gebhart/patrepeval huggingface dataset:
Stable Isotope Tracers Applied to Measuring Rates of Protein Synthesis and Breakdown in Muscle: Principles and Applications (2011)

Muscle is in a constant state of turnover, meaning that it is continuously synthesized and broken down. The balance between the rates of synthesis and breakdown determines if an individual is gaining or loosing muscle mass. It is therefore of interest in a variety of physiological circumstances to quantify the rates of muscle protein synthesis and breakdown. Tracer methodology using both radioactive and stable isotopes has been used in a wide variety of kinetic studies, including measurement of synthetic and breakdown rates of various compounds. Stable isotopes are particularly suited for the study of muscle protein metabolism, as multiple amino acid tracers can be used simultaneously, and multiple labels can be used with any individual amino acid, including labeling the nitrogen with 15N. Two basic approaches can be used to measure muscle protein synthesis. The direct incorporation of a labeled amino acid is the most conventional. This technique involves infusion or injection of tracer and measurement of subsequent incorporation into muscle protein over time. The measurement of the precursor enrichment, which is usually taken to be the free intracellular pool of the tracer amino acid, is necessary to calculate the actual rate of synthesis. Alternatively, the rate of muscle protein synthesis can be derived from the rate of uptake of an amino acid from blood. In this case incorporation of the amino acid into protein must be its only metabolic fate within the muscle. The basic principle of measuring muscle protein breakdown is to determine the rate at which intracellular amino acid tracer is diluted by the appearance of unlabeled amino acid that is not coming from the plasma. There are different approaches to accomplishing this measurement, and the choice of the optimal depends of the method used to measure protein synthesis. Ideally, methods to measure synthesis and breakdown are compatible (i.e., the same units) to enable calculation of the balance between synthesis and breakdown to determine if there is a net gain or loss in muscle protein.
Phantom materials for elastography (1997)

Acoustic and mechanical properties are reported for gelatin materials used to construct tissue-like phantoms for elasticity imaging (elastography). A device and procedure for measuring elastic properties are described. The measured compression forces were comparable to results obtained from finite element analysis when linear elastic media are assumed. Also measured were the stress relaxation, temporal stability, and melting point of the materials. Aldehyde concentration was used to increase the stiffness of the gelatin by controlling the amount of collagen cross-linking. A broad range of tissue-like elastic properties was achieved with these materials, although gels continued to stiffen for several weeks. The precision for elastic modulus measurements ranged from less than 0.1% for 100 kPa samples to 8.9% for soft (<10 kPa), sticky samples.
Raman Spectroscopic Characterization of Porcine Brain Tissue Using a Single Fiber-Optic Probe (2006)

Accurate targeting of diseased and healthy tissue has significantly been improved by MRI/CT-based navigation systems. Recently, intraoperative MRI navigation systems have proven to be powerful tools for the guidance of the neurosurgical operations. However, the widespread use of such systems is held back by the costs, the time consumption during operation, and the need for MR-compatible surgical devices. Raman spectroscopy is a nondestructive optical technique that enables real-time tissue identification and classification and has proved to be a powerful diagnostic tool in a large number of studies. In the present report, we have investigated the possibility of distinguishing different brain structures by using a single fiber-optic probe to collect Raman scattered light in the high-wavenumber region of the spectrum. For the Raman measurements, 7 pig brains were sliced in the coronal plain and Raman spectra were obtained of 11-19 anatomical structures. Adjacent brain structures could be distinguished based on their Raman spectra, reflecting the differences in their biochemical composition and illustrating the potential Raman spectroscopy holds as a guidance tool during neurosurgical procedures.
Elimination of Daudi lymphoblasts from human bone marrow using avidin- biotin immunoadsorption (1986)

Biotinylated antibodies and an avidin-Sepharose 6MB column were utilized in a novel approach to deplete selected cell populations from human bone marrow. Fluorescein-labeled Daudi lymphoblasts were mixed with bone marrow mononuclear cells in a model system, and removal of Daudi cells was quantitatively assessed with an inverted fluorescent microscope. Treatment using the biotinylated monoclonal antibody 2H7 reactive with Bp32 antigen (expressed on Daudi cells) followed by passage over avidin-Sepharose produced greater than two logs of Daudi cell removal from bone marrow. An alternative method was tested by treating cells successively with nonbiotinylated monoclonal antibody and biotinylated goat antimouse immunoglobulin followed by passage over avidin-Sepharose. Up to three logs of Daudi cells could be eliminated from bone marrow with quantitative recovery of hematopoietic progenitors. The use of biotinylated goat antimouse immunoglobulin eliminates the need to prepare a biotin conjugate of each individual monoclonal antibody. The clinical application of cellular immunoadsorption using the avidin-biotin system may prove useful in bone marrow transplantation.
Purification and characterization of the Escherichia coli thermoresistant gluconokinase encoded by the gntK gene (1996)

A thermoresistant gluconokinase encoded by the gntK gene of Escherichia coli K-12 was purified and characterized. The Km values of the purified enzyme for gluconate and ATP are 42 microM and 123 microM, respectively, and the activity was not altered by the presence of pyruvate. The enzyme was shown to function as a dimer with two identical subunits of 18.4 kDa. These characteristics appear to be distinct from those of the gluconokinase reported by E.I. Vivas, A. Liendo, K. Dawidowicz, and T. Istúriz (1994) J. Basic. Microbiol. 16, 117-122.
vNUMA: Virtual shared-memory multiprocessors (2009)

Shared memory systems, such as SMP and ccNUMA topologies, simplify programming and administration. On the other hand, systems without hardware support for shared memory, such as clusters of commodity workstations, are commonly used due to cost and flexibility considerations. In this thesis, virtualisation is proposed as a technique that can bridge the gap between these architectures. The resulting system, vNUMA, is a hypervisor with a unique feature: it provides the illusion of shared memory across separate nodes on a fast network. This allows a cluster of workstations to be transformed into a single shared memory multiprocessor, supporting existing operating systems and applications. Such an approach could also have applications for emerging highly-parallel architectures, allowing a shared memory programming model to be retained while reducing hardware complexity. To build such a system, it is necessary to meld both a high-performance hypervisor and a high-performance distributed shared memory (DSM) system. This thesis addresses the challenges inherent in both of these tasks. First, designing an efficient hypervisor layer is considered; since vNUMA is implemented on the Itanium processor architecture, this is with particular reference to Itanium processor virtualisation. Then, novel DSM protocols are developed that allow SMP consistency models to be reproduced while providing better performance than a simple atomically-consistent DSM system. Finally, the system is evaluated, proving that it can provide good performance and compelling advantages for a variety of applications.
Evaluating and Controlling the Risks of Financial Product Deregulation (1985)

The walls separating commercial banks and thrifts from non-bank financial institutions are beginning to show serious cracks. Market forces and rapid advances in technology are impelling both bank and non-bank enterprises to search for loopholes in the highly complex legal framework governing financial organizations in order to expand into new markets and to offer new services. During its first term, the Reagan Administration proposed legislation that would have permitted bank holding companies to offer virtually any financial service through separate non-bank subsidiaries Since 1984, however, Congress has been stalemated on this issue, reflecting both bitter divisions between the various financial interests involved and continued disagreement over the likely effects of financial product deregulation. This article takes advantage of the apparent hiatus in legislative activity to examine the implications of financial product deregulation for the safety of the financial system.
Sequence motifs in adenoviral DNA block immune activation by stimulatory CpG motifs (1998)

Unmethylated CpG dinucleotides in particular base contexts (CpG-S motifs) are relatively common in bacterial DNA but are rare in vertebrate DNA. B cells and monocytes have the ability to detect such CpG-S motifs that trigger innate immune defenses with production of Th1-like cytokines. Despite comparable levels of unmethylated CpG dinucleotides, DNA from serotype 12 adenovirus is immune-stimulatory, but serotype 2 is nonstimulatory and can even inhibit activation by bacterial DNA. In type 12 genomes, the distribution of CpG-flanking bases is similar to that predicted by chance. However, in type 2 adenoviral DNA the immune stimulatory CpG-S motifs are outnumbered by a 15- to 30-fold excess of CpG dinucleotides in clusters of direct repeats or with a C on the 5' side or a G on the 3' side. Synthetic oligodeoxynucleotides containing these putative neutralizing (CpG-N) motifs block immune activation by CpG-S motifs in vitro and in vivo. Eliminating 52 of the 134 CpG-N motifs present in a DNA vaccine markedly enhanced its Th1-like function in vivo, which was increased further by the addition of CpG-S motifs. Thus, depending on the CpG motif, prokaryotic DNA can be either immune-stimulatory or neutralizing. These results have important implications for understanding microbial pathogenesis and molecular evolution and for the clinical development of DNA vaccines and gene therapy vectors.
Modeling and analysis of soft-test/repair for CCD-based digital X-ray systems (2003)

Modern X-ray imaging systems evolve toward digitization for reduced cost, faster time-to-diagnosis, and improved diagnostic confidence. For the digital X-ray systems, charge coupled device (CCD) technology is commonly used to detect and digitize optical X-ray image. This paper presents a novel soft-test/repair approach to overcome the defective pixel problem in CCD-based digital X-ray systems through theoretical modeling and analysis of the test/repair process. There are two possible solutions to cope with the defective pixel problem in CCDs: one is the hard-repair approach and another is the proposed soft-test/repair approach. Hard-repair approach employs a high-yield, expensive reparable CCD to minimize the impact of hard defects on the CCD, which occur in the form of noise propagated through A/D converter to the frame memory. Therefore, less work is needed to filter and correct the image at the end-user level while it maybe exceedingly expensive to practice. On the other hand, the proposed soft-test/repair approach is to detect and tolerate defective pixels at the digitized image level; thereby, it is inexpensive to practice and on-line repair can be done for noninterrupted service. It tests the images to detect the detective pixels and filter noise at the frame memory level and caches them in a flash memory in the controller for future repair. The controller cache keeps accumulating all the noise coordinates and preprocesses the incoming image data from the A/D converter by repairing them. The proposed soft-test/repair approach is particularly devised to facilitate hardware level implementation ultimately for real-time telediagnosis. Parametric simulation results demonstrate the speed and virtual yield enhancement by using the proposed approach; thereby highly reliable, yet inexpensive, soft-test/repair of CCD-based digital X-ray systems can be ultimately realized.
The cytokines: a review of interleukins. (1997)

Over the past decade much has been elucidated concerning the cellular and molecular basis for health and disease. This increase in information has created a large gap in knowledge between the research scientist and the clinician. The following review attempts to bridge this gap by describing each of the thirteen interleukins and relating their functions to the clinical presentation of periodontal disease.
Cyclohexyl-Substituted Polyglycolides with High Glass Transition Temperatures (2007)

The substituted glycolides rac-dicyclohexylglycolide (rac-3,6-dicyclohexyl-1,4-dioxane-2,5-dione), meso-dicyclohexylglycolide, R,R-dicyclohexylglycolide, and rac-methylcyclohexylglycolide (rac-3-cyclohexyl-6-methyl-1,4-dioxane-2,5-dione) have been synthesized, and both solution and bulk polymerizations of these monomers are reported. The polymerization kinetics of these new monomers were studied and compared to data for rac-diisopropylglycolide (rac-3,6-diisopropyl-1,4-dioxane-2,5-dione) and rac-lactide. The solution polymerization rates followed the order: rac-dicyclohexylglycolide < rac-diisopropylglycolide < rac-methylcyclohexylglycolide < rac-lactide. The glass transition temperature of poly(rac-dicyclohexylglycolide) is 98 °C, consistent with a stiff polyglycolide backbone. meso-Dicyclohexylglycolide and R,R-dicyclohexylglycolide were synthesized and polymerized to study the effect of stereochemistry on the polymer properties. The glass transition temperature of meso-dicyclohexylglycolide was 96 °C, while that of poly(R,R-dicyclohexylglycolide) increased to 104 °C. While NMR spectroscopy indicated that poly(R,R-dicyclohexylglycolide) undergoes minimal racemization during polymerization, differential scanning calorimetry (DSC), X-ray diffraction (XRD), and polarized optical microscopy confirmed that the polymer was amorphous.
Structures of Multi-Branched Dextrins Produced by Saccharifying α-Amylase from Starch (1975)

From the digest of beta-limit dextrin (prepared from glutinous rice starch) with saccharifying alpha-amylase of Bacillus subtilis [EC 3.2.1.1] (BSA), two extensibely branched dextrins consisting of nine (No. 6, Fig. 1) and ten (No 7, Fig.1) glucose units were isolated by paper chromatography. Structural analysis using various enzymes revealed that No. 6 and No. 7 were both mixtures of four triply branched dextrins. They had structures which were built up with 63-alpha-glucosylmaltotriose and/or 62-alpha-glucosylmaltose as a linking unit. However, the branching configuration and the minimum alpha-1, 4-glucosidic linkages existing between two branches followed one of the three structures shown below: (see article).
Inclusion or Exclusion of Intratumoral Vessels in Relative Cerebral Blood Volume Characterization in Low-Grade Gliomas: Does It Make a Difference? (2008)

We assessed the influence of inclusion (method 1) and exclusion (method 2) of intratumoral vessels when determining maximum relative cerebral blood volume (rCBVmax) in 3 types of low-grade gliomas (LGGs): astrocytomas, oligoastrocytomas, and oligodendrogliomas. Method 1 yielded significantly higher mean rCBVmax than method 2. However, only method 2 demonstrated a significant (P = .026) association between rCBVmax and membership of a differently ranked histologic category. Exclusion of intratumoral vessels appears, therefore, preferable when determining rCBVmax in LGGs.
A Non-Chromatographic Method for the Purification of a Bivalently Active Monoclonal IgG Antibody from Biological Fluids (2009)

This paper describes a method for the purification of monoclonal antibodies (rat anti-2,4-dinitrophenyl IgG: IgG(DNP); and mouse antidigoxin IgG: IgG(Dgn)) from ascites fluid. This procedure (for IgG(DNP)) has three steps: (i) precipitation of proteins heavier than immunoglobulins with ammonium sulfate; (ii) formation of cyclic complexes of IgG(DNP) by causing it to bind to synthetic multivalent haptens containing multiple DNP groups; (iii) selective precipitation of these dimers, trimers, and higher oligomers of the target antibody, followed by regeneration of the free antibody. This procedure separates the targeted antibody from a mixture of antibodies, as well as from other proteins and globulins in a biological fluid. This method is applicable to antibodies with a wide range of monovalent binding constants (0.1 microM to 0.1 nM). The multivalent ligands we used (derivatives of DNP and digoxin) isolated IgG(DNP) and IgG(Dgn) from ascites fluid in yields of >80% and with >95% purity. This technique has two advantages over conventional chromatographic methods for purifying antibodies: (i) it is selective for antibodies with two active Fab binding sites (both sites are required to form the cyclic complexes) over antibodies with one or zero active Fab binding sites; (ii) it does not require chromatographic separation. It has the disadvantage that the structure of the hapten must be compatible with the synthesis of bi- and/or trivalent analogues.
Identification of a Linear Epitope in Sortilin That Partakes in Pro-neurotrophin Binding (2010)

Sortilin acts as a cell surface receptor for pro-neurotrophins (pro-NT) that upon complex formation with the p75 neurotrophin receptor (p75(NTR)) is able to signal neuronal cell death. Here we screened a sortilin peptide library comprising 16-mer overlapping sequences for binding of the pro-domains of nerve growth factor and brain-derived neurotrophic factor. We find that a linear surface-exposed sequence, (163)RIFRSSDFAKNF(174), constitutes an important pro-NT binding epitope in sortilin. Systematic mutational analysis revealed residues Arg(163), Phe(165), Arg(166), and Phe(170) to be critical for the interaction. Expression of a sortilin mutant in which these four amino acids were substituted by alanines disrupted pro-NT binding without affecting receptor heterodimerization with p75(NTR) or binding of ligands that selectively engages the centrally located tunnel in the beta-propeller of sortilin. We furthermore demonstrate that a peptide comprising the ligand-binding epitope can prevent pro-NT-induced apoptosis in RN22 schwannoma cells.
Predominant VHgenes expressed in innate antibodies are associated with distinctive antigen-binding sites (1999)

Antibodies to phosphatidylcholine (PtC), a common constituent of mammalian and bacterial cell membranes, represent a large proportion of the natural antibody repertoire in mice. Previous studies of several mouse strains (e.g., C57BL/6) have shown that anti-PtC antibodies are mainly encoded by the VH11 and VH12 immunoglobulin heavy chain variable region gene families. We show here, however, that VH11 and VH12 encode only a small proportion of the anti-PtC antibodies in BALB/c mice. Instead, VHQ52-encoded antibodies predominate in this strain. In addition, two-thirds of the cells expressing VHQ52 family genes use a single gene (which, interestingly, has been previously shown to predominate in the anti-oxazolone response). We also show here that in anti-PtC antibodies from all strains, the distinctive antigen-binding sites associated with VHQ52 differ substantially from those associated with VH11 and VH12. That is, VHQ52-containing transcripts preferentially use the joining region JH4 rather than JH1 and exhibit more diverse complementarity-determining region 3 (CDR3) junctions with more N-region nucleotide additions at the gene segment junctions. Thus, the VH gene family that predominates in the anti-PtC repertoire differs among mouse strains, whereas the distinctive VHDJH rearrangements (CDR3, JH) associated with each VH gene family are similar in all strains. We discuss these findings in the context of a recent hypothesis suggesting that CDR3 structure, independent of VH framework, is sufficient to define the specificity of an antibody.
Myristyl and palmityl acylation of the insulin receptor. (1987)

The presence of covalently bound fatty acids in the insulin receptor has been explored in cultured human (IM-9) lymphocytes. Both alpha (Mr = 135,000) and beta (Mr = 95,000) subunits of the receptor incorporate [3H]myristic and [3H]palmitic acids in a covalent form. The effects of alkali and hydroxylamine on the labeled subunits indicate the existence of two different kinds of fatty acid linkage to the protein with chemical stabilities compatible with amide and ester bonds. The alpha subunit contains only amide-linked fatty acid while the beta subunit has both amide- and ester-linked fatty acids. Analysis by high performance liquid chromatography after acid hydrolysis of the [3H]myristate- and [3H]palmitate-labeled subunits demonstrates the fatty acid nature of the label. Furthermore, both [3H]myristic and [3H]palmitic acids are found attached to the receptor subunits regardless of which fatty acid was used for labeling. The incorporation of fatty acids into the insulin receptor is dependent on protein synthesis and is also detectable in the Mr = 190,000 proreceptor form. Fatty acylation is a newly identified post-translational modification of the insulin receptor which may have an important role in its interaction with the membrane and/or its biological function.
The Antiviral Effects of Na,K-ATPase Inhibition: A Minireview (2018)

Since being first described more than 60 years ago, Na,K-ATPase has been extensively studied, while novel concepts about its structure, physiology, and biological roles continue to be elucidated. Cardiac glycosides not only inhibit the pump function of Na,K-ATPase but also activate intracellular signal transduction pathways, which are important in many biological processes. Recently, antiviral effects have been described as a novel feature of Na,K-ATPase inhibition with the use of cardiac glycosides. Cardiac glycosides have been reported to be effective against both DNA viruses such as cytomegalovirus and herpes simplex and RNA viruses such as influenza, chikungunya, coronavirus, and respiratory syncytial virus, among others. Consequently, cardiac glycosides have emerged as potential broad-spectrum antiviral drugs, with the great advantage of targeting cell host proteins, which help to minimize resistance to antiviral treatments, making them a very promising strategy against human viral infections. Here, we review the effect of cardiac glycosides on viral biology and the mechanisms by which these drugs impair the replication of this array of different viruses.
The SimpleScalar tool set, version 2.0 (1997)

This document describes release 2.0 of the SimpleScalar tool set, a suite of free, publicly available simulation tools that offer both detailed and high-performance simulation of modern microprocessors. The new release offers more tools and capabilities, precompiled binaries, cleaner interfaces, better documentation, easier installation, improved portability, and higher performance. This paper contains a complete description of the tool set, including retrieval and installation instructions, a description of how to use the tools, a description of the target SimpleScalar architecture, and many details about the internals of the tools and how to customize them. With this guide, the tool set can be brought up and generating results in under an hour (on supported platforms).
Study of a recombinant CHO cell line producing a monoclonal antibody by ATF or TFF external filter perfusion in a WAVE Bioreactor™ (2011)

Major advantages of perfusion are high cell numbers and high total production in a relatively small size bioreactor. Moreover, perfusion is optimal when the product of interest is unstable or if th ...