gebhart/patrepeval huggingface dataset:
The effect of dyes used to evaluate the in situ, ex-vivo, and perfused kidney. (1981)

Methylene blue, indigo carmine, and fluorescein dyes were evaluated to determine their effect on the dog kidney. Methylene blue and indigo carmine were administered intravenously and intraarterially to the in situ vascularized kidney and serial histologic appearance of the kidney was determined. The three dyes were administered intraarterially to excised kidneys that were then preserved for 1 hour in the cold and autotransplanted; and finally the three dyes were administered to the perfusate of excised kidneys that were perfused for 18 hours by cryoperfusion with an albumin perfusate and then autotransplanted. Renal function and histology were determined 5 days after autotransplantation. Methylene blue dye did not damage the in situ vascularized kidney as judged by renal histology. However, administration of methylene blue to the ex vivo kidney that was subsequently short term cold stored or perfusion stored was associated with marked apparent ischemic damage of the organ. Indigo carmine dye did not adversely affect either the in situ vascularized kidney or the short term cold stored kidney. However, with perfusion storage, indigo carmine produced apparent vasoconstriction that led to perfusion failure. Fluorescein dye was not harmful to the kidney either during short term cold storage or during perfusion preservation. It is concluded that fluorescein is the dye of choice for evaluating the vascular anatomy or macroperfusion status of the kidney.
Circulating Histones Are Mediators of Trauma-associated Lung Injury (2012)

This study elucidates a new mechanism for acute lung injury after severe trauma and proposes that circulating histones are viable therapeutic targets for improving survival outcomes in patients.
Isolating large nested deletions in bacterial and P1 artificial chromosomes by in vivo P1 packaging of products of Cre-catalysed recombination between the endogenous and a transposed loxP site (1997)

A general approach for isolating large nested deletions in P1 artificial chromosomes (PACs) and bacterial artificial chromosomes (BACs) by retrofitting with a loxP site-containing Tn10 mini-transposon is described. Cre-mediated recombination between the loxP site existing in these clones and one introduced by transposition leads to deletions and inversions of the DNA between these sites. Large deletions are selectively recovered by transducing the retrofitted PAC or BAC clones with P1 phage. The requirement that both loxP sites in the cointegrate be packaged into a P1 head ensures that only large deletions are rescued. PCR analyses identified these deletions as products of legitimate recombination between loxP sites mediated by Cre protein. BACs produce deletions much more efficiently than PACs although the former cannot be induced to greater than unit copy in cells. Mammalian cell-responsive antibiotic resistance markers are introduced as part of the transposon into genomic clone deletions for subsequent functional analysis. Most importantly, the loxP site retrofitting and P1 transduction can be performed in the same bacterial host containing these clones directly isolated from PAC or BAC libraries. These procedures should facilitate physical and functional mapping of genes and regulatory elements in these large plasmids.
ACS NEWS (2007)

RETURN TO ISSUEPREVACS NewsNEXTACS NEWSSCENES FROM THE ACS NATIONAL MEETING IN CHICAGOLINDA WANGCite this: Chem. Eng. News 2007, 85, 16, 54–55Publication Date (Print):April 16, 2007Publication History Published online29 October 2010Published inissue 16 April 2007https://pubs.acs.org/doi/10.1021/cen-v085n016.p054https://doi.org/10.1021/cen-v085n016.p054acs-newsACS PublicationsCopyright © 2007 AMERICAN CHEMICAL SOCIETY. This publication is available under these Terms of Use. This publication is free to access through this site. Learn MoreArticle Views72Altmetric-Citations-LEARN 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 PDF (709 KB) SUBJECTS:Students Get e-Alerts
Oligomeric tumour necrosis factor α slowly converts into inactive forms at bioactive levels (1992)

The stability of oligomeric human tumour necrasis factor alpha (TNF) at bioactive levels has been studied by two immunoenzymatic assays: one able to specifically detect oligomeric and not monomeric TNF (O-e.l.i.s.a.) and the other able to detect both forms (OM-e.l.i.s.a.). The selectivity of O-e.l.i.s.a. and OM-e.l.i.s.a. for oligomeric and monomeric TNF was demonstrated with isolated forms prepared by partial dissociation of recombinant TNF with 10% (v/v) dimethyl sulphoxide and gel-filtration h.p.l.c. Evidence for instability of oligomeric TNF were obtained in physiological buffers, as well as in serum and cell-culture supernatants, as a function of TNF concentration. In particular, only a half of the TNF antigen was recovered in the oligomeric form after 72 h incubation (37 degrees C) at 0.12 nM, whereas no apparent dissociation was detected at 4 nM. The structural changes observed at picomolar concentrations were rapidly reversed by raising the concentration of TNF to about 2 nM by ultrafiltration, suggesting that subunit dissociation and reassociation reactions occur in the picomolar and nanomolar range respectively. The cytolytic activity of L-M cells correlates with oligomeric-TNF levels after incubation at picomolar concentrations. Moreover, isolated oligomeric TNF was cytotoxic towards L-M cells, whereas monomeric TNF was virtually inactive. In conclusion, the results suggest that bioactive oligomeric TNF is unstable at picomolar levels and slowly converts into inactive monomers, supporting the hypothesis that quaternary-structure changes in TNF may contribute to the fine regulation of TNF cytotoxicity.
Triple helix assembly and processing of human collagen produced in transgenic tobacco plants (2000)

The use of tobacco plants as a novel expression system for the production of human homotrimeric collagen I is presented in this report. Constructs were engineered from cDNA encoding the human proalpha1(I) chain to generate transgenic tobacco plants expressing collagen I. The recombinant proalpha1(I) chains were expressed as disulfide-bonded trimers and were shown to fold into a stable homotrimeric triple helix. Moreover, the recombinant procollagen was subsequently processed to collagen as it occurs in animals. Large amounts of recombinant collagen were purified from field grown plant material. The data suggest that plants are a valuable alternative for the recombinant production of collagen for various medical and scientific purposes.
NMR spectroscopy of single neurons (2000)

The first spatially localized NMR spectra of osmolytes and metabolites from single isolated neurons have been obtained using a combination of high magnetic field strengths and NMR radio frequency (RF) microcoils. The proton spectra display peaks at high concentrations (100-300 mM) assigned to betaine and choline, and other metabolite resonances including lactate at lower concentrations in the order of 10s of millimoles. The volumes examined were approximately 10 nl, over two orders of magnitude less than previously possible. In these initial experiments; the cells were unperfused and the signal intensities of the osmolytes decrease with time, a phenomenon consistent with cell swelling. This work demonstrates the technical feasibility of NMR spectroscopy of single cells, further broadening the scope of NMR spectroscopy of living tissues from application to entire living organisms (man and animal models) and isolated tissues (perfused organs and cultured assemblies of cells) and now to single cells. Magn Reson Med 44:19-22, 2000.
Stacking classifiers for anti-spam filtering of e-mail (2001)

We evaluate empirically a scheme for combining classifiers, known as stacked generalization, in the context of anti-spam filtering, a novel cost-sensitive application of text categorization. Unsolicited commercial e-mail, or "spam", floods mailboxes, causing frustration, wasting bandwidth, and exposing minors to unsuitable content. Using a public corpus, we show that stacking can improve the efficiency of automatically induced anti-spam filters, and that such filters can be used in real-life applications.
Atomic and Molecular Manipulation with the Scanning Tunneling Microscope (1991)

The prospect of manipulating matter on the atomic scale has fascinated scientists for decades. This fascination may be motivated by scientific and technological opportunities, or from a curiosity about the consequences of being able to place atoms in a particular location. Advances in scanning tunneling microscopy have made this prospect a reality; single atoms can be placed at selected positions and structures can be built to a particular design atom-by-atom. Atoms and molecules may be manipulated in a variety of ways by using the interactions present in the tunnel junction of a scanning tunneling microscope. Some of these recent developments and some of the possible uses of atomic and molecular manipulation as a tool for science are discussed.
Targeting of porin to the outer membrane of Escherichia coli. Rate of trimer assembly and identification of a dimer intermediate. (1988)

Porin, a transmembrane protein in the outer membrane of Escherichia coli, exists in a trimeric structure which is not dissociated during sodium dodecyl sulfate-polyacrylamide gel electrophoresis at 25 degrees C. This unusual stability was utilized in the study of the conformational changes which accompany the targeting of porin to the outer membrane. A delay of 16-44 s between completion of synthesis of a monomer and its assembly into a trimer was found from the ratio of monomers to trimers found in exponentially growing cells. Pulse-chase experiments showed that rapid processing of precursor OmpF molecules was followed by assembly into sodium dodecyl sulfate-resistant oligomers with a half-time of 20 s at 30 degrees C. An intermediate in assembly was isolated by immunoprecipitation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis below 10 degrees C and was identified as a metastable dimer.
<title>Plasma Sources For X-Ray Lithography</title> (1982)

The Gas Puff Z-Pinch (GPZP) plasma X-ray source has a number of demonstrated advantages over conventional X-ray sources as applied to high throughput X-ray microlithography. The Physics International Company (PI) is presently constructing a GPZP X-ray source that has been designed for application to the microlithography industry.
Enhanced antitumor potency of polyethylene glycolylated tumor necrosis factor-alpha: a novel polymer-conjugation technique with a reversible amino-protective reagent. (1999)

We attempted to develop a novel method for the chemical modification of cytokines with synthetic polymers to increase in vivo therapeutic efficacy. A pH-reversible amino-protective reagent, dimethylmaleic anhydride (DMMAn), was used for polymer conjugation of tumor necrosis factor-alpha (TNF-alpha) with polyethylene glycol (PEG). The novel PEGylated TNF-alpha, PEG-TNF-alpha(+), which was pretreated with DMMAn before PEGylation, had 20% to 40% higher specific activity than PEG-TNF-alpha(-) (not treated with DMMAn) in vitro. Moreover, PEG-TNF-alpha(+) more potently caused tumor necrosis in Meth-A solid tumors in mice than did PEG-TNF-alpha(-). The middle fraction (M) of PEG-TNF-alpha(+), which was of the optimal degree of modification among PEG-TNF-alpha(+)s with different molecular weights, caused the highest degree of tumor hemorrhagic necrosis: 30-fold higher than native TNF-alpha and 2-fold higher than the most potent MPEG-TNF-alpha(-) that also had nearly the same molecular weight. Significantly, improvements in antitumor activity in vivo were more marked than were changes in specific activity. Furthermore, native TNF-alpha caused a dose-dependent body weight loss in mice, whereas no obvious side effects were observed in any PEG-TNF-alpha-treated mice. These results suggest that PEGylation using DMMAn is a useful for clinical cytokine delivery.
Antigenic heterogeneity of strains of Saccharomyces cerevisiae and Candida albicans recognised by serum antibodies from patients with Crohn's disease (1992)

The antigenic heterogeneity of twelve strains of Saccharomyces cerevisiae and serovar A and B strains of Candida albicans was investigated by cross-absorption of serum antibodies from a patient with Crohn's disease. On the basis of common antibody absorption patterns, eleven of the yeast strains were divided into Group 1 (five S. cerevisiae), Group 2 (two C. albicans, one S. cerevisiae) and Group 3 (three S. cerevisiae). The remaining three S. cerevisiae strains (Group 4) showed unique absorption patterns. The antigenic relationship between S. cerevisiae and C. albicans was further studied by cross-absorption of sera from eight patients with Crohn's disease. This confirmed a limited degree of cross-reaction between most strains of S. cerevisiae and C. albicans, but C. albicans serovar B significantly absorbed antibodies to more S. cerevisiae strains than did C. albicans serovar A. The results demonstrate considerable antigenic heterogeneity of S. cerevisiae and suggest that the elevated serum antibody levels to S. cerevisiae found in Crohn's disease are directed against multiple antigens.
Increase in dopaminergic neurons from mouse embryonic stem cell‐derived neural progenitor/stem cells is mediated by hypoxia inducible factor‐1α (2008)

A reliable method to induce neural progenitor/stem cells (NPCs) into dopaminergic (DAergic) neurons has not yet been established. As well, the mechanism involved remains to be elucidated. To induce DAergic differentiation from NPCs, a cytokine mixture (C-Mix) of interleukin (IL)-1beta, IL-11, leukemia-inhibitory factor (LIF), and glial-derived neurotrophic factor or low oxygen (3.5% O(2): L-Oxy) was used to treat embryonic stem (ES) cell-derived NPCs. Treatment with C-Mix increased the number of tyrosine hydroxylase (TH)-positive cells compared with controls (2.20-fold of control). The C-Mix effect was induced by mainly LIF or IL-1beta treatment. Although L-Oxy caused an increase in TH-positive cells (1.34-fold), the combination of L-Oxy with C-Mix did not show an additive effect. Increases in DA in the medium were shown in the presence of C-Mix, LIF, and L-Oxy by high-performance liquid chromatography. Gene expression patterns of neural markers [tryptophan hydroxylase (TPH), GAD67, GluT1, beta-tubulin III, glial fibrillary acidc protein, and TH] were different in C-Mix and L-Oxy treatments. Because increases in hypoxia-inducible factor (HIF)-1alpha protein were found in both treatments, we investigated the effect of HIF-1alpha on differentiation of NPCs to DAergic neurons. Inhibition of HIF-1alpha by the application of antisense oligodeoxynucleotides (ODNs) to NPCs caused a decrease in TH-positive cells induced by LIF treatment. Gene expressions of TH, GAD67, and GluT1 were decreased, and those of TPH, beta-tubulin III, and S-100beta were increased by treatment with just ODNs, indicating the importance of the endogenous effect of HIF-1alpha on neuronal differentiation. These data suggest that enhanced differentiation into DAergic neurons from ES cell-derived NPCs was induced by C-Mix or L-Oxy mediated by HIF-1alpha.
Informatics in Radiology (infoRAD) (2005)

Of the existing atlases of the brain anatomy and cerebrovasculature, none integrates the anatomy and vasculature by providing for direct manipulation of three-dimensional (3D) cerebral models. An atlas-based application was developed in four steps: (a) construction of 3D anatomic models, (b) construction of 3D vascular models, (c) interactive spatial coregistration of the anatomic and vascular models, and (d) development of functionality and a user interface for the application. Three-dimensional anatomic models were imported from an electronic brain atlas database derived from classic print atlases. A novel vascular modeling technique was developed and applied to create a vascular atlas from magnetic resonance angiographic data. The use of 3D polygonal models allows smooth navigation (rotation, zooming, panning) and interactive labeling of anatomic structures and vascular segments. This application enables the user to examine 3D anatomic structures and 3D cerebral vasculature and to gain a better understanding of the relationships between the two. The combined anatomic-vascular atlas is a user-friendly neuroeducational tool that is useful for medical students and neuroscience researchers as well as for educators in preparing teaching materials.
Cleavage reactions of bicyclic ketones derived from azoniaanthracene-ketene acetal adducts (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCleavage reactions of bicyclic ketones derived from azoniaanthracene-ketene acetal adductsDonald L. Fields and Thomas H. ReganCite this: J. Org. Chem. 1970, 35, 6, 1870–1875Publication Date (Print):June 1, 1970Publication History Published online1 May 2002Published inissue 1 June 1970https://pubs.acs.org/doi/10.1021/jo00831a033https://doi.org/10.1021/jo00831a033research-articleACS PublicationsRequest reuse permissionsArticle Views83Altmetric-Citations6LEARN 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
Deglycosylation of proteins for crystallization using recombinant fusion protein glycosidases (1996)

Obtaining high quality protein crystals remains a rate-limiting step in the determination of three-dimensional X-ray structures. A frequently encountered problem in this respect is the high or heterogeneous carbohydrate content of many eukaryotic proteins. A number of reports have demonstrated the use of enzymatic deglycosylation in the crystallization of certain glycoproteins. Although this is an attractive tool, there are some problems that hinder the more widespread use of glycosidases in crystallization. First, commercially available glycosidases are relatively expensive, which virtually prohibits their use on a large scale. Second, the glycosidase must be removed from the glycoprotein of interest following deglycosylation, which is not always straightforward. To circumvent these problems we have cloned the two most generally useful glycosidases, peptide-N-glycosidase F and endoglycosidase F1 from Flavobacterium meningosepticum, as fusion proteins with glutathione S-transferase. The fusion not only allows rapid purification of these enzymes from Escherichia coli cell extracts, but also permits rapid removal from target proteins following deglycosylation. We have used these enzymes to obtain crystals of phytase from Aspergillus ficuum and acid phosphatase from Aspergillus niger and to obtain a new crystal form of recombinant human renin.
Liquid-Infused Nanostructured Surfaces with Extreme Anti-Ice and Anti-Frost Performance (2012)

Ice-repellent coatings can have significant impact on global energy savings and improving safety in many infrastructures, transportation, and cooling systems. Recent efforts for developing ice-phobic surfaces have been mostly devoted to utilizing lotus-leaf-inspired superhydrophobic surfaces, yet these surfaces fail in high-humidity conditions due to water condensation and frost formation and even lead to increased ice adhesion due to a large surface area. We report a radically different type of ice-repellent material based on slippery, liquid-infused porous surfaces (SLIPS), where a stable, ultrasmooth, low-hysteresis lubricant overlayer is maintained by infusing a water-immiscible liquid into a nanostructured surface chemically functionalized to have a high affinity to the infiltrated liquid and lock it in place. We develop a direct fabrication method of SLIPS on industrially relevant metals, particularly aluminum, one of the most widely used lightweight structural materials. We demonstrate that SLIPS-coated Al surfaces not only suppress ice/frost accretion by effectively removing condensed moisture but also exhibit at least an order of magnitude lower ice adhesion than state-of-the-art materials. On the basis of a theoretical analysis followed by extensive icing/deicing experiments, we discuss special advantages of SLIPS as ice-repellent surfaces: highly reduced sliding droplet sizes resulting from the extremely low contact angle hysteresis. We show that our surfaces remain essentially frost-free in which any conventional materials accumulate ice. These results indicate that SLIPS is a promising candidate for developing robust anti-icing materials for broad applications, such as refrigeration, aviation, roofs, wires, outdoor signs, railings, and wind turbines.
Object Tracking by Asymmetric Kernel Mean Shift with Automatic Scale and Orientation Selection (2007)

Tracking objects using the mean shift method is performed by iteratively translating a kernel in the image space such that the past and current object observations are similar. Traditional mean shift method requires a symmetric kernel, such as a circle or an ellipse, and assumes constancy of the object scale and orientation during the course of tracking. In a tracking scenario, it is not uncommon to observe objects with complex shapes whose scale and orientation constantly change due to the camera and object motions. In this paper, we present an object tracking method based on the asymmetric kernel mean shift, in which the scale and orientation of the kernel adaptively change depending on the observations at each iteration. Proposed method extends the traditional mean shift tracking, which is performed in the image coordinates, by including the scale and orientation as additional dimensions and simultaneously estimates all the unknowns in a few number of mean shift iterations. The experimental results show that the proposed method is superior to the traditional mean shift tracking in the following aspects: 1) it provides consistent object tracking throughout the video; 2) it is not effected by the scale and orientation changes of the tracked objects; 3) it is less prone to the background clutter.