gebhart/patrepeval huggingface dataset:
Mode-of-action and evolution of methylenedioxy bridge forming P450s in plant specialized metabolism (2014)

(+)-Sesamin is a major furofran-class lignan in sesame seeds and harbors characteristic two methylenedioxy bridges (MDB) that are sequentially formed from (+)-pinoresinol via (+)-piperitol by a Sesamum indicum P450, CYP81Q1. However, the molecular basis for this unique catalytic activity of CYP81Q1 has been poorly understood. To elucidate MDB formation, we tested various natural and non-natural metabolites as substrates for CYP81Q1. A synthetic (+)-SC1mr and a naturally occurring (+)-kobusin showed inhibitory effect on the production of (+)-sesamin by CYP81Q1 unlike (+)-epipinoresinol and (−)-pinoresinol, indicating the strict diastereomer and enantiomer selectivity. Homology modeling followed by site-directed mutagenesis of CYP81Q1 showed that an amino acid residue crucial for MDB formation is a unique Ala residue (A308), located in I-helix proximal to the substrate pocket, responsible to the conserved distal-Thr residue. MDB by CYP81Q1 is produced possibly through the formation of a substrate-participated hydrogen-bonding network, since single replacement of the Ala by Thr severely and specifically lowered the MDB forming activity. This hypothesis is supported by a newly identified MDB-forming enzyme CYP81Q38 from Phryma leptostachya harboring an Ala responsible to Ala308 in CYP81Q1. An evolutional perspective of CYP81Q1 is discussed in relation to another MDB-forming CYP719As functionally conserved in Ranunculales.
m-plane (101¯) and (202¯1) GaN/AlxGa1–xN conduction band offsets measured by capacitance-voltage profiling (2014)

The reduced polarization of nonpolar and semipolar orientations of the III-Nitrides is very attractive for optoelectronics applications. Several properties of these orientations have yet to be investigated. In particular, there is no a priori reason for the band offset to be the same for different crystallographical orientations. In the present article, we report on the extraction of the GaN/AlxGa1–xN conduction band offsets through capacitance-voltage profiling for m-plane (101¯0) and (202¯1) orientations. We extracted a ΔEc:ΔEv of 50:50–60:40. We measured a non-zero hetero-interface charge for the (202¯1) orientation which made the extraction of ΔEc less reliable.
Salivary Excretion of Lithium: II. Functional Analysis (1969)

Salivary Li + was actively secreted by the cat submaxillary gland, inversely to the rate of flow, at concentrations above serum level. Stop-flow studies indicated ductal secretion of Li + by a HgCl 2 and ouabain-sensitive mechanism. Salivary secretion of Li+ did not resemble Na+ but was similiar to K+ secretion.
The Microstructure, Thermal Fatigue, and Failure Analysis of Near-Ternary Eutectic Sn-Ag-Cu Solder Joints (2004)

The electronic industry is making substantial progress toward a full transition to Pb-free soldering in the near future. At present, the leading candidate Pb-free solders are near-ternary eutectic Sn-Ag-Cu alloys. The electronic industry has begun to study both the processing behaviors and the thermo-mechanical fatigue properties of these alloys in detail in order to understand their applicability in context of current electronic card reliability requirements. In recent publications, the solidification behavior of the near-ternary eutectic Sn-Ag-Cu alloys has been reported in terms of the formation of large Ag3Sn plates and their effects on mechanical properties of Pb-free solder joints. Several methods have been employed to minimize the growth of the large Ag3Sn plates in the Sn-Ag-Cu solder joints by controlling the cooling rate during solidification, reducing Ag and/or Cu content, or adding minor alloying elements which reduce the amount of undercooling required for the nucleation of tin dendrites. In the present study, the results of accelerated thermal cycle fatigue tests are reported with the near-ternary eutectic Sn-Ag-Cu alloys of reduced Ag contents. Changes in microstructure and mechanical properties are also discussed by comparing the solder joints before and after thermal cycling.
NMR spectra of porphyrins. 29. Conformation of the propionic ester side chain in chlorophyll derivatives (1987)

The 360- and 500-MHz proton NMR spectra of the five nonequivalent protons in the C-7 propionic ester side chain of various chlorophyll derivatives have been completely analyzed in order to investigate the effect of structural variations in the chlorophyll nucleus on the side-chain conformation in solution. Analysis of the coupling constants and chemical shifts obtained shows that introduction of a central nickel atom into the chlorophyll nucleus causes profound variations in the side-chain conformation, presumably reflecting conformational changes in ring D. Less marked, but similar, effects occur upon opening of the exocyclic ring. In contrast, the introduction of δ substituents results in different, more localized, deformations, while introduction of a central magnesium atom causes little change in side-chain conformation. © 1987, American Chemical Society. All rights reserved.
Adaptive Visualization in Outdoor AR Displays (2009)

Visualizations in an Augmented Reality environment consist of a visual interaction between the presentations of virtual and real word structure. This interaction is a key element towards the generation of comprehensible visualizations, and the AR presentation has to
From Terephthalic Acid to 2,5‐Furandicarboxylic Acid: An Industrial Perspective (2016)

With the foreseeable rise of bio-based platform chemicals from starch and sucrose initially and lignocellulosic or waste feedstock streams somewhat later, the question can be raised whether new methods for defunctionalization or further functionalization will be required or can we rely on the reuse of existing catalytic conversions as a strategy? To start answering this question, we need to realize that bio-based molecules can, but most likely will not, be the same as the current petrochemical-based platform chemicals. And even if the same molecules are targeted (“drop-in”), the production routes will not be the same. Carbohydrates are the most abundant and most frequently used bio-based feedstock. They are rich in oxygen atoms, whereas the petro-based feedstocks are hydrocarbons, exclusively made up of C and H. In many cases, bio-based feedstock is overoxidized and thus a clear need for reduction, hydrogenation, dehydration, decarboxylation, and other chemistries will be needed. Perhaps an even more challenging task for these molecules is to selectively oxidize them further, as these bio-based molecules are inherently more activated due to the already present oxygen groups. This chapter provides an industrial perspective on several oxidation routes to new bio-based molecules. In particular, it focuses on the use of Co/Mn/Br catalyst systems in air oxidations, based on the Amoco Mid-Century catalyst system used for para-xylene oxidation (also see Chapter 4), as an efficient methodology for the conversion of 5-(hydroxymethyl)furfural (HMF) and 5-(methoxymethyl)furfural (MMF) to 2,5-furandicarboxylic acid (FDCA) in Avantium's YXY process. In addition, other less-studied conversions, such as methyl levulinate (ML) to succinic acid (SA), lignin to a variety of aromatic and phenolic carboxylic acids, are discussed as well.
Adaptive High Linearity Intensity Modulator for Advanced Microwave Photonic Links (2017)

This chapter, first, presents the motivation behind the need for adaptive, highly linear electro-optic modulators and an overview of the different optical linearization approaches of electro-optic modulators. Then, the figures of merits in terms of linearity performance are described and analyzed. Next, the chapter focuses on one excellent linearization approach called interferometric modulator with phase-modulating and cavity-modulating components (IMPACC). Here, we model IMPACC by simulating each of the key building blocks separately before putting them together as IMPACC modulator. This adaptive IMPACC design is compared to typical Mach-Zehnder interferometer (MZI) based modulators, and ring-assisted Mach-Zenhder interferometer (RAMZI) modulators. Theoretical analysis and results show that the IMPACC provides both superior linearity performance and unique adaptive feature that can be used to compensate for manufacturing tolerances, thus, providing extra flexibility in terms of device manufacturability as well as system integration.
Combined immunodeficiency caused by pathogenic variants in the ZAP70 C-terminal SH2 domain (2023)

Genetic characterization of an infant who presented with pneumocystis pneumonia, mycobacterial infection, and an absence of CD8 T cells revealed a novel homozygous mutation in the C-terminal SH2 domain (SH2-C) of the <i>ZAP70</i> gene (c.C343T, p.R170C). A distantly related second patient was found to be compound heterozygous for the R170C variant and a 13bp deletion in the <i>ZAP70</i> kinase domain. While the R170C mutant was highly expressed, there was an absence of TCR-induced proliferation, associated with significantly attenuated TCR-induced ZAP-70 phosphorylation and a lack of binding of ZAP-70 to TCR-ζ. Moreover, a homozygous ZAP-70 R192W variant was identified in 2 siblings with combined immunodeficiency and CD8 lymphopenia, confirming the pathogenicity of this mutation. Structural modeling of this region revealed the critical nature of the arginines at positions 170 and 192, in concert with R190, forming a binding pocket for the phosphorylated TCR-ζ chain. Deleterious mutations in the SH2-C domain result in attenuated ZAP-70 function and clinical manifestations of immunodeficiency.
The S1P1 receptor antagonist W146 induces lymphopenia in mice. Demonstration that functional antagonism of S1P1 is the mechanism of lymphopenia evoked by fingolimod-like compounds. (140.15) (2010)

Abstract Agonists of sphingosine 1-phosphate receptor 1 (S1P1) are a novel class of immunosuppressants. S1P is the endogenous agonist of S1P1 and promotes lymphocyte egress from lymph nodes (LN) into blood. However, synthetic agonists like fingolimod prevent the egress, causing systemic lymphopenia. This apparent contradiction is explained by the concept of functional antagonism, according to which synthetic S1P1 agonists induce receptor internalization, making cells unresponsive to the endogenous S1P. If this mechanism is true, S1P1 antagonists should induce lymphopenia. We have fully characterized compound W146, a S1P1 antagonist, by binding and cellular assays. We then administered W146 and several S1P1 agonists to mice and measured blood lymphocytes and plasma levels of compounds in different experimental conditions. All compounds induced lymphopenia in blood and a concomitant increase of CD4+ and CD8+ T cells in LN. These results indicated that lymphopenia evoked by W146 was due to S1P1 blockade and not to another mechanism, like cytotoxicity. By Western blot, FACS and immunocytochemistry we showed that all compounds but W146 induce S1P1 internalization. W146 is able to prevent the internalization induced by an agonist. We report, for the first time, lymphopenia with a S1P1 antagonist. Plasma levels needed to surmount the effects of endogenous S1P are achieved in our experimental conditions. Our studies strongly support the validity of the concept of functional antagonism.
Hodgkin Lymphoma has a seasonal pattern of incidence and mortality that depends on latitude (2017)

Seasonal variations in incidence and mortality after a Hodgkin lymphoma (HL) diagnosis have been previously described with partly conflicting results. The goal of this analysis is to provide a comprehensive analysis of these seasonal variations. In total, 41,405 HL cases diagnosed between 1973 and 2012 in the 18 Surveillance, Epidemiology, and End Results registries were included. Cosinor analysis and Cox proportional-hazards models were employed to analyze seasonality of incidence and mortality, respectively. HL shows a sinusoid seasonal incidence pattern (p < 0.001). Estimated incidence in March is 15.4% [95%-CI: 10.8-20.0] higher than in September. This sinusoid pattern is more pronounced at higher latitudes (p = 0.023). The risk of dying within the first three years after a HL diagnosis in winter is significantly increased compared to a HL diagnosis in summer at higher latitudes (HR = 1.082 [95%-CI: 1.009-1.161], p = 0.027). Furthermore, increasing northern latitude increases the additional mortality risk conferred by a diagnosis in winter (p<sub>interaction</sub>0.033). The seasonality patterns presented here provide epidemiological evidence that Vitamin D might play a protective role in HL. Further evidence on the direct association between Vitamin D levels and the clinical course of HL needs to be collected to advance the understanding of the role of Vitamin D in HL.
Principle and history of Natural Orifice Translumenal Endoscopic Surgery (NOTES) (2006)

The field of gastrointestinal endoscopy has been witnessing major advances over the last five decades. Developing from flexible endoscopy to endoscopic retrograde cholangiopancreatography (ERCP) in the 1950's and 70's to endoscopic ultrasound in the 80's, endoscopic technology has been transformed from serving purely diagnostic purposes to therapeutic applications. One recent major advance is the notion of using the flexible endoscope, taking it beyond the gastrointestinal lumen into what lies beyond the confines of the gastrointestinal tract. Natural orifice translumenal surgery offers the exciting potential to be safer, less invasive and possibly more cost-effective than the traditional open surgical or laparoscopic approach. The history and principles of natural orifice translumenal endoscopic surgery (NOTES), along with future implications, are outlined in this article.
The Antiviral Drug Tilorone Is a Potent and Selective Inhibitor of Acetylcholinesterase (2021)

Acetylcholinesterase (AChE) is an important drug target in neurological disorders like Alzheimer's disease, Lewy body dementia, and Parkinson's disease dementia as well as for other conditions like myasthenia gravis and anticholinergic poisoning. In this study, we have used a combination of high-throughput screening, machine learning, and docking to identify new inhibitors of this enzyme. Bayesian machine learning models were generated with literature data from ChEMBL for eel and human AChE inhibitors as well as butyrylcholinesterase inhibitors (BuChE) and compared with other machine learning methods. High-throughput screens for the eel AChE inhibitor model identified several molecules including tilorone, an antiviral drug that is well-established outside of the United States, as a newly identified nanomolar AChE inhibitor. We have described how tilorone inhibits both eel and human AChE with IC<sub>50</sub>'s of 14.4 nM and 64.4 nM, respectively, but does not inhibit the closely related BuChE IC<sub>50</sub> > 50 μM. We have docked tilorone into the human AChE crystal structure and shown that this selectivity is likely due to the reliance on a specific interaction with a hydrophobic residue in the peripheral anionic site of AChE that is absent in BuChE. We also conducted a pharmacological safety profile (SafetyScreen44) and kinase selectivity screen (SelectScreen) that showed tilorone (1 μM) only inhibited AChE out of 44 toxicology target proteins evaluated and did not appreciably inhibit any of the 485 kinases tested. This study suggests there may be a potential role for repurposing tilorone or its derivatives in conditions that benefit from AChE inhibition.
Influence of the peripheral matrix protein of vesicular stomatitis virus on the membrane dynamics of mixed phospholipid vesicles: fluorescence studies (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfluence of the peripheral matrix protein of vesicular stomatitis virus on the membrane dynamics of mixed phospholipid vesicles: fluorescence studiesJon R. Wiener, Ranajit Pal, Yechezkel Barenholz, and Robert R. WagnerCite this: Biochemistry 1983, 22, 9, 2162–2170Publication Date (Print):April 26, 1983Publication History Published online1 May 2002Published inissue 26 April 1983https://pubs.acs.org/doi/10.1021/bi00278a017https://doi.org/10.1021/bi00278a017research-articleACS PublicationsRequest reuse permissionsArticle Views38Altmetric-Citations24LEARN 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
Luminescence properties of ZnO layers grown on Si-on-insulator substrates (2006)

The authors report on the photoluminescence properties of polycrystalline ZnO thin films grown on compliant silicon-on-insulator (SOI) substrates by radio frequency magnetron sputtering. The ZnO thin films on SOI were characterized by micro-Raman and photoluminescence (PL) spectroscopy. The observation of E2high optical phonon mode near 438cm−1 in the Raman spectra of the ZnO samples represents the wurtzite crystal structure. Apart from the near-band-edge free exciton (FX) transition around 3.35eV at 77K, the PL spectra of such ZnO films also showed a strong defect-induced violet emission peak in the range of 3.05–3.09eV. Realization of such ZnO layers on SOI would be useful for heterointegration with SOI-based microelectronics and microelectromechanical systems.
Neat Resin, Adhesive and Composite Properties of Reactive Additive/PETI-5 Blends (2000)

PETI-5 (5000 g mol −1) is a relatively new adhesive and composite matrix that exhibits good processability and excellent properties. However in the fabrication of complex composite parts (i.e. skin stringer and support frames), better processability would offer distinct advantages. In an effort to improve the processability of PETI-5, a novel reactive additive was prepared and used to formulate blends. The reactive additive is a mixture of relatively simple phenylethynyl containing imides. As such, it exhibited solubility in a variety of solvents such as N-methyl-2-pyrrolidinone, a relatively low softening temperature ∼185°C) and a low melt viscosity (∼0.1–0.3 Pa s at 250°C). Neat resin blends prepared by physically mixing imide powders of the reactive additive and PETI-5 were thermally and rheologically characterized. Blends were also prepared by mixing NMP solutions of PETI-5 amide acid and the reactive additive (imide form). These solutions were subsequently used to prepare adhesive film and unidirectional carbon fibre tape using unsized IM7 fibre. The reactive additive/PETI-5 blends were used to fabricate titanium adhesive panels and composites under 0.54 MPa or less for 1 h at 350–371°C. The effect of reactive additive content on the physical, rheological, adhesive and carbon fibre laminate properties was determined. One formulation exhibited a decrease in melt viscosity (i.e. improved processability) without effecting open hole compression, compression properties after impact or microcrack behaviour. The neat resin, adhesive and composite properties of these reactive additive/PETI-5 blends and their cured polymers will be discussed.
v-Ha-ras oncogene insertion: a model for tumor progression of human small cell lung cancer. (1988)

Small cell lung cancer (SCLC) manifests a range of phenotypes in culture that may be important in understanding its relationship to non-SCLCs and to tumor progression events in patients. Most SCLC-derived cell lines, termed "classic" SCLC lines, have properties similar to SCLC tumors in patients, including high expression of neuroendocrine markers and low c-myc oncogene expression. A significant number of SCLC lines characterized as "biochemical or morphologic variant" SCLC lines have decreased levels of endocrine differentiation markers associated with increased proliferative indices, amplification of the c-myc oncogene, and growth patterns and biochemical markers more typical of non-SCLCs. To delineate further the relationships between these phenotypes and the molecular events involved, we have inserted the v-Ha-ras gene in SCLC cell lines with (biochemical variant) and without (classic) an amplified c-myc gene. These two SCLC subtypes had markedly different phenotypic responses to similar levels of expression of v-Ha-ras RNA. No biochemical or morphologic changes were observed in classic SCLC cells. In contrast, in biochemical variant SCLC cells, v-Ha-ras expression induced features typical of large cell undifferentiated lung carcinoma, including adherent monolayer growth patterns, increased cloning efficiency, increased levels of non-SCLC cell markers, ultrastructural characteristics and an acquired resistance to polyamine depletion typical of large cell carcinoma, but not SCLC, in vitro. Expression of v-Ha-ras in biochemical variant SCLC cells directly demonstrates that important transitions can occur between phenotypes of human lung cancer cells and that these may play a critical role in tumor progression events in patients. The findings provide a model system to study molecular events involved in tumor progression steps within a series of related tumor types.
Resource allocation in full-duplex OFDMA systems with partial channel state information (2015)

In this paper, we focus on a problem of joint subcarrier and rate allocation for an orthogonal frequency division multiple access (OFDMA) full-duplex (FD) system. The goal is to maximize the system's successful transmission rate (referred as goodput) subject to power constraints at the base station (BS) and uplink users alone with subcarrier constraints. Imperfect channel state information (CSI) at the transmitting nodes is taken into account in the resource allocation problem. A simple suboptimal subcarrier and rate allocation algorithm based on the necessary conditions of the optimization problem is proposed. Simulation results reveal that the proposed scheduling algorithm can substantially improve the sum-goodput over the traditional half-duplex (HD) scheduling.
Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC fromThermus thermophilusHB8 (2010)

The first step in the molybdenum cofactor (Moco) biosynthesis pathway involves the conversion of guanosine triphosphate (GTP) to precursor Z by two proteins (MoaA and MoaC). MoaA belongs to the S-adenosylmethionine-dependent radical enzyme superfamily and is believed to generate protein and/or substrate radicals by reductive cleavage of S-adenosylmethionine using an Fe-S cluster. MoaC has been suggested to catalyze the release of pyrophosphate and the formation of the cyclic phosphate of precursor Z. However, structural evidence showing the binding of a substrate-like molecule to MoaC is not available. Here, apo and GTP-bound crystal structures of MoaC from Thermus thermophilus HB8 are reported. Furthermore, isothermal titration calorimetry experiments have been carried out in order to obtain thermodynamic parameters for the protein-ligand interactions. In addition, molecular-dynamics (MD) simulations have been carried out on the protein-ligand complex of known structure and on models of relevant complexes for which X-ray structures are not available. The biophysical, structural and MD results reveal the residues that are involved in substrate binding and help in speculating upon a possible mechanism.