gebhart/patrepeval huggingface dataset:
Fully Conservative Higher Order Finite Difference Schemes for Incompressible Flow (1998)

Conservation properties of the mass, momentum, and kinetic energy equations for incompressible flow are specified as analytical requirements for a proper set of discrete equations. Existing finite difference schemes in regular and staggered grid systems are checked for violations of the conservation requirements and a few important discrepancies are pointed out. In particular, it is found that none of the existing higher order schemes for a staggered mesh system simultaneously conserve mass, momentum, and kinetic energy. This deficiency is corrected through the derivation of a general family of fully conservative higher order accurate finite difference schemes for staggered grid systems. Finite difference schemes in a collocated grid system are also analyzed, and a violation of kinetic energy conservation is revealed. The predicted conservation properties are demonstrated numerically in simulations of inviscid white noise, performed in a two-dimensional periodic domain. The proposed fourth order schemes in a staggered grid system are generalized for the case of a non-uniform mesh, and the resulting scheme is used to perform large eddy simulations of turbulent channel flow.
Large-Scale Visual Relationship Understanding (2019)

Large scale visual understanding is challenging, as it requires a model to handle the widely-spread and imbalanced distribution of 〈subject, relation, object〉 triples. In real-world scenarios with large numbers of objects and relations, some are seen very commonly while others are barely seen. We develop a new relationship detection model that embeds objects and relations into two vector spaces where both discriminative capability and semantic affinity are preserved. We learn a visual and a semantic module that map features from the two modalities into a shared space, where matched pairs of features have to discriminate against those unmatched, but also maintain close distances to semantically similar ones. Benefiting from that, our model can achieve superior performance even when the visual entity categories scale up to more than 80,000, with extremely skewed class distribution. We demonstrate the efficacy of our model on a large and imbalanced benchmark based of Visual Genome that comprises 53,000+ objects and 29,000+ relations, a scale at which no previous work has been evaluated at. We show superiority of our model over competitive baselines on the original Visual Genome dataset with 80,000+ categories. We also show state-of-the-art performance on the VRD dataset and the scene graph dataset which is a subset of Visual Genome with 200 categories.
Microstructural characterization of trabecular bone using ultrasonic backscattering and diffusion parameters (2017)

Finite differences time domain methods were utilized to simulate ultrasound propagation and scattering in anisotropic trabecular bone structures obtained from high resolution Computed Tomography (CT). The backscattered signals were collected and the incoherent contribution was extracted. The diffusion constant was calculated for propagations along and across the main direction of anisotropy, and was used to characterize the anisotropy of the trabecular microstructures. In anisotropic structures, the diffusion constant was significantly different in both directions, and the anisotropy of the diffusion constant was strongly correlated to the structural anisotropy measured on the CT images. These results indicate that metrics based on diffusion can be used to quantify the anisotropy of complex structures such as trabecular bone.
Measurement of stable isotopic enrichment and concentration of long-chain fatty acyl-carnitines in tissue by HPLC-MS (2005)

We have developed a new method for the simultaneous measurements of stable isotopic tracer enrichments and concentrations of individual long-chain fatty acyl-carnitines in muscle tissue using ion-pairing high-performance liquid chromatography-electrospray ionization quadrupole mass spectrometry in the selected ion monitoring (SIM) mode. Long-chain fatty acyl-carnitines were extracted from frozen muscle tissue samples by acetonitrile/methanol. Baseline separation was achieved by reverse-phase HPLC in the presence of the volatile ion-pairing reagent heptafluorobutyric acid. The SIM capability of a single quadrupole mass analyzer allows further separation of the ions of interest from the sample matrixes, providing very clean total and selected ion chromatograms that can be used to calculate the stable isotopic tracer enrichment and concentration of long-chain fatty acyl-carnitines in a single analysis. The combination of these two separation techniques greatly simplifies the sample preparation procedure and increases the detection sensitivity. Applying this protocol to biological muscle samples proves it to be a very sensitive, accurate, and precise analytical tool.
THE AMMONIUM TUNGSTATES.<sup>1</sup> (1902)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE AMMONIUM TUNGSTATES.1Thomas M. TaylorCite this: J. Am. Chem. Soc. 1902, 24, 7, 629–643Publication Date (Print):July 1, 1902Publication History Published online1 May 2002Published inissue 1 July 1902https://pubs.acs.org/doi/10.1021/ja02021a002https://doi.org/10.1021/ja02021a002research-articleACS PublicationsRequest reuse permissionsArticle Views199Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The benefits of nurse-led cancer follow-up (2005)

Despite the shortage in the nursing workforce, Jan Morrison argues that their clinical background and holistic approach means that nurses are best equipped to provide follow-up care for cancer patients
A mathematical model of N‐linked glycosylation (2005)

Metabolic engineering of N-linked oligosaccharide biosynthesis to produce novel glycoforms or glycoform distributions of a recombinant glycoprotein can potentially lead to an improved therapeutic performance of the glycoprotein product. A mathematical model for the initial stages of this process, up to the first galactosylation of an oligosaccharide, was previously developed by Umana and Bailey (1997) (UB1997). Building on this work, an extended model is developed to include further galactosylation, fucosylation, extension of antennae by N-acetyllactosamine repeats, and sialylation. This allows many more structural features to be predicted. A number of simplifying assumptions are also relaxed to incorporate more variables for the control of glycoforms. The full model generates 7565 oligosaccharide structures in a network of 22,871 reactions. Methods for solving the model for the complete product distribution and adjusting the parameters to match experimental data are also developed. A basal set of kinetic parameters for the enzyme-catalyzed reactions acting on free oligosaccharide substrates is obtained from the previous model and existing literature. Enzyme activities are adjusted to match experimental glycoform distributions for Chinese Hamster Ovary (CHO). The model is then used to predict the effect of increasing expression of a target glycoprotein on the product glycoform distribution and evaluate appropriate metabolic engineering strategies to return the glycoform profile to its original distribution pattern. This model may find significant utility in the future to predict glycosylation patterns and direct glycoengineering projects to optimize glycoform distributions.
Probing the Role of Cysteine Residues in Glucosamine-1-Phosphate Acetyltransferase Activity of the Bifunctional GlmU Protein from <i>Escherichia coli</i> : Site-Directed Mutagenesis and Characterization of the Mutant Enzymes (1998)

The glucosamine-1-phosphate acetyltransferase activity but not the uridyltransferase activity of the bifunctional GlmU enzyme from Escherichia coli was lost when GlmU was stored in the absence of beta-mercaptoethanol or incubated with thiol-specific reagents. The enzyme was protected from inactivation in the presence of its substrate acetyl coenzyme A (acetyl-CoA), suggesting the presence of an essential cysteine residue in or near the active site of the acetyltransferase domain. To ascertain the role of cysteines in the structure and function of the enzyme, site-directed mutagenesis was performed to change each of the four cysteines to alanine, and plasmids were constructed for high-level overproduction and one-step purification of histidine-tagged proteins. Whereas the kinetic parameters of the bifunctional enzyme appeared unaffected by the C296A and C385A mutations, 1,350- and 8-fold decreases of acetyltransferase activity resulted from the C307A and C324A mutations, respectively. The Km values for acetyl-CoA and GlcN-1-P of mutant proteins were not modified, suggesting that none of the cysteines was involved in substrate binding. The uridyltransferase activities of wild-type and mutant GlmU proteins were similar. From these studies, the two cysteines Cys307 and Cys324 appeared important for acetyltransferase activity and seemed to be located in or near the active site.
02. Preface of Design and Analysis of Experiments - 2nd Edition (1999)

Preface of the second edition of Design and Analysis of Experiments.
Common variants in LSP1, 2q35 and 8q24 and breast cancer risk for BRCA1 and BRCA2 mutation carriers (2009)

Genome-wide association studies of breast cancer have identified multiple single nucleotide polymorphisms (SNPs) that are associated with increased breast cancer risks in the general population. In a previous study, we demonstrated that the minor alleles at three of these SNPs, in FGFR2, TNRC9 and MAP3K1, also confer increased risks of breast cancer for BRCA1 or BRCA2 mutation carriers. Three additional SNPs rs3817198 at LSP1, rs13387042 at 2q35 and rs13281615 at 8q24 have since been reported to be associated with breast cancer in the general population, and in this study we evaluated their association with breast cancer risk in 9442 BRCA1 and 5665 BRCA2 mutation carriers from 33 study centres. The minor allele of rs3817198 was associated with increased breast cancer risk only for BRCA2 mutation carriers [hazard ratio (HR) = 1.16, 95% CI: 1.07-1.25, P-trend = 2.8 x 10(-4)]. The best fit for the association of SNP rs13387042 at 2q35 with breast cancer risk was a dominant model for both BRCA1 and BRCA2 mutation carriers (BRCA1: HR = 1.14, 95% CI: 1.04-1.25, P = 0.0047; BRCA2: HR = 1.18 95% CI: 1.04-1.33, P = 0.0079). SNP rs13281615 at 8q24 was not associated with breast cancer for either BRCA1 or BRCA2 mutation carriers, but the estimated association for BRCA2 mutation carriers (per-allele HR = 1.06, 95% CI: 0.98-1.14) was consistent with odds ratio estimates derived from population-based case-control studies. The LSP1 and 2q35 SNPs appear to interact multiplicatively on breast cancer risk for BRCA2 mutation carriers. There was no evidence that the associations vary by mutation type depending on whether the mutated protein is predicted to be stable or not.
Assembly of 4‐Aminoquinolines via Palladium Catalysis: A Mild and Convenient Alternative to S<sub>N</sub>Ar Methodology. (2007)

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.
Functional role of kallikrein 5 and proteinase-activated receptor 2 in eosinophilic esophagitis (2020)

Eosinophilic esophagitis (EoE) is a chronic, food antigen-driven, inflammatory disease of the esophagus and is associated with impaired barrier function. Evidence is emerging that loss of esophageal expression of the serine peptidase inhibitor, kazal type 7 (SPINK7), is an upstream event in EoE pathogenesis. Here, we provide evidence that loss of <i>SPINK7</i> mediates its pro-EoE effects via kallikrein 5 (KLK5) and its substrate, protease-activated receptor 2 (PAR2). Overexpression of <i>KLK5</i> in differentiated esophageal epithelial cells recapitulated the effect of <i>SPINK7</i> gene silencing, including barrier impairment and loss of desmoglein-1 expression. Conversely, KLK5 deficiency attenuated allergen-induced esophageal protease activity, modified commensal microbiome composition, and attenuated eosinophilia in a murine model of EoE. Inhibition of PAR2 blunted the cytokine production associated with loss of <i>SPINK7</i> in epithelial cells and attenuated the allergen-induced esophageal eosinophilia in vivo. Clinical samples substantiated dysregulated PAR2 expression in the esophagus of patients with EoE, and delivery of the clinically approved drug α1 antitrypsin (A1AT, a protease inhibitor) inhibited experimental EoE. These findings demonstrate a role for the balance between KLK5 and protease inhibitors in the esophagus and highlight EoE as a protease-mediated disease. We suggest that antagonizing KLK5 and/or PAR2 has potential to be therapeutic for EoE.
Xen Live Migration with Slowdown Scheduling Algorithm (2010)

With the increasing number of technology areas using Virtual Machine (VM) platforms, challenges exist in Virtual Machine migrating from one physical host to another. However, the complexity of these virtualized environments presents additional management challenges. Unfortunately, many traditional approaches may be either not effective well for reducing downtime or migration time, or not suitable well for Xen VMs platforms. This paper presents the design and implementation of a novel Slowdown Scheduling Algorithm (SSA) for Xen live VM migration. In our SSA methodology, the CPU resources which have been assigned to migration domain are decrease properly. That is, the dirtying page rate is reduced according to the decrease of CPU activity. Experimental results illustrate that our SSA approach can shorten both the total migration time and downtime obviously under high dirty page rate environment.
The Ranque effect (1997)

The existing theories of the Ranque effect are reviewed and their inherent inconsistencies in the interpretation of some experimental data discussed. A new approach to the vortex effect is formulated, which provides a unified explanation of all the experimental data available.
Optical phase conjugation in an azo-doped liquid crystal valve (1995)

A novel method of generating optical phase conjugation using an azo-doped liquid crystal valve is proposed for the first time. Its response time, diffraction efficiency, and threshold intensity are measured. The resolution of the device is discussed. An observation of diffraction rings caused by self-phase modulation when a low-power laser beam passes through the azo-doped liquid crystal valve is reported. Finally, these phenomena are shown to be results of the reorientation of liquid crystal molecules driven by the photoinduced isomerization, not merely an azo dye effect or a local heating effect.
<title>Calibration of scanning electron microscope magnification standards SRM484</title> (1996)

Standard Reference Material (SRM) 484 is an artifact for calibrating the magnification scale of a scanning electron microscope. Since 1977 the National Institute ofStandards and Technology (MST) has produced seven issues of SRM484 amounting to approximately 1 150 samples in all. The standards are fabricated by electroplating alternate layers ofnickel and gold onto a substrate of a Monel sheet metal. The plate is then diced, and the individual pieces are mounted on edge in a holder. Each sample is metallographically polished to obtain a smooth surface and to reveal gold lines. The samples are calibrated using a scanniig electron microscope incorporated with a laser interferometer. A piezo flexure stage carries the sample across the stationary electron beam. A backscattered electron detector detects an intensity peak at each location where the electron beam interacts with a gold line. The displacement ofthe traveled stage between lines is monitored by the interferometer. A computer program records the intensity peaks and displacement information and determines the distance (spacing) between any two peaks. The spacing is measured from a peak-to-peak algorithm rather than an edge-to-edge algorithm in order to avoid the determination ofline edge positions. Properties ofthe SRM484 and the measurement system result in recent expanded uncertainties (at the level oftwo standard deviations) of approximately 4% for 0.5 jim spacings and 0.5% for 50 tm spacings. Key words: Interferometer, Measurement uncertainty, Scanning Electron Microscope, SEM magnification, Standard Reference Material.
111In-Labeled DOTA-conjugated 6-aminohexanoic linker-containing variant of anti-epidermal growth factor receptor 2 Affibody ZHER2:342 (ABY-003) (2011)

An Affibody molecule is a chain of 58 amino acids (~6.5 kDa) that contains a modified B domain of the staphylococcal protein A and can be obtained through chemical synthesis or produced in bacteria with the use of recombinant technology (1). Because of their small size and high chemical and thermal stability, these molecules are used as radiolabeled probes for the targeted detection and treatment of malignant tumors as discussed elsewhere (1-3).The epidermal growth factor receptor 2 (HER2) is considered to be an important Affibody target because it is believed to promote the development of the malignant phenotype, it plays a role in the development of resistance to anticancer drugs and radiation therapy, it is overexpressed in several different cancer tumor cells, and it often indicates a poor prognosis for the patient (4). Several radionuclide-labeled Affibodies and their derivatives, such as ZHER2:342, have been evaluated to detect tumors expressing HER2 in preclinical studies as discussed by Tolmachev (5). Earlier, a derivative of the ZHER2:342 Affibody, designated ABY-002, which has the radiometal chelator 1,4,7,10-tetraazacyclododecane-N,N',N,N'-tetraacetic acid (DOTA) linked directly to the N-terminal valine of the molecule was constructed, radiolabeled with 111In or 68Ga, and evaluated for the imaging of malignant tumors that express HER2 (6). Although radiolabeled ABY-002 (both with 111In or 68Ga) could detect these tumors under in vivo conditions, the ZHER2:342 Affibody derivative exhibited a reduced affinity for HER2 (KD = 65 pM) compared to the parent Affibody (KD = 22 pM).From this study, it was concluded that the reduced affinity of ABY-002 for the receptor is probably due to a steric hindrance from the DOTA moiety, which is located very close to the HER2 binding site of the molecule. Tolmachev et al. decided to introduce a linker between the DOTA moiety and the HER2 binding sequence and evaluate whether this modification reduced or abolished the steric obstruction that may reduce the affinity of the Affibody for the receptor (7). The investigators placed an aliphatic linker (6-aminohexanoic acid) between DOTA and the valine on the N-terminal of ABY-002, labeled the modified Affibody (ABY-003) with 111In ([111In]-ABY-003), and evaluated the biodistribution and tumor detection properties of [111In]-ABY-003 in mice bearing HER2-expressing LS174T cell xenograft tumors (a human colon adenocarcinoma cell line showing a moderate expression level of HER2) or SKOV-3 cell xenograft tumors (a human ovarian carcinoma cell line showing a high expression level of HER2) (7).
A Laser-Plasma Positron Accelerator using Particle-Shower Plasma-Wave interactions (2018)

An all-optical laser-plasma positron accelerator is introduced and modeled using the interaction of laser-driven particle-showers with laser-driven electron plasma-waves. The principle uncovered here shows the trapping and acceleration of positrons that are part of a laser-driven electromagnetic positron-electron shower in a laser-driven plasma wave. The proof of this principle using Particle-In-Cell simulations shows the production of hundreds of MeV beams with pico-Coulomb scale charge using existing lasers. By eliminating the dependence on kilometer-scale radio-frequency accelerators, this centimeter-scale accelerator makes high-energy positron beams widely accessible.
Chiral Stationary Phases for High Performance Liquid Chromatographic Separation of Enantiomers: A Mini-Review (1984)

Abstract There has been a proliferation of papers on the use of chiral stationary phases (CSP's) to separate optical isomers in high performance liquid chromatography. The chemistry, mechanism and stability of these CSP's can vary widely. Furthermore, the applicability, availability and cost of a CSP can mean the difference between its being of passing academic interest as opposed to a technique that could have a significant impact on science and technology. Six different classes of chiral stationary phases are examined and discussed including the new chiral cyclodextrin bonded phases. The separation mechanism, strengths and limitations of the CSP's are also considered whenever such information is available.
Implication of dropping packets from the front of a queue (1993)

When congestion occurs in a packet queuing system, packets can be dropped from the rear or the front of the queue. It is demonstrated that the probability of a packet being dropped is the same in systems with rear and front packet dropping. It is shown that the probability of a packet being delayed longer than a given value in a system with front dropping is less than or equal to that in a system with rear dropping. It is further illustrated that front dropping not only improves the delay performance on an internodal link, but also provides the overall loss performance for time constrained traffic such as packet voice.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Resource Allocation in OFDMA Networks With Imperfect Channel State Information (2014)

This letter investigates the effect of imperfect channel state information (CSI) on the performance of radio resource management for a downlink multi-user OFDMA system. It is shown that the imperfect CSI introduces a signal-and-power dependent noise term, which makes the symbol error rate (SER) constellation-point dependent, and yields an error floor on the SER. In addition, a two-step multi-user channel, power and constellation allocation algorithm is proposed to maximize the total network throughput.