gebhart/patrepeval huggingface dataset:
Using acoustic radiation force as a concentration method for erythrocytes (1997)

We investigated the potential damage inflicted on erythrocytes by acoustic radiation force when the cells are concentrated by a 500-kHz ultrasonic standing wave at the pressure node. The extent of the damage was estimated from the concentrations of potassium ions, iron complexes, and lactate dehydrogenase released from the cells. After 2 min of ultrasound irradiation at 12.8 mJ/m3, the cells concentrated on the pressure node, with a cell distribution half-width of 138 microns; no significant release of intracellular components was detected, even after 15 min of irradiation. The results indicate that even small ions like potassium are not released as a result of ultrasound irradiation on cell membranes without cavitation, and they demonstrate the potential use of acoustic radiation force for concentrating living cells in biomedical applications.
Phospholipase D- and Protein Kinase C Isoenzyme-Dependent Signal Transduction Pathways Activated by the Calcitonin Receptor* (1998)

The calcitonin receptor expressed by the porcine LLC-PK1 renal tubule cells is a seven-transmembrane domain, G protein-coupled receptor activating adenylyl-cyclase and phospholipase C. Salmon calcitonin stimulated dose- and time-dependent release of the phospholipase D-dependent phosphatidylcholine product [3H] choline with an EC50 = 2.5 +/-0.3 x 10(-8) M, similar to that determined for phosphoinositide metabolism (EC50 = 4.5 +/-1.0 x 10(-8)M). The hormone failed to induce release of [3H]phosphocholine and [3H]glycerophosphocholine, ruling out activation of phosphatydilcholine-specific phospholipase C and phospholipase A. Calcitonin stimulated phosphatidic acid, a product of phospholipase D-dependent phosphatydilcholine hydrolysis. Activation of phospholipase D was confirmed by release of [3H]phosphatydilethanol, a specific and stable product in the presence of a primary alcohol. Activation of calcitonin receptor induced diacylglycerol formation, with a rapid peak followed by a prolonged increase, due to activation of phospholipase C and of phospholipase D. Consequently, the protein kinase-C alpha, but not the delta isoenzyme, was cytosol-to-membrane translocated by approximately 50% after 20 min exposure to calcitonin, whereas protein kinase-C zeta, which was approximately 40% membrane-linked in unstimulated cells, translocated by approximately 19%. The human calcitonin receptor expressed by BIN-67 ovary tumor cells, although displaying higher affinity for calcitonin, failed to activate phospholipase D and protein kinase-C in response to the hormone. This receptor lacks the G protein binding consensus site due to the presence of a 48-bp cassette encoding for a 16-amino acid insert in the predicted first intracellular loop. This modification is likely to prevent the calcitonin receptor from associating to phospholipase-coupled signaling.
Cytokine Profiles Induced by the Novel Swine‐Origin Influenza A/H1N1 Virus: Implications for Treatment Strategies (2009)

BACKGROUND. Given the apparent high mortality associated with the novel swine-origin influenza A/H1N1 virus (S-OIV) in Mexico, we aimed to study the cytokine profiles induced by S-OIV and the effect of immunomodulators. METHODS. We assayed cytokines and their messenger RNA (mRNA) levels in culture supernatants of human macrophages infected with H5N1, S-OIV California/04/2009 (S-OIV-CA), S-OIV Hong Kong/415742 (S-OIV-HK), or seasonal H1N1 with or without celecoxib and mesalazine. RESULTS. Among the 12 cytokines showing detectable levels, levels of 8 proinflammatory cytokines (interleukin [IL] 2R, IL-6, interferon [IFN] alpha, macrophage inflammatory protein [MIP] alpha, MIP-1beta, IFN-induced protein 10, regulated on activation, normal T cell expressed and secreted [RANTES], and monocyte chemotactic protein [MCP] 1) were higher in cells infected by H5N1 but similar among cells infected with H1N1, S-OIV-CA, or S-OIV-HK. The levels of the other 4 cytokines were similar for H5N1, H1N1, S-OIV-CA and S-OIV-HK. Among the 8 cytokines induced by H5N1, 6 were suppressed by celecoxib and mesalazine. The mRNA levels of tumor necrosis factor alpha, IFN-gamma, IL-6, and MCP-1 induced by H5N1 were higher than the levels of other cytokines at 12 and/or 24 h. CONCLUSIONS. No major cytokine storm, as seen in H5N1 infection, is associated with S-OIV infection of cell lines. The mainstay of treatment for uncomplicated S-OIV infections should be antiviral agents without immunomodulators. For individual S-OIV-infected patients with severe primary viral pneumonia, severe sepsis, and multiorgan failure, immunomodulators may be considered as an adjunctive therapy in clinical trials.
Reaction of quinones with thiourea. Novel route to 2-amino-6-hydroxybenzothiazoles and 2-amino-5-hydroxynaphtho[1,2-d] thiazoles (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of quinones with thiourea. Novel route to 2-amino-6-hydroxybenzothiazoles and 2-amino-5-hydroxynaphtho[1,2-d] thiazolesPhilip T. S. Lau and T. E. CompfCite this: J. Org. Chem. 1970, 35, 12, 4103–4108Publication Date (Print):December 1, 1970Publication History Published online1 May 2002Published inissue 1 December 1970https://pubs.acs.org/doi/10.1021/jo00837a003https://doi.org/10.1021/jo00837a003research-articleACS PublicationsRequest reuse permissionsArticle Views902Altmetric-Citations26LEARN 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-Alertsclose Get e-Alerts
Clustering by fast search and merge of local density peaks for gene expression microarray data (2017)

Clustering is an unsupervised approach to classify elements based on their similarity, and it is used to find the intrinsic patterns of data. There are enormous applications of clustering in bioinformatics, pattern recognition, and astronomy. This paper presents a clustering approach based on the idea that density wise single or multiple connected regions make a cluster, in which density maxima point represents the center of the corresponding density region. More precisely, our approach firstly finds the local density regions and subsequently merges the density connected regions to form the meaningful clusters. This idea empowers the clustering procedure, in which outliers are automatically detected, higher dense regions are intuitively determined and merged to form clusters of arbitrary shape, and clusters are identified regardless the dimensionality of space in which they are embedded. Extensive experiments are performed on several complex data sets to analyze and compare our approach with the state-of-the-art clustering methods. In addition, we benchmarked the algorithm on gene expression microarray data sets for cancer subtyping; to distinguish normal tissues from tumor; and to classify multiple tissue data sets.
Thin film transistor circuits integrated onto elastomeric substrates for elastically stretchable electronics (2006)

We fabricated integrated inverter circuits directly on an elastic silicone membrane substrate. Using an all-dry process, amorphous silicon thin film transistors were prepared on platforms of stiff silicon nitride, and were interconnected to inverters with elastically stretchable gold metallization. With the elastomeric substrate, rigid device islands, thin film transistors, and elastic metal interconnects, all components for an elastically stretchable active-matrix backplane have been demonstrated and integrated
Preparation of New Anti-Tubulin Ligands through a Dual-Mode, Addition−Elimination Reaction to a Bromo-Substituted α,β-Unsaturated Sulfoxide (2000)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTPreparation of New Anti-Tubulin Ligands through a Dual-Mode, Addition−Elimination Reaction to a Bromo-Substituted α,β-Unsaturated SulfoxideZhi Chen, Vani P. Mocharla, J. Matt Farmer, George R. Pettit, Ernest Hamel, and Kevin G. PinneyView Author Information Department of Chemistry and Biochemistry, P.O. Box 97348, Baylor University, Waco, Texas 76798, Cancer Research Institute and Department of Chemistry, Arizona State University, Tempe, Arizona 85287-1604, and Screening Technologies Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick Cancer Research and Development Center, Frederick, Maryland 21702 [email protected]Cite this: J. Org. Chem. 2000, 65, 25, 8811–8815Publication Date (Web):November 21, 2000Publication History Received29 March 2000Published online21 November 2000Published inissue 1 December 2000https://pubs.acs.org/doi/10.1021/jo0004761https://doi.org/10.1021/jo0004761brief-reportACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views866Altmetric-Citations37LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Inhibitors,Ligands,Oxides,Polymerization,Thiophenes Get e-Alerts
Structural and Thermodynamic Studies on Cation−Π Interactions in Lectin−Ligand Complexes:  High-Affinity Galectin-3 Inhibitors through Fine-Tuning of an Arginine−Arene Interaction (2005)

The high-resolution X-ray crystal structures of the carbohydrate recognition domain of human galectin-3 were solved in complex with N-acetyllactosamine (LacNAc) and the high-affinity inhibitor, methyl 2-acetamido-2-deoxy-4-O-(3-deoxy-3-[4-methoxy-2,3,5,6-tetrafluorobenzamido]-beta-D-galactopyranose)-beta-D-glucopyranoside, to gain insight into the basis for the affinity-enhancing effect of the 4-methoxy-2,3,5,6-tetrafluorobenzamido moiety. The structures show that the side chain of Arg144 stacks against the aromatic moiety of the inhibitor, an interaction made possible by a reorientation of the side chain relative to that seen in the LacNAc complex. Based on these structures, synthesis of second generation LacNAc derivatives carrying aromatic amides at 3'-C, followed by screening with a novel fluorescence polarization assay, has led to the identification of inhibitors with further enhanced affinity for galectin-3 (K(d) > or = 320 nM). The thermodynamic parameters describing the binding of the galectin-3 C-terminal to selected inhibitors were determined by isothermal titration calorimetry and showed that the affinity enhancements were due to favorable enthalpic contributions. These enhancements could be rationalized by the combined effects of the inhibitor aromatic structure on a cation-Pi interaction and of direct interactions between the aromatic substituents and the protein. The results demonstrate that protein-ligand interactions can be significantly enhanced by the fine-tuning of arginine-arene interactions.
Immune and Metabolic Effects of Arginine in the Surgical Patient (1988)

Arginine enhances immune function and promotes nitrogen retention in animal models, but its immunomodulatory effects in surgical patients are unknown. This randomized, prospective trial evaluated the immune and metabolic effects of supplemental L-arginine (25 g/day, n = 16) or isonitrogenous L-glycine (43 g/day, n = 14) in 30 cancer patients undergoing major operation. Two groups of patients received either arginine or glycine for 7 days after surgery as a supplement to a graduated enteral diet. Nitrogen balance was measured daily, and immune parameters were determined both before and after surgery, on Days 1, 4, and 7. The T-lymphocyte response to concanavalin A (con A) and PHA and dual marker phenotype analysis of lymphocyte (CD2, CD4, CD4/DR, CD8, CD8/DR) and macrophage (M3/DR) subsets were determined. Mean age, degree of preoperative weight loss, disease stage, number of perioperative transfusions, and calorie and nitrogen intake were similar for the groups studied. Mean daily nitrogen balance (-2.3 g/day in the arginine group vs. -3.9 g/day in the glycine group) was not significantly different between the two groups, but positive mean nitrogen balance was achieved only in the arginine group between Days 5 and 7 after surgery. Supplemental arginine significantly enhanced the mean T-lymphocyte response (stimulation index) to con A from 45 +/- 26 on postoperative Day 1 to 72 +/- 47 and 87 +/- 49 on postoperative Days 4 and 7, compared with the values of 29 +/- 15, 27 +/- 20, and 33 +/- 34 in the glycine group at the same time points, respectively. Supplemental arginine increased mean CD4 phenotype (% T-cells) on postoperative Days 1 and 7 from 25 +/- 9 to 43 +/- 14, compared with the values of 30 +/- 14 and 29 +/- 13 in the glycine group (p less than 0.05). The beneficial effect of arginine on the immune system appeared distinct from its more moderate effect on nitrogen metabolism. As a nutrient substrate, arginine was nontoxic, and may benefit surgical patients who are at increased risk of infection.
Profiling model T-cell metagenomes with short reads (2009)

ftp://ftp.bcgsc.ca/supplementary/iSSAKE.
Stereospecific Synthesis of Conformationally Constrained γ-Amino Acids: New Foldamer Building Blocks That Support Helical Secondary Structure (2009)

A highly stereoselective synthesis of novel cyclically constrained gamma-amino acid residues is presented. The key step involves organocatalytic Michael addition of an aldehyde to 1-nitrocyclohexene. After aldehyde reduction, this approach provides optically active beta-substituted delta-nitro alcohols (96-99% ee), which can be converted to gamma-amino acid residues with a variety of substituents at the alpha position. We have used these new building blocks to prepare alpha/gamma-peptide foldamers that adopt a specific helical conformation in solution and in the solid state.
Replication of poliovirus RNA containing two VPg coding sequences leads to a specific deletion event (1993)

Studies of the poliovirus genome-linked protein VPg have shown that this small viral protein is required for replication of virus-specific RNA (Q. Reuer, R. J. Kuhn, and E. Wimmer, J. Virol. 64:2967-2975, 1990). To understand the mechanism of RNA replication, we constructed a recombinant poliovirus genome encoding two tandemly arranged VPg coding sequences that were nearly identical in both nucleotide and amino acid sequence. Following transfection of this two-VPg-containing RNA into HeLa cells, we found a specific and selective deletion in the progeny virus genome. Sequence analysis of the recovered viral RNA indicated that the complete nucleotide sequence encoding the second (3C-proximal) VPg coding sequences was removed, restoring the authentic genome sequences in the poliovirus genome. Analysis of viral RNAs following transfection suggested that the deletion event occurred during genome replication. Deletion could have occurred via homologous recombination between two VPg sequences or via intramolecular deletion with loop-out of the template. In vitro translation of the two-VPg-containing transcript RNA indicated aberrant processing of the viral polyprotein. This result suggested that selection of the wild-type genotype in the transfected cells may occur at the level of viral protein synthesis.
Studies on antitumor agents. IX. Synthesis of 3'-O-benzyl-2'-deoxy-5-trifluoromethyluridine. (1989)

A practical synthesis of 3'-O-benzyl-2'-deoxy-5-trifluoromethyluridine (1), a candidate antitumor agent for clinical testing, was developed from 2'-deoxy-5-iodouridine (3). Benzylation of 2'-deoxy-5-iodo-5'-O-trityluridine (14) with benzyl bromide and sodium hydride in tetrahydrofuran gave the 3'-O-derivative (16). Benzoylation of 16 afforded the N3-benzoyl derivative (17). Coupling of 17 with trifluoromethylcopper, prepared from bromotrifluoromethane and copper powder in the presence of 4-dimethylaminopyridine, gave the 5-trifluoromethyl derivative (19) minimally contaminated with the 5-pentafluoroethyl compound. Deprotection of 19 furnished 1.
Tuning of mRNA stability through altering 3′-UTR sequences generates distinct output expression in a synthetic circuit driven by p53 oscillations (2019)

Synthetic biological circuits that can generate outputs with distinct expression dynamics are useful for a variety of biomedical and industrial applications. We present a method to control output dynamics by altering output mRNA decay rates. Using oscillatory expression of the transcription factor p53 as the circuit regulator, we use two approaches for controlling target gene transcript degradation rates based on the output gene's 3'-untranslated region (3'-UTR): introduction of copies of destabilizing AU-rich elements into the 3'-UTR or swapping in naturally occurring 3'-UTRs conferring different transcript stabilities. As a proof of principle, we apply both methods to control the expression dynamics of a fluorescent protein and visualize the circuit output dynamics in single living cells. We then use the naturally occurring 3'-UTR approach to restore apoptosis in a tunable manner in a cancer cell line deficient for caspase-3 expression. Our method can be readily adapted to regulate multiple outputs each with different expression dynamics under the control of a single naturally occurring or synthetically constructed biological oscillator.
The Immunopathogenesis of Sepsis in Elderly Patients (2005)

Prominent among the numerous events that contribute to the enhanced susceptibility of elderly patients to infection is the decline of immune function that accompanies aging. Elderly patients experience a marked decline in cell-mediated immune function and reduced humoral immune function. Age-dependent defects in T and B cell function are readily demonstrable in elderly patients, yet the essential elements of innate immunity are remarkably well preserved. The cytokine and chemokine signaling networks are altered in elderly patients and tends to favor a type 2 cytokine response over type 1 cytokine responses. The induction of proinflammatory cytokines after septic stimuli is not adequately controlled by anti-inflammatory mechanisms in elderly persons. This immune dysregulation is accompanied by a more pronounced procoagulant state in older patients. These molecular events function in concert to render elderly patients at excess risk for mortality from severe sepsis and septic shock.
Molecular dynamics simulation of winter flounder antifreeze protein variants in solution: correlation between side chain spacing and ice lattice (1993)

The solution structure of the 38 amino acid C-terminal region of the precursor for the HPLC-6 antifreeze protein from winter flounder has been investigated with molecular dynamics using the AMBER software. The simulation for the peptide in aqueous solution was carried out at a constant temperature of 0 degree C and at atmospheric pressure. The simulation covered 120 ps and the results were analyzed based on data sampled upon reaching a stable equilibrium phase. Information has been obtained on the quality of constant temperature and pressure simulations, the solution structure and dynamics, the hydrogen bonding network, the helix stabilizing role of terminal charges and the interaction with the surrounding water molecules. The Lys18-Glu22 interactions and the terminal charged residues are found to stabilize a helical structure with the side chains of Thr2, Thr13, Thr24 and Thr35 equally spaced on one side of the helix. The spacing between oxygen atoms in the hydroxyl group of the threonine side chains exhibits fluctuations of the order of 2-3 A during the 120 ps of simulation, but values simultaneously close to the repeat distance of 16.6 A between oxygen atoms along the [0112] direction in ice are observed. Furthermore, two engineered variants were studied using the same simulation protocol.
Film review (2000)

Weaving the future Weaving the Future. A video by Mark Freeman. 1997; 24 minutes, color. English commentary. Distributor: Documentary Educational Resources, 101 Morse Street, Watertown, MA 02472, U.S.A. (617) 926–0491. Video sale, $195; rental, $50.
The construction, identification and characterisation of plasmids containing human α-lactalbumin cDNA sequences (1981)

We describe the cloning of double-stranded cDNA synthesized from lactating human mammary gland total poly(A)-containing RNA, into the EcoRI site of the plasmid pAT153. Nine recombinants were shown to contain alpha-lactalbumin cDNA sequences as determined by positive hybridisation translation of complementary RNA. Restriction enzyme maps were determined for six of these. Alignment of the restriction map with the known amino acid sequence of human alpha-lactalbumin provided evidence that two plasmids, designated phO-53 and phB-35, contained the complete coding sequence of the primary translation product (pre-alpha-lactalbumin). Hybridisation studies using purified human, monkey and guinea-pig alpha-lactalbumin cDNA demonstrated that greater nucleotide sequence divergence has occurred within the rodents than the primates, and that rodent alpha-lactalbumin mRNAs retain regions of homology with primate alpha-lactalbumin mRNAs.
Adsorption of avidin on microfabricated surfaces for protein biochip applications (2001)

The adsorption of the protein avidin from hen egg white on patterns of silicon dioxide and platinum surfaces on a microchip and the use of fluorescent microscopy to detect binding of biotin are described. A silicon dioxide microchip was formed using plasma-enhanced chemical vapor deposition while platinum was deposited using radiofrequency sputtering. After cleaning using a plasma arc, the chips were placed into solutions containing avidin or bovine serum albumin. The avidin was adsorbed onto the microchips from phosphate-buffered saline (PBS) or from PBS to which ammonium sulfate had been added. Avidin was also adsorbed onto bovine serum albumin (BSA)-coated surfaces of oxide and platinum. Fluorescence microscopy was used to confirm adsorption of labeled protein, or the binding of fluorescently labeled biotin onto previously adsorbed, unlabeled avidin. When labeled biotin in PBS was presented to avidin adsorbed onto a BSA-coated microchip, the fluorescence signal was significantly higher than for avidin adsorbed onto the biochip alone. The results show that a simple, low-cost adsorption process can deposit active protein onto a chip in an approach that has potential application in the development of protein biochips for the detection of biological species.