gebhart/patrepeval huggingface dataset:
Recognition of cell‐wall peptide ligands by vancomycin group antibiotics: Studies using ion spray mass spectrometry (1995)

Abstract Non‐covalent binding of antibiotics to their target ligands represents a form of molecular recognition which is of considerable contemporary interest in bioorganic and bioanalytical chemistry. The vancomycin antibiotics, including vancomycin and ristocetin, are a family of complex glycopeptides which bind specifically to the C ‐terminal sequence X‐D‐Ala‐D‐Ala, where × is L ‐lysine, L ‐diaminopimelic acid, L ‐alanine or L ‐homoserine. It is shown that non‐covalent complexation of vancomycin and ristocetin with peptide ligands in solution, a key molecular recognition phenomenon in antibacterial chemotherapy, can be detected and analyzed in the gas phase by ionspray mass spectrometry. Using N α , N ϵ ‐diacetyl‐ L ‐Lys‐D‐Ala‐D‐Ala (Ac 2 KAA) as a representative ligand, it is further demonstrated that correlations of relative ion abundance with ligand concentrations in solution afford a direct method for measuring the binding constants of vancomycin and ristocetin complexes with target peptide sequences in bacterial cell wall. Results for ristocetin‐Ac 2 KAA ( K a = 6.25 × 10 5 l mol −1 ) and vancomycin‐Ac 2 KAA ( K a = 7.33 × 10 5 l mol −1 , are in reasonable agreement with previously values [ K a = 5.9 × 10 5 ] and 1.5 × 10 6 l mol −1 , respectively).
Treatment Trial of Oxiracetam in Alzheimer's Disease (1992)

Twenty-four carefully assessed patients with probable Alzheimer's disease were enrolled in a double-blind, placebo-controlled treatment study of oxiracetam, a nootropic agent reported to improve memory performance in patients with dementia. A broad battery of neuropsychological tests failed to reveal any improvement in the treated group or in any treated patient when individual test scores were analyzed. These findings indicate that oxiracetam is ineffective in reducing cognitive impairment due to Alzheimer's disease.
Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators (2009)

Adenosine 5'-triphosphate (ATP) is the major energy currency of cells and is involved in many cellular processes. However, there is no method for real-time monitoring of ATP levels inside individual living cells. To visualize ATP levels, we generated a series of fluorescence resonance energy transfer (FRET)-based indicators for ATP that were composed of the epsilon subunit of the bacterial F(o)F(1)-ATP synthase sandwiched by the cyan- and yellow-fluorescent proteins. The indicators, named ATeams, had apparent dissociation constants for ATP ranging from 7.4 muM to 3.3 mM. By targeting ATeams to different subcellular compartments, we unexpectedly found that ATP levels in the mitochondrial matrix of HeLa cells are significantly lower than those of cytoplasm and nucleus. We also succeeded in measuring changes in the ATP level inside single HeLa cells after treatment with inhibitors of glycolysis and/or oxidative phosphorylation, revealing that glycolysis is the major ATP-generating pathway of the cells grown in glucose-rich medium. This was also confirmed by an experiment using oligomycin A, an inhibitor of F(o)F(1)-ATP synthase. In addition, it was demonstrated that HeLa cells change ATP-generating pathway in response to changes of nutrition in the environment.
In vivo and in vitro immunological cross‐reactions between basic encephalitogen and synthetic basic polypeptides capable of suppressing experimental allergic encephalomyelitis (1973)

Abstract A significant extent of immunological cross‐reactivity has been demonstrated between the basic encephalitogenic protein of bovine origin and several synthetic amino acid copolymers which have suppressive effect on experimental allergic encephalomyelitis (EAE). This cross‐reactivity has been conclusively established on the cellular level, both in vivo by means of delayed hypersensitivity skin tests and in vitro using transformation of sensitized lymphocytes, as measured by incorporation of radioactive thymidine. The in vitro experiments have been conducted with lymph node cells from guinea pigs of both random bred and inbred strains, and on spleen and lymph node cells from rabbits. Definite cross‐reactivity was observed between the basic encephalitogen and all the synthetic copolymers which were previously shown effective in suppression of EAE, whereas ineffective copolymers or unrelated proteins did not show any cross‐reactivity. In the case of strain 2 guinea pigs and rabbit lymph node cells the cross‐reactivity in vitro was manifested by direct cross‐stimulation of the lymphocytes, whereas in random‐bred or strain 13 guinea pigs and rabbit spleen cells, the cross‐reaction was detected only by means of specific inhibition of the homologous stimulation by the heterologous antigen. A limited extent of cross‐reactivity was observed on the humoral level as well; antibodies provoked in guinea pigs against the synthetic copolymer Cop 1 cross‐reacted in the passive cutaneous anaphylaxis assay with the bovine basic encephalitogen.
Combining high‐amylose and waxy starch mutations in barley (2001)

Abstract Inbred lines, from a cross between barleys carrying the waxy and high‐amylose genes respectively, were characterised by the presence of both, either or neither of the genes and grown under field conditions. Starch granule proteins were separated by SDS‐PAGE and lines carrying the waxy gene, with or without the high‐amylose gene, had greatly reduced intensities of the 60 kDa band associated with granule‐bound starch synthase. One representative sample of each starch type was also grown under two controlled environment (CE) regimes. Starch properties were assessed on field‐ and CE‐grown samples of these genotypes and large differences were observed among starch types. Growth conditions generally had comparatively little effect on the starch properties measured. The waxy and high‐amylose genes appeared to have additive effects, both in reducing modal granule size and in increasing gelatinisation temperature significantly above that observed when only one of the genes was present. The genotype with both mutations produced a starch with phosphorus content and blue value, after removal of lipid, slightly higher than those of the waxy type and with an RVA profile similar to that of the wild type, but with lower peak and final viscosities. © 2001 Society of Chemical Industry
Handling audio and video streams in a distributed environment (1993)

Handling audio and video in a digital environment requires timely delivery of data. This paper describes the principles adopted in the design of the Pandora networked multi-media system. They attempt to give the user the best possible service while dealing with error and overload conditions.Pandora uses a sub-system to handle the multi-media peripherals. It uses transputers and associated Occam code to implement the time critical functions. Stream implementation is based on self-contained segments of data containing information for delivery, synchronisation and error recovery. Decoupling buffers are used to allow concurrent operation of multiple processing elements. Clawback buffers are used to resynchronise streams at their destinations with minimum latency.The system has proved robust in normal use, under overload, and in the presence of errors. It has been in use for a number of years.The principles involved in this design are now being used in the development of two complementary systems. One approach explodes Pandora by having the camera, microphone, speaker and display as independent units linked only by the LAN. The other approach integrates these devices as peripheral cards in a powerful workstation.
In Vitroandin VivoCytotoxic Activities of Recombinant Immunotoxin 8H9(Fv)-PE38 against Breast Cancer, Osteosarcoma, and Neuroblastoma (2004)

The 8H9 monoclonal antibody (MAb) is highly reactive with a cell surface glycoprotein expressed on human breast cancers, childhood sarcomas, and neuroblastomas but is not reactive with the cell surface of normal human tissues. This specific reactivity suggests that MAb 8H9 may be useful for targeted cancer therapy. To explore this possibility, we generated two recombinant immunotoxins (ITs) using the single-chain Fv (scFv) of MAb 8H9. Initially the 8H9(scFv) cDNA was fused to a DNA encoding a 38-kDa truncated form of Pseudomonas exotoxin (PE38) to generate the IT 8H9(scFv)-PE38. The fusion gene was expressed in Escherichia coli, and the IT was purified to near homogeneity from inclusion bodies. The purified IT showed specific cytotoxicity on nine different cancer cell lines derived from breast cancer, osteosarcoma, and neuroblastomas, known to react with MAb 8H9. The cytotoxic activity was inhibited by MAb 8H9, showing the cytotoxic activity is specific. The antitumor activity of 8H9(scFv)-PE38 was evaluated in severe combined immunodeficient mice bearing MCF-7 breast cancers or OHS-M1 osteosarcomas. The IT showed a specific dose-dependent antitumor activity at 0.075 and 0.15 mg/kg. Next, a more stable disulfide-linked IT, 8H9(dsFv)-PE38, was constructed. It was produced in high yield (16%) and showed cytotoxic and antitumor activities similar to those of 8H9(scFv)-PE38. 8H9(dsFv)-PE38 was given to two cynomolgus monkeys at doses of 0.1 and 0.2 mg/kg i.v. QOD x 3 and was well tolerated. This shows that a dose that causes significant tumor regressions in mice is well tolerated by monkeys. These results make 8H9(dsFv)-PE38 a candidate for further development as a therapeutic agent for breast cancers, osteosarcomas, and neuroblastomas.
The Alzheimer's disease assessment scale (1997)

The cognitive subscale of the Alzheimer's Disease Assessment Scale (ADAS-Cog) is used as an efficacy measure in clinical drug trials of Alzheimer's disease (AD). We used data from 1,648 AD participants in two identical 26-week multicenter drug trials to examine the distribution of baseline ADAS-Cog scores in relation to selected demographic and clinical variables, Mini-Mental State Exam (MMSE), Global Deterioration Scale (GDS), and Geriatric Evaluation by Relative's Rating Instrument (GERRI) scores. At baseline, the mean (+/-SD) MMSE score was 18 +/- 4, the ADAS-Cog score was 28 +/- 11, and most subjects were in GDS stage 4 or 5. The ADAS-Cog score was statistically significantly correlated with MMSE (R = -0.76, p < 0.0001) and GERRI (R = 0.40, p < 0.0001) total scores. Correlations among the ADAS-Cog items ranged from 0.19 to 0.59 and all were statistically significant (p < 0.0001). In a multiple regression model, younger age, male gender, older age at onset of dementia, use of concurrent estrogen, and use of concurrent anti-inflammatory agents were statistically significantly associated with superior cognitive performance. We also present data on the distribution of ADAS-Cog scores in relation to subjects' age, level of education, MMSE score, and GDS stage. Because age, MMSE score, and GDS stage (and not the ADAS-Cog) are commonly used to select subjects for AD clinical trials, our data should improve the ability of sponsors to predict ADAS-Cog scores of the subjects in their trials on the basis of the inclusion criteria used. Our data also suggest that age, gender, age at onset of dementia, level of education, and use of estrogen (in women) or anti-inflammatory drugs are related to cognitive abilities in AD. Further studies are needed to assess how and when cognitive differences related to these variables arise.
TRNA2Gln Su+2 mutants that increase amber suppression (1981)

We selected mutants of lambda pSu+2 which had an increased ability to suppress on Escherichia coli trp B9601 amber mutation on translationally stringent rpsL594 streptomycin-resistant ribosomes. tRNA2Gin Su+2 molecules produced from eight independent mutants were purified, and their ribonucleic acid sequences were determined. Two types of mutations were mapped to the tRNA2Gin Su+2(glnV) gene by this method. Both altered the pseudouridine at position 37 of the tRNA anticodon loop. Seven of the isolates were transitions (pseudouridine to cytosine), and one was a transversion (pseudouridine to adenine). These mutations resulted in Su+ transfer ribonucleic acid molecules that exhibited higher transmission coefficients than their parent Su+2 transfer ribonucleic acids. As judged by their suppressor spectra on T4 amber mutants, which were almost identical to that of Su+2, the two mutant Su+ transfer ribonucleic acids inserted glutamine at amber sites.
Nuclease-Resistant External Guide Sequence-Induced Cleavage of Target RNA by Human Ribonuclease P (1998)

External guide sequences (EGSs) are short oligoribonucleotides, which are designed to bind to a given RNA target and form a precursor tRNA-like complex. This complex can be recognized by ribonuclease P (RNase P), resulting in specific cleavage of the RNA target. To explore the potential of this class of compounds as therapeutic agents and valuable tools for gene function analysis, various chemical modifications were introduced into an all-RNA EGS molecule to confer nuclease resistance. In particular, 2'-O-methyl substitutions were incorporated into the entire sequence (i.e., A-stem, D-stem, and T-stem) except the T-loop region without loss of cleavage-inducing activity. Replacement of rU (position 54) and rC (position 56) in the T-loop with their 2'-O-methyl counterparts caused pronounced decrease in activity. Moreover, phosphorothioate backbone modification of the T-loop did not provide sufficient protection against endonucleolytic attack at the ribopyrimidine residues. Systematic modification of the T-loop with a variety of modified nucleosides and the addition of a 3'-3' inverted T at the 3'-end have generated several lead EGS prototypes, which not only exhibit wild-type activity in inducing RNase P-mediated target cleavage as compared with the all-RNA control but also remain intact in human serum for more than 24 hours. These results should provide useful insights into the design and development of oligonucleotide-based EGSs as potential regulators of gene expression.
Antibody-directed cytotoxic agents: use of monoclonal antibody to direct the action of toxin A chains to colorectal carcinoma cells. (1980)

We have constructed cell-specific cytotoxic agens by covalently coupling the A chain from diphtheria toxin or ricin toxin to monoclonal antibody directed against a colorectal carcinoma tumor-associated antigen. Antibody 1083-17-1A was modified by attachment of 3-(2-pyridyldithio)propionyl or cystaminyl groups and then treated with reduced A chain to give disulfide-linked conjugates that retained the original binding specificity of the antibody moiety. the conjugates showed cytotoxic activity for colorectal carcinoma cells in culture, but were not toxic in the same concentration range for a variety of cell lines that lacked the antigen. Under defined conditions virtually 100% of antigen-bearing cultured cells were killed, whereas cells that lacked the antigen were not affected. Conjugates containing toxin A chains coupled to monoclonal antibodies may be useful in studying functions of various cell surface components and, possibly, as tumor-specific therapeutic agents.
Aerosolized Bexarotene Inhibits Lung Tumorigenesis without Increasing Plasma Triglyceride and Cholesterol Levels in Mice (2010)

Prior studies have shown the retinoid X receptor (RXR) agonist bexarotene has preventive efficacy in rodent models of mammary and lung tumorigenesis albeit causing hypertriglyceridemia and hypercholesterolemia. We reasoned that bexarotene delivered by inhalation may provide sufficient dose directly to the respiratory tract to achieve efficacy while avoiding these side effects. In this study, the chemopreventive activity of aerosolized bexarotene was investigated in the benzo(a)pyrene [B(a)P]-induced mouse lung tumor model as assessed by tumor multiplicity and tumor load. Aerosolized bexarotene significantly decreased tumor multiplicity and tumor load by 43% and 74%, respectively. Our data showed that bexarotene can both inhibit proliferation and promote apoptosis in vivo. Our data also show that aerosolized bexarotene did not increase plasma total cholesterol and triglyceride level compared with diet group. These results indicate that aerosolization may be a safe and effective route of administering bexarotene for chemoprevention of lung cancer.
Enhanced Transdermal Delivery of Sex Hormones in Swine with a Novel Topical Aerosol (1998)

This study investigated the enhanced transdermal delivery of testosterone (Tes) and estradiol (E2) in swine in vivo with novel metered-dose topical aerosols containing the penetration enhancer padimate O (PadO) and predicted the dose deliverable in humans from the calculated drug flux across the skin. Weanling swine were catheterized and castrated under general anaesthesia and used as a conscious hypogonadal model. Tes and E2 (with and without PadO) were applied once, and venous blood samples were taken over 24 h. Tes and E2 plasma levels were determined by radioimmunoassay. After daily topical dosing of Tes for 6 days, the plasma Tes levels were determined and the transdermal flux was calculated by correcting the pseudo steady-state plasma concentration versus time profile with the clearance of an iv dose within the same swine. After a single application of the E2 aerosol over 30 cm2, or the Tes aerosol over 180 cm2, the mean AUC0-24 h when PadO was included in the spray was 14.1- and 2.0-fold greater than control, respectively (p < 0.03). After the sixth application of the Tes spray with PadO, the mean flux (+/-SE, n = 4) across swine skin in vivo was 2.12 +/- 0.35 microg/cm2.h, which gave a predicted flux in humans of 0.95 microg/cm2.h. From these data the expected plasma levels of Tes in hypogonadal men would compare well with the normal diurnal Tes profile in healthy men. These novel topical aerosols are capable of enhanced transdermal delivery of sex hormones in vivo, and they have the potential to deliver clinically relevant doses to humans.
Signal detection by complex spatial filtering (1964)

In the past, spatial filtering in coherent optical systems has been limited by the inability to realize practically a general complex filter. This paper describes a technique for realizing such a filter, and gives an application of spatial filtering to the problem of detecting isolated signals in a variety of noise backgrounds. The experimental results obtained to date indicate that this technique provides an excellent two-dimensional filtering capability that will play a key role in such problems as shape recognition and signal detection.
Efficient modification of CCR5 in primary human hematopoietic cells using a megaTAL nuclease and AAV donor template (2015)

Genetic mutations or engineered nucleases that disrupt the HIV co-receptor CCR5 block HIV infection of CD4(+) T cells. These findings have motivated the engineering of CCR5-specific nucleases for application as HIV therapies. The efficacy of this approach relies on efficient biallelic disruption of CCR5, and the ability to efficiently target sequences that confer HIV resistance to the CCR5 locus has the potential to further improve clinical outcomes. We used RNA-based nuclease expression paired with adeno-associated virus (AAV)-mediated delivery of a CCR5-targeting donor template to achieve highly efficient targeted recombination in primary human T cells. This method consistently achieved 8 to 60% rates of homology-directed recombination into the CCR5 locus in T cells, with over 80% of cells modified with an MND-GFP expression cassette exhibiting biallelic modification. MND-GFP-modified T cells maintained a diverse repertoire and engrafted in immune-deficient mice as efficiently as unmodified cells. Using this method, we integrated sequences coding chimeric antigen receptors (CARs) into the CCR5 locus, and the resulting targeted CAR T cells exhibited antitumor or anti-HIV activity. Alternatively, we introduced the C46 HIV fusion inhibitor, generating T cell populations with high rates of biallelic CCR5 disruption paired with potential protection from HIV with CXCR4 co-receptor tropism. Finally, this protocol was applied to adult human mobilized CD34(+) cells, resulting in 15 to 20% homologous gene targeting. Our results demonstrate that high-efficiency targeted integration is feasible in primary human hematopoietic cells and highlight the potential of gene editing to engineer T cell products with myriad functional properties.
O-Specific Side-Chain Toxin-Protein Conjugates as Parenteral Vaccines for the Prevention of Shigellosis and Related Diseases (1991)

Only indirect evidence has been cited to document that lipopolysaccharide-mediated virulence at the bacterial level and serum antibodies to the O-specific side chain of the lipopolysaccharide molecule may prevent shigellosis. Our proposed use of the B subunit of Shiga toxin as a carrier protein is based upon evidence (even more indirect) that serum antitoxin may reduce the severity of dysentery and diarrhea. Because animal models of disease may provide information inapplicable to the prediction of vaccine-induced protective immunity, we suggest that clinical trials in the population at risk should be started after successful completion of the safety and immunogenicity phases of vaccine development in laboratory animals and in the target population. Clinical studies of shigella vaccines are difficult because of the many causes of dysentery in a population with a high rate of intestinal disease.
Novel LQT-3 Mutation Affects Na+Channel Activity Through Interactions Between α- and β1-Subunits (1998)

The congenital long-QT syndrome (LQT), an inherited cardiac arrhythmia characterized in part by prolonged ventricular repolarization, has been linked to 5 loci, 4 of which have been shown to harbor genes that encode ion channels. Previously studied LQT-3 mutations of SCN5A (or hH1), the gene that encodes the human Na+ channel alpha-subunit, have been shown to encode voltage-gated Na+ channels that reopen during prolonged depolarization and hence directly contribute to the disease phenotype: delayed repolarization. Here, we report the functional consequences of a novel SCN5A mutation discovered in an extended LQT family. The mutation, a single A-->G base substitution at nucleotide 5519 of the SCN5A cDNA, is expected to cause a nonconservative change from an aspartate to a glycine at position 1790 (D1790G) of the SCN5A gene product. We investigated ion channel activity in human embryonic kidney (HEK 293) cells transiently transfected with wild-type (hH1) or mutant (D1790G) cDNA alone or in combination with cDNA encoding the human Na+ channel beta1-subunit (hbeta1) using whole-cell patch-clamp procedures. Heteromeric channels formed by coexpression of alpha- and beta1-subunits are affected: steady-state inactivation is shifted by -16 mV, but there is no D1790G-induced sustained inward current. This effect is independent of the beta1-subunit isoform. We find no significant effect of D1790G on the biophysical properties of monomeric alpha- (hH1) channels. We conclude that the effects of the novel LQT-3 mutation on inactivation of heteromeric channels are due to D1790G-induced changes in alpha- and beta1-interactions.
A client/server architecture for word sense disambiguation (2000)

This paper presents a robust client/server implementation of a word sense disambiguator for English. This system associates a word with its meaning in a given context using dictionaries as tagged corpora in order to extract semantic disambiguation rules. Semantic rules are used as input of a semantic application program which encodes a linguistic strategy in order to select the best disambiguation rule for the word to be disambiguated. The semantic disambiguation rule application program is part of the client/server architecture enabling the processing of large corpora.