gebhart/patrepeval huggingface dataset:
Long-range analyses of the centromeric regions of human chromosomes 13, 14 and 21: identification of a narrow domain containing two key centromeric DNA elements (1993)

Alpha-satellite, satellite 3 and satellite 1 DNA have been proposed as candidate components of a functional human centromere. Multiple subfamilies of these three DNA have recently been identified at the pericentric regions of the human acrocentric chromosomes. Using pulsed field gel electrophoresis, we have constructed long-range maps of the various centromeric markers for chromosomes 13, 14 and 21. These maps cover approximately 2.3 megabases of sequence for each chromosome, and the results demonstrate that within this centromeric region, chromosomes 13 and 21 have a similar organization that is partially shared by chromosome 14. A discrete satellite 3 domain was identified on each chromosome within the boundaries of the alpha-satellite DNA. No satellite 1 was detected within the defined centromeric regions suggesting that satellite 1 is not essential for centromere function.
Recognition of shared melanoma antigen by HLA‐A2‐restricted cytolytic T cell clones derived from human tumor‐infiltrating lymphocytes (1993)

Three melanoma-specific cytotoxic T lymphocytes (CTL) clones were derived from the tumor-infiltrating lymphocyte (TIL) of human melanoma M17, and were used to study the expression of immunogenic melanoma peptides on allogeneic tumors. Antibody inhibition studies showed that two of these TIL clones were restricted by an HLA-A2 molecule which was identified as A2.1 by gene sequencing. The third CTL clone was not restricted by HLA-A2, but by a B or C HLA antigen. HLA-A2-restricted CTL clones M17-1 and M17-2 lysed 5 and 12 out of 15 HLA-A2+ allogeneic melanomas, respectively. Since they did not lyse autologous Epstein-Barr virus B cells, HLA-A2.1-transfected P815 cells, 13 HLA-A2+ non-melanoma tumor cell lines and 10 HLA-A2- melanomas, these clones appeared specific for melanoma-restricted epitopes presented by the HLA-A2.1 molecule. We then tried to determine why a few HLA-A2+ melanomas were refractory to TIL lysis. By using a combination of flow cytometry analysis, partial cloning and sequencing of their HLA-A2 genes, we show that failure to lyse did not result from low expression or polymorphism of the HLA-A2 molecule, or from deficient expression of the adhesion molecules ICAM-1 and LFA-3 by these melanomas. Taken together, our data confirm at the clonal level the existence of shared melanoma antigens recognized by TIL in the HLA-A2.1 context. They further show that individual peptides derived from these antigens are expressed by a large majority of HLA-A2+ melanomas. Identification of such peptides appears crucial for the future of vaccination therapies.
Authoring a hypertext UNIX help manual (1995)

Operating systems require extensive help documentation. The purpose of this research is the development of a hypertext version of man for the UNIX operating system. The conversion of the man pages was facilitated by the use of several programs. This article contains a discussion of automating the conversion of standard text to hypertext.
The Particulate Methane Monooxygenase from Methylococcus capsulatus (Bath) Is a Novel Copper-containing Three-subunit Enzyme (1998)

The particulate methane monooxygenase (pMMO) is known to be very difficult to study mainly due to its unusual activity instability in vitro. By cultivating Methylococcus capsulatus (Bath) under methane stress conditions and high copper levels in the growth medium, membranes highly enriched in the pMMO with exceptionally stable activity can be isolated from these cells. Purified and active pMMO can be subsequently obtained from these membrane preparations using protocols in which an excess of reductants and anaerobic conditions were maintained during membrane solubilization by dodecyl beta-D-maltoside and purification by chromatography. The pMMO was found to be the major constituent in these membranes, constituting 60-80% of total membrane proteins. The dominant species of the pMMO was found to consist of three subunits, alpha, beta, and gamma, with an apparent molecular mass of 45, 26, and 23 kDa, respectively. A second species of the pMMO, a proteolytically processed version of the enzyme, was found to be composed of three subunits, alpha', beta, and gamma, with an apparent molecular mass of 35, 26, and 23 kDa, respectively. The alpha and alpha' subunits from these two forms of the pMMO contain identical N-terminal sequences. The gamma subunit, however, exhibits variation in its N-terminal sequence. The pMMO is a copper-containing protein only and shows a requirement for Cu(I) ions. Approximately 12-15 Cu ions per 94-kDa monomeric unit were observed. The pMMO is sensitive to dioxygen tension. On the basis of dioxygen sensitivity, three kinetically distinct forms of the enzyme can be distinguished. A slow but air-stable form, which is converted into a "pulsed" state upon direct exposure to atmospheric oxygen pressure, is considered as type I pMMO. This form was the subject of our pMMO isolation effort. Other forms (types II and III) are deactivated to various extents upon exposure to atmospheric dioxygen pressure. Under inactivating conditions, these unstable forms release protons to the buffer (approximately 10 H+/94-kDa monomeric unit) and eventually become completely inactive.
Fertilization Defects in Sperm from Mice Lacking Fertilin β (1998)

Fertilin, a member of the ADAM family, is found on the plasma membrane of mammalian sperm. Sperm from mice lacking fertilin beta were shown to be deficient in sperm-egg membrane adhesion, sperm-egg fusion, migration from the uterus into the oviduct, and binding to the egg zona pellucida. Egg activation was unaffected. The results are consistent with a direct role of fertilin in sperm-egg plasma membrane interaction. Fertilin could also have a direct role in sperm-zona binding or oviduct migration; alternatively, the effects on these functions could result from the absence of fertilin activity during spermatogenesis.
Bacterial Motility: Membrane Topology of the Escherichia coli MotB Protein (1988)

The MotB protein of Escherichia coli is an essential component of the force generators that couple proton movement across the cytoplasmic membrane to rotation of the flagellar motors. The membrane topology of MotB was examined to explore the possibility that it might form a proton channel. MotB--alkaline phosphatase fusion proteins were constructed to identify likely periplasmic domains of the MotB molecule. Fusions distal to a putative membrane-spanning segment near the amino terminus of MotB exhibited alkaline phosphatase activity, indicating that an extensive carboxyl-terminal portion of MotB may be located on the periplasmic side of the membrane. Protease treatment of MotB in spheroplasts confirmed this view. The simple transmembrane organization of MotB is difficult to reconcile with a role as a proton conductor.
Highly compacted biodegradable DNA nanoparticles capable of overcoming the mucus barrier for inhaled lung gene therapy (2015)

Gene therapy has emerged as an alternative for the treatment of diseases refractory to conventional therapeutics. Synthetic nanoparticle-based gene delivery systems offer highly tunable platforms for the delivery of therapeutic genes. However, the inability to achieve sustained, high-level transgene expression in vivo presents a significant hurdle. The respiratory system, although readily accessible, remains a challenging target, as effective gene therapy mandates colloidal stability in physiological fluids and the ability to overcome biological barriers found in the lung. We formulated highly stable DNA nanoparticles based on state-of-the-art biodegradable polymers, poly(β-amino esters) (PBAEs), possessing a dense corona of polyethylene glycol. We found that these nanoparticles efficiently penetrated the nanoporous and highly adhesive human mucus gel layer that constitutes a primary barrier to reaching the underlying epithelium. We also discovered that these PBAE-based mucus-penetrating DNA nanoparticles (PBAE-MPPs) provided uniform and high-level transgene expression throughout the mouse lungs, superior to several gold standard gene delivery systems. PBAE-MPPs achieved robust transgene expression over at least 4 mo following a single administration, and their transfection efficiency was not attenuated by repeated administrations, underscoring their clinical relevance. Importantly, PBAE-MPPs demonstrated a favorable safety profile with no signs of toxicity following intratracheal administration.
Immune pathways and defence mechanisms in honey bees Apis mellifera (2006)

Social insects are able to mount both group-level and individual defences against pathogens. Here we focus on individual defences, by presenting a genome-wide analysis of immunity in a social insect, the honey bee Apis mellifera. We present honey bee models for each of four signalling pathways associated with immunity, identifying plausible orthologues for nearly all predicted pathway members. When compared to the sequenced Drosophila and Anopheles genomes, honey bees possess roughly one-third as many genes in 17 gene families implicated in insect immunity. We suggest that an implied reduction in immune flexibility in bees reflects either the strength of social barriers to disease, or a tendency for bees to be attacked by a limited set of highly coevolved pathogens.
A framework for policy advocacy (2012)

The practice of policy advocacy has outpaced its theoretical development. Yet the importance of a theoretical grounding for advocacy has increased as advocacy organizations demand measures of efficacy, and theories of policy development need to account for advocates' contributions to the process. This article begins to address these issues by developing a conceptual framework of policy advocacy inputs, activities, and outcomes. Logic models of practitioners' advocacy programs were first synthesized into a general model. Then academic theories from social sciences and especially policy studies were reviewed and applied to hypothesize links between advocacy inputs and activities, and between activities and outcomes. The result is a conceptual framework of policy advocacy to focus academic attention on this topic, and to direct a research agenda.
STRUCTURAL AND FUNCTIONAL PROPERTIES OF TRYPANOSOMA TRANS-SIALIDASE (1994)

Sialic acids and sialidases play important roles in cellular interactions and modulate the recognition of pathogenic microbes by mammalian host cells. Protozoan parasites of the genus Trypanosoma express a unique sialic acid metabolizing enzyme. This enzyme, named trans-sialidase (TS), catalyzes the transfer of sialic acids from host glycoconjugates to acceptor molecules of the parasite plasma membrane. in African trypanosomes, the agents of sleeping sickness, TS is found only in forms developing within the insect vector, and the enzyme sialylates the major surface protein. in Trypanosoma cruzi, the causative agent of Chagas' disease in Central and South America, TS is expressed both in the insect and mammalian forms of the parasite. the T. cruzi enzyme has been biochemically characterized, and the gene encoding the enzyme has been cloned. the enzyme sialylates abundant mucin-like molecules present on the surface of the parasite. Several lines of evidence suggest that TS and sialic acid accepters on the surface of T. cruzi participate in host-parasite interactions and mediate the initial stages of the trypanosomes' invasion of host cells.
Snoring and the risk of ischemic brain infarction. (1991)

To determine if a history of snoring is a risk factor for brain infarction, I conducted a case-control study of risk factors for ischemic stroke using 177 consecutive male patients aged 16-60 (mean 49) years with acute brain infarction. For each patient I chose an age-matched (+/- 6 years) male control. Arterial hypertension, coronary heart disease, snoring (habitually or often), and heavy drinking (greater than 300 g/wk) were risk factors in the stepwise multiple logistic regression analysis. The odds ratio of snoring for brain infarction was 2.13. By McNemar's test this association increased strongly if a history of sleep apnea, excessive daytime sleepiness, and obesity were all present with snoring (odds ratio 8.00). My study indicates that snoring may be a risk factor for ischemic stroke, possibly because of the higher prevalence of an obstructive sleep apnea syndrome among snorers than nonsnorers.
Molecular characterization of Wilson disease in the Sardinian population?Evidence of a founder effect (1999)

Wilson disease (WD) in the Sardinian population has an approximate incidence of 1:7,000 live births. Mutation analysis of the WD gene in this population reported in our previous articles led us to the characterization of two common mutations and a group of 13 rare mutations accounting for the molecular defect of 8.5, 7.9, and 15.1% of the WD chromosomes. However, molecular analysis of the WD chromosomes containing the most common haplotype, which accounts for 60.5% of the WD chromosomes, failed to define the disease-causing mutation. In this study, we characterized the promoter and the 5' UTR of the WD gene sequence and carried out a mutation analysis in this DNA region from patients with the most common haplotype. The promoter is contained in a GC-rich island and shows a TATA and a CAAT consensus sequence as well as potential binding sites for transcription factors and metal response elements. In all the analyzed 92 chromosomes with this haplotype, we detected a single mutation consisting of a 15-nt deletion from position -441 to position -427 relative to the translation start site. Expression assays demonstrated a 75% reduction in the transcriptional activity of the mutated sequence compared to the normal control. By adding this mutation to those that have been already characterized, we have now defined the molecular defect in 92% of the WD chromosomes in Sardinians. The high frequency, the expected prevention by preclinical diagnosis and early treatment of the devastating effect of WD on the nervous system and liver tissue, and the feasibility to detect most of molecular defects by DNA analysis indicate that WD in the Sardinian population should be added to the list of diseases currently detected by newborn screening.
The Efficient Implementation of Reed-Solomon High Rate Erasure Resilient Codes (2006)

In this paper, we investigate the efficient implementation of Reed-Solomon high rate erasure resilient codes. Though the implementation of Reed-Solomon codes for error correction coding has been extensively investigated in the past, there is little work on the efficient implementation of Reed-Solomon codes for high rate erasure resilient coding application. In this paper, we investigate a number of technologies, including the direct inverse of the Reed-Solomon sub-generator matrix, and the scalar vector multiplication and addition on the Galois field to speed up the Reed-Solomon erasure encoding/decoding operations. Our implementation of the Reed-Solomon erasure code achieves an encoding/decoding throughput of 25 MB per second, (i.e., 200 Mbit/s), on a Pentium 2.8 GHz computer.
Primary Structure, Tissue Distribution, and Expression of Mouse Phosphoinositide-dependent Protein Kinase-1, a Protein Kinase That Phosphorylates and Activates Protein Kinase Cζ (1999)

Phosphoinositide-dependent protein kinase-1 (PDK1) is a recently identified serine/threonine kinase that phosphorylates and activates Akt and p70(S6K), two downstream kinases of phosphatidylinositol 3-kinase. To further study the potential role of PDK1, we have screened a mouse liver cDNA library and identified a cDNA encoding the enzyme. The predicted mouse PDK1 (mPDK1) protein contained 559 amino acids and a COOH-terminal pleckstrin homology domain. A 7-kilobase mPDK1 mRNA was broadly expressed in mouse tissues and in embryonic cells. In the testis, a high level expression of a tissue-specific 2-kilobase transcript was also detected. Anti-mPDK1 antibody recognized multiple proteins in mouse tissues with molecular masses ranging from 60 to 180 kDa. mPDK1 phosphorylated the conserved threonine residue (Thr402) in the activation loop of protein kinase C-zeta and activated the enzyme in vitro and in cells. Our findings suggest that there may be different isoforms of mPDK1 and that the protein is an upstream kinase that activates divergent pathways downstream of phosphatidylinositol 3-kinase.
Prevention of Gas Explosions by Controlling Oxygen Concentration (1935)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPrevention of Gas Explosions by Controlling Oxygen ConcentrationG. W. Jones and R. E. KennedyCite this: Ind. Eng. Chem. 1935, 27, 11, 1344–1346Publication Date (Print):November 1, 1935Publication History Published online1 May 2002Published inissue 1 November 1935https://doi.org/10.1021/ie50311a027RIGHTS & PERMISSIONSArticle Views92Altmetric-Citations6LEARN 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 PDF (507 KB) Get e-Alerts
Estimation of near‐surface velocities by tomography (1988)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1988Estimation of near‐surface velocities by tomographyAuthors: Xianhuai ZhuGeorge A. McMechanXianhuai ZhuCenter for Lithospheric Studies, University of Texas at Dallas and George A. McMechanCenter for Lithospheric Studies, University of Texas at Dallashttps://doi.org/10.1190/1.1892499 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1892499FiguresReferencesRelatedDetailsCited ByAngle‐Dependent TomostaticsLindsay M. Mayer, Richard D. Miller, Julian Ivanov, Tom Weis, and Bob Anderson25 June 2009 SEG Technical Program Expanded Abstracts 1988ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1988 Pages: 1359 publication data© 1988 Copyright © 1988 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 10 Feb 2005 CITATION INFORMATION Xianhuai Zhu and George A. McMechan, (1988), "Estimation of near‐surface velocities by tomography," SEG Technical Program Expanded Abstracts : 1236-1238. https://doi.org/10.1190/1.1892499 Plain-Language Summary PDF DownloadLoading ...
Distinct physiological roles of the Gq‐coupled metabotropic glutamate receptors co‐expressed in the same neuronal populations (2002)

The group I metabotropic glutamate receptors, mGluR1 and mGluR5, exhibit a high degree of sequence homology, and are often found co-expressed in the same neuronal populations. These receptors couple to a broad array of effector systems, and are implicated in diverse physiological and pathophysiological functions. Due to the high degree of sequence homology, and the findings that these receptors couple identically in recombinant systems, it has been generally assumed that these two group I mGluR subtypes would exhibit redundant function when coexpressed in the same neurons. With the advent of subtype-selective pharmacological tools, it has become possible to tease apart the functions of mGluR1 and mGluR5 in the same neuron. The emerging picture is one of diverse function, which implies differential regulation. Interestingly, the group I mGluRs are modulated by a rich variety of regulatory systems, which may explain how these receptors can mediate divergent actions when present in the same cell.
Role of muscular eNOS in skeletal arteries: Endothelium-independent hypoxic vasoconstriction of the femoral artery is impaired in eNOS-deficient mice (2016)

We previously reported that hypoxia augments α-adrenergic contraction (hypoxic vasoconstriction, HVC) of skeletal arteries in rats. The underlying mechanism may involve hypoxic inhibition of endothelial nitric oxide synthase (eNOS) expressed in skeletal arterial myocytes (16). To further explore the novel role of muscular eNOS in the skeletal artery, we compared HVC in femoral arteries (FAs) from eNOS knockout (KO) mice with that from wild-type (WT) and heterozygous (HZ) mice. Immunohistochemical assays revealed that, in addition to endothelia, eNOS is also expressed in the medial layer of FAs, albeit at a much lower level. However, the medial eNOS signal was not evident in HZ FAs, despite strong expression in the endothelium; similar observations were made in WT carotid arteries (CAs). The amplitude of contraction induced by 1 μM phenylephrine (PhE) was greater in HZ than in WT FAs. Hypoxia (3% Po2) significantly augmented PhE-induced contraction in WT FAs but not in HZ or KO FAs. No HVC was observed in PhE-pretreated WT CAs. The NOS inhibitor nitro-l-arginine methyl ester (0.1 mM) also augmented PhE contraction in endothelium-denuded WT FAs but not in WT CAs. Inhibitors specific to neuronal NOS and inducible NOS did not augment PhE-induced contraction of WT FAs. NADPH oxidase 4 (NOX4) inhibitor (GKT137831, 5 μM), but not NOX2 inhibitor (apocynin, 100 μM), suppressed HVC. Consistent with the role of reactive oxygen species (ROS), HVC was also inhibited by pretreatment with tiron or polyethylene glycol-catalase. Taken together, these data suggest that the eNOS expressed in smooth muscle cells in FAs attenuates α-adrenergic vasoconstriction; this suppression is alleviated under hypoxia, which potentiates vasoconstriction in a NOX4/ROS-dependent mechanism.
High-performance strained Si-on-insulator MOSFETs by novel fabrication processes utilizing Ge-condensation technique (2003)

Strained SOI (SSOI)-nMOSFETs with enhanced mobility up to 67% were fabricated on a strain-relaxed SiGe-on-insulator substrate using a novel Ge-condensation technique. This method, using only standard Si processes, realizes smooth SSOI surfaces without using SIMOX, wafer bonding, surface polishing or any other special processes. Relaxation ratio of the SiGe substrate was varied from 0% to 100%, resulting in the control of threshold voltage. The Ge-condensation process using conventional SOI substrates is an attractive technique for fabrication of multi-threshold SSOI-CMOS circuits with high current drive.
Local injection of RANKL facilitates tooth movement and alveolar bone remodelling (2018)

Local RANKL injection leads to increased osteoclastic activity and facilitates tooth movement, followed by subsequent alveolar bone formation; this implies a reversible transitional acceleration of bone resorption.