gebhart/patrepeval huggingface dataset:
Oxidative stability of biodiesel from soybean oil fatty acid ethyl esters (2005)

Biodiesel consists of long-chain fatty acid esters, derived from renewable sources such as vegetable oils, and its utilization is associated to the substitution of the diesel oil in engines. Depending on the raw material, biodiesel can contain more or less unsaturated fatty acids in its composition, which are susceptible to oxidation reactions accelerated by exposition to oxygen and high temperatures, being able to change into polymerized compounds. The objective of this work was to determine the oxidative stability of biodiesel produced by ethanolysis of neutralized, refined, soybean frying oil waste, and partially hydrogenated soybean frying oil waste. The evaluation was conducted by means of the Rancimat® equipment, at temperatures of 100 and 105ºC, with an air flow of 20 L h-1. The fatty acid composition was determined by GC and the iodine value was calculated. It was observed that even though the neutralized, refined and waste frying soybean oils presented close comparable iodine values, biodiesel presented different oxidative stabilities. The biodiesel from neutralized soybean oil presented greater stability, followed by the refined and the frying waste. Due to the natural antioxidants in its composition, the neutralized soybean oil promoted a larger oxidative stability of the produced biodiesel. During the deodorization process, the vegetable oils lose part of these antioxidants, therefore the biodiesel from refined soybean oil presented a reduced stability. The thermal process degrades the antioxidants, thus the biodiesel from frying waste oil resulted in lower stability, the same occuring with the biodiesel from partially hydrogenated waste oil, even though having lower iodine values than the other.
Signaling axis involving Hedgehog, Notch, and Scl promotes the embryonic endothelial-to-hematopoietic transition (2012)

During development, the hematopoietic lineage transits through hemogenic endothelium, but the signaling pathways effecting this transition are incompletely characterized. Although the Hedgehog (Hh) pathway is hypothesized to play a role in patterning blood formation, early embryonic lethality of mice lacking Hh signaling precludes such analysis. To determine a role for Hh signaling in patterning of hemogenic endothelium, we assessed the effect of altered Hh signaling in differentiating mouse ES cells, cultured mouse embryos, and developing zebrafish embryos. In differentiating mouse ES cells and mouse yolk sac cultures, addition of Indian Hh ligand increased hematopoietic progenitors, whereas chemical inhibition of Hh signaling reduced hematopoietic progenitors without affecting primitive streak mesoderm formation. In the setting of Hh inhibition, induction of either Notch signaling or overexpression of Stem cell leukemia (Scl)/T-cell acute lymphocytic leukemia protein 1 rescued hemogenic vascular-endothelial cadherin(+) cells and hematopoietic progenitor formation. Together, our results reveal that Scl overexpression is sufficient to rescue the developmental defects caused by blocking the Hh and Notch pathways, and inform our understanding of the embryonic endothelial-to-hematopoietic transition.
Adverse Reactions to Iodinated Contrast Media (2013)

The use of iodinated contrast agents for angiography dates back to the 1920s. With over 75 million contrast-requiring procedures performed annually worldwide, it is important to understand the risk factors, pathogenesis, diagnosis, prevention, and treatment of adverse reactions caused by iodinated contrast media (ICM). As contrast media have evolved from ionic, high-osmolality to nonionic, low-osmolality formulations the risk of reactions has decreased over time; however, no pretreatment protocol has been shown to eliminate all repeat reactions. Clinical alertness and early recognition of adverse reactions is of paramount importance and key for appropriate management of these patients. In this article, we review the most recent literature regarding adverse reactions to ICM and provide an insight into the pathogenesis, clinical presentation, pretreatment, and management of contrast-related reactions.
Factors determining relative sensitivity of analytes in positive mode atmospheric pressure ionization mass spectrometry (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFactors determining relative sensitivity of analytes in positive mode atmospheric pressure ionization mass spectrometryJan. Sunner, Gordon. Nicol, and Paul. KebarleCite this: Anal. Chem. 1988, 60, 13, 1300–1307Publication Date (Print):July 1, 1988Publication History Published online1 May 2002Published inissue 1 July 1988https://pubs.acs.org/doi/10.1021/ac00164a012https://doi.org/10.1021/ac00164a012research-articleACS PublicationsRequest reuse permissionsArticle Views1036Altmetric-Citations177LEARN 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 Get e-Alerts
A Novel Five Gene Signature Derived from Stem-Like Side Population Cells Predicts Overall and Recurrence-Free Survival in NSCLC (2012)

Gene expression profiling has been used to characterize prognosis in various cancers. Earlier studies had shown that side population cells isolated from Non-Small Cell Lung Cancer (NSCLC) cell lines exhibit cancer stem cell properties. In this study we apply a systems biology approach to gene expression profiling data from cancer stem like cells isolated from lung cancer cell lines to identify novel gene signatures that could predict prognosis. Microarray data from side population (SP) and main population (MP) cells isolated from 4 NSCLC lines (A549, H1650, H460, H1975) were used to examine gene expression profiles associated with stem like properties. Differentially expressed genes that were over or under-expressed at least two fold commonly in all 4 cell lines were identified. We found 354 were upregulated and 126 were downregulated in SP cells compared to MP cells; of these, 89 up and 62 downregulated genes (average 2 fold changes) were used for Principle Component Analysis (PCA) and MetaCore pathway analysis. The pathway analysis demonstrated representation of 4 up regulated genes (TOP2A, AURKB, BRRN1, CDK1) in chromosome condensation pathway and 1 down regulated gene FUS in chromosomal translocation. Microarray data was validated using qRT-PCR on the 5 selected genes and all showed robust correlation between microarray and qRT-PCR. Further, we analyzed two independent gene expression datasets that included 360 lung adenocarcinoma patients from NCI Director's Challenge Set for overall survival and 63 samples from Sungkyunkwan University (SKKU) for recurrence free survival. Kaplan-Meier and log-rank test analysis predicted poor survival of patients in both data sets. Our results suggest that genes involved in chromosome condensation are likely related with stem-like properties and might predict survival in lung adenocarcinoma. Our findings highlight a gene signature for effective identification of lung adenocarcinoma patients with poor prognosis and designing more aggressive therapies for such patients.
Design, construction, and characterization of a large synthetic human antibody phage display library (2005)

Advances in proteomic research allow the identification of several hundred protein components in complex biological specimens. Structural information is typically lost during proteomic investigations. For this reason, the rapid isolation of monoclonal antibodies specific to proteins of interest would allow the study of structurally intact biological specimens, thus providing complementary proteomic information. Here, we describe the design, construction, characterization, and use of a large synthetic human antibody phage display library (ETH-2-Gold) containing three billion individual antibody clones. A large repertoire of antibodies with similar biochemical properties was produced by appending short variable complementarity-determining region 3 (CDR3) onto three antibody germline segments (DP47, DPK22, and DPL16), which are frequently found in human antibodies. The ETH-2-Gold library exhibits efficient display of antibody fragments on filamentous phage, as assessed by immunoblot. Furthermore, the library is highly functional, since >90% of clones express soluble antibodies in bacteria and since good quality monoclonal antibodies have been isolated against 16 different antigens. The usefulness of the library as a tool for generating monoclonal antibodies for biomedical applications was tested using the C-domain of tenascin-C (a marker of angiogenesis) as antigen and showing that specific antibodies to this target were able to stain vascular structures in tumor sections.
Equilibrium acidities of carbon acids. VI. Establishment of an absolute scale of acidities in dimethyl sulfoxide solution (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEquilibrium acidities of carbon acids. VI. Establishment of an absolute scale of acidities in dimethyl sulfoxide solutionWalter S. Matthews, Joseph E. Bares, John E. Bartmess, F. G. Bordwell, Frederick J. Cornforth, George E. Drucker, Zafra Margolin, Robert J. McCallum, Gregory J. McCollum, and Noel R. VanierCite this: J. Am. Chem. Soc. 1975, 97, 24, 7006–7014Publication Date (Print):November 1, 1975Publication History Published online1 May 2002Published inissue 1 November 1975https://pubs.acs.org/doi/10.1021/ja00857a010https://doi.org/10.1021/ja00857a010research-articleACS PublicationsRequest reuse permissionsArticle Views5508Altmetric-Citations486LEARN 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 Get e-Alerts
Vascular endothelial growth factor and neovascularization in astrocytic tumors (1998)

It has been widely recognized that the vascular structure is an important factor when making a histopathological diagnosis and assessing the malignancy potential, especially of astrocytic tumors. The vascular endothelial growth factor (VEGF), which is thought to be regulated by the p53 gene, is a regulation factor for tumor neovascularization. The relationship between VEGF distribution and neovasculature was studied in 42 cases of astrocytic tumors (grades 1-4), which were obtained from surgical material, and the St Anne-Mayo grading system was applied. The relationship between the labeling indices (LI) of VEGF and LI of p53 protein in tumor cells was also studied using immunohistochemistry. The VEGF LI in high-grade malignancy potential tumors, such as grade 3 and grade 4 tumors, was significantly higher than those that were low grade. In grade 4 tumors, a significant correlation between the VEGF LI and the proliferation indices of endothelial cells of neovasculatures was observed. No significant correlation was noted between p53 LI and VEGF LI, as well as p53 LI and histopathological grade. In astrocytic tumors, expression of VEGF may be correlated to tumor neovascularization, and can be considered as an indicator of malignancy potential in astrocytic tumors.
Rapid gastric emptying of an oral glucose solution in type 2 diabetic patients. (1992)

Gastric emptying of a liquid glucose meal was measured with scintigraphic techniques in nine recently diagnosed Type 2 diabetic patients and nine sex- and age-matched nondiabetic control subjects. Seven of the nine Type 2 diabetic patients were receiving oral hypoglycemic therapy which was discontinued the evening prior to the study. The other two diabetic patients were taking no medication. The average gastric half-emptying time was 33.6 min (s.e.m. = 3.2) for the diabetic patients and 64.6 min (s.e.m. = 4.2) for the nondiabetic controls (p = 0.0005). These measurements indicate rapid gastric emptying in Type 2 diabetic patients which may contribute to worsening of glucose control in these patients.
Clinical applications of focused ultrasound—The brain (2007)

This paper provides a historic and contemporary overview of the use of focused ultrasound for treating brain disorders.
Delivery of a Peptide Radiopharmaceutical to Brain with an IgG-Avidin Fusion Protein (2011)

The genetic engineering, host cell expression, purity, identity, and in vivo brain drug targeting properties are described for a new IgG-fusion protein, designated the cTfRMAb-AV fusion protein. Avidin (AV) is fused to the carboxyl terminus of the heavy chain of the genetically engineered chimeric monoclonal antibody (mAb) against the mouse transferrin receptor (TfR). The TfRMAb binds the endogenous TfR on the blood-brain barrier (BBB), which triggers transport into brain from blood. The cTfRMAb-AV fusion protein is produced in stably transfected Chinese hamster ovary cells, which are grown in serum free medium under conditions of biotin starvation. Following affinity purification, the purity and identity of the cTfRMAb-AV fusion protein were verified by electrophoresis and Western blotting. The affinity of the cTfRMAb for the murine TfR is high, K(I) = 4.6 ± 0.5 nM, despite fusion of avidin to the antibody heavy chain. The model peptide radiopharmaceutical used in this study is the Aβ(1-40) amyloid peptide of Alzheimer's disease (AD), which in a brain-penetrating form could be used to image the amyloid plaque in brain in AD. The BBB transport and brain uptake of the [(125)I]-Aβ(1-40) peptide was measured in mice injected intravenously (IV) with the peptide either free or conjugated to the cTfRMAb-AV fusion protein. The brain uptake of the free Aβ(1-40) peptide was very low, 0.1% of injected dose (ID)/gram brain following i.v. injection, and is comparable to the brain uptake of a brain blood volume marker. However, the brain uptake of the Aβ(1-40) peptide was high, 2.1 ± 0.2% ID/gram brain, following attachment of the biotinylated peptide to the cTfRMAb-AV fusion protein. Capillary depletion analysis showed the peptide penetrated the brain parenchyma from blood. The cTfRMAb-AV fusion protein is a new drug delivery system that can target to mouse brain monobiotinylated peptide or antisense radiopharmaceuticals.
Use of phage display to probe the evolution of binding specificity and affinity in integrins (2003)

The specific binding of RGD-containing proteins to integrin is a function of both the conformation of and the local sequence surrounding the RGD motif. To study the effect of these factors on integrin binding affinity and specificity, we obtained RGD-containing ligands specific for different integrins presented on the same protein scaffold. The beta-turn region between two anti-parallel beta-strands on the loop I of tendamistat, an inhibitor of alpha-amylase, was extended by two residues and randomized in a phagemid library. This library and two subsequently constructed RGD-containing loop I libraries were biopanned with purified integrins alphaIIbbeta3, alphaVbeta3 and alphaVbeta5 individually. The sequence analysis of selected tendamistat variants and characterization by phage ELISA revealed that phage adhesion is mediated exclusively by an RGD motif located at only two out of four possible positions on loop I. Further, sequences flanking the RGD motif were specific for different integrin targets. Interestingly, selected tendamistat variants mimic natural integrin ligands, both in sequence similarity and in integrin binding specificity, indicating that various ligand specificity patterns can be generated by driving towards maximum affinity in the integrin-ligand complexes.
5-Amino-1-(chloromethyl)-1,2-dihydro-3H-benz[e]indoles:  Relationships between Structure and Cytotoxicity for Analogues Bearing Different DNA Minor Groove Binding Subunits (1999)

A series of 5-amino-seco-CBI compounds, designed for use as effectors for prodrugs, were prepared to study structure-activity relationships for the cytotoxicity of side chain analogues. Compounds were prepared by coupling 1-(chloromethyl)-5-nitro-1, 2-dihydro-3H-benz[e]indole to appropriate carboxylic acids, followed by nitro group reduction, or by coupling suitable 5-amino-protected indolines to alpha,beta-unsaturated acids, followed by deblocking. These AT-specific DNA alkylating agents were evaluated for cytotoxicity in a series of tumor cell lines (AA8, UV4, EMT6, SKOV3). For those analogues bearing an indolecarbonyl side chain, the 5'-methoxy derivative was the most cytotoxic (IC(50) 1.3 nM in AA8 cells, 4 h exposure), comparable to that of the parent CBI-TMI (5', 6',7'-trimethoxyindole) derivative (IC(50) 0.46 nM in the above assay). A subset of solubilized derivatives bearing O(CH(2))(2)NMe(2) substituents were about 10-fold less potent. For compounds containing an acryloyl linker in the side chain, the 4'-methoxycinnamoyl derivative proved the most cytotoxic (IC(50) 0. 09 nM in the above assay). A number of these 5-amino-seco-CBI-TMI analogues (including the solubilized compounds) are of interest both as cytotoxins and as components of amine-based prodrugs designed for tumor-specific activation.
Norovirus virus-like particle vaccines for the prevention of acute gastroenteritis (2013)

Noroviruses (NoVs) are the most common cause of nonbacterial acute gastroenteritis in humans worldwide. These highly infectious viruses were, until recently, commonly thought to cause a mild, self-limiting disease in healthy individuals, but increasing epidemiology shows that the incidence and severity of illness due to NoV infection is substantial and similar to diseases where immunization is widely recommended. Human NoV challenge studies have identified carbohydrate histo-blood group antigen expression as an important human susceptibility factor for many strains and correspondingly, that antibodies which block carbohydrate virus binding represent a potential correlate of protection against NoV infection and illness. Since human NoVs do not replicate in cell culture, there are numerous challenges to the development of a vaccine to prevent illness or infection. However, the development of NoV virus-like particles (VLPs) has enabled significant progress toward effective vaccine candidates designed to protect against multiple circulating NoV strains. Vaccination with NoV VLP vaccines has been shown to both induce antibodies that block virus-derived VLP carbohydrate binding and protect against homologous viral challenge in a human clinical study.
Synthetic peptides derived from the melanocyte-stimulating hormone receptor MC1R can stimulate HLA-A2-restricted cytotoxic T lymphocytes that recognize naturally processed peptides on human melanoma cells. (1997)

Human melanoma-specific HLA-A2 restricted CTLs have recently been shown to recognize antigens expressed by melanoma lines and normal melanocytes, including Melan-A/Mart-1, gp100, gp75, and tyrosinase. Herein, we define HLA-A2-restricted CTL epitopes from a recently cloned melanocortin 1 receptor (MC1R), which belongs to a new subfamily of the G-protein-coupled receptors expressed on melanomas and melanocytes. Thirty-one MC1R-derived peptides were selected on the basis of HLA-A2-specific motifs and tested for their HLA-A2 binding capacity. Of a group of 12 high or intermediate HLA-A2 binding peptides, three nonamers, MC1R244 (TILLGIFFL), MC1R283 (FLALIICNA), and MC1R291 (AIIDPLIYA), were found to induce peptide-specific CTLs from peripheral blood mononuclear cells of healthy HLA-A2+ donors after repeated in vitro stimulation with peptide-pulsed antigen-presenting cells. The CTLs raised against these three HLA-A2+-restricted peptides could recognize naturally processed peptides from HLA-A2+ melanomas and from Cos7 cells cotransfected with MC1R and HLA-A2. CTLs induced by the MC1R291 peptide (but not induced or induced only to a very low extent by the other two MCR1 peptide epitopes) showed cross-reactions with two other members of the melanocortin receptor family, which are more broadly expressed on other tissues. Taken together, our findings have implications in relation both to autoimmunity and immunotherapy of malignant melanomas.
A novel hemostatic agent: the potential role of recombinant activated factor VII (rFVIIa) in anesthetic practice. (2002)

rFVIIa is a novel hemostatic agent that shows promise in non-hemophiliac patents of a significant therapeutic role in variety of coagulopathic and hemorrhagic conditions in clinical situations ranging from thrombocytopenia, disseminated intravascular coagulation and transfusion-related coagulopathy, as well as in patients experiencing massive blood loss undergoing orthotopic liver transplantation, cardiac, orthopedic and genitourinary surgery.
Efficient loading of identical viral peptide onto class II molecules by antigenized immunoglobulin and influenza virus. (1993)

Several prior reports have identified peptides that are naturally associated with major histocompatibility complex (MHC) class II molecules on presenting cells. We have examined the delivery of a peptide from exogenous sources to MHC class II molecules. The peptide derives from the influenza virus hemagglutinin (HA) and activates a CD4+ T cell hybridoma. In functional assays of antigen presentation, this epitope is delivered effectively to T cells either in the context of influenza virus or chimeric immunoglobulin (Ig) molecules (Ig-HA) in which the peptide has replaced the CDR3 loop of the heavy chain. We find that the identical 11-mer peptide can be isolated from mouse MHC class II antigens whether the exogenous source of peptide is free HA peptide, the Ig-HA chimera, or ultraviolet-inactivated PR8 influenza virus. The Ig-HA chimera proves to be the most efficient vehicle for charging class II molecules via the exogenous route. Given the fact that self Igs represent natural long-lived carriers, we suggest that antigenized Igs have considerable potential for peptide delivery to MHC molecules in situ.
Generalized Diffusion Equation for Superconducting Alloys (1970)

Eilenberger's transportlike equations for a superconductor of type II can be simplified very much in the dirty limit. In this limit a diffusionlike equation is derived which is the generalization of the de Gennes-Maki theory for dirty superconductors to arbitrary values of the order parameter.