gebhart/patrepeval huggingface dataset:
Characterization of the Salmonella typhimurium pagC/pagD chromosomal region (1995)

The PhoP/PhoQ two-component system regulates Salmonella typhimurium genes that are essential to bacterial virulence and survival within macrophages. The best characterized of these PhoP-activated genes (pag) is pagC, which encodes a 188-amino-acid envelope protein (W. S. Pulkkinen and S. I. Miller, J. Bacteriol. 173:86-93, 1991). We here report the identification of four genes (pagD, envE, msgA, and envF) located 5' to pagC. Each gene is transcribed from its own promoter, two of which (msgA and pagD) were defined by primer extension analysis. Three of these genes (pagD, envE, and envF) are predicted to encode envelope proteins. The pagD gene is transcribed in a direction opposite from that of and adjacent to pagC and is positively regulated by PhoP/PhoQ. Transposon insertions within pagD and msgA attenuate bacterial virulence and survival within macrophages; however, deletion of pagD has no effect on virulence. The product of the envF gene is predicted to be a lipoprotein on the basis of the presence of a consensus lipid attachment site. The low G + C content of these genes and the homology of msgA to Shigella plasmid DNA suggest that this region may have been acquired by horizontal transmission.
Grain Refinement of Aluminium Alloys by Inoculation (2003)

Abstract A review is given of the studies of aluminium inoculation undertaken within the EU Network “Microstructural Engineering by Solidification Processing” (MEBSP). A wide range of studies of industrial practice of grain refining and of the fundamental mechanisms of nucleation and growth have contributed to improved understanding. Particular advances have been made in understanding the relative performance of different grain refiners.
Adopting a Resourceful Approach (1980)

An experiment with a ‘resource room’ model for special children in a comprehensive school is described Elizabeth Jones school counsellor, Banbury School Sandra Berrick head of the Special Resources Department, Carterton School
Diesel fuel derived from vegetable oils, III. Emission tests using methyl esters of used frying oil (1988)

Abstract The preparation of methyl esters of used frying oil, available as waste from restaurants and households, is described. Fuel specifications of this fuel are given, and values for gaseous (HC, CO, NO x ) and particulate emissions, measured with a vehicle powered by a turbocharged, direct injection diesel engine, are shown. The ester fuel shows slightly lower HC and CO emissions but increased NO x values compared with reference US‐2D fuel. The particulate emissions, however, are significantly lower with used frying oil. Preliminary results of an engine road test are described.
Functional and Structural Diversity in the Als Protein Family of Candida albicans (2004)

The human fungal pathogen Candida albicans colonizes and invades a wide range of host tissues. Adherence to host constituents plays an important role in this process. Two members of the C. albicans Als protein family (Als1p and Als5p) have been found to mediate adherence; however, the functions of other members of this family are unknown. In this study, members of the ALS gene family were cloned and expressed in Saccharomyces cerevisiae to characterize their individual functions. Distinct Als proteins conferred distinct adherence profiles to diverse host substrates. Using chimeric Als5p-Als6p constructs, the regions mediating substrate-specific adherence were localized to the N-terminal domains in Als proteins. Interestingly, a subset of Als proteins also mediated endothelial cell invasion, a previously unknown function of this family. Consistent with these results, homology modeling revealed that Als members contain anti-parallel beta-sheet motifs interposed by extended regions, homologous to adhesins or invasins of the immunoglobulin superfamily. This finding was confirmed using circular dichroism and Fourier transform infrared spectrometric analysis of the N-terminal domain of Als1p. Specific regions of amino acid hypervariability were found among the N-terminal domains of Als proteins, and energy-based models predicted similarities and differences in the N-terminal domains that probably govern the diverse function of Als family members. Collectively, these results indicate that the structural and functional diversity within the Als family provides C. albicans with an array of cell wall proteins capable of recognizing and interacting with a wide range of host constituents during infection.
A stateless, content-directed data prefetching mechanism (2002)

Although central processor speeds continues to improve, improvements in overall system performance are increasingly hampered by memory latency, especially for pointer-intensive applications. To counter this loss of performance, numerous data and instruction prefetch mechanisms have been proposed. Recently, several proposals have posited a memory-side prefetcher; typically, these prefetchers involve a distinct processor that executes a program slice that would effectively prefetch data needed by the primary program. Alternative designs embody large state tables that learn the miss reference behavior of the processor and attempt to prefetch likely misses.This paper proposes Content-Directed Data Prefetching, a data prefetching architecture that exploits the memory allocation used by operating systems and runtime systems to improve the performance of pointer-intensive applications constructed using modern language systems. This technique is modeled after conservative garbage collection, and prefetches "likely" virtual addresses observed in memory references. This prefetching mechanism uses the underlying data of the application, and provides an 11.3% speedup using no additional processor state. By adding less than ½% space overhead to the second level cache, performance can be further increased to 12.6% across a range of "real world" applications.
Validation of a blood plasma separation system by biomarker detection (2010)

A microfluidic system was developed for blood plasma separation at high flow rate. This system uses only hydrodynamic forces to separate plasma from whole blood. The microfluidic network features a series of constrictions and bifurcations to enhance the product yield and purity. A maximum purity efficiency of 100% is obtained on blood with entrance hematocrit level up to 30% with a flow rate of 2 mL h(-1). Flow cytometry was performed on the extracted plasma to evaluate the separation efficiency and to assess cell damage. A core target of this study was the detection of cell-free DNA from the on-chip extracted plasma. To this effect, PCR was successfully carried out off-chip on the cell-free DNA present in the plasma extracted on-chip. A house-keeping gene sequence (GAPDH) was amplified without the need for a purification after the separation, thereby showing the high quality of the plasma sample. The resulting data suggests that the system can be used as a preliminary module of a total analysis system for cell-free DNA detection in human plasma.
Structural and Functional Properties of Two Human FXYD3 (Mat-8) Isoforms (2006)

Six of 7 FXYD proteins have been shown to be tissue-specific modulators of Na,K-ATPase. In this study, we have identified two splice variants of human FXYD3, or Mat-8, in CaCo-2 cells. Short human FXYD3 has 72% sequence identity with mouse FXYD3, whereas long human FXYD3 is identical to short human FXYD3 but has a 26-amino acid insertion after the transmembrane domain. Short and long human FXYD3 RNAs and proteins are differentially expressed during differentiation of CaCo-2 cells. Long human FXYD3 is mainly expressed in nondifferentiated cells and short human FXYD3 in differentiated cells and both FXYD3 variants can be co-immunoprecipitated with a Na,K-ATPase antibody. In contrast to mouse FXYD3, which has two transmembrane domains for lack of cleavage of the signal peptide, human FXYD3 has a cleavable signal peptide and adopts a type I topology. After co-expression in Xenopus oocytes, both human FXYD3 variants associate stably only with Na,K-ATPase isozymes but not with H,K-ATPase or Ca-ATPase. Similar to mouse FXYD3, short human FXYD3 decreases the apparent K(+) and Na(+) affinity of Na,K-ATPase over a large range of membrane potentials. On the other hand, long human FXYD3 decreases the apparent K(+) affinity only at slightly negative and positive membrane potentials and increases the apparent Na(+) affinity of Na,K-ATPase. Finally, both short and long human FXYD3 induce a hyperpolarization activated current, similar to that induced by mouse FXYD3. Thus, we have characterized two human FXYD3 isoforms that are differentially expressed in differentiated and non-differentiated cells and show different functional properties.
Combined Gene Expression Profiling and RNAi Screening in Clear Cell Renal Cell Carcinoma Identify PLK1 and Other Therapeutic Kinase Targets (2011)

In recent years, several molecularly targeted therapies have been approved for clear cell renal cell carcinoma (ccRCC), a highly aggressive cancer. Although these therapies significantly extend overall survival, nearly all patients with advanced ccRCC eventually succumb to the disease. To identify other molecular targets, we profiled gene expression in 90 ccRCC patient specimens for which tumor grade information was available. Gene set enrichment analysis indicated that cell-cycle-related genes, in particular, Polo-like kinase 1 (PLK1), were associated with disease aggressiveness. We also carried out RNAi screening to identify kinases and phosphatases that when inhibited could prevent cell proliferation. As expected, RNAi-mediated knockdown of PLK1 and other cell-cycle kinases was sufficient to suppress ccRCC cell proliferation. The association of PLK1 in both disease aggression and in vitro growth prompted us to examine the effects of a small-molecule inhibitor of PLK1, BI 2536, in ccRCC cell lines. BI 2536 inhibited the proliferation of ccRCC cell lines at concentrations required to inhibit PLK1 kinase activity, and sustained inhibition of PLK1 by BI 2536 led to dramatic regression of ccRCC xenograft tumors in vivo. Taken together, these findings highlight PLK1 as a rational therapeutic target for ccRCC.
Melanocortin-5 Receptor Deficiency Reduces a Pheromonal Signal for Aggression in Male Mice (2004)

Mice lacking the melanocortin-5 receptor (MC5R) exhibit decreased sensitivity to the stimulatory effects of systemic melanocortin injections on aggressive behavior. Because the pheromone-producing preputial gland expresses the MC5R, we tested the hypothesis that decreases in preputial pheromones underlie the behavioral deficit. Here we show that MC5R deficiency decreases preputial and urine levels of the sex pheromones, alpha- and beta-farnesene, relative to wild-type mice. We also demonstrate that farnesenes potently stimulate aggression in mice. Moreover, farnesene-stimulated aggression is reduced in MC5R-deficient mice, relative to wild-type mice. Our results suggest that activation of the MC5R promotes aggression by increasing farnesene signaling.
Automated segmentation of thoracic aorta in non-contrast CT images (2008)

Aortic calcification has been shown to be related to cardiovascular disease. In this paper, we present a novel method for localization and segmentation of thoracic aorta in non-contrast CT images using dynamic programming concepts to detect and quantify aortic calcium. The localization and segmentation of the aorta are formulated as optimal path detection problems, which are solved using dynamic programming principles. We apply these methods on Hough space for aorta localization and a transformed polar coordinate space for aorta segmentation. We evaluate the proposed approach by comparing it with the manual annotations in terms of aorta location, boundary distance, and volume overlap.
Residual Carrier and Sampling Frequency Synchronization in Multiuser OFDM Systems (2006)

This contribution considers the estimation and compensation of residual multiple carrier frequency offsets (CFOs) and sampling frequency offsets (SFOs) in the uplink of a multiuser OFDM system. Based on the observation of a user-dependent phase rotation, an approximate maximum-likelihood (ML) estimator is proposed in order to estimate the CFOs and SFOs to track the phase in a post-synchronization step. Bit-error-ratio (BER) simulations show that the system performance degradation due to (small) frequency mismatches is negligible if the proposed method is applied
CdSe/CdS/SiO<SUB>2</SUB> Core/Shell/Shell Nanoparticles (2007)

Quantum dots (QD) of a CdSe-ZnS core-shell structure are coated with silica spheres to improve their stability in biological buffers and biocompatibility in fluorescence imaging. We found that it was critical to transfer quantum dots from organic phase to aqueous phase before the silica shell growth process. As a result, high quality CdSe-ZnS-SiO2 core-shell-shell nanoparticles were prepared in high yields and their size and distribution are characterized with transmission electron microscopy and dynamic light scattering, which yielded uniform sizes and narrow polydispersity. Single particle fluorescence spectroscopy on the silica-protected quantum dots showed they were stronger emitters with consistent fluorescence intensity and "on-off" behaviors than bare CdSe-ZnS nanocrystals.
Thermal degradation of cellulose in air and nitrogen at low temperatures (1979)

Abstract Thermal analysis and kinetic studies have shown that oxidative reactions are responsible for acceleration in the rates of weight loss and depolymerization of cellulose on pyrolysis in air at temperatures below 300°C. The oxidative reactions include production of hydroperoxide, carbonyl, and carboxyl groups, which have been investigated at lower temperatures along with the rates of depolymerization and production of carbon monoxide and carbon dioxide. The experimental results are consistent with an autoxidation mechanism involving initiation, propagation, and decomposition reactions. At temperatures above 300°, the rate of pyrolysis is essentially the same in both air and nitrogen, indicating that thermal degradation is independent of the oxidative reactions.
Quantitative and Sensitive Detection of Cancer Genome Amplifications from Formalin Fixed Paraffin Embedded Tumors with Droplet Digital PCR (2012)

For the analysis of cancer, there is great interest in rapid and accurate detection of cancer genome amplifications containing oncogenes that are potential therapeutic targets. The vast majority of cancer tissue samples are formalin fixed and paraffin embedded (FFPE) which enables histopathological examination and long term archiving. However, FFPE cancer genomic DNA is oftentimes degraded and generally a poor substrate for many molecular biology assays. To overcome the issues of poor DNA quality from FFPE samples and detect oncogenic copy number amplifications with high accuracy and sensitivity, we developed a novel approach. Our assay requires nanogram amounts of genomic DNA, thus facilitating study of small amounts of clinical samples. Using droplet digital PCR (ddPCR), we can determine the relative copy number of specific genomic loci even in the presence of intermingled normal tissue. We used a control dilution series to determine the limits of detection for the ddPCR assay and report its improved sensitivity on minimal amounts of DNA compared to standard real-time PCR. To develop this approach, we designed an assay for the fibroblast growth factor receptor 2 gene (<i>FGFR2</i>) that is amplified in a gastric and breast cancers as well as others. We successfully utilized ddPCR to ascertain <i>FGFR2</i> amplifications from FFPE-preserved gastrointestinal adenocarcinomas.
The pathophysiology of hyperuricaemia and its possible relationship to cardiovascular disease, morbidity and mortality (2013)

Uric acid is the end product of purine metabolism in humans. High levels are causative in gout and urolithiasis. Hyperuricaemia has also been implicated in the pathophysiology of hypertension, chronic kidney disease (CKD), congestive heart failure (CHF), the metabolic syndrome, type 2 diabetes mellitus (T2DM), and atherosclerosis, with or without cardiovascular events. This article briefly reviews uric acid metabolism and summarizes the current literature on hyperuricaemia in cardiovascular disease and related co-morbidities, and emerging treatment options.
Numerical simulation of ignition of particles of a coal–water fuel (2015)

The problem of particle ignition of coal–water fuel has been solved. The simultaneous processes of water vaporization and thermal decomposition of the solid fuel are taken into account. The conditions and characteristics of particle ignition of coal–water fuel under typical furnace conditions were determined by numerical simulation. The obtained values of the ignition delay time are in good agreement with published experimental data.
BCL2 protein is topographically restricted in tissues characterized by apoptotic cell death. (1991)

The BCL2 protooncogene encodes an inner mitochondrial membrane protein that blocks programmed cell death. BCL2 was isolated from the chromosomal breakpoint of follicular B-cell lymphoma. Transgenic mice that overexpress BCL2 display extended survival of resting B cells. In this study we use a monospecific anti-human BCL2 antibody to define the distribution of BCL2 protein within organized tissues. BCL2 is restricted within germinal centers to the follicular mantle and to portions of the light zone implicated in the selection and maintenance of plasma cells and memory B cells. BCL2 is present in the surviving T cells in the thymic medulla. All hematopoietic lineages that derive from a renewing stem cell also display BCL2. A limited number of nonlymphoid tissues demonstrate BCL2 and can be grouped as (i) glandular epithelium in which hormones or growth factors regulate hyperplasia and involution, (ii) complex differentiating epithelium such as skin and intestine characterized by long-lived stem cells, and (iii) long-lived postmitotic cells such as neurons. Within these tissues that demonstrate apoptotic cell turnover, BCL2 is often topographically restricted to long-lived or proliferating cell zones. BCL2's function as an antidote to apoptosis may confer longevity to progenitor and effector cells in these tissues.
Electrophilic Addition of Polychloroalkanes to C60:  Direct Observation of Alkylfullerenyl Cation Intermediates (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTElectrophilic Addition of Polychloroalkanes to C60: Direct Observation of Alkylfullerenyl Cation IntermediatesToshikazu Kitagawa, Harumi Sakamoto, and Ken'ichi TakeuchiView Author Information Department of Energy and Hydrocarbon Chemistry Graduate School of Engineering Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan Cite this: J. Am. Chem. Soc. 1999, 121, 17, 4298–4299Publication Date (Web):May 5, 1999Publication History Received4 January 1999Published online5 May 1999Published inissue 1 May 1999https://pubs.acs.org/doi/10.1021/ja9900048https://doi.org/10.1021/ja9900048rapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views541Altmetric-Citations55LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Absorption,Carbon,Cations,Chemical structure,Ions Get e-Alerts
FRA: Teaching Financial Accounting with a Goal‐Based Scenario (1995)

A bstract This paper reports on the development of FRA (Financial Report Analyst), an intelligent, multimedia educational software system which is designed to teach financial statement analysis to business students and professional trainees. FRA is based on a new kind of teaching architecture called a goal‐based scenario, a “learning by doing” environment in which the student acts in a realistic role and obtains helpful coaching while performing assigned tasks. In FRA, the student plays the role of a lending analyst at a bank who must make important commercial lending decisions. Usability tests of FRA have been conducted with students in the Kellogg Graduate School of Management at Northwestern University. The paper discusses: theoretical advantages of goal‐based scenarios; the architecture of FRA; and ongoing and future research.
Dynamical chaos : proceedings of a Royal Society discussion meeting held on 4 and 5 February 1987 (1987)

The leading scientists who gave these papers under the sponsorship of the Royal Society in early 1987 provide reviews of facets of the subject of chaos ranging from the practical aspects of mirror machines for fusion power to the pure mathematics of geodesics on surfaces of negative curvature. The papers deal with systems in which chaotic conditions arise from initial value problems with unique solutions, as opposed to those where chaos is produced by the introduction of noise from an external source. Table of Contents Diagnosis of Dynamical Systems with Fluctuating Parameters D. Ruelle Nonlinear Dynamics, Chaos, and Complex Cardiac Arrhythmias L. Glass, A. L. Goldberger, M. Courtemanche, and A. Shrier Chaos and the Dynamics of Biological Populations R. M. May Fractal Bifurcation Sets, Renormalization Strange Sets, and Their Universal Invariants D. A. Rand From Chaos to Turbulence in Bnard Convection A. Libchaber Dynamics of Convection N. O. Weiss Chaos: A Mixed Metaphor for Turbulence E. A. Spiegel Arithmetical Theory of Anosov Diffeomorphisms F. Vivaldi Chaotic Behavior in the Solar System J. Wisdom Chaos in Hamiltonian Systems I. C. Percival Semi-Classical Quantization, Adiabatic Invariants, and Classical Chaos W. P. Reinhardt and I. Dana Particle Confinement and Adiabatic Invariance B. V. Chirikov Some Geometrical Models of Chaotic Dynamics C. Series The Bakerian Lecture: Quantum Chaology M. V. BerryOriginally published in 1989.The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeton University Press. These paperback editions preserve the original texts of these important books while presenting them in durable paperback editions. The goal of the Princeton Legacy Library is to vastly increase access to the rich scholarly heritage found in the thousands of books published by Princeton University Press since its founding in 1905.
Adapting programming languages technologies for finite-state verification (2000)

Program verification and program transformation are two research areas that have different goals. Program verification aims to increase confidence in software through the use of formal methods and systematic testing. Program transformation rearranges the structure of programs to increase their efficiency or to make them more amenable to some other form of processing. Despite being funded under different NSF awards from the Software Engineering and Languages program on the two different areas above the authors are collaborating to apply results from both awards to develop a set of tools, called Bandera, for transforming Java programs into a form that is amenable to verification using existing model checking tools.