gebhart/patrepeval huggingface dataset:
Molecular cloning, characterization and brain mapping of the melanocortin 5 receptor in the goldfish (2003)

The melanocortin 5 receptor (MC5R) is activated by melanocyte-stimulating hormones (MSHs) and has a widespread tissue distribution, while its detailed central expression pattern and brain functions are fairly unknown. We report cloning, pharmacological characterization, tissue distribution and detailed brain mapping of melanocortin 5 receptor in goldfish (gMC5R). The goldfish orthologue protein is 69% identical to human MC5R and is conserved in important functional domains. The gMC5R showed similar potency to alpha-, beta- and gamma-MSH peptides in radioligand binding as the mammalian orthologues, while MTII and HS024 were both agonists at this receptor. The gMC5R-mRNA was found in the peripheral tissues including kidney, spleen, skin and retina, with low expression levels in the intestine, fat, muscle, gill, pituitary and ovary. In situ hybridization studies demonstrated that gMC5R transcripts are widely distributed in the goldfish brain. The gMC5R expression was found in ventral telencephalon, pre-optic area, dorsal and ventral thalamus, infundibular hypothalamus, posterior tuberculum, tectum and tegmentum mesencephali, reticular formation, vagal and facial lobes and spinal cord. The cloning and characterization of this receptor provides an important tool to elucidate its participation in neuroendocrine and behavioural control.
Fast “Wittig-Like” Reactions As a Consequence of the Inorganic Enamine Effect (2015)

The tungsten alkylidyne [CF3-ONO]W≡CC(CH3)3(THF)2 (3) {where CF3-ONO = (MeC6H3[C(CF3)2O])2N(3-)} supported by a trianionic pincer-type ligand demonstrates enhanced nucleophilicity in unusually fast "Wittig-like" reactions. Experiments are designed to provide support for an inorganic enamine effect that is the origin of the enhanced nucleophilicity. Treating complex 3 with various carbonyl-containing substrates provides tungsten-oxo-vinyl complexes upon oxygen atom transfer. The rates of reactivity of 3 are compared with the known alkylidyne (DIPP)3W≡CC(CH3)3 (DIPP = 2,6-diisopropylphenoxide). In all cases (except acetone), complex 3 exhibits significantly faster overall rates than (DIPP)3W≡CC(CH3)3. New oxo-vinyl complexes are characterized by NMR, combustion analysis and single crystal X-ray diffraction. Treating 3 with acid chlorides provides the tungsten oxo chloride species [CF3-ONO]W(O)Cl (4) and disubstituted alkynes. In the case of acetone the oxo-vinyl complex results in two rotational isomers 10syn and 10anti. The rate of isomerization was determined for the forward and reverse directions and was complimented with DFT calculations.
MICROBIAL ECOLOGY OF THE GASTROINTESTINAL TRACT (1977)

CONTENTS INTRODUCTION 107 MICROBIAL ECOLOGY AS APPLIED TO THE GASTROINTESTINAL TRACT 108 MICROBIAL HABITATS IN THE MAMMALIAN GASTROINTESTINAL TRACT ........ 110 COMPOSITION AND LOCALIZATION OF CLIMAX COMMUNITIES IN ADULTS ...... 111 Some Comments on Methods 111 The Stomach (Esophagus) 112 The Small Bowel 115 The Large Bowel 116 The Feces 118 SUCCESSION IN BABIES 119 FACTORS INFLUENCING COMPOSITION OF THE MICROBIOTA 121 Forces Exerted by the Host and Its Diet and Environment 121 Forces Resulting from Activities of the Microbes Themselves 126 HOW MICROBES IN THE BIOTA MAKE THEIR LIVING (NICHES) 127 SUMMARY AND CONCLUSIONS 129
Assessment of root-associated paenibacillus polymyxa groups on growth promotion and induced systemic resistance in pepper. (2010)

Twenty-nine P. polymyxa strains isolated from rhizospheres of various crops were clustered into five genotypic groups on the basis of BOX-PCR analysis. The characteristics of several plant growth-promoting factors among the isolates revealed the distinct attributes in each allocated group. Under gnotobiotic conditions, inoculation of pepper roots with P. polymyxa isolates significantly increased the biomass in 17 of total 29 treated plants with untreated plants. Experiments on induced systemic resistance (ISR) against bacterial spot pathogen Xanthomonas axonopodis pv. vesicatoria in pepper by P. polymyxa strains were conducted and only one isolate (KNUC265) was selected. Further studies into ISR mediation by the KNUC265 strain against the soft-rot pathogen Erwinia carotovora subsp. carotovora in tobacco demonstrated that the tobacco seedlings exposed to either bacterial volatiles or diffusible metabolites exhibited a reduction in disease severity. In conclusion, ISR and plant growth promotion triggered by P. polymyxa isolates were systemically investigated on pepper for the first time. The P. polymyxa KNUC265 strain, which elicited both ISR and plant growth promotion, could be potentially used in improving the yield of pepper and possibly of other crops.
THE PRODUCTION OF HOMOZYGOUS DEFICIENT TISSUES WITH MUTANT CHARACTERISTICS BY MEANS OF THE ABERRANT MITOTIC BEHAVIOR OF RING-SHAPED CHROMOSOMES (1938)

This lengthy article stemmed from McClintock's discovery of ring chromosomes in 1932 and research she conducted on the
 gene bm1, or brown midrib, after returning to the University of Missouri in 1938. McClintock concluded that the extent of
 variegation in a mature plant was proportional to the size of the ring that was sometimes lost at cell division.
Genetic identification of a novel hantavirus of the harvest mouse Reithrodontomys megalotis (1994)

We have cloned the S genomic segment of a novel hantavirus of the harvest mouse Reithrodontomys megalotis. The virus is phylogenetically distinct from other hantaviruses. The new hantavirus was identified in harvest mice separated by approximately 1,000 km. A wood rat (Neotoma mexicana) was found to be infected with the harvest mouse hantavirus.
Digital copyright protection (1997)

Basic encryption introduction key-based systems network-based key systems defending copyright by embedding data compressional-based tagging postscript level hacking tamper resistant tagging defending against counterfeiting.
Error analysis for a free-hand three-dimensional ultrasound system for neuronavigation (1999)

Image-guided neurosurgery that is directed by a preoperative imaging study, such as magnetic resonance (MR) imaging or computerized tomography (CT) scanning, can be very accurate provided no significant changes occur during surgery. A variety of factors known to affect brain tissue movement are not reflected in the preoperative images used for guidance. To update the information on which neuronavigation is based, the authors propose the use of three-dimensional (3-D) ultrasound images in conjunction with a finite-element computational model of the deformation of the brain. The 3-D ultrasound system will provide real-time information on the displacement of deep structures to guide the mathematical model. This paper has two goals: first, to present an outline of steps necessary to compute the location of a feature appearing in an ultrasound image in an arbitrary coordinate system; and second, to present an extensive evaluation of this system's accuracy. The authors have found that by using a stylus rigidly coupled to the 3-D tracker's sensor, they were able to locate a point with an overall error of 1.36 ± 1.67 mm (based on 39 points). When coupling the tracker to an ultrasound scanhead, they found that they could locate features appearing on ultrasound images with an error of 2.96 ± 1.85 mm (total 58 features). They also found that when registering a skull phantom to coordinates that were defined by MR imaging or CT scanning, they could do so with an error of 0.86 ± 0.61 mm (based on 20 coordinates). Based on their previous finding of brain shifts on the order of 1 cm during surgery, the accuracy of their system warrants its use in updating neuronavigation imaging data.
Phosphorylation Studies on Rat p53 Using the Baculovirus Expression System. Manipulation of the Phosphorylation State with Okadaic Acid and Influence on DNA Binding (1995)

To elucidate the role of phosphorylation of p53 we used the baculovirus expression system to obtain high yields of protein eventually in distinct phosphorylation states. Initially, we obtained only marginal phosphorylation, despite high levels of expression. Two-dimensional phosphopeptide maps exhibited the same pattern as known from rat cells although some sites were underrepresented. Coexpression of simian virus 40 (SV40) large T antigen or cyclin-dependent kinases, cdc2 or cdk2, had only marginal effects on the phosphorylation state of p53. However, when we employed the phosphatase inhibitor okadaic acid, overall phosphorylation of p53 was drastically enhanced in a dose-dependent manner and resembled that of p53 from SV40-transformed rat cells. This hyperphosphorylation resulted in enhanced binding of a consensus oligonucleotide as revealed by electrophoretic mobility shift assays. To assess the role of individual phosphorylation sites, we generated a set of mutants at putative or identified sites. All mutants retained the ability to bind wild-type conformation-specific antibody Pab1620, to complex with SV40 large T antigen, and to bind to the consensus oligonucleotide. Moreover, most mutants exhibited enhanced DNA binding upon okadaic acid treatment, except for a mutant at the cdk site which failed to do so. These data show that: (a) insect cells contain all the protein kinases necessary for phosphorylation of a mammalian protein, p53; (b) in insect cells the ratio of kinase/phosphatase activities differs from that in mammalian cells so that underphosphorylation of recombinant proteins in this system may result from high phosphatase activities rather than saturation of kinases with recombinant substrate; (c) the system can be manipulated to obtain subpopulations of recombinant protein in a desired phosphorylation state, and (d) phosphorylation may regulate the DNA-binding activity of p53.
A Multiprobe-Per-Collector Modulated Scatterer Technique for Microwave Tomography (2011)

Scattering probes with collector antennas can be utilized for microwave tomography (MWT) applications based on the modulated scatterer technique. Using this technique, we previously demonstrated a novel tomography system that utilizes a single printed-wire probe in front of each collector of a multicollector MWT system. Each collector is implemented as a multilayer Vivaldi antenna. In this letter, the number of collector antennas is reduced while maintaining the number of probes. This results in a nonuniform distribution of probes with respect to the collectors and requires special calibration techniques to infer the scattered-field at the probe location. The advantages of using such a configuration for MWT are investigated. Image reconstructions for a number of targets using data collected from this system are shown and compared to results obtained from data collected using a standard MWT system that uses only the Vivaldi antennas. It is shown that the new configuration successfully extracts useful data at the locations of the probes, resulting in good tomographic constructions.
Mapping of the Binding Site for Mannheimia haemolytica Leukotoxin within Bovine CD18 (2005)

To map the site involved in Mannheimia haemolytica leukotoxin (LktA) binding and biological activity within bovine CD18, bovine x human CD18 chimeric constructs were generated and coexpressed with bovine CD11a in K562 cells. Studies with the chimeric leukocyte function-associated antigen 1 transductants demonstrate that the site required for LktA binding and biological effects resides within amino acid residues 500 and 600 of the extracellular region of bovine CD18.
Inhibition of HIV type 1 infectivity by constrained α-helical peptides: Implications for the viral fusion mechanism (1997)

Linear peptides derived from the membrane proximal region of the gp41 ectodomain are effective inhibitors of HIV type 1 (HIV-1)-mediated fusion events. These inhibitory peptides lack structure in solution, rendering mechanistic interpretation of their activity difficult. Using structurally constrained analogs of these molecules, we demonstrate that the peptides inhibit infectivity by adopting a helical conformation. Moreover, we show that a specific face of the helix must be exposed to block viral infectivity. Recent crystal structures show that the region of gp41 corresponding to the inhibitory peptides is helical and uses the analogous face to pack against a groove formed by an N-terminal coiled-coil trimer. Our results provide a direct link between the inhibition of HIV-1 infectivity by these peptides and the x-ray structures, and suggest that the conformation of gp41 observed by crystallography represents the fusogenic state. Other agents that block HIV-1 infectivity by binding to this groove may hold promise for the treatment of AIDS.
Artificial Zinc Finger Peptide Containing a Novel His4 Domain (2000)

Zinc finger constitutes one of the most common DNA binding motifs. Although zinc finger proteins consisting of Cys2His2, Cys3His, Cys4, and Cys6 domains are known in nature, a novel His4 zinc finger protein has never been observed. Herein, we have created the first artificial His4-type zinc finger protein (H4Sp1) engineered by Cys → His mutations of the Cys2His2-type zinc finger transcription factor Sp1. The CD features of the single finger H4Sp1f2 and three-finger H4Sp1 clearly demonstrate the folding of the mutant His4 peptides by complexation with Zn(II). The NMR study of Zn(II)-H4Sp1f2 reveals that some distortions of the helical region occur due to Zn(II) coordination. The gel mobility shift assay and DNase I footprinting analysis strongly show the binding of Zn(II)-H4Sp1 to the GC-box site of duplex DNA. The methylation interference pattern of Zn(II)-H4Sp1 binding significantly resembles that of the corresponding C2H2Sp1 binding. The present artificial peptide H4Sp1 is the first example of a zinc finger containing the His4 domain. Of special interest is the fact that the zinc finger domains of H4Sp1 are folded (although not identical to the native structure) and bind DNA similar to wild-type C2H2Sp1.
Evaluation of a Laser Doppler Flowmeter for Measurement of Tissue Blood Flow (1980)

An instrument for measurement of tissue blood flow based on the laser Doppler principle was evaluated using a fluid model. A unique and linear relationship between flowmeter response and flux of red cells was demonstrated with red cell velocities and volume fractions within the normal physiological range of the microcirculatory network of the skin. Different degrees of oxygenation proved to influence the Doppler signal only to a minor extent. The study also shows that the Doppler signal is formed essentially by heterodyne mixing of light beams backscattered in static structures and moving red cells.
Gene Expression During Autograft Lumbar Spine Fusion and the Effect of Bone Morphogenetic Protein 2 (1998)

A prospective animal study of posterolateral lumbar spine arthrodesis was performed to determine the temporal and spatial pattern of gene expression and to determine the effect of recombinant human bone morphogenetic protein 2 on the gene expression pattern of a healing spine fusion mass. In Group 1, 20 adult New Zealand rabbits underwent L4-L5 posterolateral intertransverse process arthrodesis using autograft alone. Two rabbits were euthanized at each of the following points: 0,2, and 4 days, and 1, 2, 3, 4, 5, 6, and 10 weeks after surgery. The same surgical technique was used for 16 rabbits in Group II, except that the autograft first was soaked in a solution of recombinant human bone morphogenetic protein 2 before implantation. Ribonucleic acid was extracted from different regions of the fusion mass at each point and analyzed for expression of bone and cartilage related genes using reverse transcription polymerase chain reaction. A reproducible temporal sequence and spatial pattern of gene expression was found in healing spine fusions. In the central portion of the fusion mass a temporal lag in gene expression was observed that parallels the lag in healing within the central zone previously observed in histologic studies. Treatment of bone graft with recombinant human bone morphogenetic protein 2 resulted in an increase in the early expression of bone morphogenetic protein 6 which was associated with expression of higher levels of Type I collagen, osteocalcin, and other bone related genes. These findings suggest that central nonunion may be associated with delayed expression of osteoblast related genes in the central region of the forming fusion mass. The growth factor, recombinant human bone morphogenetic protein 2, increased the level of bone related gene expression throughout the fusion mass, eliminated the delay in healing within the central zone, and may decrease the likelihood of a nonunion.
Detection of Escherichia coli O157 in French food samples using an immunomagnetic separation method and the VIDASTME. coli O157 (1997)

Two commercially available screening methods, an automated enzyme-linked fluorescent immunoassay (VIDAS E. coli O157) and an immunomagnetic separation followed by culture onto cefixime tellurite sorbitol MacConkey agar (CT-SMAC), were compared for detection of Escherichia coli O157 in naturally and artificially contaminated food samples. A total of 250 naturally contaminated food samples, including raw milk cheeses, poultry, raw sausages and ground beef retail samples, were examined. Four poultry, one raw sausage and one ground beef sample were found to be positive for E. coli O157 by both methods. Of the six positive samples, five were shown to contain sorbitol-positive, O157-positive, H7-negative, motile and non-verotoxin-producing E. coli.
Polyoxypeptins A and B Produced by Streptomyces:  Apoptosis-Inducing Cyclic Depsipeptides Containing the Novel Amino Acid (2S,3R)-3-Hydroxy-3-methylproline (1999)

Potent apoptosis-inducing peptides, polyoxypeptins A (1) and B (2) were isolated from the culture broth of Streptomyces sp. by solvent extraction and column chromatography. Structural elucidation of 1 by MS and NMR analyses revealed that it is a cyclic hexadepsipeptide having a novel amino acid and a previously unrecognized N-acyl side chain. The depsipeptide consisted of 3-hydroxyleucine, N-hydroxyvaline, N-hydroxyalanine, piperazic acid, 5-hydroxyhexahydropiperazine-3-carboxylic acid, and an unusual and hitherto unreported amino acid, 3-hydroxy-3-methylproline. Alanine and valine obtained from the hydrolyzate of 1 were both in the L-configuration as concluded from chiral TLC analysis. Then, the absolute structure of 1 was determined with the relative structure obtained from X-ray crystallographic analysis, and the new amino acid was isolated and confirmed to be (2S,3R)-3-hydroxy-3-methylproline (3). MS and NMR of 2 exhibited that it is a monodeoxy compound of 1. Stereochemistry of 2 was determined by degradation studies. Both 1 and 2 at a concentration of about 0.1 &mgr;g/mL induced early cell death, nuclear fragmentation, and internucleosomal DNA scission, all of which are characteristic of apoptosis, in human pancreatic carcinoma AsPC-1 cells.
nD-SQL: A Multi-Dimensional Language for Interoperability and OLAP (1998)

We propose a multi-dimensional language called nD-SQL with the following features: (i) nD-SQL supports queries that interoperate amongst multiple relational sources with heterogeneous schemas, including RDBMS and relational data marts, overcoming the mismatch between data and schema; (ii) it supports complex forms of restructuring that permit the visualization of n- dimensional data using the three physical dimensions of the relational model, viz., row, column, and relation; (iii) it captures sophisticated aggregations involving multiple granularities, to an arbitrary degree of resolution compared to CUBE, ROLLUP, and DRILLDOWN. We propose a formal model for a federation of relational sources and illustrate nD-SQL against it. We propose an extension to relational algebra, called restructuring relational algebra (RRA), capable of restructuring and aggregation. We propose an architecture for the implementation of an nD-SQL server, based on translating nD-SQL queries into equivalent RR...
Synthesis, Characterization, and Pharmacokinetic Studies of PEGylated Glucagon-like Peptide-1 (2005)

Glucagon-like peptide-1-(7-36) (GLP-1) is a hormone derived from the proglucagon molecule, which is considered a highly desirable antidiabetic agent mainly due to its unique glucose-dependent stimulation of insulin secretion profiles. However, the development of a GLP-1-based pharmaceutical agent has a severe limitation due to its very short half-life in plasma, being primarily degraded by dipeptidyl peptidase IV (DPP-IV) enzyme. To overcome this limitation, in this article we propose a novel and potent DPP-IV-resistant form of a poly(ethylene glycol)-conjugated GLP-1 preparation and its pharmacokinetic evaluation in rats. Two series of mono-PEGylated GLP-1, (i) N-terminally modified PEG(2k)-N(ter)-GLP-1 and (ii) isomers of Lys(26), Lys(34) modified PEG(2k)-Lys-GLP-1, were prepared by using mPEG-aldehyde and mPEG-succinimidyl propionate, respectively. To determine the optimized condition for PEGylation, the reactions were monitored at different pH buffer and time intervals by RP-HPLC and MALDI-TOF-MS. The in vitro insulinotropic effect of PEG(2k)-Lys-GLP-1 showed comparable biological activity with native GLP-1 (P = 0.11) in stimulating insulin secretion in isolated rat pancreatic islet and was significantly more potent than the PEG(2k)-N(ter)-GLP-1 (P < 0.05) that showed a marked reduced potency. Furthermore, PEG(2k)-Lys-GLP-1 was clearly resistant to purified DPP-IV in buffer with 50-fold increased half-life compared to unmodified GLP-1. When PEG(2k)-Lys-GLP-1 was administered intravenously and subcutaneously into rats, PEGylation improved the half-life, which resulted in substantial improvement of the mean plasma residence time as a 16-fold increase for iv and a 3.2-fold increase for sc. These preliminary results suggest a site specifically mono-PEGylated GLP-1 greatly improved the pharmacological profiles; thus, we anticipated that it could serve as potential candidate as an antidiabetic agent for the treatment of non-insulin-dependent diabetes patients.
The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection (2002)

RNase E, a multifunctional endoribonuclease of Escherichia coli, attacks substrates at highly specific sites. By using synthetic oligoribonucleotides containing repeats of identical target sequences protected from cleavage by 2'-O-methylated nucleotide substitutions at specific positions, we investigated how RNase E identifies its cleavage sites. We found that the RNase E catalytic domain (i.e., N-Rne) binds selectively to 5'-monophosphate RNA termini but has an inherent mode of cleavage in the 3' to 5' direction. Target sequences made uncleavable by the introduction of 2'-O-methyl-modified nucleotides bind to RNase E and impede cleavages at normally susceptible sites located 5' to, but not 3' to, the protected target. Our results indicate that RNase E can identify cleavage sites by a 3' to 5' "scanning" mechanism and imply that anchoring of the enzyme to the 5'-monophosphorylated end of these substrates orients the enzyme for directional cleavages that occur in a processive or quasiprocessive mode. In contrast, we find that RNase G, which has extensive structural homology with and size similarity to N-Rne, and can functionally complement RNase E gene deletions when overexpressed, has a nondirectional and distributive mode of action.