gebhart/patrepeval huggingface dataset:
RHD gene deletion occurred in the Rhesus box (2000)

The Rh blood group antigens derive from 2 genes, RHD and RHCE, that are located at chromosomal position 1p34.1-1p36 (chromosome 1, short arm, region 3, band 4, subband 1, through band 6). In whites, a cde haplotype with a deletion of the whole RHD gene occurs with a frequency of approximately 40%. The relative position of the 2 RH genes and the location of the RHD deletion was previously unknown. A model has been developed for the RH locus using RHD- and RHCE-related nucleotide sequences deposited in nucleotide sequence databases along with polymerase chain reaction (PCR) and nucleotide sequencing. The open reading frames of both RH genes had opposite orientations. The 3' ends of the genes faced each other and were separated by about 30 000 base pair (bp) that contained the SMP1 gene. The RHD gene was flanked by 2 DNA segments, dubbed Rhesus boxes, with a length of approximately 9000 bp, 98.6% homology, and identical orientation. The Rhesus box contained the RHD deletion occurring within a stretch of 1463 bp of identity. PCR with sequence-specific priming (PCR-SSP) and PCR with restriction fragment length polymorphism (PCR-RFLP) were used for specific detection of the RHD deletion. The molecular structure of the RH gene locus explains the mechanisms for generating RHD/RHCE hybrid alleles and the RHD deletion. Specific detection of the RHD(-) genotype is now possible. (Blood. 2000;95:3662-3668)
A Multi-Component Prime-Boost Vaccination Regimen with a Consensus MOMP Antigen Enhances Chlamydia trachomatis Clearance (2016)

A C. trachomatis vaccine needs to induce a robust cellular response with broad cross-serovar coverage and a heterologous prime-boost regimen may be an approach to achieve this.
Development of bioartificial kidneys (2003)

Bioartificial kidneys, which consist of continuous haemofiltration and bioartificial tubules using tubular epithelial cells, have been studied since 1987. The bioartificial tubules consist of hollow fibre modules and tubular epithelial cells grown on the hollow fibre membranes after coating with extracellular matrices. The kinds of tubular epithelial cells, extracellular matrices and artificial membranes therefore have been investigated and then the most appropriate cell and materials have been selected on the basis of the development of bioartificial kidneys. Successful seeding to form confluent monolayers on the surfaces of hollow fibers is not easy, but this method has already been established. Renal assist devices using human renal proximal tubular epithelial cells have been used in the treatment of acute renal failure patients with endotoxemia by Humes et al., and successful treatment of acute renal failure patients with these devices was reported in 2001 and 2002, in which the improved mortality rate of those patients was shown. A bioartificial kidney, in which cDNA of multidrug resistance protein-1 was transfected into tubular epithelial cells that were then grown on the outer surfaces of hollow fibers, was used in the experimental treatment of digoxin-intoxicated dogs. Rapidly reduced digoxin levels were noted in the plasma of the dogs after treatment. Bioartificial kidneys, however, have never been used in the long-term treatment of a maintenance dialysis patient, although patients need those kidneys. In order to establish long-term treatment with a bioartificial kidney, each haemofilter has to function for more than one week without systemic anticoagulation and a bioartificial tubule must function for 3-4 weeks.
Leucocyte typing V : white cell differentiation antigens : proceedings of the Fifth International Workshop and Conference held in Boston, USA, 3-7 November, 1993 (1995)

This text provides a comprehensive description of the monoclonal antibodies that react with molecules on the surface of human leucocytes, platelets and endothelial cells. It can be used as a source of information describing the present state of our knowledge of human leucocyte differentiation antigens and it summarizes the results of a two year international collaboration to characterize these molecules by immunological, serologic, molecular, biochemical, and histochemical means.
Extracellular and intracellular mechanisms that mediate the metastatic activity of exogenous osteopontin (2009)

The results of this study revealed a complex molecular interaction as well as a dual role for osteopontin in metastasis that depends on whether tumor cells are in circulation or attached. Such context-dependent functional insights may contribute to antimetastasis strategies.
Identification of an N-Terminal Trimeric Coiled-Coil Core within Arenavirus Glycoprotein 2 Permits Assignment to Class I Viral Fusion Proteins (2006)

The lymphocytic choriomeningitis virus (LCMV) glycoprotein (GP) consists of the transmembrane subunit GP-2 and the receptor binding subunit GP-1. Both are synthesized as one precursor protein and stay noncovalently attached after cleavage. In this study, we determined the oligomeric state of the LCMV GP and expressed it in two different conformations suitable for structural analysis. Sequence analysis of GP-2 identified a trimeric heptad repeat pattern containing an N-terminal alpha-helix. An alpha-helical peptide matching this region formed a stable oligomer as revealed by gel filtration chromatography and dynamic light scattering. In contrast, a second alpha-helical peptide corresponding to a predicted C-terminal alpha-helix within GP-2 did not oligomerize. Refolding of the complete GP-2 ectodomain revealed trimeric all-alpha complexes probably representing the six-helix bundle state that is considered a hallmark of class I viral fusion proteins. Based on these results, we generated a construct consisting of the complete uncleavable LCMV GP ectodomain fused C-terminally to the trimeric motif of fibritin. Gel filtration analysis of the secreted fusion protein identified two complexes of approximately 230 and approximately 440 kDa. Both complexes bound to a set of conformational and linear antibodies. Cross-linking confirmed the 230-kDa complex to be a trimer. The 440-kDa complexes were found to represent disulfide-linked pairs of trimers, since partial reduction converted them to a complex species migrating at 250 kDa. By electron microscopy, the 230-kDa complexes appeared as single spherical particles and showed no signs of rosette formation. Our results clearly demonstrate that the arenavirus GP is a trimer and must be considered a member of the class I viral fusion protein family.
Video surveillance of interactions (2003)

This paper describes an automatic surveillance system, which performs labeling of events and interactions in an outdoor environment. The system is designed to monitor activities in an open parking lot. It consists of three components-an adaptive tracker, an event generator, which maps object tracks onto a set of pre-determined discrete events, and a stochastic parser. The system performs segmentation and labeling of surveillance video of a parking lot and identifies person-vehicle interactions, such as pick-up and drop-off. The system presented in this paper is developed jointly by MIT Media Lab and MIT Artificial Intelligence Lab.
Subarrier multiplexing based signaling and access control in optical FDM networks (2002)

A framework for subcarrier-multiplexing-based signaling and access control in optical FDM networks is presented. Fundamental node functions in optical FDM networks including channel selection, cross-connect, and add/drop are proposed. Furthermore, a subcarrier-controlled optical add/drop multiplexer is experimentally demonstrated. It is composed of an arrayed-waveguide-grating (AWG) and optical switches driven by subcarrier-multiplexed control signals. Finally, issues on multigigabit network applications are discussed.
Structural properties of DNA:RNA duplexes containing 2'-O-methyl and 2'-S-methyl substitutions: a molecular dynamics investigation (1999)

The physical properties of a DNA:RNA hybrid sequence d(CCAACGTTGG)*(CCAACGUUGG) with modifications at the C2'-positions of the DNA strand by 2'-O-methyl (OMe) and 2'-S-methyl (SMe) groups are studied using computational techniques. Molecular dynamics simu-lations of SMe_DNA:RNA, OMe_DNA:RNA and standard DNA:RNA hybrids in explicit water indicate that the nature of the C2'-substituent has a significant influence on the macromolecular conformation. While the RNA strand in all duplexes maintains a strong preference for C3'-endo sugar puckering, the DNA strand shows considerable variation in this parameter depending on the nature of the C2'-substituent. In general, the preference for C3'-endo puckering follows the following trend: OMe_DNA>DNA>SMe_DNA. These results are further corroborated using ab initio methods. Both gas phase and implicit solvation calculations show the C2'-OMe group stabilizes the C3'-endo conformation while the less electronegative SMe group stabilizes the C2'-endo conformation when compared to the standard nucleoside. The macromolecular conformation of these nucleic acids also follows an analogous trend with the degree of A-form character decreasing as OMe_DNA:RNA>DNA:RNA>SMe_DNA:RNA. A structural analysis of these complexes is performed and compared with experimental melting point temper-atures to explain the structural basis to improved binding affinity across this series. Finally, a possible correlation between RNase H activity and conformational changes within the minor groove of these complexes is hypothesized.
Cyclodextrin Drug Carrier Systems (1998)

ADVERTISEMENT RETURN TO ISSUEPREVArticleCyclodextrin Drug Carrier SystemsKaneto Uekama, Fumitoshi Hirayama, and Tetsumi IrieView Author Information Faculty of Pharmaceutical Sciences, Kumamoto University, 5-1, Oe-honmachi, Kumamoto 862-0973, Japan Cite this: Chem. Rev. 1998, 98, 5, 2045–2076Publication Date (Web):June 9, 1998Publication History Received16 October 1997Revised5 January 1998Published online9 June 1998Published inissue 30 July 1998https://doi.org/10.1021/cr970025pCopyright © 1998 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views13329Altmetric-Citations1726LEARN 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 InReddit Read OnlinePDF (324 KB) Get e-AlertsSUBJECTS:Absorption,Macrocyclic compounds,Oligosaccharides,Peptides and proteins,Pharmaceuticals Get e-Alerts
Single‐Molecule Analysis Using DNA Origami (2011)

During the last two decades, scientists have developed various methods that allow the detection and manipulation of single molecules, which have also been called "in singulo" approaches. Fundamental understanding of biochemical reactions, folding of biomolecules, and the screening of drugs were achieved by using these methods. Single-molecule analysis was also performed in the field of DNA nanotechnology, mainly by using atomic force microscopy. However, until recently, the approaches used commonly in nanotechnology adopted structures with a dimension of 10-20 nm, which is not suitable for many applications. The recent development of scaffolded DNA origami by Rothemund made it possible for the construction of larger defined assemblies. One of the most salient features of the origami method is the precise addressability of the structures formed: Each staple can serve as an attachment point for different kinds of nanoobjects. Thus, the method is suitable for the precise positioning of various functionalities and for the single-molecule analysis of many chemical and biochemical processes. Here we summarize recent progress in the area of single-molecule analysis using DNA origami and discuss the future directions of this research.
CHAPTER 1: Introduction to Food Hydrocolloids (2004)

Cereals & Grains Association is a nonprofit organization dedicated to advancing the knowledge and understanding of cereal grain science through research leadership, education, superior technical service, and advocacy.
Safety of Adenovirus-Mediated Transfer of the Human Cystic Fibrosis Transmembrane Conductance Regulator cDNA to the Lungs of Nonhuman Primates (1996)

To define the toxicity of cystic fibrosis transmembrane conductance regulator gene (CFTR) gene therapy with a replication-deficient recombinant adenovirus (Av1Cf2) in a nonhuman primate model, 10(10) plaque forming units (pfu) were instilled directly through a bronchoscope into the right lung of 5 macaques, and a lower dose of 4 x 10(6) pfu was administered to the right lung of 1 macaque. One sham-treated control received phosphate-buffered saline (PBS). The macaques were evaluated sequentially by clinical examination, vital signs, weight, hematology, blood chemistry, chest radiography, pulse oximetry, and bronchoalveolar lavage (BAL) at baseline and 3-28 days post-treatment. After the period of observation, macaques were sacrificed for autopsy and histological examination. The macaques tolerated the experimental therapy clinically with no changes in body temperature, oxygen saturation, heart rate, body weight, or blood pressure. However, 1 macaque with visible evidence of aspiration at the time of initial bronchoscopy developed tachypnea with right lower lobe (RLL) pneumonia on chest radiograph and by histology. There were no changes in Hgb, Wbc, BUN, plasma electrolytes, bilirubin, or hepatic transaminases. In the macaques that received 10(10) pfu, there was a progressive increase in the number of CD8+ lymphocytes in BAL that was maximal at 28 days. Histological examination of the treated lungs of the high-dose macaques at 3 days showed marked peribronchial and perivascular cuffing by inflammatory cells and alveolar accumulation of neutrophils and macrophages. The alveolitis appeared to be resolving at 28 days, although the perivascular and peribronchial aggregates of mononuclear cells were still present. In the high-dose macaques, BAL interleukin-8 (IL-8) was increased at all time points (256-388 pg/ml versus 1-84 pg/ml at baseline and in control), whereas IL-1 beta was increased only at days 21 and 28 (341-852 pg/ml versus 30-92 pg/ml at baseline and in control). There were no increases in BAL cell counts, IL-1 beta or IL-8, and histological changes were mild in the macaque that received 4 x 10(6) pfu. Evaluation for Av1Cf2-derived human CFTR expression using RS-PCR demonstrated expression at 3, 10, and 21, but not 28 days in macaques treated with 10(10) pfu of Av1Cf2. In situ hybridization analysis demonstrated human CFTR mRNA in the alveolar regions of the lobes that received the vector at 10 and 21 days. There was no evidence of expression after treatment with 4 x 10(6) pfu. This study showed that high-dose adenoviral vector administration to the lung achieved CFTR gene transfer and expression but was associated with increased concentrations of cytokines in BAL and alveolar inflammation. A low dose, equivalent to the maximum clinical dose currently proposed for phase I trials in human subjects, was not associated with cellular or cytokine evidence of inflammation, and histological abnormalities were mild.
Optimization of Agrobacterium‐mediated transient assays of gene expression in lettuce, tomato and Arabidopsis (2005)

Agrobacterium-mediated transient assays for gene function are increasingly being used as alternatives to genetic complementation and stable transformation. However, such assays are variable and not equally successful in different plant species. We analysed a range of genetic and physiological factors affecting transient expression following agroinfiltration, and developed a protocol for efficient and routine transient assays in several plant species. Lettuce exhibited high levels of transient expression and was at least as easy to work with as Nicotiana benthamiana. Transient expression occurred in the majority of cells within the infiltrated tissue and approached 100% in some regions. High levels of transient expression were obtained in some ecotypes of Arabidopsis; however, Arabidopsis remains recalcitrant to routine, genotype-independent transient assays. Transient expression levels often exceeded those observed in stably transformed plants. The laboratory Agrobacterium tumefaciens strain C58C1 was the best strain for use in plant species that did not elicit a necrotic response to A. tumefaciens. A wild A. tumefaciens strain, 1D1246, was identified that provided high levels of transient expression in solanaceous plants without background necrosis, enabling routine transient assays in these species.
Jump flooding in GPU with applications to Voronoi diagram and distance transform (2006)

This paper studies jump flooding as an algorithmic paradigm in the general purpose computation with GPU. As an example application of jump flooding, the paper discusses a constant time algorithm on GPU to compute an approximation to the Voronoi diagram of a given set of seeds in a 2D grid. The errors due to the differences between the approximation and the actual Voronoi diagram are hardly noticeable to the naked eye in all our experiments. The same approach can also compute in constant time an approximation to the distance transform of a set of seeds in a 2D grid. In practice, such constant time algorithm is useful to many interactive applications involving, for example, rendering and image processing. Besides the experimental evidences, this paper also confirms quantitatively the effectiveness of jump flooding by analyzing the occurrences of errors. The analysis is a showcase of insights to the jump flooding paradigm, and may be of independent interests to other applications of jump flooding.
Lysophosphatidic acid inhibits cholera toxin-induced secretory diarrhea through CFTR-dependent protein interactions (2005)

The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-regulated chloride channel localized primarily at the apical or luminal surfaces of epithelial cells that line the airway, gut, and exocrine glands; it is well established that CFTR plays a pivotal role in cholera toxin (CTX)-induced secretory diarrhea. Lysophosphatidic acid (LPA), a naturally occurring phospholipid present in blood and foods, has been reported to play a vital role in a variety of conditions involving gastrointestinal wound repair, apoptosis, inflammatory bowel disease, and diarrhea. Here we show, for the first time, that type 2 LPA receptors (LPA2) are expressed at the apical surface of intestinal epithelial cells, where they form a macromolecular complex with Na+/H+ exchanger regulatory factor-2 and CFTR through a PSD95/Dlg/ZO-1-based interaction. LPA inhibited CFTR-dependent iodide efflux through LPA2-mediated Gi pathway, and LPA inhibited CFTR-mediated short-circuit currents in a compartmentalized fashion. CFTR-dependent intestinal fluid secretion induced by CTX in mice was reduced substantially by LPA administration; disruption of this complex using a cell-permeant LPA2-specific peptide reversed LPA2-mediated inhibition. Thus, LPA-rich foods may represent an alternative method of treating certain forms of diarrhea.
Characterization of the increase in vascular permeability induced by vascular permeability factor in vivo (1993)

1. Vascular permeability factor (VPF) is a protein secreted from a variety of human and rodent tumour and normal tissue cells. In addition to mediating angiogenesis and endothelial cell growth, VPF has been reported to be a potent mediator of increased microvascular permeability in vivo. In this study we have investigated these permeability changes in vivo using a quantitative model of local plasma leakage in rabbit skin. 2. Our results reveal that VPF is a potent mediator of plasma leakage which, in the rabbit, depends on a synergistic interaction with arteriolar vasodilators such as prostaglandin E2. The requirement for an exogenous vasodilator further suggest that VPF does not act to increase blood flow in this model. 3. We show that this response does not require the presence of circulating neutrophils and in this respect is similar to direct-action permeability increasing mediators such as histamine and bradykinin. Similarly, the time course of plasma leakage induced by VPF resembles that of direct-action mediators, where the greatest response occurs over the first 30 min. In contrast, the neutrophil-dependent plasma leakage induced by the active component of zymosan-activated plasma, C5ades arg, was maintained at a similar level over 2.5 h. 4. Further, using mediator antagonists and enzyme inhibitors we demonstrate that the mechanism of action of VPF is not via activation of histamine, kinin, or platelet-activating factor pathways.
Preparation and some reactions of 3-endo-substituted tricyclo-[3.2.0.02,7]heptan-6-ones (1978)

3-endo-Substituted tricyclo[3.2.0.02,7]heptan-6-ones have been prepared by treatment of 3-endo-substituted 2-exo-halogenobicyclo[3.2.0]heptan-6-ones or 5-endo-substituted 7-anti-halogenobicyclo[2.2.1]heptan-2-ones with potassium t-butoxide. The tricyclic ketones have been treated with various nucleophiles, including cyanide ion, halide ion, water, and methanol to give the corresponding 5-endo,7-anti-disubstituted bicyclo[2.2.1]heptan-2-one exclusively.
Comparison of QTLs for seed germination under non‐stress, cold stress and salt stress in tomato (1999)

Abstract The purpose of this study was to examine whether rate of tomato seed germination under non‐stress, cold‐stress and salt‐stress conditions was under similar genetic control by identifying and comparing quantitative trait loci (QTLs) which affect germination rate under these conditions. A fast‐germinating accession (LA722) of the wild tomato species Lycopersicon pimpinellifolium Jusl. and a slow‐germinating cultivar (NC84173, maternal and recurrent parent) of tomato ( Lycopersicon esculentum Mill.) were hybridized and BC 1 and BC 1 S 1 progeny produced. The BC 1 population was used to construct a linkage map with 151 restriction fragment length polymorphism (RFLP) markers. The BC 1 S 1 population (consisting of 119 BC 1 S 1 families) was evaluated for germination under non‐stress (control), cold‐stress and salt‐stress conditions and the mean time to 50% germination (T50) in each treatment was determined. Germination analyses indicated the presence of significant (P &lt; 0.01) phenotypic correlations between T50 under control and cold stress (r = 0.71), control and salt stress (r = 0.58) and cold stress and salt stress (r = 0.67). The QTL analysis indicated the presence of genetic relationships between germination under these three conditions: a few QTLs were identified which commonly affected germination under both stress‐ (cold‐, salt‐ or both) and non‐stress conditions, and thus were called stress‐nonspecific QTLs. A few QTLs were also identified which affected germination only under cold or salt stress and thus were called stress‐specific QTLs. However, the stress‐nonspecific QTLs generally exhibited larger individual effects and together accounted for a greater portion of the total phenotypic variation under each condition than the stress‐specific QTLs. Whether the effects of stress‐nonspecific QTLs were due to pleiotropic effects of the same genes, physical linkage of different genes, or a combination of both could not be determined in this study. The results, however, indicate that the rate of tomato seed germination under different stress and nonstress conditions is partly under the same genetic control.