gebhart/patrepeval huggingface dataset:
Solid-state NMR studies of the dynamics and structure of mouse keratin intermediate filaments (1988)

The molecular dynamics and structural organization of mouse epidermal keratin intermediate filaments (IF) have been studied via solid-state nuclear magnetic resonance (NMR) experiments performed on IF labeled both in vivo and in vitro with isotopically enriched amino acids. As a probe of the organization of the peripheral glycine-rich end domains of the IF, carbon-13 NMR experiments have been performed on subfilamentous forms (prekeratin) and on IF reassembled in vitro that had been labeled with either [1-13C]glycine or [2-13C]glycine, as more than 90% of the glycines of the keratins are located in the end domains. Although cross-labeling to seryl residues was observed, the proportion of serine located in the end domains is nearly the same as that for glycine. Measurements of carbon relaxation times, nuclear Overhauser enhancements, and signal intensities show that the motions of the peptide backbone in the end domains are effectively isotropic, with average correlation times distributed over the range of 0.2-20 ns. These results indicate that the end domains of IF are remarkably flexible and have little or no structural order. To probe the structural organization of the coiled-coil rod domains of the IF, separate samples of native keratin IF, raised in primary tissue culture, were labeled with L-[1-13C]leucine, L-[2H10]leucine, or L-[2,3,3-2H3]leucine, as greater than 90% of the leucyl residues of the keratin IF types studied are located in the coiled coils which form the central core of IF.(ABSTRACT TRUNCATED AT 250 WORDS)
Antioxidant Activities of Pomegranate Fruit Extract and Its Anthocyanidins:  Delphinidin, Cyanidin, and Pelargonidin (2001)

Antioxidant activities of freeze-dried preparations of a 70% acetone extract of pomegranate (Punica granatum L.) and its three major anthocyanidins (delphinidin, cyanidin, and pelargonidin) were evaluated. Free radical scavenging activities were examined using an ESR technique with spin trapping; DMPO for hydroxyl (.OH) and superoxide (O(2)(.-) ) radicals; and [(MGD)(2)Fe(2+)] for nitric oxide (NO). Inhibitory effects on lipid peroxidation were estimated by the levels of malonaldehyde and 4-hydroxyalkenals in rat brain homogenates. Pomegranate extract exhibited scavenging activity against.OH and O(2)(.-). Anthocyanidins inhibited a Fenton reagent.OH generating system possibly by chelating with ferrous ion. Anthocyanidins scavenged O(2)(.)- in a dose-dependent manner. The ID(50) values of delphinidin, cyanidin, and pelargonidin were 2.4, 22, and 456 microM, respectively. In contrast, anthocyanidins did not effectively scavenge NO. Anthocyanidins inhibited H(2)O(2)-induced lipid peroxidation in the rat brain homogenates. The ID(50) values of delphinidin, cyanidin, and pelargonidin for them were 0.7, 3.5, and 85 microM, respectively. These findings suggest that the above anthocyanidins contribute to the antioxidant activity of pomegranate fruits.
The Rough Endoplasmic Reticulum-resident FK506-binding Protein FKBP65 Is a Molecular Chaperone That Interacts with Collagens (2008)

The rough endoplasmic reticulum-resident FK-506-binding protein FKBP65 can be isolated from chick embryos on a gelatin-Sepharose column, indicating some involvement in the biosynthesis of procollagens. The peptidylprolyl cis-trans-isomerase activity of FKBP65 was previously shown to have only marginal effects on the rate of triple helix formation (Zeng, B., MacDonald, J. R., Bann, J. G., Beck, K., Gambee, J. E., Boswell, B. A., and Bächinger, H. P. (1998) Biochem. J. 330, 109-114). Here we show that FKBP65 is a monomer in solution and acts as a chaperone molecule when tested with two classic chaperone assays: FKBP65 inhibits the thermal aggregation of citrate synthase and is active in the denatured rhodanese refolding and aggregation assay. The chaperone activity is comparable to that of protein-disulfide isomerase, a well characterized chaperone. FKBP65 delays the in vitro fibril formation of type I collagen, indicating that FKBP65 is also able to interact with triple helical collagen, and acts as a collagen chaperone.
Protease-Antiprotease Imbalance: Local Evaluation with Bronchoalveolar Lavage (1992)

The protease-antiprotease imbalance is thought to be involved in a variety of destructive lung diseases: pulmonary emphysema, chronic bronchitis, cystic fibrosis and adult respiratory distress syndrome. Bronchoalveolar lavage allowed the investigators to assess the protease-antiprotease shift in such conditions but sometimes gave conflicting results. The role of bronchoalveolar lavage as a research and diagnostic tool in diseases characterised by protease-antiprotease imbalance is reviewed, as well as its potential usefulness in the near future.
Identification by Phage Display and Characterization of Two Neutralizing Chimpanzee Monoclonal Antibodies to the Hepatitis E Virus Capsid Protein (2000)

Two monoclonal antibodies (MAbs) against the ORF2 protein of the SAR-55 strain of hepatitis E virus (HEV) were isolated by phage display from a cDNA library of chimpanzee (Pan troglodytes) gamma1/kappa antibody genes. Both MAbs, HEV#4 and HEV#31, bound to reduced, denatured open reading frame 2 (ORF2) protein in a Western blot, suggesting that they recognize linear epitopes. The affinities (equilibrium dissociation constants, K(d)) for the SAR-55 ORF2 protein were 1.7 nM for HEV#4 and 5.4 nM for HEV#31. The two MAbs also reacted in an enzyme-linked immunosorbent assay with recombinant ORF2 protein from a heterologous HEV, the Meng strain. Each MAb blocked the subsequent binding of the other MAb to homologous ORF2 protein in indirect competition assays, suggesting that they recognize the same or overlapping epitopes. Radioimmunoprecipitation assays suggested that at least part of the linear epitope(s) recognized by the two MAbs is located between amino acids 578 and 607. MAbs were mixed with homologous HEV in vitro and then inoculated into rhesus monkeys (Macaca mulatta) to determine their neutralizing ability. Whereas all control animals developed hepatitis (elevated liver enzyme levels in serum) and seroconverted to HEV, those receiving an inoculum incubated with either HEV#4 or HEV#31 were not infected. Therefore, each MAb neutralized the SAR-55 strain of HEV in vitro.
Modifying Emission Spectral Bandwidth of Phosphorescent Platinum(II) Complexes Through Synthetic Control (2017)

The design, synthesis, and characterization of a series of tetradentate cyclometalated Pt(II) complexes are reported. The platinum complexes have the general structure Pt(ppz-O-CbPy-R), where a tetradentate cyclometalating ligand is consisting of ppz (3,5-dimethyl-1-phenyl-pyrazole), CbPy (carbazolylpyridine) components, and an oxygen bridging group. Variations of the R group on the pyridyl ring with various electron withdrawing and donating substituents are shown to have profound effects on the photophysical properties of Pt complexes. Electrochemical analysis indicates that reduction process occurs mainly on the electron-accepting pyridyl group, and the irreversible oxidation process is primarily localized on the metal-phenyl portions. The studies of their photophysical properties indicate that the lowest excited state of the platinum complexes is a ligand-centered <sup>3</sup>π-π* state with minor to significant <sup>1</sup>MLCT/<sup>3</sup>MLCT character and are strongly dependent on the nature of the electron-accepting pyridyl moiety. A systematic study of the substituent effects on the pyridyl ring demonstrates that the T<sub>1</sub> state properties can be tuned by altering the functionality and positions of substituents. Importantly, it is revealed that how the emission spectra of the Pt(II) complexes can be significantly narrowed and why it can be achieved by incorporating an electron-donating group on the 4-position of the pyridyl ring. Most of the Pt(II) complexes reported here are highly emissive at room temperature in dichloromethane solutions (Φ = 1.1-95%) and in doped PMMA films (Φ = 29-88%) with luminescent lifetimes in the microsecond range (τ = 0.6-13.5 μs in solution and 0.9-11.3 μs in thin film respectively) and λ<sub>max</sub> = 442-568 nm and 440-544 nm in solution and thin film, respectively. Moreover, these complexes are neutral and thermally stable for sublimation, indicating that they can be useful for display and solid-state lighting applications.
Closed-Loop Control of Deep Brain Stimulation: A Simulation Study (2010)

Deep brain stimulation (DBS) is an effective therapy to treat movement disorders including essential tremor, dystonia, and Parkinson's disease. Despite over a decade of clinical experience the mechanisms of DBS are still unclear, and this lack of understanding makes the selection of stimulation parameters quite challenging. The objective of this work was to develop a closed-loop control system that automatically adjusted the stimulation amplitude to reduce oscillatory neuronal activity, based on feedback of electrical signals recorded from the brain using the same electrode as implanted for stimulation. We simulated a population of 100 intrinsically active model neurons in the Vim thalamus, and the local field potentials (LFPs) generated by the population were used as the feedback (control) variable for closed loop control of DBS amplitude. Based on the correlation between the spectral content of the thalamic activity and tremor (Hua , 1998), (Lenz , 1988), we implemented an adaptive minimum variance controller to regulate the power spectrum of the simulated LFPs and restore the LFP power spectrum present under tremor conditions to a reference profile derived under tremor free conditions. The controller was based on a recursively identified autoregressive model (ARX) of the relationship between stimulation input and LFP output, and showed excellent performances in tracking the reference spectral features through selective changes in the theta (2-7 Hz), alpha (7-13 Hz), and beta (13-35 Hz) frequency ranges. Such changes reflected modifications in the firing patterns of the model neuronal population, and, differently from open-loop DBS, replaced the tremor-related pathological patterns with patterns similar to those simulated in tremor-free conditions. The closed-loop controller generated a LFP spectrum that approximated more closely the spectrum present in the tremor-free condition than did open loop fixed intensity stimulation and adapted to match the spectrum after a change in the neuronal oscillation frequency. This computational study suggests the feasibility of closed-loop control of DBS amplitude to regulate the spectrum of the local field potentials and thereby normalize the aberrant pattern of neuronal activity present in tremor.
Biological and Biochemical Characterization of Variant A Subunits of Cholera Toxin Constructed by Site-Directed Mutagenesis (2001)

Cholera toxin (CT) is the prototype for the Vibrio cholerae-Escherichia coli family of heat-labile enterotoxins having an AB5 structure. By substituting amino acids in the enzymatic A subunit that are highly conserved in all members of this family, we constructed 23 variants of CT that exhibited decreased or undetectable toxicity and we characterized their biological and biochemical properties. Many variants exhibited previously undescribed temperature-sensitive assembly of holotoxin and/or increased sensitivity to proteolysis, which in all cases correlated with exposure of epitopes of CT-A that are normally hidden in native CT holotoxin. Substitutions within and deletion of the entire active-site-occluding loop demonstrated a prominent role for His-44 and this loop in the structure and activity of CT. Several novel variants with wild-type assembly and stability showed significantly decreased toxicity and enzymatic activity (e.g., variants at positions R11, I16, R25, E29, and S68+V72). In most variants the reduction in toxicity was proportional to the decrease in enzymatic activity. For substitutions or insertions at E29 and Y30 the decrease in toxicity was 10- and 5-fold more than the reduction in enzymatic activity, but for variants with R25G, E110D, or E112D substitutions the decrease in enzymatic activity was 12- to 50-fold more than the reduction in toxicity. These variants may be useful as tools for additional studies on the cell biology of toxin action and/or as attenuated toxins for adjuvant or vaccine use.
Time-to-Pulse Height Converter of Wide Range (1960)

A time-to-pulse height converter covering the range from millimicroseconds to minutes is described. A simple 5-component passive circuit for scanning times above 50 μsec is included also. The converters can measure several events per time scan related to one starting event. They are designed as plug-in units for an oscilloscope, and utilize its sweep and other circuits. The use of the converters is discussed and includes scanning of negative time and inverted operation for reduction of counting losses. Notes on testing, calibration, and dead times are given, as well as examples of nuclear experiments to which they have been applied.
Fibronectin‐binding proteins of Staphylococcus aureus mediate activation of human platelets via fibrinogen and fibronectin bridges to integrin GPIIb/IIIa and IgG binding to the FcγRIIa receptor (2005)

Staphylococcus aureus is a leading cause of infective endocarditis (IE). Platelet activation promoted by S. aureus resulting in aggregation and thrombus formation is an important step in the pathogenesis of IE. Here, we report that the fibrinogen/fibronectin-binding proteins FnBPA and FnBPB are major platelet-activating factors on the surface of S. aureus from the exponential phase of growth. Truncated derivatives of FnBPA, presenting either the fibrinogen-binding A domain or the fibronectin-binding BCD region, each promoted platelet activation when expressed on the surface of S. aureus or Lactococcus lactis, indicating two distinct mechanisms of activation. FnBPA-promoted platelet activation is mediated by fibrinogen and fibronectin bridges between the A domain and the BCD domains, respectively, to the low affinity form of the integrin GPIIb/IIIa on resting platelets. Antibodies recognizing the FnBPA A domain or the complex between the FnBPA BCD domains and fibronectin were essential for activation promoted by bacteria expressing the A domain or the BCD domain respectively. Activation was inhibited by a monoclonal antibody (IV-3) specific for the FcgammaRIIa IgG receptor on platelets. We propose that the activation of quiescent platelets by bacteria expressing FnBPs involves the formation of a bridge between the bacterial cell and the platelet surface by (i) fibronectin and fibrinogen interacting with the low affinity form of GPIIb/IIIa and (ii) by antibodies specific to FnBPs that engage the platelet Fc receptor FcgammaRIIa. Platelet activation by S. aureus clinical IE isolates from both the exponential and stationary phases of growth was completely inhibited by monoclonal antibody IV-3 suggesting that the IgG-FcgammaRIIa interaction is of fundamental importance for platelet activation mediated by this organism. This suggests new avenues for development of therapeutics against vascular infections.
pH-Dependent complexation of poly(acrylic acid) derivatives with phospholipid vesicle membranes (1984)

Poly(acrylic acid), poly(methacrylic acid), and poly(α-ethylacrylic acid) can be used to modify, in a pH-dependent manner, the properties of phospholipid vesicle membranes. Polymer-lipid complexation caw a decrease in the apparent cooperativity of the lipid melting transition. The "critical pH" for complexation may be controlled through variation of the chemical structure and the tacticity of the poly(carboxylic acid), It is suggested that an important driving force for complexation is provided by the formation of hydrogen bonds between un-ionized carboxyl groups of the polymer and the phosphodiester functions of the lipid surface.
Type II secretion in Yersinia—a secretion system for pathogenicity and environmental fitness (2012)

In Yersinia species, type III secretion (T3S) is the most prominent and best studied secretion system and a hallmark for the infection process of pathogenic Yersinia species. Type II secretion (T2S), on the other hand, is less well-characterized, although all Yersinia species, pathogenic as well as non-pathogenic, possess one or even two T2S systems. The only Yersinia strain in which T2S has so far been studied is the human pathogenic strain Y. enterocolitica 1b. Mouse infection experiments showed that at least one of the two T2S systems of Y. enterocolitica 1b, termed Yts1, is involved in dissemination and colonization of deeper tissues like liver and spleen. Interestingly, in vitro studies revealed a complex regulation of the Yts1 system, which is mainly active at low temperatures and high Mg(2+)-levels. Furthermore, the functional characterization of the proteins secreted in vitro indicates a role of the Yts1 machinery in survival of the bacteria in an environmental habitat. In silico analyses identified Yts1 homologous systems in bacteria that are known as plant symbionts or plant pathogens. Thus, the recent studies point to a dual function of the Yts1 T2S systems, playing a role in virulence of humans and animals, as well as in the survival of the bacteria outside of the mammalian host. In contrast, the role of the second T2S system, Yts2, remains ill defined. Whereas the T3S system and its virulence-mediating role has been intensively studied, it might now be time to also focus on the T2S system and its role in the Yersinia lifestyle, especially considering that most of the Yersinia isolates are not found in infected humans but have been gathered from various environmental samples.
The extracellular region of ErbB4 adopts a tethered conformation in the absence of ligand (2005)

The human ErbB family of receptor tyrosine kinases comprises the epidermal growth factor receptor (EGFR/ErbB1/HER1), ErbB2 (HER2/Neu), ErbB3 (HER3), and ErbB4 (HER4). ErbBs play fundamental roles in cell growth and differentiation events in embryonic and adult tissues, and inappropriate ErbB activity has been implicated in several human cancers. We report here the 2.4 A crystal structure of the extracellular region of human ErbB4 in the absence of ligand and show that it adopts a tethered conformation similar to inactive forms of ErbB1 and ErbB3. This structure completes the gallery of unliganded ErbB receptors and demonstrates that all human ligand-binding ErbBs adopt the autoinhibited conformation. We also show that the binding of neuregulin-1beta to ErbB4 and ErbB3 and the binding of betacellulin to both ErbB4 and ErbB1 does not decrease at low pH, unlike the binding of epidermal growth factor and transforming growth factor-alpha to ErbB1. These results indicate an important role for ligand in determining pH-dependent binding and may explain different responses observed when the same ErbB receptor is stimulated by different ligands.
Separation of Oligo/Polymers of 5-N-Acetylneuraminic Acid, 5-N-Glycolylneuraminic Acid, and 2-Keto-3-deoxy-d-glycero-d-galacto-nononic Acid by High-Performance Anion-Exchange Chromatography with Pulsed Amperometric Detector (1997)

A sensitive and efficient method to analyze oligo/ poly-sialic acids containing alpha2-8-linked 5-N-acetylneuraminic acid (Neu5Ac), 5-N-glycolylneuraminic acid (Neu5Gc), and deaminated neuraminic acid (KDN) using high-performance anion-exchange chromatography (HPAEC) with a pulsed amperometric detector (PAD-2) has been developed. Using a CarboPac PA-100 column and sodium nitrate as the pushing agent, polymers in colominic acid with degree of polymerization (DP) up to 80 were separated in 68 min. A similar DP-based resolution was also obtained on a CarboPac PA-1 column. The elution ladders of the Neu5Ac, Neu5Gc, and KDN series were sufficiently different to be used as diagnostic indices. This technique was applied to identification of the sialic acid components in a polysialoglycoprotein (PSGP) sample as well as monitoring the oligo/poly-KDN-containing fractions during the purification of KDN-containing glycoprotein (KDN-gp). The maximum DPs of oligo-Neu5Gc and oligo-KDN that can be detected in PSGP and KDN-gp hydrolysates were 11 and 8, respectively. The high sensitivity of this method was demonstrated by the quantification of Neu5Ac oligomers. Distributions of the monomer and oligo/polymers in the acid and enzymatic hydrolysates of colominic acid and PSGP under different conditions were also studied.
Regulation of Fatty Acid Elongation and Initiation by Acyl-Acyl Carrier Protein in Escherichia coli (1996)

Long chain acyl-acyl carrier protein (acyl-ACP) has been implicated as a physiological inhibitor of fatty acid biosynthesis since acyl-ACP degradation by thioesterase overexpression leads to constitutive, unregulated fatty acid production. The biochemical targets for acyl-ACP inhibition were unknown, and this work identified two biosynthetic enzymes that were sensitive to acyl-ACP feedback inhibition. Palmitoyl-ACP inhibited the incorporation of [14C]malonyl-CoA into long chain fatty acids in cell-free extracts of Escherichia coli. A short chain acyl-ACP species with the electrophoretic properties of beta-hydroxybutyryl-ACP accumulated concomitant with the overall decrease in the amount of [14C]malonyl-CoA incorporation, indicating that the first elongation cycle was targeted by acyl-ACP. All of the proteins required to catalyze the first round of fatty acid synthesis from acetyl-CoA plus malonyl-CoA in vitro were isolated, and the first fatty acid elongation cycle was reconstituted with these purified components. Analysis of the individual enzymes and the pattern of intermediate accumulation in the reconstituted system identified initiation of fatty acid synthesis by beta-ketoacyl-ACP synthase III (fabH) and enoyl-ACP reductase (fabI) in the elongation cycle as two steps attenuated by long chain acyl-ACP.
Phase II trial of paclitaxel by 3-hour infusion as initial and salvage chemotherapy for metastatic breast cancer. (1995)

Paclitaxel via 3-hour infusion, without prophylactic G-CSF, is active and safe as initial and subsequent therapy for metastatic breast cancer. The transient visual symptoms noted at higher doses seem unrelated to peak plasma paclitaxel concentration. Further studies that compare 3- and 24 hour (or other) infusion schedules are necessary to determine the optimal administration of paclitaxel in metastatic breast cancer.
A Consistent Adjacency Spectral Embedding for Stochastic Blockmodel Graphs (2012)

We present a method to estimate block membership of nodes in a random graph generated by a stochastic blockmodel. We use an embedding procedure motivated by the random dot product graph model, a particular example of the latent position model. The embedding associates each node with a vector; these vectors are clustered via minimization of a square error criterion. We prove that this method is consistent for assigning nodes to blocks, as only a negligible number of nodes will be misassigned. We prove consistency of the method for directed and undirected graphs. The consistent block assignment makes possible consistent parameter estimation for a stochastic blockmodel. We extend the result in the setting where the number of blocks grows slowly with the number of nodes. Our method is also computationally feasible even for very large graphs. We compare our method with Laplacian spectral clustering through analysis of simulated data and a graph derived from Wikipedia documents.
Point-to-Axial Chirality Transfer—A New Probe for “Sensing” the Absolute Configurations of Monoamines (2013)

A host molecule, capable of freely adopting P or M helicity, is described for molecular recognition and chirality sensing. The host, consisting of a biphenol core, binds chiral amines via hydrogen-bonding interactions. The diastereomeric complex will favor either P or M helicity as a result of minimizing steric interactions of the guest molecule with the binding cavity of the host, resulting in a detectable exciton-coupled circular dichroic spectrum. A working model is proposed that enables non-empirical prediction of the chirality of the bound amine.