gebhart/patrepeval huggingface dataset:
Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms (1999)

The current taxonomic classification of Chlamydia is based on limited phenotypic, morphologic and genetic criteria. This classification does not take into account recent analysis of the ribosomal operon or recently identified obligately intracellular organisms that have a chlamydia-like developmental cycle of replication. Neither does it provide a systematic rationale for identifying new strains. In this study, phylogenetic analyses of the 16S and 23S rRNA genes are presented with corroborating genetic and phenotypic information to show that the order Chlamydiales contains at least four distinct groups at the family level and that within the Chlamydiaceae are two distinct lineages which branch into nine separate clusters. In this report a reclassification of the order Chlamydiales and its current taxa is proposed. This proposal retains currently known strains with > 90% 16S rRNA identity in the family Chlamydiaceae and separates other chlamydia-like organisms that have 80-90% 16S rRNA relatedness to the Chlamydiaceae into new families. Chlamydiae that were previously described as 'Candidatus Parachlamydia acanthamoebae' Amann, Springer, Schönhuber, Ludwig, Schmid, Müller and Michel 1997, become members of Parachlamydiaceae fam. nov., Parachlamydia acanthamoebae gen. nov., sp. now. 'Simkania' strain Z becomes the founding member of Simkaniaceae fam. nov., Simkania negevensis gen. nov., sp. nov. The fourth group, which includes strain WSU 86-1044, was left unnamed. The Chlamydiaceae, which currently has only the genus Chlamydia, is divided into two genera, Chlamydia and Chlamydophila gen. nov. Two new species, Chlamydia muridarum sp. nov. and Chlamydia suis sp. nov., join Chlamydia trachomatis in the emended genus Chlamydia. Chlamydophila gen. nov. assimilates the current species, Chlamydia pecorum, Chlamydia pneumoniae and Chlamydia psittaci, to form Chlamydophila pecorum comb. nov., Chlamydophila pneumoniae comb. nov. and Chlamydophila psittaci comb. nov. Three new Chlamydophila species are derived from Chlamydia psittaci: Chlamydophila abortus gen. nov., sp. nov., Chlamydophila caviae gen. nov., sp. nov. and Chlamydophila felis gen. nov., sp. nov. Emended descriptions for the order Chlamydiales and for the family Chlamydiaceae are provided. These families, genera and species are readily distinguished by analysis of signature sequences in the 16S and 23S ribosomal genes.
Modèles mathématiques de l'imprécis et de l'incertain en vue d'applications aux techniques d'aide à la décision (1983)

Cette thèse est d'abord motivée par le souci d'élucider certains liens existant entre la théorie des ensembles flous et celle des probabilités, en les replaçant toutes deux dans un contexte plus général de mesures dites « d'incertitude ». Sur cette base, on développe des outils mathématiques susceptibles d'exprimer rigoureusement, de façon quantitative, les concepts duaux de possibilité et de nécessité. On montre notamment qu'on peut par là généraliser les opérations logiques ainsi que d'autres notions, telles que la cardinalité, à des ensembles dont les frontières sont mal définies, représentés par le biais d'une fonction d'appartenance, qu'on peut voir comme une distribution de possibilité. On développe, dans le cadre de la théorie des possibilités, un calcul analogue à celui des fonctions de variables aléatoires, appelé calcule des intervalles flous, qui généralise le calcule d'erreurs. Des éléments d'analyse de fonctions floues, étendant l'analyse des correspondances, sont fournis, notamment l'intégration de Riemann.<br /><br />Ces outils mathématiques sont appliqués à la formulation et à la résolution de problèmes d'analyse de la décision et de recherche opérationnelle. On étudie plus particulièrement l'agrégation de critère, l'évaluation des décisions et le choix en environnement incertain et imprécisément décrit, les algorithmes de plus courts chemins dans les graphes imprécisément valués, la programmation linéaire avec contraintes floues. On tente dans chaque cas de discuter les mérites et les limites de la théorie des possibilités par rapport à celle des probabilités, tant sur le plan de leur pouvoir descriptif que sur celui des calculs qu'elles entraînent, et des résultats qu'elles permettent d'obtenir.
TPEN, a transition metal chelator, improves myocardial protection during prolonged ischemia. (1992)

In view of the hypothesis that free radicals induced damage during ischemia and reperfusion is mediated by transition metals, we investigated the effect of the potent metal chelator TPEN (N,N,N'N'-tetrakis(-)[2-pyridylmethyl]-ethylenediamine) on cardiac function after prolonged myocardial ischemia. Isolated working rat hearts were subjected to 12 hours of cold ischemic arrest followed by reperfusion for 1 hour. The study was carried out on five groups (nine hearts in each): (1) St. Thomas' Hospital cardioplegic solution; (2) St. Thomas' Hospital cardioplegic solution with 7.5 mumol/L TPEN; (3) protection conditions as in group 2, but with TPEN administration during preischemic and reperfusion periods; (4) University of Wisconsin solution; and (5) the same conditions as in group 4 with TPEN administration during the preischemic and reperfusion periods. Significant enhancement of hemodynamic recovery was observed in the presence of TPEN throughout the experiment. The recovery of cardiac output was 24% +/- 4% in group 3, as compared to 12% +/- 4% in group 1 (p < 0.01). The postischemic left ventricular pressure recovery was 57% +/- 4% in group 3, as compared to 18% +/- 7% in group 1 (p < 0.005). The hearts in group 5 recovered, reaching 29% +/- 2% of the preischemic cardiac output and at 65% +/- 2% of the left ventricular pressure recovery (p < 0.05 versus group 3). Lactate dehydrogenase was released throughout the reperfusion. TPEN addition to groups 2 and 3 did not significantly reduce lactate dehydrogenase release; however, TPEN in University of Wisconsin solution and throughout the experiment significantly decreased lactate dehydrogenase release.(ABSTRACT TRUNCATED AT 250 WORDS)
The Human Neutrophil Respiratory Burst Oxidase (1990)

Journal Article The Human Neutrophil Respiratory Burst Oxidase Get access Robert A. Clark Robert A. Clark From the Division of Infectious Diseases, Department of Medicine, the University of Iowa College of Medicine and VA Medical Center, Iowa City Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 161, Issue 6, June 1990, Pages 1140–1147, https://doi.org/10.1093/infdis/161.6.1140 Published: 01 June 1990 Article history Received: 04 December 1989 Revision received: 02 January 1990 Published: 01 June 1990
Photonic integrated circuits for advanced communication networks (1998)

An overview is given of advanced photonic devices for multiwavelength network applications, and the potential and prospects of photonic integration are discussed
Predicting antisense oligonucleotide inhibitory efficacy: a computational approach using histograms and thermodynamic indices (1992)

Antisense oligonucleotides (ASOs) are designed to bind to a specific mRNA and selectively suppress its translation. To facilitate selection of optimal ASO targets, we have developed three thermodynamic indices to evaluate putative structural complexes important in ASO action. These indices are: a secondary structure score (Sscore), which estimates the strength of local mRNA secondary structures at the ASO target site; a duplex score (Dscore), which estimates the delta Gformation for the ASO:mRNA target sequence duplex; and a competition score (Cscore), which is the difference between the Dscore and the Sscore. We also present two histograms to graphically display these indices from different regions of the mRNA. The indices are compared to the inhibition reported in five studies of ASO-mediated suppression of gene expression. The Dscore is the most consistent predictor of ASO efficacy in four of the five studies (r2 from 0.44 to 0.99), while the results of the fifth study could not be predicted by any thermodynamic or physical index. Thus the Dscores and their histogram may prove useful in selection of ASO targets.
Thiol-containing crosslinking agent with enhanced steric hindrance (1990)

Ricin A chain immunotoxins disulfide cross-linked with conventional, sterically unhindered reagents have unsatisfactorily short circulating life times in vivo. (Acetylthio)succinic anhydride, a thiolating reagent with partial steric hindrance of the sulfur atom, does not remedy this situation. Sulfosuccinimidyl N-[3-(acetylthio)-3-methylbutyryl]-beta- alaninate, a new cross-linker in which the carbon alpha to the sulfur is doubly methylated, creates disulfide bonds 2 orders of magnitude more resistant to reduction than unhindered disulfides. Nevertheless, this deactivated thiolating agent rapidly and reliably cross-links ricin A chain and antibodies to create immunotoxins with in vitro cytotoxicities comparable to those of 2-iminothiolane-coupled conjugates.
Faster CNNs with Direct Sparse Convolutions and Guided Pruning (2016)

Phenomenally successful in practical inference problems, convolutional neural networks (CNN) are widely deployed in mobile devices, data centers, and even supercomputers. The number of parameters needed in CNNs, however, are often large and undesirable. Consequently, various methods have been developed to prune a CNN once it is trained. Nevertheless, the resulting CNNs offer limited benefits. While pruning the fully connected layers reduces a CNN's size considerably, it does not improve inference speed noticeably as the compute heavy parts lie in convolutions. Pruning CNNs in a way that increase inference speed often imposes specific sparsity structures, thus limiting the achievable sparsity levels. We present a method to realize simultaneously size economy and speed improvement while pruning CNNs. Paramount to our success is an efficient general sparse-with-dense matrix multiplication implementation that is applicable to convolution of feature maps with kernels of arbitrary sparsity patterns. Complementing this, we developed a performance model that predicts sweet spots of sparsity levels for different layers and on different computer architectures. Together, these two allow us to demonstrate 3.1--7.3$\times$ convolution speedups over dense convolution in AlexNet, on Intel Atom, Xeon, and Xeon Phi processors, spanning the spectrum from mobile devices to supercomputers. We also open source our project at https://github.com/IntelLabs/SkimCaffe.
Divergent patterns of ELAM-1, ICAM-1, and VCAM-1 expression on cytomegalovirus-infected endothelial cells. (1994)

Endothelial cells, one of several in vivo host cells for cytomegalovirus (CMV), participate in solid organ allograft rejection in part through the expression of leukocyte adhesion molecules. The hypothesis that CMV infection alters the constitutive and induced expression of ELAM-1, ICAM-1, and VCAM-1 on infected human umbilical vein endothelial cells (HUVECs) was examined. HUVECs were infected with an endothelial cell-propagated strain of CMV (VHL/E) for various periods, treated with tumor necrosis factor-alpha (TNF alpha), and examined by flow cytometry or immunohistochemically dual-labeled with monoclonal antibodies to CMV immediate early nuclear protein and ELAM-1, ICAM-1, or VCAM-1. Neither ELAM-1 nor VCAM-1 was induced on CMV-infected HUVECs, and treatment with TNF alpha treatment did not result in their induction. In contrast, ICAM-1 was induced on infected HUVECs by 24 hr postinfection. Endothelial ICAM-1 induction may represent a mechanism by which CMV infection exacerbates the recipient cellular immune response to allografts.
Direct association of fibronectin and actin molecules in vitro. (1980)

Affinity chromatography with actin-Sepharose conjugates of purified human fibronectin, normal human plasma, or serum-free culture fluid from human fibroblasts showed that fibronectin molecules can directly bind to actin. A quantitative recovery of soluble human fibronectin was accomplished by chromatography on actin immobilized on Sepharose beads. Human fibronectin molecules bound to actin-Sepharose were eluted with 0.25--0.35 M potassium bromide, and these molecules competed in a species-specific radioimmunoassay for human fibronectin. The subunits of fibronectin isolated by actin-Sepharose chromatography comigrated in SDS polyacrylamide gel electrophoresis with those of electrophoretically homogeneous fibronectin purified by conventional procedures. The efficient direct binding of fibronectin to actin suggests that interactions between these proteins might also take place in vivo but further studies are needed to elucidate the biological significance of this affinity.
Stop-flow lithography to generate cell-laden microgel particles (2008)

Encapsulating cells within hydrogels is important for generating three-dimensional (3D) tissue constructs for drug delivery and tissue engineering. This paper describes, for the first time, the fabrication of large numbers of cell-laden microgel particles using a continuous microfluidic process called stop-flow lithography (SFL). Prepolymer solution containing cells was flowed through a microfluidic device and arrays of individual particles were repeatedly defined using pulses of UV light through a transparency mask. Unlike photolithography, SFL can be used to synthesize microgel particles continuously while maintaining control over particle size, shape and anisotropy. Therefore, SFL may become a useful tool for generating cell-laden microgels for various biomedical applications.
Effects of Dapiprazole on the Reversal of Pharmacologically Induced Mydriasis (1990)

The ability of a new alpha-adrenergic antagonist, dapiprazole, to reverse mydriasis produced by phenylephrine 2.5% or 10%, tropicamide 0.5%, and the combination of phenylephrine 2.5% and tropicamide 0.5% was investigated. A double masked crossover design was used to study both efficacy of mydriatic reversal and time course. The safety of administration was evaluated as well. Subjects were optometry students and their spouses. The results demonstrate that dapiprazole is safe and effective for reversing mydriasis produced by both concentrations of phenylephrine, and partially effective in reversing mydriasis in eyes treated with tropicamide 0.5%, alone, or in combination with 2.5% phenylephrine.
Platinum(IV) Complexes with Chelating N-Heterocyclic Carbene Ligands (2010)

Platinum(II) complexes with one or two chelating bis(NHC) ligands have been oxidized by bromine as well as iodobenzene dichloride to provide the corresponding platinum(IV) carbene complexes in good yields under very mild reaction conditions. All compounds have been fully characterized by 1H and 13C NMR spectroscopy and in three cases also by solid-state structures. The NMR spectra of the novel Pt(IV) complexes show significantly shifted signals compared to their Pt(II) precursor complexes.
Secretion of a homodimeric V±CΚ T-cell receptor-immunoglobulin chimeric protein (1989)

Transfection into lymphoid cells of a chimeric T-cell receptor-immunoglobulin gene has been used to generate a secreted water-soluble form of the variable (V) domain of a human T-cell receptor alpha chain for use in structural (i.e. x-ray crystallographic) studies. The chimeric protein consists of the V alpha region of the T-cell receptor of a diphtheria toxoid-specific human T-cell clone fused to a human immunoglobulin kappa light chain constant (C) region. It is efficiently secreted by myeloma cells as a noncovalent homodimer of 65-kDa molecular mass in the absence of either immunoglobulin heavy or light chain. The V alpha C kappa protein is extensively glycosylated, and its secretion is glycosylation-dependent. Chimeric genes containing the V beta region of this particular T-cell receptor linked to immunoglobulin C kappa or C gamma 2 regions are expressed intracellularly, but the products, although glycosylated, are not secreted, nor do they assemble with the V alpha C kappa protein. This suggests that the chimeric beta chain-immunoglobulin proteins are incorrectly folded and/or processed due either to the design of the gene fusions themselves or to the absence of vital T-cell-specific accessory molecules in the myeloma host.
Direction-Specific Interactions Control Crystal Growth by Oriented Attachment (2012)

The oriented attachment of molecular clusters and nanoparticles in solution is now recognized as an important mechanism of crystal growth in many materials, yet the alignment process and attachment mechanism have not been established. We performed high-resolution transmission electron microscopy using a fluid cell to directly observe oriented attachment of iron oxyhydroxide nanoparticles. The particles undergo continuous rotation and interaction until they find a perfect lattice match. A sudden jump to contact then occurs over less than 1 nanometer, followed by lateral atom-by-atom addition initiated at the contact point. Interface elimination proceeds at a rate consistent with the curvature dependence of the Gibbs free energy. Measured translational and rotational accelerations show that strong, highly direction-specific interactions drive crystal growth via oriented attachment.
The Structural Basis of Actin Organization by Vinculin and Metavinculin (2015)

Vinculin is an essential adhesion protein that links membrane-bound integrin and cadherin receptors through their intracellular binding partners to filamentous actin, facilitating mechanotransduction. Here we present an 8.5-Å-resolution cryo-electron microscopy reconstruction and pseudo-atomic model of the vinculin tail (Vt) domain bound to F-actin. Upon actin engagement, the N-terminal "strap" and helix 1 are displaced from the Vt helical bundle to mediate actin bundling. We find that an analogous conformational change also occurs in the H1' helix of the tail domain of metavinculin (MVt) upon actin binding, a muscle-specific splice isoform that suppresses actin bundling by Vt. These data support a model in which metavinculin tunes the actin bundling activity of vinculin in a tissue-specific manner, providing a mechanistic framework for understanding metavinculin mutations associated with hereditary cardiomyopathies.
Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores (2010)

We present a novel method for integrating two single-molecule measurement modalities, namely, total internal reflection microscopy and electrical detection of biomolecules using nanopores. Demonstrated here is the electrical measurement of nanopore based biosensing performed simultaneously and in-sync with optical detection of analytes. This method makes it possible, for the first time, to visualize DNA and DNA-protein complexes translocating through a nanopore with high temporal resolution (1000 frames/s) and good signal to background. This paper describes a detailed experimental design of custom optics and data acquisition hardware to achieve simultaneous high resolution electrical and optical measurements on labeled biomolecules as they traverse through a approximately 4 nm synthetic pore. In conclusion, we discuss new directions and measurements, which this technique opens up.
Transformation of Soybean (Glycine max) by Infecting Germinating Seeds with Agrobacterium tumefaciens (1989)

The transfer of genetic material into soybean tissue was accomplished by using an avirulent strain of Agrobacterium tumefaciens which contained the binary vector pGA482. The method used for transformation requires no tissue culture steps as it involves the inoculation of the plumule, cotyledonary node, and adjacent cotyledon tissues of germinating seeds. The identification of neomycin phosphotransferase (NPT) II enzyme activity in the tissues of 16 (R(0)) soybean plants indicated that the plant expressible Nos-NPT II gene, contained within the T-DNA region from pGA482, had been transferred at least into somatic tissues. Putative transformed R(0) soybean plants were advanced to produce R(1) plants which were also assayed for the presence of the transferred Nos-NPT II gene. The combined results of these assays indicated that about 0.7% of the surviving inoculated seeds yielded transformed tissues in the R(0) plant, and that about 1/10 of these plants yielded transformed R(1) plants. The presence of the Nos-NPT II gene in DNAs isolated from both R(0) and R(1) plant was demonstrated by using genomic blot hybridization and polymerase chain reaction methods. Integration of this gene into the soybean genome was demonstrated for three R(1) soybean plants.
Strategic Information Transmission (1982)

This paper develops a model of strategic communication, in which a better-informed Sender (S) sends a possibly noisy signal to a Receiver (R), who then takes an action that determines the welfare of both. We characterize the set of Bayesian Nash equilibria under standard assumptions, and show that equilibrium signaling always takes a strikingly simple form, in which S partitions the support of the (scalar) variable that represents his private information and introduces noise into his signal by reporting, in effect, only which element of the partition his observation actually lies in. We show under further assumptions that before S observes his private information, the equilibrium whose partition has the greatest number of elements is Pareto-superior to all other equilibria, and that if agents coordinate on this equilibrium, R's equilibrium expected utility rises when agents' preferences become more similar. Since R bases his choice of action on rational expectations, this establishes a sense in which equilibrium signaling is more informative when agents' preferences are more similar.
KRDS--a tetrapeptide derived from lactotransferrin--inhibits binding of monoclonal antibody against glycoprotein IIb-IIIa on ADP-stimulated platelets and megakaryocytes (1988)

Short peptides isolated from fibrinogen and K-casein have been shown to inhibit platelet aggregation and fibrinogen binding to stimulated platelets. We studied the effects of synthetic peptides occurring in milk proteins (bovine K-casein, KNQDK, and human lactotransferrin, KRDS) and in fibrinogen (RGDS and L10) on subsequent binding of monoclonal antibodies (MoAb) against the glycoprotein (GP) IIb-IIIa complex (AP2 and P2) on adenosine diphosphate (ADP)-stimulated and unstimulated human platelets and megakaryocytes (MKs) by using an immunoperoxidase method to visualize antibody binding. Only KRDS (900 mumol/L) inhibited the binding of AP2 and P2 on ADP (5 mumol/L)- stimulated platelets, but not on unstimulated platelets. However, the binding of P2 was considerably more inhibited than that of AP2 as judged by immunoperoxidase intensity. Radiolabeled AP2 binding was inhibited by 30% with KRDS on ADP-stimulated platelets as compared with platelets incubated in the absence of ADP. KRDS did not inhibit the binding of MoAbs against GP IIIa (SZ 21), GP IIb (SZ 22), and GP Ib (SZ 2) on ADP-stimulated human platelets. Inhibition of P2 binding by KRDS was also observed in a section of MKs isolated from human bone marrow and stimulated by 15 or 20 micron ADP. A lower concentration of ADP (5 or 10 mumol/L) failed to produce any inhibition of binding. This indicates that MKs may not be equally responsive to agonists as platelets. Moreover, P2 binding inhibition was observed in a larger (P less than .001) percentage of mature MKs (29%) as compared with younger, maturing MKs (11%). The observations suggested that a functional ability possessed by platelets, namely, agonist-induced exposure of the site of interaction of KRDS, may occur at a late stage of MK development.