gebhart/patrepeval huggingface dataset:
Pharmacokinetics, metabolism, and excretion of linezolid following an oral dose of [(14)C]linezolid to healthy human subjects. (2001)

Linezolid (Zyvox), the first of a new class of antibiotics, the oxazolidinones, is approved for treatment of Gram-positive bacterial infections, including resistant strains. The disposition of linezolid in human volunteers was determined, after a 500-mg (100-microCi) oral dose of [(14)C]linezolid. Radioactive linezolid was administered as a single dose, or at steady-state on day 4 of a 10-day, 500-mg b.i.d. regimen of unlabeled linezolid (n = 4/sex/regimen). Mean recovery of radioactivity in excreta was 93.8 +/- 1.1% (range 91.2-95.2%, n = 15), of which 83.9 +/- 3.3% (range 76.7-88.4%) was in urine and 9.9 +/- 3.4% (range 5.3-16.9%) was in feces. There was no major difference in rate or route of excretion of radioactivity by dose regimen. Linezolid was excreted primarily intact, and as two inactive, morpholine ring-oxidized metabolites, PNU-142586 and PNU-142300. Other minor metabolites were characterized by high-performance liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry and (19)F NMR spectroscopy. After the single radioactive dose, linezolid was the major circulating drug-related material accounting for about 78% (male) and 93% (female) of the radioactivity area under the curve (AUC). PNU-142586 (T(max) of 3-5 h) accounted for about 26% (male) and 9% (female) of the radioactivity AUC. PNU-142300 (T(max) of 2-3 h) accounted for about 7% (male) and 4% (female) of the radioactivity AUC. Overall, mean linezolid and PNU-142586 exposures at steady-state were similar across sex. In conclusion, linezolid circulates in plasma mainly as parent drug. Linezolid and two major, inactive metabolites account for the major portion of linezolid disposition, with urinary excretion representing the major elimination route. Formation of PNU-142586 was the rate-limiting step in the clearance of linezolid.
Determinants for protein localization: beta-lactamase signal sequence directs globin across microsomal membranes. (1984)

A hybrid gene containing 182 codons of Escherichia coli beta-lactamase at the amino terminus of the corresponding protein and 141 codons of alpha-globin at the carboxyl terminus was generated by inserting chimpanzee alpha-globin cDNA into the Pst I site of plasmid pBR322. RNA transcribed in vitro from this plasmid gave a corresponding hybrid protein in a wheat germ cell-free translation system. The hybrid protein was protected from tryptic digestion and the pre-beta-lactamase signal peptide was removed when dog pancreas membrane vesicles were present during translation. A deletion mutant containing 23 codons of pre-beta-lactamase signal sequence and 5 codons of mature beta-lactamase fused to the alpha-globin cDNA gave a shorter hybrid protein that behaved similarly. However, a mutation that removed essentially all of the pre-beta-lactamase sequence gave a protein that was neither protected nor processed. Hence, at most, only the signal peptide and the first 5 amino acids of beta-lactamase were necessary to convert alpha-globin (a cytoplasmic protein) into a secretory protein.
S100A4 Expression Is an Early Event of Papillary Carcinoma of the Thyroid (2004)

These findings suggest that (1) S100A4 plays a constitutive role in papillary carcinoma and (2) S100A4 may be a useful marker for early the detection of this carcinoma.
Functional significance of the LAR receptor protein tyrosine phosphatase family in development and diseases (2004)

The protein tyrosine phosphatases (PTPs) have emerged as critical players in diverse cellular functions. The focus of this review is the leukocyte common antigen-related (LAR) subfamily of receptor PTPs (RPTPs). This subfamily is composed of three vertebrate homologs, LAR, RPTP-sigma, and RPTP-delta, as well as few invertebrates orthologs such as Dlar. LAR-RPTPs have a predominant function in nervous system development that is conserved throughout evolution. Proteolytic cleavage of LAR-RPTP proproteins results in the noncovalent association of an extracellular domain resembling cell adhesion molecules and intracellular tandem PTPs domains, which is likely regulated via dimerization. Their receptor-like structures allow them to sense the extracellular environment and transduce signals intracellularly via their cytosolic PTP domains. Although many interacting partners of the LAR-RPTPs have been identified and suggest a role for the LAR-RPTPs in actin remodeling, very little is known about the mechanisms of action of RPTPs. LAR-RPTPs recently raised a lot of interest when they were shown to regulate neurite growth and nerve regeneration in transgenic animal models. In addition, LAR-RPTPs have also been implicated in metabolic regulation and cancer. This RPTP subfamily is likely to become important as drug targets in these various human pathologies, but further understanding of their complex signal transduction cascades will be required.
Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling (2006)

Individuals with Down syndrome (DS) are predisposed to develop acute megakaryoblastic leukemia (AMKL), characterized by expression of truncated GATA1 transcription factor protein (GATA1s) due to somatic mutation. The treatment outcome for DS-AMKL is more favorable than for AMKL in non-DS patients. To gain insight into gene expression differences in AMKL, we compared 24 DS and 39 non-DS AMKL samples. We found that non-DS-AMKL samples cluster in two groups, characterized by differences in expression of HOX/TALE family members. Both of these groups are distinct from DS-AMKL, independent of chromosome 21 gene expression. To explore alterations of the GATA1 transcriptome, we used cross-species comparison with genes regulated by GATA1 expression in murine erythroid precursors. Genes repressed after GATA1 induction in the murine system, most notably GATA-2, MYC, and KIT, show increased expression in DS-AMKL, suggesting that GATA1s fail to repress this class of genes. Only a subset of genes that are up-regulated upon GATA1 induction in the murine system show increased expression in DS-AMKL, including GATA1 and BACH1, a probable negative regulator of megakaryocytic differentiation located on chromosome 21. Surprisingly, expression of the chromosome 21 gene RUNX1, a known regulator of megakaryopoiesis, was not elevated in DS-AMKL. Our results identify relevant signatures for distinct AMKL entities and provide insight into gene expression changes associated with these related leukemias.
SEED: efficient clustering of next-generation sequences (2011)

Supplementary data are available at Bioinformatics online.
A cluster-modified Poisson model for estimating defect density and yield (1990)

A simple modification of the Poisson model that accounts for defect clustering when estimating the defect density and yield of a future product is described. The Poisson yield equation is easy to use and interpret, and the composite model can be extended to a layered model without the difficulties associated with, for example, the negative binomial model. The advantage of the method is that the Poisson model, to which all yield models reduce as yields increase, can continue to be used with less effort than, more convenience than, and at least as good accuracy as other more complicated models.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Identification and nucleotide sequence of Rhizobium meliloti insertion sequence ISRm3: similarity between the putative transposase encoded by ISRm3 and those encoded by Staphylococcus aureus IS256 and Thiobacillus ferrooxidans IST2 (1991)

The insertion sequence ISRm3 was discovered simultaneously in different Rhizobium meliloti strains by probing Southern blots of total cellular DNA with 32P-labeled pTA2. This plasmid is indigenous to strain IZ450 and fortuitously contained four copies of ISRm3. By using an internal EcoRI fragment as a specific probe (pRWRm31), homology to ISRm3 was subsequently detected in over 90% of R. meliloti strains tested from different geographical locations around the world. The frequency of stable nonlethal ISRm3 transpositions was estimated to be 4 x 10(-5) per generation per cell in strain SU47 when grown in liquid culture. The entire nucleotide sequence of ISRm3 in R. meliloti 102F70 is 1,298 bp and has 30-bp terminal inverted repeats which are perfectly matched. Analysis of six copies of ISRm3 in two strains showed that a variable number of base pairs (usually eight or nine) were duplicated and formed direct repeats adjacent to the site of insertion. On one DNA strand, ISRm3 contains an open reading frame spanning 93% of its length. Comparison of the putative protein encoded with sequences derived from the EMBL and GenBank databases showed significant similarity between the putative transposases of ISRm3 from R. meliloti, IS256 from Staphylococcus aureus, and IST2 from Thiobacillus ferroxidans. These insertion sequences appear to be distantly related members of a distinct class.
ANALYSIS OF PROSTATE CANCER BY PROTEOMICS USING TISSUE SPECIMENS (2005)

Protein profiling by SELDI is relatively easy to perform and it has great potential in prostate cancer diagnosis through pattern recognition. Quantitative proteomics can potentially determine the identity of many biomarkers specific for prostate cancer.
Friends, Friendsters, and Top 8: Writing community into being on social network sites (2006)

“Are you my friend? Yes or no?” This question, while fundamentally odd, is a key component of social network sites. Participants must select who on the system they deem to be ‘Friends.’ Their choice is publicly displayed for all to see and becomes the backbone for networked participation. By examining what different participants groups do on social network sites, this paper investigates what Friendship means and how Friendship affects the culture of the sites. I will argue that Friendship helps people write community into being in social network sites. Through these imagined egocentric communities, participants are able to express who they are and locate themselves culturally. In turn, this provides individuals with a contextual frame through which they can properly socialize with other participants. Friending is deeply affected by both social processes and technological affordances. I will argue that the established Friending norms evolved out of a need to resolve the social tensions that emerged due to technological limitations. At the same time, I will argue that Friending supports pre-existing social norms yet because the architecture of social network sites is fundamentally different than the architecture of unmediated social spaces, these sites introduce an environment that is quite unlike that with which we are accustomed.
Multimodality Noninvasive Imaging for Transcatheter Aortic Valve Implantation: A Primer (2012)

Transcatheter aortic valve implantation (TAVI) has recently emerged as a treatment option for patients with severe aortic valve stenosis (AS). For patients who are deemed inoperable for surgical aortic valve replacement (SAVR), TAVI has a significant mortality benefit compared to medical therapy. This review discusses established and emerging roles for multimodality imaging and focuses on the application of these technologies for patient selection, intraprocedural guidance, and the detection and quantification of acute and chronic complications of this novel procedure.
Detailed characterization of the human aorta‐gonad‐mesonephros region reveals morphological polarity resembling a hematopoietic stromal layer (1999)

The definitive long-term repopulating human hematopoietic stem cell, which seeds the adult blood system, was previously thought to derive from the extra-embryonic yolk sac. However, there is now considerable evidence that in both avian and murine systems, yolk sac hematopoietic cells are largely a transient, embryonic population and the definitive stem cell, in fact, derives from a distinct region within the embryonic mesoderm, the aorta-gonad-mesonephros region. In the human embryo, an analogous region has been found to contain a cluster of cells distinct from, but closely associated with, the ventral endothelium of the dorsal aorta, the appearance of which is restricted both spatially and temporally. We have used antibodies recognising hematopoietic regulatory factors to further characterise this region in the human embryo. These studies indicate that all factors examined, including vascular endothelial growth factor and its receptor FLK-1, Flt-3 ligand and its receptor STK-1, and stem cell leukemia transcription factor, are expressed by both hematopoietic cells in the cluster and endothelial cells. However, there is some discontinuity in cells directly underlying the cluster. Furthermore, we have identified a morphologically distinct region of densely-packed, rounded cells in the mesenchyme directly beneath the ventral wall of the dorsal aorta, and running along its entire length. In the preumbilical AGM region, directly underlying the hematopoietic cluster, but not at more rostral and caudal levels, this region of mesenchyme expresses tenascin-C, an extracellular matrix glycoprotein known to facilitate cell-cell interactions and migration. This region of cells may therefore provide the microenvironmental support for the intraembryonic development of definitive hematopoietic stem cells, a process in which tenascin-C may play a pivotal role.
A new approach to low ripple-noise switching converters on the basis of switched-capacitor converters (1991)

A new approach to a low ripple-noise switching converter is presented. The starting circuit is a basic switched-capacitor (SC) converter cell from which several types of low ripple-noise switching converters are generated. Two generated converters are employed for switching regulators hybridized by copper thick films on alumina substrates to realize low ripple noise. As a result, the ripple noise in the output voltages is reduced to less than 5 mVpp. Finally, this approach enables design of an ideal switching converter with zero input and output current ripple.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fault Identification in Computer Network A Review and a New Approach (1995)

As computer networks increase in size, heterogeneity, complexity and pervasiveness, effective management of such networks simultaneously becomes more important and more difficult. This paper explores in detail one aspect of network management, {\em fault identification}. Fault identification is the process whereby the existence and nature of network faults are ascertained. Characteristics of the fault identification problem are explored and existing approaches are surveyed. Interestingly, much of the work in this area makes use of techniques from Artificial Intelligence, especially expert systems. Features of the fault identification problem that make it is amenable to AI approaches and resistant to more traditional algorithmic solutions are examined. Finally, a new approach to fault identification is proposed that employs an algorithm for finding dependencies among values in multiple streams of data over time. The new approach is compared to existing approaches, and it advantages and disadvantages are weighed.
A Conservative Amino Acid Mutation in the Chromosome‐Encoded Dihydrofolate Reductase Confers Trimethoprim Resistance in<i>Streptococcus pneumoniae</i> (1998)

Multidrug-resistant Streptococcus pneumoniae strains have emerged over the past decade at an alarming rate. The molecular mechanism of trimethoprim resistance was investigated in 5 pneumococcal strains isolated in the Washington, DC, area from patients with invasive infections. Cloning and sequencing of the trimethoprim resistance determinant from these pneumococci indicated that an altered chromosome-encoded dihydrofolate reductase (DHFR) was responsible for the observed resistance. Comparison of DHFR sequences from pneumococcal strains with various susceptibilities to trimethoprim, together with site-directed mutagenesis, revealed that substitution of isoleucine-100 with a leucine residue resulted in trimethoprim resistance. Hydrogen bonding between the carbonyl oxygen of isoleucine-100 and the 4-amino group of trimethoprim is proposed to play a critical role in the inhibition of DHFR by trimethoprim. This enzyme-substrate model should facilitate the design of new antibacterial agents with improved activity against S. pneumoniae.
Nonlinear optical spectroscopy of photonic metamaterials (2008)

We have obtained spectra of second-harmonic generation, third-harmonic generation, and four-wave mixing from a fishnet metamaterial around its magnetic resonance. The resonant behaviors are distinctly different from those for ordinary materials. They result from the fact that the resonance is plasmonic, and its enhancement appears through the local field in the nanostructure.
Silver Nanowires as Oxygen Reduction Electrocatalysts in an Alkaline Medium (2011)

Abstract not Available.
Minicells of <i>Bacillus subtilis</i> (1973)

After nitrosoguanidine (N-methyl-N'-nitro-N-nitrosoguanidine) mutagenesis, two Bacillus subtilis mutants (div IV-A1 and div IV-B1) were isolated that are defective in the location of division site along cell length. Both mutations were transferred into strain CU403 by transformation, and their properties were studied in the CU403 genetic background. Location of divisions in close proximity to cell pole regions in both mutants results in minicell production. Purified minicells contain a ratio of ribonucleic acid to protein comparable to that found in the parent cells. Autoradiographs of (3)H-thymine incorporation into deoxyribonucleic acid (DNA), thymine-2-(14)C incorporation into DNA, electron micrographs, and chemical analyses for DNA all fail to demonstrate DNA in the minicells. Minicells produced by both mutants are highly motile, an indication of functional energy metabolism. Electron micrographs reveal that minicells are produced by a structurally normal division mechanism and that minicells contain a normal cell surface. The div IV-A1 mutation has been mapped by PBS1 transduction linked to ura. The div IV-B1 mutation is closely linked to pheA by both PBS1 transduction and by co-transformation.
Xenon is an Inhibitor of Tissue-Plasminogen Activator: Adverse and Beneficial Effects in a Rat Model of Thromboembolic Stroke (2010)

Preclinical evidence in rodents has proven that xenon may be a very promising neuroprotective agent for treating acute ischemic stroke. This has led to the general thinking that clinical trials with xenon could be initiated in acute stroke patients in a next future. However, an unappreciated physicochemical property of xenon has been that this gas also binds to the active site of a series of serine proteases. Because the active site of serine proteases is structurally conserved, we have hypothesized and investigated whether xenon may alter the catalytic efficiency of tissue-type plasminogen activator (tPA), a serine protease that is the only approved therapy for acute ischemic stroke today. Here, using molecular modeling and in vitro and in vivo studies, we show (1) xenon is a tPA inhibitor; (2) intraischemic xenon dose dependently inhibits tPA-induced thrombolysis and subsequent reduction of ischemic brain damage; (3) postischemic xenon virtually suppresses ischemic brain damage and tPA-induced brain hemorrhages and disruption of the blood-brain barrier. Taken together, these data indicate (1) xenon should not be administered before or together with tPA therapy; (2) xenon could be a golden standard for treating acute ischemic stroke if given after tPA-induced reperfusion, with both unique neuroprotective and antiproteolytic (anti-hemorrhaging) properties.
Genetic and Biochemical Analysis of Msh2p-Msh6p: Role of ATP Hydrolysis and Msh2p-Msh6p Subunit Interactions in Mismatch Base Pair Recognition (1997)

Recent studies have shown that Saccharomyces cerevisiae Msh2p and Msh6p form a complex that specifically binds to DNA containing base pair mismatches. In this study, we performed a genetic and biochemical analysis of the Msh2p-Msh6p complex by introducing point mutations in the ATP binding and putative helix-turn-helix domains of MSH2. The effects of these mutations were analyzed genetically by measuring mutation frequency and biochemically by measuring the stability, mismatch binding activity, and ATPase activity of msh2p (mutant msh2p)-Msh6p complexes. A mutation in the ATP binding domain of MSH2 did not affect the mismatch binding specificity of the msh2p-Msh6p complex; however, this mutation conferred a dominant negative phenotype when the mutant gene was overexpressed in a wild-type strain, and the mutant protein displayed biochemical defects consistent with defects in mismatch repair downstream of mismatch recognition. Helix-turn-helix domain mutant proteins displayed two different properties. One class of mutant proteins was defective in forming complexes with Msh6p and also failed to recognize base pair mismatches. A second class of mutant proteins displayed properties similar to those observed for the ATP binding domain mutant protein. Taken together, these data suggested that the proposed helix-turn-helix domain of Msh2p was unlikely to be involved in mismatch recognition. We propose that the MSH2 helix-turn-helix domain mediates changes in Msh2p-Msh6p interactions that are induced by ATP hydrolysis; the net result of these changes is a modulation of mismatch recognition.
Effect of Gas and Kerosene Space Heaters on Indoor Air Quality: A Study in Homes of Santiago, Chile (2010)

The impact of outdoor and indoor pollution sources on indoor air quality in Santiago, Chile was investigated. Toward this end, 16 homes were sampled in four sessions. Each session included an outdoor site and four homes using different unvented space heaters (electric or central heating, compressed natural gas, liquefied petroleum gas, and kerosene). Average outdoor fine particulate matter (PM2.5) concentrations were very high (55.9 microg x m(-3)), and a large fraction of these particles penetrated indoors. PM2.5 and several PM2.5 components (including sulfate, elemental carbon, organic carbon, metals, and polycyclic aromatic hydrocarbons) were elevated in homes using kerosene heaters. Nitrogen dioxide (NO2) and ultrafine particles (UFPs) were higher in homes with combustion heaters as compared with those with electric heaters or central heating. A regression model was used to assess the effect of heater use on continuous indoor PM2.5 concentrations when windows were closed. The model found an impact only for kerosene heaters (45.8 microg m(-3)).
Chinese University Students Delegation For Musical Exchanges Visits Japan (2014)

Invited by the Japan-China Friendship Center(CJFC),an 83-member Chinese university students’delegation visited Tokyo and Hokkaido from July 9 to 16.It comprised students and teachers of the music specialty of the Central Conservatory of Music,the School of Music of the Minzu University of China and the Shanghai Conservatory of Music.
Binary-phase zone-plate arrays based on hybrid solgel glass (1998)

An organically modified silane zirconate-based solgel material is used for the fabrication of binary-phase zone-plate arrays. The synthesized hybrid solgel material has a negative tone under UV exposure and can be patterned by a UV-lithography process. The transmittance of the material is nearly 100%, and the refractive index is 1.52. Two different diffractive lens arrays with focal lengths of 5 and 42 cm have been fabricated. The average roughness of the zone surface is less than 20 nm. The diffraction efficiencies of the lens arrays are measured as a function of modulation depth and exposure dose. A diffraction efficiency of 30% is achieved.