gebhart/patrepeval huggingface dataset:
Dietary Inclusion of Wheat Bran Arabinoxylooligosaccharides Induces Beneficial Nutritional Effects in Chickens (2008)

ABSTRACT In vivo experiments were conducted to verify whether arabinoxylooligosaccharides (AXOS) obtained as low molecular mass compounds by enzymic hydrolysis from wheat bran arabinoxylan (AX) can exert nutritional effects. Two feeding trials were performed on chickens fed diets with either wheat or maize as the main component. Supplementation of bran AXOS at either 0.5% (w/w) to the wheat‐based diet or at 0.25% (w/w) to the maize‐based diet diets significantly ( P &lt; 0.05) improved the feed conversion rate without increasing the body weight of the animals, thus pointing to improved nutrient utilization efficiency. The positive effect of bran AXOS supplementation on feed utilization efficiency was similar to that obtained by adding an AX‐degrading xylanase directly to the wheat‐based diet. No significant effect on feed utilization efficiency was obtained with another type of nondigestible oligosaccharide such as fructooligosaccharides (FOS) derived from chicory roots. Bran AXOS significantly increased the level of bifidobacteria but not total bacteria in the caeca of the chickens, an effect not observed with either xylanase or FOS addition. These data suggest that bran AXOS have beneficial nutritional effects and may act as prebiotics.
Expression of the Chlamydial Genus-Specific Lipopolysaccharide Epitope in Escherichia coli (1985)

The obligate intracellular prokaryote Chlamydia trachomatis is the etiological agent of trachoma and is a primary causative pathogen of sexually transmitted genital tract disease; both diseases affect millions of people each year. The cloning of genes encoding the enzyme or enzymes producing the genus-specific lipopolysaccharide antigen of Chlamydia into Escherichia coli is reported here. The cloned chlamydial lipopolysaccharide antigen appears to be a hybrid lipopolysaccharide molecule composed of both Chlamydia and Escherichia coli components. The chlamydial lipopolysaccharide antigen is expressed on the surfaces of the viable Escherichia coli recombinants. These findings may have a significant impact on defining the role of this highly conserved antigen in the pathogenesis and diagnosis of chlamydial infections.
Automatic generation of optimum classification cascades (2008)

In this paper, we present a novel technique to automatically generate optimum classification cascades. Given a powerful classifier S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> with satisfactory accuracy and a set of N classifiers, our algorithm builds the fastest cascade that achieves an accuracy not less than that of S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> . The algorithm is fully automatic and has a complexity of O(N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) which means it is fast and scalable to large values of N.
Cell-free circulating tumor DNA in cancer (2016)

Cancer is a common cause of death worldwide. Despite significant advances in cancer treatments, the morbidity and mortality are still enormous. Tumor heterogeneity, especially intratumoral heterogeneity, is a significant reason underlying difficulties in tumor treatment and failure of a number of current therapeutic modalities, even of molecularly targeted therapies. The development of a virtually noninvasive "liquid biopsy" from the blood has been attempted to characterize tumor heterogeneity. This review focuses on cell-free circulating tumor DNA (ctDNA) in the bloodstream as a versatile biomarker. ctDNA analysis is an evolving field with many new methods being developed and optimized to be able to successfully extract and analyze ctDNA, which has vast clinical applications. ctDNA has the potential to accurately genotype the tumor and identify personalized genetic and epigenetic alterations of the entire tumor. In addition, ctDNA has the potential to accurately monitor tumor burden and treatment response, while also being able to monitor minimal residual disease, reducing the need for harmful adjuvant chemotherapy and allowing more rapid detection of relapse. There are still many challenges that need to be overcome prior to this biomarker getting wide adoption in the clinical world, including optimization, standardization, and large multicenter trials.
Novel mutations in FH and expansion of the spectrum of phenotypes expressed in families with hereditary leiomyomatosis and renal cell cancer (2005)

In combination with our previous report, we identify 31 different germline FH mutations in 56 families with HLRCC (20 missense, eight frameshifts, two nonsense, and one splice site). Our FH mutation detection rate is 93% (52/56) in families suspected of HLRCC.
Suramin inhibition of growth factor receptor binding and mitogenicity in AKR‐2B cells (1987)

Suramin, a polyanionic compound, has previously been shown to dissociate platelet-derived growth factor (PDGF) from its receptor. In the present study suramin was found to inhibit the growth of sparse cultures of AKR-2B cells in fetal bovine serum (FBS)-supplemented medium in a dose-dependent, reversible fashion. Suramin also inhibited the ability of FBS, transforming growth factor beta (TGF beta), heparin-binding growth factor type-2 (HBGF-2), and epidermal growth factor (EGF) to stimulate DNA synthesis in density-arrested cultures of AKR-2B cells. The inhibition of growth factor-stimulated mitogenicity was directly correlated to the dose of suramin required to inhibit the binding of 125I-labeled TGF beta, HBGF-2, and EGF to their cell surface receptors. Suramin affected TGF beta and HBGF-2-related events at a 10-15-fold lower dose than that required for EGF-related events. It was also noted that suramin inhibited TGF beta-stimulated soft agar colony formation of AKR-2B (clone 84A) cells as well as the spontaneous colony formation of AKR-MCA cells, a chemically transformed derivative of AKR-2B cells. This demonstrates that suramin's spectrum of action for growth factors and their receptors should be extended to include TGF beta, HBGF-2, and EGF as well as PDGF. The data further suggest that the spontaneous growth of AKR-MCA cells in soft agar is dependent on growth factor binding to cell surface receptors.
Measurement of fibrous cap thickness in atherosclerotic plaques by spatiotemporal analysis of laser speckle images (2006)

Necrotic-core fibroatheromas (NCFA) with thin, mechanically weak fibrous caps overlying lipid cores comprise the majority of plaques that rupture and cause acute myocardial infarction. Laser speckle imaging (LSI) has been recently demonstrated to enable atherosclerotic plaque characterization with high accuracy. We investigate spatio-temporal analysis of LSI data, in conjunction with diffusion theory and Monte Carlo modeling of light transport, to estimate fibrous cap thickness in NCFAs. Time-varying laser speckle images of 20 NCFAs are selected for analysis. Spatio-temporal intensity fluctuations are analyzed by exponential fitting of the windowed normalized cross-correlation of sequential laser speckle patterns to obtain the speckle decorrelation time constant, tau(rho), as a function of distance rho from the source entry location. The distance, rho', at which tau(rho) dropped to 65% of its maximum value is recorded. Diffusion theory and Monte Carlo models are utilized to estimate the maximum photon penetration depth, zmax(rho'), for a distance equal to rho', measured from LSI. Measurements of zmax(rho') correlate well with histological measurements of fibrous cap thickness (R=0.78, p<0.0001), and paired t-tests show no significant difference between the groups (p=0.4). These results demonstrate that spatio-temporal LSI may allow the estimation of fibrous cap thickness in NCFAs, which is an important predictor of plaque stability.
Near Full-Length Clones and Reference Sequences for Subtype C Isolates of HIV Type 1 from Three Different Continents (2001)

Among the major circulating HIV-1 subtypes, subtype C is the most prevalent. To generate full-length subtype C clones and sequences, we selected 13 primary (PBMC-derived) isolates from Zambia, India, Tanzania, South Africa, Brazil, and China, which were identified as subtype C by partial sequence analysis. Near full-length viral genomes were amplified by using a long PCR technique, sequenced in their entirety, and phylogenetically analyzed. Amino acid sequence analysis revealed 10.2, 6.3, and 17.3% diversity in predicted Gag, Pol, and Env protein sequences. Ten of 13 viruses were nonmosaic subtype C genomes, while all three isolates from China represented B/C recombinants. One of them was composed primarily of subtype C sequences with three small subtype B portions in gag, pol, and nef genes. Two others exhibited these same mosaic regions, but contained two additional subtype B portions at the gag/pol overlap and in the accessory gene region, suggesting ongoing B/C recombination in China. All subtype C genomes contained a prematurely truncated second exon of rev, but other previously proposed subtype C signatures, including three potential NF-kappa B-binding sites in the viral promoter-enhancer regions, were found in only a subset of these genomes.
Radiofrequency Catheter Modification of Atrioventricular Conduction to Control the Ventricular Rate during Atrial Fibrillation (1994)

A catheter technique to modify atrioventricular conduction without creating pathologic atrioventricular block is feasible in the majority of patients with symptomatic atrial fibrillation and a rapid ventricular rate refractory to drug therapy.
GANs Trained by a Two Time-Scale Update Rule Converge to a Local Nash Equilibrium (2017)

Generative Adversarial Networks (GANs) excel at creating realistic images with complex models for which maximum likelihood is infeasible. However, the convergence of GAN training has still not been proved. We propose a two time-scale update rule (TTUR) for training GANs with stochastic gradient descent on arbitrary GAN loss functions. TTUR has an individual learning rate for both the discriminator and the generator. Using the theory of stochastic approximation, we prove that the TTUR converges under mild assumptions to a stationary local Nash equilibrium. The convergence carries over to the popular Adam optimization, for which we prove that it follows the dynamics of a heavy ball with friction and thus prefers flat minima in the objective landscape. For the evaluation of the performance of GANs at image generation, we introduce the "Fréchet Inception Distance" (FID) which captures the similarity of generated images to real ones better than the Inception Score. In experiments, TTUR improves learning for DCGANs and Improved Wasserstein GANs (WGAN-GP) outperforming conventional GAN training on CelebA, CIFAR-10, SVHN, LSUN Bedrooms, and the One Billion Word Benchmark.
A Transition State Analog Inhibitor Combinatorial Library (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Transition State Analog Inhibitor Combinatorial LibraryDavid A. Campbell, Jason C. Bermak, Timothy S. Burkoth, and Dinesh V. PatelCite this: J. Am. Chem. Soc. 1995, 117, 19, 5381–5382Publication Date (Print):May 1, 1995Publication History Published online1 May 2002Published inissue 1 May 1995https://pubs.acs.org/doi/10.1021/ja00124a030https://doi.org/10.1021/ja00124a030research-articleACS PublicationsRequest reuse permissionsArticle Views97Altmetric-Citations64LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
Hyaluronan in Tissue Injury and Repair (2007)

A hallmark of tissue injury and repair is the turnover of extracellular matrix components. This review focuses on the role of the glycosaminoglycan hyaluronan in tissue injury and repair. Both the synthesis and degradation of extracellular matrix are critical contributors to tissue repair and remodeling. Fragmented hyaluronan accumulates during tissue injury and functions in ways distinct from the native polymer. There is accumulating evidence that hyaluronan degradation products can stimulate the expression of inflammatory genes by a variety of immune cells at the injury site. CD44 is the major cell-surface hyaluronan receptor and is required to clear hyaluronan degradation products produced during lung injury; impaired clearance of hyaluronan results in persistent inflammation. However, hyaluronan fragment stimulation of inflammatory gene expression is not dependent on CD44 in inflammatory macrophages. Instead, hyaluronan fragments utilize both Toll-like receptor (TLR) 4 and TLR2 to stimulate inflammatory genes in macrophages. Hyaluronan also is present on the cell surface of lung alveolar epithelial cells and provides protection against tissue damage by interacting with TLR2 and TLR4 on these parenchymal cells. The simple repeating structure of hyaluronan appears to be involved in a number of important aspects of noninfectious tissue injury and repair that are dependent on the size and location of the polymer as well as the interacting cells. Thus, the interactions between the endogenous matrix component hyaluronan and its signaling receptors initiate inflammatory responses, maintain structural cell integrity, and promote recovery from tissue injury.
Molecular Basis of Imidazolinone Herbicide Resistance in Arabidopsis thaliana var Columbia (1991)

Acetolactate synthase (ALS), the first enzyme in the biosynthetic pathway of leucine, isoleucine, and valine, is inhibited by imidazolinone herbicides. To understand the molecular basis of imidazolinone resistance, we isolated the ALS gene from an imazapyr-resistant mutant GH90 of Arabidopsis thaliana. DNA sequence analysis of the mutant ALS gene demonstrated a single-point mutation from G to A at nucleotide 1958 of the ALS-coding sequence. This would result in Ser to Asn substitution at residue 653 near the carboxyl terminal of the matured ALS. The mutant ALS gene was introduced into tobacco using Agrobacterium-mediated transformation. Imidazolinone-resistant growth of transformed calli and leaves of transgenic plants was 100-fold greater than that of nontransformed control plants. The relative levels of imidazolinone-resistant ALS activity correlated with the amount of herbicide-resistant growth in the leaves of transgenic plants. Southern hybridization analysis confirmed the existence of transferred ALS gene in the transformant showing high imazapyr resistance. The results demonstrate that the mutant ALS gene confers resistance to imidazolinone herbicides. This is the first report, to our knowledge, of the molecular basis of imidazolinone resistance in plants.
Albendazole: a Potent Inhibitor of Vascular Endothelial Growth Factor and Malignant Ascites Formation in OVCAR-3 Tumor-Bearing Nude Mice (2006)

Abstract Purpose: Angiogenesis and vessel hyperpermeability are the two factors leading to the formation of ascites. Vascular endothelial growth factor (VEGF) plays a pivotal role in malignant ascites formation. We have recently shown that albendazole inhibits peritoneal growth of human colorectal cancer cells (HT-29). The present study was designed to find out if albendazole can suppress ascites formation in ascites-producing peritoneal carcinomatosis. Experimental design: Female nude mice bearing peritoneal tumors of human ovarian cancer cells (OVCAR-3) were treated with albendazole. Following i.p. inoculation and ascites development, mice were given i.p. albendazole (150 mg/kg) or the vehicle × 3 weekly for 4 weeks. Results: Whereas vehicle-treated mice developed overt ascites requiring repeated aspiration, ascites formation in the albendazole-treated mice was markedly suppressed. As a result of this, 7 of 10 mice from the control group had to be euthanized before the course of treatment was over. Suppressed ascites production and reduced tumor vascularity observed was a result of dramatic reduction in tumor VEGF production as revealed by profoundly lower VEGF ascites fluid and plasma levels. In vitro, incubation of SKOV-3 cells with various concentrations of albendazole led to significant dose-dependent inhibition of VEGF secretion. Examination of floating tumor cells collected from the peritoneal wash revealed profound down-regulation of VEGF mRNA in albendazole-treated mice. Conclusions: These findings suggest for the first time that in nude mice bearing OVCAR-3 peritoneal tumors, by inhibiting VEGF production, albendazole abolishes tumor angiogenesis and ascites formation.
Designing and implementing malicious hardware (2008)

Hidden malicious circuits provide an attacker with a stealthy attack vector. As they occupy a layer below the entire software stack, malicious circuits can bypass traditional defensive techniques. Yet current work on trojan circuits considers only simple attacks against the hardware itself, and straightforward defenses. More complex designs that attack the software are unexplored, as are the countermeasures an attacker may take to bypass proposed defenses. We present the design and implementation of Illinois Malicious Processors (IMPs). There is a substantial design space in malicious circuitry; we show that an attacker, rather than designing one specific attack, can instead design hardware to support attacks. Such flexible hardware allows powerful, general purpose attacks, while remaining surprisingly low in the amount of additional hardware. We show two such hardware designs, and implement them in a real system. Further, we show three powerful attacks using this hardware, including a login backdoor that gives an attacker complete and highlevel access to the machine. This login attack requires only 1341 additional gates: gates that can be used for other attacks as well. Malicious processors are more practical, more flexible, and harder to detect than an initial analysis would suggest.
Wideband coding of speech using a scalable pulse codebook (2002)

Recent standardization efforts have provided motivation for research in the area of wideband speech coding (50 Hz to 7 kHz). Both the European Telecommunications Standards Institute (ETSI) in conjunction with the Third Generation Partnership Project (3GPP), and the ITU-T are currently in the process of evaluating candidate algorithms at bit rates from around 12 kbps to 32 kbps. This paper describes a code-excited linear prediction (CELP) technique used in the Motorola candidate algorithm that is scalable to a wide range of bit rates, thereby allowing the use of a ubiquitous speech model. Preliminary subjective test results indicate that the technique provides very high quality speech that meets or exceeds all requirements for both the ETSI/3GPP and ITU-T wideband speech standardization efforts.
Enhanced Delivery of Octreotide to the Brain via Transnasal Iontophoretic Administration (2004)

Transnasal drug delivery affords an opportunity to circumvent the blood-brain barrier and gain direct access to the brain. To date, this approach has used a relatively passive process relying on drug instillation high into the nasal cavity, formulation and gravity for drug delivery. The present study examined the use of an applied electrical field (transnasal iontophoresis or electrotransport) to actively drive a charged peptide, octreotide, into the rabbit brain. A simply designed electrode containing a reservoir of octreotide was placed deep into the nasal cavity on both sides. A return electrode was applied to the back of the head and a current strength of 3.0 mA was applied for 60 min. In control rabbits, electrodes were placed into the nasal cavity, but no current was applied (passive delivery). Additional control animals were given a bolus intra-arterial injection of octreotide. At the conclusion of drug delivery, animals were sacrificed and samples of brain, spinal cord, cerebrospinal fluid (CSF) and plasma were taken for measurement of octreotide levels by radioimmunoassay (RIA). In a second experiment, rabbits were exsanguinated prior to drug delivery to measure the ability of iontophoresis to transport octreotide into the brain in the absence of blood or CSF circulation. In both experiments, transnasal iontophoresis resulted in significantly elevated levels of octreotide in the brain, although results varied considerably due to electrode and tissue damage related to problems with electrode insertion into the rabbit's nasal cavity. Octreotide was present in samples extending from the olfactory bulb to the cerebellum with 2- to 13-fold increases in active compared to control/passive animals. High and sustained levels of octreotide were also present in the blood following transnasal delivery, but there were negligible amounts of octreotide in the brain following systemic administration indicating that the blood was not a significant route for drug redistribution. The results demonstrate that transnasal electrotransport is a unique, minimally invasive approach for enhancing drug delivery to the brain.
Identification of a key integrin-binding sequence in VCAM-1 homologous to the LDV active site in fibronectin (1994)

The integrin adhesion receptor alpha 4 beta 1 binds two ligands, the extracellular matrix glycoprotein fibronectin and the immunoglobulin superfamily member VCAM-1. Ligand-binding sites are contained with the HepII/IIICS domain of fibronectin, and within the homologous immunoglobulin domains 1 and 4 of VCAM-1. Previous studies have shown that the binding of each ligand to alpha 4 beta 1 is mutually exclusive, suggesting that they may employ similar mechanisms to bind receptor. Fibronectin contains at least three distinct peptide sequences that are active sites for alpha 4 beta 1 binding, two homologous sequences Leu-Asp-Val-Pro (LDVP) and Ile-Asp-Ala-Pro (IDAP), and a third related to Arg-Gly-Asp (RGD). Using a combination of site-directed mutagenesis and synthetic peptide approaches in conjunction with VCAM-1-dependent cell adhesion assays, we now report the identification of a key alpha 4 beta 1-binding sequence in both domains 1 and 4 of VCAM-1 as the tetrapeptide Ile-Asp-Ser-Pro (IDSP). Mutagenesis studies also suggest that an additional sequence in domain 1, KLEK, participates in receptor binding. Since IDSP is homologous to the LDVP and IDAP fibronectin peptides, this therefore provides a molecular explanation for the promiscuity of ligand binding by alpha 4 beta 1 and has implications for the design of synthetic VCAM-1 antagonists. The extrapolation of these findings to other integrin-binding immunoglobulin ligands is also discussed.