gebhart/patrepeval huggingface dataset:
De novo amplification within a "silent" human cholinesterase gene in a family subjected to prolonged exposure to organophosphorous insecticides. (1989)

A 100-fold DNA amplification in the CHE gene, coding for serum butyrylcholinesterase (BtChoEase), was found in a farmer expressing the "silent" CHE phenotype. Individuals homozygous for this gene display a defective serum BtChoEase and are particularly vulnerable to poisoning by agricultural organophosphorous insecticides, to which all members of this family had long been exposed. DNA blot hybridization with regional BtChoEase cDNA probes suggested that the amplification was most intense in regions encoding central sequences within BtChoEase cDNA, whereas distal sequences were amplified to a much lower extent. This is in agreement with the "onion skin" model, based on amplification of genes in cultured cells and primary tumors. The amplification was absent in the grandparents but present at the same extent in one of their sons and in a grandson, with similar DNA blot hybridization patterns. In situ hybridization experiments localized the amplified sequences to the long arm of chromosome 3, close to the site where we previously mapped the CHE gene. Altogether, these observations suggest that the initial amplification event occurred early in embryogenesis, spermatogenesis, or oogenesis, where the CHE gene is intensely active and where cholinergic functioning was indicated to be physiologically necessary. Our findings demonstrate a de novo amplification in apparently healthy individuals within an autosomal gene producing a target protein to an inhibitor. Its occurrence in two generations from a family under prolonged exposure to parathion indicates that organophosphorous poisons may be implicated in previously unforeseen long-term ecological effects.
Direct detection of point mutations by mismatch analysis: application to haemophilia B (1989)

Rapid detection of point mutations in genomic DNA has been achieved by chemical mismatch analysis of heteroduplexes formed between amplified wild-type and target sequences in the human factor IX gene. Amplification and mismatch detection (AMD) analysis of DNA from relatives of haemophilia B patients permitted carrier diagnosis by direct identification of the presence or absence of the mutation in all cases, thus eliminating the need for the informative segregation of polymorphic markers. This extends diagnostic capability to virtually all haemophilia B families. AMD analysis permits detection of all sequence variations in genomic DNA and is therefore applicable to direct diagnosis of X-linked and autosomal diseases and for identification of new polymorphisms for genetic mapping.
Phase II trials of conjugates of <em>S.typhi</em> Vi and of <em>S.paratyphi</em> A O-Speciftc polysaccharide (O-SP) conjugates in Dong Thap province, Vietnam (1998)

\4 coniugates, prepared with SPDP as a linket elicited higher levels of total serum anti-Vi than Vi alone in recruits in the U.S.
Regional pattern of hippocampus and corpus callosum atrophy in Alzheimer's disease in relation to dementia severity: evidence for early neocortical degeneration (2002)

We used volumetric MRI and analysis of areas under receiver operating characteristic (ROC) curves to directly compare the extent of hippocampus-amygdala formation (HAF) and corpus callosum atrophy in patients with Alzheimer's disease (AD) in different clinical stages of dementia. Based on neuropathological studies, we hypothesized that HAF atrophy, representing allocortical neuronal degeneration, would precede atrophy of corpus callosum, representing loss of neocortical association neurons, in early AD. HAF and corpus callosum sizes were significantly reduced in 27 AD patients (37% and 16%, respectively) compared to 28 healthy controls. In mildly- and moderately-demented AD patients, the ROC derived index of atrophy was greater for HAF volume than for total corpus callosum area. The index of atrophy of posterior corpus callosum was not significantly different from HAF at mild, moderate or severe stages of dementia. In conclusion, these findings suggest a characteristic regional pattern of allocortical and neocortical neurodegeneraton in AD. Our data indicate that neuronal loss in parietotemporal cortex (represented by atrophy of corpus callosum splenium) may occur simultaneously with allocortical neurodegeneration in mild AD. Moreover, ROC analysis may provide a statistical framework to determine atrophy patterns of different brain structures in neurodegenerative diseases in vivo.
Characterization of Hereditary Nonpolyposis Colorectal Cancer Families From a Population-Based Series of Cases (2000)

On the basis of our data, we believe that the prevalence of HNPCC in the general population is likely to be closer to 1% than to 5%. Furthermore, our study suggests that some previously reported characteristics of HNPCC, such as the proximal location of tumors in the syndrome, may not always hold true in a population-based sample.
Advances in Coupled Geomechanical and Reservoir Modeling With Applications to Reservoir Compaction (1999)

Abstract Coupled geomechanical and reservoir modeling is becoming feasible on a full field scale. This paper describes the advances of the coupled model described previously1, its extensions for modeling compaction and the application of the model in full field studies. The advances of the theory and numerical implementation since the original work1 make it practical to perform full field coupled studies with complex, realistic description of the geomechanical behaviour of the reservoir and shales, which allows prediction of stress changes, reservoir compaction and surface subsidence. These capabilities are demonstrated in field examples that analyze and predict classical pressure induced compaction in a gas field as well as thermally induced compaction in a heavy oil field. In both cases the methodology of interpreting the geomechanical laboratory and field data and its integration in the coupled modeling process was the key to obtaining a realistic predictive tool. The examples demonstrate that the technology is maturing to the point that conventional studies can be converted to coupled modeling on a fairly routine basis.
Sulfation and sulfotransferases 1: Sulfotransferase molecular biology: cDNAs and genes. (1997)

Sulfotransferase (ST) enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These reactions result in enhanced renal excretion of the sulfate-conjugated reaction products, but they can also lead to the formation of "bioactivated" metabolites. ST enzymes are members of an emerging gene superfamily that presently includes phenol ST (PST), hydroxysteroid ST (HSST), and, in plants, flavonol ST (FST) "families," members of which share at least 45% amino acid sequence identity. These families can be further subdivided into "subfamilies" that are at least 60% identical in amino acid sequence. For example, the PST family includes both PST and estrogen ST (EST) subfamilies. Amino acid sequence motifs exist within ST enzymes that are conserved throughout phylogeny. These signature sequences may be involved in the binding of 3'-phosphoadenosine-5 '-phosphosulfate, the cosubstrate for the sulfonation reaction. There are presently five known human cytosolic ST enzymes: an EST, an HSST, and three PSTs. cDNAs and genes for all of these enzymes have been cloned, and chromosomal localizations have been reported for all five genes. Genes for these human enzymes, as well as those of other mammalian cytosolic ST enzymes that have been cloned, show a high degree of structural homology, with conservation of the locations of most intron/exon splice junctions. Human ST enzyme expression varies among individuals. Functionally significant genetic polymorphisms for ST enzymes in humans have been reported, and other molecular genetic mechanisms that might be involved in the regulation of the expression of these enzymes are being explored. Knowledge of the molecular biology of cytosolic ST enzymes, when placed within a context provided by decades of biochemical research, promises to significantly enhance our understanding of the regulation of the sulfate conjugation of hormones, neurotransmitters, and drugs.
Antisense targeting of 3′ end elements involved inDUX4mRNA processing is an efficient therapeutic strategy for facioscapulohumeral dystrophy: a new gene-silencing approach (2016)

Defects in mRNA 3'end formation have been described to alter transcription termination, transport of the mRNA from the nucleus to the cytoplasm, stability of the mRNA and translation efficiency. Therefore, inhibition of polyadenylation may lead to gene silencing. Here, we choose facioscapulohumeral dystrophy (FSHD) as a model to determine whether or not targeting key 3' end elements involved in mRNA processing using antisense oligonucleotide drugs can be used as a strategy for gene silencing within a potentially therapeutic context. FSHD is a gain-of-function disease characterized by the aberrant expression of the Double homeobox 4 (DUX4) transcription factor leading to altered pathogenic deregulation of multiple genes in muscles. Here, we demonstrate that targeting either the mRNA polyadenylation signal and/or cleavage site is an efficient strategy to down-regulate DUX4 expression and to decrease the abnormally high-pathological expression of genes downstream of DUX4. We conclude that targeting key functional 3' end elements involved in pre-mRNA to mRNA maturation with antisense drugs can lead to efficient gene silencing and is thus a potentially effective therapeutic strategy for at least FSHD. Moreover, polyadenylation is a crucial step in the maturation of almost all eukaryotic mRNAs, and thus all mRNAs are virtually eligible for this antisense-mediated knockdown strategy.
RNA replication by a respiratory syncytial virus RNA analog does not obey the rule of six and retains a nonviral trinucleotide extension at the leader end (1996)

Genome analogs ("minigenomes") of Sendai and measles viruses replicate efficiently only if their nucleotide length is an even multiple of six, a requirement called the rule of six (P. Calain and L. Roux, J. Virol. 67:4822-4830, 1993; M. S. Sidhu, J. Chan, K. Kaelin, P. Spielhofer, F. Radecke, H. Schneider, M. Masurekar, P. C. Dowling, M. A. Billeter, and S. A. Udem, Virology 208:800-807, 1995). The existence of a comparable requirement was tested for respiratory syncytial virus (RSV), which also is a member of family Paramyxoviridae and whose natural genome length also is a multiple of six. An internally truncated analog of RSV positive-sense replicative intermediate RNA (antigenome) bearing the chloramphenicol acetyltransferase gene as a reporter was synthesized from cDNA in vitro. This RNA was transfected into cells which were infected with RSV as a helper. Miniantigenomic RNA was indistinguishable from previously studied negative-sense minigenome RNA in its ability to participate in transcription, RNA replication, and incorporation into transmissible particles. Sixteen miniantigenomes which were of slightly different lengths and which in aggregate represented multiples of a wide range of integers including 1 to 15 were constructed. During transfection and two serial passages, the various miniantigenomes were essentially indistinguishable with regard to the efficiency of transcription, RNA replication, and packaging into transmissible particles. Progeny minigenomes of six different mutants were recovered postpassage, copied into cDNA, cloned, and sequenced completely. The length of each of these RNAs was found to have remained unchanged during replication and passage. Thus, RSV transcription and replication appear to lack the requirement that the template length be an even multiple of an integer such as six, which for Sendai and measles viruses is obligatory for nucleocapsid function. Each of the in vitro-synthesized miniantigenomes used in transfection contained a nonviral extension of three nucleotides, GGG, on the 5' (leader) end contributed by the T7 promoter. The termini of the recovered minigenomes were examined for five mutants by RNA circularization followed by cDNA synthesis, amplification, cloning, and sequencing. Unexpectedly, each recovered minigenome contained the complement of this nonviral extension on the 3' (leader) end, showing that it had been faithfully copied and maintained during RNA replication and passage. The nonviral trinucleotide did not appear to affect the activity of the template.
Antitumor activity of esorubicin in human tumor clonogenic assay with comparisons to doxorubicin. (1984)

The new anthracycline analog, esorubicin (4'deoxy-doxorubicin, ESO), was tested against fresh biopsies of human solid tumors in vitro in clonogenic assay and the results were contrasted to those obtained with doxorubicin (DOX). ESO appeared to be significantly more potent on a weight basis than DOX in these studies, and exhibited a spectrum of antitumor activity in vitro that was in general qualitatively similar to that observed with DOX. In vitro antitumor activity was observed in a wide variety of human cancers including anthracycline-sensitive tumor types. ESO has previously been reported to have decreased cardiac toxicity in preclinical models as compared to DOX. Comparative testing of these anthracyclines on granulocyte-macrophage colony-forming units (GM-CFUs) and tumor colony forming units (TCFUs) indicated that the in vitro GM-CFU assay is more sensitive to these myelosuppressive drugs than are TCFUs, and underscores the need for in vivo studies to determine normal tissue toxicity and the therapeutic index of a drug. Early results of phase I studies suggest that with respect to myelosuppression, the maximally tolerated dose of ESO will be about half that of DOX. The increased in vitro antitumor potency observed for ESO and a spectrum of activity (even at one half the dose of DOX) supports the broad testing of ESO in the clinic to determine whether it will prove to be a more effective and less toxic anthracycline.
Identification of Bacteria by Polymerase Chain Reaction Followed by Liquid Chromatography−Mass Spectrometry (2005)

Bloodstream infections are an important cause of serious morbidity and mortality. Rapid detection and identification of specific pathogens from blood or other clinical specimens could improve the rational use of antimicrobial therapy in clinical medicine and have a great impact on the outcome of patients with systemic infections. Polymerase chain reaction using generic primers was used to amplify genomic DNA of different bacterial strains. The identification was accomplished by measuring the molecular masses of the PCR products using ion-pair reversed-phase high-performance liquid chromatography hyphenated to electrospray ionization mass spectrometry. DNA from 10 bacterial species was amplified by PCR, and the resulting amplification products were analyzed. In all cases, the measured molecular masses of the PCR products matched the theoretical value for the species-specific DNA sequence. However, three pairs of bacteria could not be distinguished since the theoretical difference in amplicon molecular mass was < 1.0 Da (different sequence, same base composition of amplicon). Determination of intra- and interday mass reproducibility resulted in relative standard deviations of 0.0030 and 0.018%, respectively. The limit of detection of the presented method was shown to be 0.5 genome equivalents/PCR. The specificity of the method in a human background was successfully tested by amplifying and analyzing 1000-10000 genome equivalents of Staphylococcus aureus spiked into human plasma.
Phosphoenolpyruvate-dependent maltose:phosphotransferase activity in Fusobacterium mortiferum ATCC 25557: specificity, inducibility, and product analysis (1994)

Phosphoenolypyruvate-dependent maltose:phosphotransferase activity was induced in cells of Fusobacterium mortiferum ATCC 25557 during growth on maltose. The disaccharide was rapidly metabolized by washed cells maintained under anaerobic conditions, but fermentation ceased immediately upon exposure of the cell suspension to air. Coincidentally, high levels of a phosphorylated derivative accumulated within the cells. Chemical and enzymatic analyses, in conjunction with data from 1H, 13C, and 31P nuclear magnetic resonance spectroscopy, established the structure of the purified compound as 6-O-phosphoryl-alpha-D-glucopyranosyl-(1-4)-D-glucose (maltose 6-phosphate). A method for the preparation of substrate amounts of this commercially unavailable disaccharide phosphate is described. Permeabilized cells of F. mortiferum catalyzed the phosphoenolpyruvate-dependent phosphorylation of maltose under aerobic conditions. However, the hydrolysis of maltose 6-phosphate (to glucose 6-phosphate and glucose) by permeabilized cells or cell-free preparations required either an anaerobic environment or addition of dithiothreitol to aerobic reaction mixtures. The first step in dissimilation of the phosphorylated disaccharide appears to be catalyzed by an oxygen-sensitive maltose 6-phosphate hydrolase. Cells of F. mortiferum, grown previously on maltose, fermented a variety of alpha-linked glucosides, including maltose, turanose, palatinose, maltitol, alpha-methylglucoside, trehalose, and isomaltose. Conversely, cells grown on the separate alpha-glucosides also metabolized maltose. For this anaerobic pathogen, we suggest that the maltose:phosphotransferase and maltose 6-phosphate hydrolase catalyze the phosphorylative translocation and cleavage not only of maltose but also of structurally analogous alpha-linked glucosides.
Plural Pronouns in Roman Plays by Shakespeare and Jonson (1991)

The paper shows that a group of Roman plays by Shakespeare and Jonson differ from a test set of other plays by the two authors in the use of plural pronouns and plural possessive adjectives. In most cases the frequency of individual plural pronoun forms is significantly higher in the Roman plays. The difference seems to reflect the Roman plays' characteristic choice of the group as its dramatic focus, in battle but also in political matters more generally Twenty-six plays, thirteen by each author, are in the study, five of them Roman plays Six plural pronoun variables are used. The comedies in the test set are strongly differentiated from the Roman plays, with generally differentiated from the roman plays, with generally markedly lower frequencies of the plural variables. The pattern for tragedies is more mixed, scores in Othello are low, but Macbeth is much more like the Roman plays on these measures, with dialogue reflecting a preoccupation with group action in war and political conspiracy.
Resistance of HIV-1 to multiple antiretroviral drugs in France (2003)

Background: Evaluating the proportion of patients with mutated drug-resistant HIV-1 strains is a major issue of current AIDS research and therapy. According to a recent study in the United States, nearly 80% of HIV-1-infected patients have virus strains that are resistant to at least one antiretroviral drug. The aim of this study was to assess the extent of multiple drug resistance among individuals followed for HIV-1 infection in France. Methods: We compiled data in a relational database for 3884 reverse transcriptase (2248 patients) and 3915 protease (2194 patients) sequences of plasma samples submitted for testing between January 1997 and March 2002 at the reference HIV AIDS hospitals located in Marseille (France). Results: Genotypic resistance to at least one nucleoside reverse transcriptase inhibitor (NRTI) was present in 78.3%, resistance to at least one non-nucleoside reverse transcriptase inhibitor (NNRTI) was present in 38.9%, and resistance to at least one protease inhibitor (PI) was present in 47.0% of plasma samples. The proportion of patients carrying a virus with multiple resistance to three categories of drugs (at least one NRTI plus at least one NNRTI plus at least one PI) peaked at 25.9% in 2000 and stabilized at 25.5% in March 2002. Conclusion: This study demonstrates the high prevalence of drug-resistant virus in a European cohort of patients currently under treatment for HIV-1 infection. New therapeutic strategies based on a more rational use of genotypic data should be worked out to prevent the development of resistance.
Imaging Sites of Receptor Dephosphorylation by PTP1B on the Surface of the Endoplasmic Reticulum (2002)

When bound by extracellular ligands, receptor tyrosine kinases (RTKs) on the cell surface transmit critical signals to the cell interior. Although signal termination is less well understood, protein tyrosine phosphatase-1B (PTP1B) is implicated in the dephosphorylation and inactivation of several RTKs. However, PTP1B resides on the cytoplasmic surface of the endoplasmic reticulum (ER), so how and when it accesses RTKs has been unclear. Using fluorescence resonance energy transfer (FRET) methods, we monitored interactions between the epidermal- and platelet-derived growth factor receptors and PTP1B. PTP1B-catalyzed dephosphorylation required endocytosis of the receptors and occurred at specific sites on the surface of the ER. Most of the RTKs activated at the cell surface showed interaction with PTP1B after internalization, establishing that RTK activation and inactivation are spatially and temporally partitioned within cells.
Transaction-Based Core Reliability (2020)

Modern microprocessor designs are becoming more vulnerable to transient faults leading to transient errors due to design trends mandating low supply voltage and reduced noise margins, shrinking feature sizes and increased transistor density for fast, low power circuits. Detecting and correcting transient errors in random logic in a processor core has become an important design goal and confronts design challenges such as input replication, error confinement and overheads minimization. Transactional Memory (TM) is a recent paradigm to improve the programmability and performance of parallel programs. TM has appeared in industry, providing hardware mechanisms for conflict detection and resolution, and checkpointing and rollback. In this paper, we leverage the features of Hardware TM (HTM) to provide processor cores with transient error detection and recovery at low hardware cost. We contribute to the current state of the art of dependable systems by proposing a novel microarchitecture.
Synthesis and GC-Eims Analyses of Optically Pure 3-Hydroxy-2-Azetidinones HavingN-Sulfonamide Drugs Side Chain (2000)

Abstract A series of new N-sulfonamides of substituted 3-hydroxy-2-azetidinones were prepared by the [2+2] cycloaddition of aldoximes, formed from the condensation of D-(R)-glyceraldehyde acetonide and the potent p-aminophenyl-N-substituted sulfonamides, with benzyloxyacetyl chloride followed by removal of the protecting groups. Obtaining both diastereoisomeric forms of β-lactams by resorting to kinetic resolution starting from racemic imino analogue is also described. The GC-EIMS, spectroscopic and analytical analyses for some of these derivatives are reported.
Making a hybrid microfluidic platform compatible for in situ imaging by vacuum-based techniques (2011)

A self-contained microfluidic-based device was designed and fabricated for in situ imaging of aqueous surfaces using vacuum techniques. The device is a hybrid between a microfluidic poly(dimethyl siloxane) block and external accessories, all portable on a small platform (10 × 8 cm2). The key feature is that a small aperture with a diameter of 2-3 μm is opened to the vacuum, which serves as a detection window for in situ imaging of aqueous surfaces. Vacuum compatibility and temperature drop due to water vaporization are the two most important challenges in this invention. Theoretical calculations and fabrication strategies are presented from multiple design aspects. In addition, results from the time-of-flight secondary ion mass spectrometry and scanning electron microscopy of aqueous surfaces are presented.