gebhart/patrepeval huggingface dataset:
GES-type and OXA-23 carbapenemase-producing Acinetobacter baumannii in Turkey (2013)

INSERM U914 ‘Emerging Resistance to Antibiotics’, Le KremlinBicetre, France; Department of Infectious Diseases and Clinical Microbiology, Ege University Medical Faculty, Izmir, Turkey; Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science, University of Fribourg, Fribourg, Switzerland; Department of Medical Microbiology, Ege University Medical Faculty, Izmir, Turkey; Intensive Care and Reanimation Unit, Ege University Medical Faculty, Izmir, Turkey
Enzymatic synthesis and chemical inversion provide both enantiomers of bioactive epoxydocosapentaenoic acids (2018)

Epoxy PUFAs are endogenous cytochrome P450 (P450) metabolites of dietary PUFAs. Although these metabolites exert numerous biological effects, attempts to study their complex biology have been hampered by difficulty in obtaining the epoxides as pure regioisomers and enantiomers. To remedy this, we synthesized 19,20- and 16,17-epoxydocosapentaenoic acids (EDPs) (the two most abundant EDPs in vivo) by epoxidation of DHA with WT and the mutant (F87V) P450 enzyme BM3 from <i>Bacillus megaterium</i> WT epoxidation yielded a 4:1 mixture of 19,20:16,17-EDP exclusively as (<i>S</i>,<i>R</i>) enantiomers. Epoxidation with the mutant (F87V) yielded a 1.6:1 mixture of 19,20:16,17-EDP; the 19,20-EDP fraction was ∼9:1 (<i>S</i>,<i>R</i>):(<i>R</i>,<i>S</i>), but the 16,17-EDP was exclusively the (<i>S</i>,<i>R</i>) enantiomer. To access the (<i>R</i>,<i>S</i>) enantiomers of these EDPs, we used a short (four-step) chemical inversion sequence, which utilizes 2-(phenylthio)ethanol as the epoxide-opening nucleophile, followed by mesylation of the resulting alcohol, oxidation of the thioether moiety, and base-catalyzed elimination. This short synthesis cleanly converts the (<i>S</i>,<i>R</i>)-epoxide to the (<i>R</i>,<i>S</i>)-epoxide without loss of enantiopurity. This method, also applicable to eicosapentaenoic acid and arachidonic acid, provides a simple, cost-effective procedure for accessing larger amounts of these metabolites.
Encircling endocardial ventriculotomy for refractory ischemic ventricular tachycardia. I. Electrophysiological effects. (1982)

The direct endocardial surgical techniques introduced for the treatment of refractory ischemic ventricular tachyarrhythmias have resulted in decreased surgical mortality rates and increased success rates in comparison to previous indirect techniques. Since the mechanism of action of one of these new techniques, the encircling endocardial ventriculotomy (EEV), is unknown, the present study was designed to clarify the electrophysiological effects of this procedure. Epicardial and intramural electrophysiology was studied in 18 dogs before and after undergoing an EEV. In the absence of induced myocardial ischemia, the procedure caused an epicardial conduction delay of 23 +/- 3 msec (p less than 0.0001) across the boundaries of the incision. When the EEV enriched acutely ischemic myocardium, it was capable in certain instances of isolating spontaneous ventricular electrical activity to the myocardium encompassed by the incision and thereby protecting the remainder of the heart from the arrhythmia. The EEV resulted in total ablation of all (2 Mv/msec) electrical activity at 20 of 48 (42%) subendocardial electrode sites and at 12 of 44 (27%) subepicardial sites monitored within the encompassed myocardium. These data suggest that although the EEV may be capable of isolating ischemic ventricular tachyarrhythmias to the encompassed myocardium, it most commonly ablates the anatomic-electrophysiological substrate necessary for the genesis and perpetuation of these arrhythmias.
Drug-metabolizing activity of human and rat liver, lung, kidney and intestine slices (2002)

1. Organ-specific biotransformation was studied in human and rat liver, lung, kidney and small intestine slices and compared on a protein basis, using four model substances. 2. Deethylation of lidocaine was highest in liver slices from both man and rat, followed by the small intestine. 3. Metabolism of testosterone was highest in liver slices, but a different overall metabolic pattern was found between the different organs. 4. Lung, kidney and intestine slices prepared from human and rat organs showed mainly an unknown metabolite of 7-ethoxycoumarin identified as 4-ethoxy-2-hydroxyphenyl propionic acid (EPPA). 5. The maximal metabolism of 7-ethoxycoumarin in slices was equal with in vivo V(max) in the rat. 6. Phase II metabolism of 7-hydroxycoumarin in kidney and intestinal slices was about 60% of the activity in liver slices. 7. In conclusion, organs other than the liver show a surprisingly high drug-metabolizing activity. Thus, the use of precision-cut slices of a combination of drug metabolizing organs in an in vitro test system from both animal and human origin is required for a proper systematic prediction of drug metabolism in man.
Exploring the Graft-To Synthesis of All-Conjugated Comb Copolymers Using Azide–Alkyne Click Chemistry (2018)

Copolymers with graft architectures possess interesting material properties distinct from their linear polymer counterparts. The effects of multidimensional architectures on the optoelectronic and physical properties of all-conjugated graft copolymers are not well-known, thus providing a large incentive for their study. In order to readily access these materials (hypothesized to have “comb” architectures), it is extremely important to investigate the methods used in their synthesis. Here we study the graft-to synthesis of comb copolymers composed of polythiophene backbones and polyselenophene side chains and identify the opportunities and challenges associated with copolymer formation. Azide-functionalized polythiophene “backbones” and acetylene-terminated polyselenophene “side chains” were synthesized in a controlled fashion using Kumada catalyst-transfer polycondensation (KCTP) polymerization and grafted together using copper-catalyzed azide–alkyne click chemistry (CuAAC). 1H NMR, GPC, and FTIR results confirm the attachment of polyselenophene side chains to the polythiophene backbone, resulting in comb copolymers with varying grafting densities. Low grafting density copolymers are readily synthesized using various backbone and side chain polymers. Midrange grafting density copolymers are more challenging but can be accessed when the availability of the graft sites on the polythiophene backbones is maximized. The synthesis of high grafting density combs remains challenging even when various modifications to the backbone and side chain polymers are implemented to improve the grafting efficiency. Problematic Glaser homocoupling of acetylene-terminated polyselenophenes was observed in certain conditions; however, this can be successfully prevented using an organic-soluble copper catalyst which is broadly applicable to many polymer–polymer CuAAC reactions. Ultimately, this investigation demonstrates a graft-to synthetic method that is useful for low- and midgrafting density all-conjugated comb copolymers, thus providing a means to further the study of these interesting multidimensional semiconducting materials.
Effect of Water Stress on in Vitro Heat Tolerance of Turfgrass Leaves1 (1983)

Abstract Seedlings of Kentucky bluegrass ( Poa pratensis L.), perennial ryegrass ( Lolium perenne L.), red fescue ( Festuca rubra L.), and weeping alkaligrass [ Puccinellia distans (L.) Parl.] were exposed to water stress prior to measuring heat tolerance of leaf blade segments. Heat tolerance was determined using an electrolyte leakage assay. Water stress pretreatments did not increase in vitro heat tolerance of turfgrass leaves.
Proneness of TLR5 deficient mice to develop colitis is microbiota dependent (2015)

Alterations in the gut microbiota have been implicated to play a role in potentiating inflammatory bowel diseases in both humans and mice. Mice lacking the flagellin receptor, toll-like receptor 5 (TLR5), are prone to develop spontaneous gut inflammation, but are significantly protected when treated with antibiotics or maintained in germ-free conditions. However, given that the incidence of spontaneous inflammation in TLR5KO mice is quite variable in conventional conditions (typically ∼10% show clear colitis), this result is far from definitive and does not rule out that TLR5KO mice might be prone to develop inflammation even in the absence of a microbiota. Herein, we demonstrate that neutralization of IL10 signaling induces colitis in 100% of TLR5KO mice which provide a more rigorous approach to evaluate the role of microbiota in gut inflammation. Mice treated with antibiotics or maintained in germ-free condition are substantially protected against IL-10R neutralization-induced colitis, underscoring that gut inflammation in TLR5KO mice is dependent upon the presence of a gut microbiota.
Nutritional components of growth of Arabica coffee genotypes cultivated under different levels of phosphorus fertilization studied by path analysis. (2015)

The high nutritional exigency of new cultivars of coffee led this study to estimate correlations between nutrient contents and to estimate their direct and indirect effects, by path analysis, over the early growth of eight genotypes of 'Coffea arabica' L, cultivated in environments with different levels of phosphorus supply. The experiment was conducted under controlled environment, following an 8 5 factorial scheme, in a completely randomized design, with four replications. The factors studied were eight genotypes of 'Coffea arabica' L. and five conditions of availability of phosphorus in the soil: 0.00, 0.18, 0.36, 0.72, and 1.44 grams of P2O5 per kilogram of soil. The growth analyses were based on dry matter, leaf area, and chlorophyll content accumulated in 150 days of cultivation. The leaf content of P, K, Ca, Mg, Zn, Cu, Fe, and Mn were used as nutritional components. The correlations were estimated and unfolded between direct and indirect effects through path analysis. Significant correlations were observed between nutritional components, and these correlations are modulated by environmental factors, such as soil type and water supply. Different levels of phosphorus fertilization promotes interactions between P Mg, K Ca, Ca Mg, Ca Mn, Ca Zn; Mg Mn, Cu Fe, Cu Mn, and Mg Zn. Some nutritional components cause strong positive effects over the early growth of genotypes of 'Coffea arabica' L.; highlighting the content of K for accumulation of biomass and development of leaf area, and Fe for chlorophyll synthesis; being possible to be explored in the indirect selection aiming to improve the early growth simultaneously to improvement of nutritional parameters.
Effects of cross-layer processing on wireless ad hoc network performance (2006)

The traditional OSI layered design used in wired networks is considered to be the bottleneck in current wireless ad hoc network's less than desirable performance. In order to support new multimedia network and to provide ubiquitous wireless access, various OSI layers and network functions must be considered together while designing the network. In this paper, we discuss the performance optimization challenges of ad hoc network and how cross-layered processing can improve its performance. We implemented a protocol stack that involves cross-layer processing including: (a) transmission rate adaptation in the MAC layer based on the channel signal strength information from physical layer and (b) congestion information from MAC layer to network routing protocol - DSR as a congestion aware routing metric for optimal route discovery. The simulation results show network performance improvement.
Solid state electroactive devices based on redox switching polymers (1995)

The redox switching of some conducting polymers was investigated. Poly(3,4- ethylenedioxythiophene) and two of its alkyl derivatives were investigated in a liquid electrolyte to probe its usefulness as a visible electrochromic device. The other type of device is based upon actively changing the surface conductivity of one active layer of the device using conducting polymer: in one state the surface conductivity is high, in the other state the surface conductivity is low. Switching speed, contrast ratio, and overall lifetime for both devices were determined and discussed.
Abstract 2075: GPCRs for pituitary adenylate cyclase activating polypeptide regulate transactivation of HER3 in non-small cell lung cancer cells (2020)

Abstract HER3, which lacks intrinsic kinase activity, plays an important role in cancer proliferation by formation of heterodimers with the EGFR or HER2 (Kiavue et al., Oncogene, 2019). Peptide GPCRs for pituitary adenylate cyclase activating polypeptide (PACAP) stimulate growth by transactivation of the EGFR and HER2 (Moody et al., JPET, 2012 and Peptides, 2019), but its effect on HER3 is unknown. The ability of PACAP to cause tyrosine phosphorylation of the EGFR, HER2 and HER3 was investigated. Using a panel of 17 non-small cell lung cancer (NSCLC) cell lines, mRNA for EGFR, HER2, HER3 was detected in 94%, 88%, and 100% of the cell lines, respectively. Addition of 100 nM PACAP but not vasoactive intestinal peptide to A549 cells increased EGFR, HER2 and HER3 tyrosine phosphorylation by 420, 240 and 190%, respectively. The increase is EGFR tyrosine phosphorylation was blocked by gefitinib or PACAP(6-38), a PAC1 antagonist. The increase in HER2 tyrosine phosphorylation caused by PACAP was inhibited by Herceptin or PACAP(6-38). The increase in HER3 tyrosine phosphorylation caused by PACAP was inhibited by the HER3 blocking antibody mAb3481 or PACAP(6-38). Immunoprecipitation experiments indicated the PACAP addition to A549 cells resulted in the formation of EGFR/HER2 and HER2/HER3 heterodimers, whereas addition of EGF resulted in EGFR/HER2 heterodimers and addition of the HER3 agonist neuregulin-1 resulted in HER2/HER3 heterodimers. Addition of N-acetyl-cysteine (antioxidant), Tiron (superoxide scavenger) or diphenylene iodonium (Nox/Duox inhibitor) impaired the ability of PACAP to cause EGFR, HER2 or HER3 transactivation. The results indicate that reactive oxygen species are essential for PACAP to cause EGFR, HER2 or HER3 transactivation in non small cell lung cancer cells. Citation Format: Terry W. Moody, Lingaku Lee, Robert T. Jensen. GPCRs for pituitary adenylate cyclase activating polypeptide regulate transactivation of HER3 in non-small cell lung cancer cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2075.
Ceramic Layer Composites in Advanced Automotive Engineering and Biomedical Applications (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation (2015)

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
Supplementary Figure 4 from A Combination of Chemoimmunotherapies Can Efficiently Break Self-Tolerance and Induce Antitumor Immunity in a Tolerogenic Murine Tumor Model (2023)

Supplementary Figure 4 from A Combination of Chemoimmunotherapies Can Efficiently Break Self-Tolerance and Induce Antitumor Immunity in a Tolerogenic Murine Tumor Model
Studies on the Organization of the Human Apolipoprotein B100 Gene (1987)

The organization of five exons of the 3' terminal end of the human apolipoprotein B 100 (apo B 100) gene 1906, 184, 115, 7572 and 374 bp long have been determined from two overlapping EMBL3 human genomic clones extending over 18 kb. They encode more than 70% of the apo B 100 amino-acid sequence. The introns between these five exons were sequenced revealing the common intron/exon splice junction sequences. The 7572 bp exon is the longest exon so far reported for mammalian genes with the proposed sequence coding for the LDL receptor binding site. Its possible relationship to apolipoprotein B 48 is discussed.
The small nuclear RNAs for pre-mRNA splicing are coordinately regulated during oocyte maturation and early embryogenesis in the mouse (1989)

The abundance and localization of snRNAs and snRNPs involved in processing and splicing of pre-mRNA has been studied during early mouse embryogenesis. The amount of U1, U2, U4, U5 and U6 RNA remains relatively constant between the postovulatory oocyte and 2-cell stage but increases three- to ten-fold in quantity between the 2-cell and blastocyst stages. Localization was examined by in situ hybridization with U1, U2 and U6 riboprobes and immunofluorescence microscopy using a monoclonal antibody to snRNP antigens. The snRNAs and snRNPs are primarily localized to the germinal vesicle in the preovulatory oocyte but are released and diluted within the cytoplasm of the oocyte during germinal vesicle breakdown and meiotic maturation. They subsequently relocalize to both pronuclei following fertilization and the nuclei of the 2-cell embryo following the first cleavage division. Since the amount of snRNA is constant during the first cleavage, the small amount of pre-mRNA that is synthesized at the time of transcriptional activation in the 2-cell embryo may be spliced and processed by snRNPs of maternal origin.
Treatment of restenotic drug-eluting stents: an intravascular ultrasound analysis. (2007)

The preintervention MSA was a major predictor of larger lumen area after repeat intervention for DES restenosis. Several IVUS studies have shown that stent dimensions do not change over time. Therefore, the MSA of the original stent implantation procedure still has the greatest impact on subsequent interventions to treat DES restenosis.
Effect of Molecular Architecture of PDMAEMA–POEGMA Random and Block Copolymers on Their Adsorption on Regenerated and Anionic Nanocelluloses and Evidence of Interfacial Water Expulsion (2015)

Block copolymers of poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) and poly(oligo(ethylene glycol) methyl ether methacrylate) (POEGMA) with varying block sizes were synthesized by consecutive reversible addition-fragmentation chain transfer (RAFT) polymerization and then exposed to cellulose substrates with different anionic charge density. The extent and dynamics of quaternized PDMAEMA-b-POEGMA adsorption on regenerated cellulose, cellulose nanofibrils (CNF), and (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO)-oxidized cellulose nanofibrils (TOCNF) was determined by using electromechanical and optical techniques, namely, quartz crystal microbalance (QCM-D) and surface plasmon resonance (SPR), respectively. PDMAEMA-b-POEGMA equilibrium adsorption increased with the anionic charge of cellulose, an indication of electrostatic interactions. Such an observation was further confirmed by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). Depending on their architecture, adsorption on TOCNF of some of the PDMAEMA-b-POEGMA copolymers produced a significant reduction in QCM frequency, as expected from large mass uptake, while surprisingly, other copolymers induced the opposite effect. This latter, remarkable behavior was ascribed to coupled water expulsion from the interface upon charge neutralization of anionic surface sites with adsorbing cationic polymer segments. These observations were further investigated with SPR and QCM-D measurements using deuterium oxide solvent exchange to determine the amount of coupled water at the TOCNF-block copolymer interface. Finally, random copolymers with similar composition adsorbed to a larger extent compared to the respective block copolymers, revealing the effect of adsorbed loops and tails as well as hydration.
Physical and functional interactions between herpes simplex virus immediate-early proteins ICP4 and ICP27 (1997)

The ordered expression of herpes simplex virus type 1 (HSV-1) genes, during the course of a productive infection, requires the action of the virus immediate-early regulatory proteins. Using a protein interaction assay, we demonstrate specific in vitro protein-protein interactions between ICP4 and ICP27, two immediate-early proteins of HSV-1 that are essential for virus replication. We map multiple points of contact between these proteins. Furthermore, by coimmunoprecipitation experiments, we demonstrate the following. (i) ICP4-ICP27 complexes are present in extracts from HSV-1 infected cells. (ii) ICP27 binds preferentially to less modified forms of ICP4, a protein that is extensively modified posttranslationally. We also demonstrate, by performing electrophoretic mobility shift assays and supershifts with monoclonal antibodies to ICP4 or ICP27, that both proteins are present in a DNA-protein complex with a noncanonical ICP4 binding site present in the HSV thymidine kinase (TK) gene. ICP4, in extracts from cells infected with ICP27-deficient viruses, is impaired in its ability to form complexes with the TK site but not with the canonical site from the alpha4 gene. However, ICP4 is able to form complexes with the TK probe, in the absence of ICP27, when overproduced in mammalian cells or expressed in bacteria. These data suggest that the inability of ICP4 from infected cell extracts to bind the TK probe in the absence of ICP27 does not reflect a requirement for the physical presence of ICP27 in the complex. Rather, they imply that ICP27 is likely to modulate the DNA binding activity of ICP4 by affecting its posttranslational modification status. Therefore, we propose that ICP27, in addition to its established role as a posttranscriptional regulator of virus gene expression, may also modulate transcription either through direct or indirect interactions with HSV regulatory regions, or through its ability to modulate the DNA binding activity of ICP4.