gebhart/patrepeval huggingface dataset:
Serum measurements of human neutrophil lipocalin (HNL) discriminate between acute bacterial and viral infections (1995)

Human neutrophil lipocalin (HNL) is a recently identified protein from human neutrophil granules. The concentrations of HNL in the circulation were measured, in a group of patients with acute infections, using a radioimmunoassay. The concentrations of HNL in patients infected by viruses and bacteria were 93.78 +/- 45.30 micrograms l-1 (SD), 404.14 +/- 355.02 micrograms l-1 (SD) in serum, and 47.81 +/- 18.18 micrograms l-1 (SD), 145.46 +/- 194.32 micrograms l-1 (SD) in plasma, respectively. The differences between the two patient groups were highly significant. There was a significant correlation between serum HNL and plasma HNL levels in bacterial infections (r = 0.73, p < 0.0001). The HNL serum levels also correlated with those of C-reactive protein (CRP) (r = 0.59, p < 0.0001). Determination of HNL in serum was more specific and sensitive than CRP in the distinction between viral and bacterial infections. At a cut-off of 155 micrograms l-1 (HNL in serum), the positive and negative predictive values for the diagnosis of bacterial infections were 92 and 96%, respectively, which were superior to the optimal predictive values of CRP. Thus, the determination of HNL level is useful in the diagnosis of acute bacterial infections.
Genotoxicity of Escherichia coli Nissle 1917 strain cannot be dissociated from its probiotic activity (2012)

Oral administration of the probiotic bacterium Escherichia coli Nissle 1917 improves chronic inflammatory bowel diseases, but the molecular basis for this therapeutic efficacy is unknown. E. coli Nissle 1917 harbors a cluster of genes coding for the biosynthesis of hybrid nonribosomal peptide-polyketide(s). This biosynthetic pathway confers the ability for bacteria to induce DNA double strand breaks in eukaryotic cells. Here we reveal that inactivation of the clbA gene within this genomic island abrogated the ability for the strain to induce DNA damage and chromosomal abnormalities in non-transformed cultured rat intestinal epithelial cells but is required for the probiotic activity of E. coli Nissle 1917. Thus, evaluation of colitis severity induced in rodent fed with E. coli Nissle 1917 or an isogenic non-genotoxic mutant demonstrated the need for a functional biosynthetic pathway both in the amelioration of the disease and in the modulation of cytokine expression. Feeding rodents with a complemented strain for which genotoxicity was restored confirmed that this biosynthetic pathway contributes to the health benefits of the probiotic by modulating its immunomodulatory properties. Our data provide additional evidence for the benefit of this currently used probiotic in colitis but remind us that an efficient probiotic may also have side effects as any other medication.
Logistic Regression—Explanation and Use (1994)

The aim of this article is to provide a simple explanation of the logistic regression process and a guide of what to look for when assessing a study involving logistic regression.
Skeletal muscle oxygenation during constant work rate exercise (1995)

We compared the slow rise in VO2 during heavy exercise (i.e., greater than lactic acidosis threshold (LAT)) with changes in muscle oxyhemoglobin+oxymyoglobin (O2Hb/O2Mb) saturation by reflectance near infrared spectroscopy. Ten subjects performed four 6-min cycle ergometer tests with two constant work rates less than and two greater than the LAT, equivalent to 20, 40, 65 and 75% peak VO2. During less than LAT exercise, O2Hb/O2Mb saturation decreased to a minimum by 2 min and then remained constant or rose slightly. For greater than LAT work rates, the initial fall in O2Hb/O2Mb saturation was greater the higher the work rate and continued to decrease with time after 3 min. Between minutes 3 and 6, the rate of decrease in O2Hb/O2Mb saturation correlated with the increase in VO2 (r = -0.69, P < 0.0001). These studies support the hypothesis that the slow rise in VO2 during heavy constant work rate exercise is associated with a progressive decline in O2Hb/O2Mb saturation in the contracting muscles themselves that may be facilitated by capillary oxyhemoglobin dissociation owing to tissue lactic acidosis (Bohr effect).
Three techniques for improving automatic synchronization between music and lyrics: Fricative detection, filler model, and novel feature vectors for vocal activity detection (2008)

Three techniques are described that improve a previously developed system for automatically synchronizing lyrics with musical audio signals. Although this system achieves state-of-the-art accuracy by extracting vocal vowels from polyphonic sound mixtures and using forced alignment between those vowels and a phoneme network of the lyrics, there was still room for improvement. The first technique detects nonexistence regions in which fricative consonant sounds do not exist, which were not utilized in the previous system, and prohibits the alignment of the fricative phonemes to those regions. The second technique inserts a filler model between phrases of the phoneme network. This model improves the accuracy of the forced alignment by ignoring inter-phrase vowel utterances not included in the lyrics. The third technique introduces novel feature vectors for vocal activity detection that enable a distance calculation between two sets of the harmonic structure without estimating their spectral envelopes. Experimental results showed that all three techniques contribute to improved synchronization.
Favorable Effects of Weak Acids on Negative-Ion Electrospray Ionization Mass Spectrometry (2004)

Despite widespread use in pharmacokinetic, drug metabolism, and pesticide residue studies, little is known about the factors governing response during reversed-phase liquid chromatography coupled with negative-ion electrospray ionization (ESI(-)) mass spectrometry. We examined the effects of various mobile-phase modifiers on the ESI(-) response of four selective androgen receptor modulators using a postcolumn infusion system. Acetic, propionic, and butyric acid improved the ESI(-) responses of analytes to varying extents at low concentrations. Formic acid suppressed ionization, as did neutral salts (ammonium formate, ammonium acetate) and bases (ammonium hydroxide, triethylamine) under most conditions. Two modifiers (2,2,2-trifluoroethanol, formaldehyde) that produce anions with high gas-phase proton affinity increased ESI(-) responses. However, the concentrations of these modifiers required to enhance ESI(-) response were higher than that of acidic modifiers, which is a phenomenon likely related to their low pK(a) values. 2,2,2-Trifluoroethanol increased response of more hydrophobic compounds but decreased response of a more hydrophilic compound. Formaldehyde improved response of all the compounds, especially the hydrophilic compound with lower surface activity. In summary, these results suggest that an ideal ESI(-) modifier should provide cations that can be easily electrochemically reduced and produce anions with small molecular volume and high gas-phase proton affinity.
Characterization of cell wall proteins from yeast and mycelial cells of Candida albicans by labelling with biotin: comparison with other techniques (1992)

Candida albicans ATCC 26555 blastoconidia and blastoconidia bearing germ tubes were metabolically labelled by incubating the cells with 14C-labelled protein hydrolysate and were subsequently tagged with biotin. Double-labelled (radioactive and biotinylated) cell wall proteins and glycoproteins were extracted from intact cells of both growth forms by treatment with 2-mercaptoethanol (beta ME) and with beta-glucanases (Zymolyase) after treatment with beta ME. The beta ME- and Zymolyase-extracts were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western blotted (immunoblotted) to nitrocellulose paper. Polyacrylamide gels were stained with Coomassie blue and processed for fluorography. Western blot analysis was performed either with peroxidase conjugated-concanavalin A (ConA) or Extravidin. Blotted proteins were also reacted with polyclonal antibodies and monoclonal antibodies against mannoprotein components from mycelial cell walls of the ATCC 26555 strain. Labelling with biotin allowed identification of a complex array of cell wall protein and glycoprotein components within a very wide molecular mass range (from 650 to 13 kDa). These appeared to be genuine cell wall components. Biotinylated high-molecular-mass glycoproteins that were not stained with Coomassie blue or that appeared as poorly resolved polydisperse bands by indirect ConA-peroxidase staining of Western blots were detected as sharply defined bands following reaction with the Extravidin-peroxidase conjugate. Biotinylated molecules retained unaltered reactivities against ConA, polyclonal antibodies, and monoclonal antibodies.
Safety of Different Dosages of Intravenous Adenosine Used in Conjunction With Diagnostic Myocardial Imaging Techniques (1993)

Adenosine-assisted myocardial perfusion imaging procedures are relatively safe for evaluating coronary artery disease. Despite 82% of patients reporting at least one side effect, only 10 (< 1%) had to discontinue adenosine. No patient suffered any residual sequelae from the adverse effects. The fixed-dose regimen is associated with fewer subjective side effects and is better tolerated than titration regimens. Appropriate safety precautions should nonetheless be taken during adenosine infusions.
Principles of electronic materials and devices (2001)

Principles of Electronic Materials and Devices, Third Edition, is a greatly enhanced version of the highly successful text Principles of Electronic Materials and Devices, Second Edition. It is designed for a first course on electronic materials given in Materials Science and Engineering, Electrical Engineering, and Physics and Engineering Physics Departments at the undergraduate level. 
The third edition has numerous revisions that include more beautiful illustrations and photographs, additional sections, more solved problems, worked examples, and end-of-chapter problems with direct engineering applications. The revisions have improved the rigor without sacrificing the original semiquantitative approach that both the students and instructors liked and valued. Some of the new end-of-chapter problems have been especially selected to satisfy various professional engineering design requirements for accreditation across international borders. Advanced topics have been collected under Additional Topics, which are not necessary in a short introductory treatment.
Table of contents

1 Elementary Materials Science Concepts 
2 Electrical and Thermal Conduction in Solids 
3 Elementary Quantum Physics 
4 Modern Theory of Solids 
5 Semiconductors 
6 Semiconductor Devices 
7 Dielectric Materials and Insulation 
8 Magnetic Properties and Superconductivity 
9 Optical Properties of Materials 
Appendix A: Bragg's Diffraction Law and X-Diffraction
Appendix B: Flux, Luminous Flux and the Brightness of Radiation
Appendix C: Major Symbols and Abbreviations 
Appendix D: Elements to Uranium 
Appendix E: Constants and Useful Information
Xylitol production from xylose mother liquor: a novel strategy that combines the use of recombinant Bacillus subtilis and Candida maltosa (2011)

In this study, we developed a biological method for the purification of xylose from xylose mother liquor and subsequent preparation of xylitol by C. maltosa-mediated biohydrogenation of xylose.
Line probe assay for rapid detection of drug-selected mutations in the human immunodeficiency virus type 1 reverse transcriptase gene (1997)

Upon prolonged treatment with various antiretroviral nucleoside analogs such as 3'-azido-3'-deoxythymidine, 2',3'-dideoxyinosine, 2',3'-dideoxycytidine, (-)- beta-L-2', 3'dideoxy-3'thiacytidine and 2',3'-didehydro-3'-deoxythymidine, selection of human immunodeficiency virus type 1 (HIV-1) strains with mutations in the reverse transcriptase (RT) gene has been reported. We designed a reverse hybridization line probe assay (LiPA) for the rapid and simultaneous characterization of the following variations in the RT gene: M41 or L41; T69, N69, A69, or D69; K70 or R70; L74 or V74; V75 or T75; M184, I184, or V184; T215, Y215, or F215; and K219, Q219, or E219. Nucleotide polymorphisms for codon L41 (TTG or CTG), T69 (ACT or ACA), V75 (GTA or GTG), T215 (ACC or ACT), and Y215 (TAC or TAT) could be detected. In addition to the codons mentioned above, several third-letter polymorphisms in the direct vicinity of the target codons (E40, E42, K43, K73, D76, Q182, Y183, D185, G213, F214, and L214) were found, and specific probes were selected. In total, 48 probes were designed and applied to the LiPA test strips and optimized with a well-characterized and representative reference panel. Plasma samples from 358 HIV-infected patients were analyzed with all 48 probes. The amino acid profiles could be deduced by LiPA hybridization in an average of 92.7% of the samples for each individual codon. When combined with changes in viral load and CD4+ T-cell count, this LiPA approach proved to be useful in studying genetic resistance in follow-up samples from antiretroviral agent-treated HIV-1-infected individuals.
Creating Interval Target Scorecards with Credit Scoring for SAS ® Enterprise Miner™ (2013)

Credit Scoring for SAS ® Enterprise Miner ™ has been widely used to develop binary target probability of default scorecards, which include scorecards for application and behavior scoring. Extending the weight-of-evidence binned scorecard methodology to interval-based targets such as loss given default and exposure at default is a natural step in the evolution of scorecard development methodologies. This paper discusses several new methods available in Credit Scoring for SAS Enterprise Miner that help build scorecards that are based on interval targets. These include cutoffs that convert the interval target to a binary form and an algorithm that maintains the continuous nature of the interval target. Each method is covered in detail, and all methods are compared to determine how they perform against known target values.
Measurement of Boundary Shear Stress in Open Channels (1990)

Research into momentum transfer in compound channel waterways is currently being undertaken at the University of Queensland. Results from this work will have application in improved design procedures. A critical component of the experimental investigation is detailed, accurate measurement of boundary shear stress distributions across the waterway. Many measurements are required and a micro-computer based system for instrument control and data logging has been developed to suit a detailed research programme.
Nanoliter Multiplex PCR Arrays on a SlipChip (2010)

The SlipChip platform was tested to perform high-throughput nanoliter multiplex PCR. The advantages of using the SlipChip platform for multiplex PCR include the ability to preload arrays of dry primers, instrument-free sample manipulation, small sample volume, and high-throughput capacity. The SlipChip was designed to preload one primer pair per reaction compartment and to screen up to 384 different primer pairs with less than 30 nanoliters of sample per reaction compartment. Both a 40-well and a 384-well design of the SlipChip were tested for multiplex PCR. In the geometries used here, the sample fluid was spontaneously compartmentalized into discrete volumes even before slipping of the two plates of the SlipChip, but slipping introduced additional capabilities that made devices more robust and versatile. The wells of this SlipChip were designed to overcome potential problems associated with thermal expansion. By using circular wells filled with oil and overlapping them with square wells filled with the aqueous PCR mixture, a droplet of aqueous PCR mixture was always surrounded by the lubricating fluid. In this design, during heating and thermal expansion, only oil was expelled from the compartment and leaking of the aqueous solution was prevented. Both 40-well and 384-well devices were found to be free from cross-contamination, and end point fluorescence detection provided reliable readout. Multiple samples could also be screened on the same SlipChip simultaneously. Multiplex PCR was validated on the 384-well SlipChip with 20 different primer pairs to identify 16 bacterial and fungal species commonly presented in blood infections. The SlipChip correctly identified five different bacterial or fungal species in separate experiments. In addition, the presence of the resistance gene mecA in methicillin resistant Staphylococcus aureus (MRSA) was identified. The SlipChip will be useful for applications involving PCR arrays and lays the foundation for new strategies for diagnostics, point-of-care devices, and immobilization-based arrays.
Synthesis and characterization of polyethylene/clay–silica nanocomposites: A montmorillonite/silica‐hybrid‐supported catalyst and in situ polymerization (2004)

Abstract A novel approach to the preparation of polyethylene (PE) nanocomposites, with montmorillonite/silica hybrid (MT‐Si) supported catalyst, was developed. MT‐Si was prepared by depositing silica nanoparticles between galleries of the MT. A common zirconocene catalyst [bis(cyclopentadienyl)zirconium dichloride/methylaluminoxane] was fixed on the MT‐Si surface by a simple method. After ethylene polymerization, two classes of nanofillers (clay layers and silica nanoparticles) were dispersed concurrently in the PE matrix and PE/clay–silica nanocomposites were obtained. Exfoliation of the clay layers and dispersion of the silica nanoparticles were examined with transmission electron microscopy. Physical properties of the nanocomposites were characterized by tensile tests, dynamic mechanical analysis, and DSC. The nanocomposites with a low nanofiller loading (&lt;10 wt %) exhibited good mechanical properties. The nanocomposite powder produced with the supported catalyst had a granular morphology and a high bulk density, typical of a heterogeneous catalyst system. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 941–949, 2004
Phase III Trial of Doxorubicin Plus Cisplatin With or Without Paclitaxel Plus Filgrastim in Advanced Endometrial Carcinoma: A Gynecologic Oncology Group Study (2004)

TAP significantly improves RR, PFS, and OS compared with AP. Evaluation of this regimen in the high-risk adjuvant setting is warranted, but close attention should be paid to the increased risk of peripheral neuropathy.
Efficient frequency comb generation in AlGaAs-on-insulator (2016)

The combination of nonlinear and integrated photonics enables Kerr frequency comb generation in stable chip-based microresonators. Such a comb system will revolutionize applications, including multi-wavelength lasers, metrology, and spectroscopy. Aluminum gallium arsenide (AlGaAs) exhibits very high material nonlinearity and low nonlinear loss. However, difficulties in device processing and low device effective nonlinearity made Kerr frequency comb generation elusive. Here, we demonstrate AlGaAs-on-insulator as a nonlinear platform at telecom wavelengths with an ultra-high device nonlinearity. We show high-quality-factor (Q > 105) micro-resonators where optical parametric oscillations are achieved with milliwatt-level pump threshold powers, which paves the way for on-chip pumped comb generation.
A linear relation between the compressibility and density of blood (2001)

By considering the blood as a mixture of ultrafiltrate and protein concentrate, the additive nature of compressibility and density from the components is utilized to deduce a linear relation between the compressibility and density for blood. This deduction also indicates that the intercept and slope of the linear relation are independent of the hematocrit, plasma protein concentration, and hemoglobin concentration of red blood cells. To verify experimentally this linear relation, saline and plasma dilutions on porcine or canine blood flowing in an extracorporeal circuit were carried out. The hematocrit of the experiments ranges from 0% to 55% and the plasma protein concentration ranges from 10 to 90 g/l. A resonance device in the circuit measured the density rhob of blood at 37 degrees C and an ultrasound system measured the sound velocity cb. The range of density is from 1,010 to 1,060 g/l and that of sound velocity is from 1,530 to 1,580 m/s. The linear relation that best fits the data of compressibility [computed as (rhob cb(2))-1] and density has a correlation coefficient of 0.9978. The linear relation is found to fit well the dependence of compressibility on density derived from the sound velocity data of human, horse, and porcine blood in the literature.
A novel pathway of human T cell activation via a 103 kD T cell activation antigen. (1987)

A novel triggering signal for human proliferating and cytotoxic T lymphocytes defined by a 103 kD T cell-specific activation antigen (Tp103) is described. Tp103 is expressed on all proliferating normal T cells but is not present, or present only in low amounts, on resting peripheral blood T lymphocytes. Cross-linking of T cell and Fc receptor-positive accessory or target cells by an antibody against Tp103 leads to activation of the T cell. The proliferative response is due to an autocrine IL 2-dependent mechanism and can be inhibited by antibodies against the IL 2 receptor or by Cyclosporin A. Resting Tp103-positive T cells also respond to anti-Tp103. Although Tp103 is not linked to the antigen receptor/T3 complex, triggering via Tp103 can be inhibited by modulation of the T3 molecule. Thus, Tp103 defines a new antigen-independent pathway of T cell activation that can be regulated via other T cell surface structures.
Binding of Bacillus thuringiensis Cry1Ac Toxin to Aminopeptidase in Susceptible and Resistant Diamondback Moths (Plutella xylostella) (1997)

Bacillus thuringiensis Cry1Ac toxin bound to a 120-kDa protein isolated from the brush border membranes of both susceptible and resistant larvae of Plutella xylostella, the diamondback moth. The 120-kDa protein was purified by Cry1Ac toxin affinity chromatography. Like Cry1Ac-binding aminopeptidase N (EC 3.4.11.2) from other insects, this protein was eluted from the affinity column with 200 mM N-acetylgalactosamine. The purified protein had aminopeptidase activity and bound Cry1Ac toxin on ligand blots. Purified aminopeptidase was recognized by antibodies to the cross-reacting determinant found on phosphatidylinositol-specific phospholipase C-solubilized proteins. The results show that the presence of Cry1Ac-binding aminopeptidase in the brush border membrane is not sufficient to confer susceptibility to Cry1Ac. Furthermore, the results do not support the hypothesis that resistance to Cry1Ac was caused by lack of a Cry1Ac-binding aminopeptidase.