gebhart/patrepeval huggingface dataset:
A New Diagnostic Method for the Detection of Endogenous Rous-Associated Virus-Type Provirus in Chickens (1992)

A quick and simple method has been developed to detect the presence or absence of the endogenous Rous-associated virus (RAV) element ev1 in chickens. The procedure consists of a one-tube multiplex polymerase chain reaction (PCR) involving three oligonucleotide primers that are specific for the upstream flanking region, the long terminal repeat (LTR), and the downstream flanking region of the proviral insert, respectively. The multiplex reaction allows for the unambiguous discrimination between ev1+/ev1+ homozygote, ev1-/ev1- homozygote, and ev1+/ev1- heterozygote birds. The method works best with purified genomic DNA as substrate, but can also be used with rapidly prepared, "crude" DNA samples. The combination of speed with the safety of a nonradioactive procedure, and the ability to perform large numbers of assays by a semi-automated procedure, make this method attractive for large-scale screening projects. The ev1 locus has been used as a model system to demonstrate the feasibility of the PCR diagnostic approach. However the same principle should be applicable to the analysis of other RAV-type ev loci, as well as endogenous elements belonging to other families of viruses as sequence information for the flanking regions of these inserts becomes available.
Measurement of cell swelling in a hypotonic medium as a rapid and sensitive test of cell injury. (1989)

A development and application of a novel test of cell damage is described. The test is based on the ability of undamaged cells to swell in the hypotonic medium. The test is much more rapid and sensitive than the tests based on staining with trypan blue or fluorescein diacetate.
Condensed phase growth of single-wall carbon nanotubes from laser annealed nanoparticulates (2001)

Single-wall carbon nanotubes (SWNT) were grown to micron lengths by laser-annealing nanoparticulate soot containing short (∼50 nm long) nanotube “seeds.” The “seeded” nanoparticulate soot was produced by restricting the time spent by an ablation plume inside an 800 °C oven following laser vaporization of a C–Ni–Co target. The soot collected from the laser vaporization apparatus was placed inside graphite crucibles under argon, and heated by a CO2 laser. In situ pyrometry was used to estimate the sample temperature. Length distributions of SWNT bundles in the unannealed and annealed samples were measured by transmission electron microscopy and field emission scanning electron microscopy. Annealing treatments exceeding 1600 °C produced no increase in nanotube length, while lower temperatures in the 1000–1300 °C range were optimal for growth. These experiments indicate that SWNT grow by the conversion of condensed phase nanomaterial during annealing, a similar mechanism to that proposed for growth during normal laser–vaporization production.
Mechanism and Kinetic of Coke Oxidation by Nonthermal Plasma in Fixed-Bed Dielectric Barrier Reactor (2019)

The formation of coke resulting from propene transformation at 623 K on a faujasite zeolite occurs according to a product shape selectivity mechanism and yields to the formation of highly alkylated polyaromatic molecules such as naphthalene, pyrene, and coronene. Their main parts are trapped in the inner cavities (supercages), poison Brønsted acid sites, and plug micropores. With a common thermal regeneration process, coke burns at 800 K, whereas this study shows that a complete regeneration of zeolite (i.e., total recovery of the native acidity and microporosity) can be achieved at 293 K by using a nonthermal plasma with a low energy consumption in a fixed-bed dielectric barrier reactor: a geometry suitable for industrial scaling. The kinetic rates of coke oxidation and the recovery of acidity and microporosity are similar. The active species (e.g., O*, O2+) are able to diffuse within the zeolite micropores and oxidize the light molecules, 36 times faster than the heavier ones. Thanks to a complete characterization of both the regenerated catalyst and the remaining coke molecules, a reaction scheme is proposed. We claim that catalyst regeneration assisted by nonthermal plasma is a real alternative to thermal combustion.
Pluripotent hematopoietic stem cells augment α-adrenergic receptor-mediated contraction of pulmonary artery and contribute to the pathogenesis of pulmonary hypertension (2020)

Pulmonary hypertension (PH) is a multicellular and progressive disease with a high mortality rate. Among many cell types, hematopoietic stem cells (HSCs) are incriminated in the pathogenesis of PH. However, our understanding of the mechanisms that increase HSCs in blood and lungs of hypertensive animals or patients and the role played by HSCs in the pathogenesis of PH remains elusive. Studies suggest that glycolysis is critical for the survival and growth of HSCs. In various cell types from hypertensive lungs of animals and patients, glycolysis and the glucose-6-phosphate dehydrogenase (G6PD) activity are increased. Herein, we demonstrated in mice that chronic hypoxia increased HSCs (CD34<sup>+</sup>, CD117<sup>+</sup>, CD133<sup>+</sup>, CD34<sup>+</sup>/CD117<sup>+</sup>, and CD34<sup>+</sup>/CD133<sup>+</sup>) in bone marrow and blood and around hypertensive pulmonary arteries in a time-dependent manner. Intriguingly, we found fewer CD133<sup>+</sup> cells in the bone marrow of C57BL/6 mice compared with Sv129J mice, and C57BL mice developed less severe chronic hypoxia-elicited PH and heart failure than Sv129J mice. Similarly, the numbers of CD34<sup>+</sup> and CD117<sup>+</sup> cells in blood of patients with pulmonary arterial hypertension (PAH) were higher (>3-fold) compared with healthy individuals. By allogeneic bone marrow transplantation, we found that GFP<sup>+</sup> bone marrow cells infiltrated the lungs and accumulated around the pulmonary arteries in lungs of hypoxic mice, and these cells contributed to increased α-adrenergic receptor-mediated contraction of the pulmonary artery cultured in hypoxia. Inhibition of G6PD activity with (3β,5α)-3,21-dihydroxypregnan-20-one, a novel and potent G6PD inhibitor, decreased HSCs in bone marrow, blood, and lungs of hypoxic mice and reduced α-agonist-induced contraction of the pulmonary artery and established hypoxia-induced PH. We did not observe CD133<sup>+</sup> cells around the pulmonary arteries in the lungs of chronically hypoxic G6PD-deficient mice. Furthermore, knockdown of G6PD and inhibition of G6PD activity: <i>1</i>) downregulated canonical and noncanonical <i>Wnt</i> and <i>Fzd</i> receptors genes; <i>2</i>) upregulated <i>Bmpr1a</i>; <i>3</i>) decreased <i>Cxcl12</i>, and <i>4</i>) reduced HSC (CD117<sup>+</sup> and CD133<sup>+</sup>) numbers. In all, our findings demonstrate unexpected function for bone marrow-derived HSCs in augmenting α-adrenergic receptor-mediated contraction of pulmonary arteries and remodeling of pulmonary arteries that contribute to increase pulmonary vascular resistance in PAH patients and hypoxic mice and suggest that G6PD, by regulating expression of genes in the WNT and BMPR signaling, contributed to increase and release of HSCs from the bone marrow in response to hypoxic stimuli.
Phase II Study of Ofatumumab in Relapsed Nodular Lymphocyte-Predominant Hodgkin Lymphoma: A Report from the German Hodgkin Study Group (2015)

Abstract Background: Nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) accounts for approximately 5% of all Hodgkin lymphoma (HL) cases. One hallmark of NLPHL is the consistent expression of CD20 on the malignant lymphocyte predominant (LP) cells. To shed more light on the role of anti-CD20 antibody treatment in relapsed NLPHL, we conducted a phase II study evaluating the fully humanized anti-CD20 antibody ofatumumab in 28 patients. Treatment consisted of 8 weekly doses (week 1: 300 mg, week 2-8: 1000 mg) of the antibody. Results: The median age of study patients was 45 years (range: 22-68) and the majority were male (64%). A median of 1 line of therapy (range: 1-5) had been applied prior to study treatment and 7/28 patients (25%) already had rituximab-containing treatment. At the final restaging 3 months after the end of treatment, response was documented in 27/28 patients (96%; 95%-CI: 84%-100%). After a median follow-up of 26 months, 1-year and 2-year progression-free survival (PFS) estimates were 93% and 80%, respectively. No patient died. Transformation into aggressive non-Hodgkin lymphoma (NHL) occurred in 2/28 patients (7.1%). No grade III/IV toxic events were observed. Conclusion: In summary, the anti-CD20 antibody ofatumumab represents a highly active and well tolerated treatment option in relapsed NLPHL. Longer follow-up is required for final conclusions. Disclosures Off Label Use: Ofatumumab in lymphocyte-predominant Hodgkin lymphoma. von Tresckow:Takeda: Consultancy; Celgene: Other: honoraria for preparation of scientific educational events; Novartis: Consultancy, Other: Travel and accomodation, Research Funding; Amgen: Other: honoraria for preparation of scientific educational events. Borchmann:Millennium: Research Funding. Engert:Takeda: Consultancy, Research Funding.
Search for supersymmetry in events with four or more charged leptons in 139 fb−1 of $$ \sqrt{s} $$ = 13 TeV pp collisions with the ATLAS detector (2021)

A bstract A search for supersymmetry in events with four or more charged leptons (electrons, muons and τ -leptons) is presented. The analysis uses a data sample corresponding to 139 fb − 1 of proton-proton collisions delivered by the Large Hadron Collider at $$ \sqrt{s} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> </mml:math> = 13 TeV and recorded by the ATLAS detector. Four-lepton signal regions with up to two hadronically decaying τ -leptons are designed to target several supersymmetric models, while a general five-lepton signal region targets any new physics phenomena leading to a final state with five charged leptons. Data yields are consistent with Standard Model expectations and results are used to set upper limits on contributions from processes beyond the Standard Model. Exclusion limits are set at the 95% confidence level in simplified models of general gauge-mediated supersymmetry, excluding higgsino masses up to 540 GeV. In R -parity-violating simplified models with decays of the lightest supersymmetric particle to charged leptons, lower limits of 1 . 6 TeV, 1 . 2 TeV, and 2 . 5 TeV are placed on wino, slepton and gluino masses, respectively.
Characterizing Search, Recognition, and Decision in the Detection of Lung Nodules on CT Scans: Elucidation with Eye Tracking (2014)

Relationships between reader search, recognition and acceptance, and overall lung nodule detection rate can be studied with eye tracking. Radiologists appear to actively search less than half of the lung parenchyma, with substantial interreader variation in volume searched, fraction of nodules included within the search volume, sensitivity for nodules within the search volume, and overall detection rate.
Perceptual learning of contrast discrimination (2010)

Introduction: Unlike many visual tasks, contrast detection and discrimination are reportedly unchanged by practice (Dorais & Sagi, 97; Adini et al, 02). We re-visited this issue and found very different data. Methods: The stimulus was a Gabor patch presented either at the visual fovea (6 cpd) or at 5 deg temporal or nasal periphery (0.75 cpd). Contrast thresholds were measured with a 2AFC staircase method. Results: (1) Among five observers who practiced foveal contrast detection and discrimination at 0, 0.3, 0.47, and 0.63 contrasts, four showed significant improvement over 4–5 days (2 hrs/day). The fifth observer started with very low thresholds and practice did not further improve performance. (2) Practice induced improvement for discriminating a vertical, 0.47 contrast foveal Gabor only partially transfers to discrimination of a horizontal Gabor, for Gabors with spatial frequency +/−1 octave away, and for Gabors at lower (0.30) and higher (0.74) contrasts, with other stimulus conditions identical. (3) Practice also improved contrast discrimination in the visual periphery. Improvement in one hemi-field only partially transfers to the other hemi-field of the same eye. (4) Practice produced much less learning in detection than in high-contrast discrimination under comparable practice conditions. Practicing detection with additional Gabor flankers did not facilitate learning in detection with no flankers when both conditions were run together. Conclusions: (1) Practice improves contrast discrimination in both foveal and peripheral vision. (2) Learning is partially general, partially specific to the stimulus spatial frequency, orientation, contrast, and retinal location, indicating that both low-level (gain) and high-level (strategy) learning is involved. (3) Contextual stimuli do not affect perceptual learning of contrast detection.
Wideband beamforming with heavily imbalanced channels (2011)

This paper studies fixed wideband beamforming with consideration of realistic channels. There has been a perception that nice beam patterns can always be formed with advanced optimization techniques. This is mostly true if the channels are ideal. But in reality it is not always true. Indeed, achieving a desirable beam pattern with an actual beamforming system can be very difficult, and this might be responsible by the fact that the channel transfer functions are neither spectrally flat nor identical across channels. Therefore, unique issues and countermeasures have to be considered in design phase. In this paper we identify the problems and find solutions via comparison study. Performance and computational load are two major issues. New architectures with parallel processing and off-board computing engines are proposed to reduce the computational pressure as well as run time and improve the performance. Both least-square minimization and convex optimization are used to synthesize the beamformer coefficients. Performance requirements like side-lobe suppression, notch/nulling and frequency invariance have to be jointly considered. Different optimization formulations are proposed to achieve a balance among these requirements. It is found that, with the measured channel data (500-MHz bandwidth, centered at 5.25 GHz), the convex-optimization beamformer can achieve 19 dB side-lobe suppression and a 59-dB notch, but this beamformer does not always turn out a feasible and/or acceptable solution. In contrast, the least-square beamformer is more robust to different parameters. It also observed that frequency invariance beamforming is not a feasible requirement for a realistic wideband beamformer. Overall speaking, the convex-optimization beamformer combined with frequency-interleave (parallel processing) offers the best beamforming performance at a reduced computational cost.
Particle scale impacts on deconstruction energy of pine residues (2022)

The goal of this Case Study was to quantify the impacts of variable moisture and ash on hammer mill throughput and energy consumption and on generation of fines that are not able to be fed to conversion, as compared to a status quo Base Case system. Also considered was convertible carbon content (minimum carbon specification) and maximum ash content and the delivered feedstock cost impacts of not being able to feed residue not meeting both specifications to the conversion reactor. Laboratory data on the impacts of input particle size and moisture content on the exit particle size were received from FCIC Subtask 5.2 from their single particle impact population balance modeling study. Additional throughput and energy consumption data were obtained from FCIC Subtask 5.2 for the same grinder with a 6 mm screen in place. These data were utilized to develop the necessary response surface equations to perform throughput analysis using discrete event simulation. Because the ash contents in the separated fines had not been analyzed in the laboratory at the time of the model runs, we chose to assume that the ash distributed proportionally with total mass into the overs and unders in the disk screen following grinding. Key takeaways from this Case Study are that it is significantly more cost effective to hammer mill the residue prior to drying, even though the grinder throughput is lower and energy consumption is higher versus drying first before grinding. An effect of dry grinding versus high moisture grinding is the production of higher amounts of fines during dry grinding, leading to significantly more of the ground feedstock being rejected by conversion for being below a minimum particle size. With wet grinding the system is still able to produce more preprocessed feedstock meeting the minimum particle size specification even though the instantaneous throughput is lower than for the case of grinding dry feedstock. Additionally, even without the higher fines production from dry grinding, the status quo would still be more costly than wet grinding because the material is rejected after the drying energy has already been input for the dry grinding case. Finally, significant reductions in drying energy are obtained by drying after grinding, and those reductions are of far greater magnitude than the grinding energy increase.
Monitoring Medication Adherence by Unannounced Pill Counts Conducted by Telephone: Reliability and Criterion-Related Validity (2008)

Unannounced telephone-based pill counts offer a feasible objective method for monitoring medication adherence.
The farnesoid X receptor agonist EDP‐305 reduces interstitial renal fibrosis in a mouse model of unilateral ureteral obstruction (2019)

Farnesoid X receptor (FXR) is a nuclear receptor that has emerged as a key regulator in the maintenance of hepatic steatosis, inflammation, and fibrosis. However, the role of FXR in renal fibrosis remains to be established. Here, we investigate the effects of the FXR agonist EDP-305 in a mouse model of tubulointerstitial fibrosis <i>via</i> unilateral ureteral obstruction (UUO). Male C57Bl/6 mice received a UUO on their left kidney. On postoperative d 4, mice received daily treatment by oral gavage with either vehicle control (0.5% methylcellulose) or 10 or 30 mg/kg EDP-305. All animals were euthanized on postoperative d 12. EDP-305 dose-dependently decreased macrophage infiltration as measured by the F4/80 staining area and proinflammatory cytokine gene expression. EDP-305 also dose-dependently reduced interstitial fibrosis as assessed by morphometric quantification of the collagen proportional area and kidney hydroxyproline levels. Finally, yes-associated protein (YAP) activation, a major driver of fibrosis, increased after UUO injury and was diminished by EDP-305 treatment. Consistently, EDP-305 decreased TGF-β1-induced YAP nuclear localization in human kidney 2 cells by increasing inhibitory YAP phosphorylation. YAP inhibition may be a novel antifibrotic mechanism of FXR agonism, and EDP-305 could be used to treat renal fibrosis.-Li, S., Ghoshal, S., Sojoodi, M., Arora, G., Masia, R., Erstad, D. J., Ferriera, D. S., Li, Y., Wang, G., Lanuti, M., Caravan, P., Or, Y. S., Jiang, L.-J., Tanabe, K. K., Fuchs, B. C. The farnesoid X receptor agonist EDP-305 reduces interstitial renal fibrosis in a mouse model of unilateral ureteral obstruction.
Computational and experimental investigations of one-step conversion of poly(carbonate)s into value-added poly(aryl ether sulfone)s (2016)

It is estimated that ∼2.7 million tons poly(carbonate)s (PCs) are produced annually worldwide. In 2008, retailers pulled products from store shelves after reports of bisphenol A (BPA) leaching from baby bottles, reusable drink bottles, and other retail products. Since PCs are not typically recycled, a need for the repurposing of the PC waste has arisen. We report the one-step synthesis of poly(aryl ether sulfone)s (PSUs) from the depolymerization of PCs and in situ polycondensation with bis(aryl fluorides) in the presence of carbonate salts. PSUs are high-performance engineering thermoplastics that are commonly used for reverse osmosis and water purification membranes, medical equipment, as well as high temperature applications. PSUs generated through this cascade approach were isolated in high purity and yield with the expected thermal properties and represent a procedure for direct conversion of one class of polymer to another in a single step. Computational investigations performed with density functional theory predict that the carbonate salt plays two important catalytic roles in this reaction: it decomposes the PCs by nucleophilic attack, and in the subsequent polyether formation process, it promotes the reaction of phenolate dimers formed in situ with the aryl fluorides present. We envision repurposing poly(BPA carbonate) for the production of value-added polymers.
Human natural killer cells promote cross‐presentation of tumor cell‐derived antigens by dendritic cells (2014)

Dendritic cells (DCs) cross-present antigen (Ag) to initiate T-cell immunity against most infections and tumors. Natural killer (NK) cells are innate cytolytic lymphocytes that have emerged as key modulators of multiple DC functions. Here, we show that human NK cells promote cross-presentation of tumor cell-derived Ag by DC leading to Ag-specific CD8(+) T-cell activation. Surprisingly, cytotoxic function of NK cells was not required. Instead, we highlight a critical and nonredundant role for IFN-γ and TNF-α production by NK cells to enhance cross-presentation by DC using two different Ag models. Importantly, we observed that NK cells promote cell-associated Ag cross-presentation selectively by monocytes-derived DC (Mo-DC) and CD34-derived CD11b(neg) CD141(high) DC subsets but not by myeloid CD11b(+) DC. Moreover, we demonstrate that triggering NK cell activation by monoclonal antibodies (mAbs)-coated tumor cells leads to efficient DC cross-presentation, supporting the concept that NK cells can contribute to therapeutic mAbs efficiency by inducing downstream adaptive immunity. Taken together, our findings point toward a novel role of human NK cells bridging innate and adaptive immunity through selective induction of cell-associated Ag cross-presentation by CD141(high) DC, a process that could be exploited to better harness Ag-specific cellular immunity in immunotherapy.
ChemInform Abstract: Matrix Isolation of Silacyclopentadienes: UV‐VIS and IR Spectra and Photochemical Interconversion. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
High-power mode-locked external cavity semiconductor laser using inverse bow-tie semiconductor optical amplifiers (1998)

This paper presents experimental results of using an inverse bow-tie gain guided semiconductor optical amplifier (SOA) as the optical gain element in a high-power external cavity semiconductor laser. An average output power of 700 mW is demonstrated in continuous-wave (CW) operation while 400 mW of average power is obtained in both passive and hybrid mode-locked operation, with subsequent optical amplification in an identical SOA. The mode-locked laser operates at a repetition rate of 1.062 GHz, owing to the interplay between the gain and saturable absorber dynamics. Optical pulses are generated with a temporal duration of 5 ps, which implies a pulse energy of 376 pJ, and a peak power of 60 W. Further reduction of the optical pulsewidth to 1.3 ps is also achieved by using dispersion compensation techniques. These results show the promise of novel SOA devices for use as gain elements in external cavity semiconductor lasers. The generated output pulse characteristics from mode-locked operation is sufficient for use in novel three-dimensional data storage applications, and in large-scale commercial printing and marking applications.