gebhart/patrepeval huggingface dataset:
Interleukin-10 and Inhibition of Innate Immunity to Yersiniae: Roles of Yops and LcrV (V Antigen) (2003)

Plague, caused by Yersinia pestis, is recognized as the most devastating acute infectious disease experienced by humankind.This notoriety is based upon the high rate of mortality, the rapid onset, and the appalling pathology associated with both the bubonic and pneumonic forms of the infection.Until recently, these extraordinary symptoms prompted investigators to describe the pestilence as a frontal assault upon the host that overwhelms innate mechanisms of defense, inevitably resulting in death caused by septic shock (10,19).It is now established, however, that the invading organisms inhibit the innate immune response, at least during the late stages of infection, thereby avoiding containment within granulomas (9).The first purpose of this review is to present two seemingly exclusive traditions that purport to define the process whereby yersiniae inhibit the generic inflammatory response.An attempt is then made to integrate these concepts.Of the 11 species of Yersinia (genus XI of the Enterobacteriaceae), those pathogenic to humans are Y. pestis and enteropathogenic Y. pseudotuberculosis and Y. enterocolitica.These three organisms share an approximately 70-kb plasmid, termed pCD in Y. pestis and pYV in the enteropathogenic species, that encodes at least one determinant required for the downregulation of inflammation (9, 75).Despite this common feature, the diseases caused by the two enteropathogenic yersiniae are chronic in nature and otherwise markedly distinct from plague (e.g., Y. pseudotuberculosis usually causes a modest mesenteric lymphadenitis in humans, and Y. enterocolitica typically promotes limited gastrointestinal disease).It is therefore remarkable that less than 20,000 years has elapsed since Y. pestis evolved from Y. pseudotuberculosis; divergence of the latter from Y. enterocolitica occurred about 1 million years earlier (1).The close relationship between Y. pestis and Y. pseudotuberculosis provides an excellent system for defining the hereditary events required for the evolution of acute disease.The known significant changes largely reflect lateral acquisition by Y. pestis of genes permitting infection by fleabite followed by dissemination through interstitial spaces and the lymphatics.In addition, the mutational loss by Y. pestis of functions required by enteropathogenic yersiniae for invasion via the small intestine may further contribute to the severity of plague (9, 75).Additional modifications of the Y. pestis genome that minimize inflammation as a mediator of innate immunity will also be addressed in this report.
Iron-oxo clusters biomineralizing on protein surfaces: Structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states (2004)

The crystal structure of the Dps-like (Dps, DNA-protecting protein during starvation) ferritin protein DpsA from the halophile Halobacterium salinarum was determined with low endogenous iron content at 1.6-A resolution. The mechanism of iron uptake and storage was analyzed in this noncanonical ferritin by three high-resolution structures at successively increasing iron contents. In the high-iron state of the DpsA protein, up to 110 iron atoms were localized in the dodecameric protein complex. For ultimate iron storage, the archaeal ferritin shell comprises iron-binding sites for iron translocation, oxidation, and nucleation. Initial iron-protein interactions occur through acidic residues exposed along the outer surface in proximity to the iron entry pore. This narrow pore permits translocation of ions toward the ferroxidase centers via two discrete steps. Iron oxidation proceeds by transient formation of tri-iron ferroxidase centers. Iron storage by biomineralization inside the ferritin shell occurs at two iron nucleation centers. Here, a single iron atom provides a structural seed for iron-oxide cluster formation. The clusters with up to five iron atoms adopt a geometry that is different from natural biominerals like magnetite but resembles iron clusters so far known only from bioinorganic model compounds.
Export of Methyl Parathion Hydrolase to the Periplasm by the Twin-Arginine Translocation Pathway inEscherichia coli (2009)

The uptake of organophosphates (OPs) is a rate-limiting factor in whole-cell biocatalysis systems. Here, we report the periplasmic secretion of methyl parathion hydrolase (MPH) by employing the twin-arginine translocation (Tat) pathway in Escherichia coli. The twin-arginine signal peptide of trimethylamine N-oxide reductase (TorA) from E. coli was used for exporting MPH to the periplasm of E. coli, alleviating the substrate uptake limitation. A periplasmic expression vector, pUTM18, coding for TorA-MPH was constructed, and the periplasmic secretion and functionality of MPH were demonstrated by cell fractionation, immunoblotting, and enzyme activity assays. The strain expressing periplasmic MPH showed 3-fold higher whole-cell activity than the control strain expressing cytoplasmic MPH. Suspended cultures also exhibited good stability, retaining almost 100% activity over a period of 2 weeks. Owing to their high activity and superior stability, these "live biocatalysts" are ideal for large-scale detoxification of OPs.
Velocity-stack and slant-stack stochastic inversion (1985)

Abstract Normal moveout (NMO) and stacking, an important step in analysis of reflection seismic data, involves summation of seismic data over paths represented by a family of hyperbolic curves. This summation process is a linear transformation and maps the data into what might be called a velocity space: a two-dimensional set of points indexed by time and velocity. Examination of data in velocity space is used for analysis of subsurface velocities and filtering of undesired coherent events (e.g., multiples), but the filtering step is useful only if an approximate inverse to the NMO and stack operation is available. One way to effect velocity filtering is to use the operator L T (defined as NMO and stacking) and its adjoint L as a transform pair, but this leads to unacceptable filtered output. Designing a better estimated inverse to L than L T is a generalization of the inversion problem of computerized tomography: deconvolving out the point-spread function after back projection. The inversion process is complicated by missing data, because surface seismic data are recorded only within a finite spatial aperture on the Earth's surface. Our approach to solving the problem of an ill-conditioned or nonunique inverse L (super -1) , brought on by missing data, is to design a stochastic inverse to L. Starting from a maximum a posteriori (MAP) estimator, a system of equations can be set up in which a priori information is incorporated into a sparseness measure: the output of the stochastic inverse is forced to be locally focused, in order to obtain the best possible resolution in velocity space. The size of the resulting nonlinear system of equations is immense, but using a few iterations with a gradient descent algorithm is adequate to obtain a reasonable solution. This theory may also be applied to other large, sparse linear operators. The stochastic inverse of the slant-stack operator (a particular form of the Radon transform), can be developed in a parallel manner, and will yield an accurate slant-stack inverse pair.
Identification of transcriptional activation and inhibitory domains in serum response factor (SRF) by using GAL4-SRF constructs. (1993)

The binding of serum response factor (SRF) to the c-fos serum response element has been shown to be essential for serum and growth factor activation of c-Fos. Since SRF is ubiquitously expressed, it has been difficult to measure the activity of SRF introduced into cells. To assay for functions of SRF in cells, we have changed its DNA binding specificity by fusing it to the DNA binding domain of GAL4. Transfection of GAL4-SRF constructs into cells has allowed us to identify SRF's transcriptional activation domain as well as domains which inhibit this activity. First, we found that the transcriptional activation domain maps to between amino acids 339 and 508 in HeLa cells and to between amino acids 414 and 508 in NIH 3T3 cells. Second, we show that in the context of GAL4-SRF constructs, there are two separate domains of SRF that can inhibit its activation domain. Although these domains overlap the DNA binding and dimerization domains of SRF, these functions were not required for inhibition. Finally, we show that one of the inhibitory domains is modular in that it can also inhibit activation when it is moved amino terminal to GAL4's DNA binding domain in an SRF-GAL4-SRF construct. The implications of these inhibitory domains for SRF regulation are discussed.
Vacuum Ultraviolet Light Source Using Electrodeless Discharge (1986)

A new type of vacuum ultraviolet light source employing electrodeless pulse discharge was studied, and the discharge conditions needed to obtain stable VUV radiation were investigated. The argon discharge spectra between 50 nm and 110 nm were studied, and the number of photons detected through a monochromator was estimated to be 2.5×10 11 cm -2 s -1 at a photon energy of 13.48 eV, a pressure of 5 mTorr of argon, and a flow rate of 12 cm 3 /min.
Cellular levels of thioredoxin associated with drug sensitivity to cisplatin, mitomycin C, doxorubicin, and etoposide. (1995)

Thioredoxin, a cellular thiol, functions as a self-defense mechanism in response to environmental stimuli, including oxidative stress. We first determined cellular levels of thioredoxin in several human bladder and prostatic cancer cell lines resistant to cis-diamminedichloroplatinum(II) (cisplatin). All cisplatin-resistant cell lines had much higher levels of thioredoxin than those in their drug-sensitive parental counterpart. We then, by introducing thioredoxin antisense expression plasmids into human bladder cancer T24 cells, established two bladder cancer cell lines that had decreased levels of thioredoxin. These thioredoxin antisense transfectants showed increased sensitivity to cisplatin and also to other superoxide-generating agents, i.e., doxorubicin, mitomycin C, etoposide, and hydrogen peroxide, as well as to UV irradiation, but not to the tubulin-targeting agents, vincristine, and colchicine. Cellular levels of thioredoxin thus appear to limit sensitivity to various superoxide-generating anticancer drugs in cancer cells.
Bi2ZnTiO6:  A Lead-Free Closed-Shell Polar Perovskite with a Calculated Ionic Polarization of 150 μC cm-2 (2006)

Bi2ZnTiO6, a lead-free analogue of PbTiO3, has been prepared by high-pressure solid-state synthesis methods. Structural analysis reveals that the tetragonal distortion (c/a ratio = 1.21) of Bi2ZnTiO6 is the largest reported for any d0 B site Pb or Bi based perovskite. Significant cation displacements result in a point-charge calculated polarization of 150 μC cm-2.
V-BLAST: an architecture for realizing very high data rates over the rich-scattering wireless channel (2002)

Information theory research has shown that the rich-scattering wireless channel is capable of enormous theoretical capacities if the multipath is properly exploited. In this paper, we describe a wireless communication architecture known as vertical BLAST (Bell Laboratories Layered Space-Time) or V-BLAST, which has been implemented in real-time in the laboratory. Using our laboratory prototype, we have demonstrated spectral efficiencies of 20-40 bps/Hz in an indoor propagation environment at realistic SNRs and error rates. To the best of our knowledge, wireless spectral efficiencies of this magnitude are unprecedented and are furthermore unattainable using traditional techniques.
Optimal Linear Estimation with State-Space Filters (1996)

In this chapter we will again consider estimation problems. However, whereas in Chapter 5 only covariance or spectral density descriptions were used for the signals, we will here adopt an alternative description based on state-space models. This will allow us to obtain a rather simple solution to the problem. In particular, it will no longer be necessary to restrict attention to stationary signals. Also, elegant sequential solutions to the problem will be possible.
The rck/p54 candidate proto-oncogene product is a 54-kilodalton D-E-A-D box protein differentially expressed in human and mouse tissues. (1995)

Expression of the RCK gene, which is a target gene on 11q23 of the t(11;14) (q23;q32) translocation in the B-cell lymphoma cell line RC-K8, was studied by Northern and Western blot analyses. The RCK gene product is a member of the D-E-A-D box protein/RNA helicase family. With the use of Northern blot analysis, a 7.5-kb transcript of the RCK gene was shown to be expressed ubiquitously in human and mouse tissues. Polyclonal antibodies against the RCK gene product were raised, and the RCK gene expression pattern was examined in human and mouse tissues. Two different polyclonal anti-rck antibodies detected a specific 54-kilodalton product named rck/p54 in the majority of human and mouse tissues tested by Western blot analysis. However, rck/p54 was shown to be very low in the human brain and was not detectable in lumbar muscle and lung tissues, although RCK mRNA is abundantly present in these tissues. It is of interest that malignant transformed human cells arising from tissues with low or no expression of rck/p54, such as neuroblastoma, glioblastoma, rhabdomyosarcoma, and lung cancer cell lines, produced a moderate amount of rck/p54 protein, suggesting that rck/p54 plays a role in tumorigenesis. In addition, the rck/p54 protein was localized to cytoplasm by immunostaining with the use of laser microscopy and by subcellular fractionation.
Vinyl Sulfonate Esters and Vinyl Sulfonamides:  Potent, Irreversible Inhibitors of Cysteine Proteases (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTVinyl Sulfonate Esters and Vinyl Sulfonamides: Potent, Irreversible Inhibitors of Cysteine ProteasesWilliam R. Roush, Stephen L. Gwaltney, Jianming Cheng, Karl A. Scheidt, James H. McKerrow, and Elizabeth HansellView Author Information Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109 Department of Chemistry, Indiana University Bloomington, Indiana 47405 Department of Pathology, University of California San Francisco, California 94121 Cite this: J. Am. Chem. Soc. 1998, 120, 42, 10994–10995Publication Date (Web):October 10, 1998Publication History Received22 May 1998Published online10 October 1998Published inissue 1 October 1998https://pubs.acs.org/doi/10.1021/ja981792ohttps://doi.org/10.1021/ja981792orapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views2704Altmetric-Citations187LEARN 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 SUBJECTS:Inhibitors,Monomers,Peptides and proteins,Sulfones,Vinyl Get e-Alerts
The Continuing Increase in the Incidence of Hepatocellular Carcinoma in the United States: An Update (2003)

The incidence of hepatocellular carcinoma continues to increase rapidly in the United States, with rates increasing the fastest in white men 45 to 54 years of age. These findings are consistent with a true increase and could be explained by consequences of hepatitis C virus acquired during the 1960s and 1970s.
Application of electromagnetic actuator using rubber film to three-degrees-of-freedom precision stage (2004)

In this study, a precision stage constructed of electromagnetic actuators using a rubber film has been developed. We have proposed an actuator, which consists of the rubber and an electromagnet as the actuator for the precision drive. This actuator (RE actuator, for short) has the following features: first, viscous damping is essentially obtained by the rubber. Second, the actuator functions also as a flexible joint. Third, since there is no sliding guide, precise positioning can be performed. As an application of the RE actuator, the XYZ precision stage has been developed. The feature of this stage is that it can be driven in the XYZ direction in spite of the monolithic structure. It is also one of the features that residual vibration does not occur after positioning. Fundamental properties of the stage are investigated, and experiments show the 20 nanometer positioning.
Regulation of phospholipid metabolism in differentiating cells from rat brain cerebral hemispheres in culture. Patterns of acetylcholine phosphocholine, and choline phosphoglycerides labeling from (methyl-14C)choline. (1976)

The uptake and metabolism of [14C]choline in dissociated rat brain embryo cell cultures was examined as a function of the extracellular choline concentration. Choline uptake did not follow normal Michaelis-Menten kinetics, but rather exhibited two components with apparent Km of 0.016 mM and 0.96 mM. At low choline concentrations (high affinity uptake) most of the [14C]choline label was present in the phosphocholine fraction prior to the appearance of label in phospholipids. At high choline concentrations (low affinity uptake) a large proportion of the radioactivity was converted into acetylcholine. The dissimilarities between the formation of phosphocholine and acetylcholine as a function of choline concentration might be explained by the existence of two mutually independent enzymatic activities with different Km affinities for choline. Kinetic data augmented by double label studies, suggested that formation of choline phosphoglyceride proceeds entirely via a phosphocholine intermediate. Nearly all radioactivity in the lipid fraction is incorporated into choline phosphoglycerides. A higher turnover rate of choline incorporation into choline phosphoglycerides, accompanied by an increase in the levels of glycerophosphocholine, was observed in older cultures as compared to younger cultures. The metabolic implications of these findings in cultured brain cells in comparison with other in vitro systems are discussed.
Convolutional Neural Networks Applied to Human Face Classification (2012)

Convolutional neural network models have covered a broad scope of computer vision applications, achieving competitive performance with minimal domain knowledge. In this work, we apply such a model to a task designed to deter automated systems. We trained a convolutional neural network to distinguish between images of human faces from computer generated avatars as part of the ICMLA 2012 Face Recognition Challenge. The network achieved a classification accuracy of 99\% on the \textit{Avatar CAPTCHA} dataset. Furthermore, we demonstrated the potential of utilizing support vector machines on the same problem and achieved equally competitive performance.
Asymmetric catalysis: An enabling science (2004)

Chirality of organic molecules plays an enormous role in areas ranging from medicine to material science, yet the synthesis of such entities in one enantiomeric form is one of the most difficult challenges. The advances being made stem from the convergence of a broader understanding of theory and how structure begets function, the developments in the interface between organic and inorganic chemistry and, most notably, the organic chemistry of the transition metals, and the continuing advancements in the tools to help define structure, especially in solution. General themes for designing catalysts to effect asymmetric induction are helping to make this strategy more useful, in general, with the resultant effect of a marked enhancement of synthetic efficiency.
Determination of Folate Vitamers in Human Serum by Stable-Isotope-Dilution Tandem Mass Spectrometry and Comparison with Radioassay and Microbiologic Assay (2004)

This stable-isotope-dilution LC/MS/MS method can quantify 5MeTHF, 5FoTHF, and FA in serum. Currently used clinical assays agree with this candidate reference method.
Understanding the Differential Performance of Rh2(esp)2 as a Catalyst for C−H Amination (2009)

Catalytic amination of saturated C-H bonds is performed efficiently with the use of Rh(2)(esp)(2). Efforts to identify pathways for catalyst degradation and/or arrest have revealed a single-electron oxidation event that gives rise to a red-colored, mixed-valence dimer, [Rh(2)(esp)(2)](+). This species is fortuitously reduced by carboxylic acid, a byproduct generated in the reaction cycle with each turnover of the diacyloxyiodine oxidant. These findings have led to the conclusion that the high performance of Rh(2)(esp)(2) is due in part to the superior kinetic stability of its one-electron oxidized form relative to other dimeric Rh complexes.
Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization. (1993)

Phi 29 DNA polymerase is able to catalyze two different synthetic reactions: protein-primed initiation and DNA polymerization. We have studied the fidelity of phi 29 DNA polymerase when carrying out these two reactions. Global fidelity was dissected into three steps: insertion discrimination, mismatch elongation, and proofreading. The insertion discrimination of phi 29 DNA polymerase in DNA polymerization ranged from 10(4) to 10(6). The efficiency of mismatch elongation was 10(5)-10(-6)-fold lower than that of a properly paired primer terminus. These factors indicate that DNA polymerization catalyzed by phi 29 DNA polymerase is a highly accurate process. Conversely, the insertion fidelity of protein-primed initiation was quite low, the insertion discrimination factor being about 10(2). Mismatch elongation discrimination was also rather low: mismatched terminal protein (TP).dNMP complexes were elongated from 2- to 6-fold more slowly than the correct TP.dNMP complex. Even more, the 3'-->5' exonuclease activity of phi 29 DNA polymerase was unable to act on the TP.dNMP initiation complex, precluding the possibility that a wrong dNMP covalently linked to TP could be excised and corrected. Therefore, protein-primed initiation can be predicted as a quite inaccurate reaction. The problem of maintaining the sequence at the DNA ends is discussed in the context of a recently described model for protein-primed initiation.