gebhart/patrepeval huggingface dataset:
Human Neutrophil Defensin and Serpins Form Complexes and Inactivate Each Other (1995)

Defensins, antimicrobial and cytotoxic peptides of neutrophils, bind to and are inactivated by blood proteins. We identified defensin interactions with alpha 1-proteinase inhibitor (alpha 1-PI), alpha 1-antichymotrypsin (alpha 1-ACT), alpha 2-antiplasmin (alpha 2-AP), and antithrombin III (AT III) and examined defensin binding to alpha 1-PI and alpha 1-ACT in more detail. Defensin interactions with either alpha 1-PI or alpha 1-ACT were not affected by iodoacetamide or high salt concentration. Preincubation of alpha 1-ACT or alpha 1-PI with increasing concentrations of defensin resulted in a progressive decrease of antiprotease activity of both inhibitors against cathepsin G and antiprotease activity of alpha 1-PI against human neutrophil elastase. At higher concentrations, defensin also ablated the inhibitory effect of normal human serum on cathepsin G and human neutrophil elastase. Both alpha 1-PI and alpha 1-ACT inhibited defensin cytotoxicity toward the human lung carcinoma cell line A549, whereas the elastase inhibitor antileukoprotease did not. Complex interactions between serpins and defensin may have a role in regulating inflammatory processes.
Fast 4D cone-beam reconstruction using the McKinnon-Bates algorithm with truncation correction and nonlinear filtering (2011)

A challenge in using on-board cone beam computed tomography (CBCT) to image lung tumor motion prior to radiation therapy treatment is acquiring and reconstructing high quality 4D images in a sufficiently short time for practical use. For the 1 minute rotation times typical of Linacs, severe view aliasing artifacts, including streaks, are created if a conventional phase-correlated FDK reconstruction is performed. The McKinnon-Bates (MKB) algorithm provides an efficient means of reducing streaks from static tissue but can suffer from low SNR and other artifacts due to data truncation and noise. We have added truncation correction and bilateral nonlinear filtering to the MKB algorithm to reduce streaking and improve image quality. The modified MKB algorithm was implemented on a graphical processing unit (GPU) to maximize efficiency. Results show that a nearly 4x improvement in SNR is obtained compared to the conventional FDK phase-correlated reconstruction and that high quality 4D images with 0.4 second temporal resolution and 1 mm<sup>3</sup> isotropic spatial resolution can be reconstructed in less than 20 seconds after data acquisition completes.
Multivariate Calibration of Infrared Spectra for Quantitative Analysis Using Designed Experiments (1988)

The principal component regression (PCR) and partial least-squares (PLS) methods are used to calibrate and validate models for quantitative prediction of the composition of mixtures from FT-IR spectra. An experimental system of two- and three-component mixtures of xylene isomers was sampled with the use of statistical experimental designs. For two-component mixtures, the prediction error of independent validation samples decreased with increasing numbers of design points in the calibration. Four design points were needed to achieve a prediction accuracy of 0.0013 weight fraction. For three-component mixtures, a Scheffé {3,3} simplex lattice design, which has ten design points, achieved an equivalent accuracy of 0.002 weight fraction. There was little difference in performance between PLS and PCR computations. The results demonstrate the application of statistical methodology to the calibration of infrared spectra and show the importance of including an adequate number of samples in the calibration. The F test on the residual spectrum is shown to be a valuable tool for the identification of spurious data.
Phase variation in streptococci of serological group B (1994)

Encapsulation is thought to be a critical virulence factor in streptococci of serological group B. In the present study two encapsulated low-density variants could be separated from their unencapsulated original strains by Percoll gradient centrifugation. The original strains had been isolated from human endocarditis and bovine mastitis. Type antigen preparations of the encapsulated human and bovine group B streptococcus reacted with type III- and type IV-specific antiserum, respectively. No comparable reactions could be observed with their unencapsulated parent strains. In contrast to the original strains, the encapsulated variants grew with uniform turbidity in fluid medium and formed diffuse colonies in soft agar. The original strains grew as granular sediment and formed compact colonies in soft agar. In addition, the original strains appeared to have a more hydrophobic surface and showed significantly greater adherence to epithelial cells. In contrast to the nonencapsulated parent strains, the encapsulated variants were less phagocytosed by polymorphonuclear leukocytes. These findings may help our understanding of the pathogenic importance of phase variants in infections with this bacterial organism.
Seismic data processing; current industry practice and new directions (1985)

Abstract The last ten years have seen an evolution in the state of the art for seismic data processing on a number of fronts. Data transformations investigated have made some types of analyses much more straightforward. Deconvolution has become a sophisticated process which includes statistical, model-based, and deterministic methods. Vibroseis processing has led to a greater understanding of the statistical limitations in recovery of the wave-field amplitude from sign-bit recording, and the deconvolution of Vibroseis data has improved. Multichannel filtering and analysis in transform domains have resulted in increasingly effective tools for noise reduction and signal enhancement. In statics analysis, surface consistency as a constraint remains a standard, and refraction analysis has become popular as a means of preconditioning data for residual statics estimation. Advances in stacking methodology have come mainly from addressing three effects: ray bending through lateral velocity variations, complex structure, and source-receiver azimuth variations. Recently many techniques of interpretation processing have been introduced with the goal of improving the estimate of earth properties, rather than generating a stacked or imaged section of higher fidelity. The interaction among related disciplines has increased and this serves to amplify the effectiveness of each discipline because they are now developing in less isolation.
Germ line transformation of the olive fly Bactrocera oleae using a versatile transgenesis marker (2006)

The olive fruit fly (olive fly) Bactrocera oleae (Dacus), recently introduced in North America, is the most destructive pest of olives worldwide. The lack of an efficient gene transfer technology for olive fly has hampered molecular analysis, as well as development of genetic techniques for its control. We have developed a Minos-based transposon vector carrying a self-activating cassette which overexpresses the enhanced green fluorescent protein (EGFP). Efficient transposase-mediated integration of one to multiple copies of this vector was achieved in the germ line of B. oleae by coinjecting the vector along with in vitro synthesized Minos transposase mRNA into preblastoderm embryos. The self-activating gene construct combined with transposase mRNA present a system with potential for transgenesis of very diverse species.
A practical guide to the monitoring and management of the complications of systemic corticosteroid therapy (2013)

Systemic corticosteroids play an integral role in the management of many inflammatory and immunologic conditions, but these agents are also associated with serious risks. Osteoporosis, adrenal suppression, hyperglycemia, dyslipidemia, cardiovascular disease, Cushing's syndrome, psychiatric disturbances and immunosuppression are among the more serious side effects noted with systemic corticosteroid therapy, particularly when used at high doses for prolonged periods. This comprehensive article reviews these adverse events and provides practical recommendations for their prevention and management based on both current literature and the clinical experience of the authors.
PA63 Channel of Anthrax Toxin:  An Extended β-Barrel (2002)

Anthrax toxin consists of three protein components: protective antigen (PA), lethal factor (LF), and edema factor (EF). PA(63), generated by protease "nicking" of whole PA, is responsible for delivering the toxin's catalytic fragments (LF and EF) to the target cell's cytosol. In planar bilayer membranes, trypsin-nicked PA makes cation-selective voltage-gated channels with a pore diameter of > or =12 A. The channels are presumed to be heptameric "mushrooms", with an extracellular "cap" region and a membrane-inserted, beta-barrel "stem". Although the crystal structure of the water-soluble monomeric form has been resolved to 2.1 A and that of the heptameric "prepore"" to 4.5 A, the structure for the membrane-bound channel (pore) has not been determined. We have engineered mutant channels that are cysteine-substituted in residues in the putative beta-barrel, and identified the residues lining the channel lumen by their accessibility to a water-soluble sulfhydryl-specific reagent. The reaction with lumen-exposed cysteinyl side chains causes a drop in channel conductance, which we used to map the residues that line the pore. Our results indicate that the beta-barrel structure extends beyond the bilayer and involves residues that are buried in the monomer. The implication is that major rearrangement of domains in the prepore cap region is required for membrane insertion of the beta-barrel stem.
Potential antimalarial agents. Derivatives of 2-chloro-1,4-naphthoquinone (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPotential antimalarial agents. Derivatives of 2-chloro-1,4-naphthoquinoneBenjamin PrescottCite this: J. Med. Chem. 1969, 12, 1, 181–182Publication Date (Print):January 1, 1969Publication History Published online1 May 2002Published inissue 1 January 1969https://pubs.acs.org/doi/10.1021/jm00301a053https://doi.org/10.1021/jm00301a053research-articleACS PublicationsRequest reuse permissionsArticle Views443Altmetric-Citations52LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Long-Term Antidepressant Treatments Result in a Tonic Activation of Forebrain 5-HT1AReceptors (1998)

We report here the first direct functional evidence of an increase in the tonic activation of postsynaptic 5-HT1A receptors by antidepressant treatments. Because 5-HT1A receptor activation hyperpolarizes and inhibits CA3 pyramidal neurons in the dorsal hippocampus, we determined, using in vivo extracellular recording, whether the selective 5-HT1A receptor antagonist WAY 100635 could disinhibit these neurons. Unexpectedly, no disinhibition could be detected in controls. However, after long-term treatment with the tricyclic antidepressant imipramine, the selective 5-HT reuptake inhibitor paroxetine, the reversible monoamine oxidase-A inhibitor befloxatone, the alpha2-adrenergic antagonist mirtazapine, or the 5-HT1A receptor agonist gepirone or multiple electroconvulsive shock (ECS) administration, WAY 100635 markedly increased (60-200%) the firing activity of CA3 pyramidal neurons. Such a disinhibition was absent in rats treated with the nonantidepressant drug chlorpromazine, in rats receiving only one ECS, or in rats receiving multiple ECSs in combination with an intrahippocampal pertussis toxin treatment to inactivate Gi/o-coupled 5-HT1A receptors. These data indicate that such antidepressant treatments, acting on entirely different primary targets, might alleviate depression by enhancing the tonic activation of forebrain postsynaptic 5-HT1A receptors.
The efficacy of DPT and oral poliomyelitis immunization schedules initiated from birth to 12 weeks of age. (1985)

Infants should receive live trivalent oral poliovirus vaccine (TOPV) and DPT immunization as early in life as possible in order to minimize the time that they are at risk of contracting these vaccine-preventable diseases. Passively acquired circulating maternal antibodies provide protection in the 1st few weeks or months of life. Although these antibodies may modify or block the serum immune response during the 1st few weeks of life, the 1st or priming dose of DPT can be given effectively after 4 weeks of age. TOPV administered to infants during the 1st week of life results in intestinal infections and local immune responses in 50-100% of infants and serum antibody responses in 30-70% of infants. The serum antibody response following TOPV administration at 4-8 weeks of age is as effective as vaccine administered to older infants. The WHO Program on Immunization recommends initiating DPT and TOPV schedules at 6 weeks of age. In countries where poliomyelitis has not been controlled, TOPV should be given at birth, or at 1st contact with the health services, then at 6 weeks of age, followed by 2 additional doses 4 weeks apart. (author's)
Techniques for transmitting digital data on the spacelab's analog video channel (1993)

A study was made of various techniques for transmitting digital data over a composite video channel, with data from experiments on the Space Shuttle Orbiter in mind. Broadcast television telecommunications schemes and other techniques described in the literature were reviewed and compared. PSK (phase shift keying) MPSK (M-ary PSK), and or PAM (pulse amplitude modulation), which can be transmitted on visible lines of a frame, unassigned lines of the VBI (vertical blanking interval), or during the HBI (horizontal blanking interval), were all judged attractive under the proper conditions. However, PAM on visible lines or during the VBI should be relatively easy to implement, provide adequate average data rates, and give acceptable BERs (bit error rates).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Use of an antisense oligonucleotide to inhibit expression of a mutated human procollagen gene (COL1A1) in transfected mouse 3T3 cells (1993)

A series of antisense oligonucleotides were developed to inhibit specifically expression of a mutated exogenous gene for collagen without inhibiting expression of an endogenous gene for the same protein. The test system consisted of mouse NIH 3T3 cells that were stably transfected with an internally deleted construct of the human gene for the pro alpha 1(I) chain of type I procollagen [Olsen et al. (1991) J. Biol. Chem. 266, 1117]. The target site was a region at the 3' end of exon 1 and the first few nucleotides of intron 1 of the exogenous human gene that differed in sequence by nine nucleotides from the sequence of the endogenous mouse gene. Expression of the two genes was assayed by Western blot with cross-reacting antibodies and by steady-state levels of mRNAs. None of the oligonucleotides were effective in concentrations up to 25 microM when administered without any carrier. However, when administered with 5 or 10 micrograms/mL lipofectin, one of the oligonucleotides in concentrations of 0.1-0.2 microM inhibited expression of the exogenous gene from 50% to 80% without significant inhibition of expression of the endogenous gene. Also, a missense version of the same oligonucleotide had no significant effect, and the inhibition observed with the most effective oligonucleotide was abolished by a single base change. Time course experiments indicated that, after a 4-h treatment, inhibition appeared at 8 h and persisted for at least 22 h.(ABSTRACT TRUNCATED AT 250 WORDS)
Parallelizing Exploration-Exploitation Tradeoffs with Gaussian Process Bandit Optimization (2012)

Can one parallelize complex exploration exploitation tradeoffs? As an example, consider the problem of optimal high-throughput experimental design, where we wish to sequentially design batches of experiments in order to simultaneously learn a surrogate function mapping stimulus to response and identify the maximum of the function. We formalize the task as a multi-armed bandit problem, where the unknown payoff function is sampled from a Gaussian process (GP), and instead of a single arm, in each round we pull a batch of several arms in parallel. We develop GP-BUCB, a principled algorithm for choosing batches, based on the GP-UCB algorithm for sequential GP optimization. We prove a surprising result; as compared to the sequential approach, the cumulative regret of the parallel algorithm only increases by a constant factor independent of the batch size B. Our results provide rigorous theoretical support for exploiting parallelism in Bayesian global optimization. We demonstrate the effectiveness of our approach on two real-world applications.
Proton uptake controls electron transfer in cytochrome c oxidase (1998)

In cytochrome c oxidase, a requirement for proton pumping is a tight coupling between electron and proton transfer, which could be accomplished if internal electron-transfer rates were controlled by uptake of protons. During reaction of the fully reduced enzyme with oxygen, concomitant with the "peroxy" to "oxoferryl" transition, internal transfer of the fourth electron from CuA to heme a has the same rate as proton uptake from the bulk solution (8,000 s-1). The question was therefore raised whether the proton uptake controls electron transfer or vice versa. To resolve this question, we have studied a site-specific mutant of the Rhodobacter sphaeroides enzyme in which methionine 263 (SU II), a CuA ligand, was replaced by leucine, which resulted in an increased redox potential of CuA. During reaction of the reduced mutant enzyme with O2, a proton was taken up at the same rate as in the wild-type enzyme (8,000 s-1), whereas electron transfer from CuA to heme a was impaired. Together with results from studies of the EQ(I-286) mutant enzyme, in which both proton uptake and electron transfer from CuA to heme a were blocked, the results from this study show that the CuA --> heme a electron transfer is controlled by the proton uptake and not vice versa. This mechanism prevents further electron transfer to heme a3-CuB before a proton is taken up, which assures a tight coupling of electron transfer to proton pumping.
Herpes simplex virus ICP0 and ICP4 immediate early proteins strongly enhance expression of a retrovirus harboured by a leptomeningeal cell line from a patient with multiple sclerosis (1993)

A leptomeningeal cell line (LM7) harbouring an unknown retrovirus was recently isolated from the cerebrospinal fluid of a patient with multiple sclerosis. However, spontaneous expression of the LM7 retrovirus in this primary culture is quite low. We present results showing that in vitro infection of LM7 cells with herpes simplex virus type 1 (HSV-1), but not that of control cells, results in (i) potent stimulation of the specific reverse transcriptase (RT) activity detected in the culture supernatant and (ii) co-expression of both typical HSV-1 virions and abundant retrovirus-like particles. Transfection of LM7 cells with plasmids expressing HSV-1 immediate early (IE) ICP0 and ICP4 proteins produced a similar enhancement of RT activity in culture supernatants with retrovirus-like particles being identifiable by electron microscopy. These effects were not observed with a plasmid expressing ICP27 or with the parental plasmid in LM7 cells, nor with any of these four plasmids in control cells. These results show that HSV IE trans-activating proteins strongly enhance the expression of the latent retrovirus present in LM7 cells. The possible role in vivo of herpesviruses as 'triggering' cofactors in the retrovirus hypothesis for multiple sclerosis aetiology is also discussed.
Efficient expression of a protein coding gene under the control of an RNA polymerase I promoter (1993)

In mammalian cells, RNA polymerase I transcripts are uncapped and retain a polyphosphate 5' terminus. It is probably for this reason that they are poorly translated as messenger RNA. We show in this report that insertion of an Internal Ribosome Entry Site (IRES) into the 5' leader of an RNA polymerase I transcript overcomes the block to translation, presumably by substituting for the 5' trimethyl G cap. Addition of an SV40 polyA addition signal also enhances protein production from the RNA polymerase I transcript. RNA Polymerase I driven expression vectors containing both elements produce protein at levels comparable to that produced from RNA polymerase II driven expression vectors which utilize a retroviral LTR. RNA Polymerase I driven expression vectors may have a variety of uses both for basic research and for practical expression of recombinant proteins.
Polymerization of different lignins by laccase (2008)

In this study the oxidative polymerization of different lignins, i.e. Flax Soda lignin, Spruce EMAL, and Eucalyptus Dioxane lignin by Trametes hirsuta laccase was compared. Initially the structures of the different lignins were compared by Fourier transform infrared spectroscopy. The reactivity of laccase with the different types of lignins in the absence of mediators was examined and verified by oxygen consumption measurements. The molecular weight distributions of treated and untreated lignins were determined by two different size exclusion chromatography methods. Furthermore, the potential of matrix-assisted laser desorption/ionisation-time of flight-mass spectroscopy for determination of the absolute molecular weights of the different lignins was evaluated. The data showed that all the technical lignins could be activated and polymerized by laccase to different degrees. The efficiency as indicated by measurements of the degree of polymerization was found to increase in the order of Spruce EMAL &lt; Eucalyptus Dioxane lignin &lt; Flax Soda lignin. Overall, this data supplies foundations for using enzymes more efficiently in the enzymatic upgrading of lignin.
Fc-fusion proteins and FcRn: structural insights for longer-lasting and more effective therapeutics (2013)

Nearly 350 IgG-based therapeutics are approved for clinical use or are under development for many diseases lacking adequate treatment options. These include molecularly engineered biologicals comprising the IgG Fc-domain fused to various effector molecules (so-called Fc-fusion proteins) that confer the advantages of IgG, including binding to the neonatal Fc receptor (FcRn) to facilitate in vivo stability, and the therapeutic benefit of the specific effector functions. Advances in IgG structure-function relationships and an understanding of FcRn biology have provided therapeutic opportunities for previously unapproachable diseases. This article discusses approved Fc-fusion therapeutics, novel Fc-fusion proteins and FcRn-dependent delivery approaches in development, and how engineering of the FcRn-Fc interaction can generate longer-lasting and more effective therapeutics.