gebhart/patrepeval huggingface dataset:
Coherent diffraction and random scattering in thiol-ene–based holographic polymer-dispersed liquid crystal reflection gratings (2006)

Bragg diffraction and random scattering in reflective holographic polymer-dispersed liquid crystal gratings are modeled using a matrix approach for a stack of low-high index layer pairs and an effective medium theory. Scattering is due to both random roughness of layer interfaces and random index variations within the layers. These are related to random liquid crystal droplet size and location as well as random orientation of the symmetry axes of bipolar droplets. Characteristic parameters governing coherent diffraction efficiency and random scattering are obtained partly from experiments, where possible, and partly from calculations based on a model of an effective medium applied to the grating. Calculations of grating transmittance are then compared to experimental transmittance spectra. Effects of scattering, primarily a decrease in baseline transmittance with wavelength and a small reduction in diffraction efficiency at the Bragg wavelength, are found to be due primarily to index inhomogeneities within the liquid-crystal-rich layers of the grating.
Slit2–Robo4 signalling promotes vascular stability by blocking Arf6 activity (2020)

Slit–Roundabout (Robo) signalling has a well-understood role in axon guidance1–5. Unlike in the nervous system, however, Slitdependent activation of an endothelial-specific Robo, Robo4, does not initiate a guidance program. Instead, Robo4 maintains the barrier function of the mature vascular network by inhibiting neovascular tuft formation and endothelial hyperpermeability induced by pro-angiogenic factors 6. In this study, we used cell biological and biochemical techniques to elucidate the molecular mechanism underlying the maintenance of vascular stability by Robo4. Here, we demonstrate that Robo4 mediates Slit2-dependent suppression of cellular protrusive activity through direct interaction with the intracellular adaptor protein paxillin and its paralogue, Hic-5. Formation of a Robo4–paxillin complex at the cell surface blocks activation of the small GTPase Arf6 and, consequently, Rac by recruitment of Arf-GAPs (ADP-ribosylation factor- directed GTPase-activating proteins) such as GIT1. Consistent with these in vitro studies, inhibition of Arf6 activity in vivo phenocopies Robo4 activation by reducing pathologic angiogenesis in choroidal and retinal vascular disease and VEGF-165 (vascular endothelial growth factor-165)-induced retinal hyperpermeability. These data reveal that a Slit2–Robo4–paxillin–GIT1 network inhibits the cellular protrusive activity underlying neovascularization and vascular leak, and identify a new therapeutic target for ameliorating diseases involving the vascular system.
The effects of hospital bed features on physical stresses on caregivers when repositioning patients in bed (2020)

Repositioning patients in bed is the most common patient handling activity and is associated with musculoskeletal disorders in caregivers. Hospital bed features may mitigate the risk of injury. The current study investigated the effect of bed features on the physical stress on caregivers. Ten nurses were recruited to perform three repositioning activities. Hand forces were recorded, and spine loading was estimated using a dynamic biomechanical model. Results demonstrated that except for the peak L5/S1 compressive load in the turning task, the use of assistive features significantly reduced the physical stresses for all repositioning activities. However, recommended thresholds for injury were still exceeded in many conditions. Compared with spinal load, hand force was much higher relative to the injury thresholds, suggesting a greater risk of shoulder and upper extremity injuries than low back injury. Mechanical lift equipment remains the safest and most robust way to reposition a patient.
Robust nonlinear parametric Gauss-Newton inversion for well-logging applications (2012)

Inclusion of the Huber error function in the framework of the Gauss-Newton inversion improves the robustness to outlier data. The robust inversion is integrated using iteratively reweighted least squares (IRLS), in conjunction with both line-search and trust-region step calculation algorithms and applied to well logging. The methodology is validated using synthetic and real well logging examples, showing that this robust Gauss-Newton inversion can automatically reject outliers with little increase in computational effort or inversion time.
Adjuvanting a subunit SARS-CoV-2 nanoparticle vaccine to induce protective immunity in non-human primates (2021)

The development of a portfolio of SARS-CoV-2 vaccines to vaccinate the global population remains an urgent public health imperative. Here, we demonstrate the capacity of a subunit vaccine under clinical development, comprising the SARS-CoV-2 Spike protein receptor-binding domain displayed on a two-component protein nanoparticle (RBD-NP), to stimulate robust and durable neutralizing antibody (nAb) responses and protection against SARS-CoV-2 in non-human primates. We evaluated five different adjuvants combined with RBD-NP including Essai O/W 1849101, a squalene-in-water emulsion; AS03, an alpha-tocopherol-containing squalene-based oil-in-water emulsion used in pandemic influenza vaccines; AS37, a TLR-7 agonist adsorbed to Alum; CpG 1018-Alum (CpG-Alum), a TLR-9 agonist formulated in Alum; or Alum, the most widely used adjuvant. All five adjuvants induced substantial nAb and CD4 T cell responses after two consecutive immunizations. Durable nAb responses were evaluated for RBD-NP/AS03 immunization and the live-virus nAb response was durably maintained up to 154 days post-vaccination. AS03, CpG-Alum, AS37 and Alum groups conferred significant protection against SARS-CoV-2 infection in the pharynges, nares and in the bronchoalveolar lavage. The nAb titers were highly correlated with protection against infection. Furthermore, RBD-NP when used in conjunction with AS03 was as potent as the prefusion stabilized Spike immunogen, HexaPro. Taken together, these data highlight the efficacy of the RBD-NP formulated with clinically relevant adjuvants in promoting robust immunity against SARS-CoV-2 in non-human primates.
Oxygen mediated gene regulation (2002)

SUMMARY: Studies of hypoxia‐inducible cis‐acting sequences from the erythropoietin gene have led to the recognition of a widespread transcriptional response to hypoxia based on the activation of a DNA‐binding complex, hypoxia‐inducible factor‐1 (HIF). Genes with functions in cellular energy metabolism, iron metabolism, catecholamine metabolism, vasomotor control and angiogenesis have subsequently been shown to be responsive to HIF, indicating a role in the coordination of oxygen supply and cellular metabolism. Hypoxia‐inducible factor‐1 is a heterodimer of two basic helix–loop–helix proteins of the PAS family, HIF‐1 alpha and HIF‐1 beta, although different isoforms of each subunit are now known to exist. When oxygen tension is lowered, HIF‐alpha subunits dimerize with HIF‐beta and activate gene transcription. Hypoxia‐inducible factor‐1‐mediated gene transcription is regulated predominantly by oxygen‐dependent destruction of HIF‐alpha via the ubiquitin‐proteasome pathway. This destruction is mediated by a ubiquitin E3 ligase complex, in which the von Hippel‐Lindau (VHL) protein (pVHL) recognizes and binds oxygen‐dependent destruction domain(s) in HIF‐alpha subunits. In VHL disease, the destruction of HIF‐alpha is blocked, at least partly explaining the phenotype. The recognition of HIF‐alpha by pVHL in normoxia has recently been shown to be conditional on enzymatic post‐translational hydroxylation of critical prolyl residues. It is hoped that a detailed understanding of these gene regulatory mechanisms may lead to therapeutically useful interventions in the future, for example by up‐regulating HIF activity in ischaemic disease or down‐regulating it in cancer.
Fluorescence‐Lifetime Imaging of DNA–Dye Interactions within Continuous‐Flow Microfluidic Systems (2007)

Licht im Tunnel: Die Kombination zeitaufgelöster Fluoreszenzbildgebung mit einem Durchfluss-Mikrofluidiksystem liefert eine leistungsfähige Methode zur Auflösung und Quantifizierung biologischer Mehrzustandssysteme mit genauer räumlicher und zeitlicher Reaktionssteuerung. Die Technik wurde zur Untersuchung von DNA-Farbstoff-Bindungswechselwirkungen genutzt. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2007/z604112_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Comparative microsomal proteomics of a model lung cancer cell line NCI-H23 reveals distinct differences between molecular profiles of 3D and 2D cultured cells (2021)

Lung cancer is the leading cause of cancer-related deaths in the USA and worldwide. Yet, about 95% of new drug candidates validated in preclinical phase eventually fail in clinical trials. Such a high attrition rate is attributed mostly to the inability of conventional two-dimensionally (2D) cultured cancer cells to mimic native three-dimensional (3D) growth of malignant cells in human tumors. To ascertain phenotypical differences between these two distinct culture conditions, we carried out a comparative proteomic analysis of a membrane fraction obtained from 3D- and 2D-cultured NSCLC model cell line NCI-H23. This analysis revealed a map of 1,166 (24%) protein species regulated in culture dependent manner, including differential regulation of a subset of cell surface-based CD molecules. We confirmed exclusive expression of CD99, CD146 and CD239 in 3D culture. Furthermore, label-free quantitation, targeting KRas proteoform-specific peptides, revealed upregulation of both wild type and monoallelic KRas4B<sup>G12C</sup> mutant at the surface of 3D cultured cells. In order to reduce the high attrition rate of new drug candidates, the results of this study strongly suggests exploiting base-line molecular profiling of a large number of patient-derived NSCLC cell lines grown in 2D and 3D culture, prior to actual drug candidate testing.
Measurements of finite-amplitude acoustic pulses radiated from focused piston sources in water (1995)

Measurements of finite-amplitude acoustic pulses radiated by a focused piston source in water are reported. Pulses with center frequency of 2.25 MHz, durations ranging from two to ten cycles, and peak sound pressures up to 3 MPa were measured with a wideband (1–20 MHz) membrane hydrophone. The combined effects of focusing, diffraction, and finite-amplitude distortion on short pulses are demonstrated. Propagation curves for the peak positive and peak negative pressure along the axis of the source are shown. The peak negative pressure, which is an important factor in cavitation dynamics, is maximized in the prefocal region and shifts closer to the source with increasing source amplitude, as predicted earlier [Averkiou etal., 3306(A) (1993)]. Tissue images during treatment with a therapeutic ultrasound device that show increased cavitation activity in the prefocal region are presented. The measurements are compared with theoretical predictions based on the KZK equation and good agreement is found. [Work supported by the National Institutes of Health.]
Uptake and molecular impact of aluminum-containing nanomaterials on human intestinal caco-2 cells (2018)

Aluminum (Al) is one of the most common elements in the earth crust and increasingly used in food, consumer products and packaging. Its hazard potential for humans is still not completely understood. Besides the metallic form, Al also exists as mineral, including the insoluble oxide, and in soluble ionic forms. Representatives of these three species, namely a metallic and an oxidic species of Al-containing nanoparticles and soluble aluminum chloride, were applied to human intestinal cell lines as models for the intestinal barrier. We characterized physicochemical particle parameters, protein corona composition, ion release and cellular uptake. Different in vitro assays were performed to determine potential effects and molecular modes of action related to the individual chemical species. For a deeper insight into signaling processes, microarray transcriptome analyses followed by bioinformatic data analysis were employed. The particulate Al species showed different solubility in biological media. Metallic Al nanoparticles released more ions than Al<sub>2</sub>O<sub>3</sub> nanoparticles, while AlCl<sub>3</sub> showed a mixture of dissolved and agglomerated particulate entities in biological media. The protein corona composition differed between both nanoparticle species. Cellular uptake, investigated in transwell experiments, occurred predominantly in particulate form, whereas ionic Al was not taken up by intestinal cell lines. Transcellular transport was not observed. None of the Al species showed cytotoxic effects up to 200 µg Al/mL. The transcriptome analysis indicated mainly effects on oxidative stress pathways, xenobiotic metabolism and metal homeostasis. We have shown for the first time that intestinal cellular uptake of Al occurs preferably in the particle form, while toxicological effects appear to be ion-related.
Natural killer (NK) cell activating factor released from murine thymocytes stimulated with an anti-tumor streptococcal preparation, OK-432. (1985)

Natural killer (NK) activity of mouse splenocytes was significantly augmented when the splenocytes were incubated for 3 to 4 hr with culture supernatants of mouse thymocytes stimulated by OK-432, an antitumor preparation from the Streptococcus pyogenes SU-strain. Antiviral activity was also detected in the culture supernatants, but IL 2 activity was not. When the culture supernatants of thymocytes stimulated by OK-432 were fractionated on a column of Blue Sepharose CL-6B, NK enhancing activity and antiviral activity were observed in partly overlapping fractions that bound to the column. However, the antiviral activity in the Blue Sepharose-bound fraction was neutralized completely by treatment with anti-IFN (alpha, beta) antiserum, whereas significant NK cell enhancing activity was still observed after treatment with anti-IFN (alpha, beta) antiserum. When the Blue Sepharose-bound fraction was subjected to gel filtration, the NK cell enhancing activity was detected in the 25,000 to 35,000 and 40,000 to 67,000 m.w. regions, but antiviral activity was observed in the over 67,000 m.w. region. These results indicate that a new kind of lymphokine, called natural killer cell activating factor (NKAF), distinct from IFN and IL 2, was found. The NKAF was found to have the following properties: its pI value is between pH 5.5 and 6.5, it binds to concanavalin A- and lentil agglutinin-Sepharose, and it is stable with pH 2-24 hr treatment. In addition, NKAF-producing cells were peanut agglutinin (PNA)-thymocytes when thymocytes were fractionated by the agglutination-sedimentation method with the use of PNA.
Designing a trace format for heap allocation events (2000)

Dynamic storage allocation continues to play an important role in the performance and correctness of systems ranging from user productivity software to high-performance servers. While algorithms for dynamic storage allocation have been studied for decades, much of the literature is based on measuring the performance of benchmark programs unrepresentative of many important allocation-intensive workloads. Furthermore, to date no standard has emerged or been proposed for publishing and exchanging representative allocation workloads. In this paper, we describe a preliminary design of a trace format for such workloads and investigate its effectiveness at representing large allocation traces. Our proposal allows for a flexible encoding of information in the trace to achieve greater compression. We evaluate our preliminary design in two dimensions. First, we measure how effective these encodings are at reducing trace size. Second we consider how a meta-level specification language could be used to describe such formats and to generate trace readers and writers automatically.
Diastereoselective Aldol Reactions with Butane‐2,3‐diacetal Protected Glyceraldehyde Derivatives. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
A microwave‐assisted process for coating polymer and glass surfaces with semiconducting ZnO submicron particles (2009)

Abstract A new method for coating glass slides with ZnO particles with an average size of 200 nm is proposed in the current article. The coating was performed under microwave radiation. Two main morphologies are found for the ZnO crystals that are deposited on glass slides. The first morphology is that of a very dense coating of ZnO hexagonal rods growing perpendicular to the glass surface. The second is the growth of ZnO flower‐like particles. In addition to coating the glass by ZnO particles, we also report on coating other polymers [poly(methyl methacrylate) plate, polycarbonate beads, Nylon 6,6 beads, and polypropylene beads) by ZnO. The morphology obtained for ZnO coated on polymers is different from that detected for coating ZnO on glass. The unorganized coating of ZnO rods on polymers has been observed. The coated glass slides were characterized by X‐ray diffraction, volumetric titration, EDS, scanning electron microscope, and optical measurements (DRS and transmittance spectroscopy). © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
F-2 Micro X-ray Fluorescence Imaging of Pharmaceutical Tablet Formulations (2004)

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Muscarinic Allosteric Modulators: Atypical Structure‐Activity‐Relationships in Bispyridinium‐type Compounds (2006)

Allosteric modulators of receptor binding are known for a variety of membrane receptors. In case of muscarinic receptors, a considerable number of structurally divergent modulators have been described. For the M2 receptor subtype which has a high sensitivity to allosteric modulation most of the allosteric agents bind to the common allosteric binding site of the receptor protein. In this study, a series of DUO compounds characterized by a bispyridinium middle chain and lateral benzyloximeether moieties of a systematically varied substitution pattern has been evaluated with regard to their allosteric potency to affect M2 receptors, whose orthosteric site was blocked by [3H]N-methylscopolamine. The variations in potency were found to be surprisingly small and the structure-activity relationships of the DUO compounds diverged from those of correspondingly substituted hexamethonio-type allosteric modulators. One has to conclude that DUO compounds bind in an "atypical" manner which is in agreement with recently reported side-directed mutagenesis and molecular modeling studies.
A run-time support environment for reconfigurable systems (2002)

This paper presents a novel FPGA Support System (FSS) that facilitates the execution of hardware-based tasks on a dynamically reconfigurable FPGA. The FSS provides the mechanisms to support the placement, execution and removal of blocks on the FPGA. A key feature of the FSS is its ability to provide communication between concurrently executing hardware blocks and software objects during the run-time of a system. The FSS was initially developed to run on a hardware platform consisting of an ARM7 processor interfaced to a Xilinx 6264 FPGA and a dual-port memory. The design, implementation and current status of the FSS are discussed, together with our initial results based on the implementation of a discrete wavelet transform application.
Thermodynamic and transport properties in Au + Au collisions at RHIC energies from the clustering of color strings (2019)

In this work, we have extracted the initial temperature from the transverse momentum spectra of charged particles in Au + Au collisions using STAR data at RHIC energies from [Formula: see text] = 7.7–200 GeV. The initial energy density [Formula: see text], shear viscosity to entropy density ratio [Formula: see text], trace anomaly [Formula: see text], the squared speed of sound [Formula: see text], entropy density, and bulk viscosity to entropy density ratio [Formula: see text] are obtained and compared with the lattice QCD calculations for (2 + 1) flavor. The initial temperatures obtained are compared with various hadronization and chemical freeze-out temperatures. The analysis of the data shows that the deconfinement-to-confinement transition possibly takes place between [Formula: see text] = 11.5 and 19.6 GeV.
Zinc Complexes with the Chelating Amido‐Imino Ligand [1‐n‐Butyl‐2‐(2,6‐diisopropylphenyl)iminoacenaphthen‐1‐yl]‐2,6‐diisopropylphenylamide (L): Synthesis, Molecular Structure and Reactivity of [(L)ZnCl]2, (L)Zn‐nBu and (L)ZnN(SiMe3)2 (2007)

Abstract Dimeric [(L)ZnCl] 2 ( 4 ) {L = [1‐ n ‐butyl‐2‐(2,6‐diisopropylphenyl)iminoacenaphthen‐1‐yl]‐2,6‐diisopropylphenylamide} was prepared by treatment of the lithium salt of the ligand (LLi) with equimolar amounts of anhydrous ZnCl 2 . Treatment of 4 with KN(SiMe 3 ) 2 affords the bis(trimethylsilyl)amido compound (L)ZnN(SiMe 3 ) 2 ( 5 ). The alkylzinc complex (L)Zn‐ n Bu ( 6 ) is the product of the reaction between the adduct LLi · n BuLi ( 3 ) and ZnCl 2 . Compounds 4 – 6 were characterized by 1 H NMR and IR spectroscopy. The molecular structures of 4 and 6 were determined by single‐crystal X‐ray analysis. In the solid state, the molecules of 4 exist as centrosymmetric, heterochiral dimers bridged by chlorine atoms, while compound 6 consists of monomeric molecules with three‐coordinate zinc atoms. The reactions of 6 with tert ‐butanol, adamanthanol, 2,5‐di‐ tert ‐butylaniline and diphenylacetonitrile do not proceed with alkane elimination but with protonation of the ligand affording the amino‐imine LH ( 7 ). (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2008)
Locating Optimal Electrodes Placement via Microelectrode Recording in General Anesthetic Patients During Deep Brain Stimulation (2012)

Deep brain stimulation (DBS) is one of promising therapy to treat advanced Parkinson's disease. During DBS operation, general anesthetic induction has been shown an alternative procedure to avoid patient's discomfort under local anesthesia. Meanwhile, microelectrode recording (MER) is a guide of optimal placement in the brain. However, the inhibition of power of neural spiking is assumed by the general anesthesia during the process. Therefore, we use median nerve stimulation (MNS) to enhance them. At the same time, the power of background noise is also enhanced. Then, it makes MER be poor to determine the optimal electrode placement. In this study, we present a methodology including spike detection, fast Fourier transformation and power spectrum analysis for analyzing MER. Through these results, MER data can be successfully utilized for tracking dorsolateral sub thalamic nucleus (STN) to ensure optimal electrode location.