gebhart/patrepeval huggingface dataset:
Commercial Serology Assays Predict Neutralization Activity Against SARS-CoV-2 (2020)

Abstract Background Currently it is unknown whether a positive serology results correlates with protective immunity against SARS-CoV-2. There are also concerns regarding the low positive predictive value of SARS-CoV-2 serology tests, especially when testing populations with low disease prevalence. Methods A neutralization assay was validated in a set of PCR confirmed positive specimens and in a negative cohort. 9,530 specimens were screened using the Diazyme SARS-CoV-2 IgG serology assay and all positive results (N=164) were reanalyzed using the neutralization assay, the Roche total immunoglobin assay, and the Abbott IgG assay. The relationship between the magnitude of a positive SARS-CoV-2 serology result and the levels of neutralizing antibodies detected was correlated. Neutralizing antibody titers (ID50) were also longitudinally monitored in SARS-CoV-2 PCR confirmed patients. Results The SARS-CoV-2 neutralization assay had a PPA of 96.6% with a SARS-CoV-2 PCR test and a NPA of 98.0% across 100 negative controls. ID50 neutralization titers positively correlated with all three clinical serology platforms. Longitudinal monitoring of hospitalized PCR confirmed COVID-19 patients demonstrates they made high neutralization titers against SARS-CoV-2. PPA between the Diazyme IgG assay alone and the neutralization assay was 50.6%, while combining the Diazyme IgG assay with either the Roche or Abbott platforms increased the PPA to 79.2% and 78.4%, respectively. Conclusions For the first time, we demonstrate that three widely available clinical serology assays positively correlate with SARS-CoV-2 neutralization activity observed in COVID-19 patients. When a two-platform screen and confirm approach was used for SARS-CoV-2 serology, nearly 80% of two-platform positive specimens had neutralization titers (ID50 &gt;50). Summary Clinical performance of a SARS-CoV-2 neutralization assay was evaluated using SARS-CoV-2 PCR confirmed patients and SARS-CoV-2 negative individuals. The neutralization assay was compared with results from SARS-CoV-2 positive serology specimens. We demonstrate that positive SARS-CoV-2 serology results correlate with the presence of neutralization activity against SARS-CoV-2. We show a high false positive rate when using a single SARS-CoV-2 serology platform to screen populations with low disease prevalence; and confirm that using a two-platform approach for COVID-19 seropositives greatly improves positive predictive value for neutralization.
Preface (2008)

ADVERTISEMENT RETURN TO BOOKPREVPrefaceNEXTPrefaceHirotoshi TamuraHirotoshi TamuraDepartment of Biochemistry and Food Science Kagawa University 2393 Miki-Cho Kita-Gun Kagawa 761-0795 JapanMore by Hirotoshi Tamura, Susan E. EbelerSusan E. EbelerDepartment of Viticulture and Enology University of California One Shields Avenue Davis, CA 95616More by Susan E. Ebeler, Kikue KubotaKikue KubotaLaboratory of Food Chemistry Department of Nutrition and Food Science Ochanomizu University 2-1-1 Otsuka Bunkyo-ku Tokyo 112-8610 JapanMore by Kikue Kubota, and Gary R. TakeokaGary R. TakeokaWestern Regional Research Center Agricultural Research Service U.S. Department of Agriculture 800 Buchanan Street Albany, CA 94710More by Gary R. TakeokaDOI: 10.1021/bk-2008-0988.pr001 This publication is free to access through this site. Learn MorePublication Date (Print):September 30, 2008Publication History Published online23 July 2009Published inprint 30 September 2008Request reuse permissions Copyright © 2008 American Chemical Society. This publication is available under these Terms of Use. Food Flavorpp xi-xiiiACS Symposium SeriesVol. 988ISBN13: 9780841274112eISBN: 9780841221314Chapter Views355Citations-LEARN ABOUT THESE METRICSChapter Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (276 KB) Get e-Alerts
Synthesis and Characterization of (Et4N)4[MoS4Cu10Cl12]:  A Polynuclear Molybdenum−Copper Cluster Containing a Central Tetrahedral MoS4 Encapsulated by Octahedral Cu6 and Tetrahedral Cu4 Arrays (1996)

A novel polynuclear Mo−Cu cluster compound (Et4N)4[MoS4Cu10Cl12] has been synthesized by the reaction of (NH4)2[MoS4], Et4NCl, and CuCl in acac/DMSO. The reaction mechanism has been monitored by dynamic 95Mo NMR spectra. X-ray single-crystal diffraction analysis reveals that the anion structure consists of a central MoS4 moiety, an octahedral Cu6 array and a tetrahedral Cu4 array, representing the addition of 10 copper atoms across the six edges and four faces of MoS4 tetrahedron. The average Mo−Cu and Mo−S distances are 2.708(8) and 2.238(7) Å, respectively.
Virtual Surgery : a Computational Engineering Approach to a Medical Problem (2010)

The aim of the study is to utilize Computational Fluid Dynamics in the process of planning surgical treatment modalities for patients with obstructive airway disorders. It is hypothesized that the ...
Doctoral Fellowships in Physical Optics (1988)

Abstract : The scattering of laser light from a single diffuser and from a cascade of two diffusers is analyzed with particular emphasis on remote sensing. It is shown that diffuser surface properties and the spacing between diffuser planes can be determined remotely. Conceptually, one measures the angular distribution of the radiation pattern or the decorrelation of the far-zone speckle pattern with respect to changes in the wavelength or the angle of incidence of an input plane wave. Keywords: Laser speckle, Cascaded diffusers, Remote sensing, Diffuser surface properties.
THE VALUE OF IMMUNOFLUORESCENCE IN THE STUDY OF HUMAN RENAL DISEASE (1971)

Immunofluorescence is a useful technique in the study of human renal diseases, both from the point of view of elucidating pathogenic mechanisms and as a diagnostic tool. The finding of characteristic staining patterns for immunoglobulins and complement indicates that many forms of glomerulonephritis are immune complex diseases and that a few are due to anti-GBM antibodies. On the other hand, in lipoid nephrosis and toxemia of pregnancy, deposits of immunoglobulins and complement are generally absent, indicating that immunologic mechanisms are probably not responsible for these glomerular diseases. The finding of fibrin or other fibrinogen derivatives in glomeruli in toxemia of pregnancy and in certain forms of glomulonephritis supports the interpretation that these substances play a pathogenic role in certain glomerular diseases. The use of immunofluorescence has led to the recognition of two previously unrecognized renal diseases: nephropathy with mesangial IgA-IgG deposits (Berger), and a tubular disorder with deposits of immunoglobulins and complement along the basement membrane.
The Effect of fuel and poison management on nuclear power systems (2014)

Statement of responsibility on title page reads: N.B. McLeod, M. Benedict, K. Uematsu, H.L. Witting, and K.S. Ram
Molecularly imprinted polymers for the extraction of imiquimod from biological samples using a template analogue strategy (2013)

Molecularly Imprinted Polymers (MIPs) against imiquimod, a highly potent immune response modifier used in the treatment of skin cancer, were synthesised using a template analogue strategy and were compared with imprints of the drug itself. An investigation of the complexation between the functional monomer and the template analogue revealed an association constant of 1376 ± 122 M−1, significantly higher than previously reported values for similar systems. The binding characteristics of the synthesised imprinted polymers were evaluated and extremely strong binding for imiquimod was observed while imprinting factors as high as 17 were calculated. When applied as sorbents in solid-phase extraction of imiquimod from aqueous, urine and blood serum samples, clean extracts and recoveries up to 95% were achieved, and it is concluded that while imiquimod imprints exhibited higher capacity for the drug, template analogue imprints are more selective. The results obtained suggest potential applications of imiquimod imprints as sorbents in rapid extraction and monitoring of undesirable systemic release of the drug.
Vapor intrusion in urban settings: effect of foundation features and source location (2011)

In many urban settings, groundwater contains volatile organic compounds, such as tricholoroethene, tetrachloroethene, benzene, etc., at concentrations that are at or slightly below non-potable groundwater standards. Some non-potable groundwater standards do not protect against human health risks that might result from vapor intrusion. Vapor intrusion is a process by which vapor phase contaminants present in the subsurface migrate through the soil and ultimately enter a building through foundation cracks. The end result is a decrease in air quality within the building. Predicting whether or not vapor intrusion will occur at rates sufficient to cause health risks is extremely difficult and depends on many factors. In many cities, a wide-range of property uses take place over a relatively small area. For instance, schools, commercial buildings and residential buildings may all reside within a few city blocks. Most conceptual site models assume the ground surface is open to the atmosphere (i.e. green space); however the effect that an impervious surface (e.g. paving) may have on vapor transport rates is not routinely considered. Using a 3-D computational fluid dynamics model, we are investigating how the presence of impervious surfaces affects vapor intrusion rates. To complement our modeling efforts, we are in the initial stages of conducting a field study in a neighborhood where vapor intrusion is occurring.
Differential diagnosis of familial adult myoclonic epilepsy (2023)

Recognition of FAME will inform prognostic and genetic counseling and diagnosis of the insidious progression, which may occur in older individuals who show mild cognitive deterioration. Distinguishing FAME from other disorders in individuals or families with this constellation of symptoms is essential to allow the identification of underlying etiology.
The catalytic domain of the cGMP‐dependent protein kinase Iα modulates the cGMP‐binding characteristics of its regulatory domain (1996)

The cGMP-dependent protein kinase Ialpha (PKG Ialpha) possesses two functional moieties, the regulatory and catalytic domains, which reside on a single polypeptide chain. Here we report on the influence of the catalytic domain on the binding of cGMP to the regulatory domain. A deletion mutant, delta352-670 of PKG Ialpha, lacking the catalytic domain, was constructed and expressed in E. coli. The purified 38 kDa mutant protein showed strong reactivity toward tryptic proteolysis at residue Arg77. Thus, a double deletion fragment delta1-77/352-670 PKG Ialpha, lacking the N-terminus, was also purified. Both proteins had functional cGMP binding, but differed kinetically from the wild-type protein. First the affinity constants for cGMP were modulated, second the constructs showed no signs of cooperative cGMP binding and third dimerization of the delta352-670 mutant was abolished. Our results provide evidence that the catalytic domain forms an intimate interaction with the regulatory domain and modulates the kinetics of cGMP binding.
The Role of Peripheral Nerve Surgery in the Treatment of Chronic Pain Associated with Amputation Stumps (2008)

Peripheral nerve surgery plays a significant role in the treatment of chronic pain associated with amputation stumps. After conservative treatment methods have been exhausted, a treatment algorithm for peripheral nerve surgery is successful in improving or resolving chronic pain and the quality-of-life issues associated with amputation patients.
Severe and Extensive Enteritis following Colectomy for Ulcerative Colitis (2012)

U lcerative colitis is an inflammatory condition usually confined to the colonic mucosa. However, inflammatory changes have been recorded in the small bowel with ulcerative colitis, specifically in ileal pouch mucosa after colectomy (ie, 'pouchitis') or in the terminal ileum with severe pancolitis (ie, 'backwash ileitis'). There have also been rare previous reports of a more diffuse and distinctive form of diffuse and extensive enteritis following total colectomy that responded to steroids or calcineurin inhibitor use (1-3). Rarely, a fatal form of diffuse enteritis following colectomy has been described (4,5). We report a dramatic presentation of severe steroid-resistant panenteritis in a patient three months after total colectomy for severe ulcerative colitis that responded to tacrolimus.
Getting Cold and Prickly on Saltland Extension (2009)

Teaching/Communication/Extension/Profession
Multiscale analysis of Galactic dust emission using complex wavelet transforms – I. Separation of Gaussian and non-Gaussian fluctuations in Herschel observations (2014)

We use anisotropic complex wavelet transforms to make a multiscale analysis of the distribution of fluctuations of dust emission at 250 μm from the Herschel infrared Galactic Plane Survey of the Herschel Space Observatory. By reproducing the Fourier power spectrum with complex wavelet transforms we show that different power distributions at each scale can have a significant effect on the measured power law. Moreover, with an iterative algorithm we separate the Gaussian and non-Gaussian part of wavelet coefficient distributions in each scale and azimuthal direction. The reconstructed map of non-Gaussian fluctuations is well correlated to small-scale structures of the 13CO emission map as well as its power spectrum which has a power-law index of −2.3. The Gaussian part of the map shows more diffuse structures with a steeper power law of −3.1. Non-Gaussian coefficients are almost undetectable at scales greater than ∼0.15 arcmin−1 (∼4–26 pc). This characteristic scale could be associated with the size of the larger molecular cloud in the region. We also demonstrate that exponentiated Gaussian random field cannot reproduce the flatter power law of the non-Gaussian component observed in the thermal dust emission, which seems to be a property of interstellar clouds.
Recommendations for whole genome sequencing in diagnostics for rare diseases (2022)

In 2016, guidelines for diagnostic Next Generation Sequencing (NGS) have been published by EuroGentest in order to assist laboratories in the implementation and accreditation of NGS in a diagnostic setting. These guidelines mainly focused on Whole Exome Sequencing (WES) and targeted (gene panels) sequencing detecting small germline variants (Single Nucleotide Variants (SNVs) and insertions/deletions (indels)). Since then, Whole Genome Sequencing (WGS) has been increasingly introduced in the diagnosis of rare diseases as WGS allows the simultaneous detection of SNVs, Structural Variants (SVs) and other types of variants such as repeat expansions. The use of WGS in diagnostics warrants the re-evaluation and update of previously published guidelines. This work was jointly initiated by EuroGentest and the Horizon2020 project Solve-RD. Statements from the 2016 guidelines have been reviewed in the context of WGS and updated where necessary. The aim of these recommendations is primarily to list the points to consider for clinical (laboratory) geneticists, bioinformaticians, and (non-)geneticists, to provide technical advice, aid clinical decision-making and the reporting of the results.
Evaluation de la charge de travail réelle des étudiants : outil d’objectivation et de réflexion et de régulation pour les enseignants (2009)

Depuis 2000, l’Ecole Polytechnique de Louvain (EPL) a mis en place un programme en pédagogie active pour les premières années de son programme. A l’occasion des réunions de concertation entre étudiants et enseignants, les étudiants se plaignent d’une surcharge de travail. De leur côté, certains enseignants estiment que les étudiants ne s’impliquent pas assez dans leur cours au profit d’autres disciplines. Une enquête a été menée durant tout le premier quadrimestre de la première année en vue de quantifier la charge de travail réelle des étudiants et de la comparer avec les estimations des enseignants. Les intérêts de cette enquête sont multiples : (1) elle permet d’objectiver les perceptions des étudiants sur leur charge de travail, (2) elle constitue un outil de coordination efficace pour l’équipe d’enseignants en charge du quadrimestre et (3) elle permet d’initier une régulation-réflexion individuelle de chaque enseignant face à l’enseignement dont il est responsable.
Genome Editing accelerated Re-Domestication” (GEaReD) – a new major direction in plant breeding (2021)

The effects of climate change, soil depletion, a growing world population putting pressure on food safety and security are major challenges for agriculture in the 21st century. The breeding success of the green revolution has decelerated and current programs can only offset the yield affecting factors. New approaches are urgently needed and we propose, “Genome Editing accelerated Re-Domestication” (GEaReD) as a major new direction in plant breeding. By combining the upcoming technologies for phenotyping, omics and artificial intelligence with the promising new CRISPR-toolkits, this approach is closer than ever. Wild relatives of current crops are often adapted to harsh environments and have a high genetic diversity. Re-domestication of wild barley or teosinte could generate new cultivars adapted to environmental changes. De novo domestication of perennial relatives like Hordeum bulbosum could counter with soil depletion and increase soil carbon. Recent research already proved the principle of re-domestication in tomato and rice and therefore laid the foundation for GEaReD.
Measurement of the ratio between the reduced and oxidized forms of coenzyme Q10 in human plasma as a possible marker of oxidative stress. (1996)

It has been postulated that lipid peroxidation plays a crucial role in the pathogenesis of atherosclerosis. As CoQ10H2 (reduced form of coenzyme Q10) is easily oxidized to CoQ10 (oxidized form of coenzyme Q10), it has been proposed that the CoQ10H2/CoQ10 ratio may be used as a possible marker of in vivo oxidative stress. However, sample preparation has an important effect on the redox status of coenzyme Q10 due to the extreme sensitivity of CoQ10H2 towards oxidation. We now report a rapid, simple isocratic HPLC procedure for the determination of CoQ10H2 and CoQ10 in plasma isopropanol extracts, and we used this method to investigate conditions by which the CoQ10H2/CoQ10 ratio can be reliably measured. Our results indicate that CoQ10H2 is unstable in whole blood, plasma, and isopropanol extracts; subsequently the CoQ10H2/CoQ10 ratio changes considerably soon after a blood sample has been obtained. The time period since blood sampling and HPLC analysis, as well as the sample pretreatment procedure, are two factors that have a profound effect on the pre-analytical variation in the determination of the CoQ10H2/CoQ10 ratio. If these two factors are properly controlled, the CoQ10H2/CoQ10 ratio may be a sensitive and practical way to measure in vivo oxidative stress. Furthermore, this indicator is independent from plasma total cholesterol concentrations, implying that groups who differ with respect to cholesterol levels may be compared directly.
Dendritic cell-derived exosomes in cancer immunotherapy: exploiting nature’s antigen delivery pathway (2005)

Dendritic cells release large quantities of exosomes, known as dexosomes. These dexosomes are heat-stable, small vesicles (60-90 nm in diameter) made up of a lipid bilayer displaying an enrichment in sphingomyelin and a decrease in phosphatidylcholine content with no measurable asymmetry. They incorporate a characteristic set of proteins, including a large quantity of tetraspanins such as CD9 and CD81, all the known antigen presenting molecules (major histocompatibility complex class I and II, CD1 a, b, c and d) and the costimulatory molecule CD86. The function of dexosomes is to transfer antigen-loaded major histocompatibility complex class I and II molecules, and other associated molecules, to naive dendritic cells, potentially leading to the amplification of the cellular immune response. In preclinical mouse models, antigen-loaded dexosomes elicit strong antitumor activity. Human dexosomes can be prepared ex vivo relatively easily from dendritic cells derived from monocytes isolated by leukapheresis of healthy individuals or cancer patients. The feasibility of using dexosomes as a cancer therapeutic vaccine has been tested in two Phase I clinical studies in melanoma and lung cancer patients, respectively. These studies demonstrate that dexosomes can be prepared from cancer patient blood cells and be safely administered. Clinical observations suggested that dexosomes can stimulate both the adaptive (T-cells) and innate (natural killer cells) cellular immune responses. This review focuses on the perspective of using dexosomes in cancer immunotherapy. Concepts for using the exosome pathway in other possible pharmacologic applications are also discussed.
Method for loading resin beds (2023)

An improved method of preparing nuclear reactor fuel by carbonizing a uranium loaded cation exchange resin provided by contacting a H.sup.+ loaded resin with a uranyl nitrate solution deficient in nitrate, comprises providing the nitrate deficient solution by a method comprising the steps of reacting in a reaction zone maintained between about 145.degree.-200.degree. C, a first aqueous component comprising a uranyl nitrate solution having a boiling point of at least 145.degree. C with a second aqueous component to provide a gaseous phase containing HNO.sub.3 and a reaction product comprising an aqueous uranyl nitrate solution deficient in nitrate.
Images of photoreceptors in living primate eyes using adaptive optics two-photon ophthalmoscopy (2010)

In vivo two-photon imaging through the pupil of the primate eye has the potential to become a useful tool for functional imaging of the retina. Two-photon excited fluorescence images of the macaque cone mosaic were obtained using a fluorescence adaptive optics scanning laser ophthalmoscope, overcoming the challenges of a low numerical aperture, imperfect optics of the eye, high required light levels, and eye motion. Although the specific fluorophores are as yet unknown, strong in vivo intrinsic fluorescence allowed images of the cone mosaic. Imaging intact ex vivo retina revealed that the strongest two-photon excited fluorescence signal comes from the cone inner segments. The fluorescence response increased following light stimulation, which could provide a functional measure of the effects of light on photoreceptors.
Energy dissipation in tapping-mode scanning force microscopy with low quality factors (1999)

The phase angle of the cantilever oscillation in tapping mode scanning force microscopy can be related to the energy dissipated per oscillation period through an analytical model that assumes a sinusoidal movement of the cantilever [J. Tamayo and R. Garcı́a, Appl. Phys. Lett. 73, 2926 (1998); J. P. Cleveland, B. Anczykowski, E. Schmid, and V. Elings, Appl. Phys. Lett. 72, 2613 (1998)]. In this work, numerical calculations of the oscillation of cantilevers with quality factors lower than 10 show a significant contribution of higher harmonics (∼5%–20%). This contribution can lead to a significant error in the energy dissipated deduced by using the model cited above. Thus, an extended relationship between the phase shift and the energy dissipated is presented, that takes into account the higher harmonics of the oscillation. These results determine the conditions for the measurement of energy dissipation in a liquid.