gebhart/patrepeval huggingface dataset:
Biochemical and biological effects of nonionic nucleic acid methylphosphonates (1981)

Oligodeoxyribonucleoside methylphosphonates with base sequences complementary to the anticodon loop of tRNALys and to the -ACCA-OH amino acid accepting stem of tRNA were prepared by chemical synthesis. Oligodeoxyadenosine methylphosphonates form stable, triple-stranded complexes with both poly(U) and poly(dT). These analogues selectively inhibit cell-free aminoacylation of tRNALys (E. coli) but have no effect on aminoacylation of tRNALys (rabbit). The extent of inhibition is temperature dependent and parallels the ability of the oligomer to bind to poly(U), which suggests that inhibition occurs as a result of oligomer binding to the -UUUU- anticodon loop of tRNALys (E. coli). The failure of the oligodeoxyadenosine methylphosphonates to inhibit tRNALys (rabbit) amino-acylation suggests that there may be a difference between the structure of tRNALys or its interaction with aminoacyl synthetase in the Escherichia coli and rabbit systems. The oligodeoxyadenosine analogues also effectively inhibit polyphenylalanine synthesis in cell-free translation systems derived from both E. coli and rabbit reticulocytes. The extent of inhibition parallels the Tm values of the oligo(A) phosphonate-poly(U) complexes and suggests that the inhibition is a consequence of complex formation with the poly(U) message. Tritium-labeled oligodeoxyribonucleoside methylphosphonates with a chain length of up to nine nucleotidyl units are taken up intact by mammalian cells in culture. All the oligomer analogues tested inhibited, to various extents, colony formation by bacterial, hamster, and human tumor cells in culture.
Combinatorial problems motivated by comma‐free codes (2004)

Abstract In the paper some combinatorial problems motivated by comma‐free codes are considered. We describe these problems, give the most significant known results and methods used, present some new results and formulate open problems. © 2004 Wiley Periodicals, Inc.
Sexually Transmitted Brucellosis in Humans (2010)

Sexual transmission of brucellosis has rarely been reported in humans. We describe 2 cases of probable sexual transmission of Brucella from husband to wife. In 1 case, orchidoepididimitis existed, whereas in the other case, the presence of Brucella in the semen in the absence of genital symptoms was demonstrated by polymerase chain reaction.
Substrate specificity of 6-O-endosulfatase (Sulf-2) and its implications in synthesizing anticoagulant heparan sulfate (2012)

Heparan sulfate (HS) 6-O-endosulfatase (Sulf) catalyzes the hydrolysis of 6-O-sulfo groups from HS polysaccharides. The resultant HS has reduced sulfation levels and displays altered biological activities. The Sulfs have been associated with several cancers and developmental problems and could function as a tool for editing specific HS structures. Here, we characterize the substrate specificity of human Sulf-2 using site-specifically radiolabeled synthetic polysaccharides. The enzyme was expressed and harvested from the conditioned medium of Chinese hamster ovary cells transfected with Sulf-2 expression plasmids. The uniquely [(35)S]sulfated polysaccharides were prepared using purified recombinant HS biosynthetic enzymes. We found that Sulf-2 is particularly effective in removing the 6-O-sulfo group residing in the trisulfated disaccharide repeating unit comprising 2-O-sulfated uronic acid and N-sulfated 6-O-sulfo glucosamine, but can also hydrolyze sulfo groups from N- and 6-O-sulfated disaccharides. In addition, we found that Sulf-2 treatment significantly decreases HS's ability to bind to platelet factor 4 (PF4), a chemokine, while binding to antithrombin is maintained. Because HS-PF4 complexes are the initiating cause of heparin-induced thrombocytopenia, this finding provides a promising strategy for developing heparin therapies with reduced side effects. Further understanding of Sulf-2 activity will help elucidate HS structure-function relationships and provide a valuable tool in tailoring HS-based anticoagulant drugs.
Small-molecule correctors of defective F508-CFTR cellular processing identified by high-throughput screening (2005)

The most common cause of cystic fibrosis (CF) is deletion of phenylalanine 508 (DeltaF508) in the CF transmembrane conductance regulator (CFTR) chloride channel. The DeltaF508 mutation produces defects in folding, stability, and channel gating. To identify small-molecule correctors of defective cellular processing, we assayed iodide flux in DeltaF508-CFTR-transfected epithelial cells using a fluorescent halide indicator. Screening of 150,000 chemically diverse compounds and more than 1,500 analogs of active compounds yielded several classes of DeltaF508-CFTR correctors (aminoarylthiazoles, quinazolinylaminopyrimidinones, and bisaminomethylbithiazoles) with micromolar potency that produced greater apical membrane chloride current than did low-temperature rescue. Correction was seen within 3-6 hours and persisted for more than 12 hours after washout. Functional correction was correlated with plasma membrane expression of complex-glycosylated DeltaF508-CFTR protein. Biochemical studies suggested a mechanism of action involving improved DeltaF508-CFTR folding at the ER and stability at the cell surface. The bisaminomethylbithiazoles corrected DeltaF508-CFTR in DeltaF508/DeltaF508 human bronchial epithelia but did not correct a different temperature-sensitive CFTR mutant (P574H-CFTR) or a dopamine receptor mutant. Small-molecule correctors may be useful in the treatment of CF caused by the DeltaF508 mutation.
Application of fetal DNA in maternal plasma for noninvasive prenatal diagnosis (2002)

Prenatal diagnosis of fetal genetic conditions is a standard part of modern obstetric care. Many of the current methods rely on invasive methods and are associated with an inherent risk of fetal loss. Consequently, there has been a long-term goal for development of noninvasive prenatal diagnostic methods. In 1997, the presence of fetal DNA in maternal plasma was first discovered through the detection of Y-chromosome-specific sequences in the plasma of women conceived with male fetuses. This discovery has opened up new possibilities in the development of noninvasive prenatal diagnostic methods through a source of fetal genetic material that could be conveniently accessible simply through the collection of a maternal peripheral blood sample. To date, there have been numerous reported applications, including fetal RhD genotyping, prenatal diagnosis of sex-linked disorders, paternally inherited genetic diseases and some pregnancy-associated conditions, including preeclampsia. More recently, there have been significant new developments with expanding number of potential applications.
Histone Deacetylase Inhibitors Decrease DNA Methyltransferase-3B Messenger RNA Stability and Down-regulate De novo DNA Methyltransferase Activity in Human Endometrial Cells (2005)

It is well known that the histone deacetylase (HDAC) inhibitor trichostatin A (TSA) acts synergistically with the DNA methyltransferase (DNMT) inhibitor 5-aza-2'-deoxycytidine (ADC) to reactivate DNA methylation-silenced genes. Moreover, in several studies, TSA was capable of inducing DNA demethylation even in the absence of ADC. Here we describe a mechanism by which HDAC inhibitors affect DNA methylation through their regulation on DNMT3B, a methyltransferase responsible for de novo DNA methylation. Using quantitative real-time PCR and Western blot analysis, we show that TSA down-regulates DNMT3B mRNA and protein expression in human endometrial cancer cells. This decrease in DNMT3B mRNA results in a significant reduction in de novo methylation activities. Further experiments indicated that TSA decreases DNMT3B mRNA stability and reduces its half-life from approximately 4 to 2.5 hours. We established that protein synthesis is required for posttranscriptional regulation, suggesting the involvement of an RNase and/or key mRNA stabilization factor(s) controlling the DNMT3B mRNA stability. Therefore, TSA may not only modify histone acetylation, but also potentially alter DNA methylation. Since the HDAC inhibitors are frequently used in epigenetic studies and are considered to be promising anticancer drugs, these new findings will have implications in both laboratory and clinical settings.
Nosocomial Pneumonia in Intubated Patients Given Sucralfate as Compared with Antacids or Histamine Type 2 Blockers (1987)

Gram-negative nosocomial pneumonia may result from retrograde colonization of the pharynx from the stomach, and this may be more likely when the gastric pH is relatively high. We studied the rate of nosocomial pneumonia among 130 patients given mechanical ventilation in an intensive care unit who were receiving as prophylaxis for stress ulcer either sucralfate (n = 61), which does not raise gastric pH, or conventional treatment with antacids, histamine type 2 (H2) blockers, or both (n = 69). At the time of randomization to treatment, the two groups were similar in age, underlying diseases, and severity of acute illness. Patients in the sucralfate group had a higher proportion of gastric aspirates with a pH less than or equal to 4 (P less than 0.001) and significantly lower concentrations of gram-negative bacilli (P less than 0.05) in gastric aspirates, pharyngeal swabs, and tracheal aspirates than did patients in the antacid-H2-blocker group. The rate of pneumonia was twice as high in the antacid-H2 group as in the sucralfate group (95 percent confidence interval, 0.89 to 4.58; P = 0.11). Gram-negative bacilli were isolated more frequently from the tracheal aspirates of patients with pneumonia who were receiving antacids or H2 blockers. Mortality rates were 1.6 times higher in the antacid-H2 group than in the sucralfate group (95 percent confidence interval, 0.99 to 2.50; P = 0.07). Although our results fell just short of statistical significance when they were analyzed according to intention to treat, they suggest that agents that elevate gastric pH increase the risk of nosocomial pneumonia in patients receiving ventilation by favoring gastric colonization with gram-negative bacilli. We conclude that in patients receiving mechanical ventilation, the use of a prophylactic agent against stress-ulcer bleeding that preserves the natural gastric acid barrier against bacterial overgrowth may be preferable to antacids and H2 blockers.
An Affinity-Enhanced Neutralizing Antibody against the Membrane-Proximal External Region of Human Immunodeficiency Virus Type 1 gp41 Recognizes an Epitope between Those of 2F5 and 4E10 (2007)

The membrane-proximal external region (MPER) of human immunodeficiency virus type 1 (HIV-1) gp41 bears the epitopes of two broadly neutralizing antibodies (Abs), 2F5 and 4E10, making it a target for vaccine design. A third Ab, Fab Z13, had previously been mapped to an epitope that overlaps those of 2F5 and 4E10 but only weakly neutralizes a limited set of primary isolates. Here, libraries of Fab Z13 variants displayed on phage were engineered and affinity selected against an MPER peptide and recombinant gp41. A high-affinity variant, designated Z13e1, was isolated and found to be approximately 100-fold improved over the parental Fab not only in binding affinity for the MPER antigens but also in neutralization potency against sensitive HIV-1. Alanine scanning of MPER residues 664 to 680 revealed that N671 and D674 are crucial for peptide recognition as well as for the neutralization of HIV-1 by Z13e1. Ab competition studies and truncation of MPER peptides indicate that Z13e1 binds with high affinity to an epitope between and overlapping with those of 2F5 and 4E10, with the minimal peptide epitope WASLWNWFDITN. Still, Z13e1 remained about an order of magnitude less potent than 4E10 against several isolates of pseudotyped HIV-1. The sum of our molecular analyses with Z13e1 suggests that the segment on the MPER of gp41 between the 2F5 and 4E10 epitopes is exposed on the functional envelope trimer but that access to the specific Z13e1 epitope within this segment is limited. Thus, the ability of MPER-bearing immunogens to elicit potent HIV-1-neutralizing Abs may depend in part on recapitulating the particular constraints that the functional envelope trimer imposes on the segment of the MPER to which Z13e1 binds.
Angiotensin Analogues Palmitoylated in Positions 1 and 4 (1997)

Lipidated angiotensin II (Ang) agonists and antagonists were synthesized and evaluated for their biological activities for eventual use an antimyoproliferative agents. Solid phase peptide synthesis was used for the assembly of the peptides with the Fmoc protection scheme. N-Acetyl-Ser1 Ang was palmitoylated on the serine hydroxyl function. The nonpalmitoylated analogue retained one-third of Ang's affinity toward the AT1 receptor on bovine adrenal cortex membranes, and the palmitoylated analogue was essentially inactive. Upon enzymatic lipolysis or mild saponification of the palmitoylated peptide, biological activity was restored. An analogous compound of Ang, N-acetyl-Ser1,beta-D-naphthylalanine8 ([NAcSer1,D-Nal8]Ang), was a pure antagonist on rabbit aorta but with lower affinity. Its O-palmitoylated form was inactive as well but was easily converted to the nonlipidated active form by lipolysis or saponification. Direct palmitoylation of [sarcosine1]Ang with palmitoyl chloride was obtained on the free phenolic hydroxyl of Tyr4 on solid phase on an otherwise fully protected peptide. This lipopeptide was fully active, was comparable to [Sar1]Ang, and exhibited strongly prolonged activity. Lipolysis and saponification under mild conditions yielded standard [Sar1]Ang. The corresponding [Sar1,D-Nal8]Ang was a potent and very long-lasting antagonist (pA2 = 8.1), and its analogous palmitoyl phenyl ester in position 4 was active in its palmitoylated form (antagonist) and, again, returned to the nonlipidated form upon saponification or lipolysis. [Sar1,Tyr4(O-octadecyl)]Ang, an analogue to Tyr-palmitoylated [Sar1]Ang with an octadecyl phenyl ether in position 4, was also prepared. Surprisingly, the ether compound was inactive. Premature hydrolysis of the palmitoyl phenyl ester peptide was excluded by HPLC analysis, and the activity of the ester peptide is attributed to a putative hydrogen bond that may be critical for biological activity. The discovery of potent biologically active lipidated antagonists of Ang gives access to potential antimyoproliferative agents with numerous application possibilities.
Identification of peptides specific for cerebrospinal fluid antibodies in multiple sclerosis by using phage libraries. (1996)

The study of the origin and pathogenetic relevance of the oligoclonal antibodies present in the cerebrospinal fluid (CSF) of multiple sclerosis (MS) patients has been hampered by a lack of specific ligands. We recently reported a general strategy, based on phage-displayed random peptide libraries, to identify ligands for disease-specific antibodies even in the absence of any information on the nature of the pathologic antigen. With this procedure, we identified several peptides specifically recognized by antibodies present in the CSF of MS patients. Using these peptides as reagents, we demonstrated that they mimic different natural epitopes and react with antibodies enriched in the CSF of MS patients. Antibodies recognizing the selected peptides are commonly found with equal frequency in the sera of MS patients and of normal individuals. In contrast, the repertoire of CSF antibodies appears to be individual-specific and is probably the result of a nonspecific immunodysregulation rather than a stereotyped response to a single antigen/agent.
Molecular Dynamics Simulations of MRI-Relevant GdIII Chelates: Direct Access to Outer-Sphere Relaxivity (2001)

The structure and dynamics of the surrounding water were studied through molecular dynamics (MD) simulations for several GdIII polyaminocarboxylate and polyaminophosphonate complexes in aqueous solution. The radial distribution functions (rdf) show that a few water molecules are bonded to the ligand through hydrogen bonds to hydrophilic groups such as carboxylates and phosphonates. Residence times are of the order of 20-25 ps for the polyaminocarboxylate and 56ps for the polyaminophosphonate chelates. No preferred orientation or bonding of water molecules is observed in the hydrophobic region of the anisotropic macrocyclic complexes. Our rdf allow calculation of the outer-sphere contribution to the nuclear magnetic resonance dispersion (NMRD) profiles using Freed's finite differences method, including electronic relaxation. The results show that the commonly used analytical force-free model is only an empirical relationship. When experimental outer-sphere NMRD profiles are available ([Gd(teta)]- and [Gd(dotp)]5-(teta=N,N',N",N"'-tetracarboxymethyl-1,4,8,11- tetraazacyclotetradecane; dotp = N,N',N",N"'-tetraphosphonatomethyl-1,4,7,10-tetraazacyclododecane) the calculated curves are in good agreement. In the case of [Gd(teta)]-, the comparison with the experimental NMRD profile has led us to predict a very fast electronic relaxation, which has been confirmed by the EPR spectrum.
New Crystallization Kinetics of Phase Change of Ge2Sb2Te5at Moderately Elevated Temperature (2002)

Based on the ellipsometric observation of the phase change of stoichiometric Ge–Sb–Te at moderately elevated temperature, we find that the kinetics of crystallization of Ge–Sb–Te is described by the modified Johnson–Mehl–Avrami (JMA) equation, which implies that the first stage of cascaded crystallization of Ge–Sb–Te is a true nucleation-dominated process such that the formation of nuclei is stimulated by preexisting nuclei.
A randomized trial of anticoagulation with warfarin and of alternating chemotherapy in extensive small-cell lung cancer by the Cancer and Leukemia Group B. (1989)

The Cancer and Leukemia Group B (CALGB) conducted a prospective randomized trial to evaluate the role of warfarin and alternating chemotherapy in extensive small-cell lung cancer (SCCL). After stratification for sex and performance status, patients were randomly assigned to receive chemotherapy with methotrexate, doxorubicin (Adriamycin; Adria Laboratories, Columbus, OH), cyclophosphamide, and lomustine (CCNU) (MACC), or MACC plus warfarin (MACC + W), or mitomycin, etoposide, cisplatin, and hexamethylmelamine alternating with MACC (MEPH/MACC). Warfarin was given continuously to maintain a prothrombin time of one and one half to twice the control values. A total of 328 patients were enrolled, and 294 were evaluable. There was a statistically significant advantage in objective response rates (complete [CR] and partial responses [PR], respectively) for MACC + W (17% and 50%) as compared with MACC alone (8% and 43%) or MEPH/MACC (10% and 38%) (P = .012). Both failure-free survival (P = .054 Wilcoxon test) and overall survival (P = .098 Wilcoxon test) were higher on MACC + W (median, 6.6 months and 9.3 months, respectively), as compared with MACC (5.0 months and 7.9 months) and MEPH/MACC (5.0 months and 7.9 months). Toxicity was comparable among the three arms, except for increased hemorrhagic events on MACC + W, which were life-threatening in four patients (4%), and lethal in two others (2%). These data support the role of warfarin in the treatment of SCCL, but do not establish its mechanism of action. Warfarin deserves further studies in SCCL, particularly in patients with limited disease.
Cathepsin K, but Not Cathepsins B, L, or S, Is Abundantly Expressed in Human Osteoclasts (1996)

Random high throughput sequencing of a human osteoclast cDNA library was employed to identify novel osteoclast-expressed genes. Of the 5475 ESTs obtained, approximately 4% encoded cathepsin K, a novel cysteine protease homologous to cathepsins S and L; ESTs for other cathepsins were rare. In addition, ESTs for cathepsin K were absent or at low frequency in cDNA libraries from numerous other tissues and cells. In situ hybridization in osteoclastoma and osteophyte confirmed that cathepsin K mRNA was highly expressed selecively in osteoclasts; cathepsins S, L, and B were not detectable. Cathepsin K was not detected by in situ hybridization in a panel of other tissues. Western blot of human osteoclastoma or fetal rat humerus demonstrated bands of 38 and 27 kDa, consistent with sizes predicted for pro- and mature cathepsin K. Immunolocalization in osteoclastoma and osteophyte showed intense punctate staining of cathepsin K exclusively in osteoclasts, with a polar distribution that was more intense at the bone surface. The abundant expression of cathepsin K selectively in osteoclasts strongly suggests that it plays a specialized role in bone resorption. Furthermore, the data suggest that random sequencing of ESTs from cDNA libraries is a valuable approach for identifying novel cell-selective genes.
Oxygen Reduction on Pd0.75Co0.25 (111) and Pt0.75Co0.25 (111) Surfaces:  An ab Initio Comparative Study (2006)

Density functional theory studies of adsorption of oxygen electroreduction intermediates and free energy profiles are used to discuss possible reaction mechanisms: one leading directly to H2O production and another having H2O2 as an intermediate, on (111) surfaces of pure Pt, pure Pd, and bimetallic systems Pd0.75Co0.25 and Pt0.75Co0.25. It is found that the calculated affinities toward the different ORR intermediates in the studied surfaces follow the Hammer-Norskov d-band model predictions. The calculated free energy profiles and the magnitude of the barriers in both mechanisms seem to favor the hypothesis that both the direct and series O2 reduction mechanisms might be operating in parallel. The highest thermodynamic barriers at (1)/4 of a monolayer atomic oxygen coverage and without solvent are located in the first hydrogenation reaction for both mechanisms.
Nanoparticles that communicate in vivo to amplify tumour targeting (2010)

Author Manuscript: 2012 May 29
Dual Source Ion Mobility-Mass Spectrometer for Direct Comparison of Electrospray Ionization and MALDI Collision Cross Section Measurements (2010)

In this report, we describe a dual ionization source ion mobility-mass spectrometer (IM-MS) instrument platform for investigations that critically compare ion mobility collision cross section (CCS) measurements obtained from different ionization methods. The instrument incorporates both matrix-assisted laser desorption ionization (MALDI) and nanoelectrospray ionization (nESI) sources. The nESI source incorporates a keyhole geometry ion funnel design which facilitates axial ion focusing, accumulation, and generation of short duration (10-30 mus) ion pulses for use with the IM-MS. The IM-MS instrument operation is independent of which ionization source is used. This allows comparisons of collision cross section measurements to be made between both ion sources with minimal differences in the instrumental arrangement. The performance of the nESI ion source is evaluated by measuring the collision cross section values of the charge states of equine cytochrome c (z = 9-16), and values are in good agreement (<2% deviation) with those previously reported in the literature. Several charge states (z = 8-11) of cytochrome c exhibit multiple cross sectional features in the ion mobility analysis. An analysis of the tryptic peptides of cytochrome c formed by both ESI and MALDI demonstrate that, on average, +1 MALDI ions are similar in CCS to +1 ESI ions and are smaller than +2 ESI ions. The ion mobility resolving power with ESI (30-35) is comparable to that obtained using MALDI (35-40), which suggests that both sources produce sufficiently narrow ion pulses for the measurement to be predominately diffusion rather than gate pulse width limited.