gebhart/patrepeval huggingface dataset:
Ligation of CD40 rescues Ramos‐Burkitt lymphoma B cells from calcium ionophore‐ and antigen receptor‐triggered apoptosis by inhibiting activation of the cysteine protease CPP32/Yama and cleavage of its substrate PARP (1996)

The new and growing family of interleukin-1beta-converting enzyme (ICE) cysteine proteases are now recognised to be major effectors of cellular death by apoptosis. Like other members of this family, the CPP32/Yama proform is activated by processing to its active heterodimeric enzyme or apopain when it likely contributes to the process of apoptosis by cleaving poly(ADP-ribose) polymerase (PARP) and thereby inhibiting much of its DNA repair activity. Apoptosis plays a fundamental role in the regulation of the immune system where it is involved in the selection of both T and B lymphocytes bearing antigen receptor (AgR) for non-self. Cells of the Ramos Epstein-Barr virus (EBV)-genome-negative Burkitt lymphoma (BL) B cell line (Ramos-BL) can be triggered into growth arrest and apoptosis by treating with the calcium ionophore ionomycin or by crosslinking their surface AgR with antibodies directed against immunoglobulin (Ig)M (anti-IgM). Ionomycin- and AgR-triggered growth arrest and apoptosis are arrested by signals transduced through the surface CD40 of Ramos-BL B cells. Both ionomycin and anti-IgM trigger activation of CPP32 and cleavage of PARP prior to the onset of apoptosis; this process is abrogated by treatment with anti-CD40 and is independent of Bcl-2 expression. A tripeptide inhibitor of ICE family cysteine proteases, Z-Val-Ala-Asp-fluoromethylketone (zVAD-fmk) inhibits ionomycin- and AgR-triggered CPP32 activation, PARP cleavage and apoptosis, but not growth arrest, in Ramos-BL B cells. Thus, in this report we demonstrate that in a physiological system, activation of endogenous members of the ICE family, including CPP32, and cleavage of the death substrate PARP act as major effectors of apoptotic death.
Design for wearability (2002)

Digital Technology is constantly improving as information becomes wireless. These advances demand more wearable and mobile form factors for products that access information. A product that is wearable should have wearability. This paper explores the concept of dynamic wearability, through design research. Wearability is defined as the interaction between the human body and the wearable object. Dynamic wearability extends that definition to include the human body in motion. Our research has been to locate, understand, and define the spaces on the human body where solid and flexible forms can rest-without interfering with fluid human movement. The result is a set of design guidelines embodied in a set of wearable forms. These wearable forms describe the three dimensional spaces on the body best suited for comfortable and unobtrusive wearability by design.
ProDy: Protein Dynamics Inferred from Theory and Experiments (2011)

ProDy is open source and freely available under GNU General Public License from http://www.csb.pitt.edu/ProDy/.
Tumor-Specific Inhibition of Membrane-Bound Complement Regulatory Protein Crry with Bispecific Monoclonal Antibodies Prevents Tumor Outgrowth in a Rat Colorectal Cancer Lung Metastases Model (2004)

Membrane-bound complement regulatory proteins (mCRP) inhibit complement-mediated tumor cell eradication in vitro and in vivo. Immunotherapy of cancer with monoclonal antibodies (mAbs) that activate complement might be hampered by expression of mCRP on tumor cells. An important strategy to improve mAb immunotherapy can be blocking or overwhelming mCRP at the tumor cells surface in a tumor-specific manner. In our study, we investigated the feasibility of this approach in vivo using bispecific mAbs (bi-mAbs). This study, performed in a syngeneic lung metastases model of rat (WAG/Rij) colorectal cancer, showed that modulation of mCRP on tumor cells resulted in significantly decreased tumor outgrowth. Opsonization of tumor cells with a bi-mAb directed against a tumor-associated antigen and rat mCRP Crry (MG4(2a)*5I2) almost completely prevented the outgrowth of lung tumors (0-7 tumors/rat; n = 17). Opsonization with mAb-cobra venom factor conjugates significantly reduced the number of lung tumors (23-59 tumors; n = 12) compared with the unconjugated MG4(2a) (175-246 tumors; n = 17; P = 0.008 and 0.014, respectively). The effect of MG4(2a)*5I2 was shown to be caused by increased complement activation due to inhibition of Crry. Moreover, prophylactic treatment with MG4(2a)*5I2 or MG4(2a) showed comparable results (3-24 and 215-472 tumors, P = 0.02; n = 6) as observed with pre-opsonized tumor cells without noticeable side effects, despite binding of MG4(2a)*5I2 to endothelium and leukocytes. These results demonstrate that Crry inhibits complement-mediated tumor cell eradication by immunotherapeutic mAbs and show that tumor-specific inhibition of complement regulatory proteins using bi-mAbs can significantly improve mAb-mediated immunotherapy.
Small Polaron Hopping in LixFePO4 Solid Solutions:  Coupled Lithium-Ion and Electron Mobility (2006)

Transition metal phosphates such as LiFePO(4) have been recognized as very promising electrodes for lithium-ion batteries because of their energy storage capacity combined with electrochemical and thermal stability. A key issue in these materials is to unravel the factors governing electron and ion transport within the lattice. Lithium extraction from LiFePO(4) results in a two-phase mixture with FePO(4) that limits the power characteristics owing to the low mobility of the phase boundary. This boundary is a consequence of low solubility of the parent phases, and its mobility is impeded by slow migration of the charge carriers. In principle, these limitations could be diminished in a solid solution, Li(x)FePO(4). Here, we show that electron delocalization in the solid solution phases formed at elevated temperature is due to rapid small polaron hopping and is unrelated to consideration of the band gap. We give the first experimental evidence for a strong correlation between electron and lithium delocalization events that suggests they are coupled. Furthermore, the exquisite frequency sensitivity of Mössbauer measurements provides direct insight into the electron hopping rate.
Bit-level systolic array for fast exponentiation in GF(2/sup m/) (1994)

This paper presents a new parallel-in-parallel-out bit-level systolic array with unidirectional data flow for computing exponentiation in GF(2/sup m/). The array is highly regular, modular, and thus well suited to very-large-scale-integration implementation. In addition, it can provide the maximum throughput in the sense of producing new results at a rate of one per clock cycle. As compared with a previously known systolic GF(2/sup m/) exponentiator with the same throughput performance, the proposed system requires much less chip area, has small latency, and is easier to incorporate fault-tolerant design.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effects of flavonoids on parietal cell acid secretion, gastric mucosal prostaglandin production and Helicobacter pylori growth. (1995)

The effect of the flavonoids flavone, flavanone and quercetin on parietal cell acid production, H+/K(+)-ATPase activity, gastric mucosal prostaglandin E2 biosynthesis and Helicobacter pylori growth was studied. All flavonoids inhibited acid production in isolated parietal cells in response to histamine and dibutyryl-cAMP stimulation (IC50 values between 26 and 139 mumol/l) and inhibited H+/K(+)-ATPase activity. Inhibition of H+/K(+)-ATPase activity was dependent on the ATP concentration. Fluorescence measurements showed that flavanone reacts with ATP. These findings indicate that the inhibitory action of flavonoids on H+/K(+)-ATPase activity is related to their ability to complex ATP. Flavone and flavanone (10 and 100 mumol/l) stimulated prostaglandin E2 production in isolated gastric mucosal cells. Furthermore, the compounds inhibited Helicobacter pylori growth in a concentration-dependent manner. From these finding it appears that flavonoids are a group of compounds which could have a therapeutic potential for treatment of gastrointestinal diseases associated with Helicobacter pylori infection.
Age-related macular degeneration: genome-wide association studies to translation (2015)

In recent years, genome-wide association studies (GWAS), which are able to analyze the contribution to disease of genetic variations that are common within a population, have attracted considerable investment. Despite identifying genetic variants for many conditions, they have been criticized for yielding data with minimal clinical utility. However, in this regard, age-related macular degeneration (AMD), the most common form of blindness in the Western world, is a striking exception. Through GWAS, common genetic variants at a number of loci have been discovered. Two loci in particular, including genes of the complement cascade on chromosome 1 and the ARMS2/HTRA1 genes on chromosome 10, have been shown to convey significantly increased susceptibility to developing AMD. Today, although it is possible to screen individuals for a genetic predisposition to the disease, effective interventional strategies for those at risk of developing AMD are scarce. Ongoing research in this area is nonetheless promising. After providing brief overviews of AMD and common disease genetics, we outline the main recent advances in the understanding of AMD, particularly those made through GWAS. Finally, the true merit of these findings and their current and potential translational value is examined.Genet Med 18 4, 283-289.
Controlled-Release Scale Inhibitor for Use in Fracturing Treatments (1995)

Abstract This paper describes results of laboratory and field testing of a solid, controlled-release scale inhibitor for use in fracturing treatments. Laboratory testing with a continuous flow apparatus has yielded inhibitor release rates under dynamic conditions. The inhibitor was tested to determine the minimum inhibitor concentration required to inhibit the formation of CaCO3, CaSO4, and BaSO4 scales in a brine. A model to predict the long-term release rate of the inhibitor was developed from data collected on the continuous flow apparatus. Data from treated wells will be compared with predictions of the model. Inhibitor release-rate testing in a continuous-flow apparatus shows that a solid, calcium-magnesium polyphosphate inhibitor has a sustained release profile. Release-rate testing shows that the inhibitor can be used up to 175°F. The inhibitor is compatible with both borate and zirconium crosslinked fracturing fluids and foamed fluids. The effective lifetime of the scale treatment can be predicted based on a model developed from laboratory data. The input variables required for the prediction include temperaturewater productionamount of inhibitorminimum effective concentration of inhibitor for the specific brine The model can be used to aid in the design of the scale inhibitor treatment.
Low-temperature manufacturing of fine pharmaceutical powders with supercritical fluid aerosolization in a Bubble Dryer® (2001)

Abstract Aerosols play an important role in thin film deposition, fine powder generation, and drug delivery. Green processes to form aerosols are needed to eliminate the use of toxic organic solvents and minimize the production of liquid wastes and the emission of halogenated and oxidant-forming organic compounds. We have developed a new patented process, Carbon Dioxide-Assisted Nebulization with a Bubble Dryer® (CAN-BD), that can generate a dense aerosol with small droplet and microbubble sizes that are dried to form particles less than 3 µm in diameter [1­9]. The process uses carbon dioxide as an aerosolization aid, and this permits drying at lower temperature than usually needed in conventional spray-drying. Intimate mixing of supercritical carbon dioxide with aqueous protein solutions causes the formation of microbubbles, which are rapidly dried in less than 5 s. The process is more environmentally benign than traditionally used methods, and is superior when thermally unstable materials are being processed. Fine-particle pharmaceutical powders can be rapidly and easily made by this new CAN-BD process, requiring less energy and eliminating residues of toxicologically or environmentally objectionable solvents. Manufacturing dry powders of pharmaceuticals for pulmonary drug delivery and increasing bioavailability are the purposes of developing and marketing the new Temco Bubble Dryer.
Molecular mass and carbohydrate structure of prostate specific antigen: Studies for establishment of an international PSA standard (1995)

Despite the widely accepted use of prostate specific antigen (PSA) as a marker of prostate cancer, this molecule has not yet been completely characterized. Past studies have well established, however, using both amino acid and cDNA sequencing techniques, that PSA contains 237 amino acids, with a molecular mass of 26,079 Da for the peptide moiety of the molecule. The present study reports analysis of this protein by ion spray mass spectrometry (ISMS) and analysis of its carbohydrate moiety by NMR spectroscopy. The predominant PSA molecular species detected by ISMS was at relative molecular mass (M(r)) of 28,430, indicating that PSA contains a carbohydrate residue of M(r) 2,351, for a total percentage of carbohydrate of 8.3%. Analysis of PSA by SDS-PAGE, however, showed a M(r) of 32,000 to 33,000, suggesting an overestimation of the molecular weight by the latter technique. The complete primary structure of the PSA carbohydrate chain was determined by NMR spectroscopy in combination with carbohydrate composition analysis. The experimentally determined carbohydrate content of PSA confirms that only one N-glycosylation site is occupied in the protein. The proposed carbohydrate structure is a diantennary N-linked oligosaccharide of the N-acetyllactosamine type, with a sialic acid group at the end of each of the two branches. In addition, our data indicate that approximately 70% of the PSA molecules contain a fucose group in the core chitobiose moiety. The calculated molecular weight of this carbohydrate structure (M(r) 2,351.8) is in excellent agreement with the predicted molecular weight of the carbohydrate group, based on the M(r) 28,430 for PSA measured by ion spray mass spectrometry and M(r) 26,079 calculated from the consensus sequence for the peptide portion of the molecule. ISMS of PSA is thus proposed as a convenient and reliable method of quality control, an indispensible step towards international standardization of this very important tumor marker for detection and monitoring of prostatic diseases, especially prostate cancer.
The issue of corrosion in dental implants: a review. (2009)

Pure titanium or titanium alloys, and to a lesser extent, zirconium, are metals that are often used in direct contact with host tissues. These metallic biomaterials are highly reactive, and on exposure to fluid media or air, quickly develop a layer of titanium dioxide (TiO2) or zirconium dioxide (ZrO2). This layer of dioxide forms a boundary at the interface between the biological medium and the metal structure, determining the degree of biocompatibility and the biological response of the implant. Corrosion is the deterioration a metal undergoes as a result of the surrounding medium (electrochemical attack), which causes the release of ions into the microenvironment. No metal or alloy is entirely inert in vivo. Corrosion phenomena at the interlace are particularly important in the evolution of both dental and orthopedic implants and one of the possible causes of implant failure after initial success. This paper comprises a review of literature and presents results of our laboratory experiments related to the study of corrosion, with special emphasis on dental implants. In situ degradation of a metallic implant is undesirable because it alters the structural integrity of the implant. The issue of corrosion is not limited to a local problem because the particles pmduced as a result could migrate to distant sites, whose evolution would require further studies.
SILVA conférence internationale sur l'arbre et la Forêt (1986)

International audience
Impairment of Hippocampal Mossy Fiber LTD in Mice Lacking mGluR2 (1996)

Subtype 2 of the metabotropic glutamate receptor (mGluR2) is expressed in the presynaptic elements of hippocampal mossy fiber-CA3 synapses. Knockout mice deficient in mGluR2 showed no histological changes and no alterations in basal synaptic transmission, paired-pulse facilitation, or tetanus-induced long-term potentiation (LTP) at the mossy fiber-CA3 synapses. Long-term depression (LTD) induced by low-frequency stimulation, however, was almost fully abolished. The mutant mice performed normally in water maze learning tasks. Thus, the presynaptic mGluR2 is essential for inducing LTD at the mossy fiber-CA3 synapses, but this hippocampal LTD does not seem to be required for spatial learning.
Efficacy, safety and immunogenicity of heptavalent pneumococcal conjugate vaccine in children (2000)

This heptavalent pneumococcal conjugate appears to be highly effective in preventing invasive disease in young children and to have a significant impact on otitis media.
C-Peptide Levels and Insulin Independence Following Autologous Nonmyeloablative Hematopoietic Stem Cell Transplantation in Newly Diagnosed Type 1 Diabetes Mellitus (2009)

clinicaltrials.gov Identifier: NCT00315133.
The Innate Immune Response to Infection (2004)

Table of Contents 1. Evolutionary Emergence and Interactions among Elements of the Innate and Combinatorial Responses, John J. Marchalonis, G. Kerr Whitfield, and Samuel F. Schluter 2. Drosophila Responses to Microbial Infection: an Overview, Jules A. Hoffman and Petros Ligoxygakis Mammalian Cells 3. Neutrophils: the Power Within, Taco W. Kujipers and Dirk Roos 4. The Biology of Macrophages, R. Tedjo Sasmono and David A. Hume 5. The Regulatory Role of Dendritic Cells in the Innate Immune Response, F. Granucci, S. Feau, I. Zanoni, G. Raimondi, N. Pavelka, C. Vizzardelli, and P. Ricciardi-Castagnoli 6. Roles of Mast Cells and Basophils in Innate Immunity, Stephen J. Galli, Devavani Chatterjea, and Mindy Tsai 7. Innate Natural Killer Cell Responses to Infection, Wayne M. Yokoyama 8. Urinary Tract Infection as a Model for Innate Mucosal Immunity, M. Samuelsson, G. Bergsten, H. Fischer, D. Karpman, I. Leijonhufvud, A.C. Lundstedt, P. Samuelsson, M.L. Svensson, B. Wullt, and C. Svanborg 9. Paneth Cells in Innate Immunity and Intestinal Inflammation, Satish Keshav Humoral Factors 10. Collectins and the Acute-Phase Response, Howard Clark, Thilo Stehle, Alan Ezekowitz, and Kenneth Reid 11. Complement and Its Receptors in Infection, Admar Verschoor and Michael C. Carroll 12. Coagulation and Innate Immunity, Charles T. Esmon Receptors 13. Toll-Like Receptors: Ligands and Signaling, Kiyoshi Takeda and Shizuo Akira 14. Toll-Like Receptors and Control of Adaptive Immunity, Gregory M. Barton, Chandrasheklar Pesare, and Ruslan Medzhitov 15. Antigen-Presenting Cell Receptors and Innate Immunity: Diversity, Recognition, and Responses, Siamon Gordon 16. The Function of Leukocyte Immunoglobulin-Like Receptors in Self-Tolerance, Viral Recognition, and Regulation of Adaptive Responses, Marco Colonna, and Winfried Barchet Effector Responses 17. Antimicrobial Peptides: Effectors of Innate Immunity, Michael Zasloff 18. Antimicrobial Proteins, Tomas Ganz and Robert I. Lehrer 19. Reactive Oxygen and Reactive Nitrogen Metabolites as Effector Molecules Against Infectious Pathogens, Christian Bogdan 20. Chemokines, Bernhard Moser 21. Lipids, K. Frank Austen and Yoshihide Kanaoka 22. Role of Innate Immunity in Microbial Infection, Peter Seiler, Ulrich Steinhoff, and Stephen H.E. Kaufmann
Production of D‐arabitol by a metabolic engineered strain of Bacillus subtilis (2006)

A novel method for D-arabitol production with a metabolically engineered Bacillus subtilis strain is described. A known transketolase-deficient and D-ribose-producing mutant of B. subtilis (ATCC 31094) was further modified by disruption of its rpi (D-ribose phosphate isomerase) gene to create a D-ribulose- and D-xylulose-producing B. subtilis strain. Expression of the D-arabitol phosphate dehydrogenase gene of Enterococcus avium in the D-ribulose- and D-xylulose-producing strain resulted in a strain of B. subtilis capable of converting D-glucose to D-arabitol with a high yield (38%) and little by-product formation.
Biosynthesis of Cholesterol and Other Sterols (2011)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTBiosynthesis of Cholesterol and Other SterolsW. David Nes*View Author InformationDepartment of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United StatesPhone: 806-743-1673. Fax: 806-742-1289. E-mail: [email protected]Cite this: Chem. Rev. 2011, 111, 10, 6423–6451Publication Date (Web):September 8, 2011Publication History Received11 January 2011Published online8 September 2011Published inissue 12 October 2011https://doi.org/10.1021/cr200021mCopyright © 2011 American Chemical SocietyRIGHTS & PERMISSIONSACS AuthorChoiceArticle Views17092Altmetric-Citations321LEARN 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 InReddit PDF (4 MB) Get e-AlertsSUBJECTS:Peptides and proteins,Steroids,Biosynthesis,Cholesterol,Fungi Get e-Alerts
Concentrations of Sialyloligosaccharides in Bovine Colostrum and Milk during the Prepartum and Early Lactation (2003)

Sialyloligosaccharides and sialylglycoconjugates in colostrum and milk are regarded to be important biological components with respect to be source of brain gangliosides in infant and to be antiinfectional components for the attack by the pathogenic bacteria and virus. Several acidic oligosaccharides have been characterised in both bovine and human milk or colostrum. The sialyloligosaccharide content of human colostrum and milk has been extensively studied, whereas that of cows milk and colostrum has received less attention. In this study, the concentrations of three sialyloligosaccharides of bovine colostrum and milk were determined at various stages during the prepartum and the first 7 d postpartum. The concentration of 3′SL (Neu5Ac(α2-3)Gal(β1-4)Glc) reached a maximum value of 0.85 mg/ml immediately following parturition while the concentrations of 6′SL (Neu5Ac(α2-6)Gal(β1-4)Glc) and 6′SLN (Neu5Ac(α2-6)Gal(β1-4)GlcNAc) of 0.14 and 0.12 mg/ml, respectively, were much lower at this initial stage, although these concentration were maximum immediately following parturition. Bovine colostrum, especially that collected immediately after parturition, may be suitable as a source of 3′SL and other sialyloligosaccharides for use as additives by the food or pharmaceutical industries.