gebhart/patrepeval huggingface dataset:
Odd–Even Effect in the Hydrophobicity of <i>n</i>-Alkanethiolate Self-Assembled Monolayers Depends upon the Roughness of the Substrate and the Orientation of the Terminal Moiety (2014)

The origin of the odd-even effect in properties of self-assembled monolayers (SAMs) and/or technologies derived from them is poorly understood. We report that hydrophobicity and, hence, surface wetting of SAMs are dominated by the nature of the substrate (surface roughness and identity) and SAM tilt angle, which influences surface dipoles/orientation of the terminal moiety. We measured static contact angles (θs) made by water droplets on n-alkanethiolate SAMs with an odd (SAM(O)) or even (SAM(E)) number of carbons (average θs range of 105.8-112.1°). When SAMs were fabricated on smooth "template-stripped" metal (M(TS)) surfaces [root-mean-square (rms) roughness = 0.36 ± 0.01 nm for Au(TS) and 0.60 ± 0.04 nm for Ag(TS)], the odd-even effect, characterized by a zigzag oscillation in values of θs, was observed. We, however, did not observe the same effect with rougher "as-deposited" (M(AD)) surfaces (rms roughness = 2.27 ± 0.16 nm for Au(AD) and 5.13 ± 0.22 nm for Ag(AD)). The odd-even effect in hydrophobicity inverts when the substrate changes from Au(TS) (higher θs for SAM(E) than SAM(O), with average Δθs |n - (n + 1)| ≈ 3°) to Ag(TS) (higher θs for SAM(O) than SAM(E), with average Δθs |n - (n + 1)| ≈ 2°). A comparison of hydrophobicity across Ag(TS) and Au(TS) showed a statistically significant difference (Student's t test) between SAM(E) (Δθs |Ag evens - Au evens| ≈ 5°; p < 0.01) but failed to show statistically significant differences on SAM(O) (Δθs |Ag odds - Au odds| ≈ 1°; p > 0.1). From these results, we deduce that the roughness of the metal substrate (from comparison of M(AD) versus M(TS)) and orientation of the terminal -CH2CH3 (by comparing SAM(E) and SAM(O) on Au(TS) versus Ag(TS)) play major roles in the hydrophobicity and, by extension, general wetting properties of n-alkanethiolate SAMs.
Harnessing Functional Plasticity of Enzymes:  A Fluorogenic Probe for Imaging 17β-HSD10 Dehydrogenase, an Enzyme Involved in Alzheimer's and Parkinson's Diseases (2007)

In this paper, we describe the development of a fluorogenic substrate for 17beta-hydroxysteroid-dehydrogenase type 10 (17beta-HSD10), which is a multifunctional metabolic enzyme fulfilling several metabolic roles (beta-oxidation of fatty acids, catabolism of isoleucine, and metabolism of steroids). In recent years, it has emerged as an important stress and pathological marker in neurons and glial cells (expression down-regulation in Parkinson's disease, up-regulation and association with beta-amyloid peptide in Alzheimer's disease). Through the iterative molecular design and chemical synthesis described herein, compound 1 was developed, which possesses all required properties for a selective optical reporter substrate: alcohol-ketone optical switching, the ability to function as a good enzyme substrate (expressed in kinetic parameters), cell permeability, and cell retention. Probe 1 provides a blue-to-green/yellow bright switch and enables non-invasive, real-time imaging of 17beta-HSD10 in live human cells. The selectivity of reporter 1 was established by the quantitative correlation of metabolic activity to protein expression in human kidney cell line HEK-293T.
Darapladib, a reversible lipoprotein-associated phospholipase A2 inhibitor, for the oral treatment of atherosclerosis and coronary artery disease. (2009)

Darapladib, under development by GlaxoSmithKline plc, is a novel inhibitor of lipoprotein-associated phospholipase A2 (PLA2), an enzyme that may link lipid metabolism with inflammation, leading to the increased stability of atherosclerotic plaques present in the major arteries. Darapladib exhibits favorable pharmacokinetics, minimal predicted drug-drug interactions, sustained blood levels with once-daily oral dosing and limited inhibition of other PLA2 isozymes. Preclinical studies in diabetic-hypercholesterolemic swine (useful for the study of human atherosclerosis mechanisms) demonstrated that darapladib attenuated the progression of arterial plaques to a higher-risk phenotype by reducing the number of inflammatory macrophages within plaques and dampening T-cell responses. Two phase II clinical trials demonstrated sustained lipoprotein-associated PLA2 inhibition with daily oral dosing, and favorable effects on markers of inflammation and plaque stability. Phase III trials are ongoing to assess the safety and efficacy of darapladib in reducing adverse clinical events in patients with atherosclerosis.
Roles of bacteriophage GVE2 endolysin in host lysis at high temperatures (2013)

The holin-endolysin system is used by double-stranded DNA phages to lyse their bacterial hosts at the terminal stage of the phage reproduction cycle. Endolysins are proteins with one of several muralytic activities able to digest the bacterial cell wall for phage progeny release. However, the functions of thermophilic bacteriophage endolysin in host lysis have not been extensively investigated. In this study, the roles of the endolysin of a thermophilic bacteriophage, GVE2, from a deep-sea hydrothermal vent, which could infect Geobacillus sp. E263 at high temperatures, were characterized. The results showed that GVE2 could lead to lysis of host cells. The confocal microscopy data showed that GFP-endolysin aggregated in GVE2-infected Geobacillus sp. E263 cells, showing the involvement of endolysin in the lysis process at high temperatures. The results revealed that the GVE2 endolysin and holin interacted directly. It was found that the endolysin could interact with the host protein ABC transporter, suggesting that host proteins might participate in the regulation of the lysis process. Therefore, our study presents a novel insight into the mechanism of the lysis process of a thermophilic bacterium by its phage at high temperatures, which should be helpful in revealing the roles of thermophilic bacteriophages in the biosphere of deep-sea hydrothermal vents.
Microphthalmia transcription factor (2001)

Mitf is a sensitive and specific marker for malignant melanoma, including the spindle-cell variant, in cytologic specimens and may be superior to the current standard melanocytic markers, S-100 protein and HMB-45 antigen.
2.5 Gbit/s CPFSK system with low central IF (1994)

A 2.5 Gbit/s coherent optical communication system is presented which uses CPFSK modulation with a central IF of only 3.75 GHz. This low IF facilitates the design of IF electronics. In experimental verification a measured sensitivity ηP = –40.9 dBm is obtained.
PMA- and ANG II-induced PKC regulation of the renal Na<sup>+</sup>-HCO<sub>3</sub><sup>−</sup>cotransporter (hkNBCe1) (2005)

The renal electrogenic Na(+)-HCO3- cotransporter (hkNBCe1) plays a major role in the bicarbonate reabsorption by the kidney. We examined how PMA- and ANG II-activated PKCs regulate hkNBCe1 expressed with or without the ANG II receptors AT(1B) in Xenopus laevis oocytes. We found that 10 nM PMA halved the hkNBCe1 current detected in voltage-clamped oocytes. A PKC-specific inhibitor GF-109203X, and a specific inhibitor of Ca-dependent conventional PKCalphabetagamma, GO-6976, significantly reduced PMA inhibition. PMA did not alter surface expression of the cotransporters, but it significantly increased hkNBCe1-PKCalphabetagamma membrane association. We found that at 10(-6) M, ANG II halved the hkNBCe1 current detected in oocytes coexpressing cotransporters with AT(1B). A PKC-specific inhibitor GF-109203X, and a PKCepsilon translocation inhibitor epsilonV1-2 peptide as well as BAPTA-AM (but not GO-6976), significantly reduced ANG II inhibition. At 10(-6) M, ANG II significantly decreased surface expression of the cotransporters and increased hkNBCe1-PKCepsilon membrane association. Additionally, we found that at 10(-11) and 10(-10) M ANG II stimulated hkNBCe1 current. This effect was blocked by BAPTA-AM and partially reduced by GF-109203X. We also found that ANG II increased intracellular Ca2+ in fluo 4-loaded oocytes. Our results suggest that 1) PMA inhibition of hkNBCe1 is mediated by Ca-dependent PKCalphabetagamma and 10 nM PMA does not induce downregulation of cotransporter surface expression. 2) ANG II (10(-6) M) inhibition of hkNBCe1 is mediated by both Ca-independent PKCepsilon and downregulation of cotransporter surface expression, possibly triggered by intracellular Ca2+ mobilization. 3) Similar to proximal tubule, acute ANG II has a biphasic effect on hkNBCe1 coexpressed with AT(1B) in X. laevis oocytes.
Shape-Dependent Activity of Ceria in Soot Combustion (2013)

In this study, a series of conventional polycrystalline ceria and single-crystalline ceria nanorods and nanocubes were prepared by hydrothermal methods, and their structural, redox, and morphological properties were investigated using XRD, SEM, HRTEM, BET, temperature-programmed reduction, and oxygen storage capacity measurements. According to HRTEM, they are characterized by exposure of different surfaces: {100} surface for nanocubes; {100}, {110}, and in part {111} for nanorods; and mainly {111} for conventional polycrystalline ceria, with a morphology dominated by {111}-enclosed octahedral particles. The presence of more-reactive exposed surfaces affects the reaction of soot oxidation positively, with an increase in activity in nanoshaped materials compared with conventional ceria. Thermal aging, although detrimental for surface area, is shown to affect morphology by promoting irregular truncation of edges and corners and development of more reactive surface combinations in all crystal shapes. It is likely that thermal treatment, starting from either cubes or octahedral particles, induces the formation of a similar particle geometry whose activity is dependent on the type of plane exposed and by the number an extension of edge and corners, thus linking reactivity of octahedral particles in conventional ceria powders with that of cubes in nanoshaped materials. The results indicate that soot oxidation is also a surface-dependent reaction, and catalyst design for this purpose should allow for surface structure morphology and its evolution against temperature.
Glaciers and Climatology; Hans W:son Ahlmann's Contribution (1949)

L. P. Kirwan, C. M:son Mannerfelt, C. G. Rossby, V. Schytt, Glaciers and Climatology; Hans W:son Ahlmann's Contribution, Geografiska Annaler, Vol. 31, Glaciers and Climate: Geophysical and Geomorphological Essays (1949), pp. 11-20
Chemistry of collagen cross-linking: biochemical changes in collagen during the partial mineralization of turkey leg tendon (1997)

With age, the proximal sections of turkey leg tendons become calcified, and this phenomenon has led to their use as a model for collagen mineralization. Mineralizing turkey leg tendon was used in this study to characterize further the composition and cross-linking of collagen in calcified tissues. The cross-link profiles of mineralizing collagen are significantly different from those of other collagenous matrices with characteristically low amounts of hydroxylysyl-pyridinoline and the presence of lysyl-pyridinoline and pyrrolic cross-links. However, the presence of the immature cross-link precursors previously reported in calcifying tissues was not supported in the present study, and was found to be due to the decalcification procedure using EDTA. Analysis of tendons from young birds demonstrated differences in the cross-link profile which indicated a higher level of hydroxylation of specific triple-helical lysines involved in cross-linking of the proximal tendon. This may be related to later calcification, suggesting that this part of the tendon is predestined to be calcified. The minimal changes in lysyl hydroxylation in both regions of the tendon with age were in contrast with the large changes in the cross-link profile, indicating differential hydroxylation of the helical and telopeptide lysine residues. Changes with age in the collagen matrix, its turnover and thermal properties in both the proximal and distal sections of the tendon clearly demonstrate that a new and modified matrix is formed throughout the tendon, and that a different type of matrix is formed at each site.
Induction of aldose reductase and xylitol dehydrogenase activities in Candida tenuis CBS 4435 (1997)

In this study the ability of various sugars and sugar alcohols to induce aldose reductase (xylose reductase) and xylitol dehydrogenase (xylulose reductase) activities in the yeast Candida tenuis was investigated. Both enzyme activities were induced when the organism was grown on d-xylose or l-arabinose as well as on the structurally related sugars d-arabinose or d-lyxose. Mixtures of d-xylose with the more rapidly metabolizable sugar d-glucose resulted in a decrease in the levels of both enzymes formed. These results show that the utilization of d-xylose by C. tenuis is regulated by induction and catabolite repression. Furthermore, the different patterns of induction on distinct sugars suggest that the synthesis of both enzymes is not under coordinate control.
Electron-beam lithography of isolated trenches with chemically amplified positive resist (2002)

Electron beam lithography has been implemented with a commercially available DUV chemically amplified positive resist. Post exposure delay stability in vacuum was found to be non-critical. Post exposure delay after removal from vacuum in our clean room is a critical variable, with a change in critical dimension of approximately 0.6 nm per minute of PEB delay. This result was achieved without amine filtration. Wafers were transported in cassettes from the e- beam exposure tool to an FSI Polaris 2000 photocluster tool. The PEB delay effect on critical dimensions can be significantly reduced by using a water soluble protective top coat with a slight change in nominal does. E-beam lithography was performed with a Leica VB6 operating at 50eV, using a n 800 micrometers field, and a 12.5 nm minimum grid size. The original CAD had a negative bias added to compensate for any proximity effect, to take advantage of dose control to achieve targeted line width, and to optimize exposure latitude. Characterization with a dual beam FIB/SEM to obtain cross-sectional SEM images, typically demonstrate a foot on plated structures from the initial resist profile. A 30 percent decease in nominal dose was observed on device wafers compared to scout wafers. Device wafers have metal structures buried below the approximate 100 nm thick plating seed layer that also cause profile changes. This is presumably due to the back scattering of the electrons from the initial area of exposure. Plating rates in isolated trenches also show a strong dependence o n the critical dimension of the narrow resist trench. Plated structures with critical dimensions of 80 nm in 0.65 microns of resist were fabricated.
Some new uses for filtered fiber-optic Raman probes:in situ drug identification andin situ and remote Raman imaging (1999)

The use of a commercially available filtered fiber-optic Raman probe is discussed for the in situ identification of illicit drugs. This probe is also shown to be useful for remote Raman measurements in a collimated beam geometry. Fiber-optic Raman imaging is discussed using single small-diameter image guides and also image guides with attached imaging GRIN lenses. Finally, a demonstration of remote Raman imaging is presented using a simple modification of the same commercially available Raman probe that was used for illicit drug measurements. Copyright © 1999 John Wiley & Sons, Ltd.
Genetic Regulation of Sporopollenin Synthesis and Pollen Exine Development (2011)

Pollen acts as a biological protector of male sperm and is covered by an outer cell wall polymer called the exine, which consists of durable sporopollenin. Despite the astonishingly divergent structure of the exine across taxa, the developmental processes of its formation surprisingly do not vary, which suggests the preservation of a common molecular mechanism. The precise molecular mechanisms underlying pollen exine patterning remain highly elusive, but they appear to be dependent on at least three major developmental processes: primexine formation, callose wall formation, and sporopollenin synthesis. Several lines of evidence suggest that the sporopollenin is built up via catalytic enzyme reactions in the tapetum, and both the primexine and callose wall provide an efficient substructure for sporopollenin deposition. Herein, we review the currently accepted understanding of the molecular regulation of sporopollenin biosynthesis and examine unanswered questions regarding the requirements underpinning proper exine pattern formation, as based on genetic evidence.
A Process for the Dehulling of High Oil‐Content Sunflower Seeds (1986)

Abstract An alternative approach to the dehulling and separation of sunflower seeds is described. The system includes a dehuller, sorting machine and air classifier. The effect of moisture content on dehulling efficiency was studied. Clean or decorticated seeds with a 1.0 to 6.4 % residual hull content were obtained under specified working conditions. The recovery range was between 91.7 % and 102.2 %.
Blockchain-based secure digital asset exchange scheme with QoS-aware incentive mechanism (2019)

As the Internet of things (IoT) is increasingly popular, the number of IoT devices such as sensors and smart equipments are growing at an astonishing rate and data generated by these devices is exploding. However, these massive IoT data, stored in the form of isolated data centers, can not be shared by others who also need it. Moreover, data exchange is now needing a secure and fair mechanism to guarantee the data provider's rights and data security. Data providers also lack the motivation to share their data, as no effective mechanism exists to reward this behavior. To solve these problems, we propose a digital asset exchange mechanism based on blockchain technology, in which we record the behavior of data publishing and exchanging into the blockchain, which can ensure the reliability and transparency of data exchange without the restriction of trusted third-party payment institutions. Especially, to inspire the data providers to share their high-quality data, we design an incentive mechanism based on QoS, which gives higher rewards to those who provide high-quality data. Experimental results of this prototype demonstrate that this mechanism is appropriate to be applied in practice.
Evolutionary Rate in the Protein Interaction Network (2002)

High-throughput screens have begun to reveal the protein interaction network that underpins most cellular functions in the yeast Saccharomyces cerevisiae. How the organization of this network affects the evolution of the proteins that compose it is a fundamental question in molecular evolution. We show that the connectivity of well-conserved proteins in the network is negatively correlated with their rate of evolution. Proteins with more interactors evolve more slowly not because they are more important to the organism, but because a greater proportion of the protein is directly involved in its function. At sites important for interaction between proteins, evolutionary changes may occur largely by coevolution, in which substitutions in one protein result in selection pressure for reciprocal changes in interacting partners. We confirm one predicted outcome of this process-namely, that interacting proteins evolve at similar rates.
Primary Resistance to PD-1 Blockade Mediated by <i>JAK1/2</i> Mutations (2016)

A key functional result from somatic JAK1/2 mutations in a cancer cell is the inability to respond to interferon gamma by expressing PD-L1 and many other interferon-stimulated genes. These mutations result in a genetic mechanism for the absence of reactive PD-L1 expression, and patients harboring such tumors would be unlikely to respond to PD-1 blockade therapy. Cancer Discov; 7(2); 188-201. ©2016 AACR.See related commentary by Marabelle et al., p. 128This article is highlighted in the In This Issue feature, p. 115.
The catalytic role of anionic phospholipids in the activation of protein C by factor Xa and expression of its anticoagulant function in human plasma (1991)

Phospholipids bearing a proportion of anionic species such as phosphatidylserine are necessary to promote the anticoagulant potential of the protein C pathway. Factor Xa (200 or 350 pM) was found to activate protein C in a thrombomodulin-independent reaction requiring only phospholipids in Al(OH)3,-adsorbed plasma resupplemented with physiological concentrations of protein C (70 nM) and protein S (130 nM). All experiments were performed in the presence of an excess of hirudin. The activity of activated protein C was assessed by the survival of factor Va. The optimal phospholipid concentration range was 5 to 25 microM with a proportion of phosphatidylserine of 50% (mol/mol) resulting in a half-life of factor Va of 7.5 min in the absence of protein S and 4.2 min in its presence. Dns-EGR-Xa, an inactive derivative of factor Xa, behaved as an apparent protector of factor Va. When replacing factor Xa, thrombin at 10 nM was not an efficient protein C activator in the absence of purified human placenta thrombomodulin. In the presence of 100 pM activated protein C, factor Va half-life was 2 min in the absence of protein S and 1.1 min in its presence in the above optimal phospholipid concentration range. The presence of protein S allowed reduction of phospholipid requirements. Annexin-V (placental anticoagulant protein-I), a potent phospholipid antagonist, fully protected factor Va from degradation by phospholipid-dependent mechanisms. Factor Va was partially protected in the plasma of a patient having experienced thrombosis associated with lupus-like anticoagulant and anti-phospholipid auto-antibodies.(ABSTRACT TRUNCATED AT 250 WORDS)
Indium 111-mercaptopyridine N-oxide-labeled human leukocytes and platelets: mechanism of labeling and intracellular location of 111In and mercaptopyridine N-oxide. (1986)

Human leukocytes and platelets were labeled in plasma with indium 111, by incubating cells first with 2-mercaptopyridine N-oxide (Merc) and then with ionic or weakly chelated 111In citrate. We investigated the mechanism by which this procedure enabled us to label cells in plasma. The interactions of 111In and Merc with cell membrane and cytoplasm were studied by homogenizing labeled cells and analyzing the homogenate by gel filtration. Studies were facilitated by use of sulfur 35-labeled Merc. Although 65% +/- 12.8% of added 111-In was incorporated in cells in presence of extracellular Merc, only 0.8% +/- 0.1% and 5.1% +/- 3.2% 35S-Merc was associated with 10(8) leukocytes and 10(10) platelets, respectively. In the absence of extracellular Merc, only 4.5% +/- 0.3% 111In was taken up by the cells. In each type of cell 83% to 99% of the cell-incorporated 35S Merc was associated with a cytoplasmic component with apparent molecular weight 5200 daltons, independently of the presence or absence of radioactive or stable indium. An approximately equal proportion of 111In was bound to similar cytoplasmic components in both types of cells. On adenosine diphosphate-induced platelet aggregation, less than 3% of platelet-bound 111In or 35S-Merc was released. These results indicate that it is the extracellular Merc that facilitates 111In labeling. It does not bind to cell membrane, but forms a lipid-soluble complex with 111In. This complex passively diffuses through the cell membrane, allows 111In to bind to cytoplasmic components, and provides a stable cell label.