gebhart/patrepeval huggingface dataset:
Calcium Affinity, Cooperativity, and Domain Interactions of Extracellular EF-hands Present in BM-40 (2000)

The structure and function of cytosolic Ca(2+)-binding proteins containing EF-hands are well understood. Recently, the presence of EF-hands in an extracellular protein was for the first time proven by the structure determination of the EC domain of BM-40 (SPARC (for secreted protein acidic and rich in cysteine)/osteonectin) (Hohenester, E., Maurer, P., Hohenadl, C., Timpl, R., Jansonius, J. N., and Engel, J. (1996) Nat. Struct. Biol. 3, 67-73). The structure revealed a pair of EF-hands with two bound Ca(2+) ions. Two unusual features were noted that distinguish the extracellular EF-hands of BM-40 from their cytosolic counterparts. An insertion of one amino acid into the loop of the first EF-hand causes a variant Ca(2+) coordination, and a disulfide bond connects the helices of the second EF-hand. Here we show that the extracellular EF-hands in the BM-40 EC domain bind Ca(2+) cooperatively and with high affinity. The EC domain is thus in the Ca(2+)-saturated form in the extracellular matrix, and the EF-hands play a structural rather than a regulatory role. Deletion mutants demonstrate a strong interaction between the EC domain and the neighboring FS domain, which contributes about 10 kJ/mol to the free energy of binding and influences cooperativity. This interaction is mainly between the FS domain and the variant EF-hand 1. Certain mutations of Ca(2+)-coordinating residues changed affinity and cooperativity, but others inhibited folding and secretion of the EC domain in a mammalian cell line. This points to a function of EF-hands in extracellular proteins during biosynthesis and processing in the endoplasmic reticulum or Golgi apparatus.
Supplementary Figure 1 from PI3Kδ Inhibitors in Cancer: Rationale and Serendipity Merge in the Clinic (2023)

&lt;p&gt;PDF file - 122K&lt;/p&gt;
L-Methionine Availability Regulates Expression of the Methionine Adenosyltransferase 2A Gene in Human Hepatocarcinoma Cells (2003)

In mammals, methionine adenosyltransferase (MAT), the enzyme responsible for S-adenosylmethionine (AdoMet) synthesis, is encoded by two genes, MAT1A and MAT2A. In liver, MAT1A expression is associated with high AdoMet levels and a differentiated phenotype, whereas MAT2A expression is associated with lower AdoMet levels and a dedifferentiated phenotype. In the current study, we examined regulation of MAT2A gene expression by l-methionine availability using HepG2 cells. In l-methionine-deficient cells, MAT2A gene expression is rapidly induced, and methionine adenosyltransferase activity is increased. Restoration of l-methionine rapidly down-regulates MAT2A mRNA levels; for this effect, l-methionine needs to be converted into AdoMet. This novel action of AdoMet is not mediated through a methyl transfer reaction. MAT2A gene expression was also regulated by 5'-methylthioadenosine, but this was dependent on 5'-methylthioadenosine conversion to methionine through the salvage pathway. The transcription rate of the MAT2A gene remained unchanged during l-methionine starvation; however, its mRNA half-life was significantly increased (from 100 min to more than 3 h). The effect of l-methionine withdrawal on MAT2A mRNA stabilization requires both gene transcription and protein synthesis. We conclude that MAT2A gene expression is modulated as an adaptive response of the cell to l-methionine availability through its conversion to AdoMet.
MCS analysis of IAEA lead-cooled fast reactor core neutronics benchmark (2018)

This paper presents the analysis of an International Atomic Energy Agency (IAEA) Lead-cooled Fast Reactor (LFR) core neutronics benchmark that was proposed under a Coordinated Research Project (CRP) on ???Small Reactors without On-site Refueling.??? The benchmark problem is based on the RBEC-M core, which is a 900 MWth lead-bismuth cooled conceptual fast reactor developed by the Russian Research Center, ???Kurchatov Institute??? (RRC KI). The benchmark is proposed to compare the performance of various simulation tools and nuclear data libraries used in the design of LFRs. Based on the foregoing, the continuous energy neutron transport Monte Carlo code MCS under development at Ulsan National Institute of Science and Technology (UNIST) has been used to analyze the RBEC-M benchmark. The purpose of this analysis is to obtain the neutronics parameters, including effective multiplication factor Keff, power profiles and core neutron spectra, defined in the benchmark. The analysis is performed with the ENDF/B-VII.0 and ENDF/B-VII.1 data libraries. The effect on the effective multiplication factor of using several axial and radial depletion zones in the active core region instead of a single depletion zone is analyzed. The effect of treating the cross sections in the unresolved resonance region with and without the Probability Table (PT) is also analyzed.
Turbo Receivers for Single User MIMO LTE-A Uplink (2009)

The paper deals with turbo detection techniques for Single User Multiple-Input-Multiple-Output (SU MIMO) antenna schemes. The context is on the uplink of the upcoming Long Term Evolution - Advanced (LTE-A) systems. Iterative approaches based on Parallel Interference Cancellation (PIC) and Successive Interference Cancellation (SIC) are investigated, and a low-complexity solution allowing to combine interstream interference cancellation and noise enhancement reduction is proposed. Performance is evaluated for Orthogonal Frequency Division Multiplexing (OFDM) and Single Carrier Frequency Division Multiplexing (SC-FDM) as candidate uplink modulation schemes for LTE-A. Simulation results show that, in a 2times2 antenna configuration, the turbo processing allows a consistent improvement of the link performance, being SC-FDM the one having higher relative gain with respect to linear detection. The turbo receiver's impact is however much reduced for both modulation schemes in a 2times4 configuration, due to the higher diversity gain provided by the additional receive antennas.
Highly Efficient Red Electrophosphorescent Devices Based on Iridium Isoquinoline Complexes: Remarkable External Quantum Efficiency Over a Wide Range of Current (2003)

Outstanding performance as an emissive dopant in organic light‐emitting devices is shown by red phosphorescent iridium complexes based on an isoquinoline framework (such as that shown in the Figure). Remarkably high efficiency can be maintained in the devices at high currents with a negligible effect from either triplet–triplet (T–T) annihilation or saturation of the excited states.
Computer simulation of effect of bipolar electrode tip to ring spacing on P wave and far field R wave sensing in atrium (2002)

Even though sensing ventricular and atrial signals for arrhythmia detection have been widely used in patients, there are issues that need to be resolved to optimize sensing. One of these issues is the detection of the far field R wave (EFRW) signal in the atria which can result in the delivery of inappropriate therapies. In the experimental setting, variables that affect near field atrial signal (P wave) and FFRW are difficult to separate. Few investigators have analyzed the issue of optimal bipolar electrode spacing for P/FFRW differentiation. A better understanding of the variables that effect P/FlFRW ratio is important for optimizing lead design and placement. In this paper, a theoretical model (see Weimin Sun and Xiaoyi Min, IEEE Trans. Biomed. Eng., vol. BME-44, p. 1237-42, 1997) of the sensed signal was utilized. This study focuses on the effect of bipolar electrode tip to ring spacing on P wave and FFRW amplitude and derivative as well as the P/FFRW ratio. Comparison between bipolar and unipolar sensing is also investigated. The model results show that the peak amplitude of P wave varies with the orientation of a bipolar electrode respect to the propagation direction of a wavefront and becomes plateau at tip to ring spacing of 10 mm or greater. However, the far field R wave amplitude increases with greater bipole spacing. Better acute signal to noise can be achieved with smaller bipole spacing. Bipolar signals have higher slew rate and comparable peak amplitude compared with unipolar signals.
Amino acid transport in membrane vesicles ofClostridium thermoautotrophicum (1990)

A proton motive force (Δp) generated by oxidation of CO in membrane vesicles of Clostridium thermoautotrophicum drove active transport of l-alanine, glycine and l-serine. The maximum rate (Vmax) for l-alanine transport was 12 × higher at 50°C than at 25°C. The apparent transport constant (Kt) for l-alanine uptake was 30–40 μM and independent of the temperature. Glycine was a substrate for the l-alanine transport system as demonstrated by the competitive inhibition of l-alanine uptake by glycine (Ki= 6 μM), by the kinetics of glycine uptake (Kt= 7 μM) and by the inhibiton of glycine uptake by l-alanine. The uptake kinetics of glycine was biphasic. l-Serine inhibited competitively also l-alanine and glycine transport but it was taken up by a separate transport system. The rate of amino acid transport, but not the Kt, was dependent on the value of the proton motive force.
Crystal structure of bis[2-(benzylamino)-6-methylpyridinato]- bis(hexahydro-2-azepinato)zirconium(IV), C38H46N6O2Zr (2003)

Abstract C 38 H 46 N 6 O 2 Zr, monoclinic, P 12 1 / c 1 (No. 14), a = 13.575(3) Å, b = 15.903(3) Å, c = 17.404(3) Å, β = 106.85(3)°, V = 3596.0 Å 3 , Z = 4, R gt (F) = 0.046, wR ref (F 2 ) = 0.126, T = 293 K.
Microcin J25, from the Macrocyclic to the Lasso Structure: Implications for Biosynthetic, Evolutionary and Biotechnological Perspectives (2004)

Microcin J25 (MccJ25) is a cyclic antibacterial peptide secreted by a fecal isolate of Escherichia coli. It exerts highly potent activity on Salmonella and Escherichia species. The microcin is recognized at the outer membrane of sensitive strains by the FhuA multifunctional protein, which belongs to the iron/siderophore receptor family, and inhibits bacterial transcription through binding to the RNA-polymerase beta' subunit. The mcjABCD genetic system carried by the wild type 50-kb pTUC100 plasmid contains four genes involved in MccJ25 production and immunity. MccJ25 results from the proteolytic cleavage of a 58-residue precursor at a specific Lys-Gly bond. The resulting mature peptide consists of 21 unmodified amino acids, mostly hydrophobic and includes a single dehydration. The initially described macrocyclic structure of MccJ25, which mostly relied on manual Edman sequencing of the thermolysin-cleaved form (t-MccJ25), involved a head-to-tail cyclisation of the 21-residue precursor. This structure did not prove to be consistent with recent IT-MS CID experiments conducted either on the native microcin or on peptides resulting from acidic or enzymatic cleavages, which are in favour of an 8-residue ring followed by a 13-residue tail. Cyclisation thus occurs between the N-terminus (Gly1) and the Glu8 side chain carboxyl group. The solution three-dimensional structure shows threading of the tail into the ring, thus forming a highly stable lasso type structure. Such a structure was described previously for enzyme inhibitors from Actinobacteria and is consistent with the ability of MccJ25 to inhibit RNA polymerase. The lasso structure is discussed in terms of phylogenetical and biotechnological perspectives.
Low Power Wake-Up in Wireless Sensor Networks Using Free Space Optical Communications (2010)

In many Wireless Sensor Network applications the desired deployment lifetime is specified in months or years. To meet very low power requirements duty cycled medium access control protocols incur increased latency in communication. In this paper, we present the use of a secondary, very low power, wake-up channel, using Free Space Optical (FSO) transmission. The FSO channel is used to send small wake-up signals, after the wake-up is received successfully the higher power radio channel is used to transfer data packets more efficiently. The FSO receiver can be powered continuously with a consumption of 317μW. The performance of the FSO transceiver has been evaluated for deployments of networks in buildings. A reliable communication range of fifteen metres can be achieved with a transmitter power consumption of 16.5mW, comparable to a WSN radio. The performance of the FSO wake-up system is compared with duty cycled radio communications and an order of magnitude improvement in latency is shown.
Vitamin D3 correlates inversely with systemic dendritic cell numbers and bone erosion in chronic rhinosinusitis with nasal polyps and allergic fungal rhinosinusitis (2011)

Vitamin D(3) (VD(3) ) is a steroid hormone that regulates bone health and numerous aspects of immune function and may play a role in respiratory health. We hypothesized that T helper type 2 (Th2) disorders, chronic rhinosinusitis with nasal polyps (CRSwNP) and allergic fungal rhinosinusitis (AFRS) would have VD(3) deficiencies, resulting in increased mature dendritic cells (DCs) and bone erosion. We conducted a retrospective study examining VD(3) levels in patients with AFRS (n = 14), CRSwNP (n = 9), chronic rhinosinusitis without nasal polyps (CRSsNP) (n = 20) and cerebrospinal fluid leak repair (non-diseased controls) (n = 14) at time of surgery. Circulating immune cell levels were determined by immunostaining and flow cytometric analysis. Plasma VD(3) and immune regulatory factors (granulocyte-macrophage colony-stimulating factor and prostaglandin E(2) ) were measured by enzyme-linked immunosorbent assay. It was observed that CRSwNP and AFRS demonstrated increased circulating DCs, while chronic rhinosinusitis without nasal polyps displayed increased circulating macrophages. CRSwNP and AFRS were to found to have insufficient levels of VD(3) which correlated inversely with circulating numbers of mature DCs, DC regulatory factors and bone erosion. CRSsNP displayed no change in circulating DC numbers or VD(3) status compared to control, but did display increased numbers of circulating macrophages that was independent of VD(3) status. Lastly, VD(3) deficiency was associated with more severe bone erosion. Taken together, these results suggest support a role for VD(3) as a key player in the immunopathology of CRSwNP and AFRS.
Diagnostic criteria for acute‐on‐chronic liver failure and related disease conditions in Japan (2022)

The Intractable Hepato-Biliary Disease Study Group of Japan, sponsored by the Ministry of Health, Labor and Wealth, proposed in 2018 that patients with cirrhosis and a Child-Pugh score of 5-9 should be diagnosed as having acute-on-chronic liver failure (ACLF) when a deterioration of liver function ("serum bilirubin level of 5.0 mg/dl or more" and "prothrombin time value of 40% or less of the standardized values and/or international normalization rates of 1.5 or more") caused by severe liver damage develops within 28 days after an acute insult, including alcohol abuse, bacterial infection, gastrointestinal bleeding, and the exacerbation of underlying liver diseases. Disease severity can be classified into 4 grades depending on the extent of the deterioration in organ functions, including liver, kidney, cerebral, blood coagulation, circulatory and respiratory functions. The Study Group has since performed an annual nationwide survey of patients with ACLF diagnosed according to the proposed diagnostic criteria as well as those with disease conditions related to ACLF. A total of 501 patients, including 183 patients diagnosed as having ACLF, seen between 2017 and 2019 were enrolled, and univariate and multivariate analyses revealed that the proposed diagnostic criteria were useful for identifying cirrhotic patients with an unfavorable outcome following an acute insult. Consequently, the Study Group determined that the proposed diagnostic criteria should be used in both clinical practice and clinical research as formal diagnostic criteria.
Crystal Growth and Conductivity Control of Group III Nitride Semiconductors and Their Application to Short Wavelength Light Emitters (1997)

Recent development of technology and understanding of the growth mechanism in heteroepitaxial growth of nitrides on highly-mismatched substrates have enabled us to grow high-quality GaN, AlGaN, GaInN and their quantum well structures. Conductivity control of both n-type and p-type nitrides has also been achieved. These achievements have led to the commercialization of high-brightness blue, green and white light-emitting diodes and to the realization of short wavelength laser diodes and high-speed transistors based on nitrides. The performance of these devices is still progressing, but still requires advances in many areas of materials science and device fabrication.
Distortion of Single‐Particle Optical Sensing (SPOS) Particle Count by Sub‐Countable Particles (2010)

Abstract Single particle optical sensing (SPOS) is a highly sensitive particle characterization technique for the measurement of the large particle (&gt; 0.5 μm) tail of a submicron particle size distribution. We have examined the SPOS technique for fumed silica dispersions which have a mass mean particle size of ~140 nm. The reported large particle population varies as a highly non‐linear function of sample concentration and is accompanied by the distortion of the particle size distribution. A similar response is also demonstrated for monodisperse polystyrene latex spheres. The source of spurious particle counts and the distortion of the particle size distribution is shown to be secondary coincidence. Model calculations indicate that the primary contributors to spurious counts are particles near the peak of the size distribution. These particles are substantially smaller than the nominal minimum 0.5 μm diameter. These findings establish the limited range of reliability for SPOS measurements when used to measure a small fraction of the total particle size distribution and establish the need for new particle characterization metrologies.
Association of anaemia, co-morbidities and red blood cell transfusion according to age groups: multicentre sub-analysis of the German Patient Blood Management Network Registry (2022)

Increasing age, co-morbidities, and preoperative anaemia are independent risk factors for complications, longer hospital length of stay, in-hospital mortality, and the need for RBC transfusion. Anaemia diagnosis and treatment should be established in all patients.
Semantics of persistence in the glib programming language (2006)

The cornerstone of object-oriented programming is the representation of data as a set of objects. In all of the widely-adopted languages that claim to support object-oriented programming, however, the lifetime of an object is bound by the lifetime of the process that instantiated it. In real applications, the lifetime of data is almost never related to the lifetime of the process that created it. This impedance mismatch necessitates a great deal of repetitive, error-prone labor. A true object-oriented design language must be a persistent language; in other words, the lifetime of an object must be independent of the lifetime of the process.Many persistent languages have been developed in research settings. Most of these languages, however, have attempted to maintain backwards compatibility with some previous, non-persistent language, such as Modula-3 or Java. Glib, on the other hand, is a programming language designed from the outset to support object persistence. I propose that Glib's constructs are simpler and more powerful than those of its predecessors, and now that I have an OOPLSA poster displaying those constructs, you can judge for yourself.
Research on numerical analysis code of oxidation behavior of hydrocarbon on diesel oxidation catalyst (2017)

A Hydrocarbon is supplied to a diesel oxidation catalyst installed in an upstream of the diesel particulate filter for burning particulate matter deposited on the diesel particulate filter. In this study, we developed a thermal fluid numerical computation fluid dynamics code including a chemical reaction rate model which shows the influence of a hydrocarbon concentration and a type on the oxidation reaction of a hydrocarbon on a diesel oxidation catalyst. First, oxidation characteristics of four types of hydrocarbon fuels (Decane, Hexadecane, Eicosane, and 1-Methylnaphthalene) were investigated using a straight flow substrate carrying a platinum palladium catalyst. 1-methylnaphthalene greatly deteriorated the oxidizing ability, but there was no significant difference in the three kinds of alkane fuels. The difference of these oxidation characteristics could be reproduced by constructing a sub model expressing the difference between the adsorption characteristics of each hydrocarbon fuel and the oxidation inhibition effect due to adsorption. Further, the oxidation characteristics of the zeolite-containing catalyst were evaluated. As a result of the evaluation, the oxidation characteristics of the decane of the linear hydrocarbon did not change when compared with the catalyst which did not contain the zeolite, but the oxidation characteristics of the aromatic hydrocarbon 1-methylnaphthalene deteriorated. It was assumed that the zeolite had high adsorption capacity of 1-methylnaphthalene and a further inhibition of a reaction by adsorption was accelerated.
Visible/Near-Infrared-Light-Induced H2 Production over g-C3N4 Co-sensitized by Organic Dye and Zinc Phthalocyanine Derivative (2014)

A new route is carried out to achieve broad spectral responsive photocatalytic H2 production over g-C3N4 co-sensitized by an indole-based D-π-A organic dye (LI-4) and an asymmetric zinc phthalocyanine derivative (Zn-tri-PcNc) with complementary absorption spectra. Experimental results indicate that both LI-4 and Zn-tri-PcNc are efficient photosensitizers of g-C3N4 for H2 production, and their co-sensitized g-C3N4 (LI-4/g-C3N4/Zn-tri-PcNc) exhibits an extremely high H2 production activity (371.4 μmol h–1) under visible/near-infrared (NIR) light (λ ≥ 420 nm) irradiation, which approximates the summation of the H2 production activity of LI-4/g-C3N4 (233.8 μmol h–1) and Zn-tri-PcNc/g-C3N4 (132.3 μmol h–1), although LI-4 and Zn-tri-PcNc can just absorb the light in the range of 400–600 and 600–750 nm, respectively. Moreover, the co-sensitized catalyst shows a broad visible/NIR light responsive range (400–800 nm) with impressively high apparent quantum yields (AQY) of 16.3, 7.7, and 1.75% at 420, 500, and 700 nm monochromatic light irradiation, respectively. The present work gives a new advance toward panchromatic light responsive photocatalytic application by combining the photosensitization of two different dyes with complementary absorption spectra on one kind of semiconductor.
Cytotoxicity and genotoxicity of Agaricus blazei methanolic extract fractions assessed using gene and chromosomal mutation assays (2008)

Functional food investigations have demonstrated the presence of substances that could be beneficial to human health when consumed. However, the toxic effects of some substances contained in foods have been determined. Reported medicinal and nutritive properties have led to the extensive commercialization of the basidiomycete fungi Agaricus blazei Murrill (sensu Heinemann), also known as Agaricus brasiliensis Wasser et al., Agaricus subrufescens Peck or the Brazilian medical mushroom (BMM). Different methanolic extract fractions (ME) of this mushroom were submitted to the cytokinesis-block micronucleus (CBMN) clastogenic assay and the hypoxanthine-guanine phosphoribosyl transferase locus (HGPRT) assay for gene mutation, both using Chinese hamster ovary cells clone K1 (CHO-K1). The results suggest that all the fractions tested possess cytotoxic and mutagenic potential but no clastogenic effects. Further information is needed on the biochemical components of the A. blazei methanol fractions to identify any substances with cytotoxic and/or mutagenicity potential. These findings indicate that A. blazei methanolic extract should not be used due to their genotoxicity and care should be taken in the use of A. blazei by the general population until further biochemical characterization of this fungi is completed.