gebhart/patrepeval huggingface dataset:
Photocatalytic Patterning using Nano-Colloidal Anatase in Aqueous Solution Process (2009)

Water-soluble titanium complexes were synthesized starting from TiCl4 as a source of Ti. TiO2 was prepared by hydrothermal treatment of the obtained Ti-malate complex. The TiO2 sample was characterized by X-ray diffraction (XRD), X-ray fluorescence analysis (XRF), Transmission electron microscopy (TEM), UV-Visible spectroscopy. The sample consisted of ～10 nm mono-dispersed anatase particles. A blue shift of absorption due to quantum size effect in the nanoscale anatase particles was observed. Transparent stable colloid suspension was obtained by dispersing the prepared nano-sized anatase into water. For the photocatalytic patterning, Ti-glycolate complex was added into the colloid solution and this resulted solution was coated on a glass substrate. After drying, the film was covered by a photomask and irradiated by UV light. The irradiated part became insoluble due to the photocatalytic reaction promoted by anatase particles. The film of masked part was removed by washing with water, and patterned film was fabricated.
Genetic evidence for role of extracellular proteinase in virulence of Candida albicans (1985)

The relationship between extracellular proteinase and the virulence for mice in Candida albicans was studied by using a set of three isolates. The set included a proteinase-producing parent (C9), a proteinase-deficient mutant derived from C9 by nitrous acid treatment (C9M1), and a spontaneous revertant (C9M1M) obtained by mouse passage of C9M1. The morphological markers and the carbon assimilation pattern were identical in these isolates. Isolate C9 produced a high level of proteinase in vitro and caused fatal infection (100%) within 21 days. The mutant produced no detectable enzymes in vitro, and all mice survived until day 22. Only 30% of the mice infected with C9M1 died between day 23 and 30. The isolates recovered from the dead mice were found to be proteinase sufficient, indicating that the mice died after the organism in tissue had reverted. The C9M1M isolate produced proteinase in vitro at 44% the level of C9 and induced fatal infection in 90% of the mice within 30 days. The number of CFU recovered from the kidneys correlated with the level of proteinase produced in vitro and, in turn, the rate of fatal infection produced by the isolates. These results support a previous observation indicating that proteinase activity is one of the virulence factors associated with C. albicans.
Two-dimensional measurement of the prompt-gamma distribution for proton dose distribution monitoring (2013)

In proton therapy, accurate monitoring of the in-vivo proton dose distribution is essential in order to deliver the planned dose to the tumor volume within a minimal safety margin. Recently, a strong correlation between the distributions of the proton dose and the prompt gammas was found, and various prompt-gamma distribution-measurement systems, including collimation-based systems, Compton cameras, knife-edge imaging systems, and ion vertex imaging systems, have been proposed. In the present study, the feasibility of proton dose distribution monitoring was tested using a two-dimensional measurement system for prompt gammas. The measurement system, developed in the present study, incorporates a vertically-aligned one-dimensional array of gamma sensors, a parallel multi-hole collimator, a precision movement system, and a digitizer- and LabVIEW-based automatic data acquisition system. A 45-MeV proton beam of 0.5 nA was delivered to a polymethyl methacrylate (PMMA) phantom, and the two-dimensional prompt-gamma distribution was measured using the developed system. The proton beam range could be quantitatively determined to within a 1.6-mm error by sigmoidal curve-fitting with the Boltzmann equation. A comparison of the prompt-gamma distribution as measured by our detection system with the proton dose distribution as measured independently by using Gafchromic EBT films positioned inside the PMMA phantom showed good agreement. Both results imply that it is, indeed, possible to confirm the patient’s proton dose distribution by using two-dimensional prompt-gamma measurements.
Solubilization and affinity purification of the alpha 2-macroglobulin receptor from human fibroblasts. (1984)

Plasma membranes showing specific binding of alpha 2-macroglobulin (alpha 2M) complexes were isolated from normal human fibroblasts. The membrane preparation was solubilized with Triton X-100, and specific binding to solubilized receptor was demonstrated by precipitation of the alpha 2M X protease receptor complexes with polyethylene glycol. The solubilized receptor could be quantitatively adsorbed on immobilized alpha 2M complexes. Adsorbed receptor was then dissociated from the alpha 2M complexes with either EDTA, bacitracin, the monoclonal anti-receptor-recognition site antibody F2B2 , or low pH. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the affinity-purified receptor preparation revealed polypeptides of 360, 130, and 83 kDa.
An Enzyme‐Linked Antiglobulin Test to Quantify Nanogram Quantities of IgG on Polystyrene Microspheres (1992)

A method is described in which polystyrene latex beads are used for constructing standard curves to estimate the number of protein molecules on cell surfaces by an enzyme-liked immunoassay test (ELAT). A series of immune globulin (IgG) dilutions in pH 9.8 carbonate buffer were coated on 3-microns microbeads by incubation overnight at 4 degrees C and subjected to ELAT. The r value of the curve derived from four assays was 0.9991. This standard curve applied to previously recorded ELAT data resulted in estimating that normal RBC have 63 +/- 19 (SD) IgG molecules and that the lower level of sensitivity of the antiglobulin test is 155 IgG molecules per RBC. The method should be useful for more precise standardization of procedures for measuring proteins on cell surfaces.
Antioxidants: A Possible Role in Kidney Protection (2003)

Oxidative stress contributes to the pathophysiology of kidney injury. Beneficial renal effects of some medications, such as angiotensin-converting enzyme inhibitors, angiotensin II type 1 receptor antagonists, calcium channel blockers, beta-blockers and lipid lowering agents depend at least partially on the ability to alleviate oxidative stress. The administration of various natural or synthetic antioxidants has been shown to be of benefit in prevention and attenuation of renal scaring in numerous animal models of kidney diseases. These include vitamins, N-acetylcysteine, alpha-lipoic acid, melatonin, dietary flavonoids and phytoestrogens, and many others. Human studies are limited in this regard. Under certain conditions, surprisingly, the antioxidant supplements may exhibit pro-oxidant properties and even worsen renal damage. To date, the evidence is insufficient to recommend antioxidant supplements in patients with kidney disease. Prospective, controlled clinical trials on safety and effectiveness of different therapeutic antioxidant strategies are indispensable.
Education for practical anesthesia (1994)

Department of Anesthesia, University Hospital, The Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA W. Bosseau Murray, Department of Anesthesia, University Hospital, The Milton S. Hershey Medical Center, P.O. Box 850, Hershey, PA 17033, USA.
Routing Symmetric Demands in Directed Minor-Free Graphs with Constant Congestion (2019)

The problem of routing in graphs using node-disjoint paths has received a lot of attention and a polylogarithmic approximation algorithm with constant congestion is known for undirected graphs [Chuzhoy and Li 2016] and [Chekuri and Ene 2013]. However, the problem is hard to approximate within polynomial factors on directed graphs, for any constant congestion [Chuzhoy, Kim and Li 2016]. Recently, [Chekuri, Ene and Pilipczuk 2016] have obtained a polylogarithmic approximation with constant congestion on directed planar graphs, for the special case of symmetric demands. We extend their result by obtaining a polylogarithmic approximation with constant congestion on arbitrary directed minor-free graphs, for the case of symmetric demands.
Resonance Light Scattering in Dye-Aggregates Forming in Dewetting Droplets (2014)

Small organic semiconducting molecules assembling into supramolecular J- and H- aggregates have attracted much attention due to outstanding optoelectronic properties. However, their easy and reproducible fabrication is not yet sufficiently developed for industrial applications, except for silver halide photography. Here we present a method based on aggregate precipitation during the phase separation and dewetting of the evaporating dye precursor solution. The smaller the precursor droplets, the more pronounced the J-aggregation. The aggregates cause the films to resonantly scatter incoming light. Because the dye aggregate extinction resonances have narrowest bandwidths, a wavelength selectivity is observed that exceeds the selectivity of localized surface plasmon resonances. The aggregation mechanism can be easily applied to periodically structured substrates, making the method appealing for photonic applications. We demonstrate this point with a 2D grating, where the narrow absorption range of the aggregates leads to wavelength specific (one color only) scattering.
S3352 Immune Checkpoint Inhibitor-Mediated Colitis Is Associated With Improved Cancer Overall Survival (2021)

Introduction: Immune checkpoint inhibitor-mediated colitis (IMC) is a common adverse event following immune checkpoint inhibitor (ICI) therapy for cancer. IMC has been associated with improved overall survival (OS) and progression-free survival (PFS), but data are limited to a single site and predominantly for melanoma patients. We sought to determine the association of IMC with OS and PFS and identify clinical predictors of IMC. Methods: We performed a retrospective case-control study including 64 ICI users who developed IMC matched according to age, sex, ICI class, and malignancy to a cohort of ICI users without IMC. We collected data on clinical characteristics and progression-free survival in both cohorts. Using univariate and multivariate logistic regression, we determined association of presence of IMC on OS, PFS, and clinical predictors of IMC. Kaplan-Meier curves were generated to compare OS and PFS between ICI users with and without IMC. Results: IMC was significantly associated with a higher OS (mean 24.3 months versus 17.7, p = 0.05) but not PFS (mean 13.7 months versus 11.9, p = 0.524). IMC was significantly associated with OS greater than 12 months (Odds ratio [OR] 2.81, 95% confidence interval [CI] 1.17-6.77). Vitamin D supplementation was significantly associated with increased risk of IMC (OR 2.48, 95% CI 1.01-6.07). Conclusion: IMC was significantly associated with improved OS and with OS greater than 12 months. In contrast to prior work, we found that vitamin D use may be a risk factor for IMC.Figure 1.: Kaplan-Meier curves of overall and progression-free survival in patients with and without IMC. A) Overall survival in patients with and without IMC. B) Progression-free survival in patients with and without IMC. IMC, immune checkpoint inhibitor-mediated colitis. HR, hazard ratio. CI, confidence interval.Table 1.: Univariate and Multivariate Predictors of IMC Among Patients Using ICI (N=128).
Reactive removal of surface oxygen by H2, CO and CO/H2 on a Au/CeO2 catalyst and its relevance to the preferential CO oxidation (PROX) and reverse water gas shift (RWGS) reaction (2014)

CO and H<sub>2</sub> compete for the same active surface (lattice) oxygen species, but with a much lower reduction efficiency of H<sub>2</sub> compared to CO and CO–H<sub>2</sub> mixtures, during removal of active oxygen from a Au/CeO<sub>2</sub> catalyst by H<sub>2</sub>, CO or CO/H<sub>2</sub> at temperatures between 30 and 300 °C.
Parallelization of Fast Monte Carlo Dose Calculation for Radiotherapy Treatment Planning on the ARMv8 Architecture (2021)

Monte Carlo (MC) simulation plays a key role in radiotherapy. Since the simulation time of the MC program cannot fully meet the clinical requirements, we use the ARM-based FT-2000+ multi-core processor for parallelization, which provides an effective solution for accelerating MC dose calculation. In this paper, we implement and verify FT-DPM, which is an OpenMP-based MC Dose Planning Method on FT-2000+. FT-DPM utilizes the parallelism of MC simulation and the advantage of ARM architecture to achieve the parallelization on ARM architecture. Meanwhile, we optimize the original DPM program in terms of memory allocation, data structure and data type. The experiments show that, compared with the original DPM code, FT-DPM obtains very accurate results and reaches the maximum speedups of 155.94 times for the electron case. The parallel program based on FT-2000+ only takes 44.1 seconds to simulate the particle transport of 100 million times, showing good clinical application potential. In addition, the speedup and efficiency of FT-DPM running on different core counts are also discussed.
The production of laminar fields with permanent magnets (1987)

With the increasing demands upon millimeter/microwave devices with regard to miniaturization, power, frequency range, etc., there have arisen requirements for strong (kOe) magnetic fields of unusual shape, confined to small regions by permanent magnetic configurations of minimal bulk. The present work describes several novel permanent magnet structures that produce uniform fields of up to several kOe confined to spaces with thicknesses an order of magnitude smaller than the other two dimensions. Such structures are potentially useful for focusing ribbonlike electron beams in devices such as orotrons. The structural principles used to accomplish this can also be used to shorten long, but efficient, (permanent magnet) transverse field sources, without loss of field strength or incurrence of flux leakage. Examples of proposed structures are discussed and analyzed.
<title>Surface acoustic wave sensor array system for trace organic vapor detection using pattern recognition analysis</title> (1993)

A sensor system using surface acoustic wave (SAW) vapor sensors has been fabricated and tested against hazardous organic vapors, simulants of these vapors, and potential background vapors. The vapor tests included two- and three-component mixtures, and covered a wide relative humidity range. The sensor system was compared of four SAW devices coated with different sorbent materials with different vapor selectivities. Preconcentrators were included to improve sensitivity. The vapor experiments were organized into a large data set analyzed using pattern recognition techniques. Pattern recognition algorithms were developed to identify two different classes of hazards. The algorithms were verified against a second data set not included in the training. Excellent sensitivity was achieved by the sensor coatings, and the pattern recognition analysis, and was also examined by the preconcentrators. The system can detect hazardous vapors of interest in the ppb range even in varying relative humidity and in the presence of background vapors. The system does not false alarm to a variety of other vapors including gasoline, jet fuel, diesel fuel and cigarette smoke.
Responsive Mesoporous Photonic Cellulose Films by Supramolecular Cotemplating (2014)

Abstract Cellulose‐based materials have been and continue to be exceptionally important for humankind. Considering the bioavailability and societal relevance of cellulose, turning this renewable resource into an active material is a vital step towards sustainability. Herein we report a new form of cellulose‐derived material that combines tunable photonic properties with a unique mesoporous structure resulting from a new supramolecular cotemplating method. A composite of cellulose nanocrystals and a urea–formaldehyde resin organizes into a chiral nematic assembly, which yields a chiral nematic mesoporous continuum of desulfated cellulose nanocrystals after alkaline treatment. The mesoporous photonic cellulose (MPC) films undergo rapid and reversible changes in color upon swelling, and can be used for pressure sensing. These new active mesoporous cellulosic materials have potential applications in biosensing, optics, functional membranes, chiral separation, and tissue engineering.
Control of Breathing by Raphe Obscurus Serotonergic Neurons in Mice (2011)

We used optogenetics to determine the global respiratory effects produced by selectively stimulating raphe obscurus (RO) serotonergic neurons in anesthetized mice and to test whether these neurons detect changes in the partial pressure of CO(2), and hence function as central respiratory chemoreceptors. Channelrhodopsin-2 (ChR2) was selectively (∼97%) incorporated into ∼50% of RO serotonergic neurons by injecting AAV2 DIO ChR2-mCherry (adeno-associated viral vector double-floxed inverse open reading frame of ChR2-mCherry) into the RO of ePet-Cre mice. The transfected neurons heavily innervated lower brainstem and spinal cord regions involved in autonomic and somatic motor control plus breathing but eschewed sensory related regions. Pulsed laser photostimulation of ChR2-transfected serotonergic neurons increased respiratory frequency (fR) and diaphragmatic EMG (dEMG) amplitude in relation to the duration and frequency of the light pulses (half saturation, 1 ms; 5-10 Hz). dEMG amplitude and fR increased slowly (half saturation after 10-15 s) and relaxed monoexponentially (tau, 13-15 s). The breathing stimulation was reduced ∼55% by methysergide (broad spectrum serotonin antagonist) and potentiated (∼16%) at elevated levels of inspired CO(2) (8%). RO serotonergic neurons, identified by their entrainment to short light pulses (threshold, 0.1-1 ms) were silent (nine cells) or had a low and regular level of activity (2.1 ± 0.4 Hz; 11 cells) that was not synchronized with respiration. These and nine surrounding neurons with similar characteristics were unaffected by adding up to 10% CO(2) to the breathing mixture. In conclusion, RO serotonergic neurons activate breathing frequency and amplitude and potentiate the central respiratory chemoreflex but do not appear to have a central respiratory chemoreceptor function.
DescribePSP and ProPSP: German Multicenter Networks for Standardized Prospective Collection of Clinical Data, Imaging Data, and Biomaterials of Patients With Progressive Supranuclear Palsy (2021)

Background: The German research networks DescribePSP and ProPSP prospectively collect comprehensive clinical data, imaging data and biomaterials of patients with a clinical diagnosis of progressive supranuclear palsy. Progressive supranuclear palsy is a rare, adult-onset, neurodegenerative disease with striking clinical heterogeneity. Since now, prospective natural history data are largely lacking. Clinical research into treatment strategies has been limited due to delay in clinical diagnosis and lack of natural history data on distinct clinical phenotypes. Methods: The DescribePSP network is organized by the German Center for Neurodegenerative Diseases. DescribePSP is embedded in a larger network with parallel cohorts of other neurodegenerative diseases and healthy controls. The DescribePSP network is directly linked to other Describe cohorts with other primary diagnoses of the neurodegenerative and vascular disease spectrums and also to an autopsy program for clinico-pathological correlation. The ProPSP network is organized by the German Parkinson and Movement Disorders Society. Both networks follow the same core protocol for patient recruitment and collection of data, imaging and biomaterials. Both networks host a web-based data registry and a central biorepository. Inclusion/exclusion criteria follow the 2017 Movement Disorder Society criteria for the clinical diagnosis of progressive supranuclear palsy. Results: Both networks started recruitment of patients by the end of 2015. As of November 2020, N = 354 and 269 patients were recruited into the DescribePSP and the ProPSP studies, respectively, and N = 131 and 87 patients received at least one follow-up visit. Conclusions: The DescribePSP and ProPSP networks are ideal resources for comprehensive natural history data of PSP, including imaging data and biological samples. In contrast to previous natural history studies, DescribePSP and ProPSP include not only patients with Richardson's syndrome, but also variant PSP phenotypes as well as patients at very early disease stages, before a diagnosis of possible or probable PSP can be made. This will allow for identification and evaluation of early biomarkers for diagnosis, prognosis, and progression.
Evaluating hand‐held radiometer derived vegetation indices for estimating above ground biomass (1992)

Abstract The potential for using vegetation indices developed from remote sensing devices, such as the GSFC Mark‐II hand‐held radiometer, to evaluate biomass has been examined in a number of studies. Relationships range from very good (r2=0.96) to very poor (r2=0.029). One problem with most of the studies is that the data were only collected during a single year, therefore, the usefulness of the relationships within and between years is difficult to evaluate. This study examined the usefulness of vegetation indices, calculated from data gathered by the GSFC Mark‐II radiometer, in assessing the amount of biomass on native grasslands. Vegetation indices derived from data gathered over two years (1989 and 1990) and during four periods throughout each growing season indicate that the ratio between near‐infrared and red spectral responses (ratio vegetation index) performed better then either the difference between the two bands or the normalized difference vegetation indices. Poor relationships were observed (r2=0.07 to r2=0.44) with the best relationships occurring in June and July. Results suggest a high degree of influence by the dead plant component and environmental factors such as sun angle, soil albedo, and atmospheric conditions. Further analysis is needed to evaluate indices acquired by other sources such as airborne‐multiband video and Landsat Thematic‐Mapper data.
Tail-labelling of DNA probes using modified deoxynucleotide triphosphates and terminal deoxynucleotidyl tranferase. Application in electrochemical DNA hybridization and protein-DNA binding assays (2011)

A simple approach to DNA tail-labelling using terminal deoxynucleotidyl transferase and modified deoxynucleoside triphosphates is presented. Amino- and nitrophenyl-modified dNTPs were found to be good substrates for this enzyme giving 3'-end stretches of different lengths depending on the nucleotide and concentration. 3-Nitrophenyl-7-deazaG was selected as the most useful label because its dNTP was efficiently incorporated by the transferase to form long tail-labels at any oligonucleotide. Accumulation of many nitrophenyl tags per oligonucleotide resulted in a considerable enhancement of voltammetric signals due to the nitro group reduction, thus improving the sensitivity of electrochemical detection of the tail-labelled probes. We demonstrate a perfect discrimination between complementary and non-complementary target DNAs sequences by tail-labelled hybridization probes as well as the ability of tumour suppressor p53 protein to recognize a specific binding site within tail-labelled DNA substrates, making the methodology useful in electrochemical DNA hybridization and DNA-protein interaction assays.
VIPER: an advanced software package to support high-throughput LC-MS peptide identification (2007)

VIPER may be downloaded free of charge at http://ncrr.pnl.gov/software/
Determining Risk for Severe Leptospirosis by Molecular Analysis of Environmental Surface Waters for Pathogenic Leptospira (2006)

Our findings data support the hypothesis that urban severe leptospirosis in the Peruvian Amazon is associated with higher concentrations of more pathogenic leptospires at sites of exposure and transmission. This combined quantitative and molecular taxonomical risk assessment of environmental surface waters is globally applicable for assessing risk for leptospiral infection and severe disease in leptospirosis-endemic regions.