gebhart/patrepeval huggingface dataset:
Embedded-Culture of Pancreatic β-Cells Derived from Transgenic Mouse Insulinoma as a Potential Source for Xenotransplantation using a Diffusion Chamber (1995)

Embedded-culture of pancreatic β-cells derived from a transgenic mouse insulinoma (MIN6 cells) was studied in vitro and in vivo. The MIN6 cells were enmeshed in an agarose-PVMA-collagen matrix for long-term maintenance. The cells formed islet-like cell clusters (ICCs) in the mixed matrix. When 10 mmol/L nicotinamide was added to these cultures the cells secreted insulin in response to various concentrations of glucose, whereas the untreated control cells were unresponsive. Both control and nicotinamide-treated MIN6 cells exhibited normal β-cell function for up to 35 days in the mixed matrix, and the cells were much better preserved with nicotinamide than without it. MIN6 cells were suspended in the mixed matrix with nicotinamide and transferred into diffusion chambers to create a bio-artificial endocrine pancreas (Bio-AEP). In streptozotocine-induced diabetic rats with implanted Bio-AEP but without any immunosuppressants, a return to normoglycaemia was observed for up to 12 wk or more after transplantation. Our results indicate that nicotinamide-treated MIN6 cells embedded in a mixed matrix should be useful for the study of xenotransplantation and the development of a bioartificial endocrine pancreas.
<i>In vitro</i> concatemerization of bacteriophage T7 DNA: Role of DNA synthesis and gene 6 exonuclease (1985)

The replication of bacteriophage T7 DNA in vivo proceeds via the synthesis of complex concatemeric intermediates which are joined via the 160 base pair terminal redundancies at either end of the phage chromosome. To gain some insight into the mode of generation of these structures, we have examined the role of DNA synthesis in the formation of concatemeric bacteriophage T7 DNA in vitro. Incubation of mature T7 DNA with T7-infected cell extracts and a deoxynucleoside [32P]triphosphate resulted in the incorporation of significant radioactivity into the DNA. Highest levels of incorporation were at the termini of the DNA and decreased toward the middle of the molecule. Incorporation was dependent upon the presence of the activity of the gene 6 exonuclease and correlated with the generation of concatemeric DNA. A model explaining the role of exonucleolytic degradation and DNA synthesis in the generation of concatemeric DNA is presented.
A Genetic Screen for Modifiers of a Kinase Suppressor of Ras-Dependent Rough Eye Phenotype in Drosophila (2000)

kinase suppressor of Ras (ksr) encodes a putative protein kinase that by genetic criteria appears to function downstream of RAS in multiple receptor tyrosine kinase (RTK) pathways. While biochemical evidence suggests that the role of KSR is closely linked to the signal transduction mechanism of the MAPK cascade, the precise molecular function of KSR remains unresolved. To further elucidate the role of KSR and to identify proteins that may be required for KSR function, we conducted a dominant modifier screen in Drosophila based on a KSR-dependent phenotype. Overexpression of the KSR kinase domain in a subset of cells during Drosophila eye development blocks photoreceptor cell differentiation and results in the external roughening of the adult eye. Therefore, mutations in genes functioning with KSR might modify the KSR-dependent phenotype. We screened approximately 185,000 mutagenized progeny for dominant modifiers of the KSR-dependent rough eye phenotype. A total of 15 complementation groups of Enhancers and four complementation groups of Suppressors were derived. Ten of these complementation groups correspond to mutations in known components of the Ras1 pathway, demonstrating the ability of the screen to specifically identify loci critical for Ras1 signaling and further confirming a role for KSR in Ras1 signaling. In addition, we have identified 4 additional complementation groups. One of them corresponds to the kismet locus, which encodes a putative chromatin remodeling factor. The relevance of these loci with respect to the function of KSR and the Ras1 pathway in general is discussed.
A mutation in the receiver domain of the <i>Agrobacterium tumefaciens</i> transcriptional regulator VirG increases its affinity for operator DNA (1994)

We fused the wild-type Agrobacterium tumefaciens virG gene and the constitutive virGN54D allele to the malE gene of Escherichia coli, and studied the binding of MBP-VirG fusions to the autoregulated virG promoter. MBP-VirGN54D protein bound this promoter with 10-fold higher affinity than MBP-VirG, and bound to vir box I with eightfold higher affinity than to vir box III. Disruption of vir box III did not alter the affinity for vir box I, suggesting a lack of cooperativity between these sites. We provide evidence that protein bound at a single vir box may have a higher oligomeric state than non-bound protein, and that a DNA distortion adjacent to vir box I may occur during activation.
Unraveling Cellular Phenotypes of Novel<i>TorsinA/TOR1A</i>Mutations (2014)

A three-nucleotide (GAG) deletion (ΔE) in TorsinA (TOR1A) has been identified as the most common cause of dominantly inherited early-onset torsion dystonia (DYT1). TOR1A encodes a chaperone-like AAA+-protein localized in the endoplasmic reticulum. Currently, only three additional, likely mutations have been reported in single dystonia patients. Here, we report two new, putative TOR1A mutations (p.A14_P15del and p.E121K) that we examined functionally in comparison with wild-type (WT) protein and two known mutations (ΔE and p.R288Q). While inclusion formation is a characteristic feature for ΔE TOR1A, elevated levels of aggregates for other mutations were not observed when compared with WT TOR1A. WT and mutant TOR1A showed preferred degradation through the autophagy-lysosome pathway, which is most pronounced for p.A14_P15del, p.R288Q, and ΔE TOR1A. Notably, blocking of the autophagy pathway with bafilomycin resulted in a significant increase in inclusion formation in p.E121K TOR1A. In addition, all variants had an influence on protein stability. Although the p.A14_P15del mutation affects the proposed oligomerization domain of TOR1A, this mutation did not disturb the ability to dimerize. Our findings demonstrate functional changes for all four mutations on different levels. Thus, both diagnostic and research genetic screening of dystonia patients should not be limited to testing for the ∆E mutation.
Stanniocalcin-1 Potently Inhibits the Proteolytic Activity of the Metalloproteinase Pregnancy-associated Plasma Protein-A (2015)

Stanniocalcin-1 (STC1) is a disulfide-bound homodimeric glycoprotein, first identified as a hypocalcemic hormone important for maintaining calcium homeostasis in teleost fish. STC1 was later found to be widely expressed in mammals, although it is not believed to function in systemic calcium regulation in these species. Several physiological functions of STC1 have been reported, although many molecular details are still lacking. We here demonstrate that STC1 is an inhibitor of the metzincin metalloproteinase, pregnancy-associated plasma protein-A (PAPP-A), which modulates insulin-like growth factor (IGF) signaling through proteolytic cleavage of IGF-binding proteins (IGFBPs). STC1 potently (Ki = 68 pm) inhibits PAPP-A cleavage of IGFBP-4, and we show in a cell-based assay that STC1 effectively antagonizes PAPP-A-mediated type 1 IGF receptor (IGF1R) phosphorylation. It has recently been found that the homologous STC2 inhibits PAPP-A proteolytic activity, and that this depends on the formation of a covalent complex between the inhibitor and the proteinase, mediated by Cys-120 of STC2. We find that STC1 is unable to bind covalently to PAPP-A, in agreement with the absence of a corresponding cysteine residue. It rather binds to PAPP-A with high affinity (KD = 75 pm). We further demonstrate that both STC1 and STC2 show inhibitory activity toward PAPP-A2, but not selected serine proteinases and metalloproteinases. We therefore conclude that the STCs are proteinase inhibitors, probably restricted in specificity to the pappalysin family of metzincin metalloproteinases. Our data are the first to identify STC1 as a proteinase inhibitor, suggesting a previously unrecognized function of STC1 in the IGF system.
Chemotoxicity of doxorubicin and surface expression of P-glycoprotein (MDR1) is regulated by the<i>Pseudomonas aeruginosa</i>toxin Cif (2008)

P-glycoprotein (Pgp), a member of the adenosine triphosphate-binding cassette (ABC) transporter superfamily, is a major drug efflux pump expressed in normal tissues, and is overexpressed in many human cancers. Overexpression of Pgp results in reduced intracellular drug concentration and cytotoxicity of chemotherapeutic drugs and is thought to contribute to multidrug resistance of cancer cells. The involvement of Pgp in clinical drug resistance has led to a search for molecules that block Pgp transporter activity to improve the efficacy and pharmacokinetics of therapeutic agents. We have recently identified and characterized a secreted toxin from Pseudomonas aeruginosa, designated cystic fibrosis transmembrane conductance regulator (CFTR) inhibitory factor (Cif). Cif reduces the apical membrane abundance of CFTR, also an ABC transporter, and inhibits the CFTR-mediated chloride ion secretion by human airway and kidney epithelial cells. We report presently that Cif also inhibits the apical membrane abundance of Pgp in kidney, airway, and intestinal epithelial cells but has no effect on plasma membrane abundance of multidrug resistance protein 1 or 2. Cif increased the drug sensitivity to doxorubicin in kidney cells expressing Pgp by 10-fold and increased the cellular accumulation of daunorubicin by 2-fold. Thus our studies show that Cif increases the sensitivity of Pgp-overexpressing cells to doxorubicin, consistent with the hypothesis that Cif affects Pgp functional expression. These results suggest that Cif may be useful to develop a new class of specific inhibitors of Pgp aimed at increasing the sensitivity of tumors to chemotherapeutic drugs, and at improving the bioavailability of Pgp transport substrates.
Limiting Conditions for the Use of Hydrolyzed Polyacrylamides in Brines Containing Divalent Ions (1983)

Abstract This paper summarizes the main parameters acting on the stability of hydrolyzed polyacrylamides in brines containing divalent ions. For dilute solutions the critical hydrolysis degree τc2+ above which the polymer may be precipitated by Ca ions is τc = 35% at room temperature and 33% at 80°C. For τ &lt; 60% the precipitated polymer redissolves at high CaCl2 or NaCl concentrations. Intrinsic viscosity measurements of the solutions near the precipitation point show a slow decrease in coil expansion and an increase in the Huggins constant as expected near θ conditions. Neither precipitation phenomena nor viscosity can be predicted from the divalent-ion content without taking into account the overall ionic environment.
Establishing lightpaths of an optical ring for distributed computing environment (2005)

We study optical lightpath networking for distributed computing environment. Lightpath networks are suitable to network-wide distributed computing because the bandwidth is assured once a lightpath is established. In this paper, we dynamically configure a unidirectional optical ring that is used for multipoint-to-multipoint communications among hosts in a group. The ring consists of multiple unidirectional lightpaths. Each host in the group is an endpoint of the lightpath. The routing of the network is usually specific to point-to-point communications. We propose a ring composition algorithm that finds the least-cost set of lightpaths of the optical ring under this routing. In this algorithm, a parent host finds a destination host of which route from the host is the least-cost route among routes to hosts in the group. We also propose backward signaling methods that are specific to the establishment of the lightpaths for the ring composition. Since the signaling for lightpath establishment is well adjusted to RSVP-TE for GMPLS, an implementation of the ring composition can be accelerated. Through simulation experiments, we find the proposed ring composition method generates lightpaths for the optical ring with less wavelength resources. The smart signaling accelerates the efficiency of network resources. The clear reduction of blocking probability of establishing a ring for a group is found from the simulation result
Zinc as a treatment for age-related macular degeneration (1998)

Evidence continues to increase that antioxidants are an important factor in the progress and development of age-related macular degeneration. While zinc supplementation fits nicely in this thesis as a mineral co-factor of vital antioxidant enzymes, the clinical evidence for oral zinc supplementation is mixed and presently inconclusive. J. Trace Elem. Exp. Med. 11:137–145, 1998. © 1998 Wiley-Liss, Inc.
The Optical Measurement of Depth (1955)

ABSTRACT The formula for vertical measurement by means of the fine adjustment of the microscope, n2/n1 × measured depth = real depth, is true, where n2 is the refractive index of the object and n, is that of the immersion medium of the objective lens. The refractive index of the mountant is unimportant. Several additional complications of this method of measurement suggest that it should not be used unless it cannot be avoided, or rough figures are required quickly.
Synthesis of Alkynyl Amino Acids and Peptides and Their Palladium-Catalyzed Coupling to Ferrocene (1999)

A method for attaching organometallics to the C-terminus of amino acids via a Pd-catalyzed two-step procedure is presented. Boc-protected enantiomerically pure amino acids 1 (a Phe, b Leu, c Met, d Ser) are reacted with 1,1-diethylpropargylamine to yield alkynyl amino acids 2. After reaction with (p-iodoanilido)ferrocene carboxylic acid 3 in the presence of 5 mol % PdCl2(PPh3)2/CuI ferrocene amino acids 4 are obtained in ca. 80% yield. The reaction does not require anhydrous conditions and tolerates functional groups such as amides, alcohols (Ser, 4d) or thioethers (Met, 4c). A complete characterization by multinuclear NMR (including 15N) is carried out. Cyclic voltammetry shows a reversible wave at about +190 mV (vs Fc/Fc+) independent of the nature of the attached amino acid. In the solid state, 2a forms a left-handed helix along the crystallographic c axis which is stabilized by hydrogen bonds as revealed by a single-crystal X-ray structure determination. A comparison of IR data in solution and the solid state suggests that hydrogen bonding is also important for the solid-state structures of ferrocene amino acids 4 but does not play a role in solution. The use of this methodology for peptide chemistry is demonstrated by labeling the dipeptide Boc-Met-Phe-OH at the C-terminus and the tripeptide Boc-Phe-Glu-Leu-OMe with ferrocene. The alkyne anchoring group in the tripeptide is introduced at the Cγ(Glu) atom at an early stage of the peptide synthesis and is not affected by subsequent deprotection and coupling reactions.
Generation of ultrahigh and tunable repetition rates in CW injection-seeded frequency-shifted feedback lasers (2013)

We show both theoretically and experimentally that frequency-shifted feedback (FSF) lasers seeded with a single frequency laser can generate Fourier transform-limited pulses with a repetition rate tunable and limited by the spectral bandwidth of the laser. We demonstrate experimentally in a FSF laser with a 150 GHz spectral bandwidth, the generation of 6 ps-duration pulses at repetition rates tunable over more than two orders of magnitude between 0.24 and 37 GHz, by steps of 80 MHz. A simple linear analytical model i.e. ignoring both dynamic and non-linear effects, is sufficient to account for the experimental results. This possibility opens new perspectives for various applications where lasers with ultra-high repetition rates are required, from THz generation to ultrafast data processing systems.
Mutations, epimutations, and the developmental programming of the maize <i>Suppressor‐mutator</i> transposable element (1989)

Information about the structure, function and regulation of the maize Suppressor-mutator (Spm) transposable element has emerged from the genetic and molecular characterization of both deletion mutations and an unconventional type of reversible genetic change (epimutation). The element is subject to an epigenetic mechanism that can either stably inactivate it or specify one of a variety of heritable programs of differential element expression in development. The essay explores the relationship between the Spm element's epigenetic developmental programming mechanism and the determinative events central to plant development and differentiation.
Regulation of T cell function by Mtv-7 gene products. (1992)

Mls-1, a superantigen encoded by the endogenous mouse mammary tumor virus Mtv-7 induces immunological tolerance through deletion of antigen-reactive T cells. A remarkable difference between this self-antigen and self-MHC antigens is that while the mouse establishes tolerance against self MHC antigens by the time of birth it does not begin to delete T cells specific for the self-superantigen until they had mounted an immuneresponse against it. An immune response occurs normally several days after birth and may be delayed experimentally for weeks before the deletion process ensues. However, for effective deletion of Mls-1 reactive T cells the mouse must be exposed to Mtv-7 positive lymphoid cells within hours after birth. In reviewing here data obtained in this and other laboratories regarding experimental induction of Mls-1 tolerance in neonatal mice we are trying to make a case for the involvement of Mtv-7 encoded antigens distinct from the superantigen. We propose that T cells reactive with non superantigenic Mtv-7 determinants pose a threat to the establishment of chimaerism between Mls-1- neonates and Mls-1+ inocula, as they may cause the rejection of Mls-1 superantigen bearing lymphocytes. Chimaerism is essential for the establishment of lasting Mls-1 tolerance.
Nonsteroidal antiinflammatory drug modulation of prosthesis pseudomembrane induced bone resorption. (1994)

Results provide a rational basis for design of animal models and/or further human studies to test the hypothesis that the prophylactic administration of an NSAID can potentially retard the pseudomembrane effected bone resorptive process associated with aseptic cemented prosthesis failure.
Generalized Analytical Framework for the Performance Assessment of Slotted Random Access Protocols (2014)

This manuscript provides a general analytical framework to accurately predict the performance of several slotted Random Access (RA) schemes such as Slotted Aloha and Diversity Slotted Aloha. Compared to past literature the proposed analytical framework allows to perform accurate performance estimation of these RA schemes exploiting state-of-the-art forward error correction schemes in the presence of packet power unbalance as it is the case in many practical systems. Furthermore, the analytical framework is also capable to accurately approximate the performance of more recent RA schemes particularly suitable for satellite communications such as Contention Resolution Diversity Slotted Aloha exploiting iterative interference cancellation techniques on top of packet repetition within the frame to further improve the RA scheme performance. The analytical results have been successfully verified against a comprehensive set of simulations covering cases of practical interest.
Site-directed mutagenesis of arginine 179 of thymidylate synthase. A nonessential substrate-binding residue. (1990)

X-ray structural studies have shown that Arg-179 of thymidylate synthase is complexed to bound inorganic phosphate or to the 5'-phosphate of the bound substrate dUMP. The importance of Arg-179 to the structure/function of thymidylate synthase is also indicated by its complete conservation among the 17 thymidylate synthases thus far sequenced. In the present work, Arg-179 has been replaced by Thr, Ala, Lys, and Glu using site-directed mutagenesis with a mixture of four synthetic oligonucleotides as primers. The mutant proteins complement thymidylate synthase-deficient Escherichia coli and show high enzyme activity. Each of these mutants has been purified to homogeneity, partially sequenced to verify the mutation, and has had its steady state kinetic parameters determined. The most significant effect of all mutations is localized to a decrease in the net rate of association of thymidylate synthase with dUMP; the Lys mutant also shows an apparent increase in the dissociation constant of the folate cofactor of the reaction. The high activity in the mutant enzymes is explained by "plasticity" of the enzyme and compensatory actions of the other Arg residues. Why the Arg-179 residue has been conserved during evolution remains an open question.
A First-Come-First-Serve Bus-Allocation Scheme Using Ticket Assignments (1981)

This paper describes a new scheme for allocating a data bus on a first-come-first-serve (FCFS) basis. When the devices connected to the bus request to become the bus-master, they are assigned distinct “ticket numbers” in the order in which the requests are generated, at which time they go into a wait state. When the bus is released by a device holding the ticket number n, it is then allocated to the device holding the ticket number n + 1. We discuss the conditions under which the scheme is a close approximation to the ideal FCFS scheme and evaluate its performance using simulation results. We also present two alternative hardware implementations of this scheme — one centralized and the other distributed. Because of its simple hardware implementation, the scheme is attractive for applications where a bus is shared, in an unbiased fashion, among a large number of devices.