gebhart/patrepeval huggingface dataset:
Characterization of the 5′-flanking transcriptional regulatory region of the human Fcγ receptor gene, Fcγ RIIA (1992)

The human Fc gamma receptor gene Fc gamma RIIA is expressed in platelets, neutrophils, monocytes and macrophages. Understanding the regulation of expression of Fc gamma RIIA will enhance our knowledge of regulated gene expression and immune function in these cells. We cloned a 3.65 kb region of the 5' end of the Fc gamma RIIA gene and characterized 3.4 kb of previously unreported sequence of the 5'-flanking region. Primer extension studies and RNase protection analyses of mRNA from HEL, K562 and U937 cells revealed multiple transcription start sites. One transcription start site mapped to a 5'-untranslated (5'UT) exon approximately 1 kb 5' to the ATG translation initiation codon, while a second start site mapped near the ATG codon. Reverse transcription combined with PCR (RT-PCR) employing an oligonucleotide in the putative 5'UT exon and an antisense oligonucleotide in the translated region yielded products which confirm that transcription starts in this 5'UT exon 881 bp upstream of the ATG codon. Sequence analysis of the RT-PCR products showed two related RNA splice products which use alternative 3'-consensus AG splice acceptor sites. Fc gamma RIIA mRNA thus has three distinct potential 5'UT regions, two alternatively spliced forms from the start site in the 5'UT exon and the third from the start site near the ATG codon. Comparisons of the human Fc gamma RIIA 5'-flanking region with human Fc gamma RI and mouse Fc gamma RII beta genes as well as with other genes expressed in megakaryocytes, neutrophils and monocytes reveal structural similarities and shared promoter elements.
Experimental and Theoretical Studies of the Redox Potentials of Cyclic Nitroxides (2008)

The redox potentials of 25 cyclic nitroxides from four different structural classes (pyrrolidine, piperidine, isoindoline, and azaphenalene) were determined experimentally by cyclic voltammetry in acetonitrile, and also via high-level ab initio molecular orbital calculations. It is shown that the potentials are influenced by the type of ring system, ring substituents and/or groups surrounding the radical moiety. For the pyrrolidine, piperidine, and isoindolines there is excellent agreement (mean absolute deviation of 0.05 V) between the calculated and experimental oxidation potentials; for the azaphenalenes, however, there is an extraordinary discrepancy (mean absolute deviation of 0.60 V), implying that their one-electron oxidation might involve additional processes not considered in the theoretical calculations. This recently developed azaphenalene class of nitroxide represents a new variant of a nitroxide ring fused to an aromatic system and details of the synthesis of five derivatives involving differing aryl substitution are also presented.
Insertional inactivation of mtrX and mtrY genes from the mithramycin gene cluster affects production and growth of the producer organism Streptomyces argillaceus (2000)

Mithramycin is an antitumor aromatic polyketide synthesized by Streptomyces argillaceus. Two genes (mtrX and mtrY) of the mithramycin gene cluster were inactivated by gene replacement. Inactivation of mtrX, that encodes an ABC excission nuclease system for DNA repair, produced a mutant that was affected in the normal rate of growth. Expression of mtrX in Streptomyces albus in a multicopy plasmid vector conferred a low increase in resistance to mithramycin. Inactivation of mtrY, that encodes a protein of unknown function, produced a 50% decrease in mithramycin biosynthesis. When mtrY was expressed in the wild-type S. argillaceus in a multicopy plasmid, this caused about 47% increase in the levels of mithramycin production. It is proposed that mtrX and mtrY could code for a secondary defense mechanism and a mithramycin regulatory element, respectively.
One-tube multiplex RT-PCR of<i>BCR-ABL</i>transcripts in analysis of patients with chronic myeloid leukaemia and acute lymphoblastic leukaemia (1998)

We describe a one-tube multiplex reverse transcription polymerase chain reaction (RT-PCR) assay for the detection of bcr-abl fusion mRNA in analysis of patients with chronic myeloid leukaemia and acute lymphoblastic leukaemia. The assay provides a quick and reliable method for the detection and analysis of chromosome translocations resulting in formation of the fusion proteins p210 (b3a2/b2a2) and p190 (e1a2). The method is based on the use of magnetic beads and sequence-specific reverse transcription primers. By combining direct mRNA isolation, reverse transcription and first-stage PCR we have reduced the number of manipulations, maintained sensitivity, and minimized the risk of contamination. A nested primer strategy is used to secure sensitivity. We also introduce a competitive one-tube RT-PCR to be able to monitor the relative quantity of transcripts using in vitro transcribed RNA as competitor.
Design and Fabrication of a Metallic Micro-Heat Pipe Based on High-Aspect-Ratio Microchannels (2007)

The cooling capacity of a micro-heat pipe is mainly governed by the magnitude of capillary pressure induced in the wick structure. For microchannel wicks, a higher capillary pressure is achievable for narrower and deeper channels. In this study, a metallic micro-heat pipe adopting high-aspect-ratio microchannel wicks is fabricated. The micromachining of high-aspect-ratio microchannels is done using the laser-induced wet etching technique in which a focused laser beam irradiates the workpiece placed in a liquid etchant along a desired channel pattern. Because of the direct writing characteristic of the laser-induced wet etching method, no mask is necessary, and the fabrication procedure is relatively simple. Deep microchannels of an aspect ratio close to 10 can be readily fabricated with little heat damage to the workpiece. The laser-induced wet etching process for the fabrication of high-aspect-ratio microchannels in 0.5 mm thick stainless steel foil is presented in detail. The shape and size variations of microchannels with respect to the process variables, such as laser power, scanning speed, number of scans, and etchant concentration, are closely examined. Also, the fabrication of a flat micro-heat pipe based on the high-aspect-ratio microchannels is demonstrated.
Automated Workload Characterization for I/O Performance Analysis in Virtualized Environments (2015)

Next generation IT infrastructures are highly driven by virtualization technology. The latter enables flexible and efficient resource sharing allowing to improve system agility and reduce costs for IT services. Due to the sharing of resources and the increasing requirements of modern applications on I/O processing, the performance of storage systems is becoming a crucial factor. In particular, when migrating or consolidating different applications the impact on their performance behavior is often an open question. Performance modeling approaches help to answer such questions, a prerequisite, however, is to find an appropriate workload characterization that is both easy to obtain from applications as well as sufficient to capture the important characteristics of the application. In this paper, we present an automated workload characterization approach that extracts a workload model to represent the main aspects of I/O-intensive applications using relevant workload parameters, e.g., request size, read-write ratio, in virtualized environments. Once extracted, workload models can be used to emulate the workload performance behavior in real-world scenarios like migration and consolidation scenarios. We demonstrate our approach in the context of two case studies of representative system environments. We present an in-depth evaluation of our workload characterization approach showing its effectiveness in workload migration and consolidation scenarios. We use an IBM System z equipped with an IBM DS8700 and a Sun Fire system as state-of-the-art virtualized environments. Overall, the evaluation of our workload characterization approach shows promising results to capture the relevant factors of I/O-intensive applications.
Semantic Keyword Selection for Automatic Video Annotation (2013)

Choosing descriptive keywords to best describe digital media content is crucial for many applications, especially those involving content-based indexing or retrieval. Traditionally such keywords are selected manually, which is labor intensive, restrictive to a limited set of words and inherently subjective to the annotator. Therefore, in this paper, we propose an automatic and objective keyword selection method for annotating video. We specifically used lecture videos and surrogate documents, e.g. transcripts, to extract potential candidate keywords. These potential keywords are then filtered based on a set of seed words to select fewer but more descriptive keywords. The seed words are extracted from the title of the video and subject category. We propose a new objective method to select top ranking keywords based on visual similarity and word sense disambiguation. To validate this approach, the selected keywords are compared to subjectively selected keywords obtained experimentally. Furthermore, the proposed ranking method is also compared to traditional term frequency inverse document frequency (TF-IDF) and state of the art latent dirichlet allocation (LDA) method. The obtained results show that the words selected by the proposed objective method correlate highly with those selected by viewers. In general, the proposed method performs better than TF-IDF and LDA.
Greek Literature (1995)

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Functional Analysis of Conserved Histidine Residues in Cephalosporium acremonium Isopenicillin N Synthase by Site-directed Mutagenesis (1996)

The isopenicillin N synthase of Cephalosporium acremonium (cIPNS) involves a catalytically important non-heme iron which is coordinated credibly to histidine residues. A comparison of the IPNS genes from various microbial sources indicated that there are seven conserved histidine residues. These were individually replaced by leucine residues through site-directed mutagenesis, and the sites of mutation were confirmed by DNA sequencing. The seven mutant genes were cloned separately into the vector pET24d for expression in Escherichia coli BL21 (DE3), and the proteins were expressed as soluble enzymes. All the resulting mutant enzymes obtained have mobilities of approximately 38 kDa, identical with the wild-type enzyme on SDS-polyacrylamide gel electrophoresis, and were also reactive to cIPNS antibodies. The enzymes were purified by ammonium sulfate precipitation and DEAE-Sephadex A-50 ion exchange chromatography, and these were analyzed for enzyme activity. A group of mutant enzymes, H49L, H64L, H116L, H126L, and H137L, were found to be enzymatically active with reduced activities of 16-93.7%, indicating that they are not essential for catalysis. Two of the mutant enzymes, H216L and H272L, were found to have lost their enzymatic activity completely, indicating that both His-216 and His-272 are crucial for catalysis. It is suggested that these histidines are likely to serve as ligands for binding to the non-heme iron in the IPNS active site. Alignment of the amino acid sequence of IPNS to related non-heme Fe(2+)-requiring enzymes indicated that the two essential histidine residues correspond to two invariant residues located in highly homologous regions. The conservation of the two closely located histidine residues indicates the possible conservation of similar iron-binding sites in these enzymes.
Insulin-like growth factor I diminishes in vivo and in vitro vascular contractility: role of vascular nitric oxide. (1996)

Although most insulin-like growth factor I (IGF-I) in the circulation is generated by the liver, the hormone is also produced locally by the vasculature, suggesting its potential importance in regulation of regional blood flow. Accordingly, we studied the effects of in vivo exposure to IGF-I (5.1 nmol, i.v.) as well as in vitro incubation (100 nM) on endothelium-intact rat tail artery contractile responses to KCl and norepinephrine (NE). Systemic administration of IGF-I resulted in transient lowering of blood pressure, with maximal reduction occurring at 15 min and a return to baseline by 60 min. Maximal contractility of rings removed from animals 90 min after a bolus injection of IGF-I, when blood pressure had returned to normal, was significantly reduced for both KCl (58%) and NE (51%) without a change in sensitivity. Similar data were obtained when rings from untreated animals were preincubated in vitro for 90 min; maximal contractility in response to KCl was decreased by 31% and that to NE by 22%. L-Nitroarginine methyl ester, an inhibitor of nitric oxide (NO) production, administered in vivo before IGF-I or added to the bath buffer reversed the attenuation. The nearly identical in vivo and in vitro results suggest that the observed diminution in contractility is a direct effect of IGF-I on the vasculature, probably mediated in large part by the release of NO. This idea is supported by our observation that IGF-I stimulates NO production in intact vessels. Further, the latency required indicates that rather complex mechanisms involving actions common on both receptor- and nonreceptor-mediated events are initiated by IGF-I and/or NO.
H1 Binding Unwinds (1996)

The preference of the linker histones to bind to superhelical DNA in comparison with linear or relaxed molecules suggests that these proteins might, in turn, change the twist and/or writhe of DNA molecules upon binding. In order to explore such a possibility, we looked for changes in the linking number of plasmid pBR322 caused by H1 binding, using assays that involve nicking and resealing of DNA strands. Two types of enzymes were used, eukaryotic topoisomerase I and prokaryotic DNA ligase. The results revealed that H1 binding causes unwinding of the DNA, with the unwinding angle being approximately 10 degrees . The globular domain of histone H1 is also capable of unwinding DNA, but to a lesser degree.
Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design (2016)

The modified Latin square design presented here uses a composite testing scheme for the evaluation of multiple performance characteristics: linear performance of individual controls, signal response within dynamic range pools of controls, and ratio detection between pairs of dynamic range pools. This compact design provides an economical sample format for the evaluation of multiple external RNA controls within a single experiment per platform. These results indicate that well-designed pools of RNA controls, spiked into samples, provide measurement assurance for endogenous gene expression studies.
Remote Sensing and Human Health: New Sensors and New Opportunities (2000)

Since the launch of Landsat-1 28 years ago, remotely sensed data have been used to map features on the earth's surface. An increasing number of health studies have used remotely sensed data for monitoring, surveillance, or risk mapping, particularly of vector-borne diseases. Nearly all studies used data from Landsat, the French Système Pour l'Observation de la Terre, and the National Oceanic and Atmospheric Administration's Advanced Very High Resolution Radiometer. New sensor systems are in orbit, or soon to be launched, whose data may prove useful for characterizing and monitoring the spatial and temporal patterns of infectious diseases. Increased computing power and spatial modeling capabilities of geographic information systems could extend the use of remote sensing beyond the research community into operational disease surveillance and control. This article illustrates how remotely sensed data have been used in health applications and assesses earth-observing satellites that could detect and map environmental variables related to the distribution of vector-borne and other diseases.
Design of a 64-channel Digital High Frequency linear array ultrasound imaging beamformer on a Massively Parallel Processor Array (2008)

In this design, an Ambric's Massively Parallel Processor Array (MPPA), which includes 336 asynchronous processors and communicates through a configurable structure of channels with a 128-bit high speed (100MHz) Input/Output (I/O) port, is used to implement the 64-channel digital beamformer. Besides the beamformer, the system is composed of 256-channel analog front-end pulser/receiver, 64-channel of Time-Gain Compensation (TGC), 64-channel of high-speed digitizer, a host PC and a PCI Express-based accelerator in the Am2045 chip with a 512 Mbytes external memory. This system is designed to handle a 256 elements linear array or a 64 elements phased array transducer. The system provides 64 channels of excitation pulsers while receiving simultaneously at a 150 MHz sampling rate with 12-bit resolution. The digitized data from all channels of one frame are first stored in the internal memory of MPPA. The coarse delays are integer multiples of the sampling clock rate. They are achieved by dynamically updating the memory addresses which are loaded in the delay coefficients table. Random Memory Access capability of MPPA enables processors to randomly access data while it is still in channels, which eliminate the necessity of moving all data from I/O ports into memory before they can be processed. The fine delays are implemented by FIR filters with an interpolation factor of 8. This technique and architecture allow dynamic receive focusing, aperture growth, spatial filtering, and scan conversion by software only.
Characterizing and circumventing sequence restrictions for synthesis of circular RNA <i>in vitro</i> (2020)

Just as eukaryotic circular RNA (circRNA) is a product of intracellular backsplicing, custom circRNA can be synthesized in vitro using a transcription template in which transposed halves of a split group I intron flank the sequence of the RNA to be circularized. Such permuted intron-exon (PIE) constructs have been used to produce circRNA versions of ribozymes, mimics of viral RNA motifs, a streptavidin aptamer, and protein expression vectors for genetic engineering and vaccine development. One limitation of this approach is the obligatory incorporation of small RNA segments (E1 and E2) into nascent circRNA at the site of end-joining. This restriction may preclude synthesis of small circRNA therapeutics and RNA nanoparticles that are sensitive to extraneous sequence, as well as larger circRNA mimics whose sequences must precisely match those of the native species on which they are modelled. In this work, we used serial mutagenesis and in vitro selection to determine how varying E1 and E2 sequences in a thymidylate synthase (td) group I intron PIE transcription template construct affects circRNA synthesis yield. Based on our collective findings, we present guidelines for the design of custom-tailored PIE transcription templates from which synthetic circRNAs of almost any sequence may be efficiently synthesized.
Multiple Residues Contribute to the Inability of Murine CCR-5 To Function as a Coreceptor for Macrophage-Tropic Human Immunodeficiency Virus Type 1 Isolates (1998)

Infection of CD4-positive cells by human immunodeficiency virus type 1 (HIV-1) requires functional interaction of the viral envelope protein with a coreceptor belonging to the chemokine receptor family of seven-membrane-spanning receptors. For the majority of macrophage-tropic HIV-1 isolates, the physiologically relevant coreceptor is the human CCR-5 (hCCR-5) receptor. Although the murine homolog of CCR-5 (mCCR-5) is unable to mediate HIV-1 infection, chimeric hCCR-5/mCCR-5 molecules containing single extracellular domains derived from hCCR-5 are effective coreceptors for certain macrophage-tropic HIV-1 isolates. Here, we have sought to identify residues in hCCR-5 critical for HIV-1 infection by substitution of mCCR-5-derived residues into the context of functional chimeric hCCR-5/mCCR-5 receptor molecules. Using this strategy, we demonstrate that residues 7, 13, and 15 in the first extracellular domain and residue 180 in the third extracellular domain of CCR-5 are important for HIV-1 envelope-mediated membrane fusion. Of interest, certain substitutions, for example, at residues 184 and 185 in the third extracellular domain, have no phenotype when introduced individually but strongly inhibit hCCR-5 coreceptor function when present together. We hypothesize that these changes, which do not preclude chemokine receptor function, may inhibit a conformational transition in hCCR-5 that contributes to HIV-1 infection. Finally, we report that substitution of glycine for valine at residue 5 in CCR-5 can significantly enhance the level of envelope-dependent cell fusion by expressing cells. The diversity of the mutant phenotypes observed in this mutational analysis, combined with their wide distribution across the extracellular regions of CCR-5, emphasizes the complexity of the interaction between HIV-1 envelope and coreceptor.
Novel heterocyclic systems from selective oxidation at the β-pyrrolic position of porphyrins (1984)

Novel heterocyclic systems in which a porphyrin pyrrole has been ring-expanded to a morpholine derivative (5), ring-contracted to an azetine derivative (6), and converted into the oxazolone derivatives (4) and (9) result from selective oxidation of 2-amino-5,10,15,20-tetraphenylporphyrin (1).
Robust sensor data collection over a long period using virtual sensing (2016)

Virtual sensing is a technique in which sensor values in a sensor network are estimated some of the time instead of taking direct measurements. Virtual sensing conserves energy on the sensor nodes, and it can be used for recovering missing data due to node or network failure, and for estimating values where permanent sensor installation is in-feasible. This paper considers the novel and challenging problem of designing an adaptive long range virtual sensing (LRVS) framework that is able to estimate values for days or months. The framework does not require any a priori modeling of generating functions for the sensor time series. A new correlation metric, called "nearest hour of the day neighbor", finds similarity in multiple time series that is able to arbitrate the hidden contexts within the data. LRVS is evaluated on data from a building-monitoring sensor network with over 100 heterogeneous, noisy sensors from different suppliers.
RNA polymerase subunit homology among cyanobacteria, other eubacteria and archaebacteria (1988)

RNA polymerase purified from vegetative cells of the cyanobacterium Anabaena sp. strain PCC 7120 contains a dissociable sigma factor and a core of five subunits: the beta', beta, and two alpha subunits characteristic of all eubacteria and an additional 66,000-molecular-weight polypeptide called gamma. Fifteen of fifteen strains of unicellular and filamentous cyanobacteria tested contained a serologically related gamma protein. Antiserum to gamma reacted with Escherichia coli beta' and the A subunit of RNA polymerase of the archaebacterium Sulfolobus acidocaldarius. Thus the evolution of the RNA polymerase beta' subunit has followed different paths in three groups of procaryotes: cyanobacteria, other eubacteria, and archaebacteria.