gebhart/patrepeval huggingface dataset:
Molecular Evolution of Receptor-Like Kinase Genes in Hexaploid Wheat. Independent Evolution of Orthologs after Polyploidization and Mechanisms of Local Rearrangements at Paralogous Loci (2001)

Hexaploid wheat is a young polyploid species and represents a good model to study mechanisms of gene evolution after polyploidization. Recent studies at the scale of the whole genome have suggested rapid genomic changes after polyploidization but so far the rearrangements that have occurred in terms of gene content and organization have not been analyzed at the microlevel in wheat. Here, we have isolated members of a receptor kinase (Lrk) gene family in hexaploid and diploid wheat, Aegilops tauschii, and barley (Hordeum vulgare). Phylogenetic analysis has allowed us to establish evolutionary relationships (orthology versus paralogy) between the different members of this gene family in wheat as well as with Lrk genes from barley. It also demonstrated that the sequences of the homoeologous Lrk genes evolved independently after polyploidization. In addition, we found evidence for gene loss during the evolution of wheat and barley. Analysis of large genomic fragments isolated from nonorthologous Lrk loci showed a high conservation of the gene content and gene organization at these loci on the homoeologous group 1 chromosomes of wheat and barley. Finally, sequence comparison of two paralogous fragments of chromosome 1B showed a large number of local events (sequence duplications, deletions, and insertions), which reveal rearrangements and mechanisms for genome enlargement at the microlevel.
Detection of Galactomannan and the 18 kDa Antigen from Aspergillus fumigatus in Serum and Urine from Cattle with Systemic Aspergillosis (1993)

Serum and urine samples from cattle with experimental and spontaneous systemic mycotic infections were tested for the presence of galactomannan and the 18 kDa antigen from Aspergillus fumigatus by an inhibition ELISA and immunoblotting, respectively. High levels of galactomannan (approximately 80 ng/ml.) were detected in serum from two of three calves experimentally infected with A. fumigatus. In two out of three cows with spontaneous acquired aspergillosis a similar amount of galactomannan was detected. Galactomannan was not found in serum samples of 20 cows which aborted due to either experimental or spontaneous placental aspergillosis. Twenty-four of forty urine samples from normal cattle reacted positively in the ELISA, consequently, the assay was not applicable on bovine urine. The 18 kDa antigen from A. fumigatus was detected in the urine from one calf out of three calves experimentally infected with aspergillosis and in the urine from one cow with spontaneous aspergillosis. It is concluded that detection of galactomannan in serum and the 18 kDa antigen in urine may be used as an aid for the diagnosis of disseminated bovine aspergillosis with the exception of placental and probably gastrointestinal localization.
Controlled Synthesis of Camptothecin−Polylactide Conjugates and Nanoconjugates (2009)

We report here a unique method of formulating camptothecin-polylactide (CPT-PLA) conjugate nanoparticles, termed nanoconjugates (NCs), through CPT/(BDI)ZnN(TMS)(2) [(BDI) = 2-((2,6-diisopropylphenyl)amido)-4-((2,6-bisalkyl)-imino)-2-pentene] mediated polymerization of lactide (LA) followed by nanoprecipitation. When CPT was used as the initiator to polymerize LA in the presence of (BDI)ZnN(TMS)(2), the polymerization was completed within hours with nearly 100% CPT loading efficiency and 100% LA conversion. CPT loading as high as 19.5% can be achieved for the CPT-polylactide (CPT-PLA) conjugate prepared at a LA/CPT ratio of 10. The steric bulk of the chelating ligands and the type of metals used had a dramatic effect on the initiation of the LA polymerization and the tendency of the ring-opening of the CPT lactone. The CPT/(BDI)ZnN(TMS)(2)-mediated LA polymerization yielded CPT-PLA conjugates with well-controlled molecular weights and narrow molecular weight distributions (1.02-1.18). The nanoprecipitation of CPT-PLA led to the formation of NCs around 100 nm in size with narrow particle size distributions. Sustained release of CPT from CPT-PLA NCs was achieved without burst release. CPT-PLA NCs were toxic to PC-3 cells with tunable IC(50) possible by adjusting the drug loading of the CPT-PLA NCs.
Transport into and out of the Nucleus (2001)

A defining characteristic of eukaryotic cells is the possession of a nuclear envelope. Transport of macromolecules between the nuclear and cytoplasmic compartments occurs through nuclear pore complexes that span the double membrane of this envelope. The molecular basis for transport has been revealed only within the last few years. The transport mechanism lacks motors and pumps and instead operates by a process of facilitated diffusion of soluble carrier proteins, in which vectoriality is provided by compartment-specific assembly and disassembly of cargo-carrier complexes. The carriers recognize localization signals on the cargo and can bind to pore proteins. They also bind a small GTPase, Ran, whose GTP-bound form is predominantly nuclear. Ran-GTP dissociates import carriers from their cargo and promotes the assembly of export carriers with cargo. The ongoing discovery of numerous carriers, Ran-independent transport mechanisms, and cofactors highlights the complexity of the nuclear transport process. Multiple regulatory mechanisms are also being identified that control cargo-carrier interactions. Circadian rhythms, cell cycle, transcription, RNA processing, and signal transduction are all regulated at the level of nucleocytoplasmic transport. This review focuses on recent discoveries in the field, with an emphasis on the carriers and cofactors involved in transport and on possible mechanisms for movement through the nuclear pores.
New Strategies in the Development of Antimicrobial Coatings: The Example of Increasing Usage of Silver and Silver Nanoparticles (2011)

Bacterial infection from medical devices is a major problem and accounts for an increasing number of deaths as well as high medical costs. Many different strategies have been developed to decrease the incidence of medical device related infection. One way to prevent infection is by modifying the surface of the devices in such a way that no bacterial adhesion can occur. This requires modification of the complete surface with, mostly, hydrophilic polymeric surface coatings. These materials are designed to be non-fouling, meaning that protein adsorption and subsequent microbial adhesion are minimized. Incorporation of antimicrobial agents in the bulk material or as a surface coating has been considered a viable alternative for systemic application of antibiotics. However, the manifestation of more and more multi-drug resistant bacterial strains restrains the use of antibiotics in a preventive strategy. The application of silver nanoparticles on the surface of medical devices has been used to prevent bacterial adhesion and subsequent biofilm formation. The nanoparticles are either deposited directly on the device surface, or applied in a polymeric surface coating. The silver is slowly released from the surface, thereby killing the bacteria present near the surface. In the last decade there has been a surplus of studies applying the concept of silver nanoparticles as an antimicrobial agent on a range of different medical devices. The main problem however is that the exact antimicrobial mechanism of silver remains unclear. Additionally, the antimicrobial efficacy of silver on medical devices varies to a great extent. Here we will review existing antimicrobial coating strategies and discuss the use of silver or silver nanoparticles on surfaces that are designed to prevent medical device related infections.
Combatting Junk Mail (1993)

We present a computational technique for combatting junk mail in particular and controlling access to a shared resource in general. The main idea is to require a user to compute a moderately hard, but not intractable, function in order to gain access to the resource, thus pre- venting frivolous use. To this end we suggest several pricing functions, based on, respectively, extracting square roots modulo a prime, the Fiat- Shamir signature scheme, and the Ong-Schnorr-Shamir (cracked) signa- ture scheme.
An introduction to data reduction: space-group determination, scaling and intensity statistics (2011)

This paper presents an overview of how to run the CCP4 programs for data reduction (SCALA, POINTLESS and CTRUNCATE) through the CCP4 graphical interface ccp4i and points out some issues that need to be considered, together with a few examples. It covers determination of the point-group symmetry of the diffraction data (the Laue group), which is required for the subsequent scaling step, examination of systematic absences, which in many cases will allow inference of the space group, putting multiple data sets on a common indexing system when there are alternatives, the scaling step itself, which produces a large set of data-quality indicators, estimation of |F| from intensity and finally examination of intensity statistics to detect crystal pathologies such as twinning. An appendix outlines the scoring schemes used by the program POINTLESS to assign probabilities to possible Laue and space groups.
Abstract 3730: Celecoxib Does Not Deteriorate Antiplatelet Effects of Aspirin and Clopidogrel in Healthy Volunteers (2008)

Background: Celecoxib, cyclooxygenase (COX)-2 inhibitor, has been reported to inhibit neointimal hyperplasia in animal studies and to reduce restenosis after coronary stenting in COREA-TAXUS clinical trial. The main concern is that celecoxib would increase thrombogenecity by inhibiting the synthesis of prostacyclin in endothelial cells. However, it is not known whether the administration of celecoxib would weaken antiplatelet effects of aspirin and clopidogrel which are used after stenting. Methods: We recruited healthy volunteers (n=40) and randomized them into five subgroups. Each subject received the medication for 6 days and blood samples were taken day 0 and 7. Celecoxib 200mg twice a day, and/or aspirin 100mg daily, and/or clopidogrel 75 mg daily was administered. We compared platelet function by using light transmittance aggregometry and arachidonic acid metabolite assay among subgroups. Results: Celecoxib single treatment did not significantly affect platelet aggregation. Dual asprin and Plavix treatment inhibited platelet aggregation by 53%, which was not affected by addition of celecoxib showing 52% inhibition (t-test: p = 0.873). The changes of prostacyclin level did not differ among each treatment group (ANOVA: p=0.193). Although statistically not significant, celecoxib seems to lower the thromboxane level further when added to antiplatelet agents. Conclusion: Celecoxib treatment did not interfere with antiplatelet effect of aspirin or clopidogrel, suggesting that celecoxib as anti-restenosis agent would be administered safely during coverage of dual antiplatelet therapy in patients with coronary stenting without increasing thrombogenecity.
MicroRNAs/TP53 feedback circuitry in glioblastoma multiforme (2012)

MicroRNAs (miRNAs) are increasingly implicated in regulating cancer initiation and progression. In this study, two miRNAs, miR-25 and -32, are identified as p53-repressed miRNAs by p53-dependent negative regulation of their transcriptional regulators, E2F1 and MYC. However, miR-25 and -32 result in p53 accumulation by directly targeting Mdm2 and TSC1, which are negative regulators of p53 and the mTOR (mammalian target of rapamycin) pathway, respectively, leading to inhibition of cellular proliferation through cell cycle arrest. Thus, there is a recurrent autoregulatory circuit involving expression of p53, E2F1, and MYC to regulate the expression of miR-25 and -32, which are miRNAs that, in turn, control p53 accumulation. Significantly, overexpression of transfected miR-25 and -32 in glioblastoma multiforme cells inhibited growth of the glioblastoma multiforme cells in mouse brain in vivo. The results define miR-25 and -32 as positive regulators of p53, underscoring their role in tumorigenesis in glioblastoma.
Epsilon protein kinase C as a potential therapeutic target for the ischemic heart (2006)

Ischemic heart disease is the leading cause of morbidity and mortality in the western world. Ischemic damage can occur by acute myocardial infarction, stable angina, cardiac stunning, and myocardial hibernation. In addition, 'scheduled' ischemic events, occurring during cardiac surgery, heart transplantation, and elective angioplasty, can also result in cardiac damage. Ischemic or pharmacological preconditioning can decrease the extent of damage to the myocardium. Although the mechanism of preconditioning-mediated cardioprotection is not fully understood, epsilonPKC has been implicated as a critical mediator of this process in animal studies. The use of isozyme-specific pharmacological tools has permitted a better elucidation of the upstream stimuli and the downstream transducers of epsilonPKC in the pathways leading to cardioprotection. While little is known about the role of epsilonPKC in these pathways in humans, animal studies suggest a potential therapeutic role of epsilonPKC. This review will focus on the role of epsilonPKC in cardiac protection and on the signal transduction cascades that have been implicated in this protection.
Structure, expression, and chromosome location of the gene for the beta subunit of brain-specific Ca2+/calmodulin-dependent protein kinase II identified by transgene integration in an embryonic lethal mouse mutant. (1992)

The transgenic mouse strain CAT40 carries in its germ line one copy of a DNA construct consisting of the chloramphenicol acetyltransferase gene and the immunoglobulin heavy-chain enhancer. We show that transgene integration has resulted in a recessive lethal mutation that leads to death of homozygous CAT40 embryos shortly after implantation. The transgene has integrated adjacent to the 3' end of the gene coding for the beta subunit of the brain-specific Ca2+/calmodulin-dependent protein kinase II (Camk-2). The complete cDNA sequence of the Camk-2 gene and most of its exon/intron structure was determined. The deduced amino acid sequence is highly homologous to the previously described rat protein. The chromosomal location of the Camk-2 locus was mapped by interspecific backcross analysis to the proximal region of mouse chromosome 11. This region lacks previously identified recessive embryonic lethal mutations. During embryonic development, Camk-2-specific transcripts are first seen in the head section of 12.5-day-old embryos, and in adult mice the gene is expressed almost exclusively in the brain. Although transcription of the Camk-2 gene in heterozygous CAT40 mice is affected by transgene integration, it is unlikely that this gene is responsible for the mutant phenotype, since it is not expressed in blastocysts and the first transcripts during normal development are detected after the death of homozygous CAT40 embryos. Transgene integration is accompanied by a large deletion of cellular DNA; death is therefore most likely caused by the loss of a gene or genes that are important for early postimplantation development.
Fusion Proteins Could Generate False Positives in Peptide Phage Display (1999)

Fusion proteins are frequently used in the functional characterization of newly discovered proteins and to identify interacting partners. In our study of hPTP1E, a cytosolic protein tyrosine phosphatase, we used glutathione S-transferase (GST)-fusion protein of the second PDZ domain to identify interacting peptide motifs by peptide phage display. A consensus motif G X X V W L G was identified and found to be specific for binding to GST-PDZ2 as determined by ELISA, peptide displacement and by protein overlay. However, using nuclear magnetic resonance (NMR), no interaction of the peptide was observed with PDZ2 alone. In co-precipitation experiments using the consensus peptide cross-linked to Affi-Gel, only GST-PDZ2 (but not PDZ2 or GST alone) could be precipitated. These data suggest that there is a potential for identification of artifacts when using fusion proteins in peptide phage display, and one should exercise caution in interpreting these results. It is critical that the interaction be verified using a second, independent system.
SYNTHESIS OF (2,3,4,6-TETRA-O-ACETYL-α-D-GLYCOPYRANOSYL) THIOPHENE DERIVATIVES AS NEW C-NUCLEOSIDE ANALOGUES1 (2001)

Treatment of 2-(2,3,4,6-tetra-O-acetyl-α-D-glucopyranosyl)ethanal (1a) and 2-(2,3,4,6-tetra-O-acetyl-α-D-galactopyranosyl)ethanal (1b) respectively with malononitrile in the presence of silica gel provided the corresponding 4-[2,3,4,6-tetra-O-acetyl-α-D-glycopyranosyl]-2-cyanocrotononitriles (2a) and (2b). Starting from 2a and 2b, respectively, cyclizations with sulfur and triethylamine yielded 5-[2,3,4,6-tetra-O-acetyl-α-D-glycopyranosyl]-2-aminothiophene-3-carbonitriles (3a) and (3b). Further cyclizations could be achieved by utilizing of triethyl orthoformate/ammonia to furnish the 6-(α-D-glycopyranosyl)thieno[2,3-d]pyrimidine-4-amines 4a and 4b.
The Role of Carotenoids in Human Health (2002)

Dietary carotenoids are thought to provide health benefits in decreasing the risk of disease, particularly certain cancers and eye disease. The carotenoids that have been most studied in this regard are beta-carotene, lycopene, lutein, and zeaxanthin. In part, the beneficial effects of carotenoids are thought to be due to their role as antioxidants. beta-Carotene may have added benefits due its ability to be converted to vitamin A. Furthermore, lutein and zeaxanthin may be protective in eye disease because they absorb damaging blue light that enters the eye. Food sources of these compounds include a variety of fruits and vegetables, although the primary sources of lycopene are tomato and tomato products. Additionally, egg yolk is a highly bioavailable source of lutein and zeaxanthin. These carotenoids are available in supplement form. However, intervention trials with large doses of beta-carotene found an adverse effect on the incidence of lung cancer in smokers and workers exposed to asbestos. Until the efficacy and safety of taking supplements containing these nutrients can be determined, current dietary recommendations of diets high in fruits and vegetables are advised.
Multicast in MPLS/BGP IP VPNs (2012)

In order for IP multicast traffic within a BGP/MPLS IP VPN (Virtual
Private Network) to travel from one VPN site to another, special
protocols and procedures must be implemented by the VPN Service
Provider. These protocols and procedures are specified in this
document. [STANDARDS-TRACK]
Invertibility of elastic layered earth parameters from precriticalP‐wave reflection amplitudes (1984)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1984Invertibility of elastic layered earth parameters from precritical P‐wave reflection amplitudesAuthors: Lawrence C. MorleyLawrence C. MorleyGolden Geophysical Corp.https://doi.org/10.1190/1.1894142 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1894142FiguresReferencesRelatedDetailsCited byReferences24 May 2016 SEG Technical Program Expanded Abstracts 1984ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1984 Pages: 856 publication data© 1984 Copyright © 1984 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 24 Mar 2005 CITATION INFORMATION Lawrence C. Morley, (1984), "Invertibility of elastic layered earth parameters from precritical P‐wave reflection amplitudes," SEG Technical Program Expanded Abstracts : 641-643. https://doi.org/10.1190/1.1894142 Plain-Language Summary PDF DownloadLoading ...
Point mutants of EHEC intimin that diminish Tir recognition and actin pedestal formation highlight a putative Tir binding pocket (2002)

Attachment to host cells by enterohaemorrhagic Escherichia coli (EHEC) is associated with the formation of a highly organized cytoskeletal structure containing filamentous actin, termed an attaching and effacing (AE) lesion. Intimin, an outer membrane protein of EHEC, is required for the formation of AE lesions, as is Tir, a bacterial protein that is translocated into the host cell to function as a receptor for intimin. We established a yeast two-hybrid assay for intimin-Tir interaction and, after random mutagenesis, isolated 24 point mutants in intimin, which disrupted Tir recognition in this system. Analysis of 11 point mutants revealed a correlation between recognition of recombinant Tir and the ability to trigger AE lesions. Many of the mutations fell within a 50-residue region near the C-terminus of intimin. Alanine-scanning mutagenesis of this region revealed four residues (Ser890, Thr909, Asn916 and Asn927) that are critical for Tir recognition. Mapping the sequences of EHEC intimin and Tir onto the crystal structure of the intimin-Tir complex of enteropathogenic E. coli predicts that each of these four intimin residues lies at the intimin-Tir interface and contributes to a pocket that interacts with Ile298 of EHEC Tir. Thus, this genetic approach to intimin function both identified residues critical for Tir binding and demonstrated a correlation between the ability to bind Tir and the ability to trigger actin focusing.
Conformational and dynamic properties of a 14 residue antifreeze glycopeptide from antarctic cod (1998)

The 1H and 13C NMR spectra of a 14-residue antifreeze glycopeptide from Antarctic cod (Tetramatomnus borchgrevinki) containing two proline residues have been assigned. 13C NMR relaxation experiments indicate motional anisotropy of the peptide, with a tumbling time in water at 5 degrees C of 3-4 ns. The relaxation data and lack of long-range NOEs are consistent with a linear peptide undergoing significant segmental motion. However, extreme values of some coupling constants and strong sequential NOEs indicate regions of local order, which are most evident at the two ATPA subsequences. Similar spectroscopic properties were observed in the 16-residue analogue containing an Arg-Ala dipeptide added to the C-terminus. Molecular modeling also showed no evidence of long-range order, but the two ATPA subsequences were relatively well determined by the experimental data. These motifs were quite distinct from helical structures or beta turns commonly found in proteins, but rather resemble sections of an extended polyproline helix. Thus, the NMR data provide a description of the local order, which is of relevance to the mechanism of action of the antifreeze activity of the antifreeze glycopeptides as well as their ability to protect cells during hypothermic storage.
Treating Heart Failure With Sildenafil (2009)

Sildenafil is a selective inhibitor of type 5 phosphodiesterase, the main phosphodiesterase isoform responsible for hydrolysis of intracellular cyclic guanosine monophosphate in the pulmonary vasculature. It improves exercise capacity and quality of life in patients with systolic heart failure, especially in those who develop secondary pulmonary hypertension. It improves peak oxygen consumption, reduces minute ventilation/carbon dioxide output slope, and acts as a selective pulmonary vasodilator during rest and exercise in patients with heart failure and pulmonary hypertension. It improves flow-mediated maximal dilatation, ergoreflex on ventilation, and breathlessness both after 3 and 6 months of treatment. Sildenafil, by improving endothelial activity and muscle perfusion, improves signaling and ventilatory efficiencies, potentially indicating a novel approach in the therapeutic management of heart failure.