gebhart/patrepeval huggingface dataset:
Studies on the recovery of crown gall tumor cells (1976)

Our previous studies have shown that, while a persistent but potentially reversible suppression of the tumorous state appears to be a characteristic feature of the vegetative phase of teratoma shoot growth in the crown gall disease of plants, a recovery from that state occurs during the reproductive phase. An analysis has now been made of the reproductive process in an attempt to define the precise stage at which recovery occurs. The results of this analysis have shown that diploid somatic cells of teratoma-derived flower parts such as those found in petals and filaments are inherently neoplastic. On the other hand, haploid cells of plants grown from anthers of the same flowers and diploid cells of F(1) generation plants grown from teratoma-derived seed have, by generally accepted criteria, recovered from the tumorous state. These findings have been interpreted to mean that the loss of neoplastic properties occurs in crown gall teratoma cells during meiosis rather than during fertilization or later stages of the reproductive process.An analysis of more than 2000 teratoma-derived tumor shoots has shown, moreover, that a recovery from the tumorous state may also occur, although apparently as a very rare event, during the vegetative phase of teratoma shoot growth.
Metabolic syndrome without obesity: Hepatic overexpression of 11β-hydroxysteroid dehydrogenase type 1 in transgenic mice (2004)

In obese humans and rodents there is increased expression of the key glucocorticoid (GC) regenerating enzyme, 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1), in adipose tissue. This increased expression appears to be of pathogenic importance because transgenic mice overexpressing 11beta-HSD1 selectively in adipose tissue exhibit a full metabolic syndrome with visceral obesity, dyslipidemia, insulin-resistant diabetes, and hypertension. In this model, while systemic plasma GC levels are unaltered, GC delivery to the liver via the portal vein is increased. 11beta-HSD1 is most highly expressed in liver where inhibition or deficiency of its activity improves glucose and lipid homeostasis. To determine the potential contribution of elevated intrahepatic GCs alone toward development of insulin-resistant syndromes we generated transgenic mice expressing increased 11beta-HSD1 activity selectively in the liver under transcriptional control of hepatic regulatory sequences derived from the human apoE gene (apoE-HSD1). Transgenic lines with 2- and 5-fold-elevated 11beta-HSD1 activity exhibited mild insulin resistance without altered fat depot mass. ApoE-HSD1 transgenic mice exhibited fatty liver and dyslipidemia with increased hepatic lipid synthesis/flux associated with elevated hepatic LXRalpha and PPARalpha mRNA levels as well as impaired hepatic lipid clearance. Further, apoE-HSD1 transgenic mice have a marked, transgene-dose-associated hypertension paralleled by incrementally increased liver angiotensinogen expression. These data suggest that elevated hepatic expression of 11beta-HSD1 may relate to the pathogenesis of specific fatty liver, insulin-resistant, and hypertensive syndromes without obesity in humans as may occur in, for example, myotonic dystrophy, and possibly, the metabolically obese, normal-weight individual.
Copepods as microbial hotspots in the ocean: effects of host feeding activities on attached bacteria (2005)

Through ingestion a copepod introduces rich organic substrates into its guts and fecal pellets, where dense bacteria may exploit them and show fast growth. Thus, a copepod and its fecal pellets may be regarded as microbial hotspots in the ocean. This study investigated the effects of copepods' feeding activities on the associated bacteria, using the Most Probable Number (MPN) method. Starved Acartia tonsa (calanoid copepod) carried a background bacteria population of 10 3 to 10 4 copepod -1 . When fed axenic cultures of algae Rhodomonas salina or Dunaliella tertiolecta, the bacterial abundance increased curvilinearly with the copepods' ingestion rates. When fed axenic cultures of diatom Thalassiosira weissflogii, the bacterial abundance showed a hump-shaped response to the ingestion rate. These observations support a conceptual model of a balance between bacteria growth stimulated by the host's feeding and bacteria loss through the host's defecation. The equivalent bacterial population density associated with the copepods was orders of magnitude higher than typical population density of marine free-living bacteria. In a time series experiment, bacteria inside the copepods' bodies increased significantly after 3 d of feeding, and the estimated bacterial growth rate was 0.89 d -1 , higher than the average growth rate for free-living pelagic bacteria. The copepods released a significant amount of bacteria via defecation when food was present, and the equivalent bacterial abundance associated with fecal pellets was 6.5 10 8 bacteria ml -1 . Bacteria recovered from A. tonsa feeding on different diets showed different growth kinetics in enrichment cultures, suggesting that diet types may be a selective force for different bacterial communities inside the host's body.
Human cellular immune response to copolymer I and myelin basic protein (1986)

Copolymer I (Cop I) is being tested as a treatment for MS because it protects animals against experimental allergic encephalomyelitis, and because there is immunologic cross-reactivity reported between Cop I and myelin basic protein (MBP). From the peripheral blood mononuclear cells of four normal individuals, we isolated helper-phenotype T-cell lines that reacted in vitro with Cop I or MBP. Cop I-reactive cell lines did not respond to MBP, nor did MBP-reactive T-cell lines respond to Cop I. Antigen-specific immune tolerance was induced in MBP-reactive cell lines by exposure to MBP in vitro, but similar exposure to Cop I did not induce tolerance in the MBP-reactive cell lines. We found no evidence of immunologic cross-reactivity between Cop I and MBP.
The Interaction of the Transforming Growth Factor-βs with Heparin/Heparan Sulfate Is Isoform-specific (1997)

We have undertaken a comparative study of the interaction of the three mammalian transforming growth factor-betas (TGF-beta) with heparin and heparan sulfate. TGF-beta1 and -beta2, but not -beta3, bind to heparin and the highly sulfated liver heparan sulfate. These polysaccharides potentiate the biological activity of TGF-beta1 (but not the other isoforms), whereas a low sulfated mucosal heparan sulfate fails to do so. Potentiation is due to antagonism of the binding and inactivation of TGF-beta1 by alpha2-macroglobulin, rather than by modulation of growth factor-receptor interactions. TGF-beta2.alpha2-macroglobulin complexes are more refractory to heparin/heparan sulfate, and those involving TGF-beta3 cannot be affected. Comparison of the amino acid sequences of the TGF-beta isoforms strongly implicates the basic amino acid residue at position 26 of each monomer as being a vital binding determinant. A model is proposed in which polysaccharide binding occurs at two distinct sites on the TGF-beta dimer. Interaction with heparin and liver heparan sulfate may be most effective because of the ability of the dimer to co-operatively engage two specific sulfated binding sequences, separated by a distance of approximately seven disaccharides, within the same chain.
A Lightweight Formation Control Methodology for a Swarm of Non-Holonomic Vehicles (2006)

Multi-vehicle swarms offer the potential for increased performance and robustness in several key robotic and autonomous applications. Emergent swarm behavior demonstrated in biological systems show performance that far outstrips the abilities of the individual members. This paper discusses a lightweight formation control methodology using conservative potential functions to ensure group cohesion, yet requiring very modest communication and control requirements for each individual node. Previous efforts have demonstrated distributed methods to navigate a vehicle swarm through a complex obstacle environment while remaining computationally simple and having low bandwidth requirements. It is shown that arbitrary formation can be held and morphed within the lightweight framework. Simulations of the lightweight framework applied to realistic non-holonomic tricycle vehicles highlight the swarm's ability to form arbitrary formations from random initial vehicle distributions and formation morphing capabilities, as well as navigate complex obstacle fields while maintaining formation. The non-holonomic constraints are used to implement realistic controls
Membrane Association and Epitope Recognition by HIV-1 Neutralizing Anti-gp41 2F5 and 4E10 Antibodies (2006)

It has been proposed that HIV-1-neutralizing 2F5 and 4E10 monoclonal antibodies recognize gp41 ectodomain pretransmembrane sequences in the context of the membrane interface. With the aim of evaluating lipid-bilayer surface effects on recognition, we use phospholipid model systems to investigate the ability of 2F5 and 4E10 to transfer into membrane interfaces and bind epitope sequences immersed therein. The experimental data support the predicted tendencies for partitioning and recognition of membrane-bound epitopes, albeit with lower affinity in the case of 2F5. Our findings support the existence of two different recognition mechanisms at membrane surfaces: the association of 2F5 with the interface possibly prevents epitope immersion into the bilayer, and 4E10 membrane association might allow recognition of the membrane-bound epitope. We discuss the relevance of these observations for the design of immunogens aimed at eliciting 2F5- and 4E10- like humoral responses.
Placenta as a Source of ‘Brain’ and ‘Pituitary’ Hormones (1982)

Placental peptides, such as human chorionic gonadotropin (hCG) and human placental lactogen (hPL), which have marked homologies to pituitary peptides, were described in the early part of this century. Recently, the presence in placenta of additional peptides previously demonstrated as occurring in other tissues, such as brain and pituitary, has been reported. Their presence in placenta has been attributed to similar embryological origin of the tissues which share these peptides, although this has by no means been proven. Placental concentrations of these recently described peptides are several orders of magnitude lower than described for their original sites of production. In many instances, definitive characterization of structural identity with their extraplacental counterparts has not been performed, but has been based on indirect evidence obtained by immunoassay or immunocytochemistry. Evidence of placental synthesis has been obtained for hCG, hPL, and pro-opiomelanocortin (the precursor molecule for adrenocorticotropic hormone (ACTH), B-lipotropin (B-LPH), alpha-melanocyte-stimulating hormone (alpha-MSH), beta-endorphin, and other thus far uncharacterized peptides). Possible functions for the recently described peptides might include actions on the maternal or fetal systems or local (paracrine) actins affecting other placental constituents, although to date no definitive physiological roles have been demonstrated.
miRBase: microRNA sequences, targets and gene nomenclature (2005)

The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets. miRBase takes over functionality from the microRNA Registry and fulfils three main roles: the miRBase Registry acts as an independent arbiter of microRNA gene nomenclature, assigning names prior to publication of novel miRNA sequences. miRBase Sequences is the primary online repository for miRNA sequence data and annotation. miRBase Targets is a comprehensive new database of predicted miRNA target genes. miRBase is available at http://microrna.sanger.ac.uk/.
Dantrolene Enhances Antisense-Mediated Exon Skipping in Human and Mouse Models of Duchenne Muscular Dystrophy (2012)

Duchenne muscular dystrophy (DMD) causes profound and progressive muscle weakness and loss, resulting in early death. DMD is usually caused by frameshifting deletions in the gene DMD, which leads to absence of dystrophin protein. Dystrophin binds to F-actin and components of the dystrophin-associated glycoprotein complex and protects the sarcolemma from contraction-induced injury. Antisense oligonucleotide-mediated exon skipping is a promising therapeutic approach aimed at restoring the DMD reading frame and allowing expression of an intact dystrophin glycoprotein complex. To date, low levels of dystrophin protein have been produced in humans by this method. We performed a small-molecule screen to identify existing drugs that enhance antisense-directed exon skipping. We found that dantrolene, currently used to treat malignant hyperthermia, potentiates antisense oligomer-guided exon skipping to increase exon skipping to restore the mRNA reading frame, the sarcolemmal dystrophin protein, and the dystrophin glycoprotein complex in skeletal muscles of mdx mice when delivered intramuscularly or intravenously. Further, dantrolene synergized with multiple weekly injections of antisense to increase muscle strength and reduce serum creatine kinase in mdx mice. Dantrolene similarly promoted antisense-mediated exon skipping in reprogrammed myotubes from DMD patients. Ryanodine and Rycal S107, which, like dantrolene, targets the ryanodine receptor, also promoted antisense-driven exon skipping, implicating the ryanodine receptor as the critical molecular target.
Probiotic isolates from unconventional sources: a review (2016)

The use of probiotics for human and animal health is continuously increasing. The probiotics used in humans commonly come from dairy foods, whereas the sources of probiotics used in animals are often the animals' own digestive tracts. Increasingly, probiotics from sources other than milk products are being selected for use in people who are lactose intolerant. These sources are non-dairy fermented foods and beverages, non-dairy and non-fermented foods such as fresh fruits and vegetables, feces of breast-fed infants and human breast milk. The probiotics that are used in both humans and animals are selected in stages; after the initial isolation of the appropriate culture medium, the probiotics must meet important qualifications, including being non-pathogenic acid and bile-tolerant strains that possess the ability to act against pathogens in the gastrointestinal tract and the safety-enhancing property of not being able to transfer any antibiotic resistance genes to other bacteria. The final stages of selection involve the accurate identification of the probiotic species.
Multimodal Input in the Car, Today and Tomorrow (2011)

With the increased functionality offered by in-vehicle systems, multimodal input is emerging as an effective means of interaction to minimize driver distraction. This article describes the current state of this technology for automotive applications, various ways to combine modalities, and outlooks toward the future.
Les chaînes de référence dans les portraits journalistiques : éléments de description (2006)

Résumé À partir d’un corpus constitué d’une quarantaine de portraits extraits du quotidien Le Monde , cet article montre que l’expression de la référence ne s’y conforme pas aux prédictions de la théorie de l’accessibilité ou la théorie du centrage. À la suite de certains auteurs, on suggère que le genre textuel conditionne fortement les modalités de la cohésion référentielle. L’inventaire et le dénombrement des SN référentiels permet en effet de distinguer, selon leur matériau grammatical et lexical, deux types de chaînes, dont les unités répondent à des principes d’alternance particuliers. Il s’agit notamment de dégager les contraintes lexicales et discursives qui pèsent sur l’emploi des SN définis, très nombreux, en tenant compte du contexte « droit » de leur occurrence.
Toward self‐assembling dendritic macromolecules from conventional monomers by a combination of living radical polymerization and irreversible terminator multifunctional initiator (2003)

Abstract TERMINI stands for irreversible terminator multifunctional initiator and represents a new concept elaborated in our laboratory for the design of novel macromolecules with complex architecture from a diversity of commercial monomers. TERMINI is a masked multifunctional initiator that quantitatively interrupts a living polymerization. After demasking, the TERMINI‐derived repeat unit provides access to a quantitative reinitiation of the same living polymerization in more than one direction, thus becoming a branching point. In this article, with a combination of self‐regulated metal‐catalyzed living radical polymerization and TERMINI, we demonstrate a new method for the divergent synthesis of dendritic poly(methyl methacrylate) containing a bifunctional core at its focal point. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 505–513, 2004
Production of sophorolipid biosurfactants by multiple species of the Starmerella (Candida) bombicola yeast clade (2010)

Sophorolipids are carbohydrate-based, amphiphilic biosurfactants that are of increasing interest for use in environmentally benign cleaning agents. Sophorolipid production was tested for 26 strains representing 19 species of the Starmerella yeast clade, including Starmerella bombicola and Candida apicola, which were previously reported to produce sophorolipids. Five of the 19 species tested showed significant production of sophorolipids: S. bombicola, C. apicola, Candida riodocensis, Candida stellata and a new species, Candida sp. NRRL Y-27208. A high-throughput matrix-assisted laser desorption/ionization-time of flight MS assay was developed that showed S. bombicola and C. apicola to produce a lactone form of sophorolipid, whereas C. riodocensis, C. stellata and Candida sp. NRRL Y-27208 produced predominantly free acid sophorolipids. Phylogenetic analysis of sequences for the D1/D2 domains of the nuclear large subunit rRNA gene placed all sophorolipid-producing species in the S. bombicola subclade of the Starmerella clade.
Preferential neuronal loss in layer III of the medial entorhinal cortex in rat models of temporal lobe epilepsy (1995)

We recently described a pronounced neuronal loss in layer III of the entorhinal cortex (EC) in patients with intractable temporal lobe epilepsy (Du et al., 1993a). To explore the pathophysiology underlying this distinct neuropathology, we examined the EC in three established rat models of epilepsy using Nissl staining and parvalbumin immunohistochemistry. Adult male rats were either electrically stimulated in the ventral hippocampus for 90 min or injected with kainic acid or lithium/pilocarpine. Animals were observed for behavioral changes for up to 6 hr and were killed 24 hr or 4 weeks after the experimental treatments. At 24 hr, all animals that had exhibited a bout of acute status epilepticus showed a consistent pattern of neuronal loss in the EC in Nissl-stained sections. Neurodegeneration was most pronounced in layer III of the medial Ec at all dorsoventral levels. A few surviving neurons were frequently present in the lesioned area. An identical pattern of nerve cell loss was also seen in the EC of rats killed 4 weeks following the treatments. This lesion was completely prevented by an injection of diazepam and pentobarbital, given 1 hr after kainic acid administration. Immunohistochemistry demonstrated a relative resistance of parvalbumin-positive neurons in layer III of the medial EC. Taken together, these experiments indicate that prolonged seizures cause a preferential neuronal loss in layer III of the medial EC and that this lesion may be related to a pathological elevation of intracellular calcium ion concentrations.
Brain-specific deletion of neuropathy target esterase/ swisscheese results in neurodegeneration (2004)

Neuropathy target esterase (NTE) is a neuronal membrane protein originally identified for its property to be modified by organo-phosphates (OPs), which in humans cause neuropathy characterized by axonal degeneration. Drosophila mutants for the homolog gene of NTE, swisscheese (sws), indicated a possible involvement of sws in the regulation of axon-glial cell interaction during glial wrapping. However, the role of NTE/sws in mammalian brain pathophysiology remains unknown. To investigate NTE function in vivo, we used the cre/loxP site-specific recombination strategy to generate mice with a specific deletion of NTE in neuronal tissues. Here we show that loss of NTE leads to prominent neuronal pathology in the hippocampus and thalamus and also defects in the cerebellum. Absence of NTE resulted in disruption of the endoplasmic reticulum, vacuolation of nerve cell bodies, and abnormal reticular aggregates. Thus, these results identify a physiological role for NTE in the nervous system and indicate that a loss-of-function mechanism may contribute to neurodegenerative diseases characterized by vacuolation and neuronal loss.
Chemistry of N-fluoropyridinium salts (2005)

This tutorial review deals with developments in the chemistry of N-fluoropyridinium salts in the past decade, including both synthetic and mechanistic aspects. Three distinct types of transformations including: i) fluorination reactions, ii) carbenoid behavior and iii) cine-/tele- substitution involving N-fluoropyridinium cation are exemplified. Procedures for fluorination of carbanions and benzenoid aromatics along with hetarylation processes yielding 2- and 4-substituted pyridines are referenced. Several new discoveries in the area, including three-component condensation reactions of in situ generated N-fluoropyridinium fluoride are described.
Frequent Dysregulation of the c-maf Proto-Oncogene at 16q23 by Translocation to an Ig Locus in Multiple Myeloma (1998)

Dysregulation of oncogenes by translocation to an IgH (14q32) or IgL (κ, 2p11 or λ, 22q11) locus is a frequent event in the pathogenesis of B-cell tumors. Translocations involving an IgH locus and a diverse but nonrandom array of chromosomal loci occur in most multiple myeloma (MM) tumors even though the translocations often are not detected by conventional cytogenetic analysis. In a continuing analysis of translocations in 21 MM lines, we show that the novel, karyotypically silent t(14;16)(q32.3;q23) translocation is present in 5 MM lines, with cloned breakpoints from 4 lines dispersed over an approximately 500-kb region centromeric to the c-maf proto-oncogene at 16q23. Another line has a t(16;22)(q23;q11), with the breakpoint telomeric to c-maf, so that the translocation breakpoints in these 6 lines bracket c-maf. Only these 6 lines overexpress c-mafmRNA. As predicted for dysregulation of c-maf by translocation, there is selective expression of one c-maf allele in 2 informative lines with translocations. This is the first human tumor in which the basic zipper c-maf transcription factor is shown to function as an oncogene.
Steric and Electrostatic Contributions to the Colloidal Properties of Nonaqueous Dispersions (1984)

Dispersions of carbon black in dodecane and kerosene have been prepared with a basic poly-isobutene succinamide, the most extensively used commercial non-aqueous dispersant. The basic anchoring groups adsorb strongly onto the acidic surface sites of the carbon black, and with 1 w% or more of dispersant (based on the carbon black) the 50 Å - long polyisobutene chains extend out into the solution to provide a steric barrier 100 Å thick between particles, as evidenced by a million-fold decrease in electrical conductivity and a twenty-fold decrease in viscosity, but with no degree whatsoever of deflocculation. Only at much higher dispersant levels is deflocculation observed. When the concentration of unadsorbed dispersant in the oil phase exceeds 0.1%, the conductivity increases as counterions form, large negative zeta-potentials develop (-140 to -300 mV), the stability ratios climb towards infinity and the dispersions become completely deflocculated.