gebhart/patrepeval huggingface dataset:
Lens gap junctions: a structural hypothesis for nonregulated low-resistance intercellular pathways. (1979)

Structural evidence is presented which suggests that gap junctions between lens fibers are adapted to remain in a low-resistance physiological state, under conditions which switch gap junctions in other tissues to a high-resistance state. The lens gap junction subunits (connexons) do not crystallize in the membrane plane in response to fixation, anoxia, lens damage, or homogenization and isolation. Rapid freezing experiments (Raviola et al.) suggest connexon resistance. Freshly homogenized liver cytoplasm does not contain an assayable factor which can crystallize connexons in lens gap junctions. Polyacrylamide gel electrophoresis of enrighed preparations of isolated lens junctions reveals a 27 +/- 2 kilodalton principal polypeptide which is similar in electrophoretic mobility to one of the principal polypeptides resolved in gels of isolated hepatocyte gap junctions. These results indicate that the whole lens may be extremely vulnerable to surface injury, perhaps even to injury of a single lens fiber.
Retrospective coregistration of functional magnetic resonance imaging data using external monitoring (2004)

Abstract Coregistration is essential for correcting head motion artifacts in functional magnetic resonance imaging (fMRI). Coregistration algorithms typically realign images through optimization of a similarity measure based on voxel signal intensities. However, coregistration can also be performed through external monitoring, whereby a tracking device measures head motion directly and independently of the imaging data. This paper describes development of external monitoring using fMRI‐compatible infrared cameras. Three subjects participated in block‐design fMRI experiments consisting of bilateral finger tapping alone and tapping combined with visuomotor tracking to produce controlled task‐correlated head motion. Functional MRI time‐series were coregistered using the external monitoring technique and a known image‐based algorithm for comparison. Over various performance characteristics, external monitoring and image‐based coregistration exhibited good agreement, in particular reducing signals correlated with millimeter task‐correlated motions by 50–100%, with a 5% difference between the two techniques. These results promise future applications and refinements of external monitoring in patient populations where head motion is especially problematic. Possibilities include 3D prospective coregistration during real‐time fMRI, coregistration of individual slices, and motion correction in anatomic MRI. Magn Reson Med 53:141–149, 2005. © 2004 Wiley‐Liss, Inc.
Pilot study of 5-azacytidine (5-AZA) and carboplatin (CBDCA) in patients with relapsed/refractory leukemia (1996)

5-azacytidine (5-AZA) and carboplatin (CBDCA) are two agents which have demonstrated antileukemic activity in a number of phase I-II trials. Their mechanisms of action and pharmacology related to cell resistance suggested suitability for combination therapy. The aim of this pilot was to evaluate the effects of this combination in the treatment of patients with relapsed/refractory acute leukemia. A total of 21 patients was enrolled. 5-azacytidine, at doses ranging from 50-150 mg/m2/day, was administered as a 2-hr infusion for 5 consecutive days. On day 3, patients began a 5-day course of CBDCA given as a 24-hr continuous intravenous infusion of 250 mg/m2/day. There were no complete remissions with this regimen. Although there were three partial responses, these were generally of short duration. Nonhematologic toxicities were mild. No correlation was seen between response and serum platinum levels. These results demonstrate that the 5-AZA/CBDCA combination is ineffective therapy for heavily pretreated patients with acute leukemia.
Cell penetration by transportan (1998)

Transportan is a 27 amino acid-long peptide containing 12 functional amino acids from the amino terminus of the neuropeptide galanin and mastoparan in the carboxyl terminus, connected via a lysine. Transportan is a cell-penetrating peptide as judged by indirect immunofluorescence using N epsilon13-biotinyl-transportan. The internalization of biotinyl-transportan is energy independent and takes place efficiently at 37 degrees, 4 degrees, and 0 degrees C. Cellular uptake of transportan is probably not mediated by endocytosis, since it cannot be blocked by treating the cells with phenylarsine oxide or hyperosmolar sucrose solution and is nonsaturable. The kinetics of internalization was studied with the aid of the 125I-labeled peptide. At 37 degrees C, the maximal intracellular concentration is reached in about 20 min. The internalized transportan is protected from trypsin. The cell-penetrating ability of transportan is not restricted by cell type, but seems to be a general feature of this peptide. In Bowes' melanoma cells, transportan first localizes in the outer membrane and cytoplasmatic membrane structures. This is followed by a redistribution into the nuclear membrane and uptake into the nuclei where transportan concentrates in distinct substructures, probably the nucleoli.
Modeling and Performance Analysis of TTE Bus Based on DSPN (2014)

The technology of Time-Triggered Ethernet(TTE)has been used in the new generation of aviation bus and developing at top speed,and the methods of modeling and performance analysis of TTE become an important meaning in its development of aerospace.Based on the working principle of message transmission of the TTE,this paper proposed a set of method of using Deterministic and Stochastic Petri Nets(DSPN)to model the TTE bus and do some related performance analysis,and also used a typical fire control system as an example for modeling and performance analysis,to illustrate the feasibility and effectiveness of the method.
Identification of an immunodominant B-cell epitope in bovine type II collagen and the production of antibodies to type II collagen by immunization with a synthetic peptide representing this epitope. (1992)

Using epitope scanning of 272 short, synthetic peptides representing the amino acid sequence of the CB-11 peptide of type II collagen, we have shown that five strains of rat, immunized with type II collagen, produce antibodies to a region 37-45 amino acids from the amino end of CB-11 peptide. Antibodies to this region always gave the highest binding values suggesting that it is an immunodominant region. Wistar rats immunized with a synthetic peptide representing this region, coupled to keyhole limpet haemocyanin, produced antibodies to this peptide which could still be detected at 1:4000 to 1:8000 dilution but none developed clinical arthritis. All sera also showed binding of antibodies to denatured bovine type II collagen but not to native type II collagen, keyhole limpet haemocyanin or to bovine serum albumin by ELISA. Sera from peptide-immunized rats were examined for antibody binding to the 272 short peptides of the CB-11 peptide and to the synthetic peptides representing shortened forms of the immunodominant region and forms of it with substituted amino acids. These results showed that the antibodies in the peptide-immunized rats were not identical to those produced to that peptide by rats immunized with type II collagen but may represent subpopulations of them. These findings suggest caution in interpreting the role of antibodies to individual peptides in arthritis induction without knowledge of their fine specificity.
Preferential Amplification of Apoptotic DNA from Plasma: Potential for Enhancing Detection of Minor DNA Alterations in Circulating DNA (2008)

Tumors release genomic DNA into the circulation of cancer patients after cellular necrosis and apoptosis. Isolation of the apoptotic fraction of plasma-circulating DNA can enhance detection of low-level mutations that can serve as tumor biomarkers (1). Because the amount of DNA circulating in the plasma of cancer patients is low, on the order of a few nanograms per milliliter of blood, the number of genes that can be examined for tumor-specific alterations is limited, a situation that reduces biomarker sensitivity. We recently applied whole-genome amplification of plasma-circulating DNA to increase the number of targets that can be analyzed from each sample, thus potentially increasing biomarker sensitivity(2). This approach yields highly-expanded DNA amounts for performing genetic screening; however, there is no preferential enrichment of smaller sized DNA fragments. We report a new method for whole-genome amplification of plasma-circulating DNA, based on ligation-mediated PCR of blunted DNA fragments (BLM-PCR)1 , which results in preferential amplification of smaller size, apoptotic DNA fragments.

Plasma-circulating DNA was extracted from blood obtained from radiation therapy patients after the patients gave informed consent and the study received institutional review board approval. Within 2–3 h of collection, whole blood was centrifuged at 2000 g for 15–30 min, plasma was separated, and plasma-circulating DNA was purified by use of a QIAamp™ MinElute Virus Spin Kit (Qiagen) and quantified via Taqman real-time-PCR. To test for v-Ki-ras2 Kirsten …
Inhibition of tolbutamide metabolism by substituted imidazole drugs in vivo: evidence for a structure‐activity relationship (1985)

Tolbutamide has been used as a model drug for an examination of the effects of eleven substituted imidazole compounds on hepatic metabolism in vivo. The 1-substituted compounds 1-methylimidazole, miconazole, clotrimazole and ketoconazole produced marked alterations in tolbutamide kinetics (increased half-life, decreased clearance). However, if there was substitution in the 2- position, irrespective of a substituent on N-1, then the compound did not appear to inhibit metabolism (e.g. 2-methylimidazole, 1,2-dimethylimidazole, methimazole, metronidazole). The 4- substituted compounds, 4-methylimidazole and cimetidine were inhibitors. A structure-activity relationship for the inhibitory actions of the substituted imidazoles is thus evident in vivo.
Involvement of Electrostatic Interactions in the Mechanism of Peptide Folding Induced by Sodium Dodecyl Sulfate Binding, (2000)

Sodium dodecyl sulfate (SDS) has consistently been shown to induce secondary structure, particularly alpha-helices, in polypeptides, and is commonly used to model membrane and other hydrophobic environments. However, the precise mechanism by which SDS induces these conformational changes remains unclear. To examine the role of electrostatic interactions in this mechanism, we have designed two hydrophilic, charged amphipathic alpha-helical peptides, one basic (QAPAYKKAAKKLAES) and the other acidic (QAPAYEEAAEELAKS), and their structures were studied by CD and NMR. The design of the peptides is based on the sequence of the segment of residues 56-70 of human platelet factor 4 [PF4(56-70), QAPLYKKIIKKLLES]. Both peptides were unstructured in water, and in the presence of neutral, zwitterionic, or cationic detergents. However, in SDS at neutral pH, the basic peptide folded into an alpha-helix. By contrast, the pH needed to be lowered to 1.8 before alpha-helix formation was observed for the acidic peptide. Strong, attractive electrostatic interactions, between the anionic groups of SDS and the cationic groups of the lysines, appeared to be necessary to initiate the folding of the basic peptide. NMR analysis showed that the basic peptide was fully embedded in SDS-peptide micelles, and that its three-dimensional alpha-helical structure could be superimposed on that of the native structure of PF4(56-70). These results enabled us to propose a working model of the basic peptide-SDS complex, and a mechanism for SDS-induced alpha-helical folding. This study demonstrates that, while the folding of peptides is mostly driven by hydrophobic effects, electrostatic interactions play a significant role in the formation and the stabilization of SDS-induced structure.
the grammar of consciousness and the consciousness of grammar (1985)

Symbolic values borrowed from Spanish into Mexicano (Nahuatl) usage simultaneously express differences in ritual status internal to peasant communities in central Mexico, but have also come to symbolize the threat to the peasant mode of production from a hostile peripheral‐capitalist marketplace. A system for examining the interaction of “voices” developed by Bakhtin applied to Mexicano discourses shows how examination of language use can contribute to the study of consciousness among proletarianizing peasant groups. [ consciousness, Nahuatl, Mexico, Bakhtin, purism in language ]
Anticipating Technological Change: Combinatorial Chemistry and the Environment (2001)

The purpose of this paper is to speculate, or suggest, how combinatorial chemistry may influence the environment and environmental policy. Technological change is frequently identified as a primary determinant of how human activities affect the environment and human health. Yet policy makers often have little opportunity to posit how technology development may change or affect current policies in the future. This paper is an attempt to look at one technology, combinatorial chemistry, and to suggest how it may or may not affect our current system. The genesis for this paper was a talk given by Dr. Paul Anderson, Vice President of Chemical and Physical Sciences, DuPont-Merck at a RAND Critical Technologies Seminar (The Critical Technologies Institute at RAND has since been renamed the Science and Technology Policy Institute). In his presentation he suggested that combinatorial chemistry would enable the simultaneous synthesis of significantly greater numbers of compounds than are routinely synthesized today.
PhaG-Mediated Synthesis of Poly(3-Hydroxyalkanoates) Consisting of Medium-Chain-Length Constituents from Nonrelated Carbon Sources in Recombinant Pseudomonas fragi (2000)

Recently, a new metabolic link between fatty acid de novo biosynthesis and biosynthesis of poly(3-hydroxy-alkanoate) consisting of medium-chain-length constituents (C(6) to C(14)) (PHA(MCL)), catalyzed by the 3-hydroxydecanoyl-[acyl-carrier-protein]:CoA transacylase (PhaG), has been identified in Pseudomonas putida (B. H. A. Rehm, N. Krüger, and A. Steinbüchel, J. Biol. Chem. 273:24044-24051, 1998). To establish this PHA-biosynthetic pathway in a non-PHA-accumulating bacterium, we functionally coexpressed phaC1 (encoding PHA synthase 1) from Pseudomonas aeruginosa and phaG (encoding the transacylase) from P. putida in Pseudomonas fragi. The recombinant strains of P. fragi were cultivated on gluconate as the sole carbon source, and PHA accumulation to about 14% of the total cellular dry weight was achieved. The respective polyester was isolated, and GPC analysis revealed a weight average molar mass of about 130,000 g mol(-1) and a polydispersity of 2.2. The PHA was composed mainly (60 mol%) of 3-hydroxydecanoate. These data strongly suggested that functional expression of phaC1 and phaG established a new pathway for PHA(MCL) biosynthesis from nonrelated carbon sources in P. fragi. When fatty acids were used as the carbon source, no PHA accumulation was observed in PHA synthase-expressing P. fragi, whereas application of the beta-oxidation inhibitor acrylic acid mediated PHA(MCL) accumulation. The substrate for the PHA synthase PhaC1 is therefore presumably directly provided through the enzymatic activity of the transacylase PhaG by the conversion of (R)-3-hydroxydecanoyl-ACP to (R)-3-hydroxydecanoyl-CoA when the organism is cultivated on gluconate. Here we demonstrate for the first time the establishment of PHA(MCL) synthesis from nonrelated carbon sources in a non-PHA-accumulating bacterium, employing fatty acid de novo biosynthesis and the enzymes PhaG (a transacylase) and PhaC1 (a PHA synthase).
Phosphorescent Nanoscale Coordination Polymers as Contrast Agents for Optical Imaging (2011)

Seeing is believing: Phosphorescent nanoscale coordination polymers (NCPs) with unprecedentedly high dye loadings were coated with thin silica shells to tune the dye release kinetics (see picture). Further functionalization of the NCP/silica particles with poly(ethylene glycol) (PEG) and PEG-anisamide enhanced their biocompatibility and targeting ability, allowing cancer-specific imaging of human lung cancer H460 cells. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The Serine Protease Domain of MASP-3: Enzymatic Properties and Crystal Structure in Complex with Ecotin (2013)

Mannan-binding lectin (MBL), ficolins and collectin-11 are known to associate with three homologous modular proteases, the MBL-Associated Serine Proteases (MASPs). The crystal structures of the catalytic domains of MASP-1 and MASP-2 have been solved, but the structure of the corresponding domain of MASP-3 remains unknown. A link between mutations in the MASP1/3 gene and the rare autosomal recessive 3MC (Mingarelli, Malpuech, Michels and Carnevale,) syndrome, characterized by various developmental disorders, was discovered recently, revealing an unexpected important role of MASP-3 in early developmental processes. To gain a first insight into the enzymatic and structural properties of MASP-3, a recombinant form of its serine protease (SP) domain was produced and characterized. The amidolytic activity of this domain on fluorescent peptidyl-aminomethylcoumarin substrates was shown to be considerably lower than that of other members of the C1r/C1s/MASP family. The E. coli protease inhibitor ecotin bound to the SP domains of MASP-3 and MASP-2, whereas no significant interaction was detected with MASP-1, C1r and C1s. A tetrameric complex comprising an ecotin dimer and two MASP-3 SP domains was isolated and its crystal structure was solved and refined to 3.2 Å. Analysis of the ecotin/MASP-3 interfaces allows a better understanding of the differential reactivity of the C1r/C1s/MASP protease family members towards ecotin, and comparison of the MASP-3 SP domain structure with those of other trypsin-like proteases yields novel hypotheses accounting for its zymogen-like properties in vitro.
Neutrophil Gelatinase-Associated Lipocalin Is Up-Regulated in Human Epithelial Cells by IL-1β, but Not by TNF-α (2003)

Synthesis of the antimicrobial protein neutrophil gelatinase-associated lipocalin (NGAL) increases dramatically in bronchial epithelial cells and alveolear type II pneumocytes during lung inflammation. IL-1beta induces a >10-fold up-regulation of NGAL expression in the type II pneumocyte-derived cell line A549 cells, whereas TNF-alpha, IL-6, and LPS had no effect. Similar IL-1beta selectivity was demonstrated in primary bronchial epithelial cells and epidermal keratinocytes and for an NGAL promoter fragment transfected into A549 cells. By deletion and substitution analysis of the NGAL promoter, a 40-bp region containing an NF-kappaB consensus site was found to control the IL-1beta-specific up-regulation. Involvement of the NF-kappaB site was demonstrated by site-directed mutagenesis, by transfection with a dominant-negative inhibitor of the NF-kappaB pathway, and by EMSA. TNF-alpha activation of NF-kappaB, in contrast, did not increase NGAL synthesis, even though induced binding of NF-kappaB to the NGAL promoter was observed in vitro. IL-1beta specificity was not contained within the NF-kappaB site of the NGAL promoter, as determined by exchanging the NGAL promoter's NF-kappaB-binding sequence with that of the IL-8 promoter or with the NF-kappaB consensus sequence and by testing the NF-kappaB-binding sequence of the NGAL promoter against the heterologous SV40 promoter. Selectivity for the IL-1 pathway was substantiated by demonstrating that NGAL promoter activity could be induced by LPS stimulation of A549 cells transiently expressing Toll-like receptor 4, which use the same intracellular signaling pathway as the IL-1R. Together, this demonstrates a selective up-regulation of NGAL by the IL-1 pathway.
A High-Molecular Mass Derivative of Trypsin-Kallikrein Inhibitor for Potential Medical Use, II[1]. Study of Inhibitory Activity (1982)

Three derivatives of poly[alpha-N beta-(2-hydroxyethyl)-DL-asparagine, beta-N alpha-(2-hydroxyethyl)-DL-asparagine] were used as soluble carrier polymers for binding the trypsin-kallikrein inhibitor (TKI). In addition to the parent polymer an anionic derivative with 19.2 mol of carboxyl groups/100 mol of residues and a hydrophobized derivative with 18.0 mol of butyl groups/100 mol of residues were also used. All carriers contained 6.6 mol of 2-(4-aminobenzamido)ethyl residues/100 mol which were used for the binding after diazotation. All derivatives retained a high inhibitory activity toward trypsin and chymotrypsin whereas the effect on kallikrein was substantially reduced. The kinetic constants were estimated under the simplifying assumption, that classical kinetic equations for the enzyme-inhibitor interaction may be applied. The equilibrium dissociation constants (5 X 10(-9) mol/l) and association rate constants (1 X 10(5) l X mol-1 X s-1) with respect to trypsin are unaffected by the two chemical modifications of the carrier. The increase in the equilibrium dissociation constant (compared to native TKI) is probably a result of the decreasing strength of the enzyme-inhibitor complex rather than a manifestation of reduced rate of diffusion of the enzyme to the active center of the polymer-bound inhibitor.
Imaging of DNA hybridization on microscopic polypyrrole patterns using scanning electrochemical microscopy (SECM): the HRP bio-catalyzed oxidation of 4-chloro-1-naphthol (2005)

We illustrate in this paper the successful combination of the direct and feedback mode of scanning electrochemical microscopy (SECM) for the writing of oligonucleotide patterns on thin gold films alongside the imaging of DNA hybridization. The patterning process was achieved using the direct mode of SECM, where the electrical field established between the SECM tip and the gold interface was used to drive the local deposition of micrometre sized polypyrrole spots to which a 15(mer) oligonucleotide (ODN) strand was linked covalently. Imaging of the deposited polypyrrole-ODNs was achieved by means of the feedback mode of SECM using Ru(NH(3))(6)(3+) as the mediator. The detection of the hybridization reaction of the ODN probes with their biotinylated complementary strands using SECM was possible after subsequent reactions with streptavidin and biotinylated horseradish peroxidase (HRP). The HRP-biocatalyzed oxidation of 4-chloro-1-naphthol (1) in the presence of H(2)O(2), and the precipitation of the insoluble product 4-chloro-1-naphthon (2) on the hybridized areas on the gold film caused a local alteration of conductivity. Such a change in conductivity was sensitively detected by the SECM tip and allowed imaging of DNA arrays in a fast and straightforward way.