gebhart/patrepeval huggingface dataset:
Comparative Analysis and Serovar-Specific Identification of Multiple-Banded Antigen Genes of Ureaplasma urealyticum Biovar 1 (1999)

Ureaplasma urealyticum is a causative agent of nongonococcal urethritis and is implicated in the pathogenesis of several other diseases. The species is divided into 14 serovars and two biovars, of which biovar 1 is most commonly isolated from clinical specimens. Reported associations between individual serovars and diseases have been difficult to confirm because of practical difficulties with serotyping. The multiple-banded antigen (MBA) is the predominant U. urealyticum antigen recognized during infections in humans and probably has a significant role in virulence. The 5' end of the MBA gene is relatively conserved but contains biovar, and possibly serovar, specificity. The 5' ends of the MBA genes of standard strains of U. urealyticum biovar 1, consisting of serovars 1, 3, 6, and 14, were amplified, cloned into pUC19, and sequenced to identify serovar-specific differences. The 5' end of the MBA gene sequence of serovar 3 was identical with the previously published sequence and differed by only three bases from that of serovar 14. Significant differences between the MBA gene sequences allowed biovar 1 to be divided into two subgroups, containing serovars 3/14 and serovars 1 and 6, respectively, using primers UMS-125-UMA269 and UMS-125-UMA269'. Serovars 1 and 6 were distinguished by restriction enzyme analysis of the amplicon and/or by PCR specific for serovar 6. These methods were used to identify and type U. urealyticum in 185 (46.3%) of 400 genital specimens from women. Biovar 1 was detected in 89.2% and biovar 2 in 18.3% of positive specimens. Of 165 specimens containing U. urealyticum biovar 1, 22.2% contained more than one serovar and 46.7, 46.1, and 25.5% contained serovars 1, 3/14, and 6, respectively. U. urealyticum was found in a significantly higher proportion of pregnant women than in sex workers and other women attending a sexually transmissible diseases clinic (P < 0.01). The methods described are relatively rapid, practicable, and specific for serotyping isolates and for direct detection and identification of individual serovars in clinical specimens containing U. urealyticum biovar 1.
Modeling of Spherical Torus Plasmas for Liquid Lithium Wall Experiments (2002)

Liquid metal walls have the potential to solve first-wall problems for fusion reactors, such as heat load and erosion of dry walls, neutron damage and activation, and tritium inventory and breeding. In the near term, such walls can serve as the basis for schemes to stabilize magnetohydrodynamic (MHD) modes. Furthermore, the low recycling characteristics of lithium walls can be used for particle control. Liquid lithium experiments have already begun in the Current Drive eXperiment-Upgrade (CDX-U). Plasmas limited with a toroidally localized limiter have been investigated, and experiments with a fully toroidal lithium limiter are in progress. A liquid surface module (LSM) has been proposed for the National Spherical Torus Experiment (NSTX). In this larger ST, plasma currents are in excess of 1 MA and a typical discharge radius is about 68 cm. The primary motivation for the LSM is particle control, and options for mounting it on the horizontal midplane or in the divertor region are under consideration. A key consideration is the magnitude of the eddy currents at the location of a liquid lithium surface. During plasma start up and disruptions, the force due to such currents and the magnetic field can force a conducting liquid off of the surface behind it. The Tokamak Simulation Code (TSC) has been used to estimate the magnitude of this effect. This program is a two dimensional, time dependent, free boundary simulation code that solves the MHD equations for an axisymmetric toroidal plasma. From calculations that match actual ST equilibria, the eddy current densities can be determined at the locations of the liquid lithium. Initial results have shown that the effects could be significant, and ways of explicitly treating toroidally local structures are under investigation.
Enhanced activity of an antisense oligonucleotide targeting murine protein kinase C-alpha by the incorporation of 2'-O-propyl modifications (1996)

We have previously described the characterization of a 20mer phosphorothioate oligodeoxynucleotide (ISIS 4189) which inhibits murine protein kinase C-alpha (PKC-alpha) gene expression, both in vitro and in vivo. In an effort to increase the antisense activity of this oligonucleotide, 2'-O-propyl modifications have been incorporated into the 5'- and 3'-ends of the oligonucleotide, with the eight central bases left as phosphorothioate oligodeoxynucleotides. Hybridization analysis demonstrated that these modifications increased affinity by approximately 8 and 6 degrees C per oligonucleotide for the phosphodiester (ISIS 7815) and phosphorothioate (ISIS 7817) respectively when hybridized to an RNA complement. In addition, 2'-O-propyl incorporation greatly enhanced the nuclease resistance of the oligonucleotides to snake venom phosphodiesterase or intracellular nucleases in vivo. The increase in affinity and nuclease stability of ISIS 7817 resulted in a 5-fold increase in the ability of the oligonucleotide to inhibit PKC-alpha gene expression in murine C127 cells, as compared with the parent phosphorothioate oligodeoxynucleotide. Thus an RNase H-dependent phosphorothioate oligodeoxynucleotide can be modified as a 2'-O-propyl 'chimeric' oligonucleotide to provide a significant increase in antisense activity in cell culture.
CHO/hPEPT1 cells overexpressing the human peptide transporter (hPEPT1) as an alternative in vitro model for peptidomimetic drugs (1999)

The present study characterized Chinese hamster ovary cells overexpressing a human intestinal peptide transporter, CHO/hPEPT1 cells, as an in vitro model for peptidomimetic drugs. The kinetic parameters of Gly-Sar uptake were determined in three different cell culture systems such as untransfected CHO cells (CHO-K1), transfected CHO cells (CHO/hPEPT1) and Caco-2 cells. Vmax in CHO/hPEPT1 cells was approximately 3-fold higher than those in Caco-2 cells and CHO-K1 cells, while Km values were similar in all cases. The uptake of beta-lactam antibiotics in CHO/hPEPT1 cells was three to twelve fold higher than that in CHO-K1 cells, indicating that CHO/hPEPT1 cells significantly enhanced the peptide transport activity. However, amino acid drugs also exhibited high cellular uptake in both CHO-K1 and CHO/hPEPT1 cells due to the high background level of amino acid transporters. Thus, cellular uptake study in CHO/hPEPT1 cells is not sensitive enough to distinguish the peptidyl drugs from amino acid drugs. The potential of CHO/hPEPT1 cells as an in vitro model for peptidomimetic drugs was also examined through the inhibition study on Gly-Sar uptake. Peptidomimetic drugs such as beta-lactam antibiotics and enalapril significantly inhibited Gly-Sar uptake whereas the nonpeptidyl compounds, L-dopa and alpha-methyldopa, did not compete with Gly-Sar for cellular uptake within the therapeutic concentrations. In conclusion, the present study demonstrates the further characterization of CHO/hPEPT1 cells as an uptake model as well as inhibition study and suggests their utility as an alternative in vitro model for drug candidates targeting the hPEPT1 transporter.
Parallel and Multiplexed Bead-Based Assays and Encoding Strategies (2003)

Advances in high throughput screening (HTS), together with the rapid progress in combinatorial chemistry, genomic and proteomic sciences have dramatically stimulated the development of a variety tools to enable the drug discovery process to become more efficient. Major future challenges in HTS include obtaining high density and good quality data based on assays that are rapid, reliable, inexpensive, sensitive, simple and miniaturised. This paper reviews the development and role of bead-based assays for HTS including DNA and single nucleotide polymorphism (SNP) assays, particularly from a multiplex perspective and evaluating the recent advances in bead-based arrays. The encoding strategies that are commonly used in bead-based assays are highlighted, while the importance of magnetic beads in genomic and proteomic purifications is discussed. In conclusion, bead-based assays offer a powerful promising approach for many aspects of drug discovery.
Optical and electrical properties of direct-current magnetron sputtered ZnO:Al films (2001)

In this study, high-quality ZnO:Al (ZAO) films were prepared by using dc reaction magnetron sputtering technology. The effect of Al doped in ZnO films on electrical and optical properties and its scattering mechanism were discussed in detail. The results showed that Al2O3 could be effectively removed by controlling oxygen flow and Al-doped concentration during deposition of ZnO:Al films. Zn, Al, and oxygen elements were well distributed through the films. For highly degenerated ZnO:Al semiconductor thin films, it was revealed that ionized impurity scattering dominated the Hall mobility of the films in the low-temperature range; while the lattice vibration became a major scattering mechanism in the high-temperature range. The grain-boundary scattering only played a major role in the ZAO films with small grain size (as compared to the electron mean-free path). The photoelectric properties of ZAO films showed that the lower resistivity (∼5×10−4 Ω cm) was obtained, and transmittance in the visible range and reflectance in the IR region were above 80% and 60%, respectively.
Evidence for defective energy homeostasis in amyotrophic lateral sclerosis: Benefit of a high-energy diet in a transgenic mouse model (2004)

Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease characterized by selective loss of motor neurons and progressive muscle wasting. Growing evidence indicates that mitochondrial dysfunction, not only occurring in motor neurons but also in skeletal muscle, may play a crucial role in the pathogenesis. In this regard, the life expectancy of the ALS G93A mouse line is extended by creatine, an intracellular energy shuttle that ameliorates muscle function. Moreover, a population of patients with sporadic ALS exhibits a generalized hypermetabolic state of as yet unknown origin. Altogether, these findings led us to explore whether alterations in energy homeostasis may contribute to the disease process. Here, we show important variations in a number of metabolic indicators in transgenic ALS mice, which in all shows a metabolic deficit. These alterations were accompanied early in the asymptomatic phase of the disease by reduced adipose tissue accumulation, increased energy expenditure, and concomitant skeletal muscle hypermetabolism. Compensating this energetic imbalance with a highly energetic diet extended mean survival by 20%. In conclusion, we suggest that hypermetabolism, mainly of muscular origin, may represent by itself an additional driven force involved in increasing motor neuron vulnerability.
Pediatric Primitive Neuroectodermal Tumors of the Central Nervous System Differentially Express Granzyme Inhibitors (2016)

We show for the first time that brain tumors express direct granzyme inhibitors (serpins) as a potential mechanism to overcome cellular cytotoxicity, which may have consequences for cellular immunotherapy.
Multispectral fingerprint imaging for spoof detection (2005)

Fingerprint systems are the most widespread form of biometric authentication. Used in locations such as airports and in PDA's and laptops, fingerprint readers are becoming more common in everyday use. As they become more familiar, the security weaknesses of fingerprint sensors are becoming better known. Numerous websites now exist describing in detail how to create a fake fingerprint usable for spoofing a biometric system from both a cooperative user and from latent prints. While many commercial fingerprint readers claim to have some degree of spoof detection incorporated, they are still generally susceptible to spoof attempts using various artificial fingerprint samples made from gelatin or silicone or other materials and methods commonly available on the web. This paper describes a multispectral sensor that has been developed to collect data for spoof detection. The sensor has been designed to work in conjunction with a conventional optical fingerprint reader such that all images are collected during a single placement of the finger on the sensor. The multispectral imaging device captures sub-surface information about the finger that makes it very difficult to spoof. Four attributes of the finger that are collected with the multispectral imager will be described and demonstrated in this paper: spectral qualities of live skin, chromatic texture of skin, sub-surface image of live skin, and blanching on contact. Each of these attributes is well suited to discriminating against particular kinds of spoofing samples. A series of experiments was conducted to demonstrate the capabilities of the individual attributes as well as the collective spoof detection performance.
A new approach to gain-bandwidth problems (1977)

A new idea for treating the broad-band matching of an arbitrary load to a resistive generator leads to a simple technique for the design of a lossless 2-port equalizer. The method is a numerical one, and only utilizes real frequency (e.g., experimental) load impedance data. No model or analytic impedance function for the load is necessary. Nor is the equalizer topology or analytic form of the system transfer function assumed. The arithmetic is well conditioned and the intricacies of gainbandwidth theory are bypassed. An example comparing the method with analytic gain-bandwidth theory is given. Two examples proceeding directly from experimental data are presented. One is the broad banding of a microwave avalanche diode reflection amplifier. The other is the gainbandwidth equalization of a microwave FET amplifier for gain taper and impedance mismatch.
Insulin‐like growth factors. (1995)

The insulin-like growth factors I and II are single chain polypeptides homologous to proinsulin. IGF I and IGF II contribute to cell regulation and stimulate protein synthesis via signaling through type 1 receptors which are homologous to insulin receptors and activate phosphorylation cascades. IGFs enhance the proliferation of chondocytes and the proliferation of their collagen and proteoglycan matrix; IGFs stimulate longitudinal (endochondral) bone growth. Throughout life, IGFs are constitutively expressed ubiquitous factors which help to maintain the survival of differentiated cells, Increased expression is found during growth and tissue repair, Six specific binding proteins, IGFBP 1-6, allow additional tissue compartment specific control of IGF activity; IGFBP production favours storage and IGFBP cleavage leads to activation.
Limb and Skin Abnormalities in Mice Lacking IKKα (1999)

The gene encoding inhibitor of kappa B (IkappaB) kinase alpha (IKKalpha; also called IKK1) was disrupted by gene targeting. IKKalpha-deficient mice died perinatally. In IKKalpha-deficient fetuses, limb outgrowth was severely impaired despite unaffected skeletal development. The epidermal cells in IKKalpha-deficient fetuses were highly proliferative with dysregulated epidermal differentiation. In the basal layer, degradation of IkappaB and nuclear localization of nuclear factor kappa B (NF-kappaB) were not observed. Thus, IKKalpha is essential for NF-kappaB activation in the limb and skin during embryogenesis. In contrast, there was no impairment of NF-kappaB activation induced by either interleukin-1 or tumor necrosis factor-alpha in IKKalpha-deficient embryonic fibroblasts and thymocytes, indicating that IKKalpha is not essential for cytokine-induced activation of NF-kappaB.
Synthesis of rigid dendritic macromolecules: enlarging the repeat unit size as a function of generation, permitting growth to continue (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of rigid dendritic macromolecules: enlarging the repeat unit size as a function of generation, permitting growth to continueJeffrey S. Moore and Zhifu XuCite this: Macromolecules 1991, 24, 21, 5893–5894Publication Date (Print):October 1, 1991Publication History Published online1 May 2002Published inissue 1 October 1991https://pubs.acs.org/doi/10.1021/ma00021a030https://doi.org/10.1021/ma00021a030research-articleACS PublicationsRequest reuse permissionsArticle Views373Altmetric-Citations90LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
SNPP: A simple network payment protocol (2003)

A protocol is proposed to securely implement payment transactions between mutually distrustful parties. This protocol is designed to operate over an open network, and can be implemented using a currently available encryption technology. A logical verification of the protocol is included, as well as a status report on its implementation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prevention of retinopathy of prematurity in preterm infants through changes in clinical practice and SpO2technology (2010)

In a large group of inborn infants <1250 g, a change in clinical practice in combination with pulse oximetry with Masimo SET, but not without it, led to significant reduction in severe ROP and need for laser therapy. Pulse oximetry selection is important in managing critically ill infants.
Genetic and biochemical evaluation of eucaryotic membrane protein topology: multiple transmembrane domains of Saccharomyces cerevisiae 3-hydroxy-3-methylglutaryl coenzyme A reductase. (1990)

Both 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase isozymes of the yeast Saccharomyces cerevisiae are predicted to contain seven membrane-spanning domains. Previous work had established the utility of the histidinol dehydrogenase protein domain, encoded by HIS4C, as a topologically sensitive monitor that can be used to distinguish between the lumen of the endoplasmic reticulum and the cytoplasm. This study directly tested the structural predictions for HMG-CoA reductase by fusing the HIS4C domain to specific sites in the HMG-CoA reductase isozymes. Yeast cells containing the HMG-CoA reductase-histidinol dehydrogenase fusion proteins grew on histidinol-containing medium if the HIS4C domain was present on the cytoplasmic side of the endoplasmic reticulum membrane but not if the HIS4C domain was targeted to the endoplasmic reticulum lumen. Systematic exchanges of transmembrane domains between the isozymes confirmed that both isozymes had equivalent membrane topologies. In general, deletion of an even number of putative transmembrane domains did not interfere with the topology of the protein, but deletion or duplication of an odd number of transmembrane domains inverted the orientation of the protein. The data confirmed the earlier proposed topology for yeast HMG-CoA reductase, demonstrated that the yeast enzymes are core glycosylated, and provided in vivo evidence that the properties of transmembrane domains were, in part, dependent upon their context within the protein.
Biology of platelet-rich plasma and its clinical application in cartilage repair (2014)

Platelet-rich plasma (PRP) is an autologous concentrated cocktail of growth factors and inflammatory mediators, and has been considered to be potentially effective for cartilage repair. In addition, the fibrinogen in PRP may be activated to form a fibrin matrix to fill cartilage lesions, fulfilling the initial requirements of physiological wound healing. The anabolic, anti-inflammatory and scaffolding effects of PRP based on laboratory investigations, animal studies, and clinical trials are reviewed here. In vitro, PRP is found to stimulate cell proliferation and cartilaginous matrix production by chondrocytes and adult mesenchymal stem cells (MSCs), enhance matrix secretion by synoviocytes, mitigate IL-1β-induced inflammation, and provide a favorable substrate for MSCs. In preclinical studies, PRP has been used either as a gel to fill cartilage defects with variable results, or to slow the progression of arthritis in animal models with positive outcomes. Findings from current clinical trials suggest that PRP may have the potential to fill cartilage defects to enhance cartilage repair, attenuate symptoms of osteoarthritis and improve joint function, with an acceptable safety profile. Although current evidence appears to favor PRP over hyaluronan for the treatment of osteoarthritis, the efficacy of PRP therapy remains unpredictable owing to the highly heterogeneous nature of reported studies and the variable composition of the PRP preparations. Future studies are critical to elucidate the functional activity of individual PRP components in modulating specific pathogenic mechanisms.
Design of TATA box-binding protein/zinc finger fusions for targeted regulation of gene expression (1997)

Fusing the TATA box-binding protein (TBP) to other DNA-binding domains may provide a powerful way of targeting TBP to particular promoters. To explore this possibility, a structure-based design strategy was used to construct a fusion protein, TBP/ZF, in which the three zinc fingers of Zif268 were linked to the COOH terminus of yeast TBP. Gel shift experiments revealed that this fusion protein formed an extraordinarily stable complex when bound to the appropriate composite DNA site (half-life up to 630 h). In vitro transcription experiments and transient cotransfection assays revealed that TBP/ZF could act as a site-specific repressor. Because the DNA-binding specificities of zinc finger domains can be systematically altered by phage display, it may be possible to target such TBP/zinc finger fusions to desired promoters and thus specifically regulate expression of endogenous genes.
Density-connected sets and their application for trend detection in spatial databases (1997)

Several clustering algorithms have been proposed for class identification in spatial databases such as earth observation databases. The effectivity of the well-known algorithms such as DBSCAN, however, is somewhat limited because they do not fully exploit the richness of the different types of data contained in a spatial database. In this paper, we introduce the concept of density-connected sets and present a significantly generalized version of DBSCAN. The major properties of this algorithm are as follows: (1) any symmetric predicate can be used to define the neighborhood of an object allowing a natural definition in the case of spatially extended objects such as polygons, and (2) the cardinality function for a set of neighboring objects may take into account the non-spatial attributes of the objects as a means of assigning application specific weights. Density-connected sets can be used as a basis to discover trends in a spatial database. We define trends in spatial databases and show how to apply the generalized DBSCAN algorithm for the task of discovering such knowledge. To demonstrate the practical impact of our approach, we performed experiments on a geographical information system on Bavaria which is representative for a broad class of spatial databases.