gebhart/patrepeval huggingface dataset:
Androgen-receptor-interacting nuclear proteins (2000)

Androgen receptor (AR) belongs to the super-family of nuclear hormone receptors that employ complex molecular mechanisms to guide the development and physiological functions of their target tissues. Our recent work has led to the identification of four novel proteins that recognize AR zinc-finger region (ZFR) both in vivo and in vitro. One is a small nuclear RING-finger protein that possesses separate interaction interfaces for AR and for other transcription activators such as Spl. The second is a nuclear serine/threonine protein kinase (androgen-receptor-interacting nuclear protein kinase; ANPK); however, the receptor itself does not seem to be a substrate for this kinase. The third one is dubbed androgen-receptor-interacting protein 3 (ARIP3) and is a novel member of the PIAS (protein inhibitor of activated STAT) protein family. The fourth protein, termed ARIP4, is a nuclear ATPase that belongs to the SNF2-like family of chromatin remodelling proteins. All four proteins exhibit a punctate nuclear pattern when expressed in cultured cells. Each protein modulates AR-dependent transactivation in co-transfection experiments; their activating functions are not restricted to AR. Current work is aimed at elucidating the biochemical and functional properties of these AR-interacting proteins and at finding the partner proteins that form complexes with them in vivo.
A ratiometric readout circuit for thermal-conductivity-based resistive gas sensors (2015)

This paper presents a readout circuit for thermal-conductivity-based resistive gas sensors. It digitizes the sensor's heat loss to its environment, which is a function of gas concentration, relative to that of a reference transducer, which is made of the same material and acts as a thermal-conductivity reference. Thus, dedicated voltage, power or temperature references are not needed. The ratiometric interface is based on a reconfigurable delta-sigma modulator that digitizes both the temperature and power ratio of the sensor and reference transducers, from which their thermal-conductivity ratio is calculated. It uses a dynamic baseline-resistance cancellation technique to relax the required dynamic range. In addition, dynamic element matching and 6-bit bias-current trimming are used to suppress errors due to transducer mismatch. The interface has been implemented in a standard 0.16 μm CMOS technology. Experimental results obtained in combination with CMOS-compatible tungsten-wire transducers show a CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> resolution of 228 ppm (1σ), which is the highest resolution reported for thermal-conductivity-based CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> sensors.
AMP-Activated Protein Kinase Regulates GLUT4 Transcription by Phosphorylating Histone Deacetylase 5 (2008)

These data reveal a signal transduction pathway linking cellular energy charge to gene transcription directed at restoring cellular and whole-body energy balance and provide new therapeutic targets for the treatment and management of insulin resistance and type 2 diabetes.
Protein kinase C alpha-mediated chronic signal transduction for immunosenescence (1997)

In CD2/protein kinase C alpha (PKC alpha)-overexpressing human CD2/rabbit PKC alpha transgenic mice, an aging-dependent increase in PKC alpha expression and a decrease in proliferative responsiveness of splenic T cells were promoted. We found that an aging-associated accumulation of CD44(high) CD45RB(low) memory CD4+ T cells in exchange for CD44(low) CD45RB(high) naive CD4+ T cells was promoted in transgenic mice. A disequilibrium between Ag-dependent generation and subsequent elimination of memory T cells in these mice was shown to underlie this phenomenon. When stimulated with Ag, the PKC alpha transgenic mice responded poorly regarding Ab production and produced cytokines biased for high IFN-gamma/IL-12 and low IL-4/IL-10 levels. These results prove, for the first time, a causal role for chronic signal transduction through PKC alpha in aging-associated immunodysfunction and provide the first animal model for genetically promoted immunosenescence.
Phonological and morphological awareness in first graders (1993)

ABSTRACT Phonological awareness is thought to be related to children's success in learning to read because it indicates an awareness of the internal structure of words. Morphological awareness, which has been found to be related to reading achievement for older students, may offer a more comprehensive measure of linguistic sensitivity because it entails not only phonological awareness, but also other aspects of linguistic knowledge. The research study reported herein was designed to investigate the extent to which phonological awareness contributes to the morphological awareness of first graders and to determine the extent to which phonological and morphological awareness account for variance in word reading. Two tasks of morphological awareness were used, one assessing judgments of morphological relations and the other assessing the production of inflected and derived forms.
A robust rate-adaptive hybrid ARQ scheme for frequency-hopped spread-spectrum multiple-access communication systems (1994)

This paper considers the application of rate-adaptive coding (RAC) to a spread spectrum multiple access (SSMA) communication system. Specifically, RAC using a variable rate Reed-Solomon (RS) code with a single decoder is applied to frequency-hopped SSMA. We show that this combination can accommodate a larger number of users compared to that with conventional fixed-rate coding. This increase is a result of a reduction in the channel interference from other users. The penalty for this improvement in most cases is a slight increase in the delay (composed of propagation and decoding delay). The throughput and the undetected error probability for a M-ary symmetric channel are analyzed, and performance results are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Analytical Chemistry of Uranium (1953)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnalytical Chemistry of UraniumC. J. RoddenCite this: Anal. Chem. 1953, 25, 11, 1598–1601Publication Date (Print):November 17, 1953Publication History Published online1 May 2002Published inissue 17 November 1953https://pubs.acs.org/doi/10.1021/ac60083a006https://doi.org/10.1021/ac60083a006research-articleACS PublicationsRequest reuse permissionsArticle Views257Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Nonionizing photoacoustic cystography in vivo (2011)

We demonstrate the feasibility of a novel and nonionizing process for bladder imaging in vivo, called photoacoustic cystography (PAC). Using a photoacoustic imaging system, we have successfully imaged a rat bladder filled with clinically used Methylene Blue (MB) dye. An image contrast of ~8 was achieved. Further, spectroscopic PAC confirmed the accumulation of MB in the bladder. Using a laser pulse energy of less than 1 mJ/cm² (1/20 of the ANSI safety limit), a deeply (1.2 cm) positioned bladder in biological tissues was clearly visible in the PA image. Our results suggest that PAC can potentially provide a nonionizing, relatively cheap, and portable tool for bladder mapping. Among our clinical interests, nonionizing PAC with an injection of MB can potentially monitor vesicoureteral reflux in children.
Functional Analysis of All Aminotransferase Proteins Inferred from the Genome Sequence of<i>Corynebacterium glutamicum</i> (2005)

Twenty putative aminotransferase (AT) proteins of Corynebacterium glutamicum, or rather pyridoxal-5'-phosphate (PLP)-dependent enzymes, were isolated and assayed among others with L-glutamate, L-aspartate, and L-alanine as amino donors and a number of 2-oxo-acids as amino acceptors. One outstanding AT identified is AlaT, which has a broad amino donor specificity utilizing (in the order of preference) L-glutamate > 2-aminobutyrate > L-aspartate with pyruvate as acceptor. Another AT is AvtA, which utilizes L-alanine to aminate 2-oxo-isovalerate, the L-valine precursor, and 2-oxo-butyrate. A second AT active with the L-valine precursor and that of the other two branched-chain amino acids, too, is IlvE, and both enzyme activities overlap partially in vivo, as demonstrated by the analysis of deletion mutants. Also identified was AroT, the aromatic AT, and this and IlvE were shown to have comparable activities with phenylpyruvate, thus demonstrating the relevance of both ATs for L-phenylalanine synthesis. We also assessed the activity of two PLP-containing cysteine desulfurases, supplying a persulfide intermediate. One of them is SufS, which assists in the sulfur transfer pathway for the Fe-S cluster assembly. Together with the identification of further ATs and the additional analysis of deletion mutants, this results in an overview of the ATs within an organism that may not have been achieved thus far.
The European Bioinformatics Institute web site: a new view (2003)

Abstract Summary: The European Bioinformatics Institute (EBI), and outstation of the European Molecular Biology laboratory, has revamped its web site for the second time since 1997 in order to address increased user demand as well as establishing better uniformity and easier accessibility for the ever growing number of users and services it offers to the community. A GRID-like hardware infrastructure has been put in place to provide round the clock services in a redundant and reliable fashion. Availability: http://www.ebi.ac.uk/ Contact: rls@ebi.ac.uk * To whom correspondence should be addressed. † EBI’s Systems group.
Information rates and power spectra of digital codes (1982)

The encoding of independent data symbols as a sequence of discrete amplitude, real variables with given power spectrum is considered. The maximum rate of such an encoding is determined by the achievable entropy of the discrete sequence with the given constraints. An upper bound to this entropy is expressed in terms of the rate distortion function for a memoryless finite alphabet source and mean-square error distortion measure. A class of simple dc-free power spectra is considered in detail, and a method for constructing Markov sources with such spectra is derived. It is found that these sequences have greater entropies than most codes with similar spectra that have been suggested earlier, and that they often come close to the upper bound. When the constraint on the power spectrum is replaced by a constraint On the variance of the sum of the encoded symbols, a stronger upper bound to the rate of dc-free codes is obtained. Finally, the optimality of the binary biphase code and of the ternary bipolar code is decided.
DNA Damage Response Pathway and Replication Fork Stress During Oligonucleotide Directed Gene Editing (2012)

Single-stranded DNA oligonucleotides (ODNs) can be used to direct the exchange of nucleotides in the genome of mammalian cells in a process known as gene editing. Once refined, gene editing should become a viable option for gene therapy and molecular medicine. Gene editing is regulated by a number of DNA recombination and repair pathways whose natural activities often lead to single- and double-stranded DNA breaks. It has been previously shown that introduction of a phosphorotioated ODN, designed to direct a gene-editing event, into cells results in the activation of γH2AX, a well-recognized protein biomarker for double-stranded DNA breakage. Using a single copy, integrated mutant enhanced green fluorescent protein (eGFP) gene as our target, we now demonstrate that several types of ODNs, capable of directing gene editing, also activate the DNA damage response and the post-translational modification of proliferating cell nuclear antigen (PCNA), a signature modification of replication stress. We find that the gene editing reaction itself leads to transient DNA breakage, perhaps through replication fork collapse. Unmodified specific ODNs elicit a lesser degree of replication stress than their chemically modified counterparts, but are also less active in gene editing. Modified phosphothioate oligonucleotides (PTOs) are detrimental irrespective of the DNA sequence. Such collateral damage may prove problematic for proliferation of human cells genetically modified by gene editing.
Discontinuous fluids (2005)

At interfaces between different fluids, properties such as density, viscosity, and molecular cohesion are discontinuous. To animate small-scale details of incompressible viscous multi-phase fluids realistically, we focus on the discontinuities in the state variables that express these properties. Surface tension of both free and bubble surfaces is modeled using the jump condition in the pressure field; and discontinuities in the velocity gradient field. driven by viscosity differences, are also considered. To obtain derivatives of the pressure and velocity fields with sub-grid accuracy, they are extrapolated across interfaces using continuous variables based on physical properties. The numerical methods that we present are easy to implement and do not impact the performance of existing solvers. Small-scale fluid motions, such as capillary instability, breakup of liquid sheets, and bubbly water can all be successfully animated.
Evolution of an endofungal Lifestyle: Deductions from the Burkholderia rhizoxinica Genome (2011)

B. rhizoxinica is the first endofungal bacterium, whose genome has been sequenced. Here, we present models of evolution, metabolism and tools for host-symbiont interaction of the endofungal bacterium deduced from whole genome analyses. Genome size and structure suggest that B. rhizoxinica is in an early phase of adaptation to the intracellular lifestyle (genome in transition). By analysis of tranporters and metabolic pathways we predict how metabolites might be exchanged between the symbiont and its host. Gene clusters for biosynthesis of secondary metabolites represent novel targets for genomic mining of cryptic natural products. In silico analyses of virulence-associated genes, secreted proteins and effectors might inspire future studies on molecular mechanisms underlying bacterial-fungal interaction.
Differentiation of bursal secretory‐dendritic cells studied with anti‐vimentin monoclonal antibody (1992)

Embryonic and posthatched differentiation of bursal secretory dendritic cells, which express vimentin intermediate filaments, were studied with anti-vimentin (clone 3B4) and anti-cytokeratin (clone Lu5) monoclonal antibodies. Anti-cytokeratin staining revealed that medullary reticular epithelial cells formed a continuous network at every age, whereas the vimentin positive cells were single and showed dendritic appearance. On the basis of location, number, shape, polarized appearance, and Ia staining, the vimentin-positive cells and secretory dendritic cells appeared to be the same cell. Secretory dendritic cell precursors entered the bursal epithelium between 11 and 13 days of embryogenesis. The first vimentin positive cell appeared in the bud of 14-day embryos. Bud formation preceded the appearance of vimentin-positive cells. These observations suggested that the secretory dendritic cell precursor did not express vimentin when it entered the epithelium. Between 15 days of embryogenesis and 2 weeks of posthatch development, the changes in vimentin staining pattern revealed a cytological differentiation of the vimentin-positive cell. During rapid bursal growth, the number of secretory dendritic cells (vimentin-positive cells) increased about 18 times possibly by proliferation of vimentin-negative precursors in the epithelial arches of the corticomedullary border.
Laser-induced graphene: preparation, functionalization and applications (2018)

Recently graphene-based materials (GBMs) have gained tremendous attention for their enormous potentials for various functional devices due to their excellent physical and chemical properties. However, the cost effective synthesis and patterning of carbon nanomaterials are a challenge, which significantly restricts its applications. Therefore, straightforward preparation and processing of GBMs in a scalable approach is still a important goal. In recent years, laser direct writing (LDW) technique provides a powerful processing method for the broad application of laser-induced graphene (LIG) which does not rely on either high temperature or toxic chemicals. This article aims to update the latest results in this rapidly evolving field and to provide critical insights to inspire more exciting developments of LIG and its functionalization. Based on the interaction mechanisms and physical effects, we comparatively review the methods of preparation and functionalization of LIG, including inducing, structuring, doping and hybriding. In this progress report, the applications of LIG and its GBMs patterned by LDW technique were discussed in the fields of optoelectronic devices, energy storage devices, biosensors and biomimetic devices.
Modeling Polarization Mode Coupling in Frequency-Selective Surfaces (2004)

An analysis of scattering from frequency-selective surfaces (FSS) is developed that correctly accounts for coupling between scattered polarization modes. This is useful for the design of FSS structures with obliquely incident radiation, such as polarization converters (polarizers) for direct broadcast satellite reception by linearly polarized ground terminal antennas. In the past, the neglect of polarization mode coupling limited the performance range of various FSS structures, such as meander-line polarizers, to near normal incidence where mode coupling is weak. The following analysis shows how a suitable pair of polarization modes can be selected to maintain modal independence. The result is a pair of independent equivalent circuits representing scattering of the two modes, together with mode transformation networks. To illustrate the theory, a four-layer meander-line polarizer is designed for an incident angle of 45/spl deg/ off normal. The resulting axial ratio is measured to be 0.3 dB at 12.45 GHz.
Tandem Infrared Multiphoton Dissociation and Collisionally Activated Dissociation Techniques in a Quadrupole Ion Trap (2001)

Tandem infrared multiphoton dissociation and collisionally activated dissociation methods are implemented in a quadrupole ion trap mass spectrometer and used to characterize an array of antibiotic ions generated by electrospray ionization. The tandem methods prove useful for probing fragmentation genealogies, evaluating the structures of lower mass fragment ions produced from higher mass molecular ions, and differentiating isobaric ions. The infrared multiphoton dissociation method is more efficient for producing an array of fragment ions over a large mass range, whereas collisionally activated dissociation is preferable for the analysis of lower m/z ions.
Regeneration of Corneal Cells and Nerves in an Implanted Collagen Corneal Substitute (2008)

We show that a simple ECM mimetic can promote regeneration of corneal cells and nerves. Gradual turnover of matrix material as part of the natural remodeling process allowed for stable integration with host tissue and restoration of mechanical properties of the organ. The simplicity in fabrication and shown functionality shows potential for ECM substitutes in future clinical applications.
Glycerol Overproduction by Engineered<i>Saccharomyces cerevisiae</i>Wine Yeast Strains Leads to Substantial Changes in By-Product Formation and to a Stimulation of Fermentation Rate in Stationary Phase (1999)

ABSTRACT Six commercial wine yeast strains and three nonindustrial strains (two laboratory strains and one haploid strain derived from a wine yeast strain) were engineered to produce large amounts of glycerol with a lower ethanol yield. Overexpression of the GPD1 gene, encoding a glycerol-3-phosphate dehydrogenase, resulted in a 1.5- to 2.5-fold increase in glycerol production and a slight decrease in ethanol formation under conditions simulating wine fermentation. All the strains overexpressing GPD1 produced a larger amount of succinate and acetate, with marked differences in the level of these compounds between industrial and nonindustrial engineered strains. Acetoin and 2,3-butanediol formation was enhanced with significant variation between strains and in relation to the level of glycerol produced. Wine strains overproducing glycerol at moderate levels (12 to 18 g/liter) reduced acetoin almost completely to 2,3-butanediol. A lower biomass concentration was attained by GPD1 -overexpressing strains, probably due to high acetaldehyde production during the growth phase. Despite the reduction in cell numbers, complete sugar exhaustion was achieved during fermentation in a sugar-rich medium. Surprisingly, the engineered wine yeast strains exhibited a significant increase in the fermentation rate in the stationary phase, which reduced the time of fermentation.
Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries (2001)

In response to thermodynamic driving forces, the domains in microphase-separated block copolymers have distinct intermaterial dividing surfaces (IMDS). Of particular interest are bicontinuous and tricontinuous, triply periodic morphologies and their mathematical representations. Level surfaces are represented by functions F: R3 → R of points (x, y, z) ∈ R3, which satisfy the equation F(x, y, z) = t, where t is a constant. Level surfaces make attractive approximations of certain recently computed triply periodic constant mean curvature (cmc) surfaces and they are good starting surfaces to obtain cmc surfaces by mean curvature flow. The functions F(x, y, z) arise from the nonzero structure factors F(hkl) of a particular space group, such that the resulting surfaces are triply periodic and maintain the given symmetries. This approach applies to any space group and can, therefore, yield desired candidate morphologies for novel material structures defined by the IMDS. We present a technique for generating such level surfaces, give new examples, and discuss certain bicontinuous cubic IMDS in detail.
Production of Lantipeptides in <i>Escherichia coli</i> (2010)

Lantipeptides are ribosomally synthesized and posttranslationally modified peptides containing thioether cross-links. We describe the preparation of seven different lantipeptides in Escherichia coli and demonstrate that this methodology can be used to incorporate nonproteinogenic amino acids.