gebhart/patrepeval huggingface dataset:
Role of gamma-carboxyglutamic acid residues in the binding of factor IXa to platelets and in factor-X activation (1992)

To study the requirements for factor-IXa binding to platelets and factor-X activation, we examined the consequences of chemical modification (factor IXMOD) or enzymatic removal (factor IXDES) of gamma-carboxyglutamic acid (Gla) residues. In the presence of factor VIIIa and factor X, there were 344 (+/- 52) binding sites/platelet for factor IXaMOD (apparent dissociation constant [kdapp] = 4.5 +/- 0.9 nmol/L) and 275 (+/- 35) sites/platelet for factor IXaDES (kdapp = 5.0 +/- 0.8 nmol/L) compared with 580 (+/-65) sites/platelet for normal factor IXa (factor IXaN) (kdapp = 0.61 +/- 0.1 nmol/L) and 300 (+/-62) sites/platelet for factor IX (kdapp = 2.9 +/- 0.29 nmol/L). The concentrations of factor IXaN, factor IXaMOD and factor IXaDES required for half-maximal rates of factor-Xa formation were 0.67 nmol/L, 3.5 nmol/L, and 6.7 nmol/L. Whereas maximal velocities (Vmax) of factor Xa formation by factor IXaMOD (approximately 0.8 nmol/L.min-1) and factor IXaN (approximately 10.5 nmol/L.min-1), turnover numbers (kcat expressed as moles of factor Xa formed per minute per mole of factor IXa bound), and values of catalytic efficiency (kcat/Km) were normal, indicating that the decreased rates of factor X activation observed with factor IXaMOD and factor IXaDES are solely a consequence of the abnormal binding of these proteins to thrombin-activated platelets in the presence of factor VIIIa and factor X. Thus, factor IXa binding to platelets is mediated in part, but not exclusively, by high-affinity Ca2+ binding sites in the Gla domain of factor IX.
Crystal Structures of Human Topoisomerase I in Covalent and Noncovalent Complexes with DNA (1998)

Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. The crystal structures at 2.1 and 2.5 angstrom resolution of reconstituted human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin is proposed on the basis of chemical and biochemical information combined with these three-dimensional structures of topoisomerase I-DNA complexes.
Principles of Digital Audio (1985)

From the Publisher:
Widely acknowledged as the bible of digital audio for both professional designers and engineering students, Principles of Digital Audio has been updated and expanded to introduce both audio and computer users to the myriad new technologies that are now transforming the field. 
Written in a highly readable style by one of the world's leading digital audio experts, the Third Edition offers complete details on advances in such areas as: 
Optical disc recording Interfacing and networking Perceptual coding theory and applications Digital audio broadcasting

This essential reference combines digital audio theory with examples of applications and provides a comprehensive database of valuable digital audio information. Included is unsurpassed coverage of digital audio fundamentals...digital audio recording and reproduction...error correction...magnetic tape storage...optical storage and transmission...compact disc formats...satellite broadcasting...MPEG coding...digital audio workstations...digital signal processing...and more. 
Filled with detailed discussions and more than 500 illustrations, the new edition of this classic guide will tell you about exciting breakthroughs in digital audio technology for the multimedia age.
Comparative Transcriptome and Secretome Analysis of Wood Decay FungiPostia placentaandPhanerochaete chrysosporium (2010)

Cellulose degradation by brown rot fungi, such as Postia placenta, is poorly understood relative to the phylogenetically related white rot basidiomycete, Phanerochaete chrysosporium. To elucidate the number, structure, and regulation of genes involved in lignocellulosic cell wall attack, secretome and transcriptome analyses were performed on both wood decay fungi cultured for 5 days in media containing ball-milled aspen or glucose as the sole carbon source. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), a total of 67 and 79 proteins were identified in the extracellular fluids of P. placenta and P. chrysosporium cultures, respectively. Viewed together with transcript profiles, P. chrysosporium employs an array of extracellular glycosyl hydrolases to simultaneously attack cellulose and hemicelluloses. In contrast, under these same conditions, P. placenta secretes an array of hemicellulases but few potential cellulases. The two species display distinct expression patterns for oxidoreductase-encoding genes. In P. placenta, these patterns are consistent with an extracellular Fenton system and include the upregulation of genes involved in iron acquisition, in the synthesis of low-molecular-weight quinones, and possibly in redox cycling reactions.
Co‐Continuous Composite Materials for Stiffness, Strength, and Energy Dissipation (2011)

Co-continuous polymer composite materials are designed and fabricated to achieve enhancements in stiffness, strength, and energy dissipation. The mutual constraints between two phases of the co-continuous structure enable enhanced dissipation by spreading of the plastic deformation and by containing cracking leading to a multitude of non-catastrophic dissipative events, which also provides damage tolerance of the co-continuous composites. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Blood–biomaterial interactions in a flow system in the presence of bacteria: Effect of protein adsorption (1995)

An in vitro continuous flow system with whole human blood was used to study blood-biomaterial interactions on a base polyurethane and three modified surfaces in the presence and absence of circulating Staphylococcus epidermidis. We hypothesized that the composition of the protein layer adsorbed on the surface of the biomaterial would influence the response of blood components and bacteria. We examined the test surfaces for adsorption of nine plasma proteins and adsorption profiles differed on the four surfaces. The positively charged surface, UC, adsorbed significantly higher amounts of fibronectin (P < .01), von Willebrand factor (P < .01), and fibrinogen (P < .05) than the other materials. As a consequence of increased adsorption of these adhesive proteins, the adhesion of platelets and bacteria was greater on UC than on any other surface. On the base polyurethane, BC, and the negatively charged surface, UA, protein adsorption was low, and these materials were largely free of adherent blood cells and bacteria. The heparinized surface, UH, adsorbed higher quantities (P < .01) of Hageman factor and high molecular weight kininogen relative to the other surfaces. Platelet adhesion, and surface coagulation were prominent on UC, and may have contributed to increased bacterial adhesion on this surface. In the presence of circulating bacteria, adsorption was generally lower than in the absence of bacteria. The pattern of protein adsorption was largely unaffected by the strain of circulating bacteria, but platelet responses (adhesion and activation) were greater in the presence of slime-producing S. epidermidis as compared to the non-slime-producing strain, suggesting that slime may have a direct activating effect on platelets.
A comprehensive set of sequence analysis programs for the VAX (1984)

The University of Wisconsin Genetics Computer Group (UWGCG) has been organized to develop computational tools for the analysis and publication of biological sequence data. A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system. The programs available and the conditions for transfer are described.
β-Amyloid Protein in Alzheimer's Disease (1991)

Beta-amyloid protein, a 42-43 amino acid polypeptide, accumulates abnormally in senile plaques and the cerebral vasculature in Alzheimer's disease. This polypeptide is derived from a membrane-associated precursor which has several isoforms expressed in many tissues. The precursor protein is processed constitutively within the beta-amyloid domain, leading to the release of the large N-terminal portion into the extracellular medium. beta-amyloid protein may be toxic to certain neuronal cell types and its early deposition may be an important event in the pathogenesis of Alzheimer's disease.
Erratum: Defining Protective Responses to Pathogens: Cytokine Profiles in Leprosy Lesions (1992)

In reference 5 of the report "Defining protective responses to pathogens: Cytokine profiles in leprosy lesions" by M. Yamamura et al. (11 Oct., p. 277), some of the primer sequences were given in the 3′→5′ rather than the 5′→3′ direction. The correct sequences should have been as follows. IL-3, ATGAGCCGCCTGCCCGTCCTG and AAGATCGCGAGGCTCAAAGTCGTCTGTTG; IL-5, ATGAGGATGCTTCTGCATTTG and TCAACTTTCTATTATCCACTCGGTGTTCATTAC; IL-7, ATGTTCCATGTTTCTTTTAGG and AGCTTTTCTTTAGTGCCCATCAAAATTTTATTCCAACA; and IL-8, ATGACTTCCAAGCTGGCCGTG and TTATGAATTCTCAGCCCTCTTCAAAAACTTCTC.
Overexpression of cytochrome P450 1B1 in advanced non-small cell lung cancer: a potential therapeutic target. (2009)

CYP1B1, EGFR and p53 overexpression are considered to be aggressive biomarkers for NSCLC, indicating that early-staged patients warrant an aggressive treatment when these factors are overexpressed in the cancer cells.
Motion-compensated video coding with adaptive perceptual quantization (1991)

The authors address the problem of adapting the Motion Picture Experts Group (MPEG) quantizer for scenes of different complexity (at bit rates around 1 Mb/s), such that the perceptual quality of the reconstructed video is optimized. Adaptive quantisation techniques conforming to the MPEG syntax can significantly improve the performance of the encoder. The authors concentrate on a one-pass causal scheme to limit the complexity of the encoder. The system employs prestored models for perceptual quality and a bit rate that have been experimentally derived. A framework is provided for determining these models as well as adapting them to locally varying scene characteristics. The variance of an 8*8 (luminance) block is basic to the techniques developed. Following standard practice, it is defined as the average of the square of the deviations of the pixels in the block from the mean pixel value.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
RNA-sequencing based identification of crucial genes for esophageal squamous cell carcinoma (2015)

These identified DEGs may be underlying targets for diagnosis and treatment of esophageal squamous cell carcinoma.
Interleukin 6 (IL-6) in serum and urine of renal transplant recipients. (1988)

Hybridoma growth factor (HGF) is a 20-25 kD protein, supporting the growth of hybridoma cells in vitro and capable of replacing feeder cells. It was shown to be produced by human monocytes and a number of cultured cell lines. Recently, HGF was found to be identical to interferon-beta 2 or 26 kD protein and BSF-2, and was renamed interleukin 6 (IL-6). Using a sensitive bio-assay we were able to measure IL-6 activity in the serum and urine of healthy volunteers and renal transplant recipients. Low levels of IL-6 were present in the serum but not in the urine of healthy individuals. In contrast, both serum and urine of renal transplant recipients contained high levels of IL-6 directly after transplantation and during acute rejection episodes. On the basis of kinetic studies of the IL-6 response, it is concluded that serial measurement of IL-6, especially in urine, may be of value in monitoring renal transplant recipients. Moreover, the sensitivity of the bioassay will allow for detailed studies as to the biological significance of IL-6 in health and disease.
Purification and characterization of protein methylase II fromHelicobacter pylori (2001)

Protein methylase II (AdoMet:protein-carboxyl O-methyltransferase, EC 2.1.1.24) was identified and purified 115-fold from Helicobacter pylori through Q-Sepharose ion exchange column, AdoHcy-Sepharose 4B column, and Superdex 200 HR column chromatography using FPLC. The purified preparation showed two protein bands of about 78 kDa and 29 kDa molecular mass on SDS-PAGE. On non-denaturing gel electrophoresis, the enzyme migrated as a single band with a molecular mass of 410 kDa. In addition, MALDI-TOF-MS analysis and Superdex 200 HR column chromatography of the purified enzyme showed a major mass signal with molecular mass values of 425 kDa and 430 kDa, respectively. Therefore, the above results led us to suggest that protein methylase II purified from H. pylori is composed of four heterodimers with 425 kDa (4x(78+29)=428 kDa). This magnitude of molecular mass is unusual for protein methylases II so far reported. The enzyme has an optimal pH of 6.0, a K(m) value of 5.0x10(-6) M for S-adenosyl-L-methionine and a V(max) of 205 pmol methyl-(14)C transferred min(-1) mg(-1) protein.
Deposition of Organic Material by the Tip of a Scanning Force Microscope (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDeposition of Organic Material by the Tip of a Scanning Force MicroscopeManfred Jaschke and Hans-Juergen ButtCite this: Langmuir 1995, 11, 4, 1061–1064Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/la00004a004https://doi.org/10.1021/la00004a004research-articleACS PublicationsRequest reuse permissionsArticle Views637Altmetric-Citations125LEARN 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
Advanced Ceramic Materials and Processes for Three-Dimensional Printing (3DP) (2006)

The University of Washington and ExOne, Inc. are collaborating in the development of advanced ceramic materials and processes for three-dimensional printing (3DP). The focus of the research to be presented is work funded by the National Science Foundation to develop a biocompatible alumina-based system for medical and dental applications. Materials design, characterization, and processing considerations will be discussed.
A Fast Wavelet-Based Reconstruction Method for Magnetic Resonance Imaging (2011)

In this work, we exploit the fact that wavelets can represent magnetic resonance images well, with relatively few coefficients. We use this property to improve magnetic resonance imaging (MRI) reconstructions from undersampled data with arbitrary k-space trajectories. Reconstruction is posed as an optimization problem that could be solved with the iterative shrinkage/thresholding algorithm (ISTA) which, unfortunately, converges slowly. To make the approach more practical, we propose a variant that combines recent improvements in convex optimization and that can be tuned to a given specific k-space trajectory. We present a mathematical analysis that explains the performance of the algorithms. Using simulated and in vivo data, we show that our nonlinear method is fast, as it accelerates ISTA by almost two orders of magnitude. We also show that it remains competitive with TV regularization in terms of image quality.
Introduction to the programming of deep brain stimulators (2002)

The clinical success of deep brain stimulation (DBS) for treating Parkinson's disease, tremor, or dystonia critically depends on the quality of postoperative neurologic management. Movement disorder specialists becoming involved with this therapy need to acquire new skills to optimally adapt stimulation parameters and medication after implantation of a DBS system. In clinical practice, the infinite number of possible parameter settings in DBS can be reduced to few relevant combinations. In this article, the authors describe a general scheme of selecting stimulation parameters in DBS and provide clinical and neurophysiological arguments for such a standardized algorithm. They also describe noninvasive technical trouble shooting by using programming features of the commercially available neurostimulation devices.
Albumin-Associated Lipids Regulate Human Embryonic Stem Cell Self-Renewal (2008)

Our discovery of the role played by albumin-associated lipids in stimulating hESC self-renewal constitutes a significant advance in the knowledge of how hESC pluripotency is maintained by extracellular factors and has important applications in the development of increasingly chemically defined hESC culture systems.
Arterial Effects of Canakinumab in Patients With Atherosclerosis and Type 2 Diabetes or Glucose Intolerance (2016)

There were no statistically significant effects of canakinumab on measures of vascular structure or function. Canakinumab reduced markers of inflammation (high-sensitivity C-reactive protein and interleukin-6), and there were modest increases in levels of total cholesterol and triglycerides. (Safety & Effectiveness on Vascular Structure and Function of ACZ885 in Atherosclerosis and Either T2DM or IGT Patients; NCT00995930).
Different mechanisms for cellular internalization of the HIV‐1 Tat‐derived cell penetrating peptide and recombinant proteins fused to Tat (2002)

Translocation through the plasma membrane is a major limiting step for the cellular delivery of macromolecules. A promising strategy to overcome this problem consists in the chemical conjugation (or fusion) to cell penetrating peptides (CPP) derived from proteins able to cross the plasma membrane. A large number of different cargo molecules such as oligonucleotides, peptides, peptide nucleic acids, proteins or even nanoparticles have been internalized in cells by this strategy. One of these translocating peptides was derived from the HIV-1 Tat protein. The mechanisms by which CPP enter cells remain unknown. Recently, convincing biochemical and genetic findings has established that the full-length Tat protein was internalized in cells via the ubiquitous heparan sulfate (HS) proteoglycans. We demonstrate here that the short Tat CPP is taken up by a route that does not involve the HS proteoglycans.
Microcapsule Modification with Peroxidase-Catalyzed Phenol Polymerization (2004)

A biocatalytic polymer synthesis on a surface of polyelectrolyte microcapsules was studied. Horseradish peroxidase assembled in nanoorganized capsule walls by alternate adsorption with linear polyions retains its activity in reactions of enzyme-catalyzed polymerization of 4-oxyphenols. It allowed controllable synthesis of a phenolic polymer layer on microcapsule walls using an outermost surface peroxidase layer as a template. By varying the phenol type, buffer pH, and reaction component concentrations, the phenolic polymer coating of the capsules with a thickness in the range 20-50 nm was formed. The polymeric products are fluorescent, which provided a good opportunity for confocal image analysis of the capsule wall structure and the attached layer. The influence of a phenolic polymer layer on the permeability of the capsule walls was investigated.
CpG Oligodeoxynucleotides and Interleukin-12 Improve the Efficacy ofMycobacterium bovisBCG Vaccination in Mice Challenged withM. tuberculosis (2000)

Mycobacterium bovis bacillus Calmette-Guérin (BCG) is the only vaccine approved for prevention of tuberculosis. It has been postulated that serial passage of BCG over the years may have resulted in attenuation of its effectiveness. Because interleukin-12 (IL-12) and oligodeoxynucleotides (ODN) containing cytidine phosphate guanosine (CpG) motifs have been shown to enhance Th1 responses in vivo, they were chosen as adjuvants to increase the effectiveness of BCG vaccination. In this report, mice were vaccinated with BCG with or without IL-12 or CpG ODN and then challenged 6 weeks later via the aerosol route with the Erdman strain of M. tuberculosis. Mice vaccinated with BCG alone showed a 1- to 2-log reduction in bacterial load compared with control mice that did not receive any vaccination prior to M. tuberculosis challenge. Moreover, the bacterial loads of mice vaccinated with BCG plus IL-12 or CpG ODN were a further two- to fivefold lower than those of mice vaccinated with BCG alone. As an immune correlate, the antigen-specific production IFN-gamma and mRNA expression in spleen cells prior to challenge were evaluated. Mice vaccinated with BCG plus IL-12 or CpG ODN showed enhanced production of IFN-gamma compared with mice vaccinated with BCG alone. Finally, granulomas in BCG-vaccinated mice were smaller and more lymphocyte rich than those in unvaccinated mice; however, the addition of IL-12 or CpG ODN to BCG vaccination did not alter granuloma formation or result in added pulmonary damage. These observations support a role for immune adjuvants given with BCG vaccination to enhance its biologic efficacy.
A Comparative Review of Thermography as a Breast Cancer Screening Technique (2009)

Breast cancer is the most frequently diagnosed cancer of women in North America. Despite advances in treatment that have reduced mortality, breast cancer remains the second leading cause of cancer induced death. Several well established tools are used to screen for breast cancer including clinical breast exams, mammograms, and ultrasound. Thermography was first introduced as a screening tool in 1956 and was initially well accepted. However, after a 1977 study found thermography to lag behind other screening tools, the medical community lost interest in this diagnostic approach. This review discusses each screening tool with a focus brought to thermography. No single tool provides excellent predictability; however, a combination that incorporates thermography may boost both sensitivity and specificity. In light of technological advances and maturation of the thermographic industry, additional research is required to confirm the potential of this technology to provide an effective non-invasive, low risk adjunctive tool for the early detection of breast cancer.