gebhart/patrepeval huggingface dataset:
Characteristics and Crystal Structure of Bacterial Inosine-5‘-monophosphate Dehydrogenase, (1999)

IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the first step unique to GTP synthesis. To provide a basis for the evaluation of IMPDH inhibitors as antimicrobial agents, we have expressed and characterized IMPDH from the pathogenic bacterium Streptococcus pyogenes. Our results show that the biochemical and kinetic characteristics of S. pyogenes IMPDH are similar to other bacterial IMPDH enzymes. However, the lack of sensitivity to mycophenolic acid and the Km for NAD (1180 microM) exemplify some of the differences between the bacterial and mammalian IMPDH enzymes, making it an attractive target for antimicrobial agents. To evaluate the basis for these differences, we determined the crystal structure of the bacterial enzyme at 1.9 A with substrate bound in the catalytic site. The structure was determined using selenomethionine-substituted protein and multiwavelength anomalous (MAD) analysis of data obtained with synchrotron radiation from the undulator beamline (19ID) of the Structural Biology Center at Argonne's Advanced Photon Source. S. pyogenes IMPDH is a tetramer with its four subunits related by a crystallographic 4-fold axis. The protein is composed of two domains: a TIM barrel domain that embodies the catalytic framework and a cystathione beta-synthase (CBS) dimer domain of so far unknown function. Using information provided by sequence alignments and the crystal structure, we prepared several site-specific mutants to examine the role of various active site regions in catalysis. These variants implicate the active site flap as an essential catalytic element and indicate there are significant differences in the catalytic environment of bacterial and mammalian IMPDH enzymes. Comparison of the structure of bacterial IMPDH with the known partial structures from eukaryotic organisms will provide an explanation of their distinct properties and contribute to the design of specific bacterial IMPDH inhibitors.
Cat-a-Cone (1997)

This paper introduces a novel user interface that integrates search and browsing of very large category hierarchies with their associated text collections. A key component is the separate but simultaneous display of the representations of the categories and the retrieved documents. Another key component is the display of multapfe selected categories simultaneously, complete with their hierarchical context. The prototype implementation uses animation and a three-dimensional graphical workspace to accommodate the category hierarchy and to store intermediate search results. Query specification in this 3D environment is accomplished via a novel method for painting Boolean queries over a combination of category labels and free text. Examples are shown on a collection of medical text. 'The Cat-a-Con. m!egrates cotegory hlerarchka into Conelhee. The name is almost a homophone of catacomb, a word whose secondary definition is a complex set of interrelated thingu
Photoaffinity behavior of a conjugate of oligonucleoside methylphosphonate, rhodamine, and psoralen in the presence of complementary oligonucleotides (1993)

A 3'-[[2-[N-(3-aminopropyl)-N-(2- hydroxyethyl)amino]ethylphosphoryl]oligodeoxyribonucleoside methylphosphonate 12-mer was synthesized using the Aha-CPG solid support [Thaden, J. and Miller, P.S. (1993) Bioconjugate Chem, companion paper in this issue]. The oligomer was conjugated at the 3' primary aliphatic amine with tetramethylrhodamine 5-isothiocyanate. The rhodamine linker/spacer was stable in 10% fetal calf serum. After enzymatic phosphorylation, the molecule was conjugated at the 5' phosphate with 4'-[N-(2-aminoethyl)aminomethyl]-4,5',8- trimethylpsoralen [(ae(AMT)]. The rhodamine/psoralen doubly-conjugated oligomer formed photoadducts with complementary single-stranded DNA and RNA oligonucleotides when irradiated with long-wavelength ultraviolet light. The efficiency of UV cross-linking slightly exceeded that of a colinear, psoralen-derivatized oligonucleoside methylphosphonate, and exhibited relationships with UV fluence and temperature that are characteristic for psoralen-conjugated methylphosphonates. The 1:1 complex formed with the oligodeoxyribonucleotide target could be detected by its red fluorescence. Mouse L949 cells grown in the presence of the double conjugate were shown by means of computer-assisted epifluorescence microscopy to have internalized it. There was an accumulation of intensely fluorescent points and spots in a juxtanuclear region of the cytoplasm, and a faint, diffuse signal in the entire cell area.
The mode of action of immunological adjuvants. (1998)

Adjuvants augment immune responses to antigens and influence the balance between cell-mediated and humoral responses, as well as the isotypes of antibodies formed. New adjuvant formulations include antigen-carrying vehicles and small molecules with immunomodulating activity. Widely used two-phase vehicles comprise liposomes and microfluidized squalene or squalane emulsions. These are believed to target antigens to antigen-presenting cells, including dendritic cells (DC), follicular dendritic cells (FDC) and B-lymphocytes. Activation of complement generates C3d, which binds CR2 (CD21) on FDC and B-lymphocytes, thereby stimulating the proliferation of the latter and the generation of B-memory. Targeting of antigens to DC may favour cell-mediated immunity. Immunomodulating agents induce the production of cytokine cascades. In a primary cascade at injection sites TNF-alpha, GM-CSF and IL-1 are produced. TNF-alpha promotes migration of DC to lymphoid tissues, while GM-CSF and IL-1 accelerate the maturation of DC into efficient antigen-presenting cells for T-lymphocytes. In a secondary cytokine cascade in draining lymph nodes, DC produce IL-12, which induces Th1 responses with the production of IFN-gamma. The cytokines elicit cell-mediated immune responses and the formation of antibodies of protective isotypes, such as IgG2a in the mouse and IgG1 in humans. Antibodies of these isotypes activate complement and collaborate with antibody-dependent effector cells in protective immune responses.
Layout based frequency dependent inductance and resistance extraction for on-chip interconnect timing analysis (1998)

It is well understood that frequency independent lumped-element circuits can be used to accurately model proximity and skin effects in transmission lines [7]. Furthermore, it is also understood that these circuits can be synthesized knowing only the high and the low frequency resistances and inductances [4]. Existing VLSI extraction tools however, are not efficient enough to solve for the frequency dependent resistances and inductances on large VLSI layouts, nor do they synthesize circuits suitable for timing analysis. We propose a rules-based method that efficiently and accurately captures the high and low frequency characteristics directly from layout shapes, and subsequently synthesizes a simple frequency independent ladder circuit suitable for timing analysis. We compare our results to other simulation results.
Adapting Adaptive Testing: Using the MicroCAT Testing System in a Local School District (1990)

What is the rationale for adapting an existing testing system instead of developing your own? What are the limitations of MicroCAT? What has to be modified in order to meet local needs and to realize the potential of adaptive testing in the context of an existing testing system?
Characterization of Graphite Fiber Surfaces with Raman Spectroscopy (1970)

Raman spectroscopy is used to characterize the fiber surface of graphite and carbon fibers. A correlation exists between the Raman spectrum of the fiber surface and the shear strength of the com posite. Effects of surface treatments are reflected in the Raman spec trum as well as the shear strength of the composite. Many graphite fibers have a weak surface layer where the graphite planes are oriented parallel to the surface.
A Generalized Sampling Method for Finite-Rate-of-Innovation-Signal Reconstruction (2008)

The problem of sampling signals that are not admissible within the classical Shannon framework has received much attention in the recent past. Typically, these signals have a parametric representation with a finite number of degrees of freedom per time unit. It was shown that, by choosing suitable sampling kernels, the parameters can be computed by employing high-resolution spectral estimation techniques. In this letter, we propose a simple acquisition and reconstruction method within the framework of multichannel sampling. In the proposed approach, an infinite stream of nonuniformly-spaced Dirac impulses can be sampled and accurately reconstructed provided that there is at most one Dirac impulse per sampling period. The reconstruction algorithm has a low computational complexity, and the parameters are computed on the fly. The processing delay is minimal just the sampling period. We propose sampling circuits using inexpensive passive devices such as resistors and capacitors. We also show how the approach can be extended to sample piecewise-constant signals with a minimal change in the system configuration. We provide some simulation results to confirm the theoretical findings.
Clinical significance of AXL kinase family in gastric cancer. (2002)

This finding indicates that a co-operative relationship exists between axllufo and nyk/mer protein kinases and this seems to play an important role in gastric cancer progression and metastasis.
Slicer function of Drosophila Argonautes and its involvement in RISC formation (2005)

Argonaute proteins play important yet distinct roles in RNA silencing. Human Argonaute2 (hAgo2) was shown to be responsible for target RNA cleavage ("Slicer") activity in RNA interference (RNAi), whereas other Argonaute subfamily members do not exhibit the Slicer activity in humans. In Drosophila, AGO2 was shown to possess the Slicer activity. Here we show that AGO1, another member of the Drosophila Argonaute subfamily, immunopurified from Schneider2 (S2) cells associates with microRNA (miRNA) and cleaves target RNA completely complementary to the miRNA. Slicer activity is reconstituted with recombinant full-length AGO1. Thus, in Drosophila, unlike in humans, both AGO1 and AGO2 have Slicer functions. Further, reconstitution of Slicer activity with recombinant PIWI domains of AGO1 and AGO2 demonstrates that other regions in the Argonautes are not strictly necessary for small interfering RNA (siRNA)-binding and cleavage activities. It has been shown that in circumstances with AGO2-lacking, the siRNA duplex is not unwound and consequently an RNA-induced silencing complex (RISC) is not formed. We show that upon addition of an siRNA duplex in S2 lysate, the passenger strand is cleaved in an AGO2-dependent manner, and nuclease-resistant modification of the passenger strand impairs RISC formation. These findings give rise to a new model in which AGO2 is directly involved in RISC formation as "Slicer" of the passenger strand of the siRNA duplex.
Pulse like hydrogen sensing response in Pd nanoparticle layers (2007)

This study reports an enhanced and unusual pulse like hydrogen sensing response in Pd nanoparticle layers. The faster H adsorption due to increased surface area and closure of conducting paths as a result of lattice expansion on hydride formation are the primary reasons for this. In comparison, Pd thin films exhibit a slow and subdued sensing response because of the overlap of the above two opposing effects and hydrogen induced lattice strain. Temperature independent conductivity in the temperature range of 20–300K confirms the presence of interparticle gaps in the case of Pd nanoparticle layers.
Feedforward Carrier Recovery for Coherent Optical Communications (2007)

We study a carrier-synchronization scheme for coherent optical communications that uses a feedforward architecture that can be implemented in digital hardware without a phase-locked loop. We derive the equations for maximum a posteriori joint detection of the transmitted symbols and the carrier phase. The result is a multidimensional optimization problem that we approximate with a two-stage iterative algorithm: The first stage is a symbol-by-symbol soft detector of the carrier phase, and the second stage is a hard-decision phase estimator that uses prior and subsequent soft-phase decisions to obtain a minimum mean-square-error phase estimate by exploiting the temporal correlation in the phase-noise process. The received symbols are then derotated by the hard-decision phase estimates, and maximum- likelihood sequence detection of the symbols follows. As each component in the carrier-recovery unit can be separately optimized, the resulting system is highly flexible. We show that the optimum hard-decision phase estimator is a linear filter whose impulse response consists of a causal and an anticausal exponential sequence, which we can truncate and implement as an finite-impulse- response filter. We derive equations for the phase-error variance and the system bit-error ratio (BER). Our results show that 4, 8, and 16 quadrature-amplitude-modulation (QAM) transmissions at 1 dB above sensitivity for BER = 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> is possible with laser beat linewidths of DeltanuT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> = 1.3 X 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> , 1.3 X 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> , and 1.5 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> when a decision-directed soft-decision phase estimator is employed.
AKT Signaling in Regulating Angiogenesis (2008)

AKT is a central signaling molecule in regulating cell survival, proliferation, tumor growth and angiogenesis. Upstream components of AKT signaling pathway such as PI3K, PTEN, and Ras are commonly mutated in many human cancers. Recently it is found that AKT plays an important role in regulating normal vascularization and pathological angiogenesis. Angiogenesis is required for tumor growth and metastasis when tumor reaches more than 1 mm in diameter. This review focuses on the role and potential mechanism of AKT signaling in regulating angiogenesis. Recent studies have shown that AKT activation is necessary and sufficient to regulate VEGF and HIF-1 expression in human cancer cells. VEGF and HIF-1 are potent inducers of angiogenesis. It was found that AKT activation induces VEGF and HIF-1 expression through its two downstream molecules HDM2 and p70S6K1. On the other hand, AKT transmits the upstream signals from growth factors, cytokines, heavy metals, and oncogenes for regulating VEGF and HIF-1 expression in human cancer cells. AKT activation and VEGF expression can be inhibited by different natural compounds used for cancer prevention. Thus, inhibition of AKT and its downstream targets offers a new approach for targeting angiogenesis, which could be important for the development of new cancer therapeutics in the future.
Interaction cloning of NS1-I, a human protein that binds to the nonstructural NS1 proteins of influenza A and B viruses (1996)

The yeast interaction trap system was used to identify, NS1-I (for NS1 interactor), which is a human protein that binds to the nonstructural NS1 protein of the influenza A virus. NS1-I is a human homolog of the porcine 17beta-estradiol dehydrogenase precursor protein, to which it is 84% identical. We detected only one NS1-I mRNA species, of about 3.0 kb, in HeLa cells, and the NS1-I cDNA was found to have a coding capacity for a 79.6-kDa protein. However, immunoblot analysis detected predominantly a 55-kDa protein in human cells, suggesting that NS1-I, like the porcine 17beta-estradiol dehydrogenase, is posttranslationally processed. Using an in vitro coprecipitation assay, we showed that NS1-I interacts with NS1 proteins from extracts of cells infected with five different influenza A virus strains as well as with the NS1 of an influenza B virus. The fact that influenza A and influenza B virus NS1 proteins bind to NS1-I suggests that this cellular protein plays a role in the influenza virus life cycle.
Characterization of the Erwinia carotovora pelB gene and its product pectate lyase (1987)

The pelB gene encodes pectate lyase B, one of three pectate lyases identified in Erwinia carotovora EC. Pectate lyase B was purified from Escherichia coli containing the pelB gene on a recombinant plasmid. The activity of the protein was optimal at a pH of 8.3. The amino acid composition, N-terminal amino acid sequence, and C-terminal peptide sequence were determined and compared with the polypeptide sequence deduced from the DNA sequence of pelB. Purified pectate lyase B started at amino acid 23 of the predicted sequence, suggesting that a 22-amino-acid leader peptide had been removed. Pectate lyase B of E. carotovora EC and pectate lyase B of E. chrysanthemi EC16 contain 352 and 353 amino acids, respectively (N. T. Keen, S. Tanaki, W. Belser, D. Dahlbeck, and B. Staskawicz, J. Bacteriol. 168:595-606, 1986). The two proteins are 72% homologous on the basis of DNA sequence data, and 75% of the amino acids are identical.
Plasmon Resonance Shifts of Au-CoatedAu2SNanoshells: Insight into Multicomponent Nanoparticle Growth (1997)

In this Letter we present a coherent description of the optical properties of a unique type of nanoparticle, metal-coated dielectric nanoparticles. These structures occur naturally in the form of Au-coated ${\mathrm{Au}}_{2}\mathrm{S}$ nanoparticles. During the course of nanoparticle growth, the plasmon-related absorption peak undergoes very large shifts in wavelength, from $\ensuremath{\sim}650$ to $\ensuremath{\sim}900\mathrm{nm}$. We show that this plasmon peak shift is purely classical in origin and is determined solely by the relative thickness of the Au shell and the ${\mathrm{Au}}_{2}\mathrm{S}$ core diameter. This understanding of the optical properties of these nanoparticles is used to elucidate the nanoparticle growth kinetics.
Identification of Bacillus anthracis via Raman Spectroscopy and Chemometric Approaches (2012)

Raman micro-spectroscopy was applied to compile a large-scale database of Raman spectra of single Bacillus endospores and to calculate classification functions, which were trained to discriminate between endospores of 66 strains from 13 Bacillus and Bacillus-related species including B. anthracis. The developed two-stage classification system comprising two support vector machines and one linear discriminant analysis classifier was then challenged by a test set of 27 samples to simulate the case of a real-world-scenario, when "unknown samples" are to be identified. In the end, all 27 test set samples including six B. anthracis strains were identified correctly. The samples thereby covered a diverse selection of species within the phylogenetically broad Bacillus genus and also included strains, which were not incorporated in the database before. All of them were correctly identified on the species level with accuracies between 88 and 100%. The sample analysis itself requires no biomass enrichment step prior to the analysis and qualifies the presented Raman spectroscopic approach to be a rapid analysis system in term of Bacillus endospore typing.
Letter: inconsistency in reporting of hypophosphataemia after intravenous iron—authors’ reply (2017)

Linked Content This article is linked to Aksan et al and Schaefer et al papers. To view these articles visit https://doi.org/10.1111/apt.14043 and https://doi.org/10.1111/apt.14231 .
Mitochondrial Carrier Homolog 2 Is a Target of tBID in Cells Signaled To Die by Tumor Necrosis Factor Alpha (2005)

BID, a proapoptotic BCL-2 family member, plays an essential role in the tumor necrosis factor alpha (TNF-alpha)/Fas death receptor pathway in vivo. Activation of the TNF-R1 receptor results in the cleavage of BID into truncated BID (tBID), which translocates to the mitochondria and induces the activation of BAX or BAK. In TNF-alpha-activated FL5.12 cells, tBID becomes part of a 45-kDa cross-linkable mitochondrial complex. Here we describe the biochemical purification of this complex and the identification of mitochondrial carrier homolog 2 (Mtch2) as part of this complex. Mtch2 is a conserved protein that is similar to members of the mitochondrial carrier protein family. Our studies with mouse liver mitochondria indicate that Mtch2 is an integral membrane protein exposed on the surface of mitochondria. Using blue-native gel electrophoresis we revealed that in viable FL5.12 cells Mtch2 resides in a protein complex of ca. 185 kDa and that the addition of TNF-alpha to these cells leads to the recruitment of tBID and BAX to this complex. Importantly, this recruitment was partially inhibited in FL5.12 cells stably expressing BCL-X(L). These results implicate Mtch2 as a mitochondrial target of tBID and raise the possibility that the Mtch2-resident complex participates in the mitochondrial apoptotic program.
Allogeneic Hematopoietic Stem Cell Transplantation (2003)

More than 30 years have passed since the first clinical application of allogeneic bone marrow transplantation to treat hematological diseases. In recent years, the availability of peripheral blood and cord blood as additional sources of stem cells other than bone marrow has expanded the applicability of hematopoietic stem cell transplantation. In addition to differences in stem cell content, immune cells in the grafts from the three sources are different in quality and quantity. As a consequence, transplants from different sources have different kinetics of hematological recovery. Stem cell sources also influence risks for developing graft-versus-host disease. In this paper, we review recently reported results of thus diversified allogeneic hematopoietic, stem cell transplantation.
Coculture Fermentations ofBifidobacteriumSpecies andBacteroides thetaiotaomicronReveal a Mechanistic Insight into the Prebiotic Effect of Inulin-Type Fructans (2009)

Four bifidobacteria, each representing a cluster of strains with specific inulin-type-fructan degradation capacities, were grown in coculture fermentations with Bacteroides thetaiotaomicron LMG 11262, a strain able to metabolize both oligofructose and inulin. In a medium for colon bacteria with inulin as the sole added energy source, the ability of the bifidobacteria to compete for this substrate reflected phenotypical variation. Bifidobacterium breve Yakult, a strain that was not able to degrade oligofructose or inulin, was outcompeted by B. thetaiotaomicron LMG 11262. Bifidobacterium adolescentis LMG 10734, a strain that could degrade oligofructose (displaying a preferential breakdown mechanism) but that did not grow on inulin, managed to become competitive when oligofructose and short fractions of inulin started to accumulate in the fermentation medium. Bifidobacterium angulatum LMG 11039(T), a strain that was previously shown to degrade all oligofructose fractions simultaneously and to be able to partially break down inulin, was competitive from the beginning of the fermentation, consuming short fractions of inulin from the moment they appeared. Bifidobacterium longum LMG 11047, representing a cluster of bifidobacteria that shared both high fructose consumption and oligofructose degradation rates and were able to perform partial breakdown of inulin, was the dominating strain in a coculture with B. thetaiotaomicron LMG 11262. These observations indicate that distinct subgroups within the large-intestinal Bifidobacterium population will be stimulated by different groups of prebiotic inulin-type fructans, a variation that could be reflected in differences concerning their health-promoting effects.