gebhart/patrepeval huggingface dataset:
Central and peripheral mechanisms by which ghrelin regulates gut motility. (2003)

Ghrelin is the recently discovered endogenous ligand for the growth hormone secretagogue receptor. This receptor had previously been characterized based on the stimulatory effect of synthetic peptides, enkephalin analogues, on growth hormone secretion by pituitary somatotrophs. Surprisingly, ghrelin is most abundant in the stomach, suggesting that it may have effects beyond the stimulation of growth hormone in the pituitary and that it is a new brain-gut peptide. There is now increasing evidence that ghrelin stimulates motor activity in the gastrointestinal tract. Thus ghrelin induces the migrating motor complex and accelerates gastric emptying. These are effects typical for motilin, the only peptide structurally related to ghrelin. Moreover, the receptors of both peptides are structurally related as well. The motor effects of ghrelin require rather high concentrations, while motilin at high concentrations stimulates growth hormone release. These data suggest cross-reactivity. However, in vitro binding and contractility studies in the rabbit, the classical model to study motilin agonists, show that ghrelin has very weak if any interaction with the motilin receptor. Similarly, in cell lines expressing the receptors for both peptides there is no evidence for cross-reactivity. This corresponds to the fact that the pharmacophore of both peptides is quite different. Therefore, the motor effects must be due to the stimulation of specific central or peripheral ghrelin receptors. In the guinea pig there is evidence from electrophysiology, immunohistochemistry and calcium imaging studies for ghrelin receptors on myenteric neurons. This provides the morphological basis for peripheral effects of ghrelin. In rats, ghrelin, but not motilin, enhances the response of muscle strips to electrical field stimulation by activating cholinergic pathways. In rabbits the opposite is true but some synthetic ghrelin agonists have weak effects which cannot be blocked by motilin antagonists. Apparently ghrelin is the functional equivalent of motilin in the rat, but in rabbits the motilin-ghrelin family may have yet unknown members. In vivo the effect of ghrelin can be blocked by vagotomy and there is evidence for ghrelin receptors on vagal afferents and in the nodose ganglion. Studies in the rat suggest that under physiological conditions circulating ghrelin does not activate the myenteric plexus, but is able to do so following vagotomy. Finally, centrally administered ghrelin also accelerates gastric emptying and ghrelin changes the activity of neurons of the central nuclei involved in signalling information from the gastrointestinal tract. It is concluded that ghrelin may affect gastrointestinal motility via specific ghrelin receptors located on myenteric, vagal and central neurons. Vagal and central pathways appear to be most important. The fact that ghrelin may reverse the effect of ileus on gastric emptying suggests that ghrelin agonists could find therapeutical application as prokinetics.
Human Heart Mitochondrial DNA Is Organized in Complex Catenated Networks Containing Abundant Four-way Junctions and Replication Forks (2009)

Analysis of human heart mitochondrial DNA (mtDNA) by electron microscopy and agarose gel electrophoresis revealed a complete absence of the -type replication intermediates seen abundantly in mtDNA from all other tissues. Instead only Y- and X-junctional forms were detected after restriction digestion. Uncut heart mtDNA was organized in tangled complexes of up to 20 or more genome equivalents, which could be resolved to genomic monomers, dimers, and linear fragments by treatment with the decatenating enzyme topoisomerase IV plus the cruciform-cutting T7 endonuclease I. Human and mouse brain also contained a population of such mtDNA forms, which were absent, however, from mouse, rabbit, or pig heart. Overexpression in transgenic mice of two proteins involved in mtDNA replication, namely human mitochondrial transcription factor A or the mouse Twinkle DNA helicase, generated abundant four-way junctions in mtDNA of heart, brain, and skeletal muscle. The organization of mtDNA of human heart as well as of mouse and human brain in complex junctional networks replicating via a presumed non- mechanism is unprecedented in mammals.
THE USE OF CONFIDENCE OR FIDUCIAL LIMITS ILLUSTRATED IN THE CASE OF THE BINOMIAL (1934)

THE USE OF CONFIDENCE OR FIDUCIAL LIMITS ILLUSTRATED IN THE CASE OF THE BINOMIAL Get access C. J. CLOPPER, B.Sc., C. J. CLOPPER, B.Sc. Search for other works by this author on: Oxford Academic Google Scholar E. S. PEARSON, D.Sc. E. S. PEARSON, D.Sc. Search for other works by this author on: Oxford Academic Google Scholar Biometrika, Volume 26, Issue 4, December 1934, Pages 404–413, https://doi.org/10.1093/biomet/26.4.404 Published: 01 December 1934
Site‐directed mutagenesis of the katG gene of Mycobacterium tuberculosis: effects on catalase–peroxidase activities and isoniazid resistance (1996)

Recent studies examining the molecular mechanisms of isoniazid (INH) resistance in Mycobacterium tuberculosis have demonstrated that a significant percentage of drug-resistant strains are mutated in the katG gene which encodes a catalase-peroxidase, and the majority of these alterations are missense mutations which result in the substitution of a single amino acid. In previous reports, residues which may be critical for enzymatic activity and the drug-resistant phenotype have been identified by evaluating INH-resistant clinical isolates and in vitro mutants. In this study, site-directed mutagenesis techniques were utilized to alter the wild-type katG gene from M. tuberculosis at 13 of these codons. The effects of these mutations were determined using complementation assays in katG-defective, INH-resistant strains of Mycobacterium smegmatis and Mycobacterium bovis BCG. This mutational analysis revealed that point mutations in the katG gene at nine of the 13 codons can cause drug resistance, and that enzymatic activity and resistance to INH are inversely related. In addition, mutations in the mycobacterial catalase-peroxidase which reduce catalase activity also decrease peroxidase activity.
Parietal Representation of Object-Based Saccades (2002)

When monkeys make saccadic eye movements to simple visual targets, neurons in the lateral intraparietal area (LIP) display a retinotopic, or eye-centered, coding of the target location. However natural saccadic eye movements are often directed at objects or parts of objects in the visual scene. In this paper we investigate whether LIP represents saccadic eye movements differently when the target is specified as part of a visually displayed object. Monkeys were trained to perform an object-based saccade task that required them to make saccades to previously cued parts of an abstract object after the object reappeared in a new orientation. We recorded single neurons in area LIP of two macaque monkeys and analyzed their activity in the object-based saccade task, as well as two control tasks: a standard memory saccade task and a fixation task with passive object viewing. The majority of LIP neurons that were tuned in the memory saccade task were also tuned in the object-based saccade task. Using a hierarchical generalized linear model analysis, we compared the effects of three different spatial variables on the firing rate: the retinotopic location of the target, the object-fixed location of the target, and the orientation of the object in space. There was no evidence of an explicit object-fixed representation in the activity in LIP during either of the object-based tasks. In other words, no cells had receptive fields that rotated with the object. While some cells showed a modulation of activity due to the location of the target on the object, these variations were small compared to the retinotopic effects. For most cells, firing rates were best accounted for by either the retinotopic direction of the movement, the orientation of the object, or both spatial variables. The preferred direction of these retinotopic and object orientation effects were found to be invariant across tasks. On average, the object orientation effects were consistent with the retinotopic coding of potential target locations on the object. This interpretation is supported by the fact that the magnitude of these two effects were roughly equal in the early portions of the trial, but around the time of the motor response, the retinotopic effects dominated. We conclude that LIP uses the same retinotopic coding of saccade target whether the target is specified as an absolute point in space or as a location on a moving object.
A potential marker protease of invasiveness, seprase, is localized on invadopodia of human malignant melanoma cells. (1994)

Seprase, a large, gelatin-degrading membrane-protease complex, is expressed at the invasive front of malignant melanoma cells on invadopodia, and its surface expression contributes to the invasive phenotype. An in vitro assay was used to determine the matrix-degrading activity of four malignant human melanoma cell lines. The lines differ in matrix-degrading activity with LOX > RPM17951 > A375 > SKMEL28. The seprase and Gelatinase A activities of these cell lines were also investigated. Seprase and active gelatinase A are found in cell membranes of LOX and RPM17951 cells but not those of SKMEL28 cells. Experiments using anti-seprase monoclonal antibodies in conjunction with a cell fractionation technique indicate that seprase consists of M(r) 97,000 polypeptides and is enriched on the ventral membrane of LOX in contact with planar extracellular matrix substratum. Confocal microscopy further substantiates our biochemical findings that seprase, as well as Gelatinase A, is localized on invadopodia membranes with a 6-fold increase of seprase and 4-fold increase of Gelatinase A intensity over the level expressed on dorsal membranes. In addition, LOX cells expressing higher levels of seprase at the cell surface, as selected by fluorescence-activated cell sorting, are significantly more degradative than LOX cells with lower seprase expression. Taken together, our data show a concordance between seprase and Gelatinase A expression on the cell surface at invadopodia and the matrix-degrading activity of human malignant melanoma cells. Seprase and major secreted proteases may act in concert to degrade components of the extracellular matrix during invasion.
Polyphosphoinositides Inhibit the Interaction of Vinculin with Actin Filaments (1999)

Binding of vinculin to adhesion plaque proteins is restricted by an intramolecular association of vinculin's head and tail regions. Results of previous work suggest that polyphosphoinositides disrupt this interaction and thereby promote binding of vinculin to both talin and actin. However, data presented here show that phosphatidylinositol 4,5-bisphosphate (PI4,5P2) inhibits the interaction of purified tail domain with F-actin. Upon re-examining the effect of PI4,5P2 on the actin and talin-binding activities of intact vinculin, we find that when the experimental design controls for the effect of magnesium on aggregation of PI4,5P2 micelles, polyphosphoinositides promote interactions with the talin-binding domain, but block interactions of the actin-binding domain. In contrast, if vinculin is trapped in an open confirmation by a peptide specific for the talin-binding domain of vinculin, actin binding is allowed. These results demonstrate that activation of the actin-binding activity of vinculin requires steps other than or in addition to the binding of PI4,5P2.
THE CONTROL OF EPIDERMAL STEM CELLS (HOLOCLONES) IN THE TREATMENT OF MASSIVE FULL-THICKNESS BURNS WITH AUTOLOGOUS KERATINOCYTES CULTURED ON FIBRIN1 (1999)

Our data demonstrate that: (i) cultured autografts bearing stem cells can indeed rapidly and permanently cover a large body surface; and (ii) fibrin is a suitable substrate for keratinocyte cultivation and transplantation. These data lend strength to the concept that the success of cell therapy at a clinical level requires cultivation and transplantation of stem cells. We therefore suggest that the proposal of a culture system aimed at the replacement of any severely damaged self-renewing tissue should be preceded by a careful evaluation of its stem cell population.
Role of RLIP76 in lung cancer doxorubicin resistance: II. Doxorubicin transport in lung cancer by RLIP76 (2003)

ATP-dependent transport of doxorubicin (DOX) by recombinant human RLIP76 has been demonstrated previously in reconstituted proteoliposomes. In the preceding communication, we demonstrated that the ATPase activity of RLIP76 was 2-fold higher in NSCLC as compared with SCLC, and it correlated with their inherent DOX resistance. Present studies were performed to determine whether greater ATPase activity of RLIP76 in NSCLC translated into greater RLIP76 mediated DOX transport, and to determine the overall contribution of RLIP76 toward total DOX transport. Consistent with the greater RLIP76 ATPase activity in NSCLC, DOX transport in artificial proteoliposomes reconstituted with purified RLIP76 from NSCLC was 1.8-fold greater than in SCLC. Anti-RLIP76 antibodies completely abrogated DOX transport in these RLIP76 proteoliposomes, whereas anti-MRP or anti-Pgp antibodies had no effect on transport. DOX transport studies in crude membrane vesicles from SCLC and NSCLC also showed a 2.1-fold higher rate of transport in NSCLC as compared with SCLC. Anti-RLIP76 IgG, which recognized only RLIP76 in crude extracts of both SCLC and NSCLC, inhibited 67+/-4% (n=12 cell lines) of total DOX transport in crude membrane vesicles from both SCLC and NSCLC. Inhibition of DOX transport by anti-MRP and anti-Pgp antibody was 35+/-7% (n=12) and 2+/-0.3% (n=12), respectively. The mixture of the three antibodies inhibited DOX transport by 95+/-3% (n=12). These studies demonstrate that DOX transport activity of RLIP76 is significantly greater in NSCLC as compared with SCLC, and that RLIP76 is the major DOX transporter in lung cancer cell lines.
Generation of Human Induced Pluripotent Stem Cells from Umbilical Cord Matrix and Amniotic Membrane Mesenchymal Cells (2010)

The umbilical cord and placenta are extra-embryonic tissues of particular interest for regenerative medicine. They share an early developmental origin and are a source of vast amounts of cells with multilineage differentiation potential that are poorly immunogenic and without controversy. Moreover, these cells are likely exempt from incorporated mutations when compared with juvenile or adult donor cells such as skin fibroblasts or keratinocytes. Here we report the efficient generation of induced pluripotent stem cells (iPSCs) from mesenchymal cells of the umbilical cord matrix (up to 0.4% of the cells became reprogrammed) and the placental amniotic membrane (up to 0.1%) using exogenous factors and a chemical mixture. iPSCs from these 2 tissues homogeneously showed human embryonic stem cell (hESC)-like characteristics including morphology, positive staining for alkaline phosphatase, normal karyotype, and expression of hESC-like markers including Nanog, Rex1, Oct4, TRA-1-60, TRA-1-80, SSEA-3, and SSEA-4. Selected clones also formed embryonic bodies and teratomas containing derivatives of the 3 germ layers, and could as well be readily differentiated into functional motor neurons. Among other things, our cell lines may prove useful for comparisons between iPSCs derived from multiple tissues regarding the extent of the epigenetic reprogramming, differentiation ability, stability of the resulting lineages, and the risk of associated abnormalities.
The US economic and social costs of Alzheimer's disease revisited. (1994)

The $536 billion and $1.75 trillion figures are minimum estimates of the long-term dollar losses to the US economy in 1991 caused by Alzheimer's disease.
Expression of the Human Multidrug Resistance and Glucocerebrosidase cDNAs from Adeno-Associated Vectors: Efficient Promoter Activity of AAV Sequences and In Vivo Delivery via Liposomes (1996)

Recombinant adeno-associated viruses (rAAV) are attractive tools for gene therapy. We designed plasmids in which the human multidrug resistance gene (hMDR1) cDNA was placed downstream from portions of the 5' end of AAV including either a 234-bp cassette or the entire AAV p5 promoter. The drug-resistant phenotype conferred by the P-glycoprotein (Pgp) efflux pump encoded by the hMDR1 cDNA was used to select NIH-3T3 cells transfected with these plasmids. The 234-bp region alone showed promoter activity similar in strength to that of the entire p5 promoter or the retroviral Harvey murine sarcoma virus long terminal repeat (LTR); this result demonstrates that the 234-bp cassette might be used as a small and efficient promoter in rAAV designed to express large genes approaching the packaging limit of AAV particles. After transfection of AAV-MDR1 vectors, the integration of MDR1 sequences into the host cell genome was demonstrated by fluorescent in situ hybridization (FISH). In addition, Southern analysis of low-molecular-weight DNA extracted from drug-resistant cells grown under continuous selection pressure indicated the persistence of nonintegrated AAV-MDR1 plasmids. Coordinate expression of Pgp and human glucocerebrosidase (hGC) was observed in drug-selected NIH-3T3 cells transfected with a bicistronic vector in which MDR1 cDNA was linked to hGC cDNA via the encephalomyocarditis internal ribosome entry site sequence. Moreover, following a single intravenous injection of the bicistronic vector complexed to cationic liposomes into recipient mice, delivery of MDR1 and GC cDNAs was achieved in all the organs we tested. Our results demonstrate that the efficiency of liposomes as vehicles for in vitro and in vivo gene delivery, the advantages of AAV-vectors, and the use of MDR1 as a selectable marker might be successfully combined in gene therapy protocols.
Chemical synthesis of oligonucleotides containing a free sulphydryl group and subsequent attachment of thiol specific probes (1985)

Oligonucleotides containing a free sulphydryl group at their 5'-termini have been synthesised and further derivatised with thiol specific probes. The nucleotide sequence required is prepared using standard solid phase phosphoramidite techniques and an extra round of synthesis is then performed using the S-triphenylmethyl O-methoxymorpholinophosphite derivatives of 2-mercaptoethanol, 3-mercaptopropan (1) ol or 6-mercaptohexan (1) ol. After cleavage from the resin and removal of the phosphate and base protecting groups, this yields an oligonucleotide containing an S-triphenylmethyl group attached to the 5'-phosphate group via a two, three or six carbon chain. The triphenylmethyl group can be readily removed with silver nitrate to give the free thiol. With the three and six carbon chain oligonucleotides, this thiol can be used, at pH 8, for the attachment of thiol specific probes as illustrated by the reaction with fluorescent conjugates of iodoacetates and maleiimides. However, oligonucleotides containing a thiol attached to the 5'-phosphate group via a two carbon chain are unstable at pH 8 decomposing to the free 5'-phosphate and so are unsuitable for further derivatisation.
Reactivity of Ferulic Acid and Its Derivatives toward Hydrogen Peroxide and Peracetic Acid (1999)

The reactions of ferulic acid and its derivatives with hydrogen peroxide and peracetic acid in lignin-retaining bleaching conditions have been investigated to determine their susceptibility to oxidative degradation. The conjugated side chain of ferulic acid and its etherified or esterified derivative was shown to be fairly stable, especially to hydrogen peroxide. The major reaction was trans-cis isomerization that possibly involved a radical mechanism but did not cause bond cleavage. The peracetic acid reaction increased the rate of trans-cis isomerization and was also accompanied by a minor cleavage of the side chain. Esterification did not have a substantial effect on the reactivity of ferulic acid, but 4-O-etherification significantly stabilized it against these two oxidants. By contrast, aldehyde substitution tremendously enhanced the susceptibility of the cinnamyl side chain to oxidative degradation, as evidenced by an intensive degradation of coniferaldehyde.
Swelling pressure of the inervertebral disc: Influence of proteoglycan and collagen contents (1985)

In this study we have considered how equilibrium water content of the human nucleus pulposus varies with applied pressure for discs of various spinal levels and of various ages. In all cases hydration decreased as pressure increased but the level of equilibrium hydration depended on the relative amounts of collagen and PG in the tissue. Provided we accounted for the exclusion of PGs from the intra-fibrillar space, the swelling pressure curve and the osmotic pressure curve of equivalent PGs were found to coincide. The result implies that under physiological hydrations the mechanical forces exerted by the collagen network of the nucleus are insignificant and that the osmotic pressure of the proteoglycans is balanced by the applied pressure arising from body weight and muscle and ligament tension alone. Since aged discs often have a low proteoglycan to collagen ratio, their equilibrium hydration also tends to be low. Moreover a far larger proportion of the total water is associated with the collagen than in the younger disc.
Stem-Loop Binding Protein, the Protein That Binds the 3′ End of Histone mRNA, Is Cell Cycle Regulated by Both Translational and Posttranslational Mechanisms (2000)

The expression of the replication-dependent histone mRNAs is tightly regulated during the cell cycle. As cells progress from G(1) to S phase, histone mRNA levels increase 35-fold, and they decrease again during G(2) phase. Replication-dependent histone mRNAs are the only metazoan mRNAs that lack polyadenylated tails, ending instead in a conserved stem-loop. Much of the cell cycle regulation is posttranscriptional and is mediated by the 3' stem-loop. A 31-kDa stem-loop binding protein (SLBP) binds the 3' end of histone mRNA. The SLBP is necessary for pre-mRNA processing and accompanies the histone mRNA to the cytoplasm, where it is a component of the histone messenger RNP. We used synchronous CHO cells selected by mitotic shakeoff and HeLa cells synchronized at the G(1)/S or the M/G(1) boundary to study the regulation of SLBP during the cell cycle. In each system the amount of SLBP is regulated during the cell cycle, increasing 10- to 20-fold in the late G(1) and then decreasing in the S/G(2) border. SLBP mRNA levels are constant during the cell cycle. SLBP is regulated at the level of translation as cells progress from G(1) to S phase, and the protein is rapidly degraded as they progress into G(2). Regulation of SLBP may account for the posttranscriptional component of the cell cycle regulation of histone mRNA.
Structure and Function of Cyclic Nucleotide-Dependent Protein Kinases (1994)

Cyclic AMP-dependent protein kinase (cAK) was first described in 19631964 (43, 132) as a cAMP-dependent glycogen synthase kinase that, in the presence of Mg/ A TP, transferred the 'V-phosphate of A TP to serines or threonines on many cellular enzymes. It was found to phosphorylate a number of proteins and was permanently named in 1968 (168). Ensuing years produced vast numbers of reports regarding properties of cAK and the signal mechanisms that elicit its activation. Many of these have been reviewed recently (8, 33,47, 85, 141, 155, 181). In 1970 cyclic GMP-de­ pendent protein kinase (cGK) was discovered (86). cGK is homologous in structure and function to cAK (24, 49, 59, 66, 93, 141, 154). The role of cGMP in physiological processes is increasingly appreciated (15, 39, 92, 94, 113, 170), but cGK is only one of several intracellular receptors for cGMP. Studies of the heterogeneity, function, and regulation of cAK and cGK have provided insight into the enzymology of diverse protein kinases and into the roles of these kinases in cellular processes.