gebhart/patrepeval huggingface dataset:
The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds (2008)

We surveyed the genetic diversity among avian influenza virus (AIV) in wild birds, comprising 167 complete viral genomes from 14 bird species sampled in four locations across the United States. These isolates represented 29 type A influenza virus hemagglutinin (HA) and neuraminidase (NA) subtype combinations, with up to 26% of isolates showing evidence of mixed subtype infection. Through a phylogenetic analysis of the largest data set of AIV genomes compiled to date, we were able to document a remarkably high rate of genome reassortment, with no clear pattern of gene segment association and occasional inter-hemisphere gene segment migration and reassortment. From this, we propose that AIV in wild birds forms transient "genome constellations," continually reshuffled by reassortment, in contrast to the spread of a limited number of stable genome constellations that characterizes the evolution of mammalian-adapted influenza A viruses.
Conformational study of N-substituted adenines by dynamic proton NMR: relatively high barrier to rotation about C6-N6 in N3,N6-disubstituted adenines (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConformational study of N-substituted adenines by dynamic proton NMR: relatively high barrier to rotation about C6-N6 in N3,N6-disubstituted adeninesAllen B. Reitz, David W. Graden, Alfonzo D. Jordan Jr., and Bruce E. MaryanoffCite this: J. Org. Chem. 1990, 55, 22, 5761–5766Publication Date (Print):October 1, 1990Publication History Published online1 May 2002Published inissue 1 October 1990https://pubs.acs.org/doi/10.1021/jo00309a021https://doi.org/10.1021/jo00309a021research-articleACS PublicationsRequest reuse permissionsArticle Views118Altmetric-Citations19LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Fast solvent screening via quantum chemistry: COSMO‐RS approach (2002)

Abstract COSMO‐RS, a general and fast methodology for the a priori prediction of thermophysical data of liquids is presented. It is based on cheap unimolecular quantum chemical calculations, which, combined with exact statistical thermodynamics, provide the information necessary for the evaluation of molecular interactions in liquids. COSMO‐RS is an alternative to structure interpolating group contribution methods. The method is independent of experimental data and generally applicable. A methodological comparison with group contribution methods is given. The applicability of the COSMO‐RS method to the goal of solvent screening is demonstrated at various examples of vapor–liquid‐, liquid–liquid‐, solid–liquid‐equilibria and vapor‐pressure predictions.
p53-independent functions of the p19<sup>ARF</sup> tumor suppressor (2000)

The p19(ARF) tumor suppressor antagonizes Mdm2 to induce p53-dependent cell cycle arrest. Individual TKO (triple knock out) mice nullizygous for ARF, p53, and Mdm2 develop multiple tumors at a frequency greater than those observed in animals lacking both p53 and Mdm2 or p53 alone, demonstrating that p19(ARF) can act independently of the Mdm2-p53 axis in tumor surveillance. Reintroduction of ARF into TKO mouse embryo fibroblasts (MEFs), but not into those lacking both p53 and ARF, arrested the cell division cycle in the G1 phase. Inhibition of the retinoblastoma protein had no effect on the ability of ARF to arrest TKO MEFs. Thus, in the absence of Mdm2, p19(ARF) interacts with other targets to inhibit cell proliferation.
Identification of a human PTS1 receptor docking protein directly required for peroxisomal protein import (1998)

The discovery of many fatal human disorders resulting from impaired peroxisomal protein import makes the functional characterization of human peroxins critical. As part of our attempt to identify novel human genes and gene products involved in the import of peroxisomal proteins, we raised antisera against peroxisomal membrane proteins. One such antiserum inhibited peroxisomal protein import in semipermeabilized mammalian cells. This "import inhibiting" antiserum, ab-MF3, specifically recognized a 57-kDa protein. Immunoblot analysis of rat liver subcellular fractions demonstrated that this protein was present exclusively in peroxisomal membranes. Functional analysis revealed that this 57-kDa molecule bound the PTS1 receptor, Pex5p, in ligand blots, suggesting it is a docking site on the peroxisomal membrane. Previous studies have identified two yeast proteins, Pex14p and Pex13p, as Pex5p-binding proteins. To facilitate the biochemical analysis of peroxisomal membrane docking proteins, we cloned and expressed the previously unidentified human Pex14p, as well as a human Pex13p that is 39 aa longer than previously reported. Recombinant Pex14p was specifically recognized by the "import inhibiting" ab-MF3 and bound Pex5p and the Src homology 3 (SH3) domain of Pex13p in ligand blots. These studies demonstrate that the ab-MF3-immunoreactive, 57-kDa peroxisomal membrane protein is Pex14p. Furthermore, this peroxin interacts with Pex5p and Pex13p(SH3) and is directly required for peroxisomal protein import.
Correction: Mucosal Healing and Fibrosis after Acute or Chronic Inflammation in Wild Type FVB-N Mice and C57BL6 Procollagen α1(I)-Promoter-GFP Reporter Mice (2012)

Background: Injury and intestinal inflammation trigger wound healing responses that can restore mucosal architecture but if chronic, can promote intestinal fibrosis. Intestinal fibrosis is a major complication of Crohn's disease. The cellular and molecular basis of mucosal healing and intestinal fibrosis are not well defined and better understanding requires well characterized mouse models.
High-linearity CMOS feedforward power amplifier for WiMAX application (2008)

A high-linearity CMOS feedforward power amplifier has been proposed. The class-C and class-AB amplifiers were combined to perform a differential circuit, which was utilized as the error amplifier to cancel the third-order nonlinear signal with the main amplifier. Therefore, the linearity of the feedforward power amplifier was improved. At the operation frequency of 2.6 GHz, the measured output IP3 and ACPR are 33.2 dBm and -59 dBc, respectively. Thus, the feedforward architecture is very suitable for high linear power amplifier design.
Selective Recognition of Glutathiolated Aldehydes by Aldose Reductase (2000)

In this study, the selectivity and specificity of aldose reductase (AR) for glutathionyl aldehydes was examined. Relative to free aldehydes, AR was a more efficient catalyst for the reduction of glutathiolated aldehydes. Reduction of glutathionyl propanal [gammaGlu-Cys(propanal)-Gly] was more efficient than that of Gly-Cys(propanal)-Gly and gamma-aminobutyric acid-Cys(propanal)-Gly suggesting a possible interaction between alpha-carboxyl of the conjugate and AR. Two active site residues, Trp20 or Ser302, were identified by molecular modeling as potential sites of this interaction. Mutations containing tryptophan-to-phenylalanine (W20F) and serine-to-alanine (S302A) substitutions did not significantly affect reduction of free aldehydes but decreased the catalytic efficiency of AR for glutathiolated aldehydes. Combined mutations indicate that both Trp20 and Ser302 are required for efficient catalysis of the conjugates. The decrease in efficiency due to W20F mutation with glutathionyl propanal was not observed with gamma-aminobutyric-Cys(propanal)-Gly or Gly-Cys-(propanal)-Gly, indicating that Trp20 is involved in binding the alpha-carboxyl of the conjugate. The effect of the S302A mutation was less severe when gammaGlu-Cys(propanal)-Glu rather than glutathionyl propanal was used as the substrate, consistent with an interaction between Ser302 and Gly-3 of the conjugate. These observations suggest that glutathiolation facilitates aldehyde reduction by AR and enhances the range of aldehydes available to the enzyme. Because the N-terminal carboxylate is unique to glutathione, binding of the conjugate with the alpha-carboxyl facing the bottom of the alpha/beta-barrel may assist in the exclusion of unrelated peptides and proteins.
Chain transfer in anionic polymerization. Determination of chain‐transfer constants by using carbon‐14‐labeled chain transfer agents (1969)

Abstract A method is described in which 14 C‐labeled chain‐transfer agents are employed to measure chain‐transfer constants in anionic polymerization as low as 10 −6 . Each chain‐transfer step incorporates one molecule of the chain‐transfer agent into the polymer so that measurement of the activity and conversion allows evaluation of the chain‐transfer constant. This method is independent of the initiator concentration and efficiency, making the technique especially useful when problems with the initiator are encountered. The experimental procedure is described in detail for the case of chain transfer to toluene in the n ‐butyllithium‐initiated polymerization of styrene, where C RH was found to be 5 × 10 −6 . A mathematical treatment is given showing the relationship between the degree of polymerization ( DP n ) and chain transfer.
Towards physiologically based treatment of patients with neuropathic pain (1990)

Neurobiology and Anesthesiology Branch, National Institute of Dental Research, National Institutes of Health, Bethesda, MD U.S.A. ∗Correspondence to: Mitchell B. Max M.D., NIDR/NIH Pain Research Clinic, National Institutes of Health, Building 10, Room 3C-405, Bethesda, MD 20852, U.S.A.
MEK/ERK Inhibitor U0126 Increases the Radiosensitivity of Rhabdomyosarcoma Cells <i>In vitro</i> and <i>In vivo</i> by Downregulating Growth and DNA Repair Signals (2011)

Multimodal treatment has improved the outcome of many solid tumors, and in some cases the use of radiosensitizers has significantly contributed to this gain. Activation of the extracellular signaling kinase pathway (MEK/ERK) generally results in stimulation of cell growth and confers a survival advantage playing the major role in human cancer. The potential involvement of this pathway in cellular radiosensitivity remains unclear. We previously reported that the disruption of c-Myc through MEK/ERK inhibition blocks the expression of the transformed phenotype; affects in vitro and in vivo growth and angiogenic signaling; and induces myogenic differentiation in the embryonal rhabdomyosarcoma (ERMS) cell lines (RD). This study was designed to examine whether the ERK pathway affects intrinsic radiosensitivity of rhabdomyosarcoma cancer cells. Exponentially growing human ERMS, RD, xenograft-derived RD-M1, and TE671 cell lines were used. The specific MEK/ERK inhibitor, U0126, reduced the clonogenic potential of the three cell lines, and was affected by radiation. U0126 inhibited phospho-active ERK1/2 and reduced DNA protein kinase catalytic subunit (DNA-PKcs) suggesting that ERKs and DNA-PKcs cooperate in radioprotection of rhabdomyosarcoma cells. The TE671 cell line xenotransplanted in mice showed a reduction in tumor mass and increase in the time of tumor progression with U0126 treatment associated with reduced DNA-PKcs, an effect enhanced by radiotherapy. Thus, our results show that MEK/ERK inhibition enhances radiosensitivity of rhabdomyosarcoma cells suggesting a rational approach in combination with radiotherapy.
Decreases in levels of serum fibronectin predict the severity of vascular leak syndrome in patients treated with ricin A chain-containing immunotoxins. (1996)

The major dose-limiting adverse effect of ricin A chain-containing immunotoxin (IT) therapy is vascular leak syndrome (VLS). Since plasma fibronectin (Fn) plays a role in maintaining microcirculatory integrity and since the gradient between plasma and tissue Fn can be altered in various pathological situations, we determined whether the administration of IT-ricin A chain to patients resulted in changes in the levels of serum Fn and, if so, whether these changes correlated with the severity of VLS. We also measured the serum levels of tumor necrosis factor alpha (TNFalpha), a proinflammatory cytokine which has been implicated in tissue damage and in interleukin 2-mediated VLS. Our results indicate that the most severe manifestations of VLS were associated with the highest pretreatment levels of Fn, the largest decreases in Fn immediately after starting IT therapy, increases in the levels of serum TNFalpha, higher concentrations of circulating IT, and the lowest numbers of circulating tumor cells. These parameters should, therefore, be useful for predicting which patients will have severe VLS.
An Efficiency and Protection Degree-Based Comparison Among the Quantitative Randomized Response Strategies (2008)

There have been many alternative strategies for implementing sampling survey on quantitative characteristic of sensitive issues by using randomized response (RR) technique. The efficiency of most of those strategies has been improved by choosing the suitable design parameters of model. However, the two different procedures with pre-assigned design parameter values cannot ensure that they possess the same protection degree to the respondents. Some earlier comparisons of those strategies are inadequate (as in Eichhorn and Hayre, 1983 Eichhorn , B. H. , Hayre , L. S. ( 1983 ). Scrambled randomized response methods for obtaining sensitive quantitative data . J. Statist. Plann. Infer. 7 : 307 – 316 .[Crossref], [Web of Science ®] , [Google Scholar]; Gupta et al., 2002 Gupta , S. , Gupta , B. , Singh , S. ( 2002 ). Estimation of sensitivity level of personal interview survey questions . J. Statist. Plann. Infer. 100 ( 2 ): 239 – 247 .[Crossref], [Web of Science ®] , [Google Scholar]). Some literature contains a more comprehensive comparison based on efficiency and protection degree to the respondents among the qualitative characteristic RR techniques (see Bhargava and Singh, 2002 Bhargava , M. , Singh , R. ( 2002 ). On the efficiency comparison of certain randomized response strategies . Metrika 55 : 191 – 197 .[Crossref], [Web of Science ®] , [Google Scholar]; Nayak, 1994 Nayak , T. K. ( 1994 ). On randomized response surveys for estimating a proportion . Commun. Statist. Theor. Meth. 23 ( 11 ): 3303 – 3321 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]; Zaizai and Zankan, 2004 Zaizai , Y. , Zankan , N. ( 2004 ). A fair comparison of the randomized response strategies . Acta Mathematica Scientia 24A ( 3 ): 362 – 368 . [Google Scholar]). As far as the comparisons are concerned that are based on efficiency and protection degree to the respondents among the quantitative characteristic RR techniques, very few related studies have been found so far. The purpose of this article is to give a more adequate comparison among those earlier quantitative characteristic RR strategies. It is found that several important differences between the results obtained in this article and some known results exist. Therefore, these earlier RR strategies should be reevaluated.
CLTC: a cluster-based topology control framework for ad hoc networks (2004)

The topology of an ad hoc network has a significant impact on its performance in that a dense topology may induce high interference and low capacity, while a sparse topology is vulnerable to link failure and network partitioning. Topology control aims to maintain a topology that optimizes network performance while minimizing energy consumption. Existing topology control algorithms utilize either a purely centralized or a purely distributed approach. A centralized approach, although able to achieve strong connectivity (k-connectivity for k /spl ges/ 2), suffers from scalability problems. In contrast, a distributed approach, although scalable, lacks strong connectivity guarantees. We propose a hybrid topology control framework, cluster-based topology control (CLTC) that achieves both scalability and strong connectivity. By varying the algorithms utilized in each of the three phases of the framework, a variety of optimization objectives and topological properties can be achieved. In this paper, we present the CLTC framework; describe topology control algorithms based on CLTC and prove that k-connectivity is achieved using those algorithms; analyze the message complexity of an implementation of CLTC, namely, CLTC-A, and present simulation studies that evaluate the effectiveness of CLTC-A for a range of networks.
Low-Temperature Plasmas for Medicine? (2009)

Can low-temperature plasma technology play a role in medicine? This is a question that many investigators today are trying hard to give a positive answer to. It did not quite start out this way. Almost two decades ago, few ldquocuriousrdquo electrical engineers and physicists with the help of few ldquobraverdquo biologists/microbiologists asked themselves more basic questions: What happens to biological cells if they were exposed to low-temperature plasma? Will they die? Will they survive? If they survive, will they come out the same or somehow ldquoinjuredrdquo? If injured, will they be able to repair the damage and recover? What kind of damage? Which plasma agent causes the damage? etc. As will be shown in this paper, some of these fundamental questions have been partially or fully answered, but until today, a complete picture has yet to emerge. This is good and not so good. It is good because if we already knew all the answers, we would not be looking forward to a more exciting research. It is not so good because after all these years, we are still quite a ways from an implementable medical application. In this review paper, the present state of knowledge regarding the effects of cold plasma on bacteria cells (prokaryotes) and on eukaryotic cells (such as mammalian cells) will be presented. As medical applications where low-temperature plasma is showing signs of success, blood coagulation and wound healing will be described.
Identification of B- and T-cell epitopes within the MTP40 protein of Mycobacterium tuberculosis and their correlation with the disease course (1991)

Synthetic peptides derived from the amino acid sequence of MTP40, a recently characterized Mycobacterium tuberculosis protein, were tested by two different immunological assays in 91 individuals. For the purposes of this study, the population was distributed in four groups: active tuberculosis (TBC) patients with elevated bacillus loads (BK+), active TBC patients with low bacillus loads (BK-), healthy individuals living in the same household with tuberculous patients (HH), and normal individuals, who had presumably never been in contact with the bacilli (control). We found that T cells of individuals belonging to the HH group showed the highest and most frequent recognition of these peptides in a T-cell proliferation assay, while their antibodies showed the lowest recognition of these peptides when tested by enzyme-linked immunosorbent assay. In contrast, TBC patients revealed an inverse pattern of immune response. Interestingly, one of these peptides (P7) was recognized by T cells of 64% of the HH individuals and by 4.5% of normal donors. Another peptide (P4) was recognized by 55% of sera from BK+ patients and by 5.5% of normal donors. The results presented here indicate the existence of T- and B-cell epitopes within the MTP40 protein. Given the particular recognition pattern of this protein, added to the fact that it appears to be a species-specific antigen of M. tuberculosis, a detailed study of the immune response to it may be useful in the design of more accurate diagnostic tests and an improved vaccine against human TBC.
Phosphorylation of streptozotocin during uptake via the phosphoenolpyruvate: sugar phosphotransferase system in Escherichia coli (1979)

Mutants of Escherichia coli K-12, Staphylococcus aureus, and Bacillus subtilis defective in the general components (enzyme I, or HPr, or both) of the phosphoenolpyruvate:sugar phosphotransferase system are shown to be resistant to the antibiotic streptozotocin. It is shown here, employing 32P-labeled phosphoenolpyruvate, that wild-type cells of E. coli phosphorylate streptozotocin, whereas with a phosphotransferase system-defective mutant of E. coli the drug is recovered in an unaltered, free form. The internal accumulation of streptozotocin at the steady-state level was about 70 times that of the concentration in the external medium. The antibacterial action of streptozotocin, as well as the uptake of the drug, was inhibited by N-acetyl-D-glucosamine. The uptake of the antibiotic was extremely sensitive to p-chloromercuribenzoate. It is concluded that streptozotocin is taken up by E. coli via the phosphoenolpyruvate:sugar phosphotransferase system and consequently accumulates in the cell at first as streptozotocin-phosphate.
Spontaneous production of anti-IFN-  and anti-IL-12 autoantibodies by thymoma cells from myasthenia gravis patients suggests autoimmunization in the tumor (2003)

Myasthenia gravis (MG) is mediated by autoantibodies to the acetylcholine receptor (AChR), expressed in muscle and rare thymic myoid cells. Most early-onset cases show thymic lymph node-type infiltrates, including pre-activated plasma cells spontaneously producing anti-AChR antibodies. Since these are not evident in the associated thymomas found in another 10% of MG patients, AChR-specific B cells must be autosensitized elsewhere. Unexpectedly, at diagnosis, >70% of MG/thymoma patients also have high-titer neutralizing autoantibodies to IFN-alpha, and >50% to IL-12; moreover, titers increase strikingly if the thymomas recur, indicating a closer tumor relationship than for anti-AChR. To investigate this, we have measured autoantibody production by cells cultured from thymomas, any available thymic remnants and blood, with or without the B cell stimulant pokeweed mitogen (PWM). To check autoantibody specificity and clonal origins, we isolated Fabs from two combinatorial libraries from producer thymus/thymoma cells. Surprisingly, thymoma cells spontaneously produced antibodies to IFN-alpha and/or IL-12 in >40% of seropositive cases, showing typical plasma cell behavior, whereas they produced anti-AChR only after PWM stimulation. We isolated 15 combinatorial Fabs to IFN-alpha (versus only one to AChR). Their strong binding in radio-immunoprecipitation and Western blots implies high affinities. The four Fabs tested neutralized anti-viral actions of IFN-alpha. The diverse V genes clearly showed ongoing antigen-driven selection. These results imply pre-activation in situ by native IFN-alpha/IL-12 expressed within a 'dangerous' tumor microenvironment. With these molecules, it should be easier to identify provoking cell type(s) that may give novel additional clues to autoimmunization against T-cell epitopes from the more complex AChR.