gebhart/patrepeval huggingface dataset:
Bentonitic Slurry in Constructing Drilled Piers (1985)

Bentonitic slurry is employed extensively in the construction of drilled shafts. While serious problems can occur, evidence is presented to show that the proper use of slurry will lead to excellent performance of drilled shafts under axial loading. Desirable properties of slurry are given and the action of slurry in stabilizing an excavation is reviewed. Several examples of specifications for the control of slurry are presented.
On the Complexity of Finite Sequences (1976)

A new approach to the problem of evaluating the complexity ("randomness") of finite sequences is presented. The proposed complexity measure is related to the number of steps in a self-delimiting production process by which a given sequence is presumed to be generated. It is further related to the number of distinct substrings and the rate of their occurrence along the sequence. The derived properties of the proposed measure are discussed and motivated in conjunction with other well-established complexity criteria.
Measurement of augmentation of 252Cf implant by 10B and 157Gd neutron capture (1994)

252Cf has been used as a brachytherapy source since the early 1970s. The dominant mechanism of interactions of 252Cf neutrons with tissue is elastic scattering. The scattered neutrons lose part of their energy, which is released as kinetic energy of the recoiling nuclei. By multiple scattering, neutrons lose their energy and eventually become thermalized (in energetic equilibrium with tissue atoms with an average energy of 0.025 eV) and do not play any role in radiotherapy. These thermal neutrons may interact with hydrogen nuclei or with nitrogen, but the cell killing effects by these reaction products are negligibly small compared to the elastic scattering by fast neutrons or by photons emitted by californium. Nonetheless, these thermal neutrons are still potentially usable for neutron capture therapy and can be used to enhance californium brachytherapy effects. Neutron capture therapy is a two-part therapy relying on the selective loading of tumor cells with compounds containing 10B or 157Gd and subsequent irradiation with thermal neutrons. To calculate neutron capture doses one has to know thermal neutron flux. This paper presents results of an experimental study of thermal neutron flux and calculations of boron neutron capture and gadolinium neutron capture doses in the vicinity of 252Cf sources.
Transduction of Well-Differentiated Airway Epithelium by Recombinant Adeno-Associated Virus Is Limited by Vector Entry (1999)

The limitations of adeno-associated virus (AAV)-mediated vectors for lung-directed gene transfer were investigated by using differentiated human respiratory epithelium in air-liquid interface cultures. Transduction efficiency was high in undifferentiated cells and was enhanced in well-differentiated cells after basolateral application of the vector or after apical application following disruption of tight junctions or pretreatment of the cultures with glycosidases. These results indicate that transduction of airway epithelia by AAV vectors is limited by entry and reinforce the importance of a physical barrier on the airway surface.
Extending genome-wide association studies to copy-number variation (2008)

Appreciating the contribution of human genome copy-number variation (CNV) to clinical phenotypes is one of the compelling genetics challenges of the coming years. It is increasingly possible to pursue such investigations as an extension of genome-wide association studies (GWAS), enabled by innovations in the design and analysis of SNP (single nucleotide polymorphism) arrays and by progress in determining the genomic locations and population-genetic properties of the CNVs that segregate in the human population. Extensions of GWAS to CNV have already resulted in discoveries of both de novo and inherited CNV that are associated with risk of common disease. This review will discuss new approaches, recent findings and the analytical challenges involved in expanding GWAS to appreciate the contribution of CNV to human phenotypes.
Cellular elimination of 2',2'-difluorodeoxycytidine 5'-triphosphate: a mechanism of self-potentiation. (1992)

2',2'-Difluorodeoxycytidine (dFdC, Gemcitabine) is a deoxycytidine analogue which, after phosphorylation to the 5'-di- and 5'-triphosphate (dFdCTP), induces inhibition of DNA synthesis and cell death. We examined the values for elimination kinetics of cellular dFdCTP and found they were dependent on cellular concentration after incubation of CCRF-CEM cells with dFdC and washing into drug-free medium. When the drug was washed out at low cellular dFdCTP levels (less than 50 microM), dFdCTP elimination was linear (t1/2 = 3.3 h), but it became biphasic at intracellular dFdCTP levels greater than 100 microM. Although the initial elimination rate was similar at all concentrations, at higher concentrations the terminal elimination rate increased with increasing cellular dFdCTP concentration, with a nearly complete inhibition of dFdCTP elimination at 300 microM. The deamination product 2',2'-difluorodeoxyuridine was the predominant extracellular catabolite at low cellular dFdCTP concentrations, whereas at high dFdCTP concentrations dFdC was the major excretion product. The dCMP deaminase inhibitor 3,4,5,6-tetrahydrodeoxyuridine transformed the monophasic dFdCTP degradation seen at low dFdCTP levels into a biphasic process, whereas the deoxycytidine deaminase inhibitor 3,4,5,6-tetrahydrouridine had no effect on dFdCTP elimination. An in situ assay indicated that dCMP deaminase activity was inhibited in whole cells, an action that was associated with a decreased dCTP:dTTP value. In addition, dFdCTP inhibited partially purified dCMP deaminase with a 50% inhibitory concentration of 0.46 mM. We conclude that dFdC-induced inhibition of dCMP deaminase resulted in a decrease of dFdCTP catabolism, contributing to the concentration-dependent elimination kinetics. This action constitutes a self-potentiation of dFdC activity.
A Gasoline Engine Concept for Improved Fuel Economy -The Lean Boost System (2000)

&lt;div class="htmlview paragraph"&gt;This paper describes the Lean Boost System, a gasoline engine concept for improved fuel economy. The system combines direct injection, lean operation and pressure charging, and allows significant reduction in swept volume, or ‘downsizing’. Engine tests have been undertaken which demonstrate the validity of the combustion concept. The strategy a typical manufacturer might adopt in order to meet future European requirements for CO&lt;sub&gt;2&lt;/sub&gt; emissions is proposed. Vehicle simulation results for typical North American and European vehicles are presented. Using the exhaust gas emission levels from engine tests and drive cycle simulation, aftertreatment requirements and configurations are considered.&lt;/div&gt;
Automatic extraction and processing of small RNAs on a multi-well/multi-channel (M&M) chip (2012)

The study of the regulatory roles in small RNAs can be accelerated by techniques that permit simple, low-cost, and rapid extraction of small RNAs from a small number of cells. In order to ensure highly specific and sensitive detection, the extracted RNAs should be free of the background nucleic acids and present stably in a small volume. To meet these criteria, we designed a multi-well/multi-channel (M&M) chip to carry out automatic and selective isolation of small RNAs via solid-phase extraction (SPE), followed by reverse-transcription (RT) to convert them to the more stable cDNAs in a final volume of 2 μL. Droplets containing buffers for RNA binding, washing, and elution were trapped in microwells, which were connected by one channel, and suspended in mineral oil. The silica magnetic particles (SMPs) for SPE were moved along the channel from well to well, i.e. in between droplets, by a fixed magnet and a translation stage, allowing the nucleic acid fragments to bind to the SMPs, be washed, and then be eluted for RT reaction within 15 minutes. RNAs shorter than 63 nt were selectively enriched from cell lysates, with recovery comparable to that of a commercial kit. Physical separation of the droplets on our M&M chip allowed the usage of multiple channels for parallel processing of multiple samples. It also permitted smooth integration with on-chip RT-PCR, which simultaneously detected the target microRNA, mir-191, expressed in fewer than 10 cancer cells. Our results have demonstrated that the M&M chip device is a valuable and cost-saving platform for studying small RNA expression patterns in a limited number of cells with reasonable sample throughput.
A specific transition state for S-peptide combining with folded S-protein and then refolding (1999)

We measured the folding and unfolding kinetics of mutants for a simple protein folding reaction to characterize the structure of the transition state. Fluorescently labeled S-peptide analogues combine with S-protein to form ribonuclease S analogues: initially, S-peptide is disordered whereas S-protein is folded. The fluorescent probe provides a convenient spectroscopic probe for the reaction. The association rate constant, kon, and the dissociation rate constant, koff, were both determined for two sets of mutants. The dissociation rate constant is measured by adding an excess of unlabeled S-peptide analogue to a labeled complex (RNaseS*). This strategy allows kon and koff to be measured under identical conditions so that microscopic reversibility applies and the transition state is the same for unfolding and refolding. The first set of mutants tests the role of the alpha-helix in the transition state. Solvent-exposed residues Ala-6 and Gln-11 in the alpha-helix of native RNaseS were replaced by the helix destabilizing residues glycine or proline. A plot of log kon vs. log Kd for this series of mutants is linear over a very wide range, with a slope of -0.3, indicating that almost all of the molecules fold via a transition state involving the helix. A second set of mutants tests the role of side chains in the transition state. Three side chains were investigated: Phe-8, His-12, and Met-13, which are known to be important for binding S-peptide to S-protein and which also contribute strongly to the stability of RNaseS*. Only the side chain of Phe-8 contributes significantly, however, to the stability of the transition state. The results provide a remarkably clear description of a folding transition state.
Prognostic implications of genetic variants in advanced non-small cell lung cancer: a genome-wide association study (2012)

The prognostic significance of inherited genetic variants in advanced-stage non-small cell lung cancer (NSCLC) patients remains unknown. In this study, we genotyped 271 817 single-nucleotide polymorphisms in 348 advanced NSCLC patients who received chemotherapy and analyzed their association with prognosis by using Cox proportional hazard regression model adjusted for known prognostic factors. Top candidate single-nucleotide polymorphisms (SNPs) were selected using the bootstrap re-sampling procedure. Median age of patient population was 56 years. Proportions of female, never smokers and adenocarcinoma were 64.9, 67.5 and 80.4%, respectively. We identified 17 top candidate SNPs related to prognosis using cut-off minimum P value of <5.0 × 10(-5) in at least 70% of 1000 bootstrap samples. These SNPs were located in the genomic regions of the FAM154A, ANKS1A, DLST, THSD7B, NCOA2, CDH8, SLC35D2, NALCN and EGF genes. The most significant SNP, rs1571228 (9p22.1:FAM154A), was significantly associated with overall survival in dominant model [AG+GG to AA, hazard ratio (HR) of death (95% CI) = 0.53 (0.42-0.67); P = 2.025 × 10(-7)]. The SNP at 4q25:EGF, rs11098063, for which some genetic variations was previously reported to be associated with prognosis, also showed significant association with overall survival in additive model [CC versus CT versus TT, HR (95% CI) = 1.00 versus 0.61 (0.47-0.78) versus 0.39 (0.19-0.79); P = 9.582 × 10(-6)]. Survival differences according to the genotype of these SNPs were independent of sex, smoking, histology and chemotherapy regimens. These results suggested the variants at multiple genetic loci might contribute to the risk of death in advanced NSCLC patients receiving chemotherapy.
Design and Testing of a 64-Channel Combinatorial Electrochemical Cell (2003)

Design, testing, and performance of a 64-channel combinatorial electrochemical cell are described. This cell is used for high-throughput screening of materials for use as Li-ion rechargeable battery electrodes. Our sealed cell has 64 separate positive electrodes and Li foil for the reference and counter electrodes. This combinatorial electrochemical cell was designed to complement our existing combinatorial materials science infrastructure. Using the combinatorial electrochemical cell decreases the time and labor associated with test cell assembly, improves the repeatability of our assembly procedure, and increases the number of compositions we can test in a given amount of time. In this paper, we demonstrate that the results from the combinatorial electrochemical cell and from conventional 2325 coin-type test cells, containing electrodes of sputtered films prepared in the same sputtering run, are identical for electrodes of the same composition. © 2003 The Electrochemical Society. All rights reserved.
Human monoclonal antibodies from stomach carcinoma patients react withhelicobacter pylori and stimulate stomach cancer cells in vitro (1994)

The human monoclonal antibodies described here react with H. pylori and cross-react with and stimulate gastric carcinoma cells. It is possible that the production of these antibodies is primarily stimulated by bacterial antigens which cause chronic gastritis and that they might be indirectly responsible for the recently described higher incidence of gastric cancer because of the simultaneous reaction and stimulation of tumor cells they cause.
Dome: parallel programming in a distributed computing environment (2002)

The Distributed object migration environment (Dome) addresses three major issues of distributed parallel programming: ease of use, load balancing, and fault tolerance. Dome provides process control, data distribution, communication, and synchronization for Dome programs running in a heterogeneous distributed computing environment. The parallel programmer writes a C++ program using Dome objects which are automatically partitioned and distributed over a network of computers. Dome incorporates a load balancing facility that automatically adjusts the mapping of objects to machines at runtime, exhibiting significant performance gains over standard message passing programs executing in an imbalanced system. Dome also provides checkpointing of program state in an architecture independent manner allowing Dome programs to be checkpointed on one architecture and restarted on another.
Phase-Locked Sampling Instruments (1965)

This paper describes a new approach to the design of RF instruments which are capable of measuring phase difference, level, distortion, and amplitude modulation of high-frequency signals from about 1 Mc/s to 1000 Mc/s or higher. The basic block consists of a modified phase-lock loop with a search and reset circuit. The input high-frequency signal is sampled, the frequency of the sampled output is locked to a reference frequency of a few kc/s, and the output waveform is a sampled replica of the input waveform. Using such a loop, measurements of RF signals can be made easily by a constant low-frequency readout circuit. Synchronization is obtained automatically for any input frequency without the need of a separate trigger circuit. Limitations as well as applications of the sampling phase-lock loop are briefly discussed.
Staphylococcus aureus golden pigment impairs neutrophil killing and promotes virulence through its antioxidant activity (2005)

Golden color imparted by carotenoid pigments is the eponymous feature of the human pathogen Staphylococcus aureus. Here we demonstrate a role of this hallmark phenotype in virulence. Compared with the wild-type (WT) bacterium, a S. aureus mutant with disrupted carotenoid biosynthesis is more susceptible to oxidant killing, has impaired neutrophil survival, and is less pathogenic in a mouse subcutaneous abscess model. The survival advantage of WT S. aureus over the carotenoid-deficient mutant is lost upon inhibition of neutrophil oxidative burst or in human or murine nicotinamide adenine dinucleotide phosphate oxidase-deficient hosts. Conversely, heterologous expression of the S. aureus carotenoid in the nonpigmented Streptococcus pyogenes confers enhanced oxidant and neutrophil resistance and increased animal virulence. Blocking S. aureus carotenogenesis increases oxidant sensitivity and decreases whole-blood survival, suggesting a novel target for antibiotic therapy.
Rubbery Graft Copolymer Electrolytes for Solid-State, Thin-Film Lithium Batteries (2004)

Graft copolymer electrolytes (GCEs) of (70:30) have been synthesized by simple free radical polymerization using a macromonomer route. Differential scanning calorimetry, transmission electron microscopy, and small angle neutron scattering confirmed the material to be microphase-separated with a domain periodicity of Over the temperature range the electrical conductivities of the lithium triflate-doped which exhibited solid-like mechanical behavior, were nearly identical to those of the liquid POEM homopolymer. Thermal and electrochemical stability studies showed the electrolyte to be stable over a wide temperature range and voltage window. Solid-state, thin-film batteries comprised of a metallic lithium anode, a thick vanadium oxide cathode, and an electrolyte of doped with proved resistant to capacity fade during extended cycling at room temperature at a discharge rate of 2/3 C and could be cycled (charged and discharged) at subambient temperature (0°C). © 2004 The Electrochemical Society. All rights reserved.
HER2/neu Gene Amplification and Protein Overexpression in Gastric and Gastroesophageal Junction Adenocarcinoma: A Review of Histopathology, Diagnostic Testing, and Clinical Implications (2012)

Amplification of the human epidermal growth factor receptor 2/neu (HER2/neu) gene and overexpression of the HER2 protein (HER2) have been shown to occur in gastric and gastroesophageal junction adenocarcinoma in a number of studies. With a dismal survival rate, patients with these cancers stand to benefit from the identification of possible molecular targets such as HER2 for both prognostic and therapeutic purposes. Although these and other carcinomas that overexpress HER2 may have a poorer prognosis and exhibit resistance to conventional chemotherapy, they have also recently been shown to respond to targeted therapy with the anti-HER2 antibody trastuzumab. Here, we briefly review the molecular biology, histopathology, diagnostic techniques, and interpretation, as well as the clinical implications, of HER2 amplification/overexpression in gastric and gastroesophageal adenocarcinoma.
CTLs Directed against HER2 Specifically Cross-React with HER3 and HER4 (2008)

The human epidermal growth factor receptor 2 (HER2) has been targeted as a breast cancer-associated Ag by T cell-based immunotherapeutical strategies such as cancer vaccines and adoptive T cell transfer. The prerequisite for a successful T cell-based therapy is the induction of T cells capable of recognizing the HER2-expressing tumor cells. In this study, we generated human cytotoxic T cell clones directed against the HER2(369-377) epitope known to be naturally presented with HLA-A*0201. Those HER2-reactive CTLs, which were also tumor lytic, exhibited a similar lysis pattern dividing the targets in lysable and nonlysable tumor cells. Several HER2-expressing tumor cells became susceptible to CTL-mediated lysis after IFN-gamma treatment and, in parallel, up-regulated molecules of the Ag-presenting machinery, indicating that the tumor itself also contributes to the success of CTL-mediated killing. Some of the HER2(369-377)-reactive T cells specifically cross-reacted with the corresponding peptides derived from the family members HER3 and/or HER4 due to a high sequence homology. The epitopes HER3(356-364) and HER4(361-369) were endogenously processed and contributed to the susceptibility of cell lysis by HER cross-reacting CTLs. The principle of "double" or "triple targeting" the HER Ags by cross-reacting T cells will impact the further development of T cell-based therapies.
L-5-Hydroxytryptophan in Depression: the First Substitution Therapy in Psychiatry? (1980)

99 ‘therapy-resistant’ depressive out-patients were treated with l-5-hydroxytrypto-phan combined with the peripheral decarboxylase inhibitor, carbidopa. This treatment produced an astonishing recovery without side effects in some 50% of the patients.
Purification of the FLP site-specific recombinase by affinity chromatography and re-examination of basic properties of the system (1987)

The FLP protein, a site-specific recombinase encoded by the 2 micron plasmid of yeast, has been purified to near homogeneity from extracts of E. coli cells in which the protein has been expressed. The purification is a three column procedure, the final step employing affinity chromatography. The affinity ligand consists of a DNA polymer with multiple FLP protein binding sites arranged in tandem repeats. This protocol yields 2 mg of FLP protein which is 85% pure. The purified protein is highly active, stable for several months at -70 degrees C and free of detectable nucleases. The molecular weight and N-terminal sequence are identical to that predicted for the FLP protein by the DNA sequence of the gene. Purified FLP protein primarily, but not exclusively, promotes intramolecular recombination. Intermolecular recombination becomes the dominant reaction when E. coli extracts containing no FLP protein are added to the reaction mixture. These extracts are not specifically required for recombination, but demonstrate that some properties previously attributed to FLP protein can be assigned to contaminating proteins present in E. coli.
Clustering Induces Redistribution of Syndecan-4 Core Protein into Raft Membrane Domains (2002)

Syndecan-4 is a heparan sulfate-carrying core protein that has been directly implicated in fibroblast growth factor 2 (FGF2) signaling. Recent studies have suggested that many signaling proteins localize to the raft compartment of the plasma cell membrane. To establish whether syndecan-4 is present in the raft compartment, we have studied the distribution of the core protein and an Fc receptor (FcR)-syndecan-4 chimera prior to and following clustering with FGF2 or antibodies. Whereas unclustered syndecan-4 was present predominantly in the non-raft membrane compartment, clustering induced extensive syndecan-4 redistribution to the rafts as demonstrated by the sucrose gradient centrifugation and life confocal microscopy. Although syndecan-4 and caveolin-1 moved in tandem, syndecan-4 was not present in caveolae, a major subset of raft compartments. We conclude that syndecan-4 clustering induces its redistribution to the non-caveolae raft compartment. This process may play an important role in syndecan-4-mediation of FGF2 signaling.
Transposon tools and methods in zebrafish (2005)

Zebrafish is an excellent model animal to study vertebrate development by genetic approaches. Hundreds of mutations affecting various processes of development have been isolated by chemical mutagenesis and insertional mutagenesis using a pseudotyped retrovirus. However, useful transposon tools and methods had not been available in zebrafish. This is mainly because no active transposable element has been found from the zebrafish genome. Recently, efficient transgenesis, gene trap, and enhancer trap methods have been developed in zebrafish by using the Tol2 and the Sleeping Beauty transposon systems. These methods should increase the usefulness of zebrafish as a model vertebrate and facilitate the study of developmental biology, genetics, and genomics.