gebhart/patrepeval huggingface dataset:
Structure of a trimeric variant of the Epstein–Barr virus glycoprotein B (2009)

Epstein-Barr virus (EBV) is a herpesvirus that is associated with development of malignancies of lymphoid tissue. EBV infections are life-long and occur in >90% of the population. Herpesviruses enter host cells in a process that involves fusion of viral and cellular membranes. The fusion apparatus is comprised of envelope glycoprotein B (gB) and a heterodimeric complex made of glycoproteins H and L. Glycoprotein B is the most conserved envelope glycoprotein in human herpesviruses, and the structure of gB from Herpes simplex virus 1 (HSV-1) is available. Here, we report the crystal structure of the secreted EBV gB ectodomain, which forms 16-nm long spike-like trimers, structurally homologous to the postfusion trimers of the fusion protein G of vesicular stomatitis virus (VSV). Comparative structural analyses of EBV gB and VSV G, which has been solved in its pre and postfusion states, shed light on gB residues that may be involved in conformational changes and membrane fusion. Also, the EBV gB structure reveals that, despite the high sequence conservation of gB in herpesviruses, the relative orientations of individual domains, the surface charge distributions, and the structural details of EBV gB differ from the HSV-1 protein, indicating regions and residues that may have important roles in virus-specific entry.
GAX collagen in the treatment of urinary incontinence in elderly women: a two year follow up (1997)

GAX collagen is an effective method of treating urinary incontinence in the elderly and especially women who have undergone previous continence procedures. The technique is easy to perform and particularly suitable in those who are frail, but if failure occurs after two years consideration needs to be given to its cost effectiveness.
<title>Remote monitoring of instrumented structures using the Internet information superhighway</title> (1994)

The requirements of sensor monitoring associated with instrumented civil structures poses potential logistical constraints on manpower, training, and costs. The need for frequent or even continuous data monitoring places potentially severe constraints on overall system performance given real-world factors such as available manpower, geographic separation of the instrumented structures, and data archiving as well as the training and cost issues. While the pool of available low wage, moderate skill workers available to the authors is sizable (undergraduate engineering students), the level of performance of such workers is quite variable leading to data acquisition integrity and continuity issues - matters that are not acceptable in the practical field implementation of such developed systems. In the case of acquiring data from the numerous sensors within the civil structures which the authors have instrumented (e.g., a multistory building, roadway/railway bridges, and a hydroelectric dam), we have found that many of these concerns may be alleviated through the use of an automated data acquisition system which archives the acquired information in an electronic location remotely accessible through the Internet global computer network. It is therefore a possible for the data monitoring to be performed at a remote location with the only requirements for data acquisition being Internet accessibility. A description of the developed scheme is presented as well as guiding philosophies.
A sensitive method for measuring protein turnover based on the measurement of 2-3H-labelled amino acids in protein (1976)

A method for measuring the rate of protein degradation is described. The method measures the change in 2-3H content of protein with time by racemization of the protein hydrolysate with acetic anhydride. The 3H on C-2 of amino acids is stable in proteins but becomes labile, owing to the action of transaminases, once the amino acids are released by proteolysis. The specific measurement of 2-3H in amino acids largely overcomes problems due to compartmentation and isotope recycling and evidence to support this claim is presented. Values for the half-life of Lemna minor (duckweed) protein determined by the new method are compared with values obtained by other methods.
Computerized Analysis of Digitized Mammograms of BRCA1 and BRCA2 Gene Mutation Carriers (2002)

The computerized analysis of mammograms suggests that mammographic patterns in carriers of BRCA1 and BRCA2 mutations differ from those of women at low risk for breast cancer. Our computer-extracted features may be useful as radiographic markers for identifying women at high risk for breast cancer.
Dark Repair of Ultraviolet-Irradiated Deoxyribonucleic Acid by Bacteriophage T4: Purification and Characterization of a Dimer-Specific Phage-Induced Endonuclease (1971)

The purification and properties of an ultraviolet (UV) repair endonuclease are described. The enzyme is induced by infection of cells of Escherichia coli with phage T4 and is missing from extracts of cells infected with the UV-sensitive and excision-defective mutant T4V(1). The enzyme attacks UV-irradiated deoxyribonucleic acid (DNA) containing either hydroxymethylcytosine or cytosine, but does not affect native DNA. The specific substrate in UV-irradiated DNA appears to be pyrimidine dimer sites. The purified enzyme alone does not excise pyrimidine dimers from UV-irradiated DNA. However, dimer excision does occur in the presence of the purified endonuclease plus crude extract of cells infected with the mutant T4V(1).
Self-heating in high-power AlGaN-GaN HFETs (1998)

We compare self-heating effects in AlGaN-GaN heterostructure field effect transistors (HFETs) grown on sapphire and SiC substrates. Heat dissipation strongly affects the device characteristics soon after the application of the source-drain voltage (in less than 10/sup -7/ s). Our results show that in HFET's with the total epilayer thickness less than 1.5 μm, the thermal impedance, /spl Theta/ is primarily determined by the substrate material and not by the material of the active layer. For our devices grown on 6H-SiC substrates, we measured /spl Theta/ of approximately 2/spl deg/C/spl middot/mm/W, which was more than an order of magnitude smaller than /spl Theta/=25/spl deg/C mm/W measured for similar AlGaN/GaN HFET's grown on sapphire. Our results demonstrate that AlGaN-GaN HFET's grown on SiC substrates combine advantages of superior electron transport properties in AlGaN/GaN heterostructures with excellent thermal properties of SiC, which should make these devices suitable for high-power electronic applications.
An investigation of the interrelationships between linear and nonlinear polarizabilities and bond-length alternation in conjugated organic molecules. (1993)

A computational method was devised to explore the relationship of charge separation, geometry, molecular dipole moment (mu), polarizability (alpha), and hyperpolariz-abilities (beta, gamma) in conjugated organic molecules. We show that bond-length alternation (the average difference in length between single and double bonds in the molecule) is a key structurally observable parameter that can be correlated with hyperpolarizabilities and is thus relevant to the optimization of molecules and materials. By using this method, the relationship of bond-length alternation, mu, alpha, beta, and gamma for linear conjugated molecules is illustrated, and those molecules with maximized alpha, beta, and gamma are described.
Frame-to-frame coherence and the hidden surface computation (1981)

Frame-to-frame coherence is the highly structured relationship that exists between successive frames of certain animation sequences. From the point of view of the hidden surface computation, this implies that parts of the scene will become visible or invisible in a predictable fashion. In this paper the frame-to-frame coherence constraints are identified and characterized for static scenes restricted to stationary, closed, convex, nonintersecting polyhedra. The animation derives from a continuous movement of the viewer. The mathematical analysis of the constraints is geometric, and leads to a characterization of the self-occlusion relationship over a single polyhedron; and to a characterization of the occlusion or change of occlusion relationship over two polyhedra. Based on these constraints, an algorithm is presented which generates successive frames in an animation sequence.
Studies on the interdependence of gp39 and B7 expression and function during antigen‐specific immune responses (1995)

Interactions between T and B cells are dynamic and regulated by interacting receptor: co-receptors. Interactions between CD40 and its ligand, gp39, and the CD28/CTLA-4 and B7 family members play a decisive role in regulating the progression of cognate interactions. The interdependence of gp39-CD40 and CD28/CTLA-B7 expression and function was studied in vitro during an antigen-induced immune response using T cells from mice expressing a transgenic T cell receptor (TCR). gp39 was induced on pigeon cytochrome c (PCC)-transgenic T cells in the presence of antigen and antigen-presenting cells. The antigen-induced expression of gp39 on transgenic T cells was inhibited by antibodies to class II major histocompatibility complex, CD4 and LFA-1, but not by CTLA-4 Ig, anti-B7-1 or anti-B7-2. These data established that the antigen-induced expression of gp39 was not dependent on co-stimulation via CD28/CTLA-4. The addition of PCC also resulted in the modest expression of B7-1 and a more robust expression of B7-2 on the cognate B cells. The addition of anti-gp39 blocked the up-regulated expression of B7-1 and partially blocked the up-regulated expression of B7-2. The addition of anti-gp39 and anti-interleukin-4 inhibited antigen-induced expression of B7-2 on B cells to near background levels. Studies on the up-regulation of B7-1 and B7-2 on resting B cells showed that soluble gp39 up-regulated B7-1 and B7-2 expression on B cells. In addition, interleukin-4 and interferon-gamma up-regulated B7-2 expression on B cells. Taken together, these data demonstrate that the antigen-induced expression of gp39 is dependent on TCR-derived signals, yet independent of CD28/CTLA-4 co-stimulatory signals. Cognate interactions also resulted in the modest enhancement of B7-1 expression and a more profound expression of B7-2 which were completely or partially dependent on gp39-CD40 interactions.
Single-Molecule Approaches to Stochastic Gene Expression (2009)

Both the transcription of mRNAs from genes and their subsequent translation into proteins are inherently stochastic biochemical events, and this randomness can lead to substantial cell-to-cell variability in mRNA and protein numbers in otherwise identical cells. Recently, a number of studies have greatly enhanced our understanding of stochastic processes in gene expression by utilizing new methods capable of counting individual mRNAs and proteins in cells. In this review, we examine the insights that these studies have yielded in the field of stochastic gene expression. In particular, we discuss how these studies have played in understanding the properties of bursts in gene expression. We also compare the array of different methods that have arisen for single mRNA and protein detection, highlighting their relative strengths and weaknesses. In conclusion, we point out further areas where single-molecule techniques applied to gene expression may lead to new discoveries.
Cerebrospinal Fluid Creatine Kinase–BB Isoenzyme Activity and Outcome After Subarachnoid Hemorrhage (1999)

The level of CSF CK-BB may help predict neurologic outcome after SAH.
The interplay between microbiome dynamics and pathogen dynamics in a murine model ofClostridium difficileInfection (2011)

Clostridium difficile infection (CDI) arises in the setting of antibiotic administration where disruption of the normal indigenous gut microbiota leads to susceptibility to C. difficile colonization and colitis. Using a murine model of CDI, we demonstrate that changes in the community structure of the indigenous gut microbiota are associated with the loss of colonization resistance against C. difficile. Several antibiotic regimens were tested in combination for the ability to overcome colonization resistance, including a five antibiotic cocktail consisting of kanamycin, gentamicin, colistin, metronidazole, and vancomycin administered in drinking water for three days, a single intraperitoneal dose of clindamycin or 10 days of cefoperazone in drinking water. Following antibiotic treatment animals were challenged with 105 colony forming units of C. difficile strain VPI 10463 via oral gavage. Animals that received the antibiotic cocktail and clindamycin prior to C. difficile challenge followed one of two clinical courses, either becoming clinically ill and moribund within 2-4 days post challenge, or remaining clinically well. Animals that became clinically ill developed histologically severe colitis. These histopathologic findings were significantly less severe in animals that remained clinically well. Analysis of 16S rRNA gene sequences retrieved from gut tissue at necropsy demonstrated that Proteobacteria dominated the gut microbiota in clinically ill animals. In contrast, the gut microbial community of clinically well animals more closely resembled untreated animals, which were dominated by members of the Firmicutes. All animals that received cefoperazone treatment prior to C. difficile challenge were clinically ill and moribund by 2-5 days post challenge in a dose dependent manner. The gut communities in these animals were dominated by C.difficile suggesting that cefoperazone treatment resulted in a greater loss in colonization resistance. Thus, the severity of colitis that arises in this system reflects the interplay between the expansion of C. difficile in the gut community and the ecologic dynamics of the indigenous microbial community as it recovers from antibiotic perturbation. We demonstrate that altering the balance of these two opposing processes alters clinical outcome and thus may lead to novel preventative and therapeutic approaches for CDI.
Acute Graft-versus-Host Disease — Biologic Process, Prevention, and Therapy (2017)

When T cells from a bone marrow donor begin to attack the host within 3 months after hematopoietic-cell transplantation, acute graft-versus-host disease results. The disease mainly affects the skin, liver, and gastrointestinal tract and is treated with immunosuppressive drugs.
Molecular cloning of the Clostridium botulinum structural gene encoding the type B neurotoxin and determination of its entire nucleotide sequence (1992)

DNA fragments derived from the Clostridium botulinum type A neurotoxin (BoNT/A) gene (botA) were used in DNA-DNA hybridization reactions to derive a restriction map of the region of the C. botulinum type B strain Danish chromosome encoding botB. As the one probe encoded part of the BoNT/A heavy (H) chain and the other encoded part of the light (L) chain, the position and orientation of botB relative to this map were established. The temperature at which hybridization occurred indicated that a higher degree of DNA homology occurred between the two genes in the H-chain-encoding region. By using the derived restriction map data, a 2.1-kb BglII-XbaI fragment encoding the entire BoNT/B L chain and 108 amino acids of the H chain was cloned and characterized by nucleotide sequencing. A contiguous 1.8-kb XbaI fragment encoding a further 623 amino acids of the H chain was also cloned. The 3' end of the gene was obtained by cloning a 1.6-kb fragment amplified from genomic DNA by inverse polymerase chain reaction. Translation of the nucleotide sequence derived from all three clones demonstrated that BoNT/B was composed of 1,291 amino acids. Comparative alignment of its sequence with all currently characterized BoNTs (A, C, D, and E) and tetanus toxin (TeTx) showed that a wide variation in percent homology occurred dependent on which component of the dichain was compared. Thus, the L chain of BoNT/B exhibits the greatest degree of homology (50% identity) with the TeTx L chain, whereas its H chain is most homologous (48% identity) with the BoNT/A H chain. Overall, the six neurotoxins were shown to be composed of highly conserved amino acid domains interceded with amino acid tracts exhibiting little overall similarity. In total, 68 amino acids of an average of 442 are absolutely conserved between L chains and 110 of 845 amino acids are conserved between H chains. Conservation of Trp residues (one in the L chain and nine in the H chain) was particularly striking. The most divergent region corresponds to the extreme carboxy terminus of each toxin, which may reflect differences in specificity of binding to neurone acceptor sites.
Nitro-Fatty Acid Inhibition of Neointima Formation After Endoluminal Vessel Injury (2009)

In summary, electrophilic nitro-fatty acids induce salutary gene expression and cell functional responses that are manifested by a clinically significant outcome, inhibition of neointimal hyperplasia induced by arterial injury.
Production of Homo- and Hetero-Dimeric Isozymes from Two Aldehyde Oxidase Genes of Arabidopsis thaliana (1999)

Polyclonal antibodies were raised against synthetic peptides or recombinant polypeptides encoded by Arabidopsis atAO-1 and atAO-2 cDNAs, which have sequences similar to maize and animal aldehyde oxidase (AO) cDNAs. Anti-atAO-1 antibodies recognized AOalpha and AObeta among the three isoforms, AOalpha, AObeta, and AOgamma, detected in Arabidopsis seedlings after native PAGE, while anti-atAO-2 antibodies reacted with AObeta and AOgamma. The polypeptide specifically recognized by each antibody was collected as the Protein-A/IgG/antigen complex. The 150- and 145-kDa polypeptides were purified by SDS-PAGE and digested with Achromobacter Protease I. From the amino acid sequences and molecular masses of the derivative peptides, it was revealed that the 150- and 145-kDa polypeptides were the products of atAO-1 and atAO-2, respectively. Molecular masses of the native forms of AOalpha, AObeta, and AOgamma were estimated as approximately 290-300 kDa. These results suggest that AOalpha and AOgamma are homodimers consisting of atAO-1 and atAO-2 products, respectively, and that AObeta is a heterodimer of the atAO-1 and atAO-2 products.
Large-Scale Synthesis, Purification, and Analysis of Oligodeoxynucleotide Phosphorothioates (1994)

Synthesis of oligonucleotides has been carried out on 1-, 2-, and 5-mmol scales using an appropriately modified automated, commercially available DNA synthesizer. The reaction cycles were optimized to obtain efficient coupling (> or = 97%). The synthesized oligonucleotide was purified by preparative reversed-phase liquid chromatography, followed by detritylation and desalting to obtain the oligonucleotides in the Na+ form. The purified oligonucleotides were characterized by 31P NMR, mass spectrometry, capillary gel electrophoresis, and ion-exchange high-performance liquid chromatography. By using these protocols, a 25-mer oligodeoxyribonucleotide can be synthesized on a 1-, 2-, or 5-mmole scale to obtain approximately 2.4, 4.8, or 12 g of purified product.
Human urokinase and porcine tissue plasminogen activator. A comparative study of the mechanism of fibrinolysis, and the effect of natural proteinase inhibitors and omega-aminocarboxylic acids. (1977)

&lt;p&gt;The dehydrogenation of ethylbenzene to styrene and of cumene to α-methylstyrene has been investigated in a fixed bed reactor over bismuth uranate Bi&lt;sub&gt;2&lt;/sub&gt;UO&lt;sub&gt;6&lt;/sub&gt; and uranium oxide as catalysts, at temperatures from 420 to 520 °C. Selectivities of 97% at a conversion of 38% for styrene and of 96% at a conversion of 66% for α-methylstyrene have been obtained in this study. Under reaction conditions Bi&lt;sub&gt;2&lt;/sub&gt;UO&lt;sub&gt;6&lt;/sub&gt; loses 67 wt% of its oxygen and metallic bismuth is formed. Uranium oxide is reduced to UO&lt;sub&gt;2&lt;/sub&gt;. The reaction pattern on both catalysts changes during the reduction. This investigation is mainly concerned with the performance of the reduced catalysts. A kinetic model, which takes into account the chemisorption of the saturated reactants and of the unsaturated reaction products, has been used to interpret the experimental data. Energies of activation are 34 kcal mol&lt;sup&gt;-1&lt;/sup&gt; for the ethylbenzene dehydrogenation and 27 kcal mol&lt;sup&gt;-1&lt;/sup&gt; for the cumene dehydrogenation. By-products formed from ethylbenzene are benzene and toluene, while cumene produces benzene, toluene, ethylbenzene and styrene.&lt;/p&gt;
Segmentation and tracking of migrating cells in videomicroscopy with parametric active contours: a tool for cell-based drug testing (2002)

This paper presents a segmentation and tracking method for quantitative analysis of cell dynamics from in vitro videomicroscopy data. The method is based on parametric active contours and includes several adaptations that address important difficulties of cellular imaging, particularly the presence of low-contrast boundary deformations known as pseudopods, and the occurence of multiple contacts between cells. First, we use an edge map based on the average intensity dispersion that takes advantage of relative background homogeneity to facilitate the detection of both pseudopods and interfaces between adjacent cells. Second, we introduce a repulsive interaction between contours that allows correct segmentation of objects in contact and overcomes the shortcomings of previously reported techniques to enforce contour separation. Our tracking technique was validated on a realistic data set by comparison with a manually defined ground-truth and was successfully applied to study the motility of amoebae in a biological research project.
Potential therapeutic applications of the cyclotides and related cystine knot mini-proteins (2007)

Cyclotides are naturally occurring mini-proteins that have a cyclic peptide backbone and a knotted arrangement of three disulfide bonds. They are remarkably stable and have a diverse range of therapeutically useful biological activities, including antimicrobial and anti-HIV activity, although their natural function appears to be as plant defence agents. Cyclotides are amenable to chemical synthesis and the potential exists to graft new bioactivities onto their cyclic cystine knot framework as a way of stabilising peptide drugs. Over the last few years, proof-of-concept that bioactive peptide epitopes can be grafted onto cyclotides and related cystine knot mini-proteins has been obtained. The cystine knot framework is tolerant to a wide range of residue substitutions and is showing great promise as a scaffold in drug design and protein engineering.