gebhart/patrepeval huggingface dataset:
Modeling Dilute Gas-Solid Turbulent Boundary Layers Using Moment Methods (2014)

The specific focus of the current effort is on modeling dilute particle-laden turbulent boundary layers in which the gas-phase carrier flow is populated with a second phase of small, dispersed solid particles possessing material densities much larger than that of the carrier flow. A novel approach known as the conditional quadrature method of moments (CQMOM) developed by Yuan and Fox [1], derived from the quadrature-based method of moments (QMOM) developed originally by McGraw [2], is being implemented to model the dispersed particles as an Eulerian phase. Both enabled and disabled inter-particle collision treatments are included in the model for a dispersed phase coupled to the fluid via a drag force acting on the particles. Simulations are conducted with a Reynolds number of 2800 based on the boundary layer thickness at the inlet to the domain. The full 3-D mesh contains 800×128×98 structured cells with overall dimensions in terms of the inlet boundary layer thickness of 80×6 ×4 in the streamwise, spanwise, and wall-normal directions, respectively. The gas-phase carrier flow is computed using Direct Numerical Simulation of the incompressible Navier-Stokes equations. The boundary layer develops spatially from a turbulent inflow condition and drives the particulate phase via drag and collisions. Comparisons are made against simulations performed using Lagrangian-based discrete particle simulation (DPS) of the dispersed phase and demonstrate the utility of the Eulerian moment method approach. Both instantaneous and time-averaged quantities are presented.
Differential activity and selectivity of N-terminal modified CXCL12 chemokines at the CXCR4 and ACKR3 receptors (2020)

Chemokines play critical roles in numerous physiologic and pathologic processes through their action on seven-transmembrane (TM) receptors. The N-terminal domain of chemokines, which is a key determinant of signaling via its binding within a pocket formed by receptors' TM helices, can be the target of proteolytic processing. An illustrative case of this regulatory mechanism is the natural processing of CXCL12 that generates chemokine variants lacking the first two N-terminal residues. Whereas such truncated variants behave as antagonists of CXCR4, the canonical G protein-coupled receptor of CXCL12, they are agonists of the atypical chemokine receptor 3 (ACKR3/CXCR7), suggesting the implication of different structural determinants in the complexes formed between CXCL12 and its two receptors. Recent analyses have suggested that the CXCL12 N-terminus first engages the TM helices of ACKR3 followed by the receptor N-terminus wrapping around the chemokine core. Here we investigated the first stage of ACKR3-CXCL12 interactions by comparing the activity of substituted or N-terminally truncated variants of CXCL12 toward CXCR4 and ACKR3. We showed that modification of the first two N-terminal residues of the chemokine (K1R or P2G) does not alter the ability of CXCL12 to activate ACKR3. Our results also identified the K1R variant as a G protein-biased agonist of CXCR4. Comparative molecular dynamics simulations of the complexes formed by ACKR3 either with CXCL12 or with the P2G variant identified interactions between the N-terminal 2-4 residues of CXCL12 and a pocket formed by receptor's TM helices 2, 6, and 7 as critical determinants for ACKR3 activation.
Application of optimization in computer-aided ophthalmic lens design (1999)

Optimization methods have long been used for computer-aided optical design. In most cases, the problems to treat are 1D. Furthermore, the number of parameters we can vary is relatively small. Ophthalmic lens design, and in particular progressive addition lens (PAL) design, is quite different from classical optical design. PAL design requires the use of nonsymmetrical diopters defined by geometrical, optical or physiological quantities calculated for each point of the lens by ray-tracing methods. The large number of parameters, the complexity of the cost function and the large number of constraints, require to implement specific descent, optimization and differentiation methods.
Triplet Sensitized Photo‐Dehydro‐Diels‐Alder Reaction (2022)

Abstract We report on the triplet sensitization of the intramolecular Photo‐Dehydro‐Diels‐Alder (PDDA) reaction of two diaryl suberates bearing methyl propiolate chromophors. Compared with the non‐sensitized irradiation, considerably increased yields could be observed. Moreover, it is possible to use the more efficient UVA lamps instead of UVB lamps. Among three investigated sensitizers (xanthone, benzophenone, thioxanthone) xanthone gave the best results.
Physical Conjugation of (Tri-) Block Copolymers to Liposomes toward the Construction of Sterically Stabilized Vesicle Systems (1998)

The physical conjugation of (tri-) block copolymer molecules to phospholipid vesicle bilayers in order to construct sterically stabilized vesicles can be carried out in two different ways: by allowing the copolymer molecules to freely participate in the small unilamellar vesicle (SUV) formation process along with the lipids or by adding the copolymer molecules to pre-formed small unilamellar liposomes. Structurally and morphologically different copolymer coated vesicle systems occur. The effect on the mean vesicle diameter and the vesicle surface characteristics is monitored by dynamic light scattering and laser Doppler electrophoresis techniques for a wide variety of block copolymer molecules of the PEO−PPO−PEO type (PEO is poly(ethylene oxide); PPO poly(propylene oxide)). Systematic investigations as a function of copolymer added concentration and molecular structure were undertaken throughout. The results indicate a dramatic increase in mean vesicle diameter when the polymer molecules are present during vesiculation, while in the case of copolymer addition to already formed liposomes the mean vesicle size follows a classic Langmuirian-type adsorption curve as a function of copolymer concentration. The ζ-potential values obtained decrease in a very similar pattern irrespective of the way of addition for the large PF127 (PEO99−PPO65−PEO99) molecule, illustrating the presence of polymer chains at the vesicle surface. For the small, more hydrophobic L61 (PEO10−PPO16−PEO10) molecule, the reduced ζ-potential value is maintained only when the copolymer molecules participate in bilayer formation, indicating absence of interaction between the polymer and the lipids when added to preformed liposomes, due to the preferred copolymer tendency to aggregate into micelles separate from the lipid bilayer particles (that eventually leads to phase separation). According to the molecular models proposed to describe the occurring lipid−copolymer interactions, addition of copolymer molecules after liposomes have been formed leads to their adsorption onto the outer liposome surface, its effectiveness being dependent on the influence that the hydrophilic (PEO) and hydrophobic (PPO) blocks exert on the copolymer molecular behaviour. Copolymer−lipid coparticipation toward bilayer formation, at low added polymer concentrations, leads to PPO block protection by arranging along with the lipids as integral parts of the vesicle bilayer, hence anchoring the PEO chains that dangle in the aqueous solution onto the vesicles. Simple geometrical considerations are also included, reinforcing the theoretical feasibility of the described models. The latter type of physically conjugating polymer chains onto vesicle surfaces is proposed as an improved alternative to the weak adsorption of amphiphilic molecules and the cumbersome chemical modification of the lipid polar headgroups to confer steric protection to liposomal surfaces.
Method for distribution, execution and management of the customized application based on software virtualization (2010)

Software virtualization allows applications and data to be put into virtual layers. We propose the method for distributing, executing and managing the customized application based on software virtualization. Customized application is composed of one or more applications, add-ons, plug-in and other various settings associated with software virtualization technique. Customized application generates the virtual boundary which separates and isolates the hard disk, memory and other resources at the execution time with a well-informed area to allow the user to write some data. So, our method ensures that customized application use a personal computer without modifying the hardware resource and without interfering with other applications in a safe state.
[Clinical characteristics of IgG4-related retroperitoneal fibrosis]. (2014)

IgG4-related RPF is a systemic autoimmune disease with favorable responses to the treatments of glucocorticoid and immunosuppressive agents.
Pathways for monolignol biosynthesis via metabolic grids: coniferyl aldehyde 5-hydroxylase, a possible key enzyme in angiosperm syringyl lignin biosynthesis (2003)

Lignins are aromatic polymers of methoxylated phenylpropanoids connected by both ether and carbon-carbon linkages, and classified into three major groups, guaiacyl lignin in softwoods (gymnosperms), guaiacyl-syringyl lignin in hardwoods (angiosperms) and guaiacyl-syringyl-p-hydroxyphenyl lignin in grasses (gramineae) on their monomeric units. In grass lignins p-coumaric acid (5∼10%) is ester linked mostly at γ-position of the propyl side chain. Biochemical studies of lignification have elucidated that 1) lignins are formed by dehydrogenative polymerization of monolignols catalyzed by peroxidase and laccase, 2) biosynthesis of monolignols is via shikimate-cinnamate pathway, 3) syringyl lignin in hardwoods is formed from the syringyl monolignol, sinapyl alcohol, derived from 5-hydroxyguaiacyl precursors, and that 4) ferulate 5-hydroxylase, coniferyl aldehyde 5-hydroxylase and probably coniferyl alcohol 5-hydroxylase are involved in the biosynthesis of the syringyl monolignol from guaiacyl monolignol precursors in respective hardwoods.(Communicated by Saburo TAMURA, M. J. A., Oct. 14, 2003)
Activation mechanisms of matrix metalloproteinases. (1997)

Matrix metalloproteinases (MMPs), also called matrixins, function in the turnover of extracellular matrix components. These enzymes are considered to play important roles in embryo development, morphogenesis and tissue remodeling, and in diseases such as arthritis, periodontitis, glomerulonephritis, atherosclerosis, tissue ulceration, and in cancer cell invasion and metastasis. All MMPs are synthesized as preproenzymes and most of them are secreted from the cells as proenzymes. Thus, the activation of these proenzymes is one of the critical steps that leads to extracellular matrix breakdown. This review describes recent progress made to elucidate the activation mechanisms of pro-matrixins which include extracellular stepwise activation common to most proMMPs, cell surface activation of progelatinase A and procollagenase 3, and intracellular activation of prostromelysin 3 and pro-membrane-type-1 MMP.
Likelihood-based deconvolution of bulk gene expression data using single-cell references (2021)

Direct comparison of bulk gene expression profiles is complicated by distinct cell type mixtures in each sample that obscure whether observed differences are actually caused by changes in the expression levels themselves or are simply a result of differing cell type compositions. Single-cell technology has made it possible to measure gene expression in individual cells, achieving higher resolution at the expense of increased noise. If carefully incorporated, such single-cell data can be used to deconvolve bulk samples to yield accurate estimates of the true cell type proportions, thus enabling one to disentangle the effects of differential expression and cell type mixtures. Here, we propose a generative model and a likelihood-based inference method that uses asymptotic statistical theory and a novel optimization procedure to perform deconvolution of bulk RNA-seq data to produce accurate cell type proportion estimates. We show the effectiveness of our method, called RNA-Sieve, across a diverse array of scenarios involving real data and discuss extensions made uniquely possible by our probabilistic framework, including a demonstration of well-calibrated confidence intervals.
Trifluorothymidine Induces Cell Death Independently of p53 (2008)

sensitivity to TFT is not dependent on the expression of wt p53.
Metamorphic Channels in Periodic Mesoporous Methylenesilica (2000)

Verbrückende Methylengruppen werden in terminale Methylgruppen überführt, wenn periodisch mesoporöse Methylensilicate, die erstmals durch Tensid-Templat-Synthese hergestellt wurden, unter kontrollierten Bedingungen (350–600°C) getempert werden. Die Methylengruppen, die zunächst Bestandteil der Kanalwände sind, werden dabei zu Methylgruppen, die in die Kanäle hineinragen (siehe Schema).
Study of BSSCO/Ag Tapes With the Help of Voltage Signal Analysis (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Properties of BSSCO/Ag tapes transporting AC current were studied by the Fourier analysis of the accompanying voltage signal. Particularly, the electrical signal in the measurement loop that is used in the standard AC loss measurement has been investigated. BSSCO/Ag tapes were studied starting from the characterization of the filament configuration, <formula formulatype="inline"> <tex>$J_{c}(B)$</tex></formula> dependence and inhomogeneity of <formula formulatype="inline"> <tex>$J_{c}$</tex></formula> distribution. These data were used as the input parameters for the numerical simulations. Initial simulations showed the necessity of replacing the simplified geometry model with detailed mutlifilamentary structure. Consequently, the higher harmonics turned out to be extremely sensitive on characterization parameters. After such refinement, the results of simulations give good agreement with measured higher harmonics of the voltage signal. This means that the analysis of higher harmonics could provide relevant information about the structure and other basic properties of the measured tape. </para>
Analysis of Telomere Maintenance Related Genes Reveals NOP10 as a New Metastatic-Risk Marker in Pheochromocytoma/Paraganglioma (2021)

One of the main problems we face with PPGL is the lack of molecular markers capable of predicting the development of metastases in patients. Telomere-related genes, such as <i>TERT</i> and <i>ATRX,</i> have been recently described in PPGL, supporting the association between the activation of immortalization mechanisms and disease progression. However, the contribution of other genes involving telomere preservation machinery has not been previously investigated. In this work, we aimed to analyze the prognostic value of a comprehensive set of genes involved in telomere maintenance. For this study, we collected 165 PPGL samples (97 non-metastatic/63 metastatic), genetically characterized, in which the expression of 29 genes of interest was studied by NGS. Three of the 29 genes studied, <i>TERT</i>, <i>ATRX</i> and <i>NOP10</i>, showed differential expression between metastatic and non-metastatic cases, and alterations in these genes were associated with a shorter time to progression, independent of <i>SDHB</i>-status. We studied telomere length by Q-FISH in patient samples and in an in vitro model. <i>NOP10</i> overexpressing tumors displayed an intermediate-length telomere phenotype without ALT, and in vitro results suggest that <i>NOP10</i> has a role in telomerase-dependent telomere maintenance. We also propose the implementation of NOP10 IHC to better stratify PPGL patients.
Supplementary Figures 1-4 from Cardiac Glycosides Inhibit p53 Synthesis by a Mechanism Relieved by Src or MAPK Inhibition (2023)

Supplementary Figures 1-4 from Cardiac Glycosides Inhibit p53 Synthesis by a Mechanism Relieved by Src or MAPK Inhibition
Structure and Origin of Artifacts in the Analysis of Plasmalogens (1996)

The determination of aldehydic compounds was achieved by gas chromatographic/mass spectrometric analysis of derived thioacetals. These were produced, together with artifacts, in a one-step reaction when plasmalogens were treated with ethane-1,2-dithiol and BF3. The artifacts were recognized to be 2-alkylidene-1,3-dithiolanes derived from phospholipids. The latter were converted by BF3 treatment into diacylglycerols, which were transformed in a complicated reaction into 2-alkyl-2-[(2-mercaptoethyl)thio]-1,3-dithiolanes. These compounds were decomposed thermally, e.g. in the injector of a gas chromatograph, in 2-alkylidene-1,3-dithiolanes. This reaction is not restricted to phospholipids but occurs with all monoacylated glycols.
Evaluation of eco‐friendly zwitterionic detergents for enveloped virus inactivation (2016)

Inclusion of a detergent in protein biotherapeutic purification processes is a simple and very robust method for inactivating enveloped viruses. The detergent Triton X-100 has been used for many years and is part of the production process of several commercial therapeutic proteins. However, recent ecological studies have suggested that Triton X-100 and its break-down products can potentially behave as endocrine disrupters in aquatic organisms, raising concerns from an environmental impact perspective. As such, discharge of Triton X-100 into the waste water treatment plants is regulated in some jurisdictions, and alternative detergents for viral inactivation are required. In this work, we report on the identification and evaluation of more eco-friendly detergents as viable replacements for Triton X-100. Five detergent candidates with low to moderate environmental impact were initially identified and evaluated with respect to protein stability, followed by proof-of-concept virus inactivation studies using a model enveloped virus. From the set of candidates lauryldimethylamine N-oxide (LDAO) was identified as the most promising detergent due to its low ecotoxicity, robust anti-viral activity (LRV >4 at validation set-point conditions with X-MuLX), and absence of any negative impact on protein function. This detergent exhibited effective and robust virus inactivation in a broad range of protein concentrations, solution conductivities, pHs, and in several different cell culture fluid matrices. The only process parameter which correlated with reduced virus inactivation potency was LDAO concentration, and then only when the concentration was reduced to below the detergent's critical micelle concentration (CMC). Additionally, this work also demonstrated that LDAO was cleared to below detectable levels after Protein A affinity chromatography, making it suitable for use in a platform process that utilizes this chromatographic mode for protein capture. All these findings suggest that LDAO may be a practical alternative to Triton X-100 for use in protein therapeutic production processes for inactivating enveloped viruses. Biotechnol. Bioeng. 2017;114: 813-820. © 2016 Wiley Periodicals, Inc.
Characteristics And Performance Of The National Synchrotron Light Source Infra-Red. Beamline (1988)

The National Synchrotron Light Source (NSLS) is a very bright, pulsed, broadband IR source. Continuously covering the spectral range from the visible to the mm wave region, it has been calculated&apos 1,2 to be one to three orders of magnitude brighter than a black-body source. At wavelengths longer than 100p, (100 cm 1) the NSLS provides more flux than a standard glbbar source, due to the different power laws governing black-body radiation and synchrotron radiation emission.
Depth Image Layers Separation (DILS) algorithm of image view synthesis based on stereo vision (2013)

A new Depth Image Layers Separation (DILS) algorithm for synthesizing inter-view images based on disparity depth map layers representation is presented. The approach is to separate the depth map into several layers identified through histogram-based clustering. Each layer is extracted using inter-view interpolation to create objects based on location and depth. DILS is a new paradigm in selecting interesting image locations based on depth, but also in producing new image representations that allow objects or parts of an image to be described without the need of segmentation and identification. The image view synthesis can reduce the configuration complexity of multi-camera arrays in 3D imagery and free-viewpoint applications. The simulation results show that depth layer separation is able to create inter-view images that may be integrated with other techniques such as occlusion handling processes. The DILS algorithm can be implemented using both simple as well as sophisticated stereo matching methods to synthesize inter-view images.
Cholinergic Dysfunction in Temporal Lobe Epilepsy (2007)

Summary: The entorhinal cortex–hippocampus complex is believed to be the site of origin of seizure activity in the majority of patients with temporal lobe epilepsy (TLE). Both these regions are enriched with cholinergic innervation, which plays a key role in the normal control of neuronal excitability and in higher cognitive processes. In TLE, anatomical and functional changes occur in all cellular components of the local neural circuit. Thus, while it is not surprising that cholinergic functions are altered in the epileptic temporal lobe, the exact nature and role of these changes in the pathogenesis of the disease are not known. In this report, we summarize the scientific background and experimental data supporting a “cholinergic hypothesis of TLE.” We conclude that while the exact role of cholinergic dysfunction in TLE is not known, there is a firm basis for suggesting that changes in the expression of key cholinergic proteins—and the associated cholinergic dysfunction—are key factors in the basic mechanisms underlying TLE.
Prognostic factors in patients with minor troponin-I elevation but without acute myocardial infarction (2006)

Creatine kinase myocardial isoform and C-reactive protein levels and age can be integrated to risk-stratify patients with minor troponin I elevation for reasons other than acute myocardial infarction.
Low-Voltage Super class AB CMOS OTA cells with very high slew rate and power efficiency (2005)

A simple technique to achieve low-voltage power-efficient class AB operational transconductance amplifiers (OTAs) is presented. It is based on the combination of class AB differential input stages and local common-mode feedback (LCMFB) which provides additional dynamic current boosting, increased gain-bandwidth product (GBW), and near-optimal current efficiency. LCMFB is applied to various class AB differential input stages, leading to different class AB OTA topologies. Three OTA realizations based on this technique have been fabricated in a 0.5-/spl mu/m CMOS technology. For an 80-pF load they show enhancement factors of slew rate and GBW of up to 280 and 3.6, respectively, compared to a conventional class A OTA with the same 10-/spl mu/A quiescent currents and /spl plusmn/1-V supply voltages. In addition, the overhead in terms of common-mode input range, output swing, silicon area, noise, and static power consumption, is minimal.
Control of Q-switched mode locking by active feedback (2001)

It is demonstrated that Q-switching dynamics in mode-locked lasers can be controlled by use of an active feedback loop. Analytic design rules for the feedback loop are presented. Suppression of Q-switched mode locking in a diode-pumped, passively mode-locked Nd:YVO(4) laser is shown experimentally and numerically.
ChemInform Abstract: A Novel Catalytic Asymmetric Route Towards Skipped Dienes with a Methyl‐Substituted Central Stereogenic Carbon. (2013)

Abstract A highly efficient method for the enantioselective synthesis of 1,4‐dienes (III) with a methyl‐substituted central carbon atom using an asymmetric allylic alkylation of diene bromides (I) is described.