gebhart/patrepeval huggingface dataset:
Protein Identification and Peptide Expression Resolver: Harmonizing Protein Identification with Protein Expression Data (2007)

Proteomic discovery platforms generate both peptide expression information and protein identification information. Peptide expression data are used to determine which peptides are differentially expressed between study cohorts, and then these peptides are targeted for protein identification. In this paper, we demonstrate that peptide expression information is also a powerful tool for enhancing confidence in protein identification results. Specifically, we evaluate the following hypothesis: tryptic peptides originating from the same protein have similar expression profiles across samples in the discovery study. Evidence supporting this hypothesis is provided. This hypothesis is integrated into a protein identification tool, PIPER (Protein Identification and Peptide Expression Resolver), that reduces erroneous protein identifications below 5%. PIPER's utility is illustrated by application to a 72-sample biomarker discovery study where it is demonstrated that false positive protein identifications can be reduced below 5%. Consequently, it is recommended that PIPER methodology be incorporated into proteomic studies where both protein expression and identification data are collected.
An efficient frequency-domain full waveform inversion method using simultaneous encoded sources (2011)

Three-dimensional full waveform inversion (FWI) still suffers from prohibitively high computational costs that arise because of the seismic modeling for multiple sources that is performed at each nonlinear iteration of FWI. Building supershots by assembling several sources allows mitigation of the number of simulations per FWI iteration, although it adds crosstalk artifacts because of interference between the individual sources of the supershots. These artifacts themselves can be reduced by encoding each individual source with a random phase shift during assembling of the sources. The source encoding method is applied to an efficient frequency-domain FWI, in which a limited number of discrete frequencies or coarsely sampled frequency groups are inverted successively following a multiscale approach. Random codes can be regenerated at each FWI iteration or for each frequency of a group during each FWI iteration, to favor the destructive summation of crosstalk artifacts over FWI iterations. Either a limited number of sources (partial assembling) or the total number of sources (full assembling) can be combined into supershots. Wide-aperture acquisition geometries such as land or marine node acquisitions are considered, to allow one to stack a large number of shots in the full computational domain and to test different partial assembling strategies involving sources that are close to or distant from each other. Two-dimensional case studies show that partial-source assembling of distant shots has a limited sensitivity to noise, for a computational saving that is roughly proportional to the number of shots assembled into the supershots. On the other hand, full assembling is more sensitive to noise, and it requires successive inversions of finely sampled frequency groups with a large number of FWI iterations. In contrast, refining the shot interval to improve the fold degrades the models when full assembling is applied to noisy data. Preliminary 3D application of the method leads to the same conclusions that 2D case studies do, with regard to the footprint of crosstalk noise in the imaging.
Hypothesis Testing with Finite Statistics (1969)

Let $X_1, X_2, \cdots$ be a sequence of independent identically distributed random variables drawn according to a probability measure $\mathscr{P}$. The two-hypothesis testing problem $H_0: \mathscr{P} = \mathscr{P}_0 \operatorname{vs.} H_1: \mathscr{P} = \mathscr{P}_1$ is investigated under the constraint that the data must be summarized after each observation by an $m$-valued statistic $T_n\varepsilon \{1, 2, \cdots, m\}$, where $T_n$ is updated according to the rule $T_{n+1} = f_n(T_n, X_{n+1})$. An algorithm with a four-valued statistic is described which achieves a limiting probability of error zero under either hypothesis. It is also demonstrated that a four-valued statistic is sufficient to resolve composite hypothesis testing problems which may be reduced to the form $H_0:p > p_0 \operatorname{vs.} H_1:p < p_0$ where $X_1, X_2, \cdots$ is a Bernoulli sequence with bias $p$.
Antagonistic and agonistic effects of transforming growth factor-beta and IL-1 in rheumatoid synovium. (1990)

We investigated potential mechanisms by which lymphocytes infiltrating rheumatoid synovium become immunosuppressed. In 20 of 22 synovial fluids and 12 of 13 synovial tissue culture supernatants, no IL-1 bioactivity could be detected in the thymocyte proliferation assay. These same preparations could, however, support proliferation of fibroblast monolayers, consistent with the presence of IL-1 and/or other fibroblast growth factors. Addition of either rheumatoid synovial fluids or synovial culture supernatants to exogenous IL-1 in the IL-1 bioassay caused marked inhibition of the assay indicative of an IL-1 inhibitor. This inhibition of IL-1 could be reversed by treating the effusions or supernatants with a neutralizing antibody to transforming growth factor-beta (TGF-beta). Furthermore, monocyte-macrophages isolated from rheumatoid synovial fluid constitutively released both latent and active TGF-beta in culture at levels sufficient to completely block the biologic activity of 100 U/ml IL-1. The production of substantial levels of TGF-beta by synovial macrophages, as well as the apparent ability of these inflammatory macrophages to activate latent TGF-beta, implicates TGF-beta not only as an important inhibitor of IL-1-induced lymphocyte proliferation, but also as a key cytokine in promoting synovial fibroblast hyperplasia and pathology.
Image appraisal for 2D and 3D electromagnetic inversion (1998)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1998Image appraisal for 2D and 3D electromagnetic inversionAuthors: David L. AlumbaughGregory A. NewmanDavid L. AlumbaughSandia National Laboratories, POI Box 5800, MS 0750 Albuquerque, NM 87185 and Gregory A. NewmanSandia National Laboratories, POI Box 5800, MS 0750 Albuquerque, NM 87185https://doi.org/10.1190/1.1820462 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1820462FiguresReferencesRelatedDetailsCited byUncertainty analysis and probabilistic segmentation of electrical resistivity images: the 2D inverse problem12 September 2017 | Geophysical Prospecting, Vol. 65 SEG Technical Program Expanded Abstracts 1998ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1998 Pages: 2092 publication data© 1998 Copyright © 1998 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 06 Jan 2005 CITATION INFORMATION David L. Alumbaugh and Gregory A. Newman, (1998), "Image appraisal for 2D and 3D electromagnetic inversion," SEG Technical Program Expanded Abstracts : 456-460. https://doi.org/10.1190/1.1820462 Plain-Language Summary PDF DownloadLoading ...
Differential Requirements for Hematopoietic Commitment Between Human and Rhesus Embryonic Stem Cells (2007)

Progress toward clinical application of ESC-derived hematopoietic cellular transplantation will require rigorous evaluation in a large animal allogeneic model. However, in contrast to human ESCs (hESCs), efforts to induce conclusive hematopoietic differentiation from rhesus macaque ESCs (rESCs) have been unsuccessful. Characterizing these poorly understood functional differences will facilitate progress in this area and likely clarify the critical steps involved in the hematopoietic differentiation of ESCs. To accomplish this goal, we compared the hematopoietic differentiation of hESCs with that of rESCs in both EB culture and stroma coculture. Initially, undifferentiated rESCs and hESCs were adapted to growth on Matrigel without a change in their phenotype or karyotype. Subsequent differentiation of rESCs in OP9 stroma led to the development of CD34(+)CD45(-) cells that gave rise to endothelial cell networks in methylcellulose culture. In the same conditions, hESCs exhibited convincing hematopoietic differentiation. In cytokine-supplemented EB culture, rESCs demonstrated improved hematopoietic differentiation with higher levels of CD34(+) and detectable levels of CD45(+) cells. However, these levels remained dramatically lower than those for hESCs in identical culture conditions. Subsequent plating of cytokine-supplemented rhesus EBs in methylcellulose culture led to the formation of mixed colonies of erythroid, myeloid, and endothelial cells, confirming the existence of bipotential hematoendothelial progenitors in the cytokine-supplemented EB cultures. Evaluation of four different rESC lines confirmed the validity of these disparities. Although rESCs have the potential for hematopoietic differentiation, they exhibit a pause at the hemangioblast stage of hematopoietic development in culture conditions developed for hESCs.
Bioconjugates of smart polymers and proteins: synthesis and applications (2004)

Abstract Over the past 20 years we have been deeply involved with the synthesis and applications of stimuli‐responsive polymer systems, especially polymer‐biomolecule conjugates. The work of Toyoichi Tanaka has been a constant inspiration for our work and this article is dedicated to him. This article summarizes the research that we have carried out along with many collaborators on polymer‐protein conjugates. We include conjugates prepared by random polymer conjugation to lysine amino groups, and also those prepared by site‐specific conjugation of the polymer to specific amino acid sites that are genetically‐engineered into the known amino acid sequence of the protein. We describe the preparation and properties of thermally‐sensitive, random conjugates to enzymes and several affinity recognition proteins. We have also prepared site‐specific conjugates to streptavidin. with temperature‐sensitive polymers, pH‐sensitive polymers, and light‐sensitive polymers. The preparation of these conjugates and their many fascinating applications are reviewed in this article.
Abstract 4280: Utilizing a selective agonist of the intermediate-affinity IL-2 receptor with an improved pharmacokinetic profile leads to an enhanced immunostimulatory response With reduced toxicity in mice (2015)

Abstract RDB 1450 is an engineered fusion protein which selectively activates the intermediate-affinity IL-2 receptor present on NK cells and memory CD8 T cells. In rodents, RDB 1450 has a half-life of 6-8 hours, compared to a half-life of minutes for recombinant human IL-2 (rhIL-2). Repeat daily dosing (QD) of RDB 1450 in mice results in marked expansion of NK cells and CD8+CD44high T cells, with minimal expansion of CD4+ regulatory T cells (Tregs). Higher QD doses elicit more pronounced effector cell expansion with modest pulmonary edema. TID delivery of the same total daily dose of RDB 1450 enhances the immunological responses in the absence of pulmonary edema. These results suggest that prolonged delivery of reduced concentrations of RDB 1450 drive the desired immune responses with improved tolerability. In contrast, high circulating concentrations of rhIL-2 are required to stimulate effector cells due to its preferential activation of Tregs at lower concentrations. The selectivity profile and favorable pharmacokinetics of RDB 1450 highlight its potential as a novel, differentiated immunotherapeutic agent for the treatment of cancer. Citation Format: Heather C. Losey, Jared E. Lopes, Reginald L. Dean, Heather Flick, Madison Gomes, Michael R. Huff, Rosemarie A. Moroso, Lei Sun, Chunhua Wang, Julie F. Waters, Juan C. Alvarez. Utilizing a selective agonist of the intermediate-affinity IL-2 receptor with an improved pharmacokinetic profile leads to an enhanced immunostimulatory response With reduced toxicity in mice. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4280. doi:10.1158/1538-7445.AM2015-4280
Homocysteine and human reproduction. (2000)

Homocysteine is an amino acid that is capable of disturbing the proper growth of cells. Hyperhomocysteinemia can lead to a non-closure of the neural tube. The underlying basis is a derangement of homocysteine metabolism due to a missense mutation of the MTHFR enzyme that has to catalyze the folate metabolic cycle furnishing sufficient methyl groups for DNA and tRNA synthesis. Folate can overcome the dysfunction of the mutation and the decreased activity of the thermolabile MTHFR. Homocysteine is also recognized as an independent risk factor for obstetrical vascular disease that can manifest itself in maternal veins (thrombosis), arteries (preeclampsia) or spiral arteries supplying the placenta (placental abruption). Low vitamin status (folic acid, vitamin B6 and B12), hyperhomocysteinemia, the MTHFR gene mutation C677T, and thrombotic factors like Protein C, Protein S. antithrombin III, factor V Leiden and Activated Protein C, are alone or in combination high risk factors for obstetrical vascular disease. Their values can be modulated by B-vitamin status and could be able to prevent disease from occurring or recurring. Placebo-randomized trials have been done in neural tube defects but are urgently needed in the vascular area. The common denominator of the effect of homocysteine on the embryo and the blood vessels (endothelium) could be sited in the process of proliferation of cells that need proper methyl groups for proper function.
Research and Optimization of Crashworthiness in Small Overlap Head-on Collision (2013)

To achieve the purpose of studying structure crashworthiness in small overlap collision, simulations were analyzed by Finite Element Method according to IIHS (The Insurance Institute for Highway Safety) regulations. Design of experiment was applied to analyze the sensitivity of each variable, and optimal design was carried out by means of approximation model technology and reliability optimizing design based on monte-carlo simulation technique in the aspects of improving crashworthiness and reducing weight. The result shows that upper rails are the main energy-absorbing parts in small overlap crash. The major factors affecting the safety in small overlap rate collision were determined through the analysis of sensitivity. By contrasting the reliability optimization with the certainty optimization of vehicles, the influence of fluctuation of design variables on quality of product was analyzed. It can be concluded that the reliability optimization is obviously superior to deterministic optimization, which is of great practical application value in engineering.
Strand Ligation in a Double-stranded DNA by T4 RNA Ligase (1996)

Abstract T4 RNA ligase was shown to ligate two DNA strands contained in a double helix with a high efficiency. Experiments on substrate and temperature dependence of this reaction supported that single-stranded ends clamped by a double-stranded region are necessary for this reaction. This finding is widely useful for DNA joining.
Meningitis Caused by Streptococcus suis in Humans (1988)

Between 1968 and 1984, 30 strains of Streptococcus suis causing meningitis were isolated in the Netherlands. Twenty-eight strains were type 2, one was type 4, and one was untypable. The average age of the patients infected with these strains was 49 years (range, 21-76 years); the male-to-female ratio was 6.5. Twenty-five patients (83%) were employed in the pork industry. Two patients (7%) died. In seven cases (23%), predisposing factors were identified. The most frequent sequela was hearing loss (54% of surviving patients). The data for these 30 patients were compared with those for 30 patients from outside the Netherlands whose cases of meningitis due to S. suis type 2 were described between 1968 and 1985. No differences were found. The estimated annual risk of developing S. suis meningitis among Dutch abattoir workers and pig breeders was approximately 3.0/100,000--a rate 1,500 times higher than that among persons not working in the pork industry.
Plasma catecholamine levels and lipid mobilization induced by yohimbine in obese and non-obese women. (1991)

Oral yohimbine administration (0.2 mg/kg) induced lipid mobilization (increase in plasma non-esterified fatty acids, NEFA) in fasting non-obese women (body mass index BMI = 20.2 +/- 0.5, age 35.5 +/- 2.7 years) without significant action on plasma glucose, insulin levels, heart rate or blood pressure during the time-course of the experiment (240 min). Plasma norpinephrine (but not epinephrine) concentrations were increased (100 percent) after oral yohimbine administration. Oral administration of propranolol (40 mg, 60 min before yohimbine) reduced the lipid-mobilizing action of yohimbine (70 percent) during the 60 min following its administration and then totally suppressed its effect until the end of the experimental period (180 min). In fasting obese women (BMI = 36.4 +/- 2.1, age 37 +/- 3.6 years), yohimbine provoked an increase in plasma NEFA levels which was not markedly different from that observed in non-obese subjects. It had no significant effect on plasma glucose, insulin levels, heart rate or blood pressure. Plasma norepinephrine increased in the same proportions. The lipid-mobilizing effect of yohimbine in women is mainly attributable to the increase in synaptic norepinephrine with a resultant increment in lipolysis by beta-adrenergic agonism. In the standard fasting conditions (12 hours) the blockade of the antilipolytic fat cell alpha 2-adrenoceptors seems to be a minor component of the lipomobilizing effect of yohimbine. Morever, when compared with non-obese women, the lipomobilizing effect of yohimbine is not enhanced in obese women.
Efficacy of LY303366 against Amphotericin B-Susceptible and -Resistant Aspergillus fumigatus in a Murine Model of Invasive Aspergillosis (1998)

LY303366 is a novel antifungal echinocandin with excellent in vitro activity against Aspergillus spp. We compared four doses (1, 2.5, 10, and 25 mg/kg of body weight) of LY303366 with amphotericin B (0.5 to 5 mg/kg) in a temporarily neutropenic murine model of invasive aspergillosis against an amphotericin B-susceptible (AF210) and an amphotericin B-resistant (AF65) Aspergillus fumigatus isolate based on in vivo response. Mice were immunosuppressed with cyclophosphamide (200 mg/kg) and infected 3 days later. Treatment started 18 h after infection and lasted for 10 days. LY303366 was given once daily intravenously for 10 days, and amphotericin B (at 0.5, 2, and 5 mg/kg) was given once daily intraperitoneally for 10 days, or only on days 1, 2, 4, and 7 (at 5 mg/kg). Kidneys and lungs from survivors were cultured on day 11. Control mice in both experiments had 90 to 100% mortality. Amphotericin B at 0.5 mg/kg and LY303366 at 1 mg/kg yielded 10 to 20% survival rates for mice infected with either AF210 or AF65. Amphotericin B at 2 and 5 (both regimens) mg/kg yielded a 70 to 100% survival rate for mice infected with AF210 but a 10 to 30% survival rate for mice infected with AF65 (P = 0.01 to 0.04 compared with AF210). Against AF210 and AF65, LY303366 at 2.5, 10, and 25 mg/kg produced a survival rate of 70 to 80%, which was as effective as amphotericin B for AF210, but superior to amphotericin B for AF65 (P < 0.03 to 0.0006). For AF65, LY303366 at 10 and 25 mg/kg/day was superior to amphotericin B at 2 and 5 mg/kg/day in reducing tissue colony counts (P = 0.01 to 0.003), and for AF210, amphotericin B at 5 mg/kg/day and at 5 mg/kg in four doses was more effective than all four regimens of LY303366 in reducing renal culture counts (P = 0.01 to 0.0001). The present study shows, for the first time, that in vivo resistance of A. fumigatus to amphotericin B exists, although this could not be detected by in vitro susceptibility assays. Furthermore, LY303366 appears to be effective against amphotericin B-susceptible and -resistant A. fumigatus infection in this model and should be further evaluated clinically.
High plasma corticosterone levels persist during frequent automatic blood sampling in rats. (2005)

Corticosterone levels in blood may be used as a marker of stress in rodents, provided that the blood sampling procedure itself is non-stressful. Automated blood sampling equipment (Accusampler) allows blood sampling without any interference with the animal and might be useful as a tool for an on-line measurement of stress markers in blood. However, the impact of the blood sampling itself on the corticosterone levels in blood is unknown. The present study was designed to evaluate whether the frequency of blood sampling influences the plasma corticosterone levels in male and female rats. During anaesthesia, a catheter was placed in the jugular vein and attached to an Accusampler. Blood samples (200 microl) were withdrawn with a high (24 samples) or low frequency (3 samples) during a six-hour period immediately after the catheter insertion. The corticosterone levels in the plasma were quantified with ELISA. The corticosterone levels persisted at high post-operation concentrations when blood was collected frequently, while the levels steadily declined significantly during low-frequency sampling. The corticosterone levels were higher in female than in male rats, but the curves were similar. The present study elucidates the importance of considering the frequency of blood withdrawal during automated blood sampling. This parameter may have an impact on the experimental results when using blood corticosterone levels as a stress marker, but also during any in vivo study where blood is collected, since high corticosterone levels may affect the normal physiology of the animals.
Nanocrystal Metal Oxide−Chlorine Adducts:  Selective Catalysts for Chlorination of Alkanes (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTNanocrystal Metal Oxide−Chlorine Adducts: Selective Catalysts for Chlorination of AlkanesNaijian Sun and Kenneth J. KlabundeView Author Information Department of Chemistry, Kansas State University Manhattan, Kansas 66506 Cite this: J. Am. Chem. Soc. 1999, 121, 23, 5587–5588Publication Date (Web):May 29, 1999Publication History Received11 January 1999Published online29 May 1999Published inissue 1 June 1999https://pubs.acs.org/doi/10.1021/ja990084fhttps://doi.org/10.1021/ja990084frapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views404Altmetric-Citations32LEARN ABOUT THESE METRICSArticle 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.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Adducts,Chlorine,Halogenation,Ions,Magnesium oxide Get e-Alerts