gebhart/patrepeval huggingface dataset:
Evaluation of PD-L1 Expression and Associated Tumor-Infiltrating Lymphocytes in Laryngeal Squamous Cell Carcinoma (2015)

Increased TILs density and PD-L1 levels are associated with better outcome in laryngeal squamous cell cancer. Assessment of TILs and PD-L1 expression could be useful to predict response to immune checkpoint inhibitors.
Michael additions in anhydrous media. A novel synthesis of oxygenated coumarins (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMichael additions in anhydrous media. A novel synthesis of oxygenated coumarinsGeorge A. Kraus and John O. PezzaniteCite this: J. Org. Chem. 1979, 44, 14, 2480–2482Publication Date (Print):July 1, 1979Publication History Published online1 May 2002Published inissue 1 July 1979https://pubs.acs.org/doi/10.1021/jo01328a031https://doi.org/10.1021/jo01328a031research-articleACS PublicationsRequest reuse permissionsArticle Views355Altmetric-Citations29LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Optimal margin computation for at-speed test (2008)

In the face of increased process variations, at-speed manufacturing test is necessary to detect subtle delay defects. This procedure necessarily tests chips at a slightly higher speed than the target frequency required in the field. The additional performance required on the tester is called test margin. There are many good reasons for margin including voltage and temperature requirements, incomplete test coverage, aging effects, coupling effects and accounting for modeling inaccuracies. By taking advantage of statistical timing, this paper proposes an optimal method of test margin determination to maximize yield while staying within a prescribed Shipped Product Quality Loss (SPQL) limit. If process information is available from wafer testing of scribe line structures or on-chip process monitoring circuitry, this information can be leveraged to determine a per-chip test margin which can further improve yield.
High-Resolution Solution Structure of the EGF-like Domain of Heregulin-α (1996)

The solution structure of the 63-residue heregulin-alpha (HRG-alpha) epidermal growth factor (EGF)-like domain, corresponding to residues 177-239 of HRG-alpha, has been determined to high resolution using data from two-dimensional and three-dimensional homo- and heteronuclear NMR spectroscopy. The structure is based on a total of 887 internuclear distance and dihedral restraints derived from data obtained using unlabeled and uniformly 15N-labeled protein samples, at pH 4.5, 20 degrees C. A total of 20 structures were calculated using a hybrid distance geometry-simulated annealing approach with the program DGII, followed by restrained molecular dynamics using the program DISCOVER. The average maximum violations are 0.12 +/- 0.01 angstroms and 1.4 +/- 0.3 degrees for distance and dihedral restraints, respectively. The backbone (N,C(alpha),C) atomic rms distribution about the mean coordinates for residues 3-23 and 31-49 is 0.29 +/- 0/07 angstroms. The N-and C-terminal residues (1-2 and 50-63) and 24-30 are disordered. Comparison of the HRG-alpha EGF-like domain structure with the previously determined structure of human EGF [Hommel et al. (1992) J. Mol. Biol. 227, 271-282] reveals a high degree of structural similarity; excluding the N-terminal region (residues 1-13), the disordered phi-loop region (residues 24-30) that contains a three-residue insertion in HRG-alpha relative to hEGF, and the disordered C-terminal region (residues 50-63), the C(alpha) alignment between the HRG-alpha and hEGF minimized mean structures has a rms difference of approximately 1 angstrom. In HRG-alpha the N-terminal residues 2-6 form a well-defined beta strand rather than being disordered as found for hEGF. This structural difference correlates with functional data which suggest that the N-terminal region of the HRG-alpha EGF-like domain is responsible for the observed receptor specificity differences between HRG-alpha and EGF.
The Role of Endogenous Corticosterone in the Late-Phase Response to Allergen Challenge in the Brown Norway Rat (1996)

The aim of this study was to assess the role of endogenous corticosterone (CCST) concentrations on the late airway response (LAR) to ovalbumin (OA). Thirty-two Brown Norway (BN) rats were sensitized to OA on Day 0, then divided into three groups. Group 1 (n = 11) received saline (1 ml, subcutaneously) at time (T) = -24, -12, and 0 h prior to a 5% OA challenge on Day 14. Group 2 (n = 11) received metyrapone (MTP), an 11 beta-hydroxylase inhibitor, (10 mg/100 g in 1 ml saline, subcutaneously) at time (T) = -24, -12, and 0 h. Group 3 (n = 10) received MTP on the same schedule as Group 2, plus CCST in the drinking water (16 micrograms/ml) from T = -24 to T = 0 h. Pulmonary resistance (RL) was measured for 8 h following OA challenge to determine early (EAR) and LAR. Blood samples were taken at T = 0 and T = 8 h to determine serum CCST levels. Bronchoalveolar lavage (BAL) fluid was collected at T = 8 h. Serum CCST levels were significantly reduced in the MTP group (235 ng/ml +/- 14 SEM) compared with control (564 +/- 38, p < 0.0001) and MTP+CCST animals (349 +/- 19, p < 0.0005). There were no differences in either baseline RL or EAR between the groups. However, the MTP group had a smaller LAR (6 ml/cm H2O/s*min +/- 2 SEM) than the control group (19 +/- 5, p < 0.02). The effect of MTP on LAR was reversed by treatment with CCST (21 +/- 3, p < 0.005). Total cell counts (p < 0.05) and eosinophils (p < 0.01) were increased in the BAL fluid of MTP rats versus control and MTP+CCST animals. We conclude that depletion of endogenous CCST in the BN rat diminishes the LAR to allergen challenge. These results indicate that physiologic levels of CCST are not necessary for development of the EAR, but they play a permissive role in the LAR to inhaled allergen.
Vitamin D3 Receptors: Structure and Function in Transcription (1991)

PERSPECTIVES AND SUMMARY 190 VITAMIN D3 HORMONE 191 Metabolism to the Active Form ......... . .... 191 Biologic Actions. ...... . ....... ......... . . . . . . ...... ..... ...... . . ... . . .. . . .... . . . . . ... 192 Transcriptional Mechanism of Action . . . . . . . . . . ....... . . . . .. . . . ...... . . 192 VITAMIN D3 RECEPTOR 193 Cellular Distribution. . 193 Biochemical Properties and Subcellular Distribution.. . .. . . . . . . . . . . . . . .. . . . . . . . . . . . . .... . . 194 Vitamin D3 Receptor Regulation.... . . . ........ . ..... . .... ........ . . . . .... .. . . . ...... 196 MOLECULAR BIOLOGY OF THE VITAMIN D3 RECEPTOR 198 Recombinant Cloning of the Vitamin D3 Receptor .... .... . ...... . . ..... .. . .. . ....... ...... 198 Steroid, Thyroid, and Retinoid Receptor Supeifamily 200 Structural Organization of the Nuclear Receptors ..... ....... . .. . . . .... . . . .. 200 Role of the Vitamin D3 Receptor in Transactivation . ........ . ...... . . . ..... . . ..... . . . . . .. 202 HUMAN SYNDROME OF HEREDITARY 1,25-DIHYDROXYVITAMIN D3 RESISTANCE 205 Vitamin DrResistant Fibroblast Model .... ......... . . ........ .. . . . . . . ...... 205 Genetic Lesions in the Vitamin D3 Receptor Chromosomal Locus . ....... . . ...... . . . .. 206 Functional Activity of Receptors Derived from Patient Genotypes 208 CONCLUSIONS 208
Angiotensin II Promotes Glucose-Induced Activation of Cardiac Protein Kinase C Isozymes and Phosphorylation of Troponin I (2001)

Activation of the protein kinase C (PKC) family is a potential signaling mechanism by which high ambient glucose concentration modulates the phenotype and physiological function of cells. Recently, the cardiac renin angiotensin system (RAS) has been reported to promote PKC translocation in the diabetic heart via the angiotensin (ANG) II type 1 receptor (AT-1R). To evaluate the molecular events coupled with high glucose-induced PKC translocation and to examine the role of endogenously released ANG II in myocyte PKC signaling, primary cultures of adult rat ventricular myocytes were exposed to normal (5 mmol/l) or high (25 mmol/l) glucose for 12-24 h. Western blot analysis indicated that adult rat ventricular myocytes coexpress six PKC isozymes (alpha, beta(1,) beta(2,) delta, epsilon, and zeta). Translocation of five PKC isozymes (beta(1), beta(2), delta, epsilon, and zeta) was detected in response to 25 mmol/l glucose. Inhibition of phospholipase C with tricyclodecan-9-yl-xanthogenate blocked glucose-induced translocation of PKC-beta(2), -delta, and -zeta. Inhibition of tyrosine kinase with genistein blocked glucose-induced translocation of PKC-beta(1) and -delta, whereas chelation of intracellular Ca(2+) with 1,2-bis(2-aminophenoxy)ethane N,N,N,'N'-tetraacetic acid blocked translocation of PKC-beta(1) and -beta(2). Enzyme-linked immunosorbent assay performed on culture media from myocytes maintained in 25 mmol/l glucose detected a twofold increase in ANG II. Addition of an AT-1R antagonist (losartan; 100 nmol/l) to myocyte cultures blocked translocation of PKC-beta(1), -beta(2), -delta, and -epsilon. Phosphorylation of troponin (Tn) I was increased in myocytes exposed to 25 mmol/l glucose. Losartan selectively inhibited Tn I serine phosphorylation but did not affect phosphorylation at threonine residues. We concluded that 1) 25 mmol/l glucose triggers the release of ANG II by myocytes, resulting in activation of the ANG II autocrine pathway; 2) differential translocation of myocyte PKC isozymes occurs in response to 25 mmol/l glucose and ANG II; and 3) AT-1R-dependent PKC isozymes (beta(1), beta(2), delta, and epsilon) target Tn I serine residues.
A bioelectrochemical study of a suspension of Escherichia coli cells metabolizing glucose and lactose (2006)

The metabolism of glucose and lactose in E. coli K-12 cells has been studied using a bioelectrochemical (BEC) approach. The magnitude and the duration of the response of a BEC anode were found to be functions of the composition of nutrient media and the concentration of bacterial cells. The amount of electricity that is generated enzymatically during the metabolism of a particular substrate depends on the activity of the relevant enzymes. This suggests that the BEC approach can be used for evaluating the activity of particular enzyme systems.
Comparison of aroma characteristics of 16 fish species by sensory evaluation and gas chromatographic analysis (2003)

Abstract The aroma properties of fish broths prepared from 16 fish species (10 saltwater, three freshwater, two anadromous and one brackish water species) were described quantitatively by reference to 10 sensory attributes. Principal component analysis (PCA) and cluster analysis of sensory attributes classified the fish into four groups. Group 1, characterised by a strong ‘green’ odour, comprised all three freshwater species (loach, pond smelt and carp), two saltwater whitefish species (snapper and conger) and eel. Group 2 included migratory coastal species (sardine, banded blue‐sprat and mackerel) and was distinguished by strong ‘fish oil’ and ‘grilled fish’ notes. Group 3 consisted of swordfish, sablefish and salmon, which exhibited a strong ‘fried chicken’ note. Group 4 included flounder, cod, tuna and goby, which were scored high for ‘cooked fish’, ‘roasted soy sauce’, ‘canned tuna’ and ‘sweet’ aromas. Partial least squares regression (PLSR) models derived from selected influential peaks in the gas chromatograms of the volatile components in the broths for each attribute were highly predictive ( R 2 ≥ 0.936). The selected peaks corresponded well to each sensory attribute. © 2003 Society of Chemical Industry
Cloning and Expression of a Potato cDNA Encoding Hydroxycinnamoyl-CoA:TyramineN-(Hydroxycinnamoyl)transferase (1999)

Hydroxycinnamoyl-CoA:tyramine N-(hydroxycinnamoyl)transferase (THT; EC 2.3.1.110) catalyzes the transfer of hydroxycinnamic acids from the respective CoA esters to tyramine and other amines in the formation of N-(hydroxycinnamoyl)amines. Expression of THT is induced by Phytophthora infestans, the causative agent of late blight disease in potato. The amino acid sequences of nine endopeptidase LysC-liberated peptides from purified potato THT were determined. Using degenerate primers, a THT-specific fragment was obtained by reverse transcription-polymerase chain reaction, and THT cDNA clones were isolated from a library constructed from RNA of elicitor-treated potato cells. The open reading frame encoding a protein of 248 amino acids was expressed in Escherichia coli. Recombinant THT exhibited a broad substrate specificity, similar to that of native potato THT, accepting cinnamoyl-, 4-coumaroyl-, caffeoyl-, feruloyl- and sinapoyl-CoA as acyl donors and tyramine, octopamine, and noradrenalin as acceptors tested. Elicitor-induced THT transcript accumulation in cultured potato cells peaked 5 h after initiation of treatment, whereas enzyme activity was highest from 5 to 30 h after elicitation. In soil-grown potato plants, THT mRNA was most abundant in roots. Genomic Southern analyses indicate that, in potato, THT is encoded by a multigene family.
Aflibercept: a Potent Vascular Endothelial Growth Factor Antagonist for Neovascular Age-Related Macular Degeneration and Other Retinal Vascular Diseases (2012)

VEGF Trap-Eye has enhanced the treatment options currently available for the management of neovascular AMD. The comparable efficacy of VEGF Trap-Eye (to other anti-VEGF agents) coupled with its longer dosing interval may decrease the number of annual office visits for patients with AMD and their caregivers.
Cleavage Preferences of the Apoptotic Endonuclease DFF40 (Caspase-activated DNase or Nuclease) on Naked DNA and Chromatin Substrates (2000)

Here we report the co-factor requirements for DNA fragmentation factor (DFF) endonuclease and characterize its cleavage sites on naked DNA and chromatin substrates. The endonuclease exhibits a pH optimum of 7.5, requires Mg(2+), not Ca(2+), and is inhibited by Zn(2+). The enzyme generates blunt ends or ends with 1-base 5'-overhangs possessing 5'-phosphate and 3'-hydroxyl groups and is specific for double- and not single-stranded DNA or RNA. DFF endonuclease has a moderately greater sequence preference than micrococcal nuclease or DNase I, and the sites attacked possess a dyad axis of symmetry with respect to purine and pyrimidine content. Using HeLa cell nuclei or chromatin reconstituted on a 5 S rRNA gene tandem array, we prove that the enzyme attacks chromatin in the internucleosomal linker, generating oligonucleosomal DNA ladders sharper than those created by micrococcal nuclease. Histone H1, high mobility group-1, and topoisomerase II activate DFF endonuclease activity on naked DNA substrates but much less so on chromatin substrates. We conclude that DFF is a useful reagent for chromatin research.
Infrared matrix isolation study of magnesium metal atom reactions. Spectra of an unsolvated Grignard species (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfrared matrix isolation study of magnesium metal atom reactions. Spectra of an unsolvated Grignard speciesBruce S. AultCite this: J. Am. Chem. Soc. 1980, 102, 10, 3480–3484Publication Date (Print):May 1, 1980Publication History Published online1 May 2002Published inissue 1 May 1980https://pubs.acs.org/doi/10.1021/ja00530a028https://doi.org/10.1021/ja00530a028research-articleACS PublicationsRequest reuse permissionsArticle Views382Altmetric-Citations33LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering (2007)

For Escherichia coli, the promoter strength can not been linked to anomalies in the -10 box and/or -35 box, and to the length of the spacer. Also a probabilistic approach to relate the promoter sequence to its strength has some drawbacks. However, by applying Partial Least Squares regression, a good correlation was found between promoter sequence and promoter strength. This PLS model can be a useful tool to rationally design a suitable promoter in order to fine tune gene expression.
Overlap between functional GI disorders and other functional syndromes: what are the underlying mechanisms? (2012)

The objective of this review is to discuss the proposed pathophysiologic mechanisms, which have been similarly studied in these conditions. These mechanisms include enhanced pain perception, altered regional brain activation, infectious etiologies, dysregulations in immune and neuroendocrine function, and genetic susceptibility. Studies suggest that these functional disorders are multifactorial, but factors which increase the vulnerability of developing these conditions are shared.
Regulation of the Cell-specific Calcitonin/Calcitonin Gene-related Peptide Enhancer by USF and the Foxa2 Forkhead Protein (2004)

An 18-bp enhancer controls cell-specific expression of the calcitonin/calcitonin gene-related peptide gene. The enhancer is bound by a heterodimer of the bHLH-Zip protein USF-1 and -2 and a cell-specific factor from thyroid C cell lines. In this report we have identified the cell-specific factor as the forkhead protein Foxa2 (previously HNF-3beta). Binding of Foxa2 to the 18-bp enhancer was demonstrated using electrophoretic mobility shift assays. The cell-specific DNA-protein complex was selectively competed by a series of Foxa2 DNA binding sites, and the addition of Foxa2 antiserum supershifted the complex. Likewise, a complex similar to that seen with extracts from thyroid C cell lines was generated using an extract from heterologous cells expressing recombinant Foxa2. Interestingly, overexpression of Foxa2 activated the 18-bp enhancer in heterologous cells but only in the presence of the adjacent helix-loop-helix motif. Likewise, coexpression of USF proteins with Foxa2 yielded greater activation than by Foxa2 alone. Unexpectedly, Foxa2 overexpression repressed activity in the CA77 thyroid C cell line, suggesting that Foxa2 may interact with additional cofactors. The stimulatory role of Foxa2 at the calcitonin/calcitonin gene-related peptide gene enhancer was confirmed by short interfering RNA-mediated knockdown of Foxa2. As seen with Foxa2 overexpression, the effect of Foxa2 knockdown also required the adjacent helix-loop-helix motif. These results provide the first evidence for combinatorial control of gene expression by bHLH-Zip and forkhead proteins.
Electrochemical Characterization of Films of Single-Walled Carbon Nanotubes and Their Possible Application in Supercapacitors (1999)

Films of single-wall carbon nanotubes (SWCNTs) were cast from suspensions in several solvents on the surface of a Pt or Au electrode. Cyclic voltammetry of the films in MeCN did not show well-resolved waves (as distinct from films of C_(60) prepared in a similar manner). However, the increase in the effective capacitance of the electrode with a SWCNT film at 0.5 V vs. an AgQRE was 283 F/g, which is about twice that of carbon electrodes in nonaqueous solvents.
Hemolysis-associated endothelial dysfunction mediated by accelerated NO inactivation by decompartmentalized oxyhemoglobin (2005)

During intravascular hemolysis in human disease, vasomotor tone and organ perfusion may be impaired by the increased reactivity of cell-free plasma hemoglobin (Hb) with NO. We experimentally produced acute intravascular hemolysis in a canine model in order to test the hypothesis that low levels of decompartmentalized or cell-free plasma Hb will severely reduce NO bioavailability and produce vasomotor instability. Importantly, in this model the total intravascular Hb level is unchanged; only the compartmentalization of Hb within the erythrocyte membrane is disrupted. Using a full-factorial design, we demonstrate that free water-induced intravascular hemolysis produces dose-dependent systemic vasoconstriction and impairs renal function. We find that these physiologic changes are secondary to the stoichiometric oxidation of endogenous NO by cell-free plasma oxyhemoglobin. In this model, 80 ppm of inhaled NO gas oxidized 85-90% of plasma oxyhemoglobin to methemoglobin, thereby inhibiting endogenous NO scavenging by cell-free Hb. As a result, the vasoconstriction caused by acute hemolysis was attenuated and the responsiveness to systemically infused NO donors was restored. These observations confirm that the acute toxicity of intravascular hemolysis occurs secondarily to the accelerated dioxygenation reaction of plasma oxyhemoglobin with endothelium-derived NO to form bioinactive nitrate. These biochemical and physiological studies demonstrate a major role for the intact erythrocyte in NO homeostasis and provide mechanistic support for the existence of a human syndrome of hemolysis-associated NO dysregulation, which may contribute to the vasculopathy of hereditary, acquired, and iatrogenic hemolytic states.
Near-Earth Asteroid Scout (2014)

Near-Earth Asteroids (NEAs) are an easily accessible object in Earth's vicinity. Detections of NEAs are expected to grow in the near future, offering increasing target opportunities. As NASA continues to refine its plans to possibly explore these small worlds with human explorers, initial reconnaissance with comparatively inexpensive robotic precursors is necessary. Obtaining and analyzing relevant data about these bodies via robotic precursors before committing a crew to visit a NEA will significantly minimize crew and mission risk, as well as maximize exploration return potential. The Marshall Space Flight Center (MSFC) and Jet Propulsion Laboratory (JPL) are jointly examining a mission concept, tentatively called 'NEA Scout,' utilizing a low-cost CubeSats platform in response to the current needs for affordable missions with exploration science value. The NEA Scout mission concept would be a secondary payload on the Space Launch System (SLS) Exploration Mission 1 (EM-1), the first planned flight of the SLS and the second un-crewed test flight of the Orion Multi-Purpose Crew Vehicle (MPCV).