 1 December 1990https://pubs.acs.org/doi/10.1021/ic00351a017https://doi.org/10.1021/ic00351a017research-articleACS PublicationsRequest reuse permissionsArticle Views191Altmetric-Citations16LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Consensus Report of the National Cancer Institute Clinical Trials Planning Meeting on Pancreas Cancer Treatment (2009)

Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer mortality, despite significant improvements in diagnostic imaging and operative mortality rates. The 5-year survival rate remains less than 5% because of microscopic or gross metastatic disease at time of diagnosis. The Clinical Trials Planning Meeting in pancreatic cancer was convened by the National Cancer Institute's Gastrointestinal Cancer Steering Committee to discuss the integration of basic and clinical knowledge in the design of clinical trials in PDAC. Major emphasis was placed on the enhancement of research to identify and validate the relevant targets and molecular pathways in PDAC, cancer stem cells, and the microenvironment. Emphasis was also placed on developing rational combinations of targeted agents and the development of predictive biomarkers to assist selection of patient subsets. The development of preclinical tumor models that are better predictive of human PDAC must be supported with wider availability to the research community. Phase III clinical trials should be implemented only if there is a meaningful clinical signal of efficacy and safety in the phase II setting. The emphasis must therefore be on performing well-designed phase II studies with uniform sets of basic entry and evaluation criteria with survival as a primary endpoint. Patients with either metastatic or locally advanced PDAC must be studied separately.
l‐Arginine fails to protect against myocardial remodelling inl‐NAME‐induced hypertension (2005)

We conclude that L-arginine failed to prevent hypertension, left ventricular hypertrophy and fibrosis development despite restoration of nitric oxide synthase activity in the left ventricle. However, L-arginine prevented the diminution of coenzyme Q levels in the left ventricle.