gebhart/patrepeval huggingface dataset:
A macrophage mRNA selectively induced by gamma-interferon encodes a member of the platelet factor 4 family of cytokines. (1990)

In order to identify novel mediators synthesized in activated macrophages, a cDNA library was prepared from cultures of the mouse macrophage cell line RAW 264.7 that had been treated with lymphokine-rich conditioned medium from mitogen-stimulated mouse spleen cells. Differential plaque hybridization identified a cDNA, designated m119, that detected a 1.6-kilobase mRNA that accumulated in response to gamma-interferon (IFN-gamma) but not in response to other macrophage activators, including IFN-alpha, IFN-beta, and lipopolysaccharide. The mRNA encoded a predicted protein of Mr 14,461 containing a 21-amino acid signal peptide. The primary structure of the predicted protein indicated that it is a member of a recently described family of cytokines related to platelet factor 4, including Gro/melanoma growth stimulatory activity and neutrophil-activating peptide/interleukin 8. The selective induction of the m119 mRNA by IFN-gamma that the predicted m119 protein mediates a macrophage activity regulated by IFN-gamma. The m119 protein may be a cytokine that affects the growth, movement, or activation state of cells that participate in immune and inflammatory responses. It is proposed that the gene encoding this protein be called mig, for monokine induced by gamma interferon.
Expression of the house dust mite allergen Der p 2 in the baker's yeast Saccharomyces cerevisiae (1998)

An expression system for Der p 2 was developed that enables the production of a soluble allergen in the culture supernatant with immunological characteristics similar to the natural allergen. In addition, yeast offers the advantage of the absence of endotoxin in comparison to E. coli. This might facilitate acceptance of recombinant allergens for in vivo applications as immunotherapy or skin-prick testing.
Novel Method for the Phase‐Transfer Catalyzed Sulfodechlorination of 1‐Chloro‐2,4‐dinitrobenzene (1981)

Mild conditions and very good yields typify the sulfodechlorination of 1‐chloro‐2,4‐dinitrobenzene with potassium disulfite to 2,4‐dinitrobenzoic acid in the presence of protonated tertiary amines as phase‐transfer catalysts; the yield and above all the purity of the product depends on the chain‐length of the alkyl moiety of the amine.
Concept, Strategies, and Feasibility of Noninvasive Insulin Delivery (2004)

Of all the approaches to date, pulmonary delivery appears to be most feasible. Ongoing phase III studies will ultimately determine safety, tolerability, and efficacy before approval for clinical use.
A phonotactic language model for spoken language identification (2005)

We have established a phonotactic language model as the solution to spoken language identification (LID). In this framework, we define a single set of acoustic tokens to represent the acoustic activities in the world's spoken languages. A voice tokenizer converts a spoken document into a text-like document of acoustic tokens. Thus a spoken document can be represented by a count vector of acoustic tokens and token n-grams in the vector space. We apply latent semantic analysis to the vectors, in the same way that it is applied in information retrieval, in order to capture salient phonotactics present in spoken documents. The vector space modeling of spoken utterances constitutes a paradigm shift in LID technology and has proven to be very successful. It presents a 12.4% error rate reduction over one of the best reported results on the 1996 NIST Language Recognition Evaluation database.
The Repeat Pattern Toolkit (RPT): analyzing the structure and evolution of the C. elegans genome. (1994)

Over 3.6 million bases of DNA sequence from chromosome III of the C. elegans have been determined. The availability of this extended region of contiguous sequence has allowed us to analyze the nature and prevalence of repetitive sequences in the genome of a eukaryotic organism with a high gene density. We have assembled a Repeat Pattern Toolkit (RPT) to analyze the patterns of repeats occurring in DNA. The tools include identifying significant local alignments (utilizing both two-way and three-way alignments), dividing the set of alignments into connected components (signifying repeat families), computing evolutionary distance between repeat family members, constructing minimum spanning trees from the connected components, and visualizing the evolution of the repeat families. Over 7000 families of repetitive sequences were identified. The size of the families ranged from isolated pairs to over 1600 segments of similar sequence. Approximately 12.3% of the analyzed sequence participates in a repeat element.
Keratinocyte–Melanocyte Interactions During Melanosome Transfer (2001)

The epidermal-melanin unit is composed of one melanocyte and approximately 36 neighboring keratinocytes, working in synchrony to produce and distribute melanin. Melanin is synthesized in melanosomes, transferred to the dendrite tips, and translocated into keratinocytes, forming caps over the keratinocyte nuclei. The molecular and cellular mechanisms involved in melanosome transfer and the keratinocyte-melanocyte interactions required for this process are not yet completely understood. Suggested mechanisms of melanosome transfer include melanosome release and endocytosis, direct inoculation ('injection'), keratinocyte-melanocyte membrane fusion, and phagocytosis. Studies of the keratinocyte receptor protease-activated receptor-2 (PAR-2) support the phagocytosis theory. PAR-2 controls melanosome ingestion and phagocytosis by keratinocytes and exerts a regulatory role in skin pigmentation. Modulation of PAR-2 activity can enhance or decrease melanosome transfer and affects pigmentation only when there is keratinocyte-melanocyte contact. Moreover, PAR-2 is induced by UV irradiation and inhibition of PAR-2 activation results in the prevention of UVB-induced tanning. The role of PAR-2 in mediating UV-induced responses remains to be elucidated.
Immunoglobulin domain interface exchange as a platform technology for the generation of Fc heterodimers and bispecific antibodies (2017)

Bispecific antibodies (bsAbs) are of significant importance to the development of novel antibody-based therapies, and heavy chain (Hc) heterodimers represent a major class of bispecific drug candidates. Current technologies for the generation of Hc heterodimers are suboptimal and often suffer from contamination by homodimers posing purification challenges. Here, we introduce a new technology based on biomimicry wherein the protein-protein interfaces of two different immunoglobulin (Ig) constant domain pairs are exchanged in part or fully to design new heterodimeric domains. The method can be applied across Igs to design Fc heterodimers and bsAbs. We investigated interfaces from human IgA CH3, IgD CH3, IgG1 CH3, IgM CH4, T-cell receptor (TCR) α/β, and TCR γ/δ constant domain pairs, and we found that they successfully drive human IgG1 CH3 or IgM CH4 heterodimerization to levels similar to or above those of reference methods. A comprehensive interface exchange between the TCR α/β constant domain pair and the IgG1 CH3 homodimer was evidenced by X-ray crystallography and used to engineer examples of bsAbs for cancer therapy. Parental antibody pairs were rapidly reformatted into scalable bsAbs that were free of homodimer traces by combining interface exchange, asymmetric Protein A binding, and the scFv × Fab format. In summary, we successfully built several new CH3- or CH4-based heterodimers that may prove useful for designing new bsAb-based therapeutics, and we anticipate that our approach could be broadly implemented across the Ig constant domain family. To our knowledge, CH4-based heterodimers have not been previously reported.
Alkali-Swellable and Alkali-Soluble Thickener Technology (1989)

Carboxyl-containing copolymers that are prepared by the addition polymerization of ethylenically unsaturated monomers and that swell or solubilize to thicken aqueous media on neutralization are commonly referred to as alkali-swellable or alkali-soluble thickeners (ASTs collectively). These thickeners are broadly classified as either conventional (presumably nonassociative) or associative, depending on their chemical architecture and dominant mechanism of thickening. ASTs prepared by emulsion polymerization and supplied in latex form have received the greatest commercial acceptance. These polymers consist of conventional alkali-swellable or -soluble emulsions (ASE) and those that are classified associative by hydrophobe modification (hydrophobically modified alkali-swellable or -soluble emulsions, HASE). This review examines various aspects of AST technology, including chemical composition, thickening mechanisms, methods of polymerization, and factors affecting the swelling and dissolution behavior of these polymers.
Biosynthesis of asparagine-linked oligosaccharides in Saccharomyces cerevisiae: the alg2 mutation (1993)

In the yeast Saccharomyces cerevisiae, the alg2 mutation causes temperature-sensitive growth and abnormal accumulation of the lipid-linked oligosaccharide Man2GlcNAc2-PP-Dol (Jackson et al., Arch. Biochem. Biophys., 272, 203-209, 1989; Huffaker and Robbins, Proc. Natl. Acad. Sci. USA, 80, 7466-7470, 1983). A gene having the function and genomic location of ALG2 was cloned from libraries based on the multicopy plasmid YEp24 and on the centromere plasmid YCp50. Alg2 mutants transformed with plasmids containing ALG2 regained the capacity to grow and to synthesize lipid-linked oligosaccharides normally at the previously non-permissive temperature. ALG2 was essential for viability in haploid and diploid yeast. The ALG2 gene was transcribed into a single mRNA of 1.7 kb in size. The stability of ALG2 mRNA, assessed after thermal inactivation of RNA polymerase II in an rpb1-1 mutant (Herrick et al., Mol. Cell. Biol., 10, 2269-2284, 1990) was very low, with a t1/2 of < 5 min. The ALG2 transcript accumulation was growth dependent, and it was at least an order of magnitude lower in stationary phase cells compared to exponentially growing cells. The putative translation product of ALG2 contained a potential dolichol recognition domain similar to that found in all three glycosyltransferases of the lipid-linked pathway that have been sequenced.(ABSTRACT TRUNCATED AT 250 WORDS)
Characterization of a β-Actin mRNA Zipcode-Binding Protein (1997)

Localization of beta-actin mRNA to the leading edge of fibroblasts requires the presence of conserved elements in the 3' untranslated region of the mRNA, including a 54-nucleotide element which has been termed the "zipcode" (E. Kislauskis, X. Zhu, and R. H. Singer, J. Cell Biol. 127:441-451, 1994). In order to identify proteins which bind to the zipcode and possibly play a role in localization, we performed band-shift mobility assays, UV cross-linking, and affinity purification experiments. A protein of 68 kDa was identified which binds to the proximal (to the coding region) half of the zipcode with high specificity (ZBP-1). Microsequencing provided unique peptide sequences of approximately 15 residues each. Degenerate primers corresponding to the codons derived from the peptides were synthesized and used for PCR amplification. Screening of a chicken cDNA library resulted in isolation of several clones providing a DNA sequence encoding a 67.7-kDa protein with regions homologous to several RNA-binding proteins, such as hnRNP E1 and E2, and with consensus mRNA recognition motif with RNP1 and 2 motifs and a putative REV-like nuclear export signal. Antipeptide antibodies were raised in rabbits which bound to ZBP-1 and coimmunoprecipitated proteins of 120 and 25 kDa. The 120-kDa protein was also obtained by affinity purification with the RNA zipcode sequence, along with a 53-kDa protein, but the 25-kDa protein appeared only in immunoprecipitations. Mutation of one of the conserved sequences within the zipcode, an ACACCC element in its proximal half, greatly reduced its protein binding and localization properties. These data suggest that the 68-kDa ZBP-1 we have isolated and cloned is an RNA-binding protein that functions within a complex to localize beta-actin mRNA.
Calcium Phosphate Transfection (1999)

This unit contains two methods of calcium phosphate-based eukaryotic cell transfection, protocols that can be used for both transient and stable transfections. In the protocols, plasmid DNA is introduced to monolayer cell cultures via a precipitate that adheres to the cell surface. The Basic Protocol uses a HEPES-buffered solution to form a calcium phosphate precipitate that is directly layered onto the cells. In the alternate high-efficiency method, a BES-buffered system is used that allows the precipitate to form gradually in the medium and is then dropped onto the cells. The alternate method is particularly efficient for stable transformation of cells with circular plasmid DNA, and may be helpful with linear or genomic DNA. Both methods of transfection require very high-quality plasmid DNA, which can be prepared as described in the second Support Protocol. Transfection efficiency in some cell lines can be increased by shocking the cells with glycerol or dimethyl sulfoxide (DMSO) as described in the first Support Protocol.
Mesenteric Vasodilation Mediated by Endothelial Anandamide Receptors (1999)

Cannabinoids, including the endogenous ligand anandamide (arachidonyl ethanolamide), elicit pronounced hypotension in rats via activation of peripherally located CB1 cannabinoid receptors, which have been also implicated in endotoxin (lipopolysaccharide [LPS])-induced hypotension. The present study was designed to test the role of vascular CB1 receptors in cannabinoid- and endotoxin-induced mesenteric vasodilation. In the isolated, buffer-perfused rat mesenteric arterial bed precontracted with phenylephrine, anandamide induced long-lasting (up to 60 minutes) dose-dependent vasodilation (ED50: 79+/-3 nmol; maximal relaxation: 77+/-2%), inhibited by 0.5 to 5.0 micromol/L of the selective CB1 receptor antagonist SR141716A. Low doses of the calcium ionophore ionomycin also caused mesenteric vasodilation inhibited by SR141716A. The metabolically stable analogue R-methanandamide elicited mesenteric vasodilation (ED50: 286+/-29 nmol), whereas the potent synthetic CB1 receptor agonists WIN 55212-2 and HU-210 caused no change in vascular tone or only a minor dilator effect not affected by SR141716A, respectively. The endogenous ligand 2-arachidonyl glycerol caused no change in vascular tone, whereas Delta9-tetrahydrocannabinol and arachidonic acid caused mesenteric vasoconstriction. After endothelial denudation, the dilator response to anandamide was slightly reduced and was no longer inhibited by SR141716A. In preparations from LPS-pretreated rats, SR141716A alone caused a significant and prolonged increase in perfusion pressure, whereas it had no such effect in control preparations perfused in vitro with or without LPS or after endothelial denudation in preparations from rats pretreated with LPS. We conclude that anandamide-induced mesenteric vasodilation is mediated by an endothelially located SR141716A-sensitive "anandamide receptor" distinct from CB1 cannabinoid receptors and that activation of such receptors by an endocannabinoid, possibly anandamide, contributes to LPS-induced mesenteric vasodilation in vivo.
Review article: the role of butyrate on colonic function (2007)

Although most studies point towards beneficial effects of butyrate, more human in vivo studies are needed to contribute to our current understanding of butyrate-mediated effects on colonic function in health and disease.
Beat radiation from dipoles near a photonic band edge (1993)

We consider a model for two nearly identical, slightly detuned dipoles that radiate in frequency near a photonic band edge such that one dipole is in the band while the other is in the gap. The dipole in the gap does not radiate directly, but its presence can be detected by beats that occur in the power output of the dipole that is in the band. Hence it is possible to detect properties of and perhaps to excite gap dipoles if they are coupled by local modes to dipoles that are located in the frequency band.
Nuclear magnetic resonance studies of the protonation sequence of some oxaaza macrocyclic compounds (1990)

The sequences of protonation of a series of oxatriaza and dioxadiaza macrocyclic compounds have been studied by 1H and 13C n.m.r. spectroscopy. It is shown that Sudmeier and Reilley's quantitative approach to derive sequences of protonation suffers from several limitations when applied to these (and other) polyaza macrocycles due to the lack of suitable models, but the indications directly provided by the corresponding potentiometric and n.m.r. titration curves may complement the information required for this purpose. The results obtained suggest that the 12-membered oxatriaza and dioxadiaza macrocycles adopt different and more compact conformations when the nitrogen atoms are derivatized (e.g. with methyl or acetate groups); this results in stronger electrostatic repulsions of consecutive protonated nitrogen atoms of the ring, leading to changeable base strength and to protonation–deprotonation steps that produce ‘anomalous’ n.m.r. titration curves. In the case of the N-acetate derivatives, the interpretation of the trends is further complicated by the possibility of formation of CO2–⋯ HN+ intramolecular hydrogen bonds. The data now available make it possible to predict approximate values for the protonation constants of the various basic centres for the 12-membered polyoxapolyaza macrocycles and, consequently, the corresponding percentages of protonation at different pH values.
The discovery of mRNA interferases: Implication in bacterial physiology and application to biotechnology (2006)

Escherichia coli contains a large number of suicide or toxin genes, whose expression leads to cell growth arrest and eventual cell death. This raises intriguing questions as to why E. coli contains so many toxin genes and what are their roles in bacterial physiology. Among these, MazF has been shown to be a sequence-specific endoribonuclease, which cleaves mRNAs at ACA sequences to completely inhibit protein synthesis. MazF is therefore called mRNA interferase. A number of other mRNA interferases with different cleavage specificities have been discovered not only in E. coli, but also in other bacteria including Mycobacterium tuberculosis. Induction of MazF in the cell leads to cellular dormancy termed quasi-dormancy. In spite of complete cell growth inhibition, cells in the quasi-dormant state are fully capable of energy metabolism, amino acids and nucleic acids biosynthesis and RNA and protein synthesis. The quasi-dormancy may be implicated in cell survival under stress conditions and may play a major role in pathogenicity of M. tuberculosis. The quasi-dormant cells provide an intriguing novel biotechnological system producing only a protein of interest in a high yield. MazF causing Bak-dependent programmed cell death in mammalian cells may be used as a tool for gene therapy against cancer and AIDS. The discovery of a novel way to interfere with mRNA function by mRNA interferases opens a wide variety of avenues in basic as well as applied and clinical sciences.
A Programmable 512 GOPS Stream Processor for Signal, Image, and Video Processing (2008)

A 34-million transistor stream processor system-on-chip (SoC) for signal, image, and video processing contains 80 parallel integer ALUs organized into 16 data-parallel lanes with a 5-ALU VLIW per lane, two CPU cores, and I/Os. Implemented in a 0.13 <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">mu</i> m CMOS technology, sixteen 800 MHz data-parallel lanes combine to deliver performance of 512 8-bit GOPS or 256 16-bit GOPS, or 128 billion 16-bit multiply-accumulates per second GMACs), with a power efficiency of 82 pJ/MAC.
A continuous skeletonization method based on level sets (2002)

A robust and efficient method in 2D and 3D for the calculation of skeletons for arbitrary objects is presented. The method is based on the calculation of the distance function with respect to the object boundary. This is combined, in a post processing step, with a new indicator to identify the skeleton, which coincides with the singularity set of the distance map. The indicator is defined as a suitable function of certain local momenta of this distance map and allows a robust and accurate computation of the distance from the skeleton set. This distance is then extended, again via the level set method, onto the whole space. Several applications in 2D and 3D are presented.
Integrins can collaborate with growth factors for phosphorylation of receptor tyrosine kinases and MAP kinase activation: roles of integrin aggregation and occupancy of receptors. (1996)

Integrins mediate cell adhesion, migration, and a variety of signal transduction events. These integrin actions can overlap or even synergize with those of growth factors. We examined for mechanisms of collaboration or synergy between integrins and growth factors involving MAP kinases, which regulate many cellular functions. In cooperation with integrins, the growth factors EGF, PDGF-BB, and basic FGF each produced a marked, transient activation of the ERK (extracellular signal-regulated kinase) class of MAP kinase, but only if the integrins were both aggregated and occupied by ligand. Transmembrane accumulation of total tyrosine-phosphorylated proteins, as well as nonsynergistic MAP kinase activation, could be induced by simple integrin aggregation, whereas enhanced transient accumulation of the EGF-receptor substrate eps8 required integrin aggregation and occupancy, as well as EGF treatment. Each type of growth factor receptor was itself induced to aggregate transiently by integrin ligand-coated beads in a process requiring both aggregation and occupancy of integrin receptors, but not the presence of growth factor ligand. Synergism was also observed between integrins and growth factors for triggering tyrosine phosphorylation of EGF, PDGF, and FGF receptors. This collaborative response also required both integrin aggregation and occupancy. These studies identify mechanisms in the signal transduction response to integrins and growth factors that require various combinations of integrin aggregation and ligands for integrin or growth factor receptors, providing opportunities for collaboration between these major regulatory systems.
Use-Dependent Effects of Amyloidogenic Fragments of β-Amyloid Precursor Protein on Synaptic Plasticity in Rat HippocampusIn Vivo (2001)

The Alzheimer's disease-related beta-amyloid precursor protein (beta-APP) is metabolized to a number of potentially amyloidogenic peptides that are believed to be pathogenic. Application of relatively low concentrations of the soluble forms of these peptides has previously been shown to block high-frequency stimulation-induced long-term potentiation (LTP) of glutamatergic transmission in the hippocampus. The present experiments examined how these peptides affect low-frequency stimulation-induced long-term depression (LTD) and the reversal of LTP (depotentiation). We discovered that beta-amyloid peptide (Abeta1-42) and the Abeta-containing C -terminus of beta-APP (CT) facilitate the induction of LTD in the CA1 area of the intact rat hippocampus. The LTD was frequency- and NMDA receptor-dependent. Thus, although low-frequency stimulation alone was ineffective, after intracerebroventricular injection of Abeta1-42, it induced an LTD that was blocked by d-(-)-2-amino-5-phosphonopentanoic acid. Furthermore, an NMDA receptor-dependent depotentiation was induced in a time-dependent manner, being evoked by injection of CT 10 min, but not 1 hr, after LTP induction. These use- and time-dependent effects of the amyloidogenic peptides on synaptic plasticity promote long-lasting reductions in synaptic strength and oppose activity-dependent strengthening of transmission in the hippocampus. This will result in a profound disruption of information processing dependent on hippocampal synaptic plasticity.