gebhart/patrepeval huggingface dataset:
Both isoforms of human UDP-glucose:glycoprotein glucosyltransferase are enzymatically active (2014)

Being recognized as an important constituent of the glycoprotein folding cycle, uridine diphosphate-glucose:glycoprotein glucosyltransferase (UGGT) has been a subject of intense study. Up to now, it is two isoforms, UGGT1 and 2 have been identified, which share ∼ 50% amino acid identity. UGGT1 is a well-documented enzyme which functions as a folding sensor in the endoplasmic reticulum, by the virtue of its ability to transfer a glucose residue to non-glucosylated high-mannose-type glycans of immature glycoproteins exhibiting non-native conformation. On the other hand, direct evidence to support the glucosyltransferase activity of UGGT2 has been lacking, leaving it unclear as to whether it has any function in the glycoprotein folding process. This study aimed to reveal the property of human UGGT2 by using synthetic substrates such as fluorescently labeled glycans and N-glycosylated proteins. The analysis, for the first time, revealed the glucosyltransferase activity of UGGT2, whose specificity was shown to be quite similar to UGGT1, in terms of both glycan specificity and preferential recognition of proteins having non-native conformations. Finally, Sep15 was found to form the heterodimeric complex with both isoforms of UGGT and markedly enhanced its glucosyltransferase activity.
Activation of the Receptor for Advanced Glycation End Products Triggers a p21 -dependent Mitogen-activated Protein Kinase Pathway Regulated by Oxidant Stress (1997)

Advanced glycation end products (AGEs) exert their cellular effects on cells by interacting with specific cellular receptors, the best characterized of which is the receptor for AGE (RAGE). The transductional processes by which RAGE ligation transmits signals to the nuclei of cells is unknown and was investigated. AGE-albumin, a prototypic ligand, activated p21(ras) in rat pulmonary artery smooth muscle cells that express RAGE, whereas nonglycated albumin was without effect. MAP kinase activity was enhanced at concentrations of AGE-albumin, which activated p21(ras) and NF-kappaB. Depletion of intracellular glutathione rendered cells more sensitive to AGE-mediated activation of this signaling pathway. In contrast, signaling was blocked by preventing p21(ras) from associating with the plasma membrane or mutating Cys118 on p21(ras) to Ser. Signaling was receptor-dependent, because it was prevented by blocking access to RAGE with either anti-RAGE IgG or by excess soluble RAGE. These data suggest that RAGE-mediated induction of cellular oxidant stress triggers a cascade of intracellular signals involving p21(ras) and MAP kinase, culminating in transcription factor activation. The molecular mechanism that triggers this pathway likely involves oxidant modification and activation of p21(ras).
Novel prenyltransferase gene encoding farnesylgeranyl diphosphate synthase from a hyperthermophilic archaeon, Aeropyrum pernix (2000)

Prenyltransferases catalyse sequential condensations of isopentenyl diphosphate with allylic diphosphates. Previously, we reported the presence of farnesylgeranyl diphosphate (FGPP) synthase activity synthesizing C25 isoprenyl diphosphate in Natronobacterium pharaonis which is a haloalkaliphilic archaeon having C20-C25 diether lipids in addition to C20-C20 diether lipids commonly occurring in archaea [Tachibana, A. (1994) FEBS Lett. 341, 291-294]. Recently, it was found that a newly isolated aerobic hyperthermophilic archaeon, Aeropyrum pernix, had only C25-C25 diether lipids, not the usual C20-containing lipids [Morii, H., Yagi, H., Akutsu, H., Nomura, N., Sako, Y. & Koga, Y. (1999) Biochim. Biophys. Acta 1436, 426-436]. In this report, we describe the isoloation from A. pernix of the novel prenyltransferase gene, fgs, encoding FGPP synthase. The protein encoded by fgs was expressed in Escherichia coli as a glutathione S-transferase fusion protein and produced FGPP as a final product. Phylogenetic analysis of fgs with other prenyltransferases revealed that the short-chain prenyltransferase family is divided into three subfamilies: bacterial subfamily I, eukaryotic subfamily II, and archaeal subfamily III. fgs is clearly contained within the archaeal geranylgeranyl diphosphate (GGPP) synthase group (subfamily III), suggesting that FGPP synthase evolved from an archaeal GGPP synthase with an alteration in product specificity.
Estimation of Melting Points of Organic Compounds (2004)

A combination of additive group contributions and nonadditive molecular parameters is employed to estimate the normal melting points of 1215 organic compounds. The melting points are calculated from the ratio of the total phase change enthalpy and entropy of melting. The total phase change enthalpy of melting is calculated from the enthalpic group contributions, whereas the total phase change entropy of melting is estimated using a semiempirical equation based on only two nonadditive molecular parameters. The average absolute error in estimating the melting points of these organic compounds is 33.2 K. This is a relatively low value considering the wide range of pharmaceutically and environmentally relevant organic compounds included in this data set.
Cytokeratin-based CTC counting unrelated to clinical follow up. (2013)

This case report study shows the interest of a comparative and kinetic analysis of different methods for CTCs detection combined with their evaluation according to the clinical follow up. Our results should open up an area for future research and validation in larger clinical cohorts.
The Cyclization and Polymerization of Bacterially Expressed Proteins Using Modified Self-splicing Inteins (1999)

Mini-inteins derived from Synechocystis sp. (Ssp DnaB intein) and Mycobacterium xenopi (Mxe GyrA intein) that have been modified to cleave peptide bonds at their C and N termini, respectively, were cloned in-frame to the N and C termini of a target protein. Peptide bond cleavage of the modified inteins generated an N-terminal cysteine and a C-terminal thioester on the same protein. These complementary reactive groups underwent intra- or intermolecular condensation to generate circular or polymeric protein species with a new peptide bond at the site of ligation. Three cyclic peptides, BBP, an organ specific localization peptide; RGD, an inhibitor of platelet aggregation; and CDR-H3/C2, which inhibits HIV-1 replication, were isolated using the two-intein system. BBP, RGD, and CDR-H3/C2 had masses of 977.1, 1119.9, and 2098.6 g/mol, respectively, as determined by matrix-assisted laser desorption-time of flight mass spectrometry, which agreed well with the values of 977.2, 1120.3, and 2098.3 g/mol, respectively, predicted for the cyclic species. This system was used to cyclize proteins as large as 395 amino acids. Furthermore, multimers of thioredoxin were formed upon concentration of the reactive species, indicating the potential to form novel biomaterials based on fibrous proteins.
RATCHET BONDS: MAXIMUM REFUNDING EFFICIENCY AT MINIMUM TRANSACTION COST (1999)

Callable bonds, which are widely used by corporate borrowers to manage interest rate risk, have several major drawbacks. Foremost is the transaction cost of refunding. In addition, poor execution—calling too early or too late—is common, causing a transfer of wealth from shareholders to bondholders. The Ratchet bond captures the advantages of a callable bond—the ability to lower interest costs when rates decline—while eliminating its undesirable features. If rates fall after issuance, the coupon of a Ratchet bond automatically resets to the yield of a specified Treasury bond plus some fixed spread. The resulting “step‐down” cash flow pattern resembles that of a sequence of callable bonds that are refunded to the same original maturity date. The Tennessee Valley Authority was the first to use this innovative structure. In June 1998, they sold $575 million 6.75%“PARRS” with a 30‐year maturity and annual rate resets beginning after five years. Moreover, as this article went to print, TVA announced its intent to sell another large Ratchet issue with features virtually identical to the PARRS described in this article.
Highly Scalable Horizontal Channel 3-D NAND Memory Excellent in Compatibility With Conventional Fabrication Technology (2013)

We developed a stacked horizontal channel type floating gate (HC-FG) NAND memory; a 3-D stacked NAND array composed of conventional FG cells. With this cell structure, a wide program/erase (P/E) window is obtained, accompanied by superior read disturb immunity, P/E endurance, and data retention. In addition, we propose a low-cost layer select transistor (LST) that is easily integrated with the HC-FG cell. Because the 3-D memory composed of the HC-FG cell and the LST has good compatibility with conventional fabrication technology, further bit cost scaling is expected.
Target classification and localization in habitat monitoring (2004)

We are developing an acoustic habitat-monitoring sensor network that recognizes and locates specific animal calls in real time. We investigate the system requirements of such a real-time acoustic monitoring network. We propose a system architecture and a set of lightweight collaborative signal processing algorithms that achieve real-time behavior while minimizing inter-node communication to extend the system lifetime. In particular, the target classification is based on spectrogram pattern matching while the target localization is based on beamforming using time difference of arrival (TDOA). We describe our preliminary implementation on a commercial off the shelf (COTS) testbed and present its performance based on testbed measurements.
The synthetic utility of heteroaromatic azido compounds. Part VII. Preparation of some 2‐ and 4‐substituted thieno[3,2‐d]pyrimidines (1980)

Abstract Synthetically useful scission reactions of some 1 H ‐1,2,3‐triazolo[1,5‐ a ]thieno[3,2‐ d ]pyrimidines have been studied. The net result of these reactions is an elimination of nitrogen, and a 1,1‐addition of the cleaving agent, forming 2‐substituted thieno[3,2‐ d ]pyrimidines. The mechanism of the scission is discussed, and a concomitant nucleophilic attack and expulsion of nitrogen is proposed. An unusual reaction between the unsubstituted triazole‐fused parent compound ( 1 ) and bromine in alkaline medium is also reported.
Opsonophagocytic Killing Antibody toPseudomonas aeruginosaMucoid Exopolysaccharide in Older Noncolonized Patients with Cystic Fibrosis (1987)

The principal cause of morbidity and mortality in cystic fibrosis is persistent respiratory colonization with mucoid strains of Pseudomonas aeruginosa. To investigate possible mechanisms of resistance to this organism, we studied serum from 16 older (greater than or equal to 12 years) patients not colonized with mucoid P. aeruginosa, 11 older (greater than or equal to 14 years) colonized patients, 10 younger (less than or equal to 11 years) noncolonized patients, and 20 healthy adults. The samples from the older patients not colonized with mucoid P. aeruginosa contained antibody specific to the mucoid-exopolysaccharide antigen, which could mediate bacterial killing in conjunction with complement and white cells (titers of 4 to 80). These opsonophagocytic killing antibodies were not detected in samples from the 20 normal controls (P less than 0.0001 vs. noncolonized older patients) or 9 of 10 younger (less than or equal to 11 years) noncolonized patients (P = 0.0072 vs. noncolonized older patients). Although the patients with chronic colonization had higher titers of serum opsonophagocytic killing antibody than did the older noncolonized patients (P = 0.0005), these antibodies were not specific to the mucoid-exopolysaccharide antigen. We conclude that there is an association between mucoid-exopolysaccharide-specific opsonophagocytic killing antibody and a lack of detectable P. aeruginosa colonization in a subset of older, relatively healthy patients with cystic fibrosis.
Regulation of the superoxide-generating NADPH oxidase by a small GTP-binding protein and its stimulatory and inhibitory GDP/GTP exchange proteins. (1992)

The superoxide-generating NADPH oxidase system in phagocytes consists of at least membrane-associated cytochrome b558 and three cytosolic components named SOCI/NCF-3/sigma 1/C1, SOCII/NCF-1/p47-phox, and SO-CIII/NCF-2/p67-phox. p47-phox and p67-phox were isolated, and their primary structures were determined, but SOCI has not been well characterized. In the present study, we first purified SOCI to homogeneity from the cytosol fraction of the differentiated HL-60 cells. The purified SOCI was a small GTP-binding protein (G protein) with a M(r) of about 22,000. The guanosine 5'-(3-O-thio)triphosphate-bound form, but not the GDP-bound form, of this small G protein showed the SOCI activity. The partial amino acid sequence of SOCI thus far determined was identical to the amino acid sequence deduced from the cDNA encoding rac2 p21. None of the purified small G proteins, including Ki-ras p21, smg p21B/rap1B p21, rhoA p21, and rac1 p21, showed the SOCI activity. These results indicate that SOCI is a small G protein very similar, if not identical, to rac2 p21. The GDP/GTP exchange reaction of SOCI was stimulated and inhibited by stimulatory and inhibitory GDP/GTP exchange proteins for small G proteins, named smg GDS and rho GDI, respectively. The NADPH oxidase activity was also stimulated and inhibited by smg GDS and rho GDI, respectively. These results indicate that the superoxide-generating NADPH oxidase system is regulated by both smg GDS and rho GDI through rac2 p21 or the rac2-related small G protein in phagocytes.
Platelet membrane glycoprotein IIb-IIIa complex incorporated into phospholipid vesicles. Preparation and morphology. (1985)

Platelet membrane glycoproteins (GP) IIb and IIIa have been identified as platelet aggregation sites. These glycoproteins form a heterodimer complex (GP IIb-IIIa) in the presence of Ca2+. To study the morphology of this glycoprotein complex in membranes, we incorporated GP IIb-IIIa into artificial phospholipid vesicles using a detergent (octyl glucoside) dialysis procedure. Phosphatidylserine-enriched vesicles (70% phosphatidylserine, 30% phosphatidylcholine) incorporated approximately 90% of the GP IIb-IIIa as determined by sucrose flotation. Glycoprotein IIb-IIIa incorporation into the vesicles was unaffected by ionic strength, suggesting a hydrophobic interaction between the glycoprotein and the phospholipid. In both intact platelets or phospholipid vesicles, GP IIb was susceptible to neuraminidase hydrolysis, indicating that most of the glycoprotein complexes were oriented toward the outside of the platelets or vesicles. The morphology of GP IIb-IIIa in the phospholipid vesicles was observed by negative staining electron microscopy. Individual GP IIb-IIIa complexes appeared as spikes protruding as much as 20 nm from the vesicle surface. Each spike consisted of a GP IIb "head," which was distal to the vesicle and was supported by the GP IIIa "tails." The GP IIb-IIIa complex appeared to be attached to the vesicle membrane by the tips of the GP IIIa tails. Treatment of vesicles with EGTA dissociated the GP IIb-IIIa complex. The dissociated glycoproteins remained attached to the phospholipid vesicles, indicating that both GP IIb and GP IIIa contain membrane-attachment sites. These data suggest a possible structural arrangement of the GP IIb-IIIa complex in whole platelets.
Association between anaplastic lymphoma kinase rearrangements (rALK) and the clinical activity of IPI-504 (retaspimycin hydrochloride), a novel Hsp90 inhibitor, in patients with non-small cell lung cancer (NSCLC). (2010)

7517 Background: Oncogenic ALK gene rearrangements (rALK) recently have been identified in approximately 3-5% of all NSCLC, particularly in non-smoking patients (pts) with epidermal growth factor receptor (EGFR) wild-type tumors. IPI-504 is a potent, water-soluble heat shock protein 90 (Hsp90) inhibitor that is being evaluated in a clinical study of patients with NSCLC, stratified by EGFR status. In preclinical models, ALK is a client protein of the Hsp90 chaperone; therefore, a retrospective analysis of the ALK status of pts in this trial was conducted. Methods: A nonrandomized phase II trial investigating the safety and antitumor activity of IPI-504 as a single agent was performed. Eligible pts had advanced NSCLC that progressed after treatment with at least one tyrosine kinase inhibitor. The primary endpoint was response rate, assessed via central, independent radiology review. rALK was assessed centrally with a fluorescent in situ hybridization (FISH) break-apart assay. Results: 76 pts were enrolled. 15 pts had tissue available for analysis of the ALK gene. See Table below. Conclusions: rALK may be a useful biomarker predicting response to therapy with IPI-504. These clinical data are the first to suggest that NSCLC pts with rALK may preferentially respond to Hsp90 inhibition. Validation is ongoing in a prospective extension of this clinical trial. Clinical activity based on molecular characterization N ORR CBR Overall 76 5 (6.6%) 20 (26.3%) EGFR mutant 24 1 (4.2%) 8 (33.4%) EGFR wild type 42 4 (9.5%) 12 (28.5%) EGFR unknown 10 0 0 Known ALK fusion status 15 3 (20%) 6 (40%) rALK positive 3 2 (66.7%) 3 (100%) rALK negative 12 1 (8.3%) 3 (25%) Abbreviations: ORR, overall response rate (all partial responses); CBR, clinical benefit rate (partial response or stable disease maintained for at least 12 weeks). Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Infinity Infinity Infinity
A CMOS image sensor with pseudorandom pixel placement for clear imaging (2009)

The picture element (pixel) in conventional image sensors, such as CCD or CMOS imager, are placed in the form of a lattice for ease of implementation. Lattice placement of pixels intrinsically has directional dependency on the clarity of image representation; in other words, the image clarity is significantly dependent on the directions of the objects in the image, such as lines. For example, horizontal lines are perfectly represented by lattice pixels, while slanted lines have jagged edges. In this paper, we propose a pseudorandom pixel placement architecture for clear imaging with solving the directional dependency problems. We also discuss our evaluation of its characteristics based on the designed layout of CMOS image sensor with pseudorandom pixel placement, as well as its implementation.
Microscopic Measurement of pH with Iridium Oxide Microelectrodes (2000)

Microscopic pH electrodes were produced by deposition of hydrous iridium oxide onto carbon fiber microelectrodes. The electrodes exhibit two linear regions of potentiometric response between pH 2-6 and pH 6-12. The electrodes respond to pH changes within 50 ms, and an equilibrium value is reached within 30 s. By using these electrodes as probes in the scanning electrochemical microscope, dynamic pH changes occurring at or near a surface can be measured and pH maps of the surface can be generated. Vertical pH profiles and images of pH were obtained at substrates where electrochemical (oxidation and reduction of H2O2, hydrogen evolution) or enzymatic (glucose oxidase) reactions involving proton transfers occur.
Squamous Cell Carcinoma (2012)

Photodynamic therapy (PDT) is an established and useful modality for the clinical non-invasive treatment of cancer. This therapy requires a photosensitizing agent(photosensitizer) selectively taken up by tumor cells, visible light, and molecular oxygen to generate highly reactive oxygen species (ROS),which ultimately cause tumor destruction.The specificity achieved from drug uptake selectivity combined with light targeting makes PDT an appealing approach. PDT consists of three phases:excitation of photosensitizers (PS) by light, production of ROS, and induction of cell death (Triesscheijn et al., 2006). In the first phase, irradiated light of a suitable wavelength, typically visible or near-infrared, excites the PS molecules. The light is generally selected to correspond with the maximum absorption wavelength of the PS. The PS molecules then absorb light energy and change to an excited singlet state. These excited molecules can fall back to their native state with emission of fluorescence. Thus, all PS molecules are also examples of fluorescent molecules. On the other hand, the molecules also have the ability to undergo an electron spin conversion to their triplet state followed by the transfer of this energy to oxygen molecules or to other substrate molecules in the surroundings which then react with oxygen.
Differential permeability of the proximal and distal rabbit small bowel (1972)

The permeability of the proximal and distal rabbit intestine for two to six carbon polyhydric alcohols was compared. Intestinal segments were mounted in chambers that permitted the measurement of the unidirectional flux across the brush border membrane. For both proximal and distal intestine, the permeability for a series of polyhydric alcohols decreased with increasing size. The proximal intestine was more permeable for four, five, and six carbon polyhydric alcohols than distal intestine. This regional permeability difference can be attributed to variations in the permeability characteristics of the brush border specifically. The uptake of alcohols was nonsaturable and was not inhibited by phlorizine or n-ethylmaleimide. The results are compatible with the concept that the brush border membrane has properties similar to artificial porous membranes and that the equivalent radius of the pores of the proximal intestine exceeds that of the distal gut.
Soluble BAFF Levels Inversely Correlate with Peripheral B Cell Numbers and the Expression of BAFF Receptors (2011)

The TNF family member protein BAFF/BLyS is essential for B cell survival and plays an important role in regulating class switch recombination as well as in the selection of autoreactive B cells. In humans, increased concentrations of soluble BAFF are found in different pathological conditions, which may be as diverse as autoimmune diseases, B cell malignancies, and primary Ab deficiencies (PAD). Because the mechanisms that regulate BAFF levels are not well understood, we newly developed a set of mAbs against human BAFF to study the parameters that determine the concentrations of soluble BAFF in circulation. Patients with PAD, including severe functional B cell defects such as BTK, BAFF-R, or TACI deficiency, were found to have higher BAFF levels than asplenic individuals, patients after anti-CD20 B cell depletion, chronic lymphocytic leukemia patients, or healthy donors. In a comparable manner, mice constitutively expressing human BAFF were found to have higher concentrations of BAFF in the absence than in the presence of B cells. Therefore, our data strongly suggest that BAFF steady-state concentrations mainly depend on the number of B cells as well as on the expression of BAFF-binding receptors. Because most patients with PAD have high levels of circulating BAFF, the increase in BAFF concentrations cannot compensate defects in B cell development and function.
A 0.5-μm-thick polycrystalline silicon Schottky diode with rectification ratio of 106 (2002)

Polycrystalline Si films, 0.5-μm thick, were obtained as a result of metal-induced growth by sputtering from a Si target on 25 nm thick Ni prelayers at 525 °C. Silicon grew heteroepitaxially on the NiSi2 layer formed due to the reaction between the sputtered Si atoms and Ni. Schottky diodes were fabricated on the Si films by deposition of a Schottky metal on the front surface of the film while Ni disilicide provided an intimate ohmic contact at the back. A Pd/n-Si diode using an n-Si film annealed for 2 h at 700 °C in forming gas demonstrated a rectification ratio of 106, while an as-deposited p-Si film provided an Al/p-Si diode with rectification of five orders of magnitude. Schottky barrier properties are briefly discussed.