gebhart/patrepeval huggingface dataset:
Proinflammatory functions of vascular endothelial growth factor in alloimmunity (2003)

Vascular endothelial growth factor (VEGF), an established angiogenesis factor, is expressed in allografts undergoing rejection, but its function in the rejection process has not been defined. Here, we initially determined that VEGF is functional in the trafficking of human T cells into skin allografts in vivo in the humanized SCID mouse. In vitro, we found that VEGF enhanced endothelial cell expression of the chemokines monocyte chemoattractant protein 1 and IL-8, and in combination with IFN-gamma synergistically induced endothelial cell production of the potent T cell chemoattractant IFN-inducible protein-10 (IP-10). Treatment of BALB/c (H-2d) recipients of fully MHC-mismatched C57BL/6 (H-2b) donor hearts with anti-VEGF markedly inhibited T cell infiltration of allografts and acute rejection. Anti-VEGF failed to inhibit T cell activation responses in vivo, but inhibited intragraft expression of several endothelial cell adhesion molecules and chemokines, including IP-10. In addition, whereas VEGF expression was increased, neovascularization was not associated with acute rejection, and treatment of allograft recipients with the angiogenesis inhibitor endostatin failed to inhibit leukocyte infiltration of the grafts. Thus, VEGF appears to be functional in acute allograft rejection via its effects on leukocyte trafficking. Together, these observations provide mechanistic insight into the proinflammatory function of VEGF in immunity.
Highly conserved residue arginine-15 is required for the Ca2+-dependent properties of the γ-carboxyglutamic acid domain of human anticoagulation Protein C and activated Protein C (1997)

The function of the rigidly conserved amino acid residue R15 in the Ca2+/phospholipid-dependent properties of the gamma-carboxyglutamic acid (Gla)-containing domain (GD) of human Protein C (PC) were investigated through site-directed mutagenesis strategies. A series of recombinant (r) mutants, namely r-[R15K]PC, r-[R15H]PC, r-[R15L]PC, and r-[R15W]PC, were constructed, expressed and purified, and their relevant properties investigated. As revealed by intrinsic fluorescence analysis, all of the variant proteins underwent Ca2+-dependent structural transitions. Nonetheless, they displayed altered binding properties to acidic phospholipid vesicles, and also did not interact with a monoclonal antibody specific for the type of Ca2+-dependent conformation of the GD that characterizes the wild-type protein. On conversion into their activated forms, these variant enzymes possessed less than 10% of the ex vivo plasma anticoagulant activity of wild-type r-PC. Similar activities were found when the r-active PC mutants were assayed directly for inactivation of factor Va and factor VIII, in the complete prothrombinase and tenase complexes respectively. We conclude that R15 is a critical residue in allowing the GD of PC, and probably of other proteins of this class, to adopt a Ca2+-dependent conformation that allows functional phospholipid binding, thus explaining the strict conservation of this amino acid residue in GD modules of various proteins. As a result of an analysis of structural models of the Ca2+-GD complex of PC, it is postulated that hydrogen bonds between the side chain of R15 and the functionally important Gla16 residue, as well as between the side chain of R15 and the carbonyl oxygen in the peptide bond of H10, are critical for adoption of a Ca2+-dependent conformation of the GD that allows functional phospholipid binding.
Subcellular mRNA Localization in Animal Cells and Why It Matters (2009)

Subcellular localization of messenger RNAs (mRNAs) can give precise control over where protein products are synthesized and operate. However, just 10 years ago many in the broader cell biology community would have considered this a specialized mechanism restricted to a very small fraction of transcripts. Since then, it has become clear that subcellular targeting of mRNAs is prevalent, and there is mounting evidence for central roles for this process in many cellular events. Here, we review current knowledge of the mechanisms and functions of mRNA localization in animal cells.
Biofilms in dermatology. (2012)

Biofilms are diverse communities of microorganisms embedded within a self-produced matrix of extracellular polymeric substance which are firmly attached to biotic or abiotic surfaces. Approximately 80% of all human infections are associated with biofilms and evidence for their role in an ever-growing number of cutaneous disorders is constantly unfolding. Biofilms present a difficult challenge to clinicians due to their persistent nature, inability to be cultured with standard techniques, and resistance to conventional antimicrobial therapy. Although limited treatment options are presently available, better understanding of the molecular biology of biofilms and their pathogenicity will likely lead to the development of novel anti-biofilm agents for clinical use.
Integrating RFID Technology into a Drug Administration System (2005)

Errors in the administration of drugs to patients, along with other types of adverse drug events (ADEs), have proven to be very costly to the healthcare sector. One commonly proposed solution to the problem is the use of barcodes to uniquely identify both patients and drugs. The size of the ADE problem, and the success of a limited number of barcode-based systems, has prompted US healthcare regulators to endorse, or even mandate, their use. However, it has been suggested that limitations of barcodes adversely affect the usability of such systems, and that RFID technology offers a more suitable alternative. This paper documents the design and development of an extension to an existing barcode-based anaesthetic drug identification system, IDAS, which would allow it to functionally replace barcodes with RFID technology. The design is informed by a review of RFID application case studies, experiments with RFID hardware, and observation and interviews of anaesthetists. A demonstration of the prototype system suggests that RFID technology could functionally replace barcodes, but significant issues remain to be addressed.
PARP-2 Interacts with TTF-1 and Regulates Expression of Surfactant Protein-B (2006)

Thyroid transcription factor 1 (TTF-1/Nkx-2.1) plays a critical role in lung morphogenesis and regulates the expression of lungspecific genes, including the surfactant proteins required for pulmonary function after birth. The activity of TTF-1 is influenced by its interactions with other transcription factors and coactivators, including CBP/p300 and SRC-1. In this study, we have identified poly(ADP-ribose) polymerases (PARP-2 and PARP-1) as TTF-1 interacting proteins that influence its transcriptional activity. Endogenous PARP-2 was coimmunoprecipitated from transformed mouse lung epithelial cell (MLE15) extracts with TTF-1 and was identified by mass spectrometry. PARP-1 and Ku70/Ku80 were also coimmunoprecipitated from the cell extracts with TTF-1. The E domain of PARP-2 interacted via the C-terminal domain of TTF-1. Both PARP-1 and PARP-2 enhanced the activity of the promoter of surfactant protein-B (Sftpb gene) but not other surfactant proteins in vitro. PARP-2 was selectively expressed in epithelial cells of the conducting and peripheral lung tubules of the fetal mouse lung from embryonic day 12.5 and was detected in bronchial epithelial cells in the adult lung at cellular sites consistent with that of surfactant protein B. PARP-2 and PARP-1 interact with TTF-1 and regulate the expression of surfactant protein B, a protein required for lung function.
Magnetic resonance imaging enhanced by superparamagnetic iron oxide particles: Usefulness for distinguishing between focused ultrasound‐induced blood–brain barrier disruption and brain hemorrhage (2008)

T2*-weighted images-either with and without SPIO enhancement-may differentiate focused ultrasound-induced BBB disruption from brain hemorrhage.
Image-based dynamic measurement for vehicle steering control (2005)

An image sensing technique is developed in this study using image plane analysis to measure the dynamic motion variables of a vehicle based on the road scene viewed from a camera inside the vehicle. Some motion variables such as heading angle, lateral deviation, yaw rate, and sideslip angle of the vehicle are measured and could be further used for steering control systems such as automatic steering and four-wheel steering system. An experimental car is set up to verify the image sensing method. The vehicle is equipped with a V8 video camera to record the road scene viewed from a moving vehicle. To examine the proposed image sensing method, other measuring process is utilized to manually measure the motion variables based on the traces of the vehicle left on the road. The recorded video data are used to test the image sensing technique in an off-line manner in the laboratory to obtain motion information. Some experimental results for the situation of straight road show that the proposed sensing technique is feasible.
Down-regulation of mRNA for the low density lipoprotein receptor in transgenic mice containing the gene for human cholesteryl ester transfer protein. Mechanism to explain accumulation of lipoprotein B particles. (1993)

To evaluate the effects of cholesteryl ester transfer protein (CETP) on apoB-containing lipoproteins, we analyzed plasma lipoproteins from three different lines of human CETP transgenic mice, with plasma CETP concentration ranging from low (1.5 microgram/ml) to high levels (8.5 micrograms/ml). With increasing CETP concentration, very low density lipoprotein and low density lipoprotein (LDL) cholesteryl ester (CE) and apoB were progressively increased, and high density lipoprotein CE was decreased. To investigate the mechanism of accumulation of lipoproteins containing apoB (lipoprotein B), the abundance of hepatic LDL receptor mRNA was determined. LDL receptor mRNA was reduced as a result of CETP expression, with maximum repression to about 48% of the level of non-transgenic mice. Among the different lines of CETP transgenic mice there was an inverse relationship between plasma CETP concentration and hepatic LDL receptor mRNA abundance (r = -0.94, p < 0.01). CETP expression also led to increased cholesterol and cholesteryl ester content in liver and to decreased abundance of mRNAs encoding 3-hydroxy-3-methylglutaryl-coenzyme A reductase and 7-alpha-hydroxylase. Thus, CETP expression results in increased cholesteryl ester concentration in very low density lipoprotein and LDL, probably reflecting both CE transfer from high density lipoprotein and accumulation of lipoprotein B particles. The accumulation of lipoprotein B particles results from CETP-mediated down-regulation of liver LDL receptors, possibly due to enhanced return of cholesterol to the liver.
Perspectives in Animal Health:  Old Targets and New Opportunities (2001)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTPerspectives in Animal Health: Old Targets and New OpportunitiesPeter T. MeinkeView Author Information Department of Medicinal Chemistry, Merck Research Laboratories, P.O. Box 2000, RY800-B101, Rahway, New Jersey 07065-0900 Cite this: J. Med. Chem. 2001, 44, 5, 641–659Publication Date (Web):February 6, 2001Publication History Received11 November 1999Published online6 February 2001Published inissue 1 March 2001https://pubs.acs.org/doi/10.1021/jm990564hhttps://doi.org/10.1021/jm990564hreview-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1180Altmetric-Citations33LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Animal health,Pharmaceuticals,Receptors,Therapeutics,Toxicity Get e-Alerts
A comprehensive delay macro modeling for submicrometer CMOS logics (1999)

The increasing need for high-performance, cost-effective, application-specific integrated circuits, associated to the reduction of design cycle time, compels designers to manage and optimize the circuit speed performance at each step of the design flow. Circuits are usually designed at gate level; the gate selection or sizing and their placement are driven by estimated delay, hence the need for accurate estimations at the logical level. In the submicrometer range, the gap between gate-level logical estimations and transistor-level electrical simulations dramatically increases. We propose here a comprehensive analytical modeling of the speed performance of CMOS gates with an accuracy comparable to electrical simulators. A design-oriented expression of delay is first developed for CMOS inverters, considering input slope, input-to-output capacitance coupling, and short-circuit current effects. The extension to more complex gates is proposed using a serial array reduction technique taking account of the gate input dependency and the input-slope-induced nonlinearity. Validations are obtained over a large range of design, load, and input slope conditions by comparison with SPICE simulations (level 6 with 0.65-/spl mu/m foundry specified card model) used as a reference.
Low-Carbohydrate-Diet Score and the Risk of Coronary Heart Disease in Women (2006)

Our findings suggest that diets lower in carbohydrate and higher in protein and fat are not associated with increased risk of coronary heart disease in women. When vegetable sources of fat and protein are chosen, these diets may moderately reduce the risk of coronary heart disease.
Realizing All-Spin–Based Logic Operations Atom by Atom (2011)

An ultimate goal of spintronic research is the realization of concepts for atomic-scale all-spin-based devices. We combined bottom-up atomic fabrication with spin-resolved scanning tunneling microscopy to construct and read out atomic-scale model systems performing logic operations. Our concept uses substrate-mediated indirect exchange coupling to achieve logical interconnection between individual atomic spins. Combined with spin frustration, this concept enables various logical operations between inputs, such as NOT and OR.
Substrate Requirements for Transglutaminases (1995)

Thirteen recombinant alpha A-crystallin mutants were constructed that differed in the type of amino acid residue directly preceding the sole amine donor lysine for transglutaminases in this protein. The capacity of these mutants to be cross-linked to amine acceptor substrates by tissue transglutaminase and factor XIII was assessed. Two different biotinylated glutamine-containing oligopeptides were used as amine acceptor probes. It appears that the type of residue preceding the amine donor lysine has a considerable influence on the substrate potential of alpha A-crystallin for transglutaminases. This influence shows qualitatively similar trends for tissue transglutaminase and factor XIII and is irrespective of the amine acceptor probe. In general, glycine or aspartic acid before the amine donor lysine has the strongest adverse effects on substrate reactivity, and proline, histidine, and tryptophan are less favorable. Valine, arginine, and phenylalanine, and to a more variable or somewhat lesser extent also serine, alanine, leucine, tyrosine, and asparagine, have an enhancing effect. This pattern of preference is largely in agreement with that observed for the limited number of characterized amine donor lysines in protein substrates for transglutaminases. It can be concluded that tissue transglutaminase and factor XIII have a rather broad yet clearly differentiated tolerance with respect to the residue preceding the amine donor lysine substrate in native proteins.
Modulated Coding for Digital Communication Systems Under ISI/Multipath Fading and Jamming (2000)

Abstract : This report describes the main research achievements during the time period cited above on the research project in the area of telecommunications. The main achievements include the systematic study of modulated codes that are convolutional codes defined on real/complex field over intersymbol interference, multipath, jamming channels. We obtained the joint maximum-likelihood decoding, and the MMSE-DFE decoding algorithms. We proved the existence of the coding gain compared to the uncoded AWGN channel. We also obtained space-time modulated codes for multiple transmit and multiple receive antenna systems. A new precoded OFDM system was also obtained which is robust to spectral-nulls.
Anti-CD43 Inhibits Monocyte-Endothelial Adhesion in Inflammation and Atherogenesis (1997)

Recruitment of blood monocytes into tissues is a central event in the inflammatory response and in atherogenesis. The mechanisms leading to monocyte adhesion and migration through endothelium are not completely defined. We recently reported that MAb L11, against the leukocyte sialomucin CD43, blocks T-lymphocyte binding to lymph node and Peyer's patch high endothelial venules (HEV) and inhibits T-cell extravasation from the blood into organized secondary lymphoid tissues. We have now assessed the ability of L11 to inhibit monocyte-endothelial (EC) interactions and trafficking. L11 blocks binding of WEHI78/24 cells, a murine monocytoid cell line, to inflamed lymph node HEV and inhibits recruitment of monocytes and neutrophils to thioglycollate-inflamed peritoneum. Because monocyte adhesion to the endothelium and diapedesis in lesion-prone regions of the vasculature is among the earliest events in atherogenesis, leading to formation of lipid-laden foam cells, the ability of L11 to block monocyte recognition of aortic endothelial cells was assessed in a novel ex vivo assay of monocyte binding to intact rabbit aortic endothelium. Cholesterol feeding of rabbits induces enhanced aortic adhesiveness for monocytes and WEHI78/24 monocytoid cells, and this adhesion is inhibited by L11. The inhibitory effect of L11 is additive with that of a cocktail of anti-L-selectin and anti-alpha4 and beta2 integrin monoclonal antibodies. Thus, CD43 represents a novel target for manipulation of monocyte recruitment in inflammation and atherogenesis.
Characterization of δ-Guaiene Synthases from Cultured Cells of Aquilaria, Responsible for the Formation of the Sesquiterpenes in Agarwood (2010)

The resinous portions of Aquilaria plants, called agarwood, have been used as medicines and incenses. Agarwood contains a great variety of sesquiterpenes, and a study using cultured cells of Aquilaria showed the production of sesquiterpenes (α-guaiene, α-humulene, and δ-guaiene) to be induced by treatment with methyl jasmonate (MJ). In this study, the accumulation and production of sesquiterpenes were quantified. The amounts accumulated and produced reached a maximum at 12 h, and the most abundant product was α-humulene at 6 h and δ-guaiene after 12 h. However, a headspace analysis of the cells revealed that α-humulene is likely to be volatilized; so overall, the most abundant sesquiterpene in the cells was δ-guaiene. A cDNA library from RNA isolated from MJ-treated cells was screened using PCR methodologies to isolate five clones with very similar amino acid sequences. These clones were expressed in Escherichia coli, and enzymatic reactions using farnesyl pyrophosphate revealed that three of the clones yielded the same compounds as extracted from MJ-treated cells, the major product being δ-guaiene. These genes and their encoded enzymes are the first sesquiterpene synthases yielding guaiane-type sesquiterpenes as their major products to be reported. Expression of a fourth terpene synthase gene in bacteria resulted in the accumulation of the protein in insoluble forms. Site-directed mutagenesis of the inactive clone and three-dimensional homology modeling suggested that the structure of the N-terminal domain was important in facilitating proper folding of the protein to form a catalytically active structure.
Distinct signals in human immunodeficiency virus type 1 Pr55 necessary for RNA binding and particle formation (1992)

The human immunodeficiency virus type 1 (HIV-1) gag gene product Pr55 self-assembles to form virus-like particles when expressed in Spodoptera frugiperda cells using recombinant baculoviruses. The particles resemble immature HIV and are released from the infected cell into the culture medium. Using this system we have progressively truncated the gag open reading frame from the C terminus and examined each deleted gag protein for its particle-producing capability. We show that deletion of Pr6 and deletions that progressively remove the distal region of the Pr7 domain, including one Cys-His box thought to function as an RNA capture signal, do not affect particle formation. However deletion of two Cys-His boxes causes production of slightly larger particles with altered sedimentation properties. Sequence-specific North-Western assays using an RNA probe representative of the HIV-1 packaging signal revealed specific RNA binding by all mutants that maintained both Cys-His boxes. However, deletion of one Cys-His box reduced RNA binding substantially and loss of two Cys-His boxes abolished binding entirely. We conclude that HIV-1 gag particle formation per se does not require viral RNA encapsidation, but that it may act as a cofactor in the condensation of the immature core. Further deletion of gag sequences upstream of the Cys-His boxes led to the abolition of particle-forming ability, and we show that one boundary of the gag sequence necessary for particle formation lies within eight amino acids spanning one of the known protease cleavage sites at the C terminus of Pr24.
Phosphorylation of the Eukaryotic Translation Initiation Factor eIF4E Contributes to Its Transformation and mRNA Transport Activities (2004)

The eukaryotic translation initiation factor eIF4E is dysregulated in a wide variety of human cancers. In the cytoplasm, eIF4E acts in the rate-limiting step of translation initiation whereas in the nucleus, eIF4E forms nuclear bodies and promotes the nucleo-cytoplasmic export of a subset of growth-promoting mRNAs including cyclin D1. The only known post-translational modification of eIF4E is its phosphorylation at S209. Many studies have examined the role of phosphorylation on cap-dependent translation. However, no studies to date have explored the role of phosphorylation on the ability of eIF4E to transform cells. Using mutagenesis and separately a small molecular inhibitor of eIF4E phosphorylation, we show that eIF4E phosphorylation enhances both its mRNA transport function and its transformation activity in cell culture. Thus, phosphorylation of nuclear eIF4E seems to be an important step in control of the mRNA transport and thus the transforming properties of eIF4E.
Formation of ice nanotube with hydrophobic guests inside carbon nanotube (2005)

A composite ice nanotube inside a carbon nanotube has been explored by molecular-dynamics and grand canonical Monte Carlo simulations. It is made from an octagonal ice nanotube whose hollow space contains hydrophobic guest molecules such as neon, argon, and methane. It is shown that the attractive interaction of the guest molecules stabilizes the ice nanotube. The guest occupancy of the hollow space is calculated by the same method as applied to clathrate hydrates.