gebhart/patrepeval huggingface dataset:
Mapping the active sites of bovine thrombin, factor IXa, factor Xa, factor XIa, factor XIIa, plasma kallikrein, and trypsin with amino acid and peptide thioesters: development of new sensitive substrates (1981)

The subsite specificities of bovine factor IXa, factor Xa, factor XIa, factor XIIa, thrombin, plasma kallikrein, and trypsin were mapped with amino acid, dipeptide, and longer peptide thioester substrates. Each substrate contained a P1 Arg residue. The P1' residues included thiol residues which are analogues of valine, leucine, and isoleucine, respectively, and the P2 residue included 12 representative amino acid residues. Longer substrates with the sequence at the antithrombin III reactive site and at the zymogen activation site of various coagulation factors were also studied. The enzymatic hydrolysis of the thioesters was measured in the presence of 4,4'-dithiodipyridine which provides a very sensitive assay for the free thiol. The thioesters were excellent substrates for the coagulation factors studied, and the kcat/Km values for the best thioester substrates were higher than those previously reported for most of these enzymes. Thrombin and plasma kallikrein were the most active of the coagulation factors toward the thioester substrates. The best substrate for thrombin was Z-Gly-Arg-SCH2C6H5, although substrates containing proline in the P2 position were also quite effective. Some of the better substrates for plasma kallikrein had a P2 Phe or Trp residue. Factor IXa was the least reactive of the coagulation factors and hydrolyzed only four of the dipeptide thioesters. Substrates with bulky hydrophobic groups such as Phe or Trp in the P2 position were the most reactive with factor IXa. Factor Xa hydrolyzed all the thioester substrates tested, the most reactive being Z-Gly-Arg-SCH2C6H5. This is consistent with the fact that glycine and arginine are present in the P2 and P1 positions, respectively, of the factor Xa sensitive bonds in prothrombin which is the physiological substrate for factor Xa. Bovine factor XIa showed the least amount of specificity of the various coagulation factors and was quite reactive toward all of the thioester substrates. The most sensitive substrate for this enzyme was also Z-Gly-Arg-SCH2C6H5. Factor XIIa preferred the dipeptide with a P2 Phe, although the simpler thioester Z-Arg-SCH2CH(CH3)2 was more reactive. Trypsin hydrolyzed all of the thioester substrates at a high rate and showed little substrate specificity. With all enzymes studied, extension of the thioester substrate beyond P2 or the P1' thiol leaving group did not lead to an improvement in hydrolysis. Due to their high kcat/Km values and the ease of detecting the thiol leaving group, thioester substrates should be extremely useful for future studies of coagulation proteases.
Penetratin and Related Cell-Penetrating Cationic Peptides Can Translocate Across Lipid Bilayers in the Presence of a Transbilayer Potential (2003)

Fluorescent-labeled derivatives of the Antennapedia-derived cell-penetating peptide penetratin, and of the simpler but similarly charged peptides R(6)GC-NH(2) and K(6)GC-NH(2), are shown to be able to translocate into large unilamellar lipid vesicles in the presence of a transbilayer potential (inside negative). Vesicles with diverse lipid compositions, and combining physiological proportions of neutral and anionic lipids, are able to support substantial potential-dependent uptake of all three cationic peptides. The efficiency of peptide uptake under these conditions is strongly modulated by the vesicle lipid composition, in a manner that suggests that more than one mechanism of peptide uptake may operate in different systems. Remarkably, peptide uptake is accompanied by only minor perturbations of the overall barrier function of the lipid bilayer, as assessed by assays of vesicle leakiness under the same conditions. Fluorescence microscopy of living CV-1 and HeLa cells incubated with the labeled peptides shows that the peptides accumulate in peripheral vesicular structures at early times of incubation, consistent with an initial endosomal localization as recently reported, but gradually accumulate in the cytoplasm and nucleus during more extended incubations (several hours). Our findings indicate that these relatively hydrophilic, polybasic cell-penetrating peptides can translocate through lipid bilayers by a potential- and composition-dependent pathway that causes only minimal perturbation to the overall integrity and barrier function of the bilayer.
Ceramide synthases and ceramide levels are increased in breast cancer tissue (2009)

Several in vitro studies have correlated dysfunction of the sphingolipid-signaling pathway with promotion of tumor cell growth as well as progression and resistance of tumors to chemotherapeutic agents. As ceramides (Cer) constitute the structural backbones of all sphingolipids, we investigated the endogenous ceramide levels in 43 malignant breast tumors and 21 benign breast biopsies and compared them with those of normal tissues using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). The total ceramide levels in malignant tumor tissue samples were statistically significantly elevated when compared with normal tissue samples. Upregulation of the total ceramide level averaged 12-fold and 4-fold higher than normal tissue samples, for malignant tumors and benign tissues, respectively. Specifically, the levels of C(16:0)-Cer, C(24:1)-Cer and C(24:0)-Cer were significantly raised in malignant tumors as compared with benign and normal tissue. The augmentation of the various ceramides could be assigned to an increase of the messenger RNA levels of ceramide synthases (CerS) LASS2 (longevity assurance), LASS4 and LASS6. Notably, elevated levels of C(16:0)-Cer were associated with a positive lymph node status, indicating a metastatic potential for this ceramide. Moreover, the levels of C(18:0)-Cer and C(20:0)-Cer were significantly higher in estrogen receptor (ER) positive tumor tissues as compared with ER negative tumor tissues. In conclusion, progression in breast cancer is associated with increased ceramide levels due to an upregulation of specific LASS genes.
Solution Structure of the E-Domain of Staphylococcal Protein A (1996)

The E-domain of staphylococcal protein A is one of five homologous IgG-binding domains designated E, D, A, B, and C that comprise the extracellular portion of protein A. The E-domain binds tightly to Fc fragments of IgG and binds certain Fv fragments with micromolar affinity. To explore further the structural features of Fc binding by protein A, and as a first step in developing a structural understanding of E-domain/Fv complex formation, we have determined the solution structure of the uncomplexed E-domain using 2D homonuclear and heteronuclear NMR spectroscopy. Complete 1H and 15N resonance assignments were obtained, and the structure was determined from 383 NOE-derived distance restrains, 34 phi and 19 chi 1 dihedral angle restraints, and 54 restraints for 27 H-bonds. 3JH alpha-H beta coupling constants and long-range NOEs involving Phe11 indicate the side chain exists in more than one conformation with differing chi 1 values. NOE restraints that were incompatible with chi 1 = -60 degrees were removed from one set of structure calculations, and those incompatible with chi 1 = 180 degrees were removed from a second set to allow Phe11 to explore both rotamer wells. Thus, two sets of 20 final structures, having no distance or dihedral angle restraint violations greater than 0.12 A or 1.6 degrees, respectively, represent the solution structure of the E-domain. Backbone atomic rms differences with respect to the mean coordinates for each set of 20 structures for residues 8-53 averaged 0.41 +/- 0.06 and 0.35 +/- 0.06 A. No significant differences in the overall structure result from the different orientations of Phe11. The solution structure of the E-domain consists of three alpha-helices that pack together to form a compact helical bundle. A detailed comparison between the E-domain ensembles and the previously determined structure for the B-domain in complex with Fc indicates that only the 180 degrees chi 1 rotamer of Phe11 is competent for binding; the -60 degrees chi 1 rotamer must reorient to 180 degrees to create a cavity that is filled by Ile253 from the CH2 domain of Fc in the Fc-bound complex.
Talimogene Laherparepvec Improves Durable Response Rate in Patients With Advanced Melanoma (2015)

T-VEC is the first oncolytic immunotherapy to demonstrate therapeutic benefit against melanoma in a phase III clinical trial. T-VEC was well tolerated and resulted in a higher DRR (P < .001) and longer median OS (P = .051), particularly in untreated patients or those with stage IIIB, IIIC, or IVM1a disease. T-VEC represents a novel potential therapy for patients with metastatic melanoma.
High speed patterning of a metal silicide using scanned probe lithography (1999)

We describe a simple high-speed process for patterning metal silicides with an atomic force microscope (AFM). The process uses a thin AFM-generated oxide to block Pt diffusion during the formation of Pt silicide. Because the process requires only ∼1 nm of oxide, high write speeds and fine lateral resolution are achieved. We find that by maintaining ambient moisture at the tip–sample interface we can under optimal tip conditions achieve a minimum exposure time of ∼300 ns for a 30 nm size pixel which corresponds to a maximum write speed of ∼10 cm/s.
Protein PAB, an Albumin-binding Bacterial Surface Protein Promoting Growth and Virulence (1996)

The anaerobic bacterium Peptostreptococcus magnus is a human commensal and pathogen. Previous work has shown that strains of P. magnus isolated from patients with gynecological disease (vaginosis) frequently express an immunoglobulin (Ig) light chain-binding protein called protein L. Here we report that strains isolated from localized suppurative infections bind human serum albumin (HSA), whereas commensal isolates bind neither Ig nor HSA. The HSA-binding protein PAB was extracted from the bacterial surface or isolated from the culture supernatant of the P. magnus strain ALB8. Protein PAB was shown to have two homologous HSA-binding domains, GA and uGA. GA is absent in the sequence of a related protein from another P. magnus strain and shows a high degree of homology to the HSA-binding domains of streptococcal protein G. Therefore GA is believed to have recently been shuffled as a module from genes of other bacterial species into the protein PAB gene. This GA module was shown to exhibit a much higher affinity for HSA than uGA and was also found to be present in all of the isolates tested from localized suppurative infections, indicating a role in virulence. Moreover, when peptostreptococci or streptococci expressing the GA module were grown in the presence of HSA, the growth rate was substantially increased. Thus, the HSA binding activity of the GA module adds selective advantages to the bacteria, which increases their virulence in the case of P. magnus strains.
General method for calculating helical parameters of polymer chains from bond lengths, bond angles, and internal‐rotation angles (1967)

Abstract Helical conformations of infinite polymer chains may be described by the helical parameters, d and θ (the translation along the helix axis and the angle of rotation about the axis per repeat unit), pi (the distance of the i th atom from the axis), d ij , and d ij (the translation along the axis and the angle of rotation, respectively, on passing from the i th atom to the j th). A general method has been worked out for calculating all those helical parameters from the bond lengths, bond angles, and internal‐rotation angles. The positions of the main chain and side chain atoms with respect to the axis may also be calculated. All the equations are applicable to any helical polymer chain and are readily programmed for electronic computers. A method is also presented for calculating the partial derivatives of helical parameters with respect to molecular parameters.
Clinical Prevalence, Antimicrobial Susceptibility, and Geographic Resistance Patterns of Enterococci: Results from the SENTRY Antimicrobial Surveillance Program, 1997–1999 (2001)

As part of the SENTRY Antimicrobial Resistance Surveillance Program, a total of 4998 strains of enterococci isolated from 1997 to 1999 were processed. The occurrence of enterococcal infections by species and site of infection was analyzed, as were the occurrence of vancomycin-resistant enterococci (VRE) and their resistance phenotypes and genotypes. Trends in antimicrobial susceptibility to a variety of agents (including experimental compounds) were also reported. Enterococci accounted for >9% of isolates from all bloodstream infections (BSIs) in North America. Ampicillin was active against strains from Latin America and Europe but not against those from the United States and Canada. US isolates were considerably more resistant to vancomycin (17% resistant strains in 1999) than were those from patients in the rest of the world. The highest proportion of VRE was observed among BSI isolates (81.7%). Quinupristin-dalfopristin, chloramphenicol, and doxycycline were the most active agents tested against VRE. The results of this study confirm the worldwide trend in increasing occurrence of enterococci and the emerging pattern of antimicrobial resistance among such isolates.
Size effects in the excited electronic states of small colloidal CdS crystallites (1984)

This paper reports experimental studies of the development of bulk optical properties as a function of crystallite size for the inorganic direct gap semiconductor CdS. Small crystallites are synthesized via colloidal chemical techniques, and their optical properties are studied in situ at extreme dilution. The crystallites are characterized via high resolution transmission electron microscopy. Direct images show (111) lattice planes, and establish the crystallite structures as close to those of excised fragments of bulk CdS (zinc-blende cubic). Large crystallites (&amp;gt; 100 Å average diameter) show an optical absorption, in colloidal solution, close to that of bulk crystalline material. However, small crystallites of 30 Å average diameter show a large blue shift (∼0.8 eV) in absorption edge (effective band gap), and an intensification of edge absorption relative to absorption at higher energy regions. These observations can be understood as quantum size effects resulting from confinement of an electron and hole in a small volume. 40 Å average size crystallites show a smaller shift (∼0.25 eV), and corresponding changes in their fluorescence, and resonance Raman excitation, spectra.
Effects of Surgical Trauma and Cardiopulmonary Bypass on Active Thrombin Concentrations and the Rate of Thrombin Inhibition in vivo (2003)

The in vivo concentration of active thrombin and the second-order rate constant for the inhibition of thrombin by antithrombin (k(inh)) were estimated in patients undergoing cardiopulmonary bypass (CPB) based on measured levels of hemostatic markers in combination with a computer model of the patient's hemostatic and vascular systems. At baseline k(inh) = 0.6 +/- 0.1 microM(-1) s(-1) leaving 270 +/- 101 fM of active thrombin in the circulation. These factors were unchanged after sternotomy. Soon after heparin administration and the start of CPB, k(inh) increased 25-fold resulting in decreased active thrombin. After CPB and heparin neutralization, k(inh) decreased to 8-fold above baseline allowing active thrombin levels to rise. Both factors had returned to normal 2 h after surgery. We conclude that CPB with heparinization results in a rapid increase in thrombin inhibition leading to decreased active thrombin levels in vivo.
A framework for cost-effective peer-to-peer content distribution (2003)

No abstract available.
The Influence of Pyridostigmine Administration on Human Neuromuscular Functions—Studies in Healthy Human Subjects (1991)

Pyridostigmine has a protective effect against organophosphate poisoning when given in a dosage of 30 mg three times daily causing 20–40% cholinesterase inhibition. To test its safety in the human neuromuscular system, a double-blind study on 35 subjects divided into two matched groups was performed. One group was treated with pyridostigmine in a dose of 30 mg three times daily and the other group was treated similarly with placebo, both for a 10-day period. The resultant average cholinesterase inhibition in the treatment group was 23%. Muscle strength and endurance were tested before, during (on the 8th day), and after treatment. Electrodiagnostic studies, including nerve conduction, electromyography, and response to repetitive stimulation, were carried out on four subjects of the treatment group and on two subjects of the placebo group, both before and during treatment (eighth day). Isometric handgrip strength, isokinetic elbow flexor, and extensor strength did not differ between groups as a result of the treatment. Knee flexor and extensor isokinetic strength showed a small (but statistically significant) trend to improve more during placebo treatment, whereas knee extensor endurance decreased slightly in the placebo group. Both these effects are probably due to large fluctuations in performance of the placebo group, whereas the treatment group performance was quite constant. They probably do not represent any adverse effect of pyridostigmine. No electrophysiological changes were found in any of the subjects during treatment. We conclude that pyridostigmine does not cause any significant neuromuscular effect in healthy subjects when taken in a dosage of 90 mg daily for 8 days, causing 20–30% inhibition of Cholinesterase.
The Role of Cystathionine β-Synthase in Homocysteine Metabolism (2005)

Cystathionine beta-synthase (CBS) is the first enzyme in the transsulfuration pathway, catalyzing the conversion of serine and homocysteine to cystathionine and water. The enzyme contains three functional domains. The middle domain contains the catalytic core, which is responsible for the pyridoxal phosphate-catalyzed reaction. The C-terminal domain contains a negative regulatory region that is responsible for allosteric activation of the enzyme by S-adenosylmethionine. The N-terminal domain contains heme, and this domain regulates the enzyme in response to redox conditions. Besides its canonical reaction, CBS can catalyze alternative reactions that produce hydrogen sulfide, a novel neuromodulator in the brain. Mutations in human CBS result in homocystinuria, an autosomal recessive disorder characterized by defects in a variety of different organ systems. The most common CBS allele is 833T>C (I278T), which is associated with pyridoxine-responsive homocystinuria. A complementation system in S. cerevisiae has been developed for analysis of human CBS mutations. Using this system, it has been discovered that deletion of the C-terminal domain of CBS can suppress the functional defects of many patient-derived mutations. This finding suggests it may be possible to develop drugs that interact with the C-terminal domain of CBS to treat elevated homocysteine in humans.
Fluorination with XeF2.144. Effect of Geometry and Heteroatom on the Regioselectivity of Fluorine Introduction into an Aromatic Ring (1998)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTFluorination with XeF2.1 44. Effect of Geometry and Heteroatom on the Regioselectivity of Fluorine Introduction into an Aromatic RingMarko Zupan, Jernej Iskra, and Stojan StavberView Author Information Laboratory of Organic and Bioorganic Chemistry, Faculty of Chemistry and Chemical Technology, and J. Stefan Institute, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia Cite this: J. Org. Chem. 1998, 63, 3, 878–880Publication Date (Web):January 13, 1998Publication History Received12 August 1997Published online13 January 1998Published inissue 1 February 1998https://pubs.acs.org/doi/10.1021/jo971496ehttps://doi.org/10.1021/jo971496ebrief-reportACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views637Altmetric-Citations8LEARN 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 SUBJECTS:Aromatic compounds,Functionalization,Halogenation,Organic reactions,Selectivity Get e-Alerts
Sequence-specific polypeptoids: A diverse family of heteropolymers with stable secondary structure (1998)

We have synthesized and characterized a family of structured oligo-N-substituted-glycines (peptoids) up to 36 residues in length by using an efficient solid-phase protocol to incorporate chemically diverse side chains in a sequence-specific fashion. We investigated polypeptoids containing side chains with a chiral center adjacent to the main chain nitrogen. Some of these sequences have stable secondary structure, despite the achirality of the polymer backbone and its lack of hydrogen bond donors. In both aqueous and organic solvents, peptoid oligomers as short as five residues give rise to CD spectra that strongly resemble those of peptide alpha-helices. Differential scanning calorimetry and CD measurements show that polypeptoid secondary structure is highly stable and that unfolding is reversible and cooperative. Thermodynamic parameters obtained for unfolding are similar to those obtained for the alpha-helix to coil transitions of peptides. This class of biomimetic polymers may enable the design of self-assembling macromolecules with novel structures and functions.
Sensitive and fast mutation detection by solid phase chemical cleavage (1996)

We have developed a solid phase chemical cleavage method (SpCCM) for screening large DNA fragments for mutations. All reactions can be carried out in microtiterwells from the first amplification of the patient (or test) DNA through the search for mutations. The reaction time is significantly reduced compared to the conventional chemical cleavage method (CCM), and even by using a uniformly labelled probe, the exact position and nature of the mutation can be revealed. The SpCCM is suitable for automatization using a workstation to carry out the reactions and a fluorescent detection-based DNA sequencing system to analyze the cleaved fragments.
Elevated cerebrospinal fluid and blood concentrations of oxytocin following its intranasal administration in humans (2013)

There has been an unprecedented interest in the modulatory effects of intranasal oxytocin on human social cognition and behaviour, however as yet no study has actually demonstrated that this modality of administration increases concentrations of the peptide in the brain as well as blood in humans. Here using combined blood and cerebrospinal fluid (CSF) sampling in subjects receiving either 24 IU of oxytocin (n = 11) or placebo (n = 4) we have shown that oxytocin levels significantly increased in both plasma and CSF. However, whereas oxytocin plasma concentrations peaked at 15 min after intranasal administration and decreased after 75 min, CSF concentrations took up to 75 min to reach a significant level. Moreover, there was no correlation (r = <0.10) between oxytocin plasma and CSF concentrations. Together, these data provide crucial insights into the plasma and CSF kinetics of intranasally administered oxytocin.