gebhart/patrepeval huggingface dataset:
X-Ray Photoacoustic Spectroscopy of ZnO Thin Film (1993)

The hard X-ray photoacoustic spectrum of ZnO thin film has been obtained in the EXAFS (extended X-ray absorption fine structure) region using synchrotron radiation. It is shown that information on EXAFS is included in the X-ray photoacoustic signal intensity and phase spectra which reflect the heat production processes in ZnO thin film. However, the results showed that the increases and changes in the photoacoustic signal intensity were different from those of the photoacoustic signal phase in the EXAFS region.
Separation and recycling of cotton from cotton/PET blends by depolymerization of PET catalyzed by bases and ionic liquids (2014)

The recycling of post consumer cotton textile waste is highly requested, due to the high environmental impact of cotton production. Often cotton is mixed in blends with polyethylene terephthalate (PET). For the generation of high value products from recycled cotton, it essential that PET is separated from the cotton first. In this contribution, the depolymerization of PET in cotton / PET blend is investigated for the separation of PET from cotton fibers. Ionic liquids and NaOH are used as catalysts for the depolymerization reaction in ethylene glycol (glycolysis). It will be shown that ionic liquids have no significant influence on the conversion of PET. However, 99% conversion is achieved in this process with 2 w/w % NaOH as catalyst. This enables the selective depolymerization of PET in presence of cotton and gives rise to an easy separation of cotton from cotton / PET blends.Paper for the 14th World Textile Conference, May 26th-28th2014, Bursa, Turkey.
A Short Synthesis of Fusaric Acid and Analogues (1989)

Abstract Fusaric acid (5-n-butyl-pyridine-2-carboxylic acid) and other substituted picolinic acid derivatives are synthesized in two steps from readily available α,β-unsaturated hydrazones and 2-chloroacrylonitrile in high yield.
Pleiotropic influence of triiodothyronine on thymus physiology. (1993)

It is well demonstrated that the thymus gland is under neuroendocrine control. Thymic endocrine function can be modulated by a variety of hormones including those secreted by the thyroid gland. This prompted us to investigate putative influences of T3 in further aspects of thymus physiology. We showed that T3-treated animals exhibited an increase in thymus weight, cellularity and cycling cells. Moreover, Thy1+ thymocytes as well as CD4-CD8 defined subsets were augmented in absolute numbers, whereas PgP.1+ cells increased in both absolute and percentage values. In parallel, the total numbers of thymic nurse cells were also increased. Regarding the expression of extracellular matrix components (ECM) by microenvironmental cells, we observed an enhancement in the intrathymic ECM upon T3 in vivo treatment. Similar effects were found in vitro by treating a thymic epithelial cell line or thymic nurse cell-derived epithelial cultures with T3. This treatment also increased the expression of ECM receptors by thymic epithelial cultures. Interestingly, an enhancement in thymocyte/thymic epithelial cell adhesion ratio was observed after T3 treatment of epithelial cells. Our data suggest that T3 exerts a pleiotropic effect upon thymus physiology, stimulating thymocyte differentiation, not only by modulating epithelial cell hormonal secretion but also their production of ECM proteins and respective receptors.
Effective determination of surface potential landscapes from metal-organic nanoporous network overlayers (2019)

Abstract Determining the scattering potential landscape for two-dimensional superlattices provides key insight into fundamental quantum electron phenomena. Theoretical and semiempirical methods have been extensively used to simulate confinement effects of the two-dimensional electron gas (2DEG) on superlattices with a single scatterer in the form of vicinal surfaces and dislocation networks or isolated structures such as quantum corrals and vacancy islands. However, the complexity of the problem increases when the building blocks (or scatterers) are heterogeneous, as in metal-organic nanoporous networks (MONNs), since additional potentials may come into play. Therefore, the parametrization of the surface potential landscape is often inaccurate, leading to incorrect scattering potentials. Here, we address this issue with a combination of scanning tunneling microscopy/spectroscopy, angle resolved photoemission spectroscopy and Kelvin probe force microscopy measurements together with electron plane-wave expansion simulations on a MONN grown on Cu(111). This experimental-theory approach, enables us to capture the 2DEG response to the intricate scattering potential landscape, and reveals systematic modeling procedures. Starting from a realistic geometry of the system, we determine the repulsive scattering potentials for both molecules and coordinated metal adatoms, the latter contradicting the established simulation framework. Moreover, we reveal local asymmetries and subtle renormalization effects of the 2DEG that relate to the interaction of the MONN and the underlying substrate.
Confidence intervals under order restrictions (2013)

In this paper, we consider the problem of constructing confidence intervals (CIs) for <i>G</i> independent normal population means subject to linear ordering constraints. For this problem, CIs based on asymptotic distributions, likelihood ratio tests and bootstraps do not have good properties particularly when some of the population means are close to each other. We propose a new method based on defining intermediate random variables that are related to the original observations and using the CIs of the means of these intermediate random variables to restrict the original CIs from the separate groups. The coverage rates of the intervals are shown to exceed, but be close to, the nominal level for two groups, when the ratio of the variances is assumed known. Simulation studies show that the proposed CIs have coverage rates close to nominal levels with reduced average widths. Data on half-lives of an antibiotic are analyzed to illustrate the method.
Supplementary Figure 5 from SGEF Is Regulated via TWEAK/Fn14/NF-κB Signaling and Promotes Survival by Modulation of the DNA Repair Response to Temozolomide (2023)

&lt;p&gt;Supplementary Figure 5. SGEF is required for BRCA1 recruitment to H2A.X foci following TMZ treatment.&lt;/p&gt;
Underbalanced Drilling and Completion of Sand-Prone Tight Gas Reservoirs in Southern North Sea (2007)

Abstract This paper describes the application of underbalanced horizontal wells to develop some different tight gas reservoirs in the Netherlands section of the Southern North Sea. Underbalanced well design presented specific issues related to the nature of these reservoirs. The construction and production experience to date is evaluated and compared against similar wells drilled offshore UK. Also the benefits of the underbalanced horizontal well concept are reviewed.
Interneuron Simplification and Loss of Structural Plasticity As Markers of Aging-Related Functional Decline (2018)

Changes in excitatory neuron and synapse structure have been recognized as a potential physical source of age-related cognitive decline. Despite the importance of inhibition to brain plasticity, little is known regarding aging-associated changes to inhibitory neurons. Here we test for age-related cellular and circuit changes to inhibitory neurons of mouse visual cortex. We find no substantial difference in inhibitory neuron number, inhibitory neuronal subtypes, or synapse numbers within the cerebral cortex of aged mice compared with younger adults. However, when comparing cortical interneuron morphological parameters, we find differences in complexity, suggesting that arbors are simplified in aged mice. <i>In vivo</i> two-photon microscopy has previously shown that in contrast to pyramidal neurons, inhibitory interneurons retain a capacity for dendritic remodeling in the adult. We find that this capacity diminishes with age and is accompanied by a shift in dynamics from balanced branch additions and retractions to progressive prevalence of retractions, culminating in a dendritic arbor that is both simpler and more stable. Recording of visually evoked potentials shows that aging-related interneuron dendritic arbor simplification and reduced dynamics go hand in hand with loss of induced stimulus-selective response potentiation (SRP), a paradigm for adult visual cortical plasticity. Chronic treatment with the antidepressant fluoxetine reversed deficits in interneuron structural dynamics and restored SRP in aged animals. Our results support a structural basis for age-related impairments in sensory perception, and suggest that declines in inhibitory neuron structural plasticity during aging contribute to reduced functional plasticity.<b>SIGNIFICANCE STATEMENT</b> Structural alterations in neuronal morphology and synaptic connections have been proposed as a potential physical basis for age-related decline in cognitive function. Little is known regarding aging-associated changes to inhibitory neurons, despite the importance of inhibitory circuitry to adult cortical plasticity and the reorganization of cortical maps. Here we show that brain aging goes hand in hand with progressive structural simplification and reduced plasticity of inhibitory neurons, and a parallel decline in sensory map plasticity. Fluoxetine treatment can attenuate the concurrent age-related declines in interneuron structural and functional plasticity, suggesting it could provide an important therapeutic approach for mitigating sensory and cognitive deficits associated with aging.
Protective HLA Class I Alleles That Restrict Acute-Phase CD8+T-Cell Responses Are Associated with Viral Escape Mutations Located in Highly Conserved Regions of Human Immunodeficiency Virus Type 1 (2008)

The control of human immunodeficiency virus type 1 (HIV-1) associated with particular HLA class I alleles suggests that some CD8(+) T-cell responses may be more effective than others at containing HIV-1. Unfortunately, substantial diversities in the breadth, magnitude, and function of these responses have impaired our ability to identify responses most critical to this control. It has been proposed that CD8 responses targeting conserved regions of the virus may be particularly effective, since the development of cytotoxic T-lymphocyte (CTL) escape mutations in these regions may significantly impair viral replication. To address this hypothesis at the population level, we derived near-full-length viral genomes from 98 chronically infected individuals and identified a total of 76 HLA class I-associated mutations across the genome, reflective of CD8 responses capable of selecting for sequence evolution. The majority of HLA-associated mutations were found in p24 Gag, Pol, and Nef. Reversion of HLA-associated mutations in the absence of the selecting HLA allele was also commonly observed, suggesting an impact of most CTL escape mutations on viral replication. Although no correlations were observed between the number or location of HLA-associated mutations and protective HLA alleles, limiting the analysis to mutations selected by acute-phase immunodominant responses revealed a strong positive correlation between mutations at conserved residues and protective HLA alleles. These data suggest that control of HIV-1 may be associated with acute-phase CD8 responses capable of selecting for viral escape mutations in highly conserved regions of the virus, supporting the inclusion of these regions in the design of an effective vaccine.
Detection of 2‐Amino‐1‐methyl‐6‐(4‐hydroxyphenyl)imidazo[4,5‐b]pyridine in Broiled Beef (1992)

2-Amino-1-methyl-6-(4-hydroxyphenyl)imidazo[4,5-b]pyridine (4'-OH-PhIP) showed mutagenicity in Salmonella typhimurium TA98 in the presence of S9 mix, inducing 180 revertants per 100 micrograms. Since creatinine, tyrosine and glucose, which are present in meat, are expected to be involved in the formation of 4'-OH-PhIP, its presence in broiled beef was examined. 4'-OH-PhIP was detected in broiled beef by high-performance liquid chromatography and UV-spectrometry after extraction with 0.1 N HCl and purification by blue cotton treatment and ion exchange column chromatography. Its level was estimated to be 21.0 ng per g of broiled beef, which is comparable to that of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP).
Expression and characterization of a structural and functional domain of the mannitol-specific transport protein involved in the coupling of mannitol transport and phosphorylation in the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli (1993)

The mannitol-specific transport protein in Escherichia coli, EIImtl, consists of three structural and functional domains: a hydrophilic EIII-like domain (the A domain); a hydrophobic transmembrane domain (the C domain); and a second hydrophilic domain (the B domain) which connects the A and C domains together. The A domain contains the first phosphorylation site, His554, while the B domain contains the second phosphorylation site, Cys384. The phosphoryl group which is needed for the active transport of mannitol is sequentially transferred from P-enolpyruvate via the two phosphorylation sites to mannitol bound to the substrate binding site. In this paper, the expression, purification, and initial characterization of the B domain, IIBmtl, are described. Oligonucleotide-directed mutagenesis was used to produce an amber stop codon (TAG) and HindIII restriction site in a flexible loop between the B and A domains in the subcloned gene fragment coding for IIBAmtl (van Weeghel et al., 1991c). The gene fragment coding for IIBmtl was then subcloned behind strong promoters, located in two different expression/mutagenesis vectors, which directed the expression of the 15.3-kDa polypeptide in Escherichia coli. The domain was purified from E. coli crude cell extracts by using Q-Sepharose Fast Flow, S-Sepharose Fast Flow, and hydroxylapatite column steps. This purification procedure resulted in 1 mg of pure IIBmtl/g of cell, wet weight. The purified B domain was analyzed in vitro for its catalytic activity with membranes containing the phosphorylation site mutant form of EIImtl, C384S, and with the transmembrane domain, IICmtl. The B domain, together with purified IIA, was able to restore the P-enolpyruvate-dependent phosphorylation activity of the membrane-bound C domain. Steady-state mannitol phosphorylation kinetics at saturating EI, HPr, and IIAmtl yielded an apparent Km of P-IIBmtl for IICmtl of 200 microM and an apparent Vmax of 71 nmol of mtl-P min-1 mg of membrane protein)-1. This Vmax value is comparable to that of wild-type EIImtl measured under the same experimental conditions.
Antigenic and Mutational Analyses of Herpes Simplex Virus Glycoprotein B Reveal Four Functional Regions (2007)

Glycoprotein B (gB), along with gD, gH, and gL, is essential for herpes simplex virus (HSV) entry. The crystal structure of the gB ectodomain revealed it to be an elongated multidomain trimer. We generated and characterized a panel of 67 monoclonal antibodies (MAbs). Eleven of the MAbs had virus-neutralizing activity. To organize gB into functional regions within these domains, we localized the epitopes recognized by the entire panel of MAbs and mapped them onto the crystal structure of gB. Most of the MAbs were directed to continuous or discontinuous epitopes, but several recognized discontinuous epitopes that showed some resistance to denaturation, and we refer to them as pseudo-continuous. Each category contained some MAbs with neutralizing activity. To map continuous epitopes, we used overlapping peptides that spanned the gB ectodomain and measured binding by enzyme-linked immunosorbent assay. To identify discontinuous and pseudocontinuous epitopes, a purified form of the ectodomain of gB, gB(730t), was cleaved by alpha-chymotrypsin into two major fragments comprising amino acids 98 to 472 (domains I and II) and amino acids 473 to 730 (major parts of domains III, IV, and V). We also constructed a series of gB truncations to augment the other mapping strategies. Finally, we used biosensor analysis to assign the MAbs to competition groups. Together, our results identified four functional regions: (i) one formed by residues within domain I and amino acids 697 to 725 of domain V; (ii) a second formed by residues 391 to 410, residues 454 to 475, and a less-defined region within domain II; (iii) a region containing residues of domain IV that lie close to domain III; and (iv) the first 12 residues of the N terminus that were not resolved in the crystal structure. Our data suggest that multiple domains are critical for gB function.
Revised dynamical theory of thermoplastic deformation (1975)

A method of quantifying the influence of the surface charge on the deformation of thermoplastics has been proposed. The results obtained from our analysis are compared with measurements of the spatial frequency distribution of thermoplastic frost deformation. The agreement between theory and experiment is found to be satisfactory in view of the approximations made in analysis.
Copper-Catalyzed Carboxylation of C–F Bonds with CO2 (2019)

An effective Cu-catalyzed selective formal carboxylation of C–F bonds with an atmospheric pressure of CO2 is reported. A variety of gem-difluoroalkenes, gem-difluorodienes, and α-trifluoro-methyl alkenes show high reactivity and selectivity for this ipso monocarboxylation. Under mild conditions, diverse important α-fluoroacrylic acids and α,α-difluorocarboxylates are obtained in good-to-high yields. Moreover, this operationally simple protocol features good functional group tolerance, is readily scalable, and the resulting products are readily converted into bioactive α-fluorinated carbonyl compounds, indicating potential application in biochemistry and drug discovery. Mechanistic studies reveal that fluorinated boronate esters might be vital intermediates in this transformation.
Network‐aware optimization of communications for parallel matrix multiplication on hierarchical HPC platforms (2015)

Summary Communications on hierarchical heterogeneous high‐performance computing platforms can be optimized based on topology and performance information. For MPI, as a major programming tool for such platforms, a number of topology‐aware and performance‐aware implementations of collective operations have been proposed for optimal scheduling of messages. This approach improves performance of application and does not require to modify application source code. However, it is applicable to collective operations only and does not affect the parts of the application that are based on point‐to‐point exchanges. In this paper, we address the problem of efficient execution of data‐parallel applications on interconnected clusters and present optimizations that improve data partition by taking into account the entire communication flow of the application. This approach is also non‐intrusive to the source code but application specific. For illustration, we use parallel matrix multiplication, where the matrices are partitioned into irregular two‐dimensional rectangles assigned to different processors and arranged in columns, and the processors communicate over this partition vertically and horizontally. By rearranging the rectangles, we can minimize communications between different levels of the network hierarchy. Finding the optimal arrangement is NP‐complete; therefore, we propose two heuristic approaches based on evaluation of the communication flow on the given network topology. We demonstrate the correctness and efficiency of the proposed approaches by experimental results on multicore nodes and interconnected heterogeneous clusters. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Copper complexes of bis(thiosemicarbazones): from chemotherapeutics to diagnostic and therapeutic radiopharmaceuticals (2011)

The molecules known as bis(thiosemicarbazones) derived from 1,2-diones can act as tetradentate ligands for Cu(II), forming stable, neutral complexes. As a family, these complexes possess fascinating biological activity. This critical review presents an historical perspective of their progression from potential chemotherapeutics through to more recent applications in nuclear medicine. Methods of synthesis are presented followed by studies focusing on their potential application as anti-cancer agents and more recent investigations into their potential as therapeutics for Alzheimer's disease. The Cu(II) complexes are of sufficient stability to be used to coordinate copper radioisotopes for application in diagnostic and therapeutic radiopharmaceuticals. Detailed understanding of the coordination chemistry has allowed careful manipulation of the metal based properties to engineer specific biological activities. Perhaps the most promising complex radiolabelled with copper radioisotopes to date is Cu(II)(atsm), which has progressed to clinical trials in humans (162 references).
Arrays of Aperture Antennas (2015)

Arrays of aperture antennas find wide application because of their flexibility and their ability to provide shaped patterns with low sidelobes. These find wide application because of their flexibility and their ability to provide shaped patterns with low sidelobes. This chapter discusses planar arrays and mutual coupling, including the basic radiation patterns of arrays with aperture antennas. One implication in the use of an array is the mutual coupling that occurs between elements, and the analysis of this effect in aperture antennas is discussed. The chapter describes the physical aspects of mutual coupling by means of an asymptotic approach, and outlines a general approach for arbitrary shapes. It also discusses on the element‐by‐element approach for finite arrays. Two of the many approaches possible are described: the moment method approach and the method of weighted residuals. It is especially important to consider the effect of mutual coupling in the design.
Non‐covalent Interactions and Charge Transfer between Propene and Neutral Yttrium‐Doped and Pure Gold Clusters (2019)

The dopant and size-dependent propene adsorption on neutral gold (Au<sub>n</sub> ) and yttrium-doped gold (Au<sub>n-1</sub> Y) clusters in the n=5-15 size range are investigated, combining mass spectrometry and gas phase reactions in a low-pressure collision cell and density functional theory calculations. The adsorption energies, extracted from the experimental data using an RRKM analysis, show a similar size dependence as the quantum chemical results and are in the range of ≈0.6-1.2 eV. Yttrium doping significantly alters the propene adsorption energies for n=5, 12 and 13. Chemical bonding and energy decomposition analysis showed that there is no covalent bond between the cluster and propene, and that charge transfer and other non-covalent interactions are dominant. The natural charges, Wiberg bond indices, and the importance of charge transfer all support an electron donation/back-donation mechanism for the adsorption. Yttrium plays a significant role not only in the propene binding energy, but also in the chemical bonding in the cluster-propene adduct. Propene preferentially binds to yttrium in small clusters (n<10), and to a gold atom at larger sizes. Besides charge transfer, relaxation also plays an important role, illustrating the non-local effect of the yttrium dopant. It is shown that the frontier molecular orbitals of the clusters determine the chemical bonding, in line with the molecular-like electronic structure of metal clusters.