gebhart/patrepeval huggingface dataset:
The Glycosyltransferase Domain of Penicillin-Binding Protein 2a from Streptococcus pneumoniae Catalyzes the Polymerization of Murein Glycan Chains (2003)

The bacterial peptidoglycan consists of glycan chains of repeating beta-1,4-linked N-acetylglucosaminyl-N-acetylmuramyl units cross-linked through short peptide chains. The polymerization of the glycans, or glycosyltransfer (GT), and transpeptidation (TP) are catalyzed by bifunctional penicillin-binding proteins (PBPs). The beta-lactam antibiotics inhibit the TP reaction, but their widespread use led to the development of drug resistance in pathogenic bacteria. In this context, the GT catalytic domain represents a potential target in the antibacterial fight. In this work, the in vitro polymerization of glycan chains by the extracellular region of recombinant Streptococcus pneumoniae PBP2a, namely, PBP2a* (the asterisk indicates the soluble form of the protein) is presented. Dansylated lipid II was used as the substrate, and the kinetic parameters K(m) and k(cat)/K(m) were measured at 40.6 micro M (+/- 15.5) and 1 x 10(-3) M(-1) s(-1), respectively. The GT reaction catalyzed by PBP2a* was inhibited by moenomycin and vancomycin. Furthermore, the sequence between Lys 78 and Ser 156 is required for enzymatic activity, whereas it is dispensable for lipid II binding. In addition, we confirmed that this region of the protein is also involved in membrane interaction, independently of the transmembrane anchor. The characterization of the catalytically active GT domain of S. pneumoniae PBP2a may contribute to the development of new inhibitors, which are urgently needed to renew the antibiotic arsenal.
Antibodies directed against phosphothreonine residues as potent tools for studying protein phosphorylation (1989)

Here we report the development of novel antibodies which specifically react with phosphothreonine residues [anti-(P-Thr)antibodies]. The specificity of the antibodies was assessed in radioimmunoassays where we could demonstrate that half-maximal and maximal binding of the antibodies to plates coated with BSA - P-Thr occurred at serum dilutions of 1:4000 and 1:1000, respectively. P-Thr inhibited antibody binding with a half-maximal effect at 40 microM. P-Ser was 200-fold less potent while P-Tyr was essentially ineffective. Anti-(P-Thr) antibodies could specifically bind to phosphothreonine-containing proteins on Western blots. Using such a procedure we could demonstrate enhanced threonine phosphorylation of the EGF receptor upon treatment of intact unlabeled A431 cells with EGF. We could further demonstrate antibodies binding to proteins present in extracts of rat hepatoma cells (Fao). P-Thr at 10 microM completely inhibited antibody binding while P-Ser, P-Tyr, Thr or Ser, each present at tenfold higher concentrations, had no such inhibitory effect. Anti-(P-Thr) antibodies were also capable of specifically immunoprecipitating 32P-labeled phosphoproteins present in Triton extracts of Fao cells. Immunoprecipitation of proteins of 38 kDa, 55 kDa, 85 kDa, 100 kDa and 155 kDa was inhibited by 1 mM P-Thr but not by P-Tyr. These findings suggest that anti-(P-Thr) antibodies could be powerful tools in studies aimed at monitoring alterations in threonine phosphorylation of specific proteins as they occur under physiological conditions in response to various extracellular stimuli. Identification of such proteins can be conveniently monitored by immunoblotting.
Neurotransmission in Epilepsy (1995)

Some evidence indicates that in some types of focal epilepsy the enhanced excitability is due in part to impaired gamma-aminobutyric acid (GABA)ergic inhibitory feedback. One form that this can take is impaired excitatory input to GABAergic interneurons. Enhanced excitatory receptor sensitivity, most characteristically involving N-methyl-D-aspartate (NMDA) receptors, has been identified in kindled rodents and in focal epilepsy in humans. Drugs that enhance GABA-mediated inhibition are anticonvulsant in many syndromes of generalized and focal epilepsy. Mechanisms through which this occurs include direct interaction with the GABA/benzodiazepine (BZD) receptor (BZDs, barbiturates, chlormethiazole), inhibition of GABA-transaminase (vigabatrin, VGB) and blocking GABA uptake (tiagabine, TGB). Glutamate receptor antagonists (both NMDA and non-NMDA antagonists) are potent anticonvulsants in many animal models of epilepsy. Whether pure glutamate receptor antagonists will have a clinical role as antiepileptic drugs (AEDs) remains to be established.
Biodegradable polyurethanes for implants. II. In vitro degradation and calcification of materials from poly(ϵ‐caprolactone)–poly(ethylene oxide) diols and various chain extenders (2002)

Linear, biodegradable, aliphatic polyurethanes with various degrees of hydrophilicity were synthesized in bulk at 50-100 degrees C. The ratios between the hydrophilic and hydrophobic segments were 0:100, 30:70, 40:60, 50:50, and 70:30, respectively. The hydrophilic segment consisted of poly(ethylene oxide) (PEO) diol (molecular weight = 600 or 2000) or the poly(ethylene-propylene-ethylene oxide) (PEO-PPO-PEO) diol Pluronic F-68 (molecular weight = 8000). The hydrophobic segment was made of poly(epsilon-caprolactone) diol (molecular weight = 530, 1250, or 2000). The chain extenders were 1,4-butane diol and 2-amino-1-butanol. The diisocyanate was aliphatic hexamethylene diisocyanate. The polymers absorbed water in an amount that increased with the increasing content of the PEO segment in the polymer chain. The total amount of absorbed water did not exceed 2% for the poly(ester urethane)s and was as high as 212% for some poly(ester ether urethane)s that behaved in water like hydrogels. The polymers were subjected to in vitro degradation at 37 +/- 0.1 degrees C in phosphate buffer solutions for up to 76 weeks. The poly(ester urethane)s showed 1-2% mass loss at 48 weeks and 1.1-3.8% mass loss at 76 weeks. The poly(ester ether urethane)s manifested 1.6-76% mass loss at 48 weeks and 1.6-96% mass loss at 76 weeks. The increasing content and molecular weight of the PEO segment enhanced the rate of mass loss. Similar relations were also observed for polyurethanes from PEO-PPO-PEO (Pluronic) diols. Materials obtained with 2-amino-1-butanol as the chain extender degraded at a slower rate than similar materials synthesized with 1,4-butane diol. All the materials already manifested a progressive decrease in the molecular weight in the first month of in vitro aging. The rate of molecular weight loss was higher for poly(ester ether urethane)s than for poly(ester urethane)s. For poly(ester ether urethane)s, the rate of molecular weight loss was higher for materials containing Pluronic than for those containing PEO segments. All polymers calcified in vitro. The susceptibility to calcification increased with material hydrophilicity. The progressive deposition of calcium salt on the film surfaces resulted in the formation of large crystal aggregates, the structure of which depended on the chemical composition of the calcified material. Needle-like aggregates, resembling brushite, formed on the hydrophobic polyurethane, and plate-like crystals formed on the highly hydrophilic material. The calcium-to-phosphorus atomic ratio of the crystals growing on the samples was dependent on the chemical composition of the material and varied from 0.94 to 1.55.
Assessing Depression in Schizophrenia: The Calgary Depression Scale (1993)

Since existing depression scales were designed for assessment of depression in non-psychotic populations, such scales have items which do not distinguish depressed from non-depressed psychotic subjects. The authors describe a new scale, the Calgary Depression Scale, which was designed for the assessment of depression in schizophrenia. The scale was derived from two existing scales by factor analysis and reliability analysis. It has been further tested in two new samples. In the first it has been shown to be reliable, congruent with a self-report scale and valid. In the second sample it has been shown that there is no overlap with negative or extrapyramidal symptoms.
Wall stress and patterns of hypertrophy in the human left ventricle. (1975)

It is generally recognized that chronic left ventricular (LV) pressure overload results primarily in wall thickening and concentric hypertrophy, while chronic LV volume overload is characterized by chamber enlargement and an eccentric pattern of hypertrophy. To assess the potential role of the hemodynamic factors which might account for these different patterns of hypertrophy, we measured LV wall stresses throughout the cardiac cycle in 30 patients studied at the time of cardiac catheterization. The study group consisted of 6 subjects with LV pressure overload, 18 with LV volume overload, and 6 with no evidence of heart disease (control). LV pressure, meridional wall stress (sigman), wall thickness (h), and radius (R) were measured in each patient throughout the cardiac cycle. For patients with pressure overload, LV peak systolic and end diastolic pressures were significantly increased (220 plus or minus 6/23 plus or minus 3 mm Hg) compared to control (117 plus or minus 7/10 plus or minus 1 mm Hg, P less than 0.01 for each). However, peak systolic and end diastolic (sigman) were normal (161 plus or minus 24/23 plus or minus 3 times 10-3 dyn/cm-2) compared to control (151 plus or minus 14/17 plus or minus 2 times 10-3 dyn/cm-2, NS), reflecting the fact that the pressure overload was exactly counterbalanced by increased wall thickness (1.5 plus or minus 0.1 cm for pressure overload vs. 0.8 plus or minus 0.1 cm for control, P less than 0.01). For patients with volume overload, peak systolic (sigman) was not significantly different from control, but end diastolic (sigmam) was consistently higher than normal (41 plus or minus 3 times 10-3 dyn/cm-2 for volume overload, 17 plus or minus 2 times 10-3 dyn/cm-2 for control, P less than 0.01). LV pressure overload was associated with concentric hypertrophy, and an increased value for the ratio of wall thickness to radius (h/R ratio). In contrast, LV volume overload was associated with eccentric hypertrophy, and a normal h/R ratio. These data suggest the hypothesis that hypertrophy develops to normalize systolic but not diastolic wall stress. We propose that increased systolic tension development by myocardial fibers results in fiber thickening just sufficient to return the systolic stress (force per unit cross-sectional area) to normal. In contrast, increased resting or diastolic tension appears to result in gradual fiber elongation or lengthening which improves efficiency of the ventricular chamber but cannot normalize the diastolic wall stress.
A nucleolar mechanism controlling cell proliferation in stem cells and cancer cells (2002)

The unique property of stem cells to self-renew suggests specific mechanisms that regulate their cell-cycle progression. In the present study, we identify a novel protein, nucleostemin, found in the nucleoli of CNS stem cells, embryonic stem cells, and several cancer cell lines and preferentially expressed by other stem cell-enriched populations. It contains an N-terminal basic domain and two GTP-binding motifs. When stem cells differentiate, nucleostemin expression decreases rapidly prior to cell-cycle exit both in vitro and in vivo. Depletion or overexpression of nucleostemin reduces cell proliferation in CNS stem cells and transformed cells. Mutation analysis indicates that excessive nucleostemin, particularly mutants that lack the GTP-regulatory domain, prevents cells from entering mitosis and causes apoptosis in a p53-dependent manner. The N-terminal basic domain specifies nucleolar localization, the p53 interaction, and is required for the cell death caused by overexpression. This work describes a novel nucleolar mechanism that controls the cell-cycle progression in CNS stem cells and cancer cells.
Dissection of measles virus V protein in relation to its ability to block alpha/beta interferon signal transduction (2004)

Interferon (IFN)-alpha and -beta are the main cytokines for innate immune responses against viral infections. To replicate efficiently in the hosts, viruses have evolved various countermeasures to the IFN response. The V protein of measles virus (MV) has been shown to block IFN-alpha/beta signalling. Here, the wild-type IC-B strain of MV was shown to grow comparably in the presence and absence of IFN-alpha, whereas replication of the Edmonston tag strain recovered from cloned DNA was strongly suppressed in its presence. The V protein of the IC-B strain, but not the Edmonston tag strain, blocked IFN-alpha signalling. The V protein of the Edmonston strain from the ATCC also inhibited IFN-alpha signalling. There were three amino acid differences between the V proteins of the Edmonston ATCC and tag strains, and substitutions of both residues at positions 110 and 272 were required for the Edmonston ATCC V protein to lose IFN-antagonist activity. The P protein of the IC-B strain, which shares the N-terminal 231 aa residues with the V protein, also inhibited IFN-alpha signalling. Indeed, fragments comprising only those 231 residues of the IC-B and Edmonston ATCC V proteins, but not the Edmonston tag V protein, were able to block IFN-alpha signalling. However, the N-terminal region of the Edmonston tag V protein, when attached to the C-terminal region of the Edmonston ATCC V protein, inhibited IFN-alpha signalling. Taken together, our results indicate that both the N- and C-terminal regions contribute to the IFN-antagonist activity of the MV V protein.
Scalable parallel building blocks for custom data analysis (2011)

We present a set of building blocks that provide scalable data movement capability to computational scientists and visualization researchers for writing their own parallel analysis. The set includes scalable tools for domain decomposition, process assignment, parallel I/O, global reduction, and local neighborhood communicationtasks that are common across many analysis applications. The global reduction is performed with a new algorithm, described in this paper, that efficiently merges blocks of analysis results into a smaller number of larger blocks. The merging is configurable in the number of blocks that are reduced in each round, the number of rounds, and the total number of resulting blocks. We highlight the use of our library in two analysis applications: parallel streamline generation and parallel Morse-Smale topological analysis. The first case uses an existing local neighborhood communication algorithm, whereas the latter uses the new merge algorithm.
Effects of branching and molecular weight of surface-bound poly(ethylene oxide) on protein rejection (1995)

To understand better the origin of protein rejection observed with surface-bound poly(ethylene oxide) (or PEO), we have measured fibrinogen adsorption for a series of linear and branched, low-molecular-weight PEOs bound to solid polystyrene surfaces. The results show that a dependence on molecular weight is found below 1500 g mol-1 for linear PEO. Branched PEOs are less effective at protein rejection than linear PEOs. The branched PEOs have smaller exclusion volumes (from GPC) than the corresponding linear PEOs, consistent with restriction in conformational freedom for the branched compounds. The protein rejection results are interpreted in terms of entropy changes that result upon protein adsorption. In addition, some practical problems in preparation of PEO glycidyl ethers have been clarified, thus making these PEO derivatives more useful for surface modification.
Safe and bodywide muscle transduction in young adult Duchenne muscular dystrophy dogs with adeno-associated virus (2015)

The ultimate goal of muscular dystrophy gene therapy is to treat all muscles in the body. Global gene delivery was demonstrated in dystrophic mice more than a decade ago using adeno-associated virus (AAV). However, translation to affected large mammals has been challenging. The only reported attempt was performed in newborn Duchenne muscular dystrophy (DMD) dogs. Unfortunately, AAV injection resulted in growth delay, muscle atrophy and contracture. Here we report safe and bodywide AAV delivery in juvenile DMD dogs. Three ∼2-m-old affected dogs received intravenous injection of a tyrosine-engineered AAV-9 reporter or micro-dystrophin (μDys) vector at the doses of 1.92-6.24 × 10(14) viral genome particles/kg under transient or sustained immune suppression. DMD dogs tolerated injection well and their growth was not altered. Hematology and blood biochemistry were unremarkable. No adverse reactions were observed. Widespread muscle transduction was seen in skeletal muscle, the diaphragm and heart for at least 4 months (the end of the study). Nominal expression was detected in internal organs. Improvement in muscle histology was observed in μDys-treated dogs. In summary, systemic AAV gene transfer is safe and efficient in young adult dystrophic large mammals. This may translate to bodywide gene therapy in pediatric patients in the future.
A steady‐state mass balance model of the polycarbonate–CO2 system reveals a self‐regulating cell growth mechanism in the solid‐state microcellular process (2001)

Abstract A simple mechanism regulating polymer mobility is demonstrated to determine initial and final growth states of solid‐state microcellular foams. This mechanism, governed by the extent of plasticization of the polymer by the dissolved gases, is examined with a mass balance model and results from foam growth experiments. Polycarbonate was exposed to CO 2 , which acted as both a plasticizing gas and a physical blowing agent driving foam growth. The polycarbonate specimens were saturated to the equilibrium gas concentration at 25 °C for CO 2 pressures of 1–6 MPa in 1‐MPa increments. Equilibrated specimens were heated in a glycerin bath until thermal equilibrium was reached, and a steady foam structure was attained. Glycerin bath temperatures of 30–150 °C in 10 °C increments were examined. Using knowledge of gas solubility, the equation of state for CO 2 , the effective glass‐transition temperature as a function of gas concentration, and a model for mass balance within a solid‐state foam, we demonstrate that foam growth terminates when sufficient gas is driven from the polycarbonate matrix into the foam cells. The foam cell walls freeze at the elevated bath temperature because of gas transport from the polycarbonate matrix and the associated rise in the polymer glass‐transition temperature to that of the heated bath. © 2001 John Wiley &amp; Sons, Inc. J Polym Sci B: Polym Phys 39: 868–880, 2001
Effects of caffeine on mating frequency and pre-copulation and copulation durations in Drosophila prosaltans. (1995)

Parameters of sexual behaviour were studied in Drosophila prosaltans treated with 2,500 micrograms/ml of caffeine per 1 ml of banana culture medium. The mating frequency and copulation duration were greater in control than in treated flies, while the pre-copulation duration was greater in treated flies than in controls. Statistical analysis showed that for the pre-copulation duration the difference was significant.
Phase III Trial Assessing Bevacizumab in Stages II and III Carcinoma of the Colon: Results of NSABP Protocol C-08 (2010)

Bevacizumab for 1 year with mFOLFOX6 does not significantly prolong DFS in stages II and III colon cancer. However, a significant but transient effect during bevacizumab exposure was observed in the experimental arm. We postulate that this observation reflects a biologic effect during bevacizumab exposure. Given the lack of improvement in DFS, the use of bevacizumab cannot be recommended for use in the adjuvant treatment of patients with colon cancer.
Serum Calcium and Magnesium Levels in Chronic Schizophrenics (1983)

Serum calcium and magnesium levels were studied during neuroleptic treatment in a group of 29 chronic schizophrenic inpatients who had previously remained drug free for at least 4 weeks. The drug-free values of both electrolytes were not significantly different between patients and controls. In three patients who developed catatonic stupor during the drug-free period, calcium was significantly increased at the onset of the catatonic manifestations. Both electrolytes were significantly decreased in the whole group during treatment; the magnitude of the decrease was independent of the neuroleptic used. No correlation was found between the observed increase in prolactin and calcium changes. Patients who remained free of extra-pyramidal symptoms had a higher mean drug-free magnesium to calcium ratio compared to those who developed such symptoms. Our study provides evidence for an interconnection between serum electrolyte changes and neuroleptic drug action.
The concept of Fermi level pinning at semiconductor/liquid junctions. Consequences for energy conversion efficiency and selection of useful solution redox couples in solar devices (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe concept of Fermi level pinning at semiconductor/liquid junctions. Consequences for energy conversion efficiency and selection of useful solution redox couples in solar devicesAllen J. Bard, Andrew B. Bocarsly, Fu Ren F. Fan, Erick G. Walton, and Mark S. WrightonCite this: J. Am. Chem. Soc. 1980, 102, 11, 3671–3677Publication Date (Print):May 1, 1980Publication History Published online1 May 2002Published inissue 1 May 1980https://pubs.acs.org/doi/10.1021/ja00531a001https://doi.org/10.1021/ja00531a001research-articleACS PublicationsRequest reuse permissionsArticle Views6230Altmetric-Citations432LEARN 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