gebhart/patrepeval huggingface dataset:
Quantitative measurement of regional lung ventilation using 3He MRI (2002)

A new strategy for a quantitative measurement of regional pulmonary ventilation using hyperpolarized helium-3 (3He) MRI has been developed. The method employs the build-up of the signal intensity after a variable number of (3)He breaths. A mathematical model of the signal dynamics is presented, from which the local ventilation, defined as the fraction of gas exchanged per breath within a given volume, is calculated. The model was used to create ventilation maps of coronal slices of guinea pig lungs. Ventilation values very close to 1 were found in the trachea and the major airways. In the lung parenchyma, regions adjacent to the hilum showed values of 0.6-0.8, whereas 0.2-0.4 was measured in peripheral regions. Monte Carlo simulations were used to investigate the accuracy of the method and its limitations. The simulations revealed that, at presently attainable signal-to-noise ratios, the ventilation parameter can be determined with a relative uncertainty of <5% over a wide range of values.
Migration Inhibitory Factor-Binding Sarcolectin from Human Placenta is Indistinguishable from a Subfraction of Human Serum Albumin (1994)

Human sarcolectin is known as growth promoter and interferon-alpha/beta antagonist. Besides N-acetylneuraminic acid-dependent cell agglutination it also binds to a macrophage migration inhibitory factor (MIF). Several types of negatively charged carbohydrates interfere with this binding, indicating importance of a negatively charged cluster. Since human serum albumin that has very similar properties in gel electrophoretic analysis can also bind to this factor with a comparatively reduced extent, sarcolectin and albumin are compared biochemically and immunologically. Their peptide maps, generated by cleavage with cyanogen bromide and N-chlorosuccinimide, reveal no differences. The N-terminal sequences are identical up to the fourteenth position that have unequivocally been determined. Reactivities to anti-human serum albumin antibody that inhibits binding of sarcolectin to MIF are similar. Fractionation of human albumin by chromatography on hydroxyapatite yields a subfraction with increased specific activity, measured by extent of inhibition of sarcolectin-MIF interaction. It exhibits the same inhibitory capacity as a similarly derived subfraction from sarcolectin. Interestingly, rabbit and pig serum albumins are as active as human albumin to inhibit binding of sarcolectin to MIF, whereas hamster, mouse, horse and bovine albumin preparations were ineffective up to 2.5 mg/ml. Thus, sarcolectin appears to be a subfraction of human serum albumin whose functionally relevant molecular peculiarities are presently unknown. Neither treatment with organic solvents nor with lipases, but exposure to trypsin, chymotrypsin and pronase can impair sarcolectin's ability to bind MIF.
Exon eight APC mutations account for a disproportionate number of familial adenomatous polyposis families (1994)

The familial adenomatous polyposis gene, APC, has recently been identified. Detection of APC mutations will facilitate genetic screening in family members at risk for this disease. The length of APC makes it impractical to examine the entire coding sequence in each new family encountered. Identification of mutation cluster regions within the gene has therefore become a priority. Initial reports suggested that exon eight might contain a disproportionate number of mutations. This study describes direct sequencing of exon eight in 21 unrelated Australians with familial adenomatous polyposis. Mutations were detected in three of the 21 subjects (14%). Two were previously described point mutations changing an arginine to a stop codon. The third was a novel two base-pair deletion producing a frameshift and downstream stop codon. All three mutations segregated with the disease gene in their respective families. Three at risk children from two of these families were studied and shown not to have inherited the disease producing mutation. These results confirm that exon eight is a frequent site of mutation in familial adenomatous polyposis and should be examined routinely in families requesting genetic screening.
Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction (2005)

Abstract We report a strategy for conjugated polymer (CP)-based optical DNA detection with improved selectivity. The high sensitivity of CP-based biosensors arises from light harvesting by the CP and the related amplified fluorescent signal transduction. We demonstrate that the use of magnetic microparticles significantly improves the selectivity of this class of DNA sensors. Compared with previously reported DNA sensors with CP amplification, this novel sensing strategy displays excellent discrimination against non-cognate DNA in the presence of a protein mixture or even human serum. We also demonstrate that the magnetically assisted DNA sensor can conveniently identify even a single-nucleotide mismatch in the target sequence.
Blood flow to primary tumors and lymph node metastases in SMT-2A tumor-bearing rats following intravenous flunarizine. (1984)

Tumor blood flow is an important determinant of the efficacy of presently available antineoplastic treatment modalities. Using 113Sn-labeled microspheres, 25 micron in diameter, we measured blood flow to primary tumors and regional lymph node metastases in conscious SMT-2A mammary adenocarcinoma-bearing syngeneic rats following a single i.v. bolus injection of the calcium entry blocker, flunarizine. Tumor blood flow increased in a biphasic dose-dependent fashion; at a dose of 1 mg/kg, primary tumor blood flow increased approximately 50% (p less than 0.001) without a significant change in heart rate or blood pressure. The increase in flow was distributed to both the peripheral viable and central necrotic regions of the tumor and was still detectable 45 min following administration of the drug. A similar increase in blood flow was demonstrated for lymph node metastases (p less than 0.001).
Cell-of-origin chromatin organization shapes the mutational landscape of cancer (2015)

Cancer is a disease potentiated by mutations in somatic cells. Cancer mutations are not distributed uniformly along the human genome. Instead, different human genomic regions vary by up to fivefold in the local density of cancer somatic mutations, posing a fundamental problem for statistical methods used in cancer genomics. Epigenomic organization has been proposed as a major determinant of the cancer mutational landscape. However, both somatic mutagenesis and epigenomic features are highly cell-type-specific. We investigated the distribution of mutations in multiple independent samples of diverse cancer types and compared them to cell-type-specific epigenomic features. Here we show that chromatin accessibility and modification, together with replication timing, explain up to 86% of the variance in mutation rates along cancer genomes. The best predictors of local somatic mutation density are epigenomic features derived from the most likely cell type of origin of the corresponding malignancy. Moreover, we find that cell-of-origin chromatin features are much stronger determinants of cancer mutation profiles than chromatin features of matched cancer cell lines. Furthermore, we show that the cell type of origin of a cancer can be accurately determined based on the distribution of mutations along its genome. Thus, the DNA sequence of a cancer genome encompasses a wealth of information about the identity and epigenomic features of its cell of origin.
Automatic kidney segmentation in CT images based on multi-atlas image registration (2014)

Kidney segmentation is an important step for computer-aided diagnosis or treatment in urology. In this paper, we present an automatic method based on multi-atlas image registration for kidney segmentation. The method mainly relies on a two-step framework to obtain coarse-to-fine segmentation results. In the first step, down-sampled patient image is registered with a set of low-resolution atlas images. A coarse kidney segmentation result is generated to locate the left and right kidneys. In the second step, the left and right kidneys are cropped from original images and aligned with another set of high-resolution atlas images to obtain the final results respectively. Segmentation results from 14 CT angiographic (CTA) images show that our proposed method can segment the kidneys with a high accuracy. The average Dice similarity coefficient and surface-to-surface distance between segmentation results and reference standard are 0.952 and 0.913mm. Furthermore, the kidney segmentation in CT urography (CTU) and CTA images of 12 patients were performed to show the feasibility of our method in CTU images.
Coronary atherosclerotic wall thickening and vascular reactivity in humans. Elevated high-density lipoprotein levels ameliorate abnormal vasoconstriction in early atherosclerosis. (1994)

Coronary vasomotor responses to the endothelium-dependent dilator acetylcholine and to sympathetic stimulation by cold pressor test correlate with local atherosclerotic wall thickening. Thus, the degree of abnormal local vascular reactivity is closely related to the extent of atherosclerotic "plaque load" in human epicardial arteries in vivo. Elevated HDL cholesterol serum levels ameliorate abnormal vasoconstriction at any given extent of atherosclerotic wall thickening, suggesting that HDL cholesterol exerts a beneficial effect on abnormal vascular reactivity, a fundamental functional disturbance associated with coronary atherosclerosis.
Diameter-Selective Synthesis of Semiconductor Nanowires (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTDiameter-Selective Synthesis of Semiconductor NanowiresMark S. Gudiksen and Charles M. LieberView Author Information Department of Chemistry and Chemical Biology Harvard University, Cambridge, Massachusetts 02138 Cite this: J. Am. Chem. Soc. 2000, 122, 36, 8801–8802Publication Date (Web):August 22, 2000Publication History Received6 June 2000Published online22 August 2000Published inissue 1 September 2000https://pubs.acs.org/doi/10.1021/ja002008ehttps://doi.org/10.1021/ja002008erapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views2296Altmetric-Citations300LEARN 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:Catalysts,Colloids,Nanowires,Semiconductors,Wires Get e-Alerts
Determining the transgene containment level provided by chloroplast transformation (2007)

Plastids (chloroplasts) are maternally inherited in most crops. Maternal inheritance excludes plastid genes and transgenes from pollen transmission. Therefore, plastid transformation is considered a superb tool for ensuring transgene containment and improving the biosafety of transgenic plants. Here, we have assessed the strictness of maternal inheritance and the extent to which plastid transformation technology confers an increase in transgene confinement. We describe an experimental system facilitating stringent selection for occasional paternal plastid transmission. In a large screen, we detected low-level paternal inheritance of transgenic plastids in tobacco. Whereas the frequency of transmission into the cotyledons of F(1) seedlings was approximately 1.58 x 10(-5) (on 100% cross-fertilization), transmission into the shoot apical meristem was significantly lower (2.86 x 10(-6)). Our data demonstrate that plastid transformation provides an effective tool to increase the biosafety of transgenic plants. However, in cases where pollen transmission must be prevented altogether, stacking with other containment methods will be necessary to eliminate the residual outcrossing risk.
Design, fabrication and characterization of dispersive mirrors for ultrafast lasers (2010)

The design, fabrication and characterization of the dispersive multilayers are presented in this paper. Two kinds of dispersive mirror (High dispersion and 700-900nm Gires-Tournois mirrors) are designed by employing Particle Swarm Optimization method which demonstrates fast convergence speed and less dependence on the initial parameters. The mirrors are experimentally fabricated by home-made dual ion beam sputtering system with stable deposition rate and high density. A white light interferometry is built for precisely measuring the dispersion properties. A novel wavelet-based differentiation approach is introduced with considerable resistance to measurement error. The good agreement between the measured and designed results verifies the accuracy of both the fabrication and characterization method. Finally, two applications of Yb-doped photonic crystal fiber laser and Ti:Sapphire crystal oscillation cavity, which use our fabricated mirrors for dispersion compensation, are presented. Good output characteristics of both the two ultrafast laser systems are obtained.
Made-to-order metal-organic frameworks for trace carbon dioxide removal and air capture (2014)

Direct air capture is regarded as a plausible alternate approach that, if economically practical, can mitigate the increasing carbon dioxide emissions associated with two of the main carbon polluting sources, namely stationary power plants and transportation. Here we show that metal-organic framework crystal chemistry permits the construction of an isostructural metal-organic framework (SIFSIX-3-Cu) based on pyrazine/copper(II) two-dimensional periodic 4(4) square grids pillared by silicon hexafluoride anions and thus allows further contraction of the pore system to 3.5 versus 3.84 Å for the parent zinc(II) derivative. This enhances the adsorption energetics and subsequently displays carbon dioxide uptake and selectivity at very low partial pressures relevant to air capture and trace carbon dioxide removal. The resultant SIFSIX-3-Cu exhibits uniformly distributed adsorption energetics and offers enhanced carbon dioxide physical adsorption properties, uptake and selectivity in highly diluted gas streams, a performance, to the best of our knowledge, unachievable with other classes of porous materials.
A Pseudopressure-Pseudotime Transformation for the Analysis of Gas Well Closed Chamber Tests (1993)

ABSTRACT This paper presents methods for the analysis of gas-well, closed-chamber tests. It is shown that, in most cases, pseudopressure and pseudotime can be used to correlate gas-well, closed-chamber test results with the analogous liquid, slug-test solutions. This allows data from gas-well, closed-chamber tests to be analyzed using slug-test analysis procedures that assume single-phase flow of a slightly compressible liquid of constant compressibility and viscosity within the reservoir. Multirate analysis techniques were found to be applicable to gas-well, closed-chamber tests in terms of pseudopressure and time, not pseudotime.
bcl-2 Rearrangements in de novo diffuse large cell lymphoma. Association with distinctive clinical features (1993)

Analysis of bcl-2 rearrangements in de novo diffuse large cell lymphoma may identify a subset of patients with unusual clinical features.
Potent Metalloporphyrin Peroxynitrite Decomposition Catalyst Protects Against the Development of Doxorubicin-Induced Cardiac Dysfunction (2003)

Thus, peroxynitrite plays a key role in the pathogenesis of DOX-induced cardiac failure. Targeting peroxynitrite formation may represent a new cardioprotective strategy after DOX exposure or in other conditions associated with peroxynitrite formation, including myocardial ischemia/reperfusion injury.
Conservation, Preservation, and Digitization (1986)

Considerable attention has been focused recently on the problems of conservation and preservation of library materials. Particularly daunting are the scale of the problems and the enormous ongoing investment that will be required to address them. Currently proposed approaches include extensive microfilming of material, deacidification, and other repair measures. It is proposed that digital technologies be used to accomplish simultaneously the aims of conservation and improved access to materials. Various technologies are reviewed. Such an approach to conservation would form a natural extension to the current growth of electronic publishing, online catalogs, and online databases of journal abstracts. Furthermore, it would provide the greatest return for the massive investment that will be needed to save our deteriorating collections.
A Transition from Cellulose Swelling to Cellulose Dissolution by o-Phosphoric Acid:  Evidence from Enzymatic Hydrolysis and Supramolecular Structure (2006)

ADVERTISEMENT RETURN TO ISSUEPREVNoteA Transition from Cellulose Swelling to Cellulose Dissolution by o-Phosphoric Acid: Evidence from Enzymatic Hydrolysis and Supramolecular StructureY.-H. Percival Zhang, Jingbiao Cui, Lee R. Lynd, and Lana R. KuangView Author Information Biological Systems Engineering Department, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, Center for Nanomaterials Research, Dartmouth College, Hanover, New Hampshire 03755, and Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755 Cite this: Biomacromolecules 2006, 7, 2, 644–648Publication Date (Web):January 17, 2006Publication History Received21 October 2005Revised7 December 2005Published online17 January 2006Published inissue 1 February 2006https://pubs.acs.org/doi/10.1021/bm050799chttps://doi.org/10.1021/bm050799cbrief-reportACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views7118Altmetric-Citations440LEARN 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:Absorption,Cellulose,Dissolution,Hydrolysis,Peptides and proteins Get e-Alerts
Inhibition of Staphylococcal Enterotoxin A–Induced Superantigenic and Lethal Activities by a Monoclonal Antibody to Toxic Shock Syndrome Toxin–1 (2001)

Staphylococcal toxic shock syndrome is caused by a family of related superantigens that includes toxic shock syndrome toxin-1 (TSST-1) and staphylococcal enterotoxins (SEs) A, B, and C. The cross-inhibitory activity against SEA by a novel anti-TSST-1 monoclonal antibody (MAb), MAb5, which also cross-inhibits SEB-induced superantigenic activities, was investigated. MAb5 blocked SEA binding to human monocytes, cross-neutralized SEA-induced T cell mitogenesis and TNF-alpha secretion in human peripheral blood mononuclear cells, and prevented lethality in mice. Epitope mapping revealed that MAb5 binds to residues SEA(154-161) within the central alpha helix that is structurally highly conserved among TSST-1, SEA, and SEB. The cross-inhibitory activity of MAb5 is likely due to steric hindrance of this conserved motif, although the precise function of this motif shared among related staphylococcal superantigens remains to be further elucidated.
1-(((7,7-Dimethyl-2(S)-(2(S)-amino-4-(methylsulfonyl)butyramido)bicyclo[2.2.1]heptan-1(S)-yl)methyl)sulfonyl)-4-(2-methylphenyl)piperazine (L-368,899): An Orally Bioavailable, Non-Peptide Oxytocin Antagonist with Potential Utility for Managing Preterm Labor (1994)

Modifications to the previously reported spiroindenylpiperidine camphor-sulfonamide oxytocin (OT) antagonist L-366,509 have produced a new series of o-tolylpiperazine (TP) camphor-sulfonamides. A number of analogues in the TP series that incorporate a modified or unmodified L-methionine sulfone amide at the C2 endo position on the camphor ring exhibit high affinity for OT receptors (IC50 = 1.3-15 nM) and good selectivity for binding to OT versus arginine vasopressin V1a and V2 receptors. Several of these analogues were additionally characterized as potent antagonists of OT-stimulated contractions of the isolated and/or in situ rat uterus. Compound 7 (L-368,899) exhibited the best overall profile of OT receptor affinity (IC50 = 8.9 nM, rat uterus; 26 nM, human uterus), potency for inhibition of OT-stimulated contractions of the isolated rat uterus (pA2 = 8.9) and in situ rat uterus (AD50 = 0.35 mg/kg after intravenous (i.v.) administration and 7.0 mg/kg after intraduodenal administration), aqueous solubility (3.7 mg/mL at pH 5.0), and oral bioavailability in several species (35% (rat), 25% (dog), and 21% (chimpanzee) as estimated from radioreceptor determination of drug levels in plasma after oral and i.v. dosing). On the basis of these favorable properties, 7 has begun clinical testing for use as an oral and i.v. tocolytic agent. Molecular modeling alignment studies have provided support for the hypothesis that the TP camphor-sulfonamide portion of the non-peptide structures may serve as a mimetic of the important D-AA2-Ile3 dipeptide (AA = aromatic amino acid) found in many potent OT antagonists from the cyclic hexapeptide and OT analogue structural classes.
Color discrimination problems in digital TV systems (2005)

As large-scale direct view TV screens such as LCD flat panels or plasma displays become more and more affordable, consumers not only expect to buy a ‘big screen’ but to also get ‘great picture quality’. To enjoy the big picture, its viewing distance is significantly reduced. Consequently, more artifacts related to digital compression techniques show above the threshold of visual detectability. The artifact that caught our attention can be noticed within uniform color patches. It presents itself as ‘color blobs’ or color pixel clustering. We analyze the artifact’s color characteristics in RGB and CIELAB color spaces and underline them by re-synthesizing an artificial color patch. To reduce the visibility of the artifact, we elaborate several linear methods, such as low pass filtering and additive white gaussian noise and verify, whether they could correct or mask the visible artifacts. From the huge list of nonlinear filter methods we analyze the effect of high frequency dithering and pixel shuffling, also based on the idea that spatial visual masking should dominate signal correction. By applying shuffling, we generate artificial high frequency components within the uniform color patch. As a result, the artifact characteristics change significantly and its visibility is strongly reduced.