gebhart/patrepeval huggingface dataset:
Kaposi's Sarcoma-Associated Herpesvirus vCyclin Open Reading Frame Contains an Internal Ribosome Entry Site (2001)

We have previously examined the transcription and splicing of open reading frames (ORFS) 71 (K13), 72, and 73 of Kaposi's sarcoma-associated herpesvirus (KSHV) in the primary effusion lymphoma cell line BCP-1 (latently infected with KSHV) (45). The three genes encoded by these ORFs (for vFLIP, vCyclin, and latency-associated nuclear antigen [LANA]) are transcribed from a common transcription start site in BCP-1 cells during both latency and the lytic cycles. The resulting transcript is spliced to yield a 5.32-kb message encoding LANA, vCyclin, and vFLIP and a 1.7-kb bicistronic message encoding vCyclin and vFLIP. To investigate whether the vFLIP protein could be expressed from this vCyclin/vFLIP message, we utilized a bicistronic luciferase reporter system. The genes for Renilla and firefly luciferases (which utilize different substrates) were cloned in tandem downstream from a T7 RNA polymerase promoter. Fragments of DNA immediately upstream from the initiating codon of vFLIP were cloned between the two luciferase genes. The relative expression of the two luciferases, one directed by the putative internal ribosome entry site (IRES) sequences and the other by cap-dependent ribosome scanning, was used to compare the activities of the different DNA fragments. A minimum fragment of 233 bp within the coding region of vCyclin was found to direct efficient expression of the downstream cistron (firefly luciferase). The activity of this IRES was orientation dependent and unaffected by methods used to inhibit cap-dependent translation. This is the first demonstration of an IRES element encoded by a DNA virus and may represent a novel mechanism through which KSHV controls protein expression.
The Sort-Merge-Shrink join (2006)

One of the most common operations in analytic query processing is the application of an aggregate function to the result of a relational join. We describe an algorithm called the Sort-Merge-Shrink (SMS) Join for computing the answer to such a query over large, disk-based input tables. The key innovation of the SMS join is that if the input data are clustered in a statistically random fashion on disk, then at all times, the join provides an online, statistical estimator for the eventual answer to the query as well as probabilistic confidence bounds. Thus, a user can monitor the progress of the join throughout its execution and stop the join when satisfied with the estimate's accuracy or run the algorithm to completion with a total time requirement that is not much longer than that of other common join algorithms. This contrasts with other online join algorithms, which either do not offer such statistical guarantees or can only offer guarantees so long as the input data can fit into main memory.
Photocatalytic bacterial inactivation by TiO2-coated surfaces (2013)

The aim of this study was the evaluation of the photoactivated antibacterial activity of titanium dioxide (TiO2)-coated surfaces. Bacterial inactivation was evaluated using TiO2-coated Petri dishes. The experimental conditions optimized with Petri dishes were used to test the antibacterial effect of TiO2-coated ceramic tiles. The best antibacterial effect with Petri dishes was observed at 180, 60, 30 and 20 min of exposure for Escherichia coli, Staphylococcus aureus, Pseudomonas putida and Listeria innocua, respectively. The ceramic tiles demonstrated a photoactivated bactericidal effect at the same exposure time. In general, no differences were observed between the antibacterial effect obtained with Petri dishes and tiles. However, the photochemical activity of Petri dishes was greater than the activity of the tiles.Results obtained indicates that the TiO2-coated surfaces showed a photoactivated bactericidal effect with all bacteria tested highlighting that the titania could be used in the ceramic and building industry for the production of coated surfaces to be placed in microbiologically sensitive environments, such as the hospital and food industry.
GAP1, a novel selection and counter-selection marker for multiple gene disruptions inSaccharomyces cerevisiae (2001)

Volume 16, p. 1111–1119, 2000. Page 1113, column 2, line 17 to line 20: Should read: “The direct repeats (DR1 and DR2) were derived from the Ashbya gossypii LEU2 (AgLEU2) gene and obtained by PCR amplification using plasmid pFA6-kanMX3…︁” Throughout the paper, ‘hisG’ should read as AgLEU2, ‘Salmonella typhimurium’ as ‘Ashbya gossypii’ and ‘hisG1’ and ‘hisG2’ as ‘DR1’ and ‘DR2’, respectively.
Nuclear Cloning, Epigenetic Reprogramming, and Cellular Differentiation (2004)

Almost half a century ago the technique of nucleartransplantation (NT) was pioneered in amphibians (Gurdon 1999; Di Berardino et al. 2003). These experimentsdemonstrated that nuclei of somatic cells are totipotentbut that the ability to generate live animals decreases withthe developmental age of the donor nucleus. The generation of Dolly from an adult mammary gland cell demonstrated that at least some cells within an adult organismretain totipotency and are able to direct development of anew animal (Wilmut et al. 1997). After Dolly, additionalmammalian species were successfully cloned from somatic cells, albeit with a low efficiency, as in most casesonly 0.5–10% of reconstructed oocytes develop into apparently healthy adults (Rideout et al. 2001)...
Dynamic control of a moving platform using the CAREN system to optimize walking invirtual reality environments (2009)

Virtual reality (VR) technology offers the opportunity to expose patients to complex physical environments without physical danger and thus provides a wide range of opportunities for locomotor training or the study of human postural and walking behavior. A VR-based locomotor training system has been developed for gait rehabilitation post-stroke. A clinical study has shown that persons after stroke are able to adapt and benefit from this novel system wherein they walk into virtual environments (VEs) on a self-paced treadmill mounted on a platform with 6 degrees of freedom. This platform is programmed to mimic changes in the terrain encountered in the VEs. While engaging in these VEs, excessive trunk movements and speed alterations have been observed, especially during the pitch perturbations accompanying uphill or downhill terrain changes. An in-depth study of the subject's behavior in relation to the platform movements revealed that the platform rotational axes need to be modified, as previously shown by Barton et al, and in addition did not consider the subject's position on the treadmill. The aim of this study was to determine an optimal solution to simulate walking in real life when engaging in VEs.
Subcutaneous interleukin-2 plus interferon alfa-2a in metastatic renal cancer: an outpatient multicenter trial. (1993)

This outpatient low-dose subcutaneous regimen induced mild toxicity, a modest response rate, and an excellent median survival duration in previously untreated patients. Phase III trials are now needed to compare IL-2 plus IFN with IL-2 alone or to various IL-2/IFN regimens. However, the major task is to identify unique new agents with activity in renal cancer.
Nuclear Magnetic Resonance in the Cesium Halides (1958)

The chemical shifts, the spin-lattice relaxation times, the isotropic exchange coupling $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{A}$, and the pseudo-dipolar exchange coupling $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{B}$ between cation and anion nuclear spins have been determined in a single crystal of CsBr. The results are: ${\ensuremath{\sigma}}_{\mathrm{Cs}}=(\ensuremath{-}1.9\ifmmode\pm\else\textpm\fi{}0.4)\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}4}$, ${\ensuremath{\sigma}}_{\mathrm{Br}}=(\ensuremath{-}2.5\ifmmode\pm\else\textpm\fi{}0.3)\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}4}$, ${({T}_{1})}_{\mathrm{Cs}}=1050\ifmmode\pm\else\textpm\fi{}40$ sec, ${({T}_{1})}_{\mathrm{Br}}=0.105\ifmmode\pm\else\textpm\fi{}0.020$ sec, ${h}^{\ensuremath{-}1}|\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{A}|=55$ ${\mathrm{sec}}^{\ensuremath{-}1}$, ${h}^{\ensuremath{-}1}\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{B}=15 or \ensuremath{-}89$ ${\mathrm{sec}}^{\ensuremath{-}1}$. Similar, but less complete, data have been obtained for a single crystal of CsI and a CsCl powder.The results are discussed in terms of existing theories for the chemical shift and exchange interactions in solids. An average of 25% covalent bonding per ion is deduced.The large ratio of ${T}_{1}$ for Cs and Br, respectively, sets an upper limit to the quadrupole moment of ${\mathrm{Cs}}^{133}$: $|Q|&lt;0.004\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}24}$ ${\mathrm{cm}}^{2}$. This large difference in the spin-lattice interactions between the nuclear species is responsible for some new effects. The decay time ${T}_{2e}$ for the transverse ${\mathrm{Cs}}^{133}$ magnetization is proportional to ${{H}_{1}}^{2}({\ensuremath{\nu}}_{\mathrm{Cs}})$ for a wide power range of the radio-frequency field at the ${\mathrm{Cs}}^{133}$ Larmor frequency. It is furthermore possible to build up a transverse ${\mathrm{Cs}}^{133}$ magnetization by applying, simultaneously with ${H}_{1}({\ensuremath{\nu}}_{\mathrm{Cs}})$, a radio-frequency field ${{H}_{1}}^{\mathrm{Br}}(\ensuremath{\nu})$ at a frequency $\ensuremath{\nu}=\frac{{\ensuremath{\nu}}_{\mathrm{Br}}\ifmmode\pm\else\textpm\fi{}{\ensuremath{\gamma}}_{\mathrm{Cs}}{{H}_{1}}^{\mathrm{Cs}}}{2\ensuremath{\pi}}$. Here ${\ensuremath{\nu}}_{\mathrm{Br}}$ is the bromine precession frequency.A theory of these effects shows that the relatively weak interaction constants $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{A}$ and $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{B}$ between cesium and halogen spins can be determined with much higher accuracy than would have been possible from the usual second moment determinations.
A flexible, tendon-controlled device for endoscopy (2002)

The authors introduce the slide motion scheme, which provides smooth movement of the endoscope stem with only three continuously controlled degrees of freedom. Such movement is accomplished by implementing a series of relative motions between an outer tube and intermittently stiff spines insides. The strength and stability of the locking mechanism, which exhibits the property of intermittent stiffness, is also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Novel technique for mode selection in a large-mode-area fiber laser (2010)

A novel method for selectively exciting a single-spatial-mode (fundamental or higher-order) in a high-power multi-mode fiber laser resonator is presented. Preliminary results for a cladding-pumped Tm-doped silica fiber laser are discussed.
Some Implementations of the Boxplot (1989)

Abstract An increasing number of statistical software packages offer exploratory data displays and summaries. For one of these, the graphical technique known as the boxplot, a selective survey of popular software packages revealed several definitions. These alternative constructions arise from different choices in computing quartiles and the fences that determine whether an observation is “outside” and thus plotted individually. We examine these alternatives and their consequences, discuss related background for boxplots (such as the probability that a sample contains one or more outside observations and the average proportion of outside observations in a sample), and offer recommendations that lead to a single standard form of the boxplot.
Safety, infectivity, transmissibility and immunogenicity of rhesus rotavirus vaccine (MMU 18006) in infants (1986)

In an attempt to evaluate the immunogenicity, infectivity, transmissibility and safety of rhesus rotavirus vaccine (RRV) MMU 18006, 27 infants ages 5 to 20 months participated in two randomized, double-blind placebo controlled trials, one in a day care setting to allow for child to child contact and close surveillance and the other on an outpatient basis. Fourteen infants (mean age, 8.3 months) received 105 plaqueforming units of RRV and 13 (mean age, 11.1 months) received placebo. In the eight infants who participated in the vaccine trial in the day care setting, there was no evidence of transmissibility of RRV, by either stool excretion or seroconversion. The data from both trials showed RRV to be 100% infective and immunogenic in the vaccinees. There were no gastrointestinal side effects although there was an association between vaccine administration and fever occurring on Days 3 and 4. Based on these encouraging preliminary results, further work is proceeding to evaluate this vaccine at lower doses in this age group of infants.
BvgAS-mediated signal transduction: analysis of phase-locked regulatory mutants of Bordetella bronchiseptica in a rabbit model (1994)

Members of the Bordetella genus alternate between two distinct phenotypic phases in response to changes in their environment. This switch, termed phenotypic modulation, is mediated by the BvgAS sensory transduction system. We developed an animal model based on the interaction of Bordetella bronchiseptica with one of its natural hosts, the rabbit. To investigate the importance of BvgAS signal transduction, we constructed constitutive (RB53) and Bvg- (RB54) phase-locked derivatives of a wild-type strain, RB50. RB50 and RB53, but not RB54, established respiratory infections in B. bronchiseptica-free rabbits with an intranasal 50% infective dose of less than 200 organisms, and the course of the infection closely resembled that observed with naturally infected rabbits. Bacteria were recovered from the nasal cavity, larynx, trachea, and lungs in similar numbers from RB50- and RB53-infected rabbits, yet no pathology was detected by histological examination of lung and tracheal sections. The antibody responses in rabbits inoculated with RB50 or RB53 were quantitatively and qualitatively indistinguishable; high titers of antibodies were generated primarily against Bvg(+)-phase-specific antigens. No response against flagella, a Bvg- phase factor, was detected. Assessment of bacteria associated with alveolar macrophages indicated that only a small percentage of bacteria, if any, appear to be residing within lung macrophages. We also tested the ability of these strains to survive in a nutrient poor environment, conditions which may be encountered within certain niches in the host or in an environmental reservoir. The Bvg- phase was advantageous for growth under these conditions. Our results indicate the Bvg+ phase is sufficient for establishment of respiratory tract infection in the rabbit and the normal BvgAS-mediated response to environmental signals is not required during initial colonization. The Bvg- phase may play a role at later stages of infection, including persistence, transmission, or survival in the environment.
LDL Receptor–Related Protein and the Vascular Wall (2005)

LDL receptor-related protein 1 (LRP1) is highly expressed in the vascular wall and is mainly associated with macrophages and vascular smooth muscle cells (VSMCs). Overexpression of LRP1 in atherosclerotic lesions has been demonstrated in several animal models and human lesions. Clinical studies have suggested a relation between alterations in LRP1 expression and coronary heart disease. Indeed, it has been demonstrated that LRP1 gene expression is increased in blood mononuclear cells from patients with coronary obstruction and that the LRP1 mRNA-protein expression ratio is altered in coronary patients. Taken together, these results seem to suggest that LRP1 may be a pivotal receptor in the etiology of atherosclerosis. Our group has contributed to the elucidation of the physiopathologic role of LRP1 in the vascular wall by demonstrating that LRP1-mediated, matrix-retained LDL internalization could be crucial for VSMC-foam cell formation, that LRP1 is upregulated by lipid during human atherosclerotic lesion progression, and that LRP1-mediated aggregated LDL uptake causes the prothrombotic transformation of the vascular wall. Therefore, LRP1 seems to play a pathologic function during atherosclerotic lesion progression; however, LRP1 also seems to be essential for embryonic development and for the maintenance of vascular integrity. The protective effect of LRP1 in the vessel wall seems to be mainly due to its role in controlling certain signaling pathways. In this review, we will focus on the description of the main physiopathologic functions of LRP1 in the vascular wall.
The use of Huygens' equivalence principle for solving the volume integral equation of scattering (1993)

An algorithm is introduced to solve the volume integral equation of scattering. A volume scatterer is first divided into N subscatterers. Then the subscatterers are divided into four groups, and the groups are in turn divided into four subgroups and so on. By using the idea found in many fast algorithms, a smaller problem can hence be nested within a larger problem. Moreover, by way of Huygen's equivalence principle, the scattering properties of a group of subscatterers in a volume can be replaced by a group of subscatterers distributed on a surface enclosing the volume. This idea is used as the basis of an algorithm which solves the scattering problem in several stages, where at each stage the interaction matrix algorithm is first used to find the scattering solution of each subgroup of subscatterers. Subscatterers are then replaced by equivalent surface subscatterers which are used in the next stage. This results in a reduction in the number of subscatterers at every stage. This algorithm can be shown to have a CPU time asymptotically proportional to N/sup 1.5/ for N subscatterers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
What are Coatings? (2006)

Introduction to coatings including annual volume and value of major classes of coatings. General discussion of components of coatings. Relative importance of different classes of resin binders.
Comparison of Bevacizumab, Ranibizumab, and Pegaptanib In Vitro: Efficiency and Possible Additional Pathways (2008)

At clinical doses, bevacizumab and ranibizumab are equally potent in neutralizing VEGF. To neutralize VEGF completely in this system, a fraction of the clinical dose is needed. Ranibizumab is more efficient at neutralizing VEGF when diluted. Pegaptanib showed no effect in this system, which might help explain the clinical experience regarding this drug. A direct effect of ranibizumab and bevacizumab on VEGF protein expression indicates additional pathways of VEGF inhibitors.
Hydrogen Storage in Pillared Li-Dispersed Boron Carbide Nanotubes (2008)

Ab initio density-functional theory study suggests that pillared Li-dispersed boron carbide nanotubes are capable of storing hydrogen with a mass density higher than 6.0 wt% and a volumetric density higher than 45 g/L. The boron substitution in carbon nanotube greatly enhances the binding energy of Li atom to the nanotube, and this binding energy (∼2.7 eV) is greater than the cohesive energy of lithium metal (∼1.7 eV), preventing lithium from clustering at high lithium doping concentration. The adsorption energy of hydrogen on the Li-dispersed boron carbide nanotube is in the range of 10−24 kJ/mol, suitable for reversible H2 adsorption/desorption at room temperature. The aim of this theoretical study is to stimulate future experimental tests on the hydrogen-storage capability in porous boron−carbon systems (e.g., microporous boron carbides) with sufficiently large interior surfaces coated with submonolayer lithium.
Modeling and control of a multi-phase induction machine with structural unbalance (1996)

The multiphase winding structure provides an induction machine with capabilities of starting and running even with one or more of its stator phases open-circuited. However, when operated with such a structurally unbalanced condition, the dynamic properties of the machine will change drastically from its balanced operation condition. For example, field-oriented control strategies developed for a balanced winding structure will no longer function properly and could lead to catastrophic consequences. In this paper, a unified approach to the modeling and field-oriented control of dual three phase induction machine with one phase open is presented. Using the concept of vector space decomposition, the proposed technique is established on the basis of the asymmetrical winding structure directly, and thus provides a precise, physically insightful tool to the modeling and control of induction machines with structural unbalance.
Human IgE mRNA expression by peripheral blood lymphocytes stimulated with interleukin 4 and pokeweed mitogen (1990)

Expression of human IgE mRNA by peripheral blood lymphocytes (PBL) and an IgE-producing myeloma cell line, U-266, was examined by Northern blot hybridization and compared with IgE levels in culture supernatants. A 2.35-kb IgE mRNA was detected in unstimulated atopic PBL and U-266 cells but not in normal PBL, and its levels correlated with IgE protein levels in the supernatant. Upon stimulation with interleukin 4, a new 1.75-kb transcript was revealed in both atopic and normal PBL but not in U-266 cells. Its expression did not correlate with IgE levels in the supernatant. Pokeweed mitogen also induced the expression of the 1.75-kb transcript without concomitant induction of IgE synthesis by normal PBL and even suppressed the spontaneous expression of the 2.35-kb transcript and IgE protein synthesis by atopic PBL. Interferon-gamma, which suppressed both the 2.35-kb transcript and IgE protein production, had no inhibitory effect on the 1.75-kb transcript. Expression of the 1.75-kb transcript was already high after 2 days of stimulation and peaked around day 4. The length of the transcript is smaller than that of mRNA coding for secreted human IgG and IgA and contains all four C epsilon exon sequences, suggesting it might be a truncated transcript without v region and might be a human counterpart of the murine germ-line C epsilon transcript.
Tumour necrosis factor-alpha expression in tumour islets confers a survival advantage in non-small cell lung cancer (2010)

The expression of TNFalpha in the tumour islets of patients with NSCLC is associated with improved survival suggesting a role in the host anti-tumour immunological response. The expression of TNFalpha by macrophages and mast cells is critical for this relationship.
Adaptive spherical lens (1984)

This paper reports the creation of a tandem liquid crystal cell arrangement capable of simulating the performance of a spherical lens. Electrical modulation of the index of refraction creates focusing behavior. The modulation is induced by a set of electrodes whose individual voltages are arranged to provide a cylindrical exit wave front for a uniform plane-wave input. Two such cells with orthogonal electrodes arranged in cascade create spherical lens performance. Experimental evidence using a lens with a relatively small number of electrodes is presented. Applications for such structures, once improved, would include real-time focus adjustment for optical disk readers and hand-held photographic equipment as well as aberration compensation for long path-length optical systems.
Error filtering, pair assembly and error correction for next-generation sequencing reads (2015)

Supplementary data are available at Bioinformatics online.
Prevention Conference VI: Diabetes and Cardiovascular Disease (2002)

The American Heart Association makes every effort to avoid any actual or potential conflicts of interest that may arise as a result of an outside relationship or a personal, professional,