gebhart/patrepeval huggingface dataset:
A modular approach to the computer simulation of a passenger car powertrain incorporating a diesel engine and continuously variable transmission (1994)

Much engine research is aimed at measuring and reducing emissions at steady engine speeds and loads. However vehicle engine emissions produced during transient operation represent a significant proportion of total vehicle emissions. The work described concerns the design of a controller for an integrated powertrain, directed at reducing emissions during the full transient range of conditions. To optimise the controller, it is necessary to have an accurate representation of the powertrain. A modular simulation of the system has been produced and validated against experimental data. This paper describes the modelling process and discusses the validation of the computer models against experimental data. The simulation includes models of a Ford, 1.8IDI TCi Diesel engine, CTX continuously variable transmission with hydraulic controller and Orion car. It has been used to predict transient powertrain and vehicle behaviour. The engine model calculates the torque developed based upon the driver input and the effects of the turbocharger. The transmission and vehicle are represented by dynamic theoretical models. The engine model can be replaced by one consisting of several theoretically based dynamic models used in conjunction with an empirical cylinder model to determine emissions. It uses emissions data obtained from a steady state engine test facility to predict values under real conditions. Implications affecting the design of a powertrain controller are drawn from the results. Control strategies are being developed which can be tested initially on the computer models and then on a test rig and a test vehicle.
Detecting Circulating Tumor Cells: Current Challenges and New Trends (2013)

Circulating tumor cells (CTCs) in the blood stream play a critical role in establishing metastases. The clinical value of CTCs as a biomarker for early cancer detection, diagnosis, prognosis, prediction, stratification, and pharmacodynamics have been widely explored in recent years. However, the clinical utility of current CTC tests is limited mainly due to methodological constraints. In this review, the pros and cons of the reported CTC assays are comprehensively discussed. In addition, the potential of tumor cell-derived materials as new targets for CTC detection, including circulating tumor microemboli, cell fragments, and circulating DNA, is evaluated. Finally, emerging approaches for CTC detection, including telomerase-based or aptamer-based assays and cell functional analysis, are also assessed. Expectantly, a thorough review of the current knowledge and technology of CTC detection will assist the scientific community in the development of more efficient CTC assay systems.
Hydrolysis of Glycerol Trioleate and Extraction of Its Fatty acid Under CO2 Supercritical Conditions. (1995)

藻類の生産する有用物質の一つとして高度脂肪酸に着目し,それら脂肪酸の簡便な回収法の開発を目的に,CO2超臨界流体中で脂質の加水分解及び生成した脂肪酸の抽出を試みた.CO2流体に水を導入し,分解容器の温度250℃,圧力8MPaに保つことにより,中性脂質の標準物質として用いたトリオレイソの加水分解は,ほぼ100%進行した.さらに同一流路,容器で,水の導入をやめ,CO2の超臨界流体密度を0.55g/cm3以上に保つことにより,生成したオレイン酸を選択的に抽出することができた・抽出条件の一一つとして,温度80℃,圧力20MPaが選択される.本加水分解及び抽出条件では不飽和結合をもつ高度脂肪酸の変成は認められず,脂質の加水分解と生成脂肪酸の抽出は同一流路で,温度と圧力のみを変えることで容易に達成される.
Analysis of Full-Length Metagenomic 16S Genes by SMRT ® Sequencing (2013)

Assaying 16S CCS Above: Raw read length distributions for sequencing of full-length 16S (~1500 bp) amplicons. The dotted vertical line denotes the minimum read length for CCS. Left: Mean quality-values for fulllength 16S CCS sequences by raw read length. High-throughput sequencing of the 16S rRNA gene has become a valuable tool for characterizing microbial communities. However, the short read lengths produced by second-generation sequencing introduce bias and cannot provide taxonomic classification below the genus level, limiting biological insight. The best results are therefore obtained with full-length sequences of the 16S gene, however doing so with Sanger sequencing is time-consuming, costly, and low-throughput. SMRT® Sequencing has been used previously to analyze 16S amplicons[1], but to our knowledge no attempts have been made to analyze full-length (~1500 bp) 16S. In this study, we evaluate the PacBio® RS and PacBio® RS II for full-length 16S rRNA gene sequencing and community profiling. We profiled four microbial communities (Cecum, Soil, Water, and a Mock control) for bacterial 16S, archaeal 16S, and fungal ITS using barcoded primers. Sample data was evaluated with rDnaTools[2], a custom pipeline that integrates the widely used Mothur suite[3] with PacBio-specific utilities. Each SMRT Cell of full-length 16S data generated 17-24k CCS reads, of which between 10-16k had >99% predicted concordance to the reference. Community samples were predicted to contain between 2.3-15 times as many species as phyla, with abundance levels as low as 0.05%. SMRT® Sequencing therefore represents a novel platform for community analysis, allowing for high depth and unprecedented sensitivity. 1. Export CCS Sequence Data from Bas.H5 2. Filter Sequences by Quality 3. Group Sequences by Barcode and/or Primer 4. Align Sequences to Reference 5. Filter Partial Alignment Reads (<80%) 6. Identify & Remove Chimeric Sequences 7. Pre-Cluster Sequences 8. Calculate Distance Matrix 9. Cluster Sequences 10.Generate OTU Consensus Sequences 11.Classify Clusters based on the Consensus 12.Summarize OTUs Analysis of 16S CCS sequences was carried out with standard tools from the Mothur package (http://www.mothur.org)[3] where possible. Where existing tools were not well suited for analyzing SMRT sequence data, custom scripts were written using Python. The complete analysis pipeline, and all custom scripts are available for download on GitHub (https://github.com/bnbowman/rDnaTools). Steps highlighted in bold are implemented with custom scripts.
Laser Linewidth Tolerance for 16-QAM Coherent Optical Systems Using QPSK Partitioning (2010)

The laser linewidth tolerance for 16-ary quadrature amplitude modulation (16-QAM) coherent optical systems is investigated using a quaternary phase-shift-keying (QPSK) partition scheme. The different stages needed to partition the square-16-QAM into QPSK constellations for carrier phase estimation are discussed. It is shown that at 1 dB above sensitivity at a bit-error rate of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> , a combined linewidths symbol duration product of 1 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> is tolerable. The performance of the algorithm with different bits resolution in the analog-to-digital converter is also presented.
Susceptibility to Paget's Disease of Bone Is Influenced by a Common Polymorphic Variant of Osteoprotegerin (2004)

The G1181 allele was significantly over-represented in PDB patients (chi(2) = 5.7, df = 1, p = 0.017, adjusted alpha = 0.024), equivalent to an odds ratio for PDB of 1.55 (95% CI: 1.11-2.16). The distribution of TNFRSF11B haplotypes significantly differed in sporadic PDB cases and controls (chi(2) = 30.2, df = 9, p < 0.001) because of over-representation of haplotypes containing the G1181 allele in cases. The family study showed that the most common haplotype containing the G1181 allele was transmitted more frequently than expected to 140 individuals with familial PDB (chi(2) = 7.35, df = 1, p < 0.01), and the transmission disequilibrium was even more pronounced in a subgroup of 78 familial PDB patients who did not carry mutations of the SQSTM1 gene (chi(2) = 8.44, df = 1, p < 0.005). We conclude that the G1181 allele of TNFRSF11B, encoding lysine at codon 3 of the OPG protein, predisposes to the development of sporadic PDB and familial PDB that is not caused by SQSTM1 mutations.
Comparative organization and function of the major histocompatibility complex of domesticated cattle (1999)

This review focuses on recent advances in research on the bovine major histocompatibility complex (BoLA), with specific reference to the genetic organization, polymorphism and function of the class II genes. The BoLA region is unlike the MHC of humans and mice in that a large inversion has moved several class II genes, including the TAP/LMP cluster, close to the centromere of bovine chromosome 23. Therefore, close linkage of MHC genes and other genes associated with the MHC in humans and mice does not appear to be required for normal immunological function. In cattle, polymorphism in the class IIa genes influences both the magnitude and the epitope specificity of antigen-specific T-cell responses to foot-and-mouth disease virus peptides. Disease association studies have demonstrated that BoLA alleles affect the subclinical progression of bovine leukemia virus (BLV) infection. This association is strongly correlated with the presence of specific amino acid motifs within the DRB3 antigen-binding domain. In addition to the practical significance of these findings, the association between BoLA and BLV provides a unique model to study host resistance to retrovirus infection in a non-inbred species. These studies contribute to our understanding of the evolution of the MHC in mammals, to the development of broadly effective vaccines, and to breeding strategies aimed at improving resistance to infectious diseases.
A Homogeneous and Noncompetitive Immunoassay Based on the Enhanced Fluorescence Resonance Energy Transfer by Leucine Zipper Interaction (2002)

Fluorescence resonance energy transfer (FRET) between two GFP variants is a powerful technique to describe protein-protein interaction in a biological system. However, it has a limitation that the two variants tethered to the respective proteins have to be in sufficient proximity upon binding, which is often difficult to attain by simple N- or C-terminal fusions. Here we describe a novel method to significantly enhance FRET between GFP variant-tagged proteins with the use of leucine zippers. For the homogeneous sandwich immunoassay of a high molecular weight antigen human serum albumin (HSA), two separate single-chain Fvs recognizing distant epitopes of HSA were respectively fused with fluorescence donor ECFP or acceptor EYFP, and FRET between the two was analyzed by fluorescence spectrometry. Because these two proteins did not give any detectable FRET uponantigen addition, we tethered each protein with a leucine zipper motif (c-Jun or FosB) at the C-terminus to help the neighborhood of the GFP variants. Upon antigen addition, the new pairs showed significant antigen-dependent FRET. By exchanging the binding domains, the method will find a range of applications for the assay of other proteins and their interactions in vitro or in vivo.
Engineered humanized diabodies for microPET imaging of prostate stem cell antigen-expressing tumors (2008)

We have previously demonstrated preclinical in vivo targeting of prostate stem cell antigen (PSCA) using a humanized anti-PSCA 2B3 monoclonal antibody (mAb). However, humanization resulted in 5-fold loss of apparent affinity relative to the parental mAb (1 nM). In this study, diabodies (scFv dimers of 55 kDa) were generated from 2B3 including variants with different linker lengths as well as back-mutations to original murine residues to improve affinity. Parental 2B3 (p2B3) and back-mutated 2B3 (bm2B3) diabodies (Dbs) with five- or eight-amino acid linkers (p2B3-Db5, p2B3-Db8, bm2B3-Db5 and bm2B3-Db8) were evaluated for binding to PSCA by flow cytometry and affinities were determined by surface plasmon resonance. Back-mutation restored the affinity from 5.4 to 1.9 nM. Stability, evaluated by size exclusion, revealed that diabodies with eight-residue linkers existed as a mixture of dimeric and monomeric species at low concentrations (<or =1 mg/ml). Shortening the linker from eight to five residues improved dimer stability, notably in the bm2B3-Db8 compared with bm2B3-Db5. Both p2B3-Db8 and bm2B3-Db8 were radioiodinated with (124)I and evaluated by serial micro-positron emission tomography imaging in mice bearing LAPC-9 human prostate cancer xenografts. Localization in LAPC-9 xenografts was seen at 4 h, whereas at 20 h most of the activity had cleared from the tumor. Highest tumor-to-background contrast ratios and best images were obtained at 12 h. Although the higher affinity bm2B3-Db8 demonstrated improved tumor retention at later time points (20 h), it did not improve tumor targeting or imaging compared with p2B3-Db8 at 12 h.
Ceruloplasmin enhances DNA damage induced by hydrogen peroxidein vitro (2000)

Ceruloplasmin (Cp) was found to promote the oxidative damage to DNA, as evidenced by the formation of 8-hydroxy-2'-deoxyguanosine and strand breaks, when incubated with H2O2 in vitro. The capacity of Cp to enhance oxidative damage to DNA was inhibited by hydroxyl radical scavengers such as sodium azide and mannitol, a metal chelator, diethylenetriaminepentaacetic acid, and catalase. Although the oxidized protein resulted in an increase in the content of carbonyl groups, the ferroxidase activity and the proteolytic susceptibility were not significantly altered. The release of a portion of Cu from Cp was observed, and conformational alterations were indicated by the changes in fluorescence spectra. Based on these results, we suggest that damage to DNA is mediated in the H2O2/Cp system via the generation of *OH by released Cu2+ and/or loosely bound Cu exposed from oxidatively damaged Cp through the conformational change. The release of Cu from Cp during oxidative stress could enhance the formation of reactive oxygen species and could also potentiate cellular damage.
Bone cancer pain: the effects of the bisphosphonate alendronate on pain, skeletal remodeling, tumor growth and tumor necrosis (2004)

Patients with metastatic breast, lung or prostate cancer frequently have significant bone cancer pain. In the present report we address, in a single in vivo mouse model, the effects the bisphosphonate alendronate has on bone cancer pain, bone remodeling and tumor growth and necrosis. Following injection and confinement of green fluorescent protein-transfected murine osteolytic tumor cells into the marrow space of the femur of male C3H/HeJ mice, alendronate was administered chronically from the time the tumor was established until the bone cancer pain became severe. Alendronate therapy reduced ongoing and movement-evoked bone cancer pain, bone destruction and the destruction of sensory nerve fibers that innervate the bone. Whereas, alendronate treatment did not change viable tumor burden, both tumor growth and tumor necrosis increased. These data emphasize that it is essential to utilize a model where pain, skeletal remodeling and tumor growth can be simultaneously assessed, as each of these can significantly impact patient quality of life and survival.
Certain properties of .ALPHA.-glucosidase from Mucor racemosus. (1977)

The substrate and inhibitor specificities, and α-glucosyltransfer products of the purified α-glucosidase from the mycelia of Mucor racemosus were investigated. The enzyme hydrolyzed maltose, maltotriose, phenyl α-maltoside, isomaltose, soluble starch, and amylose liberating glucose, but did not act on sucrose. The enzyme hydrolyzed phenyl α-maltoside into glucose and phenyl α-glucoside. Maltotriose was the main α-glucosyltransfer product formed from maltose, and isomaltose was that from soluble starch. Tris and turanose inhibited the enzyme activity, but PCMB and EDTA did not. The enzyme hydrolyzed amylose liberating α-glucose. The enzyme was a glycoprotein containing 4.1% of neutral sugar. The neutral sugar was identified as mannose in the acid hydrolyzate of the enzyme.
Heterocyclic series. X. 1,3,9-Triazaphenothiazine ring system, a new phenothiazine ring (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHeterocyclic series. X. 1,3,9-Triazaphenothiazine ring system, a new phenothiazine ringCharles O. OkaforCite this: J. Org. Chem. 1975, 40, 19, 2753–2755Publication Date (Print):September 1, 1975Publication History Published online1 May 2002Published inissue 1 September 1975https://doi.org/10.1021/jo00907a010RIGHTS & PERMISSIONSArticle Views233Altmetric-Citations21LEARN 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 InReddit PDF (468 KB) Get e-Alerts Get e-Alerts
Development and characterization of human monoclonal antibodies that neutralize multiple TGFβ isoforms (2015)

Transforming growth factor (TGF)β levels are elevated in, and drive the progression of, numerous disease states such as advanced metastatic cancer and systemic and ocular fibrosis. There are 3 main isoforms, TGFβ1, 2, and 3. As multiple TGFβ isoforms are involved in disease processes, maximal therapeutic efficacy may require neutralization of 2 or more of the TGFβ isoforms. Fully human antibody phage display libraries were used to discover a number of antibodies that bind and neutralize various combinations of TGFβ1, 2 or 3. The primary panning did not yield any uniformly potent pan-isoform neutralizing antibodies; therefore, an antibody that displayed potent TGFβ 1, 2 inhibition, but more modest affinity versus TGFβ3, was affinity matured by shuffling with a light chain sub-library and further screening. This process yielded a high affinity pan-isoform neutralizing clone. Antibodies were analyzed and compared by binding affinity, as well as receptor and epitope competition by surface plasmon resonance methods. The antibodies were also shown to neutralize TGFβ effects in vitro in 3 assays: 1) interleukin (IL)-4 induced HT-2 cell proliferation; 2) TGFβ-mediated IL-11 release by A549 cells; and 3) decreasing SMAD2 phosphorylation in Detroit 562 cells. The antibodies' potency in these in vitro assays correlated well with their isoform-specific affinities. Furthermore, the ability of the affinity-matured clone to decrease tumor burden in a Detroit 562 xenograft study was superior to that of the parent clone. This affinity-matured antibody acts as a very potent inhibitor of all 3 main isoforms of TGFβ and may have utility for therapeutic intervention in human disease.
Hydrogel-Based Non-Autologous Cell and Tissue Therapy (2000)

Many diseases are closely tied to deficient or subnormal metabolic and secretory cell functions. Milder forms of these diseases can be managed by a variety of treatments. However, it is often extremely difficult or even impossible to imitate the moment-to-moment fine regulation and the complex roles of the hormone, factor or enzyme that is not sufficiently produced by the body. Immunoisolated transplantation is one of the most promising approaches to overcome the limitations of current treatments. Non-autologous (transformed) cell lines and allogeneic and xenogeneic cells/tissues that release the therapeutic substances are enclosed in immunoprotective microcapsules. The microcapsules avoid a lifetime of immunosuppressive therapy while excluding an immune response in the host. Research in this direction has shown the feasibility of microcapsules based on hydrogels (particularly of alginate) for transplantation of non-autologous cells and tissue fragments. Numerous technical accomplishments of the immunoisolation method have recently made possible the first successful long-term clinical applications. However, realizing the potential of immunoisolated therapy requires the use of several factors that have received limited attention in the past but are important for the formulation of hydrogel-based immunoisolation systems that are highly versatile, potentially economical and can gain medical approval.
Gene Expression Profiling Reveals Potential Biomarkers of Human Hepatocellular Carcinoma (2007)

We suggest that a diagnostic signature approach using a combined score of these five biomarkers rather than a single marker may improve the prediction accuracy of HCC patients, including those with normal serum AFP and smaller-sized tumors.
Catalytic mechanism of Escherichia coli ribonuclease III: kinetic and inhibitor evidence for the involvement of two magnesium ions in RNA phosphodiester hydrolysis (2005)

Escherichia coli ribonuclease III (RNase III; EC 3.1.24) is a double-stranded(ds)-RNA-specific endonuclease with key roles in diverse RNA maturation and decay pathways. E.coli RNase III is a member of a structurally distinct superfamily that includes Dicer, a central enzyme in the mechanism of RNA interference. E.coli RNase III requires a divalent metal ion for activity, with Mg2+ as the preferred species. However, neither the function(s) nor the number of metal ions involved in catalysis is known. To gain information on metal ion involvement in catalysis, the rate of cleavage of the model substrate R1.1 RNA was determined as a function of Mg2+ concentration. Single-turnover conditions were applied, wherein phosphodiester cleavage was the rate-limiting event. The measured Hill coefficient (n (H)) is 2.0 +/- 0.1, indicative of the involvement of two Mg2+ ions in phosphodiester hydrolysis. It is also shown that 2-hydroxy-4H-isoquinoline-1,3-dione--an inhibitor of ribonucleases that employ two divalent metal ions in their catalytic sites--inhibits E.coli RNase III cleavage of R1.1 RNA. The IC50 for the compound is 14 microM for the Mg2+-supported reaction, and 8 microM for the Mn2+-supported reaction. The compound exhibits noncompetitive inhibitory kinetics, indicating that it does not perturb substrate binding. Neither the O-methylated version of the compound nor the unsubstituted imide inhibit substrate cleavage, which is consistent with a specific interaction of the N-hydroxyimide with two closely positioned divalent metal ions. A preliminary model is presented for functional roles of two divalent metal ions in the RNase III catalytic mechanism.
Isolation, culture, and transplantation of human hepatocytes. (1982)

The in situ two-step collagenase perfusion technique used for the isolation of hepatocytes from rat liver was adapted into a procedure applicable to pieces of human liver obtainable from surgical procedures. Human hepatocytes obtained by this method were maintained in primary culture for 10 days. The cellular changes observed at the light microscopic and electron microscopic levels are described. The changes in microsomal enzymes as a function of the age of the cultures were also measured. Exposure of the human hepatocytes to procarcinogens known to be metabolized by rodent liver resulted in unscheduled DNA synthesis. The isolated hepatocytes were also transplanted into two-thirds partially hepatectomized athymic nude mice. The transplanted cells formed nodules with characteristic hepatic architecture. These studies demonstrate that hepatocytes obtained from human liver by the described modified collagenase technique can be used for in vitro studies in chemical carcinogenesis.