gebhart/patrepeval huggingface dataset:
Demonstration of Unidirectional Single-Stranded DNA Translocation by PcrA Helicase:  Measurement of Step Size and Translocation Speed (1999)

Using a fluorescent sensor for inorganic phosphate, the kinetics of ATP hydrolysis by PcrA helicase were measured in the presence of saturating concentrations of oligonucleotides of various lengths. There is a rapid phase of inorganic phosphate release that is equivalent to several turnovers of the ATPase, followed by slower steady-state ATP hydrolysis. The magnitude of the rapid phase is governed by the length of single-stranded DNA, while the slow phase is independent of its length. A kinetic model is presented in which the rapid phase is associated with translocation along single-stranded DNA, after the PcrA binds randomly along the DNA. There is a linear relationship between the length of single-stranded DNA and both the duration and amplitude of the rapid phase. These data suggest that the translocation activity occurs at 50 bases/s in unidirectional single-base steps, each requiring the hydrolysis of 1 ATP molecule.
Combined Core Needle Biopsy and Fine-Needle Aspiration With Ancillary Studies Correlate Highly With Traditional Techniques in the Diagnosis of Nodal-Based Lymphoma (2011)

Core needle biopsy (CNB) and fine-needle aspiration (FNA) are increasingly replacing excisional lymph node biopsy in the diagnosis of lymphomas. However, evaluation of CNB and FNA remains challenging owing to limited architectural information and the more detailed subclassification of lymphomas required by the WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues. Our study is the largest study to assess diagnostic accuracy of CNB and FNA in conjunction with ancillary studies. We analyzed 263 cases and a diagnosis was established in 237, of which 193 were completely subclassified. In cases in which excisional biopsy was available as a reference for comparison, CNB and FNA had a sensitivity of 96.5%, a specificity of 100%, a positive predictive value of 100%, and a negative predictive value of 90%. CNB and FNA with ancillary studies represent a viable alternative in the diagnosis of lymphoma, as long as the number and size of cores for morphologic studies are not compromised.
The dynamic bubble trap reduces microbubbles in extracorporeal circulation and high intensity transient signals in the middle cerebral artery: a case report (2003)

Microemboli during extracorporeal circulation (ECC) might be a reason for postoperative neuropsychological dysfunction. This case report shows that reduction of microbubbles in the arterial line, as well as high intensity transient signals (HITS) in the middle cerebral artery (MCA), could be accomplished by use of a dynamic bubble trap (DBT) during routine coronary artery bypass graft (CABG) surgery in a 63-year-old male. The DBT was placed after the arterial filter, an ultrasound Doppler device was used for detection of microemboli before and after the DBT. HITS were measured by a transcranial ultrasound Doppler in both MCAs. For first 32 min of ECC, the DBTwas excluded; 54 916 microbubbles and 507 HITS were counted. In the next 30 min, blood flow was directed through the DBT. This led to a significant reduction of microbubbles from 55 888 to 18 237; accordingly, only 120 HITS were registered. A DBT, integrated in ECC for routine CABG, effectively reduces air bubbles, thus protecting the cerebrovascular system from microembolization, as demonstrated by lower HITS counts.
Integration between terrestrial and satellite networks: the PPDR-TC vision (2014)

Wireless communication technologies are critical for public protection and disaster relief (PPDR) professionals during the emergency operations that follow natural or man-made disasters, scenarios in which commercial terrestrial networks often fail to provide the necessary support. The reason is threefold: they simply get disrupted by the disaster, they cannot sustain the sudden surge of network demand or they fail to deliver the necessary bandwidth and/or other QoS guarantees. In every PPDR operation reliable voice communications are critical, especially in the very early stages of the response; nevertheless, there is an increasing demand from the PPDR community for a wider range of data-centric services. While current technologies used for PPDR operations provide a rich set of voice-centric services, they are unable to sustain high-bandwidth data-oriented applications. As the PPDR-TC EU consortium, we propose a hybrid approach to tackle the question of determining the future architecture for Pan-European PPDR networks based on the integration of Terrestrial and Satellite technologies, presenting our first simulation results on the integration of LTE and Satellite Networks.
Circulating Tumor DNA: Measurement and Clinical Utility (2017)

Circulating tumor DNA (ctDNA) is a component of the "naked" DNA found in blood. It can be isolated from plasma and represents combined genetic material from the primary tumor and metastases. Quantitative and qualitative information about a cancer, including mutations, can be derived using digital polymerase chain reaction and other technologies. This "liquid biopsy" is quicker and more easily repeated than tissue biopsy, yields real-time information about the cancer, and may suggest therapeutic options. All stages of cancer therapy have the ability to benefit from ctDNA, starting with screening for cancer before it is clinically apparent. During treatment of metastatic disease, it is useful to predict response and monitor disease progression. Currently, ctDNA is used in the clinic to select patients who may benefit from epidermal growth factor receptor-targeted therapy in non-small cell lung cancer. In the future, ctDNA technology promises useful applications in every part of clinical oncology care.
Neuere Erkenntnisse zur Polymerisation von Blausäure (1974)

Abstract Für die Polymerisation der Blausäure werden zwei grundsätzlich verschiedene Mechanismen diskutiert, von denen einer den schrittweisen Aufbau des Polymeren, ausgehend von Blausäure als Monomerem, vorsieht, während der andere auf dem Dimeren der Blausäure als dem eigentlichen polymerisierenden „Monomeren”︁ beruht. Für die „Dimerpolymerisation”︁ wird neben dem anionischen noch ein carbenoider Mechanismus in Betracht gezogen. Es wurden verschiedene N ‐Alkyl‐substituierte Blausäuredimere hergestellt. Sie zeigten keinen Carbencharakter und waren relativ stabil. Ihre Umsetzungen mit Blausäure wurden studiert. Dabei wurde eine Reihe von Additionsprodukten erhalten, die weitgehend den schrittweisen Polymerisationsmechanismus favorisieren.
Surface-enhanced Raman scattering microchip fabricated by femtosecond laser (2010)

We report a surface-enhanced Raman scattering (SERS) microchip that is capable of measuring SERS signals of liquid samples with high sensitivity. The microdevice is an integration of a silicon-based SERS substrate, a multimode optical fiber (MMF), and a microchannel embedded in the photosensitive glass fabricated by the femtosecond laser followed by thermal treatment, wet etching, and annealing. The performance of the SERS microchip is evaluated by measuring rhodamine 6G using a 632.8 nm He-Ne laser at 4.3 mW excitation power, which reveals that the detection limit is lower than 10(-10) M at a 1 s short accumulation time.
POChP—Choroba Zbyt Rzadko Rozpoznawana Nie Tylko we Wczesnym Okresie (2007)

Przewlekła obturacyjna choroba płuc (POChP) jest chorobą bardzo rozpowszechnioną [...]
The use of tri(n‐butyl)phosphate detergent mixtures to inactivate hepatitis viruses and human immunodeficiency virus in plasma and plasma's subsequent fractionation (1990)

The treatment of plasma with organic solvent/detergent mixtures at the time of plasma collection or pooling could reduce the exposure of technical staff to infectious viruses and enhance the viral safety of the final product. Treatment of plasma for 4 hours with 2-percent tri(n-butyl)phosphate (TNBP) at 37 degrees C, with 1-percent TNBP and 1-percent polyoxyethylensorbitan monooleate (Tween 80) at 30 degrees C, or with 1-percent TNBP and 1-percent polyoxyethylene ethers, (Triton X-45) at 30 degrees C resulted in the rapid and complete inactivation of greater than or equal to 10(4) tissue culture-infectious doses (TCID50) of vesicular stomatitis and Sindbis viruses, which are used as surrogates. Treatment of plasma with TNBP and TNBP and Tween-80 was shown to inactivate greater than or equal to 10(4) TCID50 of human immunodeficiency virus. TNBP treatment of plasma contaminated with 10(6) chimpanzee-infectious doses (CID50) of hepatitis B virus and 10(5) CID50 of non-A,non-B hepatitis virus prevented the transmission of hepatitis to chimpanzees. Immediately after treatment of plasma with 2-percent TNBP, the recovery of factors VIII, IX, and V and antithrombin III was 80, 90, 40, and 100 percent, respectively. Recovery of all factors was greater than or equal to 90 percent after treatment with TNBP and detergent mixtures. Treated plasma was fractionated by standard techniques into antihemophilic factor and prothrombin complex concentrates, immune globulin, and albumin. Prior treatment with TNBP or TNBP and detergent did not affect the separations of desired proteins. Therefore, it appears possible to inactivate viruses in plasma before the execution of standard fractionation procedures.(ABSTRACT TRUNCATED AT 250 WORDS)
Mode coupling in a Penning trap:<i>π</i>pulses and a classical avoided crossing (1990)

An inhomogeneous radiofrequency electric field can couple the cyclotron and axial modes of a single ion in a Penning trap. The classical equations of motion are the same as those of a driven quantum-mechanical two-level system. We discuss an analog of the \ensuremath{\pi} pulse, which can exchange mode actions, and an analog of the avoided crossing. Experimental illustrations are presented.
Economic Evaluation of Methyl Bromide Alternatives for the Production of Tomatoes in North Carolina (2008)

Partial budget analysis was used to evaluate soil treatment alternatives to methyl bromide (MeBr) based on their efficacy and cost-effectiveness in the production of tomato ( Solanum lycopersicum ). The analysis was conducted for the mountain tomato production region based on 6 years of field test data collected in Fletcher, NC. Fumigation alternatives evaluated included 61.1% 1,3-dichloropropene + 34.7% chloropicrin (Telone-C35™), 60.8% 1,3-dichloropropene + 33.3% chloropicrin (InLine), 99% chloropicrin (Chlor-o-pic), 94% chloropicrin (TriClor EC), 42% metam sodium (4.26 lb/gal a.i., Vapam), and 50% iodomethane + 50% chloropicrin (Midas). The MeBr formulation was 67% methyl bromide and 33% chloropicrin (Terr-O-Gas). Chloropicrin applied at 15 gal/acre provided the greatest returns with an additional return of $907/acre relative to MeBr. Telone-C35 provided an additional return of $848/acre and drip-applied metam sodium provided an additional return of $137/acre. The return associated with broadcast applied metam sodium was about equal to the estimated return a grower would receive when applying MeBr. Fumigating with a combination of chloropicrin and metam sodium; shank-applied chloropicrin at 8 gal/acre; drip-applied chloropicrin, Midas, or InLine; and the nonfumigated soil treatment all resulted in projected losses of $156/acre, $233/acre, $422/acre, $425/acre, $604/acre, and $2133/acre, respectively, relative to MeBr. Although technical issues currently associated with some of the MeBr alternatives may exist, results indicate that there are economically feasible fumigation alternatives to MeBr for production of tomatoes in North Carolina.
Production of gamma interferon by natural killer cells from Toxoplasma gondii-infected SCID mice: regulation by interleukin-10, interleukin-12, and tumor necrosis factor alpha (1994)

Previous studies of mice have implicated natural killer (NK) cells as mediators of protective activity against Toxoplasma gondii through their production of gamma interferon (IFN-gamma). In the present study, we have compared NK-cell activity in infected and uninfected SCID mice. Our data reveal that infection results in increased levels of IFN-gamma in serum and elevated NK-cell activity but that these NK cells were not cytotoxic for T. gondii-infected P815 cells. Treatment with anti-IFN-gamma antibody abrogated the increase in NK-cell activity and resulted in earlier mortality of infected mice. In vivo treatment with anti-asialo GM1 antiserum reduced NK cell activity and levels of IFN-gamma in serum but did not alter time to death. Spleen cells from infected mice produced higher levels of IFN-gamma than those from uninfected mice when stimulated in vitro with live T. gondii or parasite antigen preparations. Further analysis revealed that interleukin 10 (IL-10) inhibited, whereas tumor necrosis factor alpha (TNF-alpha) and IL-12 enhanced, IFN-gamma production by spleen cells from infected or uninfected mice. The combination of IL-12 and TNF-alpha induced higher levels of IFN-gamma from whole spleen cells of infected mice than from those of uninfected mice. Depletion of the adherent cell population from the spleen cells of infected mice led to a significant reduction in the levels of IFN-gamma produced after stimulation with IL-12 plus TNF-alpha. Similar results did not occur with cells from uninfected mice. These data indicate that other cytokines produced by the adherent cell population from infected mice may be involved in maximal production of IFN-gamma by NK cells stimulated with IL-12 and TNF-alpha. To assess the importance of endogenous IL-12, a polyclonal anti-IL-12 was administered to infected SCID mice. This treatment led to earlier mortality, indicating that endogenous IL-12 mediates resistance to T. gondii.
Timing and Energy Resolution of New Near-UV SiPMs Coupled to <formula formulatype="inline"><tex Notation="TeX">${\rm LaBr}_3$</tex> </formula>:Ce for TOF-PET (2014)

The high light output and fast decay time of LaBr<sub>3</sub>:Ce scintillation detectors leads to excellent timing performance. To realize the potential of timing resolution with LaBr<sub>3</sub>:Ce we have investigated the performance with SiPMs, which enable 1-to-1 coupling to individual crystals, and which have been optimized for the near-ultraviolet (NUV) scintillation light emission of LaBr<sub>3</sub>:Ce. Coincidence timing resolution (CTR) of 100 ps was measured for a 4×4×5 mm<sup>3</sup> LaBr<sub>3</sub>:30%Ce crystal directly coupled to a large-area 4×4 mm<sup>2</sup> NUV-SiPM. Results show very little dependence on temperature, in the range of -20° to 20°C, and bias voltage, from 2 V to 5 V over breakdown. Optimal performance was achieved at an over-voltage (OV) range of 3 V - 5 V, at which high gain and high photon detection efficiency are achieved. Though saturation was evident at 511 keV, an energy resolution of 6.8% was measured after correcting for non-linearity. We also measured a CTR of 110 ps for a 4×4×5mm<sup>3</sup> LaBr<sub>3</sub>:5%Ce crystal and 245 ps for a 4×4×30 mm<sup>3</sup> LaBr<sub>3</sub>:5%Ce crystal using the NUV-SIPM. The poorer timing measurement for the 30-mm long crystal is due mainly to a systematic shift in the time pick-off as a function of the depth-of-interaction. The excellent temperature stability, fast rise time, high gain, and low noise of the NUV-SiPM make it a practical and highly appealing photodetector for the readout of a LaBr<sub>3</sub>:Ce TOF-PET detector.
Does an Eye Tracker Tell the Truth about Visualizations?: Findings while Investigating Visualizations for Decision Making (2012)

For information visualization researchers, eye tracking has been a useful tool to investigate research participants' underlying cognitive processes by tracking their eye movements while they interact with visual techniques. We used an eye tracker to better understand why participants with a variant of a tabular visualization called `SimulSort' outperformed ones with a conventional table and typical one-column sorting feature (i.e., Typical Sorting). The collected eye-tracking data certainly shed light on the detailed cognitive processes of the participants; SimulSort helped with decision-making tasks by promoting efficient browsing behavior and compensatory decision-making strategies. However, more interestingly, we also found unexpected eye-tracking patterns with SimulSort. We investigated the cause of the unexpected patterns through a crowdsourcing-based study (i.e., Experiment 2), which elicited an important limitation of the eye tracking method: incapability of capturing peripheral vision. This particular result would be a caveat for other visualization researchers who plan to use an eye tracker in their studies. In addition, the method to use a testing stimulus (i.e., influential column) in Experiment 2 to verify the existence of such limitations would be useful for researchers who would like to verify their eye tracking results.
Saccharomyces cerevisiae exhibits a sporulation-specific temporal pattern of transcript accumulation. (1985)

Cultures of the yeast Saccharomyces cerevisiae that are heterozygous for the mating type (MATa/MAT alpha) undergo synchronous meiosis and spore formation when starved for nitrogen and supplied with a nonfermentable carbon source such as acetate. Haploid and homozygous MAT alpha/MAT alpha and MATa/MATa diploid cells incubated under the same conditions fail to undergo meiosis and are asporogenous. It has not yet been firmly established that gene expression during sporulation is controlled at the level of transcript accumulation. To examine this question, we used cloned genes that encode a variety of "housekeeping" functions to probe Northern blots to assay the appearance of specific transcripts in both sporulating and asporogenous S. cerevisiae. In sporulating cells, each transcript showed a characteristic pattern of accumulation, reaching a maximum relative abundance at one of several different periods. In contrast, in both asporogenous haploid MATa and diploid MAT alpha/MAT alpha cells, all transcripts accumulated with similar kinetics. These results suggest a sporulation-specific pattern for transcript appearance. During these studies, high levels of several different transcripts were observed at unexpected times in sporulating cells. Histone (H)2A and (H)2B1 transcripts, although most abundant during premeiotic DNA synthesis, remained at one-third to one-half maximal levels after its end and were found in mature ascospores. Their appearance at this time is in sharp contrast to vegetative cells in which these histone transcripts are only found just before and during the period of DNA synthesis. Furthermore, transcripts from GAL10 and CDC10 genes, which are believed to be dispensable for sporulation, were much more abundant in sporulating cells than in asporogenous cells and vegetative cells grown on glucose or acetate. The presence of these transcripts did not appear to be due to a general activation of transcription because each accumulated with different kinetics. In addition, the transcript for at least one gene, HO, that is also dispensable for sporulation was not detected. The increased abundance of transcripts from some genes not required for sporulation leads us to propose that genes preferentially expressed during sporulation need not be essential for this differentiation.
Cellular processing of copper-67-labeled monoclonal antibody chCE7 by human neuroblastoma cells. (1995)

Monoclonal antibody chCE7, an internalizing neuroblastoma-specific chimeric antibody, was derivatized with the macrocyclic amine ligand 4-[(1,4,8,11-tetraazacyclotetradec-1-yl)-methyl] benzoic acid tetrahydrochloride and labeled with the potential therapeutic nuclide 67Cu. Using pulse labeling and an acid elution endocytosis assay, 67Cu-chCE7 was found to be internalized into human neuroblastoma (SKN-AS) cells at a similar rate and to a similar extent as 125I-labeled chCE7. Uptake of 67Cu-chCE7 and 125I-chCE7 into the acid stable (intracellular) pool proceeded with similar kinetics during the first 2 h of internalization. However, in contrast to 125I-chCE7-loaded cells, at later times intracellular radioactivity kept increasing in the case of 67Cu-chCE7-loaded cells. It was shown that this effect is due to the intracellular accumulation of a low M(r) degradation product consisting of the 67Cu-4[(1,4,8,11-tetraazacyclotetradec-1-yl)-methyl] benzoic acid complex, possibly with a short peptide attached to it. Degradation of both 125I-chCE7 and 67Cu-chCE7 was inhibited by chloroquine, indicating endosomal or lysosomal degradation, and a 43,000 M(r) fragment was found to be the major high M(r) degradation product in both cases. Although at times between 4 and 6 h of internalization intracellular breakdown of 67Cu-chCE7 was found to proceed more slowly, the major difference between the two immunoconjugates resides in the prolonged cellular retention of the 67Cu-chCE7 metabolite.
Whole-program optimization of object-oriented languages (1996)

This dissertation examines the use of whole-program optimization as a way of improving the performance of object-oriented programming languages. Although object-oriented programming conveys a number of software engineering benefits, heavy application of its trademark feature, dynamic dispatching, imposes severe performance penalties when programs are compiled using traditional compilation techniques. Several new techniques that rely on whole-program optimization are described, and these techniques substantially improve the performance of object-oriented programs written in Cecil, Java, C++, and Modula-3. Among the new techniques is class hierarchy analysis, which provides the compiler with knowledge of the class hierarchy of the entire program. This is an especially important optimization, becaus...
Urokinase-Type Plasminogen Activator Receptor Is Internalized by Different Mechanisms in Polarized and Nonpolarized Madin–Darby Canine Kidney Epithelial Cells (1999)

Accumulated data indicate that endocytosis of the glycosylphosphatidyl-inositol-anchored protein urokinase plasminogen activator receptor (uPAR) depends on binding of the ligand uPA:plasminogen activator inhibitor-1 (PAI-1) and subsequent interaction with internalization receptors of the low-density lipoprotein receptor family, which are internalized through clathrin-coated pits. This interaction is inhibited by receptor-associated protein (RAP). We show that uPAR with bound uPA:PAI-1 is capable of entering cells in a clathrin-independent process. First, HeLaK44A cells expressing mutant dynamin efficiently internalized uPA:PAI-1 under conditions in which transferrin endocytosis was blocked. Second, in polarized Madin-Darby canine kidney (MDCK) cells, which expressed human uPAR apically, the low basal rate of uPAR ligand endocytosis, which could not be inhibited by RAP, was increased by forskolin or phorbol ester (phorbol 12-myristate 13-acetate), which selectively up-regulate clathrin-independent endocytosis from the apical domain of epithelial cells. Third, in subconfluent nonpolarized MDCK cells, endocytosis of uPA:PAI-1 was only decreased marginally by RAP. At the ultrastructural level uPAR was largely excluded from clathrin-coated pits in these cells and localized in invaginated caveolae only in the presence of cross-linking antibodies. Interestingly, a larger fraction of uPAR in nonpolarized relative to polarized MDCK cells was insoluble in Triton X-100 at 0 degreesC, and by surface labeling with biotin we also show that internalized uPAR was mainly detergent insoluble, suggesting a correlation between association with detergent-resistant membrane microdomains and higher degree of clathrin-independent endocytosis. Furthermore, by cryoimmunogold labeling we show that 5-10% of internalized uPAR in nonpolarized, but not polarized, MDCK cells is targeted to lysosomes by a mechanism that is regulated by ligand occupancy.