gebhart/patrepeval huggingface dataset:
Introduction to the Molecular Biology of Baculoviruses (2003)

Over the last 10 years, baculovirus expression vectors have become a very popular and effective means with which to produce recombinant proteins in large quantities (1–5). Posttranslational modifications of the gene products of these insect viruses closely parallel glycosylation, fatty acid acylation, and phosphorylation in mammalian cells (reviewed in 6). Scaleup of insect cells in culture has also been largely perfected, making purification of large quantities of recombinant proteins a reality (7). In addition, baculoviruses offer an ecologically acceptable and effective alternative to chemicals for the control of forest and agricultural insect pests (8,9). Their demonstrated safety as expression vectors and pest management tools is the result of limited host specificity and lack of resemblance to mammalian viruses. The development of the baculovirus expression system was facilitated by the establishment of insect cell lines that support the replication of one subgroup, the nuclear polyhedrosis viruses (NPVs). The ability to propagate baculoviruses in cell culture has also allowed extensive study of their molecular biology (10). The model virus in these studies is the Autographa californica NPV (AcNPV). Although it was first isolated from the alfalfa looper (Autographa californica), it multiplies readily in cell lines derived from both the fall armyworm (Spodopterafrugiperda) and the cabbage looper (Trichoplusia ni). Most expression vectors are based on AcNPV infection of Spodoptera frugiperda cells. However, the production of heterologous proteins in silkworm (Bombyx mori; Bm) larvae relies on infection with recombinant BmNPV (4). The baculovirus expression system is based on introduction of the foreign gene into nonessential regions of the viral genome through allelic replacement. Production of the recombinant protein is achieved following infection of insect cells or larvae with the newly engineered virus.
The crystallographic fast Fourier transform. Recursive symmetry reduction (2007)

Algorithms are presented for maximally efficient computation of the crystallographic fast Fourier transform (FFT). The approach is applicable to all 230 space groups and allows reduction of both the computation time and the memory usage by a factor equal to the number of symmetry operators. The central idea is a recursive reduction of the problem to a series of transforms on grids with no special points. The maximally efficient FFT for such grids has been described in previous papers by the same authors. The interaction between the grid size factorization and the symmetry operators and its influence on the algorithm design are discussed.
Enhancement by histamine of NMDA-mediated synaptic transmission in the hippocampus (1993)

Histamine is a neuromodulator in the brain, and the hippocampus is one of the regions of the brain that is innervated by histaminergic neurons. When applied to cultured hippocampal neurons, histamine selectively increased by up to tenfold the amplitude of the component of synaptic transmission that was mediated by N-methyl-D-aspartate (NMDA) receptors. Spontaneous miniature synaptic currents and the current elicited by applied NMDA also were enhanced, indicating that the histamine effect was expressed primarily postsynaptically. These results suggest that histamine may modulate processes involving NMDA receptors, such as the induction of long-term potentiation.
SELDI proteinchip MS: a platform for biomarker discovery and cancer diagnosis (2002)

Identification and understanding the structures, interactions and functions of all of a cell's proteins is one of the major goals of the postgenome era. The genome project has produced a wealth of information that is greatly expounding the genetic basis of cancer. However, it falls short in not allowing for accurate prediction of what is happening at the protein level in a cancer cell or a body fluid proteome. It is the hope that, by deciphering the alterations in the cancer proteome, biomarkers and patterns of biomarkers will be found that will lead to improvements in early detection, diagnosis and treatment monitoring. To achieve this goal, rapid high-throughput proteomic technologies will be required. The SELDI ProteinChip Biomarker mass spectrometry system appears to have potential in this effort, both for biomarker discovery and as a potential clinical diagnostic assay platform.
Phase III Study by the Norwegian Lung Cancer Study Group: Pemetrexed Plus Carboplatin Compared With Gemcitabine Plus Carboplatin As First-Line Chemotherapy in Advanced Non–Small-Cell Lung Cancer (2009)

PURPOSE To compare pemetrexed/carboplatin with a standard regimen as first-line therapy in advanced non-small-cell lung cancer NSCLC. PATIENTS AND METHODS Patients with stage IIIB or IV NSCLC and performance status of 0 to 2 were randomly assigned to receive pemetrexed 500 mg/m(2) plus carboplatin area under the curve (AUC) = 5 (Calvert's formula) on day 1 or gemcitabine 1,000 mg/m(2) on days 1 and 8 plus carboplatin AUC = 5 on day 1 every 3 weeks for up to four cycles. The primary end point was health-related quality of life (HRQoL) defined as global quality of life, nausea/vomiting, dyspnea, and fatigue reported on the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire C30 and the lung cancer-specific module LC13 during the first 20 weeks. Secondary end points were overall survival and toxicity. Results Four hundred thirty-six eligible patients were enrolled from April 2005 to July 2006. Patients who completed the baseline questionnaire were analyzed for HRQoL (n = 427), and those who received > or = one cycle of chemotherapy were analyzed for toxicity (n = 423). Compliance of HRQoL questionnaires was 87%. There were no significant differences for the primary HRQoL end points or in overall survival between the two treatment arms (pemetrexed/carboplatin, 7.3 months; gemcitabine/carboplatin, 7.0 months; P = .63). The patients who received gemcitabine/carboplatin had more grade 3 to 4 hematologic toxicity than patients who received pemetrexed/carboplatin, including leukopenia (46% v 23%, respectively; P < .001), neutropenia (51% v 40%, respectively; P = .024), and thrombocytopenia (56% v 24%, respectively; P < .001). More patients on the gemcitabine/carboplatin arm received transfusions of RBCs and platelets, whereas the frequencies of neutropenic infections and thrombocytopenic bleedings were similar on both arms. CONCLUSION Pemetrexed/carboplatin provides similar HRQoL and survival when compared with gemcitabine/carboplatin with less hematologic toxicity and less need for supportive care.
Deep penetration of a portion of Escherichia coli SecA protein into model membranes is promoted by anionic phospholipids and by partial unfolding. (1992)

SecA protein, a principal component of the protein export machinery of Escherichia coli, is found both in the cytoplasm and inner membrane of cells. Previous in vitro and in vivo studies demonstrated that the interaction of SecA with the inner membrane requires the presence of physiological levels of anionic (acidic) phospholipids. In this report the degree of SecA insertion into model membranes and the conformational changes associated with this event have been examined. The extent of association of SecA with model membranes was determined by photolabeling with a hydrophobic reagent, and the depth of insertion of the protein into the phospholipid bilayer was determined by the amount of quenching of SecA fluorescence by both brominated and spin-labeled phospholipids. These methods demonstrated that SecA penetrates deep within the acyl chain region of the phospholipid bilayer. It was also found that SecA penetration into vesicles was associated with a major conformational change in the protein. This change can be induced by higher temperatures and involves a partial unfolding event as judged by differential scanning calorimetry, SecA fluorescence and increased sensitivity to proteolysis. These properties suggest the induction of a molten-globule-like conformation in a portion of the SecA polypeptide. This change was also induced at lower temperatures by the presence of membranes containing a physiological amount of the anionic phospholipid, phosphatidylglycerol. The partial unfolding and concomitant deep insertion of SecA into membranes may aid in the insertion of precursor proteins into the inner membrane and may influence possible interactions between SecA and the integral membrane export machinery components.
Presence of complement-fixing anti-endothelial cell antibodies in systemic lupus erythematosus. (1984)

Vasculitis in systemic lupus erythematosus (SLE) is associated with the deposition of IgG and complement in blood vessel walls. However, it is not known whether immune injury to endothelial cells is a part of this process. Therefore, we used a solid phase radioimmunoassay to study the ability of IgG from normal human sera and sera from patients with SLE to bind to endothelial cells. In this assay, cultured human umbilical venous endothelial cells were sequentially incubated with normal or SLE sera, goat anti-human IgG, and 125I-labeled staphylococcal protein A (*SPA). After exposure to normal sera, 2.5 +/- 0.5% (mean +/- SD) of the added *SPA bound to the cells, whereas after exposure to SLE sera 13.8 +/- 7.6% of the added *SPA bound to these cells. This difference in binding was highly significant (P less than 0.001). Binding was partially reduced when SLE sera were preincubated with B-lymphocytes or monocytes, but not after exposure to erythrocytes, platelets, or T lymphocytes. Incubation of endothelial cells with the 7S fraction of SLE sera or with the F(ab')2 fragment of SLE-IgG resulted in the deposition of greater than 80% as much IgG as was deposited on endothelial cells by whole serum. However, since higher molecular weight fractions (greater than 7S) of SLE sera were also active, we tested the capacity of endothelial cells to bind IgG complexes. Endothelial cells bound heat-aggregated IgG (HA-IgG) in a saturable manner at one log concentration below the binding of normal monomeric IgG. Binding of HA-IgG to endothelial cells was markedly enhanced by preincubation with a serum source of complement. Both HA-IgG and SLE-IgG also bound to freshly obtained endothelial cells in suspension, as detected by automated fluorescence flow cytometry. Binding of SLE-IgG and HA-IgG to endothelium initiated complement activation, deposition of the third component of complement, and disruption of the monolayer. In addition, SLE-IgG and HA-IgG caused endothelial cells to secrete prostacyclin and caused the adherence of platelets, confirmed by scanning electron microscopy. These studies demonstrate that IgG anti-endothelial antibodies are present in the sera of patients with active SLE. These sera may also contain IgG complexes that are capable of binding to endothelial cells. The association of IgG and complement with endothelial cells may initiate vascular injury in SLE and other human disorders.
Non-symmetrical dielectric relaxation behaviour arising from a simple empirical decay function (1970)

The empirical dielectric decay function γ(t)= exp –(t/τ0)β may be transformed analytically to give the frequency dependent complex dielectric constant if β is chosen to be 0.50. The resulting dielectric constant and dielectric loss curves are non-symmetrical about the logarithm of the frequency of maximum loss, and are intermediate between the Cole-Cole and Davidson-Cole empirical relations. Using a short extrapolation procedure, good agreement is obtained between the empirical representation and the experimental curves for the α relaxation in polyethyl acrylate. It is suggested that the present representation would have a general application to the α relaxations in other polymers. The Hamon approximation, with a small applied correction, is valid for the present function with β= 0.50 in the range log(ωτ0) > –0.5, but cannot be used at lower frequencies.
Methyl- and (Trifluoromethyl)alkene Peptide Isosteres:  Synthesis and Evaluation of Their Potential as β-Turn Promoters and Peptide Mimetics (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTMethyl- and (Trifluoromethyl)alkene Peptide Isosteres: Synthesis and Evaluation of Their Potential as β-Turn Promoters and Peptide MimeticsPeter Wipf, Todd C. Henninger, and Steven J. GeibView Author Information Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 Cite this: J. Org. Chem. 1998, 63, 18, 6088–6089Publication Date (Web):August 14, 1998Publication History Received3 June 1998Published online14 August 1998Published inissue 1 September 1998https://pubs.acs.org/doi/10.1021/jo981057vhttps://doi.org/10.1021/jo981057vrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views1526Altmetric-Citations123LEARN 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 SUBJECTS:Alcohols,Amides,Aziridines,Hydrocarbons,Peptides and proteins Get e-Alerts
Genome-Wide Association between Branch Point Properties and Alternative Splicing (2010)

The branch point (BP) is one of the three obligatory signals required for pre-mRNA splicing. In mammals, the degeneracy of the motif combined with the lack of a large set of experimentally verified BPs complicates the task of modeling it in silico, and therefore of predicting the location of natural BPs. Consequently, BPs have been disregarded in a considerable fraction of the genome-wide studies on the regulation of splicing in mammals. We present a new computational approach for mammalian BP prediction. Using sequence conservation and positional bias we obtained a set of motifs with good agreement with U2 snRNA binding stability. Using a Support Vector Machine algorithm, we created a model complemented with polypyrimidine tract features, which considerably improves the prediction accuracy over previously published methods. Applying our algorithm to human introns, we show that BP position is highly dependent on the presence of AG dinucleotides in the 3' end of introns, with distance to the 3' splice site and BP strength strongly correlating with alternative splicing. Furthermore, experimental BP mapping for five exons preceded by long AG-dinucleotide exclusion zones revealed that, for a given intron, more than one BP can be chosen throughout the course of splicing. Finally, the comparison between exons of different evolutionary ages and pseudo exons suggests a key role of the BP in the pathway of exon creation in human. Our computational and experimental analyses suggest that BP recognition is more flexible than previously assumed, and it appears highly dependent on the presence of downstream polypyrimidine tracts. The reported association between BP features and the splicing outcome suggests that this, so far disregarded but yet crucial, element buries information that can complement current acceptor site models.
An approach to rheological and electrokinetic behaviour of lipidic vesicles covered with chitosan biopolymer (2007)

The rheological and electrokinetic properties of soybean lecithin vesicles prepared from concentrated soy lecithin dispersions (250 g/L) obtained by slow swelling under shear conditions and mixed with chitosan biopolymer solutions were studied. The rheological behaviour of lecithin–chitosan vesicles was determined by shear stress against shear rate measurements, as well as by the variation on the hysteresis loop area. The results were compared with the rheopectic behaviour of soy lecithin dispersions without chitosan. An important change on the rheological properties of the complex dispersion was observed, depicting in a thixotropic behaviour with a plastic character in the presence of chitosan. This observation indicates that chitosan promotes the transition of planar sheets into closed structures, such as vesicles. The influence on the rheological and the electrokinetic behaviours of several electrolytes, such as NaCl, CaCl2 and AlCl3 with concentrations ranging between 10−5 and 10−2 mol/L were also studied. In all of the cases, an estimation of the diameters of the closed structures was obtained.
Elements of a single MAP kinase cascade in Saccharomyces cerevisiae mediate two developmental programs in the same cell type: mating and invasive growth. (1994)

Diploid Saccharomyces cerevisiae strains starved for nitrogen undergo a developmental transition from a colonial form of growth to a filamentous pseudohyphal form. This dimorphism requires a polar budding pattern and elements of the MAP kinase signal transduction pathway essential for mating pheromone response in haploids. We report here that haploid strains exhibit an invasive growth behavior with many similarities to pseudohyphal development, including filament formation and agar penetration. Haploid filament formation depends on a switch from an axial to a bipolar mode of bud site selection. Filament formation is distinct from agar penetration in both haploids and diploids. We find that the same components of the MAP kinase cascade necessary for diploid pseudohyphal development (STE20, STE11, STE7, and STE12) are also required for both filament formation and agar penetration in haploids. Thus, haploid yeast cells can enter either of two developmental pathways: mating or invasive growth, both of which depend on elements of a single MAP kinase cascade. Our results provide a novel developmental model to study the dynamics of signal transduction, with implications for higher eukaryotes.
Nucleosomal DNA property database. (1999)

The current version of the database is available at http://wwwmgs.bionet.nsc. ru/system/BDNAvideo/. C-code of the recognition program may be found in the section FEATURE. WWW-available programs for testing arbitrary sequences are accessible at http://wwwmgs.bionet.nsc. ru/Programs/bDNA/NA_bDNA.htm/. The links to the mirror site(s) can be found at http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++.
Preparation of Partially Substituted 1-Halo- and 1,4-Dihalo-1,3-dienes via Reagent-Controlled Desilylation of Halogenated 1,3-Dienes (2006)

Depending on the desilylation reagents used, 1-halo-1,4-bis(trimethylsilyl)-1,3-butadienes afforded either 1-halo-1-trimethylsilyl-1,3-butadienes or 1-halo-4-trimethylsilyl-1,3-butadienes in excellent yields with excellent selectivity, respectively, when treated with CF3COOH or with NaOMe. These monosilylated 1,3-butadiene products could be further desilylated to generate their corresponding halobutadienes via the above reagent-controlled desilylation reaction. When 1,4-dihalo-1,4-bis(trimethylsilyl)-1,3-dienes were treated with MeONa/MeOH at room temperature, desilylation of both of the two trimethylsilyl groups took place to afford their corresponding 1,4-dihalo-1,3-dienes in excellent yields. The commonly used desilylation reagent CF3COOH did not work for these dihalobutadienes.
Efficient Initiation of HCV RNA Replication in Cell Culture (2000)

Hepatitis C virus (HCV) infection is a global health problem affecting an estimated 170 million individuals worldwide. We report the identification of multiple independent adaptive mutations that cluster in the HCV nonstructural protein NS5A and confer increased replicative ability in vitro. Among these adaptive mutations were a single amino acid substitution that allowed HCV RNA replication in 10% of transfected hepatoma cells and a deletion of 47 amino acids encompassing the interferon (IFN) sensitivity determining region (ISDR). Independent of the ISDR, IFN-alpha rapidly inhibited HCV RNA replication in vitro. This work establishes a robust, cell-based system for genetic and functional analyses of HCV replication.
cDNA cloning and characterization of human Δ5-desaturase involved in the biosynthesis of arachidonic acid (2000)

Two human expressed sequence tag (EST) cDNA sequences with identity with Delta(5)- and Delta(6)-desaturases from a filamentous fungus, Mortierella alpina, were identified from the LifeSeq(R) database of Incyte Pharmaceuticals, Inc. (Palo Alto, CA, U.S.A.). An oligonucleotide complementary to the 3' EST cDNA sequences was used to screen human liver cDNA using rapid amplification of cDNA ends (RACE)-PCR. The amplified DNA fragment had 98% identity with a putative open reading frame (ORF) predicted from a human genomic sequence, and encoded 444 amino acids. Expression of this ORF in mouse fibroblast cells demonstrated that the encoded protein was a Delta(5)-desaturase, as determined by the conversion of dihomo-gamma-linolenic acid (C(20:3,n-6)) into arachidonic acid (C(20:4,n-6)). The human Delta(5)-desaturase contained a predicted N-terminal cytochrome b(5)-like domain, as well as three histidine-rich domains. A tissue expression profile revealed that this gene is highly expressed in fetal liver, fetal brain, adult brain and adrenal gland. A search of the existing databases led to localization of this ORF within a 14 kb interval flanked by the flap endonuclease-1 (FEN1) and vitelliform macular dystrophy (Best's disease; VMD2) loci of chromosome 11q12.
The matrilins – adaptor proteins in the extracellular matrix (2005)

The matrilins form a four-member family of modular, multisubunit matrix proteins, which are expressed in cartilage but also in many other forms of extracellular matrix. They participate in the formation of fibrillar or filamentous structures and are often associated with collagens. It appears that they mediate interactions between collagen-containing fibrils and other matrix constituents, such as aggrecan. This adaptor function may be modulated by physiological proteolysis that causes the loss of single subunits and thereby a decrease in binding avidity. Attempts to study matrilin function by gene inactivation in mouse have been frustrating and so far not yielded pronounced phenotypes, presumably because of the extensive redundancy within the family allowing compensation by one family member for another. However, mutations in matrilin-3 in humans cause different forms of chondrodysplasias and perhaps also hand osteoarthritis. As loss of matrilin-3 is not critical in mouse, these phenotypes are likely to be caused by dominant negative effects.