gebhart/patrepeval huggingface dataset:
The Palladium Catalyzed Nucleophilic Substitution of Aryl Halides by Thiolate Anions (1980)

Abstract In the presence of a catalytic amount of tetrakis(triphenylphosphine) palladium, phenyl and methyl or methoxyphenyl iodides and bromides were found to react with thiolate anions in alcoholic solvents, to give the corresponding aryl sulfides in excellent yield. The reaction is useful to prepare symmetrical or unsymmetrical diaryl sulfides and aryl alkyl sulfides. The reaction mechanism does not involve aryl halide radical anions, but is thought to involve oxidative addition of aryl halide to Pd(0), nucleophilic substitution on the adduct followed by reductive elimination.
Miniature urea sensor based on H(+)-ion sensitive field effect transistor and its application in clinical analysis. (1992)

An urea-ENFET (Enzyme field effect transistor) probe was made by covering one of the grids of the dual ISFET (Ion sensitive field effect transistor) with a membrane of cross-linked bovine serum albumin (BSA)-urease and the other with cross-linked BSA, and the response characteristics of the probe was then tested through differential measurements. In different concentrations of phosphate buffer, the sensor responded to various concentrations of urea solution within 10-60s. From the calibration curve plotted on logarithmic scales a linear concentration range of 1.0-8.0 mg/dl was acquired, and the correlation coefficient and response sensitivity were 0.997 and 50mV/dec. (mg/dl), respectively. However, in dilute urea solution, the sensor responded linearly to the contents of urea over the range of concentration of 0.1-1.0 mg/dl with a correlation coefficient of 0.998 and a response sensitivity of 12-15mV/mg/dl. The standard deviation and the variation coefficient for 20 performances responding to 100mg/dl urea in 0.01M pH7.0 phosphate buffer were found to be 1.39mV and 1.44%, respectively. The urea-ENFET was used for the determination of BUN (Blood urea nitrogen) and the BUN values were compared with those determined by enzymatic method, the repression equation and correlation coefficient for 50 assays were y = -0.1272 + 0.9695x and r = 0.9912, respectively. When the urea-ENFET was used for determining urea either in buffer solution or in serum for 250 runs over a period of 1.5 months (the enzyme FET was stored at 4 degrees C between measurements during this period), the observed decrease of response sensitivity was only about 10%.(ABSTRACT TRUNCATED AT 250 WORDS)
Spread Spectrum Acquisition and Tracking Performance for Shuttle Communication Links (1978)

The spread spectrum acquisition and tracking performance for the Shuttle <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</tex> -band and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ku</tex> -band communication links are analyzed and compared to test results. The <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</tex> -band link requirements are more severe than those of the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ku</tex> -band links, hence, different despreader designs were developed for the two systems. The <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</tex> -band despreader acquires pseudonoise code lock by examining all possible code phases in half chip steps while the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ku</tex> -band despreader acquires pseudonoise code lock by continuously sweeping a tau-jitter loop. Both despreaders employ a tau-jitter loop for code tracking. The code tracking performance is computed for the tau-jitter loop and compared to that of the more complex delay lock loop.
Rat collagenase. Cloning, amino acid sequence comparison, and parathyroid hormone regulation in osteoblastic cells. (1990)

We have isolated clones for rat collagenase from a rat osteoblastic cell cDNA library. These clones have been sequenced and the amino acids deduced. The calculated molecular weight is 51,352 for the proenzyme and 42,229 for the active enzyme. The deduced amino acid sequence was compared to those previously reported for: 1) human collagenase, 2) rat transin 1 (stromelysin), 3) human stromelysin, and 4) rabbit collagenase. The number of amino acids conserved was 47, 47, 50, and 47%, respectively. We also compared the collagenase mRNA and protein in different rat cells (osteoblast, uterine smooth muscle, synovial fibroblast) and determined that in rat uterine cells the message is slightly larger, although collagenase protein in all three cell types was identical in size. Parathyroid hormone dramatically induces the 2.9-kilobase collagenase mRNA in the rat osteoblastic cells, UMR 106-01. Nuclear run-on studies in UMR 106-01 cells demonstrated a 4-8-fold induction in the rate of synthesis of collagenase mRNA at 2 and 4 after parathyroid hormone treatment, with steady state levels of mRNA increased 100-fold at 4 h. Thus, parathyroid hormone regulation of the collagenase gene in UMR 106-01 cells is in part transcriptional.
Automatic delineation of white matter fascicles by localization based upon anatomical spatial relationships (2013)

Delineation of white matter fascicles is generally achieved with tractography by specifying seeding and exclusion regions of interest (ROIs) defined by anatomical landmarks. In practice, the most popular approach has been to manually draw the ROIs for each scan which requires extensive training, is strongly subject to inter- and intra-expert variability and is highly time consuming. Fully automatic localization of the ROIs is of central interest, particularly for white matter investigations involving a large number of subjects. In this work, we propose an original approach in which the ROIs are localized using the fuzzy set theory by discovering stable anatomical spatial relationships in the brain anatomy. Our approach relies on a learning procedure, in which stable relationships are identified from a limited number of training templates supplied with manually delineated ROIs. For a new subject, the spatial relationships are applied and the ROIs localized. We show that our approach enables successful automatic delineation of the ROIs in the individual. Importantly, we show that this localization is robust across subjects age.
Ewald summation for systems with slab geometry (1999)

We propose a modification in the three-dimensional Ewald summation technique for calculations of long-range Coulombic forces for systems with a slab geometry that are periodic in two dimensions and have a finite length in the third dimension. The proposed method adds a correction term to the standard Ewald summation formula. To test the current method, molecular dynamics simulations on water between Pt(111) walls have been carried out. For a more direct test, the calculation of the pair forces between two point charges has been also performed. An excellent agreement with the results from simulations using the rigorous two dimensional Ewald summation technique were obtained. We observed that a significant reduction in computing time can be achieved when the proposed modification is used.
Amplitude, duration and predictablity of long hop trans-horizon X-band signals over the sea (1992)

A 10.71 GHz trans-horizon radio link of 254.1 km across the English Channel (La Manche) between Brittany and Dorsct has been continuously monitored for two yean. The distribution of signal strength measured in dB relative to free spaa is normal and the duration of threshold exctedanco, is lognormal. The correlation between weekly average signal amplitude and weekly average maximum daily local temperature at the receiver site is good. Correlation with other meteorological parameten is also discussed together with cyclic daily and monthly variabilities.
Mannitol, Dextromethorphan, and Catalase Minimize Ischemic Damage to Retinal Pigment Epithelium and Retina (1993)

We studied the recovery of retinal pigment epithelium and retinal function after 80 minutes of pressure-induced ischemia in rabbits. Just before restoring circulation, we gave intravenous mannitol (an osmotic agent and free-radical scavenger), dextromethorphan (an N-methyl-D-aspartate receptor antagonist), or catalase (an antioxidant enzyme). Mannitol has not previously been shown to be protective for retinal or retinal pigment epithelial ischemia. At 24 hours after reperfusion, the electroretinogram b-wave was reduced to 37% of preischemic amplitude in untreated eyes, but it recovered to 67% to 80% after treatment with all three agents. The c-wave was replaced by a negative slow PIII response in control eyes and in seven of 12 catalase-treated eyes, but it recovered by 58% to 82% in the remaining catalase-treated eyes and all the mannitol- and dextromethorphan-treated eyes. Histologic examination confirmed that retinal pigment epithelium as well as retina had been damaged by the ischemia. The effects of mannitol seem of special interest, since the drug has a dual mechanism of action and is clinically available.
Examination of the effects of epidermal growth factor on the production of urokinase and the expression of the plasminogen activator receptor in a human colon cancer cell line. (1989)

The expression of the plasminogen activator, urokinase, and the display of its receptor in response to growth factors were examined in a serum-free adapted colon cancer cell line, CBSsf. Cells propagated in protein-free medium secreted 6.5 +/- 1.0 ng/ml of urokinase/10(6) cells in a 3-day period as determined by enzyme-linked immunosorbent assay. Inclusion of insulin or transferrin into the protein-free medium was without effect on this parameter. However, addition of epidermal growth factor (EGF) to the protein-free medium resulted in a 50% reduction in this parameter. This change was also reflected in the plasminogen-dependent solubilization of immobilized radioactive laminin. Plasminogen-supplemented conditioned medium derived from CBSsf cells grown in protein-free medium solubilized 135,000 +/- 25,000 dpm/10(6) cells of radioactive substrate. This value was decreased to 59,000 +/- 6,000 when conditioned medium was collected in the presence of EGF. Dose-response curves indicated that, while 0.5 ng/ml of EGF were suboptimal for the suppression of urokinase secretion, a concentration of 5.0 ng/ml had a maximum effect on this measurement. Northern hybridization studies indicated that the reduced plasminogen activator reflected, at least in part, translation of a less abundant transcript. Examination of the colon carcinoma cell line for altered urokinase receptor display revealed that EGF caused a dose-dependent increase in the amount of radioactive urokinase bound. This did not reflect reduced occupation of binding sites with endogenous ligand. Scatchard manipulation of the binding data indicated that the increased amount of radioactive plasminogen activator bound to cells cultured with EGF reflected an increase in receptor number from 7,500 to 13,000 sites/cell. Time course studies revealed that the decrease in urokinase secretion precedes changes in receptor display by 5 h. A 60% reduction in assayable urokinase was demonstrated in the conditioned medium from cells treated with the growth peptide for 10 h. However, a 24-h period was required to observe an increase (80%) in the amount of radioligand bound to EGF-treated cells. These data suggest EGF to be a regulator of both urokinase production and urokinase receptor display in a colon cancer cell line.
Die Erweiterung des genetischen Codes (2004)

Abstract Chemiker sind in der Lage, nahezu jede niedermolekulare organische Verbindung zu synthetisieren. Dennoch sind unsere Möglichkeiten zur rationalen Modifizierung von Proteinen sehr begrenzt, und das, obwohl diese an nahezu allen Lebensprozessen teilnehmen. Bei den meisten Proteinen beschränken sich die Modifikationen weitgehend auf Substitutionen der zwanzig Standard‐Aminosäuren untereinander. Hier beschreiben wir jüngste Fortschritte, die es ermöglichen, den genetischen Code von prokaryotischen und eukaryotischen Organismen um neue Bausteine zu erweitern. Es wurden bereits mehr als dreißig neuartige Aminosäuren in eindeutigen Triplett‐ und Quadruplett‐Codons genetisch codiert, darunter fluoreszierende und redoxaktive Aminosäuren, glycosylierte Aminosäuren und Aminosäuren mit Keto‐, Azid‐, Acetylen‐ und Schweratomfunktionen in den Seitenketten. Mit dem Wegfall der Einschränkungen, die durch den begrenzten Satz von zwanzig Aminosäuren vorgegeben sind, sollte es möglich sein, Proteine und sogar gesamte Organismen mit neuen oder verbesserten Eigenschaften zu generieren.
CD34 expression in primary cutaneous malignant melanoma: apropos of a case and review of the aberrant melanoma phenotype (2005)

We present a case of malignant melanoma of nodular subtype, which strongly expressed CD34. The spectrum of abnormal phenotypes in malignant melanoma is reviewed, and a possible explanation for the presence of CD34 is discussed. This case demonstrates the potential of malignant melanoma to express CD34, defining an infrequently recognized aberrant phenotype. Whether or not expression of this marker is associated with a more aggressive clinical course remains to be determined.
Mechanism-based inactivation of human liver microsomal cytochrome P-450 IIIA4 by gestodene (1990)

A series of 17 alpha-acetylenic steroids was examined with regard to ability to inactivate human liver microsomal cytochrome P-450 (P-450) IIA4, an enzyme involved in the oxidation of a number of drugs, carcinogens, and steroids, including estrogens and progestogens. Of the eight compounds tested, gestodene was found to be particularly active as a mechanism-based inactivator of P-450 IIIA4. Inhibition of both microsomal nifedipine oxidation and 17 alpha-ethynylestradiol (EE) 2-hydroxylation was dependent upon NADPH and gestodene concentration. Rates of inactivation were pseudo first order-values of kinactivation = 0.4 min-1 and Ki = 46 microM and a partition ratio of 9 were calculated. The kinactivation is approximately 50-fold greater than estimated for EE and is one of the highest reported for P-450 mechanism-based inactivators. Spectrally detectable P-450 was also destroyed in microsomes, but several experiments indicate that little covalent binding to amino acid residues of P-450 IIIA4 occurs. Microsomal inactivation of P-450 could be blocked by the presence of other P-450 IIIA4 substrates, and several activities catalyzed by other P-450s were not inhibited under conditions in which greater than 90% of P-450 IIIA4 was inactivated. Consideration of structure/activity relationships among the 17 alpha-acetylenic steroids examined indicates that the delta 15 double bond is critical but is not in itself sufficient for the inactivation process, which is postulated to result from attack of P-450 on the substituted acetylenic carbon and lead to porphyrin N-alkylation. The effectiveness of this mechanism-based inactivator may account for reports of increased estrogen and steroid levels in some women using gestodene in oral contraceptives.
&lt;title&gt;Optical Disk Media Parameters And Their Relationship To Equipment Design&lt;/title&gt; (1983)

Optical disk media para.oeters are examined with respect to recording capability, dimensional constraints, and the necessary interface with recording equipment. The parameters discussed include recording properties such as Media sensitivity and recorded signal quality. The mechanical dimensional tolerances required to proimote media. interchange ability, and to permit effective optical tracking and focus control are also discussed. The stated values reflect the current understanding of requirewents for automated, optical disk systems, and the reasons for the selection of these values are presented. A recording equipment of primary interest is the multidisk jukebox, with its requirements for disk protection and automated. deployment. Consequently, emphasis is given to the interface of disk media with the optical and mechanical subsystems of random-access, multiple-disk equipment.
Protease B of the lysosomelike vacuole of the yeast Saccharomyces cerevisiae is homologous to the subtilisin family of serine proteases. (1987)

The PRB1 gene of Saccharomyces cerevisiae encodes the vacuolar endoprotease protease B. We have determined the DNA sequence of the PRB1 gene and the amino acid sequence of the amino terminus of mature protease B. The deduced amino acid sequence of this serine protease shares extensive homology with those of subtilisin, proteinase K, and related proteases. The open reading frame of PRB1 consists of 635 codons and, therefore, encodes a very large protein (molecular weight, greater than 69,000) relative to the observed size of mature protease B (molecular weight, 33,000). Examination of the gene sequence, the determined amino-terminal sequence, and empirical molecular weight determinations suggests that the preproenzyme must be processed at both amino and carboxy termini and that asparagine-linked glycosylation occurs at an unusual tripeptide acceptor sequence.
Universal Correspondence Network (2016)

We present a deep learning framework for accurate visual correspondences and demonstrate its effectiveness for both geometric and semantic matching, spanning across rigid motions to intra-class shape or appearance variations. In contrast to previous CNN-based approaches that optimize a surrogate patch similarity objective, we use deep metric learning to directly learn a feature space that preserves either geometric or semantic similarity. Our fully convolutional architecture, along with a novel correspondence contrastive loss allows faster training by effective reuse of computations, accurate gradient computation through the use of thousands of examples per image pair and faster testing with $O(n)$ feed forward passes for $n$ keypoints, instead of $O(n^2)$ for typical patch similarity methods. We propose a convolutional spatial transformer to mimic patch normalization in traditional features like SIFT, which is shown to dramatically boost accuracy for semantic correspondences across intra-class shape variations. Extensive experiments on KITTI, PASCAL, and CUB-2011 datasets demonstrate the significant advantages of our features over prior works that use either hand-constructed or learned features.
The Role of Acidification for Antimicrobial Activity of Atmospheric Pressure Plasma in Liquids (2010)

Abstract Water disinfection by indirect plasma treatment was investigated using a surface dielectric barrier discharge (DBD). Liquid was neither part of the discharge electrode configuration nor stirred during plasma treatment. High concentrations (10 6 –10 8 cfu·mL −1 ) of Escherichia coli and Staphylococcus aureus have been completely inactivated within 5–15 min, depending on liquid sample volume. Inactivation occurred in non‐buffered liquids, only, where pH decrease was found. Measurements of pH, nitrate, and nitrite concentrations after DBD plasma or NO gas treatment lead to the conclusion that nitric acid formation from plasma‐generated reactive nitrogen species are the main source of liquid acidification. Incubation of bacteria in nitric acid alone did not result in comparable inactivation effects. Increase of H 2 O 2 concentration was found as a result of plasma treatment of liquids but not after treatment by NO gas. Therefore, synergistic action of both reactive oxygen and nitrogen species are discussed to be responsible for antimicrobial plasma effects. magnified image
Overexpression of Prostate-Specific <i>TMPRSS2(exon 0)-ERG</i> Fusion Transcripts Corresponds with Favorable Prognosis of Prostate Cancer (2009)

The expression of TMPRSS2(exon 0)-ERG fusion transcripts in prostate cancer is associated with a less-aggressive biological behavior.
An "Endless" Route to Cyclic Polymers (2002)

A new synthetic route to cyclic polymers has been developed in which the ends of growing polymer chains remain attached to a metal complex throughout the entire polymerization process. The approach eliminates the need for linear polymeric precursors and high dilution, drawbacks of traditional macrocyclization strategies, and it effectively removes the barrier to producing large quantities of pure cyclic material. Ultimately, the strategy offers facile access to a unique macromolecular scaffold that may be used to meet the increasing demand of new applications for commercial polymers. As a demonstration of its potential utility, cyclic polyethylenes were prepared and found to exhibit a variety of physical properties that were distinguishable from their linear analogs.
Resistance to Celiac Disease in Humanized HLA-DR3-DQ2-Transgenic Mice Expressing Specific Anti-Gliadin CD4+ T Cells (2009)

Celiac disease is a chronic inflammatory enteropathy caused by cellular immunity to dietary gluten. More than 90% of patients carry HLA-DQ2 encoded by HLA-DQA1*05 and DQB1*02, and gluten-specific CD4(+) T cells from intestinal biopsies of these patients are HLA-DQ2-restricted, produce Th1 cytokines and preferentially recognize gluten peptides deamidated by tissue transglutaminase. We generated mice lacking murine MHC class II genes that are transgenic for human CD4 and the autoimmunity and celiac disease-associated HLA-DR3-DQ2 haplotype. Immunization with the alpha-gliadin 17-mer that incorporates the overlapping DQ2-alpha-I and DQ2-alpha-II epitopes immunodominant in human celiac disease generates peptide-specific HLA-DQ2-restricted CD4(+) T cells. When exposed to dietary gluten, naive or gliadin-primed mice do not develop pathology. Coincident introduction of dietary gluten and intestinal inflammation resulted in low-penetrance enteropathy and tissue transglutaminase-specific IgA. Two further strains of transgenic mice expressing HLA-DR3-DQ2 and human CD4, one with a NOD background and another TCR transgenic having over 90% of CD4(+) T cells specific for the DQ2-alpha-II epitope with a Th1 phenotype, were also healthy when consuming gluten. These humanized mouse models indicate that gluten ingestion can be tolerated without intestinal pathology even when HLA-DQ2-restricted CD4(+) T cell immunity to gluten is established, thereby implicating additional factors in controlling the penetrance of celiac disease.
Design of porphyrin-based conjugated microporous polymers with enhanced singlet oxygen productivity (2016)

Novel porphyrin-based conjugated microporous polymers displayed high O<sub>2</sub>(<sup>1</sup>Δ<sub>g</sub>) production, were stable in organic solvents, and did not undergo measurable photobleaching.
Performance characterization of the Pentium Pro processor (2002)

In this paper, we characterize the performance of several business and technical benchmarks on a Pentium Pro processor based system. Various architectural data are collected using a performance monitoring counter tool. Results show that the Pentium Pro processor achieves significantly lower cycles per instruction than the Pentium processor due to its out of order and speculative execution, and non-blocking cache and memory system. Its higher clock frequency also contributes to even higher performance.