gebhart/patrepeval huggingface dataset:
A proteoglycan with HNK-1 antigenic determinants is a neuron-associated ligand for cytotactin. (1987)

Cytotactin is an extracellular matrix protein that is involved in neuron-glia adhesion and is found in both neural and nonneural sites. It is synthesized by glia but not by neurons. In this study, we have examined the binding of cytotactin to a variety of extracellular matrix components using uniform microscopic beads (Covaspheres) that could be labeled and then linked to purified molecules. Cytotactin-coated beads bound well to neurons, and this binding was strongly inhibited by anti-cytotactin antibodies but not by anti-neural cell adhesion molecule (anti-N-CAM) antibodies. In contrast, the binding of N-CAM-coated beads to neurons was inhibited by anti-N-CAM antibodies and not by anti-cytotactin antibodies. To identify a neuronal ligand for cytotactin, we tested several molecules for their ability to block the binding of cytotactin-coated beads to cells. A proteoglycan-containing fraction that copurified with cytotactin from brain extracts strongly inhibited binding, whereas neither a heparan sulfate proteoglycan from Engelbreth-Holm-Swarm tumor cells nor soluble cytotactin itself had a significant inhibitory effect. The neural proteoglycan also inhibited the binding of cytotactin-coated beads to fibroblasts. Digestion with chondroitinase, heparitinase, and hyaluronidase as well as immunological analyses suggested that the predominant species in the active fraction was a chondroitin sulfate proteoglycan with a Mr280,000 core protein bearing HNK-1 antigenic determinants and also indicated that hyaluronic acid was present in this fraction. In experiments on in vitro synthesis, it was found that the proteoglycan was synthesized in culture by embryonic chicken brain tissue but not by embryonic chicken glial cells. A series of binding experiments was performed on appropriately derivatized beads to confirm that the proteoglycan is a ligand for cytotactin and to check for the possibility that other extracellular matrix proteins might interact with one or the other member of this binding couple. Proteoglycan-coated beads and cytotactin-coated beads coaggregated readily. The aggregation was inhibitable by anti-cytotactin antibodies, soluble cytotactin, or soluble proteoglycan. Addition of laminin inhibited the binding of cytotactin-coated beads to proteoglycan-coated beads or to cells; this is consistent with data indicating that laminin interacts with a component of the proteoglycan-containing fraction. In contrast, fibronectin bound to cytotactin, but it did not bind to proteoglycan or interfere with the binding of cytotactin to proteoglycan. The results of this study are in accord with the idea that the functions of extracellular matrix components during neural and nonneural development may be modulated both by competition for shared cell surface receptors and by a network of molecular interactions among the matrix components themselves.
Towards heterogeneous multimedia information systems: the Garlic approach (2002)

Provides an overview of the Garlic project, a new project at the IBM Almaden Research Center. The goal of this project is to develop a system and associated tools for the management of large quantities of heterogeneous multimedia information. Garlic permits traditional and multimedia data to he stored in a variety of existing data repositories, including databases, files, text managers, image managers, video servers, and so on; the data is seen through a unified schema expressed in an object-oriented data model and can be queried and manipulated using an object-oriented dialect of SQL, perhaps through an advanced query/browser tool that we are also developing. The Garlic architecture is designed to be extensible to new kinds of data repositories, and access efficiency is addressed via a "middleware" query processor that uses database query optimization techniques to exploit the native associative search capabilities of the underlying data repositories.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cellular Aging Reflected by Leukocyte Telomere Length Predicts Advanced Atherosclerosis and Cardiovascular Disease Risk (2010)

Our findings indicate a differential role of telomere shortening in the various stages of atherosclerosis, with preferential involvement in advanced vessel pathology and acute vascular syndromes.
Glucose Catabolism in Cancer Cells (2001)

One of the most common signatures of highly malignant tumors is their capacity to metabolize more glucose to lactic acid than their tissues of origin. Hepatomas exhibiting this phenotype are dependent on the high expression of type II hexokinase, which supplies such tumors with abundant amounts of glucose 6-phosphate, a significant carbon and energy source especially under hypoxic conditions. Here we report that the distal region of the hepatoma type II hexokinase promoter displays consensus motifs for hypoxia-inducible factor (HIF-1) that overlap E-box sequences known to be related in other gene promoters to glucose response. Moreover, we show that subjecting transfected hepatoma cells to hypoxic conditions activates the type II hexokinase promoter almost 3-fold, a value that approaches 7-fold in the presence of glucose. Consistent with these findings is the induction under hypoxic conditions of the HIF-1 protein. Reporter gene analyses with a series of nested deletion mutants of the hepatoma type II hexokinase promoter show that a significant fraction of the total activation observed under hypoxic conditions localizes to the distal region where the overlapping HIF-1/E-box sequences are located. Finally, DNase I footprint analysis with a segment of the promoter containing these elements reveals the binding of several nuclear proteins. In summary, these novel studies identify and characterize a marked glucose-modulated activation response of the type II hexokinase gene to hypoxic conditions within highly glycolytic hepatoma cells, a property that may help assure that such cells exhibit a growth and survival advantage over their parental cells of origin.
Analysis of the Conjugal Transfer System of the Pheromone- Independent Highly Transferable Enterococcus Plasmid pMG1: Identification of a tra Gene ( traA ) Up-Regulated during Conjugation (2002)

pMG1 (65.1 kbp) is a pheromone-independent Enterococcus faecium conjugative plasmid conferring gentamicin resistance. pMG1 is able to transfer to enterococci at a high frequency in broth mating experiments, and it does not respond to the sex pheromones which are involved in the high-frequency transfer system of some conjugative plasmids in Enterococcus faecalis. To analyze regulation of tra gene expression in pMG1, transcripts of pMG1 were examined during conjugation. RNA samples were prepared from mating mixtures 20, 40, 80, and 160 min after initiation of mating and were subsequently analyzed by Northern hybridization by using a variety of pMG1 DNA fragments as probes. One transcript of gene 71ORF2 increased to the maximal level 20 min after the start of mating. The level of this transcript decreased after 40 min of mating to the same level as the level in the control donor culture. The increase was not observed in cultures of the donor cells or recipient cells. These findings suggested that the increase was a conjugation-specific event. The 71ORF2 gene of pMG1 was disrupted by using the suicide vector pMG226 carrying an erythromycin resistance gene that is expressed in enterococci. The transfer frequencies of mutant plasmid pMG229, which had a disrupted 71ORF2 gene in pMG1, and the parent plasmid pMG1 were 1.6 x 10(-7) and 1.1 x 10(-3) per donor cell, respectively, in broth mating experiments, and the transfer frequencies of pMG229 and pMG1 were 2.7 x 10(-3) and 8.5 x 10(-2) per donor cell, respectively, in filter mating experiments. This indicated that the transfer frequency of plasmid pMG229 was reduced during broth mating and was not altered during filter mating. 71ORF2, which is designated traA, is a gene involved in the tra gene system for conjugation, and the product of this gene is associated with the formation or stabilization of mating aggregates during broth mating.
Effect of executive compensation and share ownership on financial performance of listed deposit money banks in Nigeria (2020)

It has remained a paradox whether people will be motivated if they believe that strong effort will lead to good performance and good performance will lead to desired rewards. Studies in this area have reported conflicting findings. To this end, the study examines the effect of executive compensation and share ownership on financial performance of listed Deposit Money Banks in Nigeria. Executive compensation variables were proxied with Chief Executive Officer (CEO) Pay, Chairman&rsquo;s compensation and highest paid director, while percentage of shares owned by executive represent the share ownership. Financial performance was measured using net interest margin. Robust Ordinary Least Square regression technique was used for the estimation, while Stata 13 was employed as tool of data analysis. Secondary source of data was utilized and were obtained from the annual reports and accounts of the banks over the period 2007-2018. Robustness tests such as normality test of error term, multicollinearity and heteroscedasticity tests were conducted to validate the results. The findings reveal that, CEO Pay has significant positive effect on financial performance of banks, while chairmen compensation and highest paid director have negative influence on financial performance of banks. Furthermore, the increase in share ownership of the executives in the banking sector is an effective means through which the financial performance of the banks could be enhanced. It is therefore recommended that the management should tie the payment of CEO of the banks to performance. The regulators such as Central Bank of Nigeria and Securities and Exchange Commission) should encourage the banks management to be mindful when increasing the level of compensation paid to chairmen and highest paid directors without commensurate share ownership in the banks by them as they may become complacent towards encouraging increased financial performance. &nbsp; Key words: Net interest margin, executive compensation, share ownership and pay-performance theory.
Expression of Recombinant Human Tropoelastin in Saccharomyces cerevisiae Containing a Synthetic Gene with a High Codon Adaptation Index Coupled to the SUC2 Invertase Signal Sequence (2001)

Tropoelastin is the soluble precursor of vertebrate elastin,but the gene is absent in lower eukaryotes, which are not organized into complex multicellular arrays. A synthetic gene encoding human tropoelastin with a high codon adaptation index was examined for expression in Saccharomyces cerevisiae. The expression of tropoelastin transcript increased. ∼20-fold following induction. The native cytoplasm-expressed form of tropoelastin was not detected. In contrast, N-terminal fusion of the SUC2 invertase signal sequence of the yeast to tropoelastin led to the production of intracellular full-length protein and enhanced its stability in vivo. There was no evidence of extracellular secretion of the protein.We conclude that eukaryotic cells are capable of expressing and retaining undegraded tropoelastin in the absence of a vertebrate-specific protein partner. Tropoelastin was directed to the yeast endoplasmic reticulum through the interim presence of the SUC2 signal peptide sequence.
Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry I.Profiling an unfractionated tryptic digest (2001)

The proteome of normal male urine from a commercial pooled source has been examined using direct liquid chromatography-tandem mass spectrometry (LC-MS/MS). The entire urinary protein mixture was denatured, reduced and enzymatically digested prior to LC-MS/MS analysis using a hybrid-quadrupole time-of-flight mass spectrometer (Q-TOF) to perform data-dependent ion selection and fragmentation. To fragment as many peptides as possible, the mixture was analyzed four separate times, with the mass spectrometer selecting ions for fragmentation from a subset of the entire mass range for each run. This approach requires only an autosampler on the HPLC for automation (i.e, unattended operation). Across these four analyses, 1.450 peptide MS/MS spectra were matched to 751 sequences to identify 124 gene products (proteins and translations of expressed sequence tags). Interestingly, the experimental time for these analyses was less than that required to run a single two-dimensional gel.
Biocomposites developed using water‐plasticized wheat gluten as matrix and jute fibers as reinforcement (2011)

Abstract Biocomposites developed from wheat gluten using water without any chemicals as plasticizer and jute fibers as reinforcement have much better flexural and tensile properties than similar polypropylene composites reinforced with jute fibers. Wheat gluten is an inexpensive and abundant co‐product derived from renewable resources and is biodegradable but non‐thermoplastic. Previous attempts at developing biocomposites from wheat gluten have used plasticizers such as glycerol or chemical modifications to make gluten thermoplastic. However, plasticizers have a considerably negative effect on the mechanical properties of the composites and chemical modifications make wheat gluten less biodegradable, expensive and/or environmentally unfriendly. In the research reported, we developed composites from wheat gluten using water as a plasticizer without any chemicals. Water plasticizes wheat gluten but evaporates during compression molding and therefore does not affect the mechanical properties of the composites. The effect of composite fabrication conditions on the flexural, tensile and acoustic properties was studied in comparison to polypropylene composites reinforced with jute fibers. Wheat gluten composites had flexural strength (20 MPa), tensile strength (69 MPa) and tensile modulus (7.7 GPa) values approximately twice those of polypropylene composites. Water is an effective plasticizer for wheat gluten and could be used to develop various types of inexpensive and biodegradable wheat gluten‐based thermoplastics. Copyright © 2011 Society of Chemical Industry
The Influence of Charge Distribution on Self-Association and Viscosity Behavior of Monoclonal Antibody Solutions (2012)

The present work investigates the influence of electrostatic surface potential distribution of monoclonal antibodies (MAbs) on intermolecular interactions and viscosity. Electrostatic models suggest MAb-1 has a less uniform surface charge distribution than MAb-2. The patches of positive and negative potential on MAb-1 are predicted to favor intermolecular attraction, even in the presence of a small net positive charge. Consistent with this expectation, MAb-1 exhibits a negative second virial coefficient (B₂₂), an increase in static structure factor, S((q→0)), and a decrease in hydrodynamic interaction parameter, H((q→0)), with increase in MAb-1 concentration. Conversely, MAb-2 did not show such heterogeneous charge distribution as MAb-1 and hence favors intermolecular repulsion (positive B₂₂), lower static structure factor, S((q→0)), and repulsion induced increase in momentum transfer, H((q→0)), to result in lower viscosity of MAb-2. Charge swap mutants of MAb-1, M-5 and M-7, showed a decrease in charge asymmetry and concomitantly a loss in self-associating behavior and lower viscosity than MAb-1. However, replacement of charge residues in the sequence of MAb-2, M-10, did not invoke charge distribution to the same extent as MAb-1 and hence exhibited a similar viscosity and self-association profile as MAb-2.
TGB A phase in a series of swallowtailed chiral liquid crystals (1998)

A homologous series of chiral materials, 1-butylpentyl (S)-2-{6-[4-(4'-alkoxyphenyl)- benzoyloxy]-2-naphthyl}propionates, BPmPBNP (m=6-16), derived from a chiral moiety, (S)-2-(6-hydroxy-2-naphthyl)propionic acid, in conjunction with a swallowtail group attached to the external side of the chiral centre, has been synthesized and their mesomorphic phases have been studied. There were two frustrated phases: a blue (BP) phase and a twist-grain- boundary (TGBA) phase found enantiotropically in all materials. It is worth noting that, depending on the nature of the terminal chain length, two types of filament textures were observed in the TGB A phase: a vermis (filament) texture and a spiral filament texture. The formation of the TGB A phase was rationalized as due to the steric effect caused by the swallowtail of the materials. All materials exhibited a wide temperature range of the SmA phase, but only three materials (m=12, 13 and 16) possessed a monotropic SmC* phase over a narrow temperature range, indicating that the swallowtailed materials inhibit the formation of a tilted smectic phase.
Neovascular glaucoma: a review (2016)

Neovascular glaucoma (NVG) is a secondary glaucoma generally associated with poor visual prognosis. The development of new vessels over the iris and the iridocorneal angle can obstruct aqueous humor outflow and lead to increased intraocular pressure. The underlying pathogenesis in most cases is posterior segment ischemia, which is most commonly secondary to proliferative diabetic retinopathy or central vein retinal occlusion. The neovascularization process in the eye is driven by the events that alter the homeostatic balance between pro-angiogenic factors, such as the <i>vascular endothelial growth factor</i> and anti-angiogenic factors, such as the pigment-epithelium-derived factor. Early diagnosis of this condition through slit lamp examination of the iris, iridocorneal angle and retina can help to avoid the development of goniosynechia and obstruction of aqueous humor outflow, with consequent intraocular pressure elevation. Historically, NVG treatment was focused on reducing the posterior segment ischemic process that caused the formation of new vessels, through panretinal photocoagulation. Recently, several studies have investigated the application of intravitreal anti-VEGF therapies in NVG. If clinical treatment with the use of hypotensive topical drops is not sufficient, laser and/or surgical procedures are required for intraocular pressure control.
Plant genome editing with TALEN and CRISPR (2017)

Genome editing promises giant leaps forward in advancing biotechnology, agriculture, and basic research. The process relies on the use of sequence specific nucleases (SSNs) to make DNA double stranded breaks at user defined genomic loci, which are subsequently repaired by two main DNA repair pathways: non-homologous end joining (NHEJ) and homology directed repair (HDR). NHEJ can result in frameshift mutations that often create genetic knockouts. These knockout lines are useful for functional and reverse genetic studies but also have applications in agriculture. HDR has a variety of applications as it can be used for gene replacement, gene stacking, and for creating various fusion proteins. In recent years, transcription activator-like effector nucleases and clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR associated protein 9 or CRISPR from Prevotella and Francisella 1 have emerged as the preferred SSNs for research purposes. Here, we review their applications in plant research, discuss current limitations, and predict future research directions in plant genome editing.
Plants with the Midas Touch: Formation of Gold Nanoparticles by Alfalfa Plants (2002)

In the well-known Greek legend the touch of King Midas would convert anything to metallic gold. Recently, a team working at SSRL lead by Professor Jorge Gardea-Torresdey from the University of Texas at El Paso have shown that ordinary alfalfa plants can accumulate very small particles (nanoparticles) of metallic gold (1). The best-known materials that contain nanoparticles of metallic gold are gold colloids. These lack the familiar metallic luster, but show bright colors which range from red, violet or blue, depending upon the size of the nanoparticles (2,3). Colloidal gold has traditionally been used to color materials such as glass (e.g. gold ruby glass and cranberry glass) and enamels (e.g. famille rose enamels) since the 16 century. The earliest report of a colloidal gold preparation may be in the Bible. The book of Exodus reports that Moses destroyed the golden calf in a manner that may have resulted in an aqueous (water-based) gold colloid, which he then forced the Israelites to drink. In modern times gold colloids are imbibed for a variety of ailments (despite little or no evidence of any health-related benefits), but the most important applications may be in the field of nano-technology (see 1, and refs therein).
application in microarrays (2006)

In this paper, we introduce a modified version of linear discriminant analysis, called the “shrunken centroids regularized discriminant analysis” (SCRDA). This method generalizes the idea of the “nearest shrunken centroids” (NSC) (Tibshirani et al., 2003) into the classical discriminant analysis. The SCRDA method is specially designed for classification problems in high dimension low sample size situations, for example, microarray data. Through both simulated data and real life data, it is shown that this method performs very well in multivariate classification problems, often outperforms the PAM method (using the NSC algorithm) and can be as competitive as
Combining shape regression model and isophotes curvature information for eye center localization (2014)

The localization of eye centers technique is used in several applications. In this paper, we combine the face shape model to eye center location method to obtaining robustness in eye center localization from a low-resolution image. We make use of shape regression approach and combine it to the eye-center localization using isophote curvature features which has shown its advantage from previous work. In the experiments, we use BioID datasets to test our approach for accurate eye center location and robustness to changes in illumination and pose. We demonstrate that our approach can achieve an improvement of the robustness of eye center localization while the accuracy at eye center localization e≤0.1 and e≤0.15 have achieve 0.918 and 0.977 respectively.