gebhart/patrepeval huggingface dataset:
Intraoperative 1-Hour Electrical Nerve Stimulation Enhances Outcomes of Nerve–Muscle-Endplate Band Grafting Technique for Muscle Reinnervation (2017)

Background Increasing evidence suggests that 1-hour electrical nerve stimulation during surgery improves nerve regeneration and functional recovery. However, it remains unknown if this approach has beneficial effects on the outcomes of our recently developed nerve–muscle-endplate band grafting-native motor zone (NMEG-NMZ) technique for muscle reinnervation. Methods In this study, NMEG-NMZ transplantation was performed in a rat model. The right sternomastoid muscle was experimentally denervated and immediately reinnervated by implanting a NMEG harvested from the ipsilateral sternohyoid (SH) muscle into the NMZ of the target muscle. Before implantation of the NMEG, the SH nerve branch innervating the NMEG was subjected to intraoperative 1-hour continuous electrical stimulation (20 Hz). Three months after surgery, the degree of functional recovery was evaluated with muscle force measurement and the extent of nerve regeneration and endplate reinnervation was examined using histological and immunohistochemical methods. Results A combination of NMEG-NMZ with electrical nerve stimulation resulted in a greater degree of functional recovery than the NMEG-NMZ alone. The mean muscle force of the treated muscles was 90% of the contralateral control. The muscle mass was recovered up to 90% of the control. The mean number and percentage of area of the regenerated axons in the treated muscles was computed to be 81 and 84% of the control muscles, respectively. On average, 83% of the denervated endplates in the treated muscles were reinnervated by regenerated axons. Conclusion Intraoperative brief nerve stimulation promotes nerve regeneration, endplate reinnervation, and functional recovery of the muscles reinnervated with NMEG-NMZ technique.
Cloning and Characterization of an Arabidopsis thaliana Topoisomerase I Gene (1992)

cDNA and genomic clones encoding DNA topoisomerase I were isolated from Arabidopsis thaliana lambdagt11 and lambdaFix libraries by low stringency hybridization with a Saccharomyces cerevisiae TOP1 probe. The cDNA clones include a 2748-base pair open reading frame predicting an amino acid sequence that is highly homologous to sequences encoded by TOP1 from yeast and human sources. The sequence of the upstream genomic region reveals two putative TATA-like elements and a purine-rich region, but no other obvious controlling elements. Southern blot analysis shows that the gene is present as a single copy in the Arabidopsis genome. When expressed in a S. cerevisiae top1 mutant under the control of the GAL1 promoter, the gene complements the phenotype caused by loss of topoisomerase activity and directs the expression of a protein that cross-reacts with a human anti-topoisomerase I antibody.
MultiCoil: A program for predicting two‐and three‐stranded coiled coils (1997)

A new multidimensional scoring approach for identifying and distinguishing trimeric and dimeric coiled coils is implemented in the MultiCoil program. The program extends the two-stranded coiled-coil prediction program PairCoil to the identification of three-stranded coiled coils. The computations are based upon data gathered from a three-stranded coiled-coil database comprising 6,319 amino acid residues, as well as from the previously constructed two-stranded coiled-coil database. In addition to identifying coiled coils not predicted by the two-stranded database programs, MultiCoil accurately classifies the oligomerization states of known dimeric and trimeric coiled coils. Analysis of the MultiCoil scores provides insight into structural features of coiled coils, and yields estimates that 0.9% of all protein residues form three-stranded coiled coils and that 1.5% form two-stranded coiled coils. The MultiCoil program is available at http:/(/)theory.lcs.mit.edu/multicoil.
Antioxidants in fruits and vegetables – the millennium’s health (2001)

Abstract Some of the most exciting research in the last decade has been the discovery of a group of nutrients, which have protective effects against cell oxidation. These naturally occurring compounds impart bright colour to fruits and vegetables and act as antioxidants in the body by scavenging harmful free radicals, which are implicated in most degenerative diseases. Epidemiological studies have established a positive correlation between the intake of fruits and vegetables and prevention of diseases like atheroscelerosis, cancer, diabetes, arthritis and also ageing. So pronounced has been their effect on ageing that they have been called ‘fountains of youth’. Fruits and vegetables have thus had conferred on them the status of ‘functional foods’, capable of promoting good health and preventing or alleviating diseases. Phenolic flavonoids, lycopene, carotenoids and glucosinolates are among the most thoroughly studied antioxidants. The present review highlights the potential of fruits and vegetables rich in antioxidants, their health benefits and the effect of processing on the bioavailability of these nutrients. The paper also reviews some of the important methods used to determine the antioxidant activity.
Circulating and tissue endothelin immunoreactivity in hypercholesterolemic pigs. (1993)

This study suggests a role for endothelin as an early participant and a marker for the endothelial dysfunction in hypercholesterolemia as well as a participant in the atherogenic process.
Merosin, a protein specific for basement membranes of Schwann cells, striated muscle, and trophoblast, is expressed late in nerve and muscle development. (1988)

We have identified a tissue-specific basement membrane-associated protein by using monoclonal antibodies prepared against a protein fraction of human placenta. In immunofluorescence, the monoclonal antibodies stained basement membranes of Schwann cells, striated muscle, and trophoblast, whereas no reaction was seen with any other basement membrane or tissue structure. In antibody-affinity chromatography of proteolytic digests of human placenta, a 65-kDa polypeptide was bound by these monoclonal antibodies. Rabbit antisera and monoclonal antibodies raised against the isolated 65-kDa polypeptide stained human and monkey tissues identically to the original monoclonal antibodies and reacted with an 80-kDa polypeptide in tissue extracts prepared without proteolysis. The 65-kDa and 80-kDa polypeptides were shown to be immunologically distinct from laminin, type IV collagen, fibronectin, and major serum proteins. They presumably represent a novel basement membrane-associated protein, which we have named merosin. No merosin immunoreactivity could be detected in cultures of any of 28 established cell lines. In developing mouse tissues, merosin staining first appeared at the newborn stage. The restricted tissue distribution and late developmental appearance of merosin suggest that the protein has a tissue-specific function associated with a high level of differentiation.
Code-book driven glottal pulse analysis (2003)

A code-book approach is developed for glottal-pulse modeling of speech. The authors extend previous methods of glottal pulse analysis, suggesting a practical scheme suitable for speech coding and compression. The scheme is based on using a codebook of glottal pulse signals, thereby allowing for efficient minimization of an objective measure of distortion, consistent with ordinary CELP (code-excited linear prediction) analysis. Subjective and objective quality, as well as analysis complexity, compare favorably with established methods, such as stochastic 1024-CELP coders. Moreover, the proposed coder is robust. >
Modulation of Endothelial Cell Function by Normal Polyspecific Human Intravenous Immunoglobulins (1998)

Intravenous immunoglobulin (IVIg) is increasingly used in the treatment of autoimmune and inflammatory diseases, including vasculitides and Kawasaki disease. However, the outcome of IVIg interaction with endothelial cells of the vascular bed is not clear as yet. We have investigated the effect of IVIg on the in vitro activation of human endothelial cells, as assessed by cell proliferation and reverse transcription-polymerase chain reaction-detected expression of mRNA coding for adhesion molecules (intercellular adhesion molecule-1 and vascular cellular adhesion molecule-1), chemokines (monocyte chemoattractant protein-1, macrophage colony-stimulating factor, and granulocyte-macrophage colony-stimulating factor), and proinflammatory cytokines (tumor necrosis factor-alpha, interleukin-1beta, and interleukin-6). IVIg inhibited proliferation of endothelial cells in a time-dependent manner. This effect was dependent on both Fc and F(ab')2 fragments of the immunoglobulin molecule and was fully reversible. Tumor necrosis factor-alpha and interleukin-1beta also inhibited thymidine incorporation, but to a lesser degree. IVIg had no effect on basal levels of mRNA coding for the adhesion molecules, chemokines, and proinflammatory cytokines. IVIg fully down-regulated the expression induced by tumor necrosis factor-alpha or interleukin-1beta of mRNA coding for these molecules. Thus, blockade of cellular proliferation and of cytokine-induced expression of adhesion molecules, chemokines, and cytokines may explain the therapeutic effect of IVIg in vascular and inflammatory disorders.
Thermodynamic Stability of Carbonic Anhydrase:  Measurements of Binding Affinity and Stoichiometry Using ThermoFluor (2005)

ThermoFluor (a miniaturized high-throughput protein stability assay) was used to analyze the linkage between protein thermal stability and ligand binding. Equilibrium binding ligands increase protein thermal stability by an amount proportional to the concentration and affinity of the ligand. Binding constants (K(b)) were measured by examining the systematic effect of ligand concentration on protein stability. The precise ligand effects depend on the thermodynamics of protein stability: in particular, the unfolding enthalpy. An extension of current theoretical treatments was developed for tight binding inhibitors, where ligand effect on T(m) can also reveal binding stoichiometry. A thermodynamic analysis of carbonic anhydrase by differential scanning calorimetry (DSC) enabled a dissection of the Gibbs free energy of stability into enthalpic and entropic components. Under certain conditions, thermal stability increased by over 30 degrees C; the heat capacity of protein unfolding was estimated from the dependence of calorimetric enthalpy on T(m). The binding affinity of six sulfonamide inhibitors to two isozymes (human type 1 and bovine type 2) was analyzed by both ThermoFluor and isothermal titration calorimetry (ITC), resulting in a good correlation in the rank ordering of ligand affinity. This combined investigation by ThermoFluor, ITC, and DSC provides a detailed picture of the linkage between ligand binding and protein stability. The systematic effect of ligands on stability is shown to be a general tool to measure affinity.
Bacteriophage SP6-specific RNA polymerase. I. Isolation and characterization of the enzyme. (1982)

SP6 is a small, virulent bacteriophage which grows on Salmonella typhimurium LT2. It is morphologically similar to Escherichia coli bacteriophage T7 and its relatives, but appears to be genetically distinct. After infection a bacteriophage-specific RNA polymerase is induced in infected cells. SP6 RNA polymerase is a stable enzyme and is easily purified to homogeneity in good overall yield. The activity resides in a single polypeptide chain of Mr = 96,000. Synthesis of RNA by SP6 RNA polymerase requires a DNA template and Mg2+ ion and is strongly stimulated by either bovine serum albumin of spermidine. Thiol-reactive reagents inhibit the enzyme, suggesting the presence of essential sulfhydryl residues. RNA synthesis requires native SP6 RNA as template; DNAs from other bacteriophages including T3 and T7 are inert; hence, SP6 RNA polymerase possesses a stringent promoter specificity similar to, but distinct from that of the other phage RNA polymerases. The SP6 RNA polymerase is also highly active in synthesis of poly(rG) with poly(dI) . (dC) as template. This reaction is unlikely to involve promoter-like sites, but it appears to reflect a general catalytic capacity of the polymerase, since cleavage of the SP6 RNA polymerase with trypsin, which completely eliminates SP6-transcribing activity, has little effect on poly(rG) synthesis. Hence, it appears that the catalytic portion of the polymerase can be separated from the RNA polymerase holoenzyme.
The Perinuclear Matrix as a Structural Element of the Mouse Sperm Nucleus1 (1992)

The mouse sperm nucleus, after the removal of protamines and DNA, consisted of a skeletal structure that conformed to the original nuclear shape. Sperm were extracted with 1% SDS, and the Isolated nuclei, along with the enveloping perinuclear theca, were incubated in 25 mM dithiothreitol, and exposed to different reagents in an effort to displace the protamines, Pt and P2. Protamines, labeled with [3Hiarglnine, were displaced from the nucleus by Cad2 consisted of 230 protein spots, with M,s in the range of 70 000 to 8000 and pls of 7.5 to -4.7, respectively. Monoclonal antibodies prepared against perinuclear matrices bound to specific proteins on IEF immunoblots and, based on light and electron microscopic observations, to discrete domains of the sperm perinuclear theca and nucleus.
The design of a battery-operated fluorescent lamp (1989)

The author presents the design of a battery-supplied fluorescent lamp for automotive, emergency, or portable light sources. Each fluorescent tube has its own driver circuit that exhibits high efficiency (over 80%), simple design, and low cost. The driver circuit operates at a high frequency (50 kHz) and has an electronic ballast control, symmetrical tube driving, and semiresonance ignition. These operating conditions are optimal, and they provide a long tube life and high illumination.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Defects of embryonic organogenesis resulting from targeted disruption of the N-myc gene in the mouse (1993)

The highest expression of the N-myc gene occurs during embryonic organogenesis in the mouse ontogeny, with the peak of expression around embryonic day 9.5. Homozygous N-myc-deficient mice, produced by germline transmission of a disrupted allele in ES cells, developed normally to day 10.5, indicating dispensability of N-myc expression in the earlier period, but later accumulated organogenic abnormalities and died around day 11.5. The most notable abnormalities were found in the limb bud, visceral organs (lung, stomach, liver and heart) and the central/peripheral nervous systems, and were highly correlated with the site of N-myc expression. The limb buds and the lungs excised from N-myc-deficient mutant embryos were placed in culture to allow their development to stages beyond the point of death of the embryos. Analyses indicated that the mutant limbs failed to develop distal structures and the development of bronchi from the trachea was defective in the lungs. The latter defect was largely corrected by addition of fetal calf serum to the culture medium, suggesting that an activity missing in the mutant lung was replenished by a component of the serum. The phenotype of N-myc-deficient mutant embryos indicated requirement of the N-myc function in many instances of tissue interactions in organogenesis and also in cell-autonomous regulation of tissue maturation.
Method for Quantitative Proteomics Research by Using Metal Element Chelated Tags Coupled with Mass Spectrometry (2006)

The mass spectrometry-based methods with a stable isotope as the internal standard in quantitative proteomics have been developed quickly in recent years. But the use of some stable isotope reagents is limited by the relative high price and synthetic difficulties. We have developed a new method for quantitative proteomics research by using metal element chelated tags (MECT) coupled with mass spectrometry. The bicyclic anhydride diethylenetriamine-N,N,N',N' ',N' '-pentaacetic acid (DTPA) is covalently coupled to primary amines of peptides, and the ligand is then chelated to the rare earth metals Y and Tb. The tagged peptides are mixed and analyzed by LC-ESI-MS/MS. Peptides are quantified by measuring the relative signal intensities for the Y and Tb tag pairs in MS, which permits the quantitation of the original proteins generating the corresponding peptides. The protein is then identified by the corresponding peptide sequence from its MS/MS spectrum. The MECT method was evaluated by using standard proteins as model sample. The experimental results showed that metal chelate-tagged peptides chromatographically coeluted successfully during the reversed-phase LC analysis. The relative quantitation results were accurate for proteins using MECT. DTPA modification of the N-terminal of peptides promoted cleaner fragmentation (only y-series ions) in mass spectrometry and improved the confidence level of protein identification. The MECT strategy provides a simple, rapid, and economical alternative to current mass tagging technologies available.
Inside OLE 2 : the fast track to buiding powerful object-oriented applications (1993)

With the introduction of OLE version 2, Object Linking and Embedding becomes much more than a mechanism for linking data. Now it provides a new programming model for transforming Windows into a truly object-oriented development environment. The author tells experienced Windows programmers how to take advantage of OLE 2 to develop next-generation applications that will take Windows to a new level.
Role of Heparan Sulfate 2-O-Sulfotransferase in Prostate Cancer Cell Proliferation, Invasion, and Growth Factor Signaling (2011)

Heparan-sulfate proteoglycans (HSPGs) are required for maximal growth factor signaling in prostate cancer progression. The degree of sulfate modification on the covalently attached heparan sulfate (HS) chains is one of the determining factors of growth factor-HSPG interactions. Sulfate groups are transferred to HS chains via a series of O-sulfotransferases. In the present study, we demonstrate that Heparan sulfate 2-O-sulfotransferase (2OST) is essential for maximal proliferation and invasion of prostate cancer cells in the LNCaP-C4-2B model. We also show that a decrease in invasion due to 2OST siRNA is associated with an increase in actin and E-cadherin accumulation at the cell surface. 2OST expression correlates with increasing metastatic potential in this model. We demonstrate that 2OST expression is upregulated by the stress-inducible transcription factors HIF1α, ATF2, and NFκB. Chromatin immunoprecipitation analysis suggests that HIF1α and ATF2 act directly on the 2OST promoter, while NFκB acts indirectly.
Lymphomas of Follicles: Mantle Cell and Follicle Center Cell Lymphomas (1993)

Lymphomas of Follicles: Mantle Cell and Follicle Center Cell Lymphomas Get access Dennis D. Weisenburger, M.D., Dennis D. Weisenburger, M.D. From the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska Address reprint requests to Dr. Weisenburger: Department of Pathology and Microbiology, University of Nebraska Medical Center, 600 South 42nd Street, Omaha, NE 68198. Search for other works by this author on: Oxford Academic Google Scholar Wing C. Chan, M.D. Wing C. Chan, M.D. From the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska Search for other works by this author on: Oxford Academic Google Scholar American Journal of Clinical Pathology, Volume 99, Issue 4, 1 April 1993, Pages 409–420, https://doi.org/10.1093/ajcp/99.4.409 Published: 01 April 1993 Article history Received: 26 October 1992 Accepted: 30 October 1992 Published: 01 April 1993
On the Temperature Dependence of Cooperative Relaxation Properties in Glass-Forming Liquids (1965)

A molecular-kinetic theory, which explains the temperature dependence of relaxation behavior in glass-forming liquids in terms of the temperature variation of the size of the cooperatively rearranging region, is presented. The size of this cooperatively rearranging region is shown to be determined by configuration restrictions in these glass-forming liquids and is expressed in terms of their configurational entropy. The result of the theory is a relation practically coinciding with the empirical WLF equation. Application of the theory to viscosimetric experiments permits evaluation of the ratio of the kinetic glass temperature Tg (derived from usual ``quasistatic'' experiments) to the equilibrium second-order transition temperature T2 (indicated by either statistical-mechanical theory or extrapolations of experimental data) as well as the hindrance-free energy per molecule. These parameters have been evaluated for fifteen substances, the experimental data for which were available. Hindrance-free energies were found to be of the magnitude to be expected from consideration of molecular interaction energies. The values of Tg/T2 thus obtained for these fifteen widely differing materials were found to be nearly the same, i.e., 1.30±8.4%. Values for Tg/T2 of nearly the same magnitude were derived by Bestul and Chang from calorimetric data.