gebhart/patrepeval huggingface dataset:
Suppression of the negative effect of minor arginine codons on gene expression; preferential usage of minor codons within the first 25 codons of the<i>Escherichia coli</i>genes (1990)

AGA and AGG codons for arginine are the least used codons in Escherichia coli, which are encoded by a rare tRNA, the product of the dnaY gene. We examined the positions of arginine residues encoded by AGA/AGG codons in 678 E. coli proteins. It was found that AGA/AGG codons appear much more frequently within the first 25 codons. This tendency becomes more significant in those proteins containing only one AGA or AGG codon. Other minor codons such as CUA, UCA, AGU, ACA, GGA, CCC and AUA are also found to be preferentially used within the first 25 codons. The effects of the AGG codon on gene expression were examined by inserting one to five AGG codons after the 10th codon from the initiation codon of the lacZ gene. The production of beta-galactosidase decreased as more AGG codons were inserted. With five AGG codons, the production of beta-galactosidase (Gal-AGG5) completely ceased after a mid-log phase of cell growth. After 22 hr induction of the lacZ gene, the overall production of Gal-AGG5 was 11% of the control production (no insertion of arginine codons). When five CGU codons, the major arginine codon were inserted instead of AGG, the production of beta-galactosidase (Gal-CGU5) continued even after stationary phase and the overall production was 66% of the control. The negative effect of the AGG codons on the Gal-AGG5 production was found to be dependent upon the distance between the site of the AGG codons and the initiation codon. As the distance was increased by inserting extra sequences between the two codons, the production of Gal-AGG5 increased almost linearly up to 8 fold. From these results, we propose that the position of the minor codons in an mRNA plays an important role in the regulation of gene expression possibly by modulating the stability of the initiation complex for protein synthesis.
Group Asynchronous Browsing on the World Wide Web (1995)

The goal of our Group Asynchronous Browsing (GAB) research is to provide tools for people to leverage the information hunting and gathering activities of other people or groups of people on the World Wide Web. To date we have focused on taking advantage of the personal subject indices that are being constructed today with bookmarks or hotlists of widely available browsers. We have also concentrated on monitoring URLs that may themselves serve as living resources on particular subject areas. In support of the former, we have created a server that collects and merges bookmark/hotlist files of participating users. The server can serve subsets of these merged bookmark files to either standard HTML client browsers or to a client built with the multiscale visualization tool Pad++. For the latter, we have built a tool called WebWatch that can monitor URLs of interest and alert users when significant updates appear.
An analysis of Internet inter-domain topology and route stability (2002)

The Internet routing fabric is partitioned into several domains. Each domain represents a region of the fabric administered by a single commercial entity. Over the past two years, the routing fabric has experienced significant growth. From more than a year's worth of inter-domain routing traces, we analyze the Internet inter-domain topology, its route stability behavior, and the effect of growth on these characteristics. Our analysis reveals several interesting results. Despite growth, the degree distribution and the diameter of the inter-domain topology have remained relatively unchanged. Furthermore, there exists a four-level hierarchy of Internet domains classified by degree. However, connectivity between domains is significantly non-hierarchical. Despite increased connectivity at higher levels in the topology, the distribution of paths to prefixes from the backbone remained relatively unchanged. There is evidence that both route availability and the mean reachability duration have degraded with Internet growth.
Sera from patients with heparin-induced thrombocytopenia generate platelet-derived microparticles with procoagulant activity: an explanation for the thrombotic complications of heparin-induced thrombocytopenia (1994)

Heparin-induced thrombocytopenia is characterized by moderate thrombocytopenia and thrombotic complications, whereas quinine/quinidine-induced thrombocytopenia usually presents with severe thrombocytopenia and bleeding. Using flow cytometry and assays of procoagulant activity, we investigated whether sera from patients with these immune drug reactions could stimulate normal platelets to generate platelet-derived microparticles with procoagulant activity. Sera or purified IgG from patients with heparin-induced thrombocytopenia stimulated the formation of platelet-derived microparticles in a heparin-dependent fashion. Further studies showed that heparin-induced thrombocytopenia sera also produced a marked increase in procoagulant activity. In contrast, sera from patients with quinine- or quinidine-induced thrombocytopenia did not generate platelet-derived microparticles nor generate increased procoagulant activity. However, quinine/quinidine-induced thrombocytopenia sera produced a significant increase in the binding of IgG to platelets in a drug-dependent fashion, whereas sera from patients with heparin-induced thrombocytopenia demonstrated no drug-dependent binding of IgG to platelets. We also observed increased levels of circulating microparticles in patients with acute heparin-induced thrombocytopenia compared with control patients. Our observations indicate that the generation of procoagulant platelet-derived microparticles in vivo is a plausible explanation for the thrombotic complications observed in some patients with heparin-induced thrombocytopenia.
Abnormalities in the handling of intracellular bacteria in Crohn’s disease: a link between infectious etiology and host genetic susceptibility (2008)

The etiology of Crohn's disease (CD) is still poorly understood, but recent advances have highlighted the importance of the innate immune system and the critical relationship between the gut flora and the intestinal mucosa. Several combinations of genetic factors predisposing to CD have been described, with the most significant replicable associations including genes for intracellular receptors of bacterial cell walls (NOD2/CARD15) and for bacterial clearance and antigen processing via autophagy (ATG16L1 and IRGM). One theoretical link between susceptibility genes NOD2/CARD15, ATG16L1, and IRGM is that CD is primarily induced by the presence of a dysfunctional immunological response to persistent infection by intracellular bacterial pathogens such as Mycobacterium avium subspecies paratuberculosis or adherent-invasive Escherichia coli, both first-rank candidates on the basis of host genetic susceptibility, which concerns impaired functions in the defense against intracellular bacteria.
Antimalarial Linear Lipopeptides from a Panamanian Strain of the Marine Cyanobacterium <i>Lyngbya </i><i>majuscula</i> (2007)

As part of the Panama International Cooperative Biodiversity Groups (ICBG) project, two new (2, 4) and two known (1, 3) linear alkynoic lipopeptides have been isolated from a Panamanian strain of the marine cyanobacterium Lyngbya majuscula. Carmabin A (1), dragomabin (2), and dragonamide A (3) showed good antimalarial activity (IC50 4.3, 6.0, and 7.7 microM, respectively), whereas the nonaromatic analogue, dragonamide B (4), was inactive. The planar structures of all four compounds were determined by NMR spectroscopy in combination with mass spectrometry, and their stereoconfigurations were established by chiral HPLC and by comparison of their optical rotations and NMR data with literature values.
Quantum Transport: Atom to Transistor (2005)

This book presents the conceptual framework underlying the atomistic theory of matter, emphasizing those aspects that relate to current flow. This includes some of the most advanced concepts of non-equilibrium quantum statistical mechanics. No prior acquaintance with quantum mechanics is assumed. Chapter 1 provides a description of quantum transport in elementary terms accessible to a beginner. The book then works its way from hydrogen to nanostructures, with extensive coverage of current flow. The final chapter summarizes the equations for quantum transport with illustrative examples showing how conductors evolve from the atomic to the ohmic regime as they get larger. Many numerical examples are used to provide concrete illustrations and the corresponding Matlab codes can be downloaded from the web. Videostreamed lectures, keyed to specific sections of the book, are also available through the web. This book is primarily aimed at senior and graduate students
Soluble VEGF receptor Flt1: the elusive preeclampsia factor discovered? (2003)

status: Published
Thermal and electrical conductivity of approximately 100-nm permalloy, Ni, Co, Al, and Cu films and examination of the Wiedemann-Franz Law (2015)

We present measurements of thermal and electrical conductivity of polycrystalline permalloy (Ni-Fe), aluminum, copper, cobalt, and nickel thin films with thickness $&lt;200$ nm. A micromachined silicon-nitride membrane thermal-isolation platform allows measurements of both transport properties on a single film and an accurate probe of the Wiedemann--Franz (WF) law expected to relate the two. Through careful elimination of possible effects of surface scattering of phonons in the supporting membrane, we find excellent agreement with WF in a thin Ni-Fe film over nearly the entire temperature range from 77 to 325 K. All other materials studied here deviate somewhat from the WF prediction of electronic thermal conductivity with a Lorenz number, $L$, suppressed from the free-electron value by $10%\phantom{\rule{4.pt}{0ex}}\text{to}\phantom{\rule{4.pt}{0ex}}20%$. For Al and Cu we compare the results to predictions of the theoretical expression for the Lorenz number as a function of $T$. This comparison indicates two different types of deviation from expected behavior. In the Cu film, a higher than expected $L$ at lower $T$ indicates an additional thermal conduction mechanism, while at higher $T$ lower than expected values suggests an additional inelastic scattering mechanism for electrons. We suggest the additional low-$T\phantom{\rule{4pt}{0ex}}L$ indicates a phonon contribution to thermal conductivity and consider increased electron-phonon scattering at grain boundaries or surfaces to explain the high-$T$ reduction in $L$.
VDB (2013)

We have developed a novel hierarchical data structure for the efficient representation of sparse, time-varying volumetric data discretized on a 3D grid. Our “VDB”, so named because it is a Volumetric, Dynamic grid that shares several characteristics with B+trees, exploits spatial coherency of time-varying data to separately and compactly encode data values and grid topology. VDB models a virtually infinite 3D index space that allows for cache-coherent and fast data access into sparse volumes of high resolution. It imposes no topology restrictions on the sparsity of the volumetric data, and it supports fast (average O (1)) random access patterns when the data are inserted, retrieved, or deleted. This is in contrast to most existing sparse volumetric data structures, which assume either static or manifold topology and require specific data access patterns to compensate for slow random access. Since the VDB data structure is fundamentally hierarchical, it also facilitates adaptive grid sampling, and the inherent acceleration structure leads to fast algorithms that are well-suited for simulations. As such, VDB has proven useful for several applications that call for large, sparse, animated volumes, for example, level set dynamics and cloud modeling. In this article, we showcase some of these algorithms and compare VDB with existing, state-of-the-art data structures.
Solid phase microextraction with thermal desorption using fused silica optical fibers (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolid phase microextraction with thermal desorption using fused silica optical fibersCatherine L. Arthur and Janusz. PawliszynCite this: Anal. Chem. 1990, 62, 19, 2145–2148Publication Date (Print):October 1, 1990Publication History Published online1 May 2002Published inissue 1 October 1990https://pubs.acs.org/doi/10.1021/ac00218a019https://doi.org/10.1021/ac00218a019research-articleACS PublicationsRequest reuse permissionsArticle Views10795Altmetric-Citations4079LEARN 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 Get e-Alerts
The Biosynthesis of Ricinoleic Acid by <i>Claviceps purpurea</i> (1966)

The major source ofricinoleic acid (D-12-hydroxy-9-octadecenoic acid) is the oil of the castor bean (Ricinus communis), where it occurs as a mixture of simple triglycerides. The precursor of ricinoleic acid in this system has been shown to be oleic acid and not linoleic acid (James,
Using Stationary-Dynamic Camera Assemblies for Wide-area Video Surveillance and Selective Attention (2006)

In this paper, we present a prototype video surveillance system that uses stationary-dynamic (or master-slave) camera assemblies to achieve wide-area surveillance and selective focus-of-attention. We address two critical issues in deploying such camera assemblies in real-world applications: off-line camera calibration and on-line selective focus-ofattention. Our contributions over existing techniques are twofold: (1) in terms of camera calibration, our technique calibrates all degrees-of-freedom (DOFs) of both stationary and dynamic cameras, using a closed-form solution that is both efficient and accurate, and (2) in terms of selective focus-of-attention, our technique correctly handles dynamic changes in the scene and varying object depths. This is a significant improvement over existing techniques that use an expensive and non-adaptable table-look-up process.
Primase-polymerases are a functionally diverse superfamily of replication and repair enzymes (2015)

Until relatively recently, DNA primases were viewed simply as a class of proteins that synthesize short RNA primers requisite for the initiation of DNA replication. However, recent studies have shown that this perception of the limited activities associated with these diverse enzymes can no longer be justified. Numerous examples can now be cited demonstrating how the term 'DNA primase' only describes a very narrow subset of these nucleotidyltransferases, with the vast majority fulfilling multifunctional roles from DNA replication to damage tolerance and repair. This article focuses on the archaeo-eukaryotic primase (AEP) superfamily, drawing on recently characterized examples from all domains of life to highlight the functionally diverse pathways in which these enzymes are employed. The broad origins, functionalities and enzymatic capabilities of AEPs emphasizes their previous functional misannotation and supports the necessity for a reclassification of these enzymes under a category called primase-polymerases within the wider functional grouping of polymerases. Importantly, the repositioning of AEPs in this way better recognizes their broader roles in DNA metabolism and encourages the discovery of additional functions for these enzymes, aside from those highlighted here.
Detection of Increased Fecal Carcinoembryonic Antigen and Its Characterization as a Membrane‐bound Form in Colorectal Carcinoma and Other Gastrointestinal Disorders (1989)

The levels and character of carcinoembryonic antigen (CEA) in feces were investigated by sandwich radioimmunometric assay using anti-CEA monoclonal antibodies NCC-CO-411 and NCC-CO-432. Mean CEA concentration was significantly higher (P less than 0.001) in the feces from patients with colorectal carcinoma and other gastrointestinal disorders as compared to normal adults. More than 90% of the fecal CEA was trapped by a 0.22 micron membrane filter and solubilized by treatment with 1% Triton X-100 or phosphatidyl-inositol specific phospholipase C. In hydrophobic chromatography, most of the fecal CEA was eluted at the lowest (NH4)2SO4 concentration while serum CEA appeared in the more hydrophilic fractions. These results suggest that the majority of CEA exists in feces as an amphiphilic molecule or a membrane-bound form. The increase of fecal CEA may reflect the destruction and abrasion of epithelial cells in various gastrointestinal disorders.
Rapid and reproducible characterization of sickling during automated deoxygenation in sickle cell disease patients (2019)

In sickle cell disease (SCD), sickle hemoglobin (HbS) polymerizes upon deoxygenation, resulting in sickling of red blood cells (RBCs). These sickled RBCs have strongly reduced deformability, leading to vaso-occlusive crises and chronic hemolytic anemia. To date, there are no reliable laboratory parameters or assays capable of predicting disease severity or monitoring treatment effects. We here report on the oxygenscan, a newly developed method to measure RBC deformability (expressed as Elongation Index - EI) as a function of pO<sub>2</sub> . Upon a standardized, 22 minute, automated cycle of deoxygenation (pO<sub>2</sub> median 16 mmHg ± 0.17) and reoxygenation, a number of clinically relevant parameters are produced in a highly reproducible manner (coefficients of variation <5%). In particular, physiological modulators of oxygen affinity, such as, pH and 2,3-diphosphoglycerate showed a significant correlation (respectively R = -0.993 and R = 0.980) with Point of Sickling (PoS<sub>5%</sub> ), which is defined as the pO<sub>2</sub> where a 5% decrease in EI is observed during deoxygenation. Furthermore, in vitro treatment with antisickling agents, including GBT440, which alter the oxygen affinity of hemoglobin, caused a reproducible left-shift of the PoS, indicating improved deformability at lower oxygen tensions. When RBCs from 21 SCD patients were analyzed, we observed a significantly higher PoS in untreated homozygous SCD patients compared to treated patients and other genotypes. We conclude that the oxygenscan is a state-of-the-art technique that allows for rapid analysis of sickling behavior in SCD patients. The method is promising for personalized treatment, development of new treatment strategies and could have potential in prediction of complications.
Infrared Radiation Sensors of &lt;I&gt;Melanophila acuminata&lt;/I&gt; (Coleoptera: Buprestidae): A Thermopneumatic Model (2005)

A description of the ne structure of the infrared radiation (IR) sensor of Melanophila acuminata (De Geer) and of the role of the wings during ight in mechanically modulating incoming IR into on and off pulses, supports a thermopneumatic model of IR perception by this insect. The model postulates that pulsed IR, corresponding to wavelengths emitted by res, enters an enclosed, airtight, thick-walled cavity in each sensor through an apical epicuticular waveguide and is absorbed by a thin, chitinous endocuticular lamella of the cavity wall. The lamella is heated and in turn heats and expands the enclosed air that then compresses a basal cuticular cap that displaces the tubular body of the sensor, triggering a dendritic impulse and transducing an action potential in the neuron. This process is possible because of the absorption by the chitinous lamella of the wavelengths of IR emitted by res resulting in extraordinary IR wavelength discrimination, radiant energy sensitivity, and rapid response time. These properties distinguish the sensor from temperature sensors of insects, sometimes erroneously designated as IR sensors, that respond relatively slowly to broadband wavelength radiation.
Sex Steroids and Growth Factors Differentially Regulate the Growth and Differentiation of Cultured Human Endometrial Stromal Cells* (1991)

We have studied the interaction between growth factors and sex steroids in regulating human endometrial stromal cell growth and differentiation using an in vitro serum-free cell culture model system. None of the growth factors [epidermal growth factor (EGF), basic fibroblast growth factor (bFGF), insulin, insulin-like growth factor-I (IGF-I), IGF-II, or platelet-derived growth factor] stimulated the growth of human endometrial stromal cells grown in progestin-free medium. However, the growth of progestin-treated cultures was dramatically increased by EGF, bFGF, or platelet-derived growth factor, but not by insulin, IGF-I, or IGF-II. Estrogen could not substitute for progesterone in this protocol, and coadministration of estrogen with progestin did not enhance the response over that to progesterone alone. In contrast to their positive effects on growth, only EGF, not bFGF, stimulated stromal cell differentiation, as measured by an increase in PRL, laminin, and fibronectin production; moreover, stimulation of differentiation was dependent upon the presence of progestin in the culture medium. Thus, human endometrial stromal cell growth is 1) regulated by a discrete set of growth factors, only a subset of which regulates stromal cell differentiation; and 2) regulation of stromal cell growth and stromal cell differentiation by growth factors is progestin dependent. Our results provide direct evidence for interaction between growth factors and sex steroids in the regulation of stromal cell growth and differentiation in vitro and suggest that growth factors may be absolutely required in conjunction with progesterone for the decidual response in vivo.
Mechanism of release of soluble forms of tumor necrosis factor/lymphotoxin receptors by phorbol myristate acetate-stimulated human THP-1 cells in vitro. (1993)

The mechanism involved in the release of the soluble forms of 55 and 75 kDa TNF and lymphotoxin (LT) membrane receptors was studied in a continuous human monocytic cell line, THP-1, in vitro. THP-1 cells were found to spontaneously release soluble forms of both 55 and 75 kDa TNF/LT receptors. Release was up-regulated by PMA, and optimal release was achieved at 10(-8) M PMA. Serine protease inhibitors such as PMSF,3,4 dichloroisocoumarin, N alpha-p-tosyl-L-lysine chloromethyl ketone (TLCK), and N-tosyl-L-phenylalanine chloromethyl ketone (TPCK) were found to inhibit the production of both soluble TNF/LT receptors. PMSF (2 mM) also blocked receptors shedding from paraformaldehyde-fixed THP-1 cells coincubated with conditioned media from PMA-stimulated THP-1 cells. Colchicine at 1 and 10 microM stimulated the production of both soluble TNF/LT receptors, but the PMA-induced release of both soluble TNF/LT receptors was inhibited. It appears that the PMA-induced release of soluble TNF/LT receptors involves serine proteases in the extracellular space where the soluble parts of the TNF/LT receptors are cleaved directly off the cell membrane.