gebhart/patrepeval huggingface dataset:
Chemoselective Tryptophan Labeling with Rhodium Carbenoids at Mild pH (2009)

Significant improvements have been made to a previously reported tryptophan modification method using rhodium carbenoids in aqueous solution, allowing the reaction to proceed at pH 6-7. This technique is based on the discovery that N-(tert-butyl)hydroxylamine promotes indole modification with rhodium carbenoids over a broad pH range (2-7). This methodology was demonstrated on peptide and protein substrates, generally yielding 40-60% conversion with excellent tryptophan chemoselectivity. The solvent accessibility of the indole side chains was found to be a key factor in successful carbenoid addition, as demonstrated by conducting the reaction at temperatures high enough to cause thermal denaturation of the protein substrate. Progress toward the expression of proteins bearing solvent accessible tryptophan residues as reactive handles for modification with rhodium carbenoids is also reported.
Copatching and Lipid Raft Association of Different Viral Glycoproteins Expressed on the Surfaces of Pseudorabies Virus-Infected Cells (2004)

Pseudorabies virus (PRV) is a swine alphaherpesvirus that is closely related to human herpes simplex virus (HSV). Both PRV and HSV express a variety of viral envelope glycoproteins in the plasma membranes of infected cells. Here we show that at least four major PRV glycoproteins (gB, gC, gD, and gE) in the plasma membrane of infected swine kidney cells and monocytes seem to be linked, since monospecific antibody-induced patching of any one of these proteins results in copatching of the others. Further, for all four PRV glycoproteins, monospecific antibody-induced patches were enriched in GM1, a typical marker of lipid raft microdomains, but were excluded for transferrin receptor, a nonraft marker, suggesting that these viral proteins may associate with lipid rafts. However, only gB and, to a lesser extent, gE were found in lipid raft fractions by using detergent floatation assays, indicating that gC and gD do not show strong lipid raft association. Addition of methyl-beta-cyclodextrin (MCD), a cholesterol-depleting agent that is commonly used to disrupt lipid rafts, only slightly reduced copatching efficiency between the different viral proteins, indicating that other factors, perhaps tegument-glycoprotein interactions, may be important for the observed copatching events. On the other hand, MCD strongly reduced polarization of the antibody-induced viral glycoprotein patches to a cap structure, a gE-dependent process that has been described for specific PRV- and HSV-infected cells. Therefore, we hypothesize that efficient gE-mediated capping of antibody-antigen patches may require the lipid raft-associated signal transduction machinery.
Searching for Novel Cancer Chemopreventive Plants and their Products:The Genus Zanthoxylum (2011)

The genus Zanthoxylum (Rutaceae) comprises about 250 species, of which many are used as food, often as condiments, substituting pepper due to the pungent taste of fruits, seeds, leaves, and bark, and therapeutic remedies especially in Eastern Asian countries and in Central America. The whole plant is also consumed as an ingredient of soups and salads. The aim of this review is to examine in detail from a phytochemical and pharmacological point of view what is reported in the current literature about the anti-cancer and chemopreventive properties of phytopreparations or individual active compounds obtained from edible plants belonging to this genus.
Genetics of Campylobacter and Heliobacter (1992)

This article reviews the current state of genetic analysis of Campylobacter and Helicobacter. Chromosomal genes cloned from Campylobacter and Helicobacter species are listed along with the method used to identify the cloned gene. Campylobacter plasmid genes that have been cloned and expressed in Escherichia coli and that specify resistance to tetracycline, kanamycin, or chloramphenicol are presented. This review also examines our current knowledge of genetic exchange in Campylobacter, including conjugative plasmid transfer, natural transformation, electrotransformation, and bacteriophage transduction. In Helicobacter, natural transformation has been described and both plasmids and bacteriophages have been observed. Plasmid cloning vectors have been constructed for Campylobacter. Available vectors are discussed and restriction maps of some useful vectors that we have constructed are included. The genome sizes of C. jejuni and C. coli are approximately 1.7 megabases (Mb), whereas the genome size of H. pylori ranges from l.60 to l.73 Mb. The positions of various genes on the C. jejuni and C. coli genome maps have been determined using both homologous and heterologous DNA probes. Genomic maps of these organisms are presented.
Identification of plasma proteins facilitated by enrichment on particulate surfaces: Analysis by two‐dimensional electrophoresis and N‐terminal microsequencing (1997)

Plasma protein adsorption on intravenously injectable drug carriers is regarded as an important factor for the fate of the particles in the body after their administration. Therefore, the plasma protein adsorption patterns on a number of different carrier systems were analyzed in vitro employing two-dimensional electrophoresis (2-DE). The particulate systems presented in this study were polystyrene (PS) model particles, PS nanoparticles surface-modified by adsorption of a surfactant, a commercial fat emulsion, and magnetic iron oxide particles used as contrast agents in magnetic resonance imaging. Most of the spots in the plasma protein adsorption patterns could be identified by matching the resulting 2-DE gels with a reference map of human plasma proteins. Several other proteins that indicated preferentially adsorbed proteins on the surface of the particles investigated have either not been identified on the reference map, or their identity was found to be ambiguous. The relevant proteins are all present in plasma in low abundance. Since these proteins were strongly enriched on the surface of the particles, the resulting spots on the 2-DE gels were successfully identified by N-terminal microsequencing. With this approach, two chains of spots, designated PLS:6 and PLS:8, were determined on a plasma reference map: inter-alpha-trypsin inhibitor family heavy chain-related protein (also named PK-120) and a dimer of fibrinogen gamma, respectively. Plasma gelsolin is presented in a 2-DE adsorption pattern of PS model particles. One of the main proteins adsorbed by droplets of a commercial fat emulsion was identified as apoliprotein H. Moreover, the positions of apolipoproteins apoC-II and apoC-III were also verified on the 2-DE protein map of human plasma. Thus, protein adsorption experiments of the kind presented in this study are increasing our insight into human plasma proteins.
HLA-G EXPRESSION PROTECTS PORCINE ENDOTHELIAL CELLS AGAINST NATURAL KILLER CELL-MEDIATED XENOGENEIC CYTOTOXICITY1,2 (1999)

Expression of HLA-G on PAECs protected xenogeneic PAECs against human polyclonal NK cell-mediated lysis. These results indicate that the expression of HLA-G alone in the absence of other nonclassical HLA class I molecules is sufficient to inhibit human NK cell lysis. These findings suggest methods utilizing HLA-G to overcome NK cell-mediated cytotoxicity against porcine endothelial cells, considered the first cell type effected during xenograft cellular rejection.
Synthesis and characterisation of layered double hydroxide dispersions in organic solvents (2014)

Aqueous Miscible Organic Solvent Treatment (AMOST) Mg<sub>3</sub>AlCO<sub>3</sub>–LDHs have been prepared using twelve different (AMO) solvents.
PxF, a prenylated protein of peroxisomes. (1994)

CAAX farnesyltransferase attaches a farnesyl group to proteins that terminate in the sequence CAAX, where C is cysteine, A is an aliphatic amino acid, and X is typically methionine or serine. A limited number of substrates for the CAAX farnesyltransferase have been identified in cultured cells. These include p21ras proteins and the nuclear lamins A and B. We describe here the use of a CAAX farnesyltransferase inhibitor, together with a hamster cell line that exhibits efficient uptake of [3H]mevalonate, as a means of identifying novel farnesylated proteins. One candidate protein was purified and its attached prenyl group identified as farnesyl. The predicted amino acid sequence of this protein, deduced from a cloned cDNA, terminates with the tetrapeptide Cys-Leu-Ile-Met, which conforms to the consensus sequence for recognition by farnesyltransferase. This farnesylated protein, designated PxF, is localized to the outer surface of peroxisomes as determined by indirect immunofluorescence and electron microscopy.
Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs (2003)

We considered 12 subcellular locations in eukaryotic cells: chloroplast, cytoplasm, cytoskeleton, endoplasmic reticulum, extracellular medium, Golgi apparatus, lysosome, mitochondrion, nucleus, peroxisome, plasma membrane, and vacuole. We constructed a data set of proteins with known locations from the SWISS-PROT database. A set of SVMs was trained to predict the subcellular location of a given protein based on its amino acid, amino acid pair, and gapped amino acid pair compositions. The predictors based on these different compositions were then combined using a voting scheme. Results obtained through 5-fold cross-validation tests showed an improvement in prediction accuracy over the algorithm based on the amino acid composition only. This prediction method is available via the Internet.
Abstracts (pp. 1&ndash;50) (2009)

Endothelium-dependent hyperpolarization of smooth muscle cells serves to synchronize and limit changes in resistance artery diameter. A diffusible 'factor' and/or direct heterocellular electrical coupling can underlie this physiological control, and both often act in parallel. Thus, depending on the tissue and the presence of myoendothelial gap junctions (between endothelial and smooth muscle cells), activation of K channels by factors such as nitric oxide, superoxide anion, cytochrome P 450 metabolites or K ion can each overall evoke the same dilator responses as that evoked by spread of hyperpolarization from endothelial cells following the opening of Ca 2+ -activated K channels. However, we still do not know how important the relative sub-cellular localization of each of the various channels and signalling intermediates contributing to these pathways are in ensuring effective integration of the overall vascular dilator response. Once a resistance artery or arteriole is hyperpolarized, the overall response manifests as bidirectional spread of current and subsequent dilatation along the longitudinal length of vessels. This ability of the vessel work in this area and discuss our recent data showing that discrete and rational arrangement of K channels, connexins and possibly other key proteins in membrane microdomains may be crucial to ensure the effective control of artery diameter, both locally and over distance.
Isolation and culture of hamster ectoplacental cone trophoblasts: an in vitro study on the cell types and their growth pattern (1996)

The method of isolation of trophoblast cell types from ectoplacental cone of hamster embryo of day 8 post coitum (plug day as day 1) and examination of their growth pattern in vitro is presented in this study. Based on their size, three types of trophoblast cells were identified. (1) the smaller cells having clear cytoplasm formed the major portion (70% to 80%) of the total cell population (2) moderately bigger cells having mono or binucleated appearance and containing minute granules in the nuclear region formed 5% to 10% and (3) extra large and multinucleated cells shared 10% to 20% of the total cell number. While the smaller and slightly bigger cells showed moderate growth the larger ones had extensive growth and were seen to acquire different shapes on extending the duration of culture, such as fusiform, dumb-bell, polygonal, rectangular or flowery. The extremities of the cytoplasmic growth of these cells were seen to be thickened at one end giving the impression of a pad-like structure. The significance of these adaptations are not known at present.
Design of rate-compatible structured LDPC codes for hybrid ARQ applications (2009)

In this paper, families of rate-compatible protograph-based LDPC codes that are suitable for incrementalredundancy hybrid ARQ applications are constructed. A systematic technique to construct low-rate base codes from a higher rate code is presented. The base codes are designed to be robust against erasures while having a good performance on error channels. A progressive node puncturing algorithm is devised to construct a family of higher rate codes from the base code. The performance of this puncturing algorithm is compared to other puncturing schemes. Using the techniques in this paper, one can construct a rate-compatible family of codes with rates ranging from 0.1 to 0.9 that are within 1 dB from the channel capacity and have good error floors.
A knowledge-based approach to organizing retrieved documents (1999)

When people use computer-based tools to find answers to general questions, they often are faced with a daunting list of search results or &amp;quot;hits&amp;quot; returned by the search engine. Many search tools address this problem by helping users to make their searches more specific. However, when dozens or hundreds of documents are relevant to their question, users need tools that help them to explore and to understand their search results, rather than ones that eliminate a portion of those results. In this paper, we present DynaCat, a tool that dynamically categorizes search results into a hierarchical organization by using knowledge of important kinds of queries and a model of the domain terminology. Results from our evaluation show that DynaCat helps users find answers to those important types of questions more quickly and easily than when they use a relevance -ranking system or a clustering system. Introduction Current information-retrieval tools usually return results that cons...
Atypicality of Atypical Antipsychotics (2005)

If the definition of "atypical" antipsychotic is considered to be freedom from extrapyramidal symptoms, then, based on a comprehensive review of available data and clinical experience, clozapine and quetiapine appear to be the only true atypicals.
Expression of extracellular superoxide dismutase in the human male reproductive tract, detected using antisera raised against a recombinant protein (1998)

Mammalian spermatozoa are particularly susceptible to the deleterious effects of reactive oxygen species and lipid peroxidation, which ultimately lead to impaired fertility. A number of enzymes are present in the male reproductive tract which may play a role in preventing oxidative damage; in particular, the epididymis is the site of synthesis and secretion of large amounts of extracellular superoxide dismutase (eSOD). In order to study the distribution of eSOD in the male reproductive tract, and distinguish it from other related superoxide dismutase isoenzymes (e.g. cytosolic SOD), polyclonal antisera have been raised against a recombinant human eSOD fusion protein, expressed in bacterial cells. This protein was expressed from a synthetic gene fragment, using preferred Escherichia coli codons, designed to overcome the problems associated with the high guanine+cytosine content of the natural human eSOD transcript. Using this antiserum, eSOD can be readily detected in a range of human reproductive tissues as well as in human seminal plasma. However, the presence of similar levels of eSOD in the seminal plasma of vasectomized men (probably of prostatic origin) precludes its use as a simple diagnostic indicator of eSOD activity levels in the epididymis.
A conserved family of elav-like genes in vertebrates. (1995)

A large family of genes encodes proteins with RNA recognition motifs that are presumed to bind RNA and to function in posttranscriptional regulation. Neural-specific members of this family include elav, a gene required for correct differentiation and maintenance of neurons in Drosophila melanogaster, and a related gene, HuD, which is expressed in human neuronal cells. I have identified genes related to elav and HuD in Xenopus laevis, zebrafish, and mouse that define a family of four closely related vertebrate elav-like genes (elrA, elrB, elrC, and elrD) in fish, frogs, and mammals. In addition to protein sequence conservation, a segment of the 3'-untranslated sequence of elrD is also conserved, implying a functional role in elrD expression. In adult frogs, elrC and elrD are exclusively expressed in the brain, whereas elrB is expressed in brain, testis, and ovary. During Xenopus development, elrC and elrD RNAs are detected by late gastrula and late neurula stages, respectively, whereas a nervous system-specific elrB RNA species is expressed by early tadpole stage. Additional elrB transcripts are detected in the ovary and early embryo, demonstrating a maternal supply of mRNA and possibly of protein. These expression patterns suggest a role for different elav-like genes in early development and neuronal differentiation. Surprisingly, elrA is expressed in all adult tissues tested and at all times during development. Thus, the widely expressed elrA is expected to have a related function in all cells.
Use of photoactivatable sphingolipid analogues to monitor lipid transport in mammalian cells (1997)

Photoactivatable derivatives of ceramide, glucosylceramide (GlcCer) and sphingomyelin {3-(p-azido-m-[125I]iodophenyl)propionylceramide, 3-(p-azido-m-[125I]iodophenyl)propionyl-GlcCer and 3-(p-azido-m-[125I]iodophenyl)propionylsphingomyelin} were synthesized in an attempt to identify compartment-specific proteins involved in sphingolipid sorting or metabolism. In HT29 and BHK cells the ceramide analogue entered the cell by monomeric diffusion, as evidenced by the probe's efficient internalization at low temperature (4 degrees C). In contrast, the photoactivatable GlcCer was internalized only at elevated temperatures (37 degrees C), presumably reflecting an endocytic mechanism of uptake. The photoactivatable ceramide was mainly metabolized to the corresponding sphingomyelin analogue, but small amounts of GlcCer and galactosylceramide were also synthesized. The newly synthesized photoreactive sphingomyelin was subsequently transported to the cell surface, a process that was effectively inhibited by the presence of brefeldin A. The incubation of cells with photoactivatable analogues at 4 degrees C, followed by illumination, led to the association of sphingolipid with a specific subset of proteins. The protein labelling pattern of ceramide differed from that of glucosylceramide. A further shift in labelling pattern was apparent when the cells were incubated with the lipid analogues at 37 degrees C. Moreover, most of the proteins labelled by photoreactive sphingomyelin seemed to be detergent-insoluble, which is indicative of a location in sphingolipid-rich microdomains at the plasma membrane. The potential of applying photoactivatable sphingolipids to further define and identify the role of distinct proteins in sphingolipid biosynthesis, transport and sorting, is discussed.
Diversity and diversification of HLA-A,B,C alleles. (1989)

The nucleotide sequences encoding 14 HLA-A,B,C and 5 ChLA-A,B,C molecules have been determined. Combining these sequences with published data has enabled the polymorphism in 40 HLA-A,B,C and 9 ChLA-A,B,C alleles to be analyzed. Diversity is generated through assortment of point mutations by recombinational mechanisms including gene and allelic conversions. The distribution and frequency of silent and replacement substitutions indicate that there has been positive selection for allelic diversity in the 5' part of the gene (exons 1 to 3) and for allelic homogenization and locus specificity in the 3' part of the gene (exons 4 to 8). These differences may correlate with the lengths of converted sequences in the two parts of the gene and frequency of the CpG dinucleotide. Locus-specific divergence of HLA-A,B, and C demonstrates that recombinational events involving alleles of a locus have been more important than conversion between loci. This contrasts with the predominance of gene conversion events in the evolution of mutants of the H-2Kb gene. However, a striking example of gene conversion involving HLA-B and C alleles of an oriental haplotype has been found. Comparison of human and chimpanzee alleles reveals extensive sharing of polymorphisms, confirming that diversification is a slow process, and that much of contemporary polymorphism originated in ancestral primate species before the emergence of Homo sapiens. There is less polymorphism at the HLA-A locus compared to HLA-B, with greater similarity also being seen between HLA-A and ChLA-A alleles than between HLA-B and ChLA-B alleles. Although greater diversity is seen in the 5' "variable" exons of HLA-B compared to HLA-A, there is increased heterogeneity in the 3' "conserved" exons of HLA-A compared to HLA-B.
Synthesis of enzymatically active human α‐l‐iduronidase in Arabidopsis cgl (complex glycan‐deficient) seeds (2005)

As an initial step to develop plants as systems to produce enzymes for the treatment of lysosomal storage disorders, Arabidopsis thaliana wild-type (Col-0) plants were transformed with a construct to express human alpha-l-iduronidase (IDUA; EC 3.2.1.76) in seeds using the promoter and other regulatory sequences of the Phaseolus vulgaris arcelin 5-I gene. IDUA protein was easily detected on Western blots of extracts from the T(2) seeds, and extracts contained IDUA activity as high as 2.9 nmol 4-methylumbelliferone (4 MU)/min/mg total soluble protein (TSP), corresponding to approximately 0.06 microg IDUA/mg TSP. The purified protein reacted with an antibody specific for xylose-containing plant complex glycans, indicating its transit through the Golgi complex. In an attempt to avoid maturation of the N-linked glycans of IDUA, the same IDUA transgene was introduced into the Arabidopsis cgl background, which is deficient in the activity of N-acetylglucosaminyl transferase I (EC 2.4.1.101), the first enzyme in the pathway of complex glycan biosynthesis. IDUA activity and protein levels were significantly higher in transgenic cgl vs. wild-type seeds (e.g. maximum levels were 820 nmol 4 MU/min/mg TSP, or 18 microg IDUA/mg TSP). Affinity-purified IDUA derived from cgl mutant seeds showed a markedly reduced reaction with the antibody specific for plant complex glycans, despite transit of the protein to the apoplast. Furthermore, gel mobility changes indicated that a greater proportion of its N-linked glycans were susceptible to digestion by Streptomyces endoglycosidase H, as compared to IDUA derived from seeds of wild-type Arabidopsis plants. The combined results indicate that IDUA produced in cgl mutant seeds contains glycans primarily in the high-mannose form. This work clearly supports the viability of using plants for the production of human therapeutics with high-mannose glycans.
The use of fast Fourier transform for the estimation of power spectra: A method based on time averaging over short, modified periodograms (1967)

The use of the fast Fourier transform in power spectrum analysis is described. Principal advantages of this method are a reduction in the number of computations and in required core storage, and convenient application in nonstationarity tests. The method involves sectioning the record and averaging modified periodograms of the sections.