gebhart/patrepeval huggingface dataset:
Carbohydrate structures of recombinant soluble human CD4 expressed in Chinese hamster ovary cells (1991)

Infection of T-lymphocytes and macrophages by human immunodeficiency virus (HIV) is mediated by the binding of the HIV envelope glycoprotein to the cell-surface receptor glycoprotein CD4. A soluble, recombinant CD4 molecule (rCD4), produced by expression of a truncated CD4 gene in Chinese hamster ovary (CHO) cells [Smith et al. (1987) Science 238, 1704-1707], is in clinical trials as a potential therapeutic agent in the treatment of acquired immunodeficiency syndrome (AIDS). In the present study, the structures of the Asn-linked oligosaccharides of soluble rCD4 have been elucidated. The rCD4 molecule has two potential sites for N-glycosylation, Asn-271 and Asn-300. Tryptic glycopeptides containing either of the sites were purified by reversed-phase HPLC, and their oligosaccharides were released enzymatically. The structures of the oligosaccharides were determined by methylation analysis, high-pH anion-exchange chromatography, fast-atom bombardment mass spectrometry, and 1H NMR spectroscopy at 500 MHz. Asn-271 was found to carry diantennary N-acetyllactosamine-type ("complex") oligosaccharides, of which 8% were asialo, 55% were monosialyl, and 37% were disialyl. Approximately 18% of these structures contained fucose alpha(1-->6) linked to the reducing GlcNAc residue. Two different hybrid structures were found to account for 34% of the oligosaccharides attached to Asn-300. The remainder of the oligosaccharides attached to Asn-300 were diantennary N-acetyllactosamine-type, of which 10% were asialo, 61% were monosialyl, and 29% were disialyl. Approximately 9% of the hybrid structures and 40% of the N-acetyllactosamine structures at Asn-300 were found to contain fucose alpha(1-->6) linked to the innermost GlcNAc residue.
The Use of Prophylactic Antibacterials in Plastic Surgery (1985)

A questionnaire designed to determine the pattern of usage of prophylactic antibacterials, similar to one used a decade ago, was distributed to plastic surgeons, of whom 1718 responded. The pattern of antibacterial use in 8 major categories and 55 separate operations and circumstances was reviewed. The timing and the influence of various modifying factors was evaluated. The data present the pattern of antibacterial use by plastic surgeons at this point and time, that is, what is "usual and customary".
Structure and function of human IgA Fc receptors (Fc alpha R). (1996)

Receptors for the Fc region of IgA are expressed by many human cell types, especially phagocytes located in mucosal areas, where IgA is the prevalent antibody isotype. Binding of IgA-opsonized particles (e.g., bacteria, viruses) to Fc alpha R may trigger a plethora of cell-mediated immune effector functions designed to rid the body of the foreign invader. The IgA receptor present on myeloid cells such as neutrophils, eosinophils, and monocytes (Fc alpha RI or CD89) is a transmembrane glycoprotein that binds both IgA isotypes with similar affinity. Genetic characterization showed Fc alpha RI to be a more distantly related member of the Ig receptor gene family. Recently, Fc alpha RI was found to associate with the FcR gamma-chain signaling molecule through a unique charge-based mechanism. Fc alpha RI is, thus, connected to the intracellular machinery via the ITAM signaling motifs located within the cytoplasmic tail of FcR gamma-chain. Evidence exists in support of receptors for IgA (distinct from Fc alpha RI) on human T and B cells. IgA Fc receptors may, therefore, play a role in both the induction and control of an efficient (mucosal) immune response.
A New Class of Propylthiouracil Analogs: Comparison of 5'-Deiodinase Inhibition and Antithyroid Activity* (1986)

After in vivo administration, propylthiouracil (PTU) inhibits not only thyroid iodide uptake and organification, but also T4 5'-deiodinase activity in most peripheral organs. The present report describes the effects of some previously untested 6-substituted 2-thiouracil derivatives on in vivo and in vitro iodide uptake and organification, and on T4 5'-deiodinase activity in liver and pituitary homogenates. When added to homogenates, many analogs were as potent or more potent than PTU in inhibiting hepatic T4 5'-deiodinase activity. Three derivatives, 6-anilino-2-thiouracil (A compound), 6-(p-ethylanilino)2-thiouracil (B compound), and 6-(p-n-butylanilino) 2-thiouracil (C compound), which were among the most potent inhibitors of hepatic T4 5'-deiodinase, when added in vitro inhibited T4 5'-deiodinase activity in liver homogenates after in vivo administration. When added to pituitary homogenates prepared from hypothyroid rats, these compounds also significantly inhibited pituitary T4 5'-deiodinase activity. In a concentration of 1 mM in the presence of 20 mM dithiothreitol, the percent inhibition of pituitary T4 5'-deiodinase activity was 19.7 +/- 7.4 (mean +/- SE), 34.0 +/- 3.2, 47.3 +/- 3.1, and 89.0 +/- 1.0 for PTU and the A, B, and C compounds, respectively (P less than 0.05 for all groups vs. one another and vehicle). Despite their ability to inhibit hepatic T4 5'-deiodinase activity, none of the 13 analogs tested altered thyroid iodide uptake or organification after administration of 0.1 mg/rat. PTU, in the same dose, inhibited thyroid iodide uptake by 78.2 +/- 2.4% (P less than 0.001) and thyroid iodide organification by 36.4 +/- 7.3% (P less than 0.01). Furthermore, the A, B, and C compounds did not inhibit thyroid iodide uptake or iodide organification when administered in higher doses of 5, 5, and 1 mg/rat, respectively. In contrast to these in vivo results, the A, B, and C compounds were more potent than PTU in inhibiting iodide organification in a purified thyroid peroxidase system and in porcine thyroid slices. The concentrations causing 50% inhibition of iodide organification in the purified thyroid peroxidase system were 30, 7, 8, and 14 microM for PTU and the A, B, and C compounds, respectively. However, PTU was far more potent in inhibiting iodide organification in intact incubated thyroid lobes compared to the A, B, and C compounds.(ABSTRACT TRUNCATED AT 400 WORDS)
Immunological comparison of microbial TPP-dependent non-oxidative Î±-keto acid decarboxylases (1986)

Antigenic, and hence possible evolutionary, relationships amongst various TPP-dependent non-oxidative α-keto acid decarboxylases were determined by the Ouchterlony double diffusion method and by measuring the degree of antibody-induced enzyme inhibition. The results show that: (a) phenylglyoxylate decarboxylases of various wild-type strains of Acinetobacter calcoaceticus are antigenically indistinguishable; (b) there seems to be no antigenic cross-reactivity between the phenylglyoxylate decarboxylase of A. calcoaceticus and of Pseudomonas aeruginosa or Pseudomonas putida; and (c) no antigenic homology can be detected amongst phenylglyoxylate decarboxylase and phenylpyruvate decarboxylase of A. calcoaceticus and pyruvate decarboxylase of brewers' yeast.
Complete Reconstitution of the Human Coenzyme A Biosynthetic Pathway via Comparative Genomics (2002)

The biosynthesis of CoA from pantothenic acid (vitamin B5) is an essential universal pathway in prokaryotes and eukaryotes. The CoA biosynthetic genes in bacteria have all recently been identified, but their counterparts in humans and other eukaryotes remained mostly unknown. Using comparative genomics, we have identified human genes encoding the last four enzymatic steps in CoA biosynthesis: phosphopantothenoylcysteine synthetase (EC ), phosphopantothenoylcysteine decarboxylase (EC ), phosphopantetheine adenylyltransferase (EC ), and dephospho-CoA kinase (EC ). Biological functions of these human genes were verified using a complementation system in Escherichia coli based on transposon mutagenesis. The individual human enzymes were overexpressed in E. coli and purified, and the corresponding activities were experimentally verified. In addition, the entire pathway from phosphopantothenate to CoA was successfully reconstituted in vitro using a mixture of purified recombinant enzymes. Human recombinant bifunctional phosphopantetheine adenylyltransferase/dephospho-CoA kinase was kinetically characterized. This enzyme was previously suggested as a point of CoA biosynthesis regulation, and we have observed significant differences in mRNA levels of the corresponding human gene in normal and tumor cells by Northern blot analysis.
Computing with Neural Circuits: A Model (1986)

A new conceptual framework and a minimization principle together provide an understanding of computation in model neural circuits. The circuits consist of nonlinear graded-response model neurons organized into networks with effectively symmetric synaptic connections. The neurons represent an approximation to biological neurons in which a simplified set of important computational properties is retained. Complex circuits solving problems similar to those essential in biology can be analyzed and understood without the need to follow the circuit dynamics in detail. Implementation of the model with electronic devices will provide a class of electronic circuits of novel form and function.
Photosensitive impregnated porous glass (1983)

Porous glass, impregnated with photosensitive organometallic compounds such as transition metal carbonyls, demonstrates induced optical changes when exposed to light. Both optical absorption and refractive index changes can be induced and are permanent after heating. Examples of high resolution optical patterns produced by this process are shown.
Temperature dependence of minority and majority carrier mobilities in degenerately doped GaAs (1995)

Measured minority and majority carrier mobility temperature dependencies in heavily doped n- and p-GaAs are compared. Majority carrier mobilities in heavily doped GaAs are essentially temperature (T) independent while minority carrier mobilities exhibit a roughly 1/T dependence. Majority carrier freezeout, which reduces both majority–minority carrier and ionized impurity scattering, is shown not to be responsible for the 1/T minority carrier mobility dependence. The difference in minority and majority carrier mobility T dependencies is explained in terms of the increased degree of degeneracy of majority carriers with decreased temperature, which decreases majority–minority carrier scattering.
Antibody Engineering for the Development of Therapeutic Antibodies (2005)

Therapeutic antibodies represent one of the fastest growing areas of the pharmaceutical industry. There are currently 19 monoclonal antibodies in the market that have been approved by the FDA and over 150 in clinical developments. Driven by innovation and technological developments, therapeutic antibodies are the second largest biopharmaceutical product category after vaccines. Antibodies have been engineered by a variety of methods to suit a particular therapeutic use. This review describes the structural and functional characteristics of antibody and the antibody engineering for the generation and optimization of therapeutic antibodies.
Coding Macromolecules: Inputting Information in Polymers Using Monomer-Based Alphabets (2015)

International audience
DROPLET ANALYSIS WITH ELECTROSPRAY IONIZATION MASS SPEC- TROMETRY USING AN INTEGRATED GLASS MICROCHIP (2010)

We describe an integrated microchip for droplet analysis with electrospray ionization mass spectrometry (ESI-MS). The chip integrated multiple modules of droplet generator, droplet extraction interface, and monolithic ESI-emitter. A novel droplet extraction interface based on a hydrophilic tongue structure was developed to transfer droplet from segmented phase to aqueous phase with high reliability and high controllability. The performance was evaluated in the analysis of peptide angiotensin, and high sensitive and stable results were obtained. The present system was further applied to identify the product from peptide alkylation reaction in droplet, demonstrating its ability in online monitoring of actual droplet microreactions.
In vitro and in vivo activity of human recombinant granulocyte-macrophage colony-stimulating factor in dogs. (1990)

Although it is well documented that human granulocyte-macrophage colony-stimulating factor (GM-CSF) controls the production and functional activity of human and nonhuman primate granulocytes and macrophages, relatively little is known about its effects on cells obtained from other species. The molecular cloning of the complementary DNA for human GM-CSF has made it possible to determine the cross-reactivity of the purified recombinant human material (rhGM-CSF) on cells of other species. The results presented herein show that specific receptors for human GM-CSF exist on dog bone marrow cells and mature circulating dog granulocytes. The number of the receptors and the apparent binding affinity of the rhGM-CSF to its receptors on granulocytes were similar to those observed either on human or monkey cells. In cultures of dog bone marrow cells, rhGM-CSF was capable of promoting colony formation in a dose-dependent manner. Human GM-CSF also primed dog granulocytes for increased production of reactive oxygen metabolites in response to either phorbolmyristic acetate-or zymosan-activated dog serum. In vivo, s.c. administration to healthy dogs of rhGM-CSF in daily doses of 15, 50, or 150 micrograms/kg body weight over a period of 7-20 days induced a dose-dependent rise of up to a maximum of a fourfold increase in peripheral WBC counts. The rise in WBC counts was mainly due to elevated neutrophil levels, but an increase in the numbers of monocytes and eosinophils was also observed. However, the rhGM-CSF-induced leukocytosis in dogs was not as dramatic as that observed in nonhuman primates. In all rhGM-CSF-treated dogs, circulating platelet counts dropped to nadir levels of about 20%-30% of normal numbers. Dogs that were treated with 150 micrograms/kg rhGM-CSF developed specific antibodies after about 10-12 days of treatment. These antibodies were able to neutralize the effect of rhGM-CSF in in vitro assays. In vivo WBC counts began to decline when specific antibodies developed, but they never dropped below normal levels. Taken together, the results suggest that human GM-CSF does not appear to exhibit absolute species specificity.
Tree Matching Problems with Applications to Structured Text Databases (1992)

Tree matching is concerned with finding the instances, or matches, of a given pattern tree in a given target tree. We introduce ten interrelated matching problems called tree inclusion problems. A specific tree inclusion problem is defined by specifying the trees that are instances of the patterns. The problems differ from each other in the amount of similarity required between the patterns and their instances. We present and analyze algorithms for solving these problems, and show that the computational complexities of the problems range from linear to NP-complete. The problems are motivated by the study of query languages for structured text databases. The structure of a text document can be described by a context-free grammar, and text collections can be represented as collections of parse trees. Matching-based operations are an intuitive basis for accessing the contents of structured text databases. In &amp;quot;G-grammatical&amp;quot; tree inclusion problems the target tree is a parse tree over a co...
Expression of Thymosin beta4 in Murine Bone Marrow Endothelial Cells, HL-60 Cells and Human Peripheral Blood Mononuclear Cells. (2001)

To investigate the relationship between the growth situation of the cells and the expression level of thymosin beta4, the specific primer of thymosin beta4 was selected to test the expression of thymosin-beta gene in murine bone marrow endothelial cells in different proliferation states and in HL-60 cells and peripheral blood mononuclear cells by RT-PCR. The results showed that the expression level of thymosin beta4 in the murine bone marrow endothelial cells with active proliferation was high, otherwise it was low. The thymosin beta4 gene expression level was higher in HL-60 cells than that in human peripheral blood mononuclear cells. It was suggested that the expression level of thymosin beta4 mRNA is closely related to cell growth.
The Synthesis of the Sixteen Possible 2′-O-Methyl MMI Dimer Phosphoramidites: Building Blocks for the Synthesis of Novel Antisense Oligonucleotides (1997)

Abstract The synthesis of Methylene(methylimino) or MMI linked nucleoside dimers in all sixteen possible configurations has been accomplished via a reductive coupling of a nucleosidic aldehyde with an hydroxylamine. This has allowed us to prepare all of the necessary 2′-O-methyl MMI dimer building blocks necessary for use in an antisense motif.
Bipolar and tetrapolar transfer impedance measurementsfrom volume conductor (2000)

Bipolar and tetrapolar impedance measurements from a volume of biological tissue are compared. In the bipolar case, sensitivity is always positive and decreases with depth. However, for tetrapolar measurements the mean sensitivity is found to be zero over the surface plane, rising to a maximum at a depth proportional to electrode spacing.
Quantitative reverse transcription-polymerase chain reaction detection of cytokeratin 20 in noncolorectal lymph nodes. (2001)

These results characterize low-level, epithelial cell-specific CK20 expression in infiltrated lymph nodes from subjects with noncolorectal cancer types and demonstrate the potential advantages of detecting circulating epithelial cells by quantitative PCR.
Social structure of Risso’s dolphins (Grampus griseus) at the Azores: a stratified community based on highly associated social units (2008)

In this study, we present for the first time a model for the social structure of Risso’s dolphins ( Grampus griseus Cuvier, 1812). Over the period 2004–2006, 1028 Risso’s dolphins were identified at Pico island, Azores. Individuals sighted on 10 or more occasions were included in the analysis of social structure (n = 183). High resighting rates indicate strong site fidelity for at least part of the population. We found that individuals form stable, long-term bonds organised in pairs or in clusters of 3–12 individuals. Social structure is stratified based on age and sex classes, with strong associations between adult males and between adult females. We suggest that clusters form the basic units of Risso’s dolphin society. Thirteen pods consisting solely of adults, likely males, and 3 pods consisting of mother–calf pairs were identified. Males are organised in stable, long-term associations of varying size that occur throughout the complete range of behavioural states observed. For females, associations can be of similar strength, but the time scale may vary depending on the presence of nursing calves. As subadults, associations also occur (pair formation), but are less stable than those observed for adults. We propose a new model for Risso’s dolphin societies known as a stratified social organisation, which differs from the fission–fusion and matrilineal society models.
SYNTHESIS AND APPLICATION OF SOME NEW 5-SULFONYLHETEROCYCLO-8-QUINOLINOL DERIVATIVES (1992)

Abstract A new series of 5-(4′-arylidine-3′-methyl-5′-oxo-4′,5′-dihydropyrazol-1-yl-sulfonyl)-8-quinolinols (la-c) were prepared via the reaction of 5-(3′-methyl-5′-oxo-4′,5′-dihydropyrazol-l-yl-sulfonyl)-8-quinolinols with selected aldehydes. These compounds were condensed with hydrazine, hydroxylamine, urea and thiourea to give 5-(3′-methyl-5′-acetyl-4′-substituted pyrazolo-[3′,4′-c]pyrazol-l-yl-sulfonyl)-8-quinolinols (2a-c), 5-[3′-methyl-4′-substituted pyrazol-1-yl-sulfonyl-[3′,4′-c]isoxazolo-]quinolinols (3a-c) and 5-[3′-methyl-4′-substituted pyrazol-1-yl-sulfonyl[3′,4′-c]pyrimidine-6′ one (thione)]-8-quinolinols (4a-c, 5a-c) respectively. Metal chelate of 2a.b.d and 3a,b,d with Fe2+, Cu2+, Hg2+ have been synthesized and characterized by elemental and IR spectral analysis. The synthesized compounds were biologically screened in vitro to study the structure activity relationship and the effect of complexation and the type of metal cation on the more biologically active compounds.
Introns and gene expression: Cellular constraints, transcriptional regulation, and evolutionary consequences (2014)

A gene's "expression profile" denotes the number of transcripts present relative to all other transcripts. The overall rate of transcript production is determined by transcription and RNA processing rates. While the speed of elongating RNA polymerase II has been characterized for many different genes and organisms, gene-architectural features - primarily the number and length of exons and introns - have recently emerged as important regulatory players. Several new studies indicate that rapidly cycling cells constrain gene-architecture toward short genes with a few introns, allowing efficient expression during short cell cycles. In contrast, longer genes with long introns exhibit delayed expression, which can serve as timing mechanisms for patterning processes. These findings indicate that cell cycle constraints drive the evolution of gene-architecture and shape the transcriptome of a given cell type. Furthermore, a tendency for short genes to be evolutionarily young hints at links between cellular constraints and the evolution of animal ontogeny.
Lipid modifications of G protein subunits. (1991)

Myristoylated recombinant proteins can be synthesized in Escherichia coli by concurrent expression of the enzyme myristoyl-CoA:protein N-myristoyl-transferase with its protein substrates (Duronio, R.J., Jackson-Machelski, E., Heuckeroth, R.O., Olins, P. O., Devine, C.S., Yonemoto, W., Slice, L. W., Taylor, S. S., and Gordon, J. I. (1990) Proc. Natl. Acad. Sci. U. S.A. 87, 1506-1510). Expression of the G protein subunit Go alpha in this system results in the synthesis of two forms of the protein; these were separated on a column of heptylamine-Sepharose. Purification of the more abundant form of Go alpha yielded a product that has a blocked amino terminus. Chemical analysis of the fatty acids released by acid hydrolysis of the protein revealed myristic acid. The second form of the protein was not myristoylated. Myristoylated and nonmyristoylated recombinant Go alpha were compared with brain Go alpha (which is myristoylated) for their ability to interact with G protein beta gamma subunits. The nonmyristoylated recombinant protein clearly had a reduced affinity for beta gamma, while the myristoylated recombinant protein was indistinguishable from native Go alpha in its subunit interactions. Thus, myristoylation increases the affinity of alpha subunits for beta gamma. We propose that the function of myristoylation of G protein alpha subunits is, at least in part, to facilitate formation of the heterotrimer and the localization of alpha to the plasma membrane.