gebhart/patrepeval huggingface dataset:
Dual-Energy CT-Scanning Applications in Rock Characterization (2004)

Abstract The use of dual-energy CT-scanning for evaluating reservoir rocks is not a new technique. It involves scanning the same location within the rock twice, using a different X-ray energy each time. Wellington and Vinegar, in a 1987 paper stated that one image proportional only to bulk density and another proportional to atomic number can be obtained by scanning the sample at high (above 100 kV, Compton scattering dominant) and low (well below 100 kV, Photoelectric absorption dominant) X-ray energies. They generated CT slices showing density and atomic number variations. Although dual-energy scanning has been used quite successfully in fluid flow visualization studies, especially in the case of three-phase flow, its use has been limited in the field of petrophysical core characterization. Part of the problem is due to the unavailability of appropriate software and procedures to generate the bulk density and atomic number images from the high and low-energy CT data and part is due to the lack of necessary steps to utilize the density and atomic number data to characterize the cores. Commercially available software can now allow generating the density and atomic number images from the dual-energy data. This paper describes some techniques to utilize the density and atomic number data to better characterize the reservoir rocks. This technique was first applied to small plug samples of known petrophysical properties for validation purposes. After that, it was applied to a 60 ft-long section of preserved core from an Upper Jurassic carbonate reservoir in Saudi Arabia, which was CT-scanned at two different X-ray energies at 5 cm (2 inch) intervals. Interesting qualitative results were obtained that can improve our understanding of the carbonates. This paper also shows step-by-step instructions for calculating porosity values from the approximate mineral compositions.
Particle Deflection in a Poly(dimethylsiloxane) Microchannel Using a Propagating Surface Acoustic Wave: Size and Frequency Dependence (2013)

We study the effect of a propagating surface acoustic wave (PSAW) with different frequencies on particles with different sizes in microfluidic channels. We find that the deflection critically depends on the applied frequency as well as on the particle size. For fixed frequencies, large particles are deflected and migrate perpendicular to the flow direction while smaller particles only follow the streamlines of the flow field. However, with increasing frequency of the PSAW above a size dependent limit, small particles are also actuated. This relation can be characterized by the wavenumber k and the particle radius r using the parameter κ = k · r. For the onset of deflection, we find a critical value κc ≅ 1.28 ± 0.20. Finally, we demonstrate how this device can be used for particle separation.
The wobble motor: design, fabrication and testing of an eccentric-motion electrostatic microactuator (2003)

The basic characteristics and advantages of microelectromechanical systems, machines constructed of small moving subelements which have characteristic dimensions in the range of about 0.5 to 500 mu m, are reviewed; design problems are considered; and particular attention is given to the wobble motor (WM) developed by S.C. Jacobsen et al. (1989) using electrodischarge machining (EDM). Fifteen EDM WMs have been constructed and utilized for experimental purposes. WM explorations have demonstrated that micro systems can be quite easily constructed by means other than etching silicon. Experiments aimed at generating simple preliminary data have been conducted, and results compare reasonably to analytical studies. Results reported include stall torque measurements, speed measurements, torque-speed measurements, and wear measurements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The kinetics of 1,4‐butanediol diglycidyl ether crosslinking of dermal sheep collagen (2000)

Dermal sheep collagen was crosslinked with 1,4-butanediol diglycidyl ether (BDDGE) or modified with glycidyl isopropyl ether (PGE). The reduction in amine groups as a function of time was followed to study the overall reaction kinetics of collagen with either BDDGE or PGE. Linearization of the experimental data resulted in a reaction order of 2 with respect to the amine groups in the PGE masking reaction, whereas a reaction order of 2.5 was obtained in the BDDGE crosslinking reaction. The reaction orders were independent of the pH in the range of 8.5–10.5 and the reagent concentration (1–4 wt %). The reaction order with respect to epoxide groups was equal to 1 for both reagents. As expected, the reaction rate was favored by a higher reagent concentration and a higher solution pH. Because the BDDGE crosslinking reaction occurs via two distinct reaction steps, the content of pendant epoxide groups in the collagen matrix was determined by treating the collagen with either O-phosphoryl ethanolamine or lysine methyl ester. The increase in either phosphor or primary amine groups was related to the content of pendant groups. Crosslinking at pH 9.0 resulted in a low reaction rate but in a high crosslink efficacy, especially after prolonged reaction times. A maximum concentration of pendant epoxide groups was detected after 50 h. Reaction at pH 10.0 was faster, but a lower crosslinking efficacy was obtained. At pH 10.0, the ratio between pendant epoxide groups and crosslinks was almost equal to 1 during the course of the crosslinking reaction. © 2000 John Wiley & Sons, Inc. J Biomed Mater Res, 51, 541–548, 2000.
Time of injury affects urinary biomarker predictive values for acute kidney injury in critically ill, non-septic patients (2013)

NGAL, KIM-1, pi- and alpha-GST displayed unique and mutually incomparable time dependent characteristics during the development of non-sepsis related AKI. Therefore, the time-relationship between the biomarker measurements and the injurious event influences the individual test results.
Correction: Inactivation of the CovR/S Virulence Regulator Impairs Infection in an Improved Murine Model of Streptococcus pyogenes Naso-Pharyngeal Infection (2013)

Streptococcus pyogenes is a leading cause of pharyngeal infection, with an estimated 616 million cases per year. The human nasopharynx represents the major reservoir for all S. pyogenes infection, including severe invasive disease. To investigate bacterial and host factors that influence S. pyogenes infection, we have devised an improved murine model of nasopharyngeal colonization, with an optimized dosing volume to avoid fulminant infections and a sensitive host strain. In addition we have utilized a refined technique for longitudinal monitoring of bacterial burden that is non-invasive thereby reducing the numbers of animals required. The model was used to demonstrate that the two component regulatory system, CovR/S, is required for optimum infection and transmission from the nasopharynx. There is a fitness cost conferred by covR/ S mutation that is specific to the nasopharynx. This may explain why S. pyogenes with altered covR/S have not become prevalent in community infections despite possessing a selective advantage in invasive infection.
Visualization of in Vivo Direct Interaction between HIV-1 TAT and Human Cyclin T1 in Specific Subcellular Compartments by Fluorescence Resonance Energy Transfer (2001)

Human cyclin T1, a component of the P-TEFb kinase complex, was originally identified through its biochemical interaction with the Tat transactivator protein of human immunodeficiency virus type 1 (HIV-1). Current understanding suggests that binding of Tat to P-TEFb is required to promote efficient transcriptional elongation of viral RNAs. However, the dynamics and the subnuclear localization of this process are still largely unexplored in vivo. Here we exploit high resolution fluorescence resonance energy transfer (FRET) to visualize and quantitatively analyze the direct interaction between Tat and cyclin T1 inside the cells. We observed that cyclin T1 resides in specific subnuclear foci which are in close contact with nuclear speckles and that Tat determines its redistribution outside of these compartments. Consistent with this observation, strong FRET was observed between the two proteins both in the cytoplasm and in regions of the nucleus outside of cyclin T1 foci and overlapping with Tat localization. These results are consistent with a model by which Tat recruits cyclin T1 outside of the nuclear compartments where the protein resides to promote transcriptional activation.
Investigation of the Irreversible Capacity Loss in the Layered LiNi[sub 1∕3]Mn[sub 1∕3]Co[sub 1∕3]O[sub 2] Cathodes (2005)

The irreversible capacity (IRC) loss in the first cycle at 3.0-4.6 V of layered cathodes has been investigated as a function of synthesis temperature (600-900°C), and compared with that of . The IRC values in both the systems increase with decreasing synthesis temperature and show a linear relationship with the Brunauer-Emmett-Teller surface area although the increase is faster with . Additionally, the IRC is found to exhibit a relationship to an irreversible anodic peak observed in cyclic voltammograms at around 4.5 V, which becomes prominent with decreasing synthesis temperature and increasing Mn content in .
Zur Veröffentlichung von Unterrichtseinheiten (1996)

Veröffentlichte Unterrichtseinheiten gibt es in großer Zahl. In den letzten Jahren mehren sich die Anzeichen, daß publizierte Unterrichtsmodelle in Zukunft ihr Aussehen grundlegend verändern werden. Diese Entwicklung verdient Aufmerksamkeit, denn in der Lehrerausbildung und in der eigenen Fort- und -weiterbildung kommt veröffentlichten Unterrichtseinheiten ein hoher Stellenwert zu.
Branched DNA (bDNA) Technology for Direct Quantification of Nucleic Acids: Design and Performance (1998)

The branched DNA (bDNA) assay represents a significant advance in the direct quantification of nucleic acid molecules for research and clinical applications. Other methods for the detection and quantification of nucleic acid molecules, such as polymerase chain reaction (PCR) and nucleic acid sequence-based amplification (NASBA), involve molecular amplification of target nucleic acids followed by detection of amplified products. While these target amplification methods can be extremely sensitive, they suffer from two major disadvantages. First, it is difficult to obtain reproducible quantification since the target nucleic acid must be extracted and amplified in order to measure it. Second, numerous precautions must be taken to avoid false positive results caused by contamination of samples with PCR products and carryover from other specimens. A new departure from target amplification methods, the bDNA assay, directly measures nucleic acid molecules by boosting the reporter signal, rather than by replicating target sequences as the means of detection (Figure 1), and hence it is not subject to the errors inherent in the extraction and amplification of target nucleic acids. An ideal tool for nucleic acid quantification, the bDNA assay detects nucleic acid molecules at their physiological concentration, yields highly reproducible quantification, and eliminates false positives due to contamination.
Effect of standardized aqueous extract of Withania somniferaon tests of cognitive and psychomotor performance in healthy human participants (2013)

These results suggest that Withania somnifera extract can improve cognitive and psychomotor performance and may, therefore, be a valuable adjunct in the treatment of diseases associated with cognitive impairment.
A novel in vivo assay for the analysis of protein-protein interaction (1999)

The Ras Recruitment System (RRS) is a method for identification and isolation of protein-protein interaction. The method is based on translocation of cytoplasmic mammalian Ras protein to the inner leaflet of the plasma membrane through protein-protein interaction. The system is studied in a temperature-sensitive yeast strain where the yeast Ras guanyl nucleotide exchange factor is inactive at 36 degrees C. Protein-protein interaction results in cell growth at the restrictive temperature. We developed a gene reporter assay for the analysis of protein-protein interaction in mammalian cells. Ras activation in mammalian cells induces the mitogen-activated kinase cascade (MAPK), which can be monitored using Ras-dependent reporter genes. This greatly extends the usefulness of the system and provides a novel assay for protein-protein interaction in mammalian cells.
Production of recombinant soluble human integrin α4β1 (2000)

Integrin alpha4beta1 is a major leukocyte adhesion receptor that is a key target for the development of anti-inflammatory therapeutics. With the dual long-term goals of developing a reagent for use in high-throughput inhibitor screening assays and for crystallisation trials and subsequent structure determination, we have generated a recombinant soluble alpha4beta1 receptor. Both subunits were truncated prior to the transmembrane domains by site-directed mutagenesis and expressed using baculovirus infection of insect cells. The molecular weights of the recombinant subunits were as expected for post-translationally unmodified protein. In addition, as observed for the native subunit, a proportion of the alpha4 subunit was proteolytically processed into two fragments. ELISA and solid phase ligand-binding assays were performed to investigate the folding and functionality of the soluble integrin. The data suggest that the receptor was correctly folded and that it bound recombinant ligands with similar kinetics to the native molecule.
An Improvement of the Two-Path Algorithm Transfer Logic for Acoustic Echo Cancellation (2007)

Adaptive filters for echo cancellation generally need update control schemes to avoid divergence in case of significant disturbances. The two-path algorithm avoids the problem of unnecessary halting of the adaptive filter when the control scheme gives an erroneous output. Versions of this algorithm have previously been presented for echo cancellation. This paper presents a transfer logic which improves the convergence speed of the two-path algorithm for acoustic echo cancellation, while retaining the robustness. Results from simulations show an improved performance, and a fixed-point DSP implementation verifies the performance in real-time
Profile of Escherichia coli O157:H7 pathogen responsible for hamburger-borne outbreak of hemorrhagic colitis and hemolytic uremic syndrome in Washington (1993)

We analyzed Escherichia coli O157:H7 isolates from stool samples of five patients who had bloody diarrhea and were infected during a large food-borne outbreak of hemorrhagic colitis in Washington state. The isolates were assessed for Shiga-like toxin profile, adherence and plasmid traits, mouse virulence, capsule, and enterohemolysin production. The profiles of the five isolates were indistinguishable from each other and similar to that of E. coli O157:H7 strain EDL933, an organism responsible for a similar hamburger-associated food poisoning episode in 1982.
Protein expression profiles in human breast ductal carcinoma and histologically normal tissue (1997)

Reference two-dimensional (2-D) gels are presented for human breast ductal carcinoma and histologically normal tissue. Whole biopsy fragments were analyzed, including epithelial and nonepithelial components. Thirty-five spots have been assigned by gel matching to the human liver SWISS-2DPAGE reference map and/or to the human primary keratinocyte IPG map from the Danish Center for Human Genome. N-terminal microsequencing was applied to confirm randomly chosen matching assignments and to identify six new spots. Protein expression profiles in ductal carcinoma and in normal breast tissue appeared to be similar, except for a pattern consisting of 32 spots, which were highly expressed in all carcinoma specimens, and less intense and occasionally undetectable in normal tissue. This difference was statistically significant. Assignment has been obtained for several spots, namely GRP94, GRP78, GRP75, mitochondrial HSP60, calreticulin, protein disulfide isomerase, peptidyl-prolyl cis-trans isomerase, collagen-binding protein 2, fructose bisphosphate aldolase, glyceraldehyde-3-phosphate dehydrogenase, thioredoxin, cytochrome c oxidase VA subunit, tubulin beta isoform and macrophage migration inhibitory factor (MIF). The cancer- and tissue-specificity of the described pattern was assessed by matching to the Swiss-2DPAGE human liver, hepatoma, lymphoma, erythroleukemia reference maps. The pattern of 32 spots was found to be indicative of epithelial neoplasia.
Solid-Phase Peptide Synthesis (1998)

Methods for synthesizing peptides are divided conveniently into two categories solution and solid-phase (SPPS) Solution synthesis retains value in large-scale manufacturing and for specialized laboratory applications. However, the need to optimize reaction conditions, yields, and purification procedures for essentially every intermediate (each of which has unpredictable solubility and crystallization characteristics) renders solution methods time-consuming and labor-intensive Consequently, most workers now requiring peptides for then research opt for the more accessible solidphase approach In this chapter, an overview of SPPS is presented. For brevity, only commercially available reagents and derivatives utilized for synthesis will be considered here The reader 1s referred to a number of excellent, comprehensive reviews (1–9) for further discussion of the solid-phase technique.
Four molecular pathways of T cell adhesion to endothelial cells: roles of LFA-1, VCAM-1, and ELAM-1 and changes in pathway hierarchy under different activation conditions. (1991)

T cell adhesion to endothelium is critical to lymphocyte recirculation and influx into sites of inflammation. We have systematically analyzed the role of four receptor/ligand interactions that mediate adhesion of peripheral human CD4+ T cells to cultured human umbilical vein endothelial cells (HUVEC): T cell LFA-1 binding to ICAM-1 and an alternative ligand ("ICAM-X"), T cell VLA-4 binding to VCAM-1, and T cell binding to ELAM-1. Contributions of these four pathways depend on the activation state of both the T cell and HUVEC, and the differentiation state of the T cell. ELAM-1 plays a significant role in mediating adhesion of resting CD4+ T cells to activated HUVEC. LFA-1 adhesion dominates with PMA-activated T cells but the strength and predominant LFA-1 ligand is determined by the activation state of the HUVEC; while ICAM-1 is the dominant ligand on IL-1-induced HUVEC, "ICAM-X" dominates binding to uninduced HUVEC. Adhesion via VLA-4 depends on induction of its ligand VCAM-1 on activated HUVEC; PMA activation of T cells augments VLA-4-mediated adhesion, both in the model of T/HUVEC binding and in a simplified model of T cell adhesion to VCAM-1-transfected L cells. Unlike LFA-1 and VLA-4, ELAM-1-mediated adhesion is not increased by T cell activation. Differential expression of adhesion molecules on CD4+ T cell subsets understood to be naive and memory cells also regulates T/HUVEC adhesion. Naive T cell adhesion to HUVEC is mediated predominantly by LFA-1 with little or no involvement of the VLA-4 and ELAM-1 pathways. In contrast, memory T cells bind better to HUVEC and utilize all four pathways. These studies demonstrate that there are at least four molecular pathways mediating T/HUVEC adhesion and that the dominance/hierarchy of these pathways varies dramatically with the activation state of the interacting cells and the differentiation state of the T cell.
Biosynthesis of D-alanyl-lipoteichoic acid: cloning, nucleotide sequence, and expression of the Lactobacillus casei gene for the D-alanine-activating enzyme (1992)

The D-alanine-activating enzyme (Dae; EC 6.3.2.4) encoded by the dae gene from Lactobacillus casei ATCC 7469 is a cytosolic protein essential for the formation of the D-alanyl esters of membrane-bound lipoteichoic acid. The gene has been cloned, sequenced, and expressed in Escherichia coli, an organism which does not possess Dae activity. The open reading frame is 1,518 nucleotides and codes for a protein of 55.867 kDa, a value in agreement with the 56 kDa obtained by electrophoresis. A putative promoter and ribosome-binding site immediately precede the dae gene. A second open reading frame contiguous with the dae gene has also been partially sequenced. The organization of these genetic elements suggests that more than one enzyme necessary for the biosynthesis of D-alanyl-lipoteichoic acid may be present in this operon. Analysis of the amino acid sequence deduced from the dae gene identified three regions with significant homology to proteins in the following groups of ATP-utilizing enzymes: (i) the acid-thiol ligases, (ii) the activating enzymes for the biosynthesis of enterobactin, and (iii) the synthetases for tyrocidine, gramicidin S, and penicillin. From these comparisons, a common motif (GXXGXPK) has been identified that is conserved in the 19 protein domains analyzed. This motif may represent the phosphate-binding loop of an ATP-binding site for this class of enzymes. A DNA fragment (1,568 nucleotides) containing the dae gene and its putative ribosome-binding site has been subcloned and expressed in E. coli. Approximately 0.5% of the total cell protein is active Dae, whereas 21% is in the form of inclusion bodies. The isolation of this minimal fragment without a native promoter sequence provides the basis for designing a genetic system for modulating the D-alanine ester content of lipoteichoic acid.
A Low-Light CMOS Contact Imager With an Emission Filter for Biosensing Applications (2008)

In this paper, a fully functional low light 128 X 128 contact image sensor for cell detection in biosensing applications is presented. The imager, fabricated in 0.18 mum CMOS technology, provides low-noise operation by employing both a modified version of the active reset (AR) technique and a modified version of the active column sensor (ACS) readout method. High-sensitivity, low noise performance of the presented sensor is well-suited for fluorescence imaging. For this purpose, an emission filter was fabricated and integrated with the sensor. The filter was fabricated using PDMS and Sudan II Blue dye mix, spin-coated and deposited in a class 1000 clean room. The designed filter is suitable for excitation at wavelengths below 340 nm and emission at 450 nm and above. The fabricated imager architecture and operation are described, noise analysis is presented and measurements from a test chip are shown. Experimental results using live neurons from the pond snail, Lymnaea stagnalis, and fluorescence polystyrene micro-beads prove the functionality of the fabricated system and indicate its biocompatiblity.
Introduced plant diseases (2003)

With the introduction of plants and plant products comes associated plant diseases. Diseases are particularly insidious because they may show few or no symptoms on the hosts with which they have evolved. However, native species that are susceptible to these new diseases are likely to have very low resistance or tolerance. Introduced plant diseases have probably had stronger impacts on native plant communities than have their original plant hosts. In some cases, introduced diseases have changed the species composition of forests in a major way.
Reduced hippocampal metabolism in MCI and AD (2005)

The new HipMask technique provides accurate and rapid assessment of the hippocampus on PET without the use of regions of interest. Hippocampal glucose metabolism reductions are found in both mild cognitive impairment and Alzheimer disease and contribute to their diagnostic classification. These results suggest re-examination of prior voxel-based analysis 2-[18F]fluoro-2-deoxy-d-glucose PET studies that failed to report hippocampal effects.