gebhart/patrepeval huggingface dataset:
Atorvastatin, an HMG-COA reductase inhibitor and efficient lipid-regulating agent. Part I. Synthesis of ring-labeled [14C6]atorvastatin (1999)

Pyrrole-ring labeled [14C]atorvastatin (Lipitor®, CI-981), [R-(R*,R*)]-2-(4-fluorophenyl)-β,γ-dihydroxy-5-(1-methylethyl)-3-phenyl-4-[(phenylamino)-carbonyl]-1H-[3-14C]pyrrole-1-heptanoic acid calcium salt (2:1) (15), was synthesized in a 5-step synthesis from [7-14C]benzaldehyde (5) with an overall yield of 6.9 to 9.6%. Thus, Knoevenagel condensation of 5 with isobutyryl-acetanilide (6) gave 4-methyl-3-oxo-N-phenyl-2-(phenyl[14C]methylene)-pentamide (7). Stetter condensation of (7) with p-fluorobenzaldehyde (8), in the presence of the catalyst 3-ethyl-5-(2-hydroxyethyl)-4-methylthiazolium bromide (9) and triethylamine, gave the key labeled intermediate diketone, 4-fluoro-α-(2-methyl-1-oxopropyl)-γ-oxo-N,β-diphenylbenzene[3-14C]butaneamide (10). Reaction of 10 with the protected chiral dihydroxyaminoheptanoic ester, [4R-cis]]-1,1-dimethylethyl-6-(2-aminoethyl)-2,2-dimethyl-1,3-dioxane-4-acetate (11), synthesized separately, gave atorvastatin in its protected form, [4R-cis]-1,1-dimethylethyl-6-[2[2-(4-fluorophenyl)-5-(1-methylethyl)-3-phenyl-4-[(phenylamino)carbonyl]-1H-[3-14C]pyrrol-1-yl]ethyl]-2,2-dimethyl-1,3-dioxane-4-acetate (12). Deprotection of 12 led to the sodium salt 13. Subsequent calcium salt formation gave the ring-labeled atorvastatin 15. Copyright © 1999 John Wiley & Sons, Ltd.
Positive Predictive Value of Specific Mammographic Findings according to Reader and Patient Variables (2009)

Five percent of invasive cancers were identified with asymmetry, and asymmetry is more weakly associated with cancer in screening examinations than are mass, calcifications, and architectural distortion.
The signal for glucose repression of the lactose-galactose regulon is amplified through subtle modulation of transcription of the Kluyveromyces lactis Kl-GAL4 activator gene. (1992)

Induction of the lactose-galactose regulon is strongly repressed by glucose in some but not all strains of Kluyveromyces lactis. We show here that in strongly repressed strains, two to three times less Kl-GAL4 mRNA is synthesized and that expression of structural genes in the regulon such as LAC4, the structural gene for beta-galactosidase, is down regulated 40-fold or more. Comparative analysis of strains having a strong or weak repression phenotype revealed a two-base difference in the promoter of the Kl-GAL4 (also called LAC9) positive regulatory gene. This two-base difference is responsible for the strong versus the weak repression phenotype. The two base changes are symmetrically located in a DNA sequence having partial twofold rotational symmetry (14 of 21 bases). We hypothesize that this region functions as a sensitive regulatory switch, an upstream repressor sequence (URS). According to our model, the presence of glucose in the culture medium signals, by an unidentified pathway, a repressor protein to bind the URS. Binding reduces transcription of the Kl-GAL4 gene so that the concentration of the Kl-GAL4 protein falls below the level needed for induction of LAC4 and other genes in the regulon. For strains showing weak glucose repression, we hypothesize that the two base changes in the URS reduce repressor binding so that the regulon is not repressed. Our results illustrate an important principle of genetic regulation: a small (2- to 3-fold) change in the concentration of a regulatory protein can produce a large (40-fold or greater) change in expression of structural genes. This mechanism of signal amplification could play a role in many biological phenomena that require regulated transcription.
ProtoSphere (2010)

Filling objects densely with sets of non overlapping spheres has been investigated for centuries. Once started as a pure intellectual challenge, today, sphere packings have diverse applications in a wide spectrum of scientific and engineering disciplines, for example in automated radiosurgical treatment planning, investigation of processes such as sedimentation, compaction and sintering, in powder metallurgy for three-dimensional laser cutting, in cutting different natural crystals, the discrete element method is based on them, and so forth.
Image Reconstruction in Ring Array Ultrasound Tomography by Means of Enhancing the Sinogram (2013)

The Ring Array Ultrasound Tomography is the system which has been used for breast cancer detection. The system is potentially developed due to unmovable mechanically, safe and obtainable high resolution image. The study means to reconstruct ring array ultrasound tomography by reposition and spline-interpolation data into parallel beam Sinogram. The study was conducted with numerical and experimental object by 16 and 32 transducer positions to obtain 31x31 pixels of images. Sinogram was repaired by an RMSD method and reconstructed by the SCFBP method. The results indicate that the methods of Sinogram enhancement can only improve the image of 0.02%. The study showed that 16 transducers had produced a blur image and been dissimilar to the object, but 32 transducers could generate a good image but it is still worse than parallel beam.
Tandem Gold(I)-Catalyzed Cyclization/Electrophilic Cyclopropanation of Vinyl Allenes (2007)

We have developed an expedient method for the synthesis of polycyclic compounds from propargyl acetates or vinyl allenes involving up to three Au(I)-catalyzed elemental steps: 3,3-rearrangement, metalla-Nazarov reaction, and electrophilic cyclopropanation. The reaction proceeds under very mild conditions and in short times. The mechanism has been studied by DFT computations.
TRPC3 positively regulates reactive oxygen species driving maladaptive cardiac remodeling (2016)

Reactive oxygen species (ROS) produced by NADPH oxidase 2 (Nox2) function as key mediators of mechanotransduction during both physiological adaptation to mechanical load and maladaptive remodeling of the heart. This is despite low levels of cardiac Nox2 expression. The mechanism underlying the transition from adaptation to maladaptation remains obscure, however. We demonstrate that transient receptor potential canonical 3 (TRPC3), a Ca<sup>2+</sup>-permeable channel, acts as a positive regulator of ROS (PRROS) in cardiomyocytes, and specifically regulates pressure overload-induced maladaptive cardiac remodeling in mice. TRPC3 physically interacts with Nox2 at specific C-terminal sites, thereby protecting Nox2 from proteasome-dependent degradation and amplifying Ca<sup>2+</sup>-dependent Nox2 activation through TRPC3-mediated background Ca<sup>2+</sup> entry. Nox2 also stabilizes TRPC3 proteins to enhance TRPC3 channel activity. Expression of TRPC3 C-terminal polypeptide abolished TRPC3-regulated ROS production by disrupting TRPC3-Nox2 interaction, without affecting TRPC3-mediated Ca<sup>2+</sup> influx. The novel TRPC3 function as a PRROS provides a mechanistic explanation for how diastolic Ca<sup>2+</sup> influx specifically encodes signals to induce ROS-mediated maladaptive remodeling and offers new therapeutic possibilities.
Near-Equilibrium Chemical Force Microscopy (2008)

Molecular force spectroscopy experiments probe the stochastic kinetics of individual intermolecular bond rupture under external loading. While there are numerous examples describing rupture kinetics under fast-loading, far from equilibrium conditions, bond rupture at slow loading rates near equilibrium conditions is seldom explored. We use an analytical and numerical approach to show that rupture forces in this qualitatively different regime reach an equilibrium plateau value that is a function of the probe stiffness and the free energy difference between the bound and dissociated state of the bond. Chemical force microscopy measurements of the interaction between a small number of well-defined COOH functional groups confirm these predictions and show the expected scaling of the force plateau values with the square root of the probe stiffness. Finally, we discuss the implications of these results for the interpretation of force spectroscopy experiments.
Comparison of a Commercial Real-Time PCR Assay for <i>tcdB</i> Detection to a Cell Culture Cytotoxicity Assay and Toxigenic Culture for Direct Detection of Toxin-Producing <i>Clostridium difficile</i> in Clinical Samples (2008)

Rapid detection of toxin-producing strains of Clostridium difficile is essential for optimal management of patients with C. difficile infection. The BD GeneOhm (San Diego, CA) Cdiff assay, a real-time PCR assay that amplifies tcdB, was compared to a cell culture neutralization assay (Wampole C. difficile Toxin B [TOX-B] test; TechLab, Blacksburg, VA) and to toxigenic culture. Using liquid (n = 273) and soft (n = 131) stool specimens from 377 symptomatic patients, all testing was performed on the same day by independent laboratory staff according to the manufacturers' protocols. Toxigenic bacterial culture was performed as follows. A 0.5-ml aliquot of stool was heated to 80 degrees C for 10 min, followed by inoculation onto modified cycloserine cefoxitin fructose agar with and without horse blood (Remel, Lenexa, KS) and into prereduced chopped-meat broth. Of the 404 stool specimens tested, 340 were negative and 40 were positive (10.0% prevalence) both by PCR for tcdB and by cytotoxin production. The overall agreement between the BD GeneOhm Cdiff assay and the TOX-B test was 94.8% (380/401). When the TOX-B test was used as the reference method, the initial sensitivity, specificity, and positive and negative predictive values of the BD GeneOhm Cdiff assay were 90.9% (40/44), 95.2% (340/357), 70.2% (40/57), and 98.8% (340/344), respectively. When toxigenic culture was used as the "gold standard," the sensitivity, specificity, and positive and negative predictive values of the BD GeneOhm Cdiff assay were 83.6%, 98.2%, 89.5%, and 97.1%, respectively, and those of the TOX-B test were 67.2%, 99.1%, 93.2%, and 94.4%, respectively. PCRs for three samples were inhibited upon initial testing; one sample was resolved upon retesting. One sample produced nonspecific cytotoxin results. The BD GeneOhm Cdiff assay performed well compared to a standard cell culture neutralization assay and to toxigenic culture for the detection of toxigenic C. difficile directly from fecal specimens.
Making mashups with marmite (2007)

There is a tremendous amount of web content available today, but it is not always in a form that supports end-users' needs. In many cases, all of the data and services needed to accomplish a goal already exist, but are not in a form amenable to an end-user. To address this problem, we have developed an end-user programming tool called Marmite, which lets end-users create so-called mashups that re-purpose and combine existing web content and services. In this paper, we present the design, implementation, and evaluation of Marmite. An informal user study found that programmers and some spreadsheet users had little difficulty using the system.
Polymer Vesicles with a Red Cell‐like Surface Charge: Microvascular Imaging and in vivo Tracking with Near‐Infrared Fluorescence (2009)

Polymersomes are block copolymer-based vesicles whose long circulation times or "stealth" in vivo coupled with the loading and controlled release of drugs, siRNA, and other compounds has made them attractive for delivery. A brushy corona of non-ionic polyethylene glycol (PEG) likely contributes stealth, but red blood cells (RBCs) possess a negatively charged glycocalyx and circulate much longer. Polyanionic block copolymers were therefore mixed into polymersomes which were also labeled with a near IR fluorophore to quantify biodistribution in live mice and excised organs. Charge shifts tissue distribution, and high resolution imaging of vesicles in blood capillaries further shows that organ cultures can provide deeper insight into microscale transport within tissue microenvironments.
A Method for System Matrix Construction and Processing for Reconstruction of In-Beam PET Data (2007)

At present, positron emission tomography (PET) is the only available technique for an in-situ, non-invasive monitoring of the dose delivery precision in highly conformal ion beam therapy. At the heavy ion therapy facility at the Gesellschaft fur Schwerionenforschung (GSI) Darmstadt, Germany, an in-beam PET scanner is operated for quality assurance monitoring, simultaneously to the therapeutic irradiation. The dedicated reconstruction algorithm and data acquisition system were developed to fit specific conditions of in-beam PET (dual-head, limited-angle geometry, very low counting statistics). In this work we propose a precise technique for calculating and processing the geometric component of the system matrix and analyze the influence of the system matrix on the quality of reconstructed in-beam PET image. We show that for in-beam PET data the maximum likelihood expectation maximization (MLEM) algorithm is robust to errors in the system matrix and produces acceptable results even for a system matrix calculated with poor quality, whereas the quality of images reconstructed with the randomly filled subsets expectation maximization algorithm (RFS-EM) depends more on the accuracy of the system matrix.
cDNA cloning and characterization of a ligand for the Cek5 receptor protein-tyrosine kinase. (1994)

We have isolated a murine cDNA encoding a ligand for the Cek5 receptor protein-tyrosine kinase (RPTK), a member of the Eph/Eck RPTK subfamily. Sequence analysis predicts an open reading frame of 345 amino acids with a predicted molecular mass of 38 kDa. Metabolic labeling and immunoprecipitation of cells transfected with a cDNA encoding the Cek5 ligand revealed the mature protein to have an apparent molecular mass of 45 kDa. The extracellular domain of the Cek5 ligand shows a 27% sequence identity at the protein level to B61, a ligand for the related Eck RPTK (Bartley, T. D., et al. (1994) Nature 368, 558-560). Consistent with the presence of a transmembrane domain, flow cytometry analysis revealed the Cek5 ligand to be expressed on the cell surface. The expressed Cek5 ligand is functionally active as it induces autophosphorylation of the Cek5 RPTK.
Dominance of interface effects in SRO-SiO/sub 2/-SRO DEIS structures for EAROMs (1988)

Current injection at silicon-rich oxide (SRO)-thermal oxide and SRO-CVD (chemical-vapor-deposited) oxide interfaces is shown to be interface-limited. I-V characteristics for both interfaces fit a model for injection enhancement that depends on the curvature of Si islands in the SRO. Results indicate that only a fraction of the Si islands contribute to the injection. The asymmetry observed in dual-electron-injector structures (DEIS) can be explained by a 2.5-times difference in the number of islands between top and bottom injecting interfaces.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The <i>Pseudomonas aeruginosa rhlG</i> Gene Encodes an NADPH-Dependent β-Ketoacyl Reductase Which Is Specifically Involved in Rhamnolipid Synthesis (1998)

A Pseudomonas aeruginosa gene homologous to the fabG gene, which encodes the NADPH-dependent beta-ketoacyl-acyl carrier protein (ACP) reductase required for fatty acid synthesis, was identified. The insertional mutation of this fabG homolog (herein called rhlG) produced no apparent effect on the growth rate and total lipid content of P. aeruginosa cells, but the production of rhamnolipids was completely abrogated. These results suggest that the synthetic pathway for the fatty acid moiety of rhamnolipids is separate from the general fatty acid synthetic pathway, starting with a specific ketoacyl reduction step catalyzed by the RhlG protein. In addition, the synthesis of poly-beta-hydroxyalkanoate (PHA) is delayed in this mutant, suggesting that RhlG participates in PHA synthesis, although it is not the only reductase involved in this pathway. Traits regulated by the quorum-sensing response, other than rhamnolipid production, including production of proteases, pyocyanine, and the autoinducer butanoyl-homoserine lactone (PAI-2), were not affected by the rhlG mutation. We conclude that the P. aeruginosa rhlG gene encodes an NADPH-dependent beta-ketoacyl reductase absolutely required for the synthesis of the beta-hydroxy acid moiety of rhamnolipids and that it has a minor role in PHA production. Expression of rhlG mRNA under different culture conditions is consistent with this conclusion.
The Application of Advanced PDC Concepts Proves Effective in South Texas (1996)

Summary Over the years, a variety of problems with polycrystalline diamond compact (PDC) bit design and application has been documented, with "bit whirl" being identified as the cause of many inherent problems. The goal of most PDC manufacturers, and the subject of this paper, is development of a better-performing, "whirl-resistant" PDC bit design. Similarly, the goal for most operators is the lower cost resulting from effective application of such bits. Toward those ends, a cooperative development effort between operators and a manufacturer was undertaken to apply advanced concepts effectively to the design, manufacture, and application of a new series of PDC bits in south Texas. Adoption of design concepts, such as force-balanced cutting structures, asymmetric blade layouts, spiral blade designs, and tracking cutter arrangements, proved effective in countering the destructive effects of bit whirl, and allowed PDC bits to be used in harder formations. Summaries of both operational and economic performance confirm the success of the undertaking.
Kitasatospora cheerisanensis sp. nov., a new species of the genus Kitasatospora that produces an antifungal agent (1999)

An actinomycete, strain YC75T, which produced bafilomycin-like antifungal compounds, was identified as a member of the genus Kitasatospora on the basis of morphological and chemotaxonomic characteristics. The strain produced the aerial and fragmenting vegetative mycelia consisting of straight chains of 20 or more smooth-surfaced spores. Submerged spores were formed in tryptic soy broth. No soluble pigments were formed. Whole-cell hydrolysates contained glucose and mannose, but not galactose. The 16S rDNA sequence of YC75T was compared with those of the other representative kitasatosporae and streptomycetes. Strain YC75T formed a significant monophyletic clade with Kitasatospora phosalacinea. The levels of DNA relatedness between strain YC75T and representatives of the genus Kitasatospora ranged from 16 to 59% including K. phosalacinea (28 and 40%). It is clear from polyphasic evidence that the isolate should be classified as Kitasatospora cheerisanensis sp. nov., whose type strain is YC75T (= KCTC 2395T). The presence of galactose in whole-cell hydrolysates may not be a stable chemical marker for the genus Kitasatospora.
Abdominal Sacrocolpopexy: A Comprehensive Review (2004)

Sacrocolpopexy is a reliable procedure that effectively and consistently resolves vaginal vault prolapse. Patients should be counseled about the low, but present risk, of reoperation for prolapse, stress incontinence, and complications. Prospective trials are needed to understand the effect of sacrocolpopexy on functional outcomes.
Visualization of Intrathoracically Disseminated Solid Tumors in Mice with Optical Imaging by Telomerase-Specific Amplification of a Transferred Green Fluorescent Protein Gene (2004)

Abstract Currently available methods for detection of tumors in vivo such as X-ray, computed tomography, and ultrasonography are noninvasive and have been well studied; the images, however, are not specific for tumors. Direct optical imaging of tumor cells in vivo that can clearly distinguish them from surrounding normal tissues may be clinically useful. Here, we describe a new approach to visualizing tumors whose fluorescence can be detected using tumor-specific replication-competent adenovirus (OBP-301, Telomelysin) in combination with Ad-GFP, a replication-deficient adenovirus expressing green fluorescent protein (GFP). Human telomerase reverse transcriptase is the catalytic subunit of telomerase, which is highly active in cancer cells but quiescent in most normal somatic cells. We constructed an adenovirus 5 vector in which the human telomerase reverse transcriptase promoter element drives expression of E1A and E1B genes linked with an internal ribosome entry site and showed that OBP-301 replicated efficiently in human cancer cells, but not in normal cells such as human fibroblasts. When the human lung and colon cancer cell lines were infected with Ad-GFP at a low multiplicity of infection, GFP expression could not be detected under a fluorescence microscope; in the presence of OBP-301, however, Ad-GFP replicated in these tumor cells and showed strong green signals. In contrast, coinfection with OBP-301 and Ad-GFP did not show any signals in normal cells such as fibroblasts and vascular endothelial cells. We also found that established subcutaneous tumors could be visualized after intratumoral injection of OBP-301 and Ad-GFP. A549 human lung tumors and SW620 human colon tumors transplanted into BALB/c nu/nu mice were intratumorally injected with 8 × 105 plaque-forming units of Ad-GFP in combination with 8 × 106 plaque-forming units of OBP-301. Within 3 days of treatment, the fluorescence of the expressed GFP became visible by a three-chip color cooled charged-coupled device camera in these tumors, whereas intratumoral injection of Ad-GFP alone could not induce GFP fluorescence. Moreover, intrathoracic administration of Ad-GFP and OBP-301 could visualize disseminated A549 tumor nodules in mice after intrathoracic implantation. Our results indicate that intratumoral or intrathoracic injection of Ad-GFP in combination with OBP-301 might be a useful diagnostic method that provides a foundation for future clinical application.
ChemInform Abstract: TAUTOMERISM OF HETEROCYCLIC COMPOUNDS, VI. SYNTHESIS AND REACTIONS OF BIFUNCTIONAL CHLOROFORMAMIDINES (1976)

Abstract Die trisubstituierten, bifunktionellen Harnstoffe (I) werden mit Hilfe des Chlorierungsreagenzes Triphenylphosphin/Tetrachlorkohlenstoff in die bifunktionellen Chlorformamidine (II) übergeführt.
Considerations for accurate gene expression measurement by reverse transcription quantitative PCR when analysing clinical samples (2014)

Reverse transcription quantitative PCR is an established, simple and effective method for RNA measurement. However, technical standardisation challenges combined with frequent insufficient experimental detail render replication of many published findings challenging. Consequently, without adequate consideration of experimental standardisation, such findings may be sufficient for a given publication but cannot be translated to wider clinical application. This article builds on earlier standardisation work and the MIQE guidelines, discussing processes that need consideration for accurate, reproducible analysis when dealing with patient samples. By applying considerations common to the science of measurement (metrology), one can maximise the impact of gene expression studies, increasing the likelihood of their translation to clinical tools.