gebhart/patrepeval huggingface dataset:
Metabolome and metaboproteome remodeling in nuclear reprogramming (2013)

Nuclear reprogramming resets differentiated tissue to generate induced pluripotent stem (iPS) cells. While genomic attributes underlying reacquisition of the embryonic-like state have been delineated, less is known regarding the metabolic dynamics underscoring induction of pluripotency. Metabolomic profiling of fibroblasts vs. iPS cells demonstrated nuclear reprogramming-associated induction of glycolysis, realized through augmented utilization of glucose and accumulation of lactate. Real-time assessment unmasked downregulated mitochondrial reserve capacity and ATP turnover correlating with pluripotent induction. Reduction in oxygen consumption and acceleration of extracellular acidification rates represent high-throughput markers of the transition from oxidative to glycolytic metabolism, characterizing stemness acquisition. The bioenergetic transition was supported by proteome remodeling, whereby 441 proteins were altered between fibroblasts and derived iPS cells. Systems analysis revealed overrepresented canonical pathways and interactome-associated biological processes predicting differential metabolic behavior in response to reprogramming stimuli, including upregulation of glycolysis, purine, arginine, proline, ribonucleoside and ribonucleotide metabolism, and biopolymer and macromolecular catabolism, with concomitant downregulation of oxidative phosphorylation, phosphate metabolism regulation, and precursor biosynthesis processes, prioritizing the impact of energy metabolism within the hierarchy of nuclear reprogramming. Thus, metabolome and metaboproteome remodeling is integral for induction of pluripotency, expanding on the genetic and epigenetic requirements for cell fate manipulation.
Measurement of nuclear effects on ψ(2S) production in p-Pb collisions at $$ \sqrt{s_{\mathrm{NN}}} $$ = 8.16 TeV (2020)

A bstract Inclusive ψ (2S) production is measured in p-Pb collisions at the centre-of-mass energy per nucleon-nucleon pair $$ \sqrt{s_{\mathrm{NN}}} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:msub> <mml:mi>s</mml:mi> <mml:mi>NN</mml:mi> </mml:msub> </mml:msqrt> </mml:math> = 8 . 16 TeV, using the ALICE detector at the CERN LHC. The production of ψ (2S) is studied at forward (2 . 03 &lt; y cms &lt; 3 . 53) and backward ( − 4 . 46 &lt; y cms &lt; − 2 . 96) centre-of-mass rapidity and for transverse momentum p T &lt; 12 GeV/ c via the decay to muon pairs. In this paper, we report the integrated as well as the y cms - and p T -differential inclusive production cross sections. Nuclear effects on ψ (2S) production are studied via the determination of the nuclear modification factor that shows a strong suppression at both forward and backward centre-of-mass rapidities. Comparisons with corresponding results for inclusive J/ ψ show a similar suppression for the two states at forward rapidity (p-going direction), but a stronger suppression for ψ (2S) at backward rapidity (Pb-going direction). As a function of p T , no clear dependence of the nuclear modification factor is found. The relative size of nuclear effects on ψ (2S) production compared to J/ ψ is also studied via the double ratio of production cross sections [ σ ψ (2S) /σ J /ψ ]pPb / [ σ ψ (2S) /σ J /ψ ] pp between p-Pb and pp collisions. The results are compared with theoretical models that include various effects related to the initial and final state of the collision system and also with previous measurements at $$ \sqrt{s_{\mathrm{NN}}} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:msub> <mml:mi>s</mml:mi> <mml:mi>NN</mml:mi> </mml:msub> </mml:msqrt> </mml:math> = 5 . 02 TeV.
MR systems for MRI‐guided interventions (2008)

The field of MR imaging has grown from diagnosis via morphologic imaging to more sophisticated diagnosis via both physiologic and morphologic imaging and finally to the guidance and control of interventions. A wide variety of interventional procedures from open brain surgeries to noninvasive focused ultrasound ablations have been guided with MR and the differences between diagnostic and interventional MR imaging systems have motivated the creation of a new field within MR. This review discusses the various systems that research groups and vendors have designed to meet the requirements of interventional MR and suggest possible solutions to those requirements that have not yet been met. The common requirements created by MR imaging guidance of interventional procedures are reviewed and different imaging system designs will be independently considered. The motivation and history of the different designs are discussed and the ability of the designs to satisfy the requirements is analyzed.
MSK1 and MSK2 Inhibit Lipopolysaccharide-Induced Prostaglandin Production via an Interleukin-10 Feedback Loop (2013)

Prostaglandin production is catalyzed by cyclooxygenase 2 (cox-2). We demonstrate here that MSK1 and MSK2 (MSK1/2) can exert control on the induction of cox-2 mRNA by Toll-like receptor (TLR) agonists. In the initial phase of cox-2 induction, MSK1/2 knockout macrophages confirmed a role for MSK in the positive regulation of transcription. However, at later time points both lipopolysaccharide (LPS)-induced prostaglandin and cox-2 protein levels were increased in MSK1/2 knockout. Further analysis found that while MSKs promoted cox-2 mRNA transcription, following longer LPS stimulation MSKs also promoted degradation of cox-2 mRNA. This was found to be the result of an interleukin 10 (IL-10) feedback mechanism, with endogenously produced IL-10 promoting cox-2 degradation. The ability of IL-10 to do this was dependent on the mRNA binding protein TTP through a p38/MK2-mediated mechanism. As MSKs regulate IL-10 production in response to LPS, MSK1/2 knockout results in reduced IL-10 secretion and therefore reduced feedback from IL-10 on cox-2 mRNA stability. Following LPS stimulation, this increased mRNA stability correlated to an elevated induction of both of cox-2 protein and prostaglandin secretion in MSK1/2 knockout macrophages relative to that in wild-type cells. This was not restricted to isolated macrophages, as a similar effect of MSK1/2 knockout was seen on plasma prostaglandin E2 (PGE2) levels following intraperitoneal injection of LPS.
Synthetic Agonists of Toll-like Receptors and Therapeutic Applications (2019)

In recent years a number of innate immune receptors, such as retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs), absent in melanoma 2 (AIM2)-like receptors (ALRs), stimulator of interferon genes (STING), nucleotide oligomerization domain (NOD)-like receptors, and Toll-like receptors (TLRs), which recognize exogenous and endogenous nucleic acid molecular patterns, have been discovered. This chapter is focused on the chemistry of oligonucleotides which recognize and modulate immune responses specifically through TLRs 3, 7, 8, and 9. These TLRs are expressed in endosomes of many cells of the immune system. Known ligands of these receptors include viral double-stranded RNA for TLR3, viral single-stranded RNA for TLR7 and TLR8, and bacterial and viral DNA containing unmethylated CpG motifs for TLR9. Structure–activity relationship studies of synthetic oligonucleotides, with the goal of creating novel agonists of TLR3, 7, 8, and 9, have been conducted to modulate immune responses mediated through targeted receptors. Preclinical proof of concept studies of agonists of TLR3, 7, 8, and 9 for various diseases have been reported. A number of TLR9-agonist candidates have advanced to clinical trials, including for treatment of cancers, allergies, asthma, and infectious diseases, and also as adjuvants with vaccines. Recently, a hepatitis B (HepB) vaccine containing a TLR9 agonist as an adjuvant has been approved.
A novel design approach for small dual-band Sierpinski gasket monopole antennas (2002)

We propose a novel design technique for a small dual-band Sierpinski gasket monopole antenna using the first and second resonant bands by controlling the flare angle and the similarity factor of the Sierpinski gasket. A ratio less than 2 has been successfully achieved between the first and second bands.
Efficiency of a Directly Driven Generator for Hydrokinetic Energy Conversion (2013)

An experimental setup for hydrokinetic energy conversion comprising a vertical axis turbine, a directly driven permanent magnet generator, and a control system has been designed and constructed for deployment in the river Dalälven in Sweden. This paper is devoted to discussing the mechanical and electrical design of the generator used in the experimental setup. The generator housing is designed to be water tight, and it also acts as a support structure for the turbine shaft. The generator efficiency has been measured in the range of 5–16.7 rpm, showing that operation in the low velocity range up to 1.5 m/s is possible with a directly driven generator.
Experimental Study of Moving Man Detection by Acoustic Forward Scattering Radar System (2017)

The article explores the possibility of detection of people on the base of their sound shadow (sound blocking) when people cross the baseline in the Acoustic Forward Scatter Radar System (AFSRS). Experimental sound shadows have been obtained from moving people crossing AFSRS at different sound frequencies and different distances of people to the receiver. The sound shadow parameters of moving people, i.e. length of target shadow and peak Signal-to-Noise Ratio have been evaluated. The algorithm under investigation can be applied to create a network of sound barriers.
Shannon Meets Nyquist: Capacity Limits of Sampled Analog Channels (2011)

We explore two fundamental questions at the intersection of sampling theory and information theory: how is channel capacity affected by sampling below the channel’s Nyquist rate, and what sub-Nyquist sampling strategy should be employed to maximize capacity. In particular, we first derive the capacity of sampled analog channels for two prevalent sampling mechanisms: filtering followed by sampling and sampling following filter banks. Connections between sampling and MIMO Gaussian channels are illuminated based on this analysis. Optimal prefilters that maximize capacity are identified for both cases, as well as several kinds of channels for which these sampling mechanisms are optimal to maximize capacity at sub-Nyquist rates. We also highlight connections between sampled analog channel capacity and minimum mean squared error estimation from sampled data. In particular, it is shown that for both filtering and filter-bank sampling strategies, the filters maximizing capacity and minimizing mean squared error are equivalent. We also investigate a more general sampling strategy by adding modulation banks to filter-bank sampling. This general sampling method subsumes most nonuniform sampling techniques applied in both theory and practice. We also show a connection between this general sampling method and MIMO Gaussian channels. We then identify the optimal sampling strategy for piece-wise flat sampled
Operation and performance of the ATLAS Tile Calorimeter in Run 1 (2018)

The Tile Calorimeter is the hadron calorimeter covering the central region of the ATLAS experiment at the Large Hadron Collider. Approximately 10,000 photomultipliers collect light from scintillating tiles acting as the active material sandwiched between slabs of steel absorber. This paper gives an overview of the calorimeter's performance during the years 2008-2012 using cosmic-ray muon events and proton-proton collision data at centre-of-mass energies of 7 and 8 TeV with a total integrated luminosity of nearly 30 fb <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow></mml:mrow> <mml:mrow><mml:mo>-</mml:mo> <mml:mn>1</mml:mn></mml:mrow> </mml:msup> </mml:math> . The signal reconstruction methods, calibration systems as well as the detector operation status are presented. The energy and time calibration methods performed excellently, resulting in good stability of the calorimeter response under varying conditions during the LHC Run 1. Finally, the Tile Calorimeter response to isolated muons and hadrons as well as to jets from proton-proton collisions is presented. The results demonstrate excellent performance in accord with specifications mentioned in the Technical Design Report.
Immune checkpoint inhibitors in gynecologic cancers with lessons learned from non-gynecologic cancers (2016)

After years of very little success, a better understanding of the pivotal role of the tumor microenvironment in suppressing anticancer immunity and the exploration of treatment regimens using immune checkpoint inhibitors alone or in combination have finally led to the development of effective cancer immunotherapies and to improve survival of patients with certain types of advanced cancers. While the clinical experience with immune checkpoint inhibitors in gynecologic cancer patients remains limited, early signal of clinical activity strongly suggest that immunotherapy will play a significant role in the year to come in at least a subset of gynecologic cancer patients.
Performance Enhancement of Poly(lactic acid) and Sugar Beet Pulp Composites by Improving Interfacial Adhesion and Penetration (2008)

Sugar beet pulp (SBP), the residue from the sugar extraction process, contains abundant dietary fibers and is mainly used for feedstuff. In this study, poly(lactic acid) (PLA) and SBP composites were prepared using a twin screw extruder. The phase structure, thermal properties, mechanical properties, and water absorption of the composites were studied. The molecular weight change of PLA in the composites was also studied. Polymeric diphenylmethane diisocyanate (pMDI) was used as a coupling agent and resulted in significant increases in mechanical properties and water resistance. The tensile strength of the PLA/SBP (70/30 w/w) composite was only 56.9% that of neat PLA, but it was increased to 80.3% with the addition of 0.5% pMDI and further increased to 93.8% at 2% pMDI. With 50% SBP and 2% pMDI, the tensile strength of the composite was 87.8% of that of neat PLA. The microstructure of the composites indicated that the addition of pMDI greatly improved the wettability of the SBP particles by PLA and increased the penetration of PLA into the porous SBP. Consequently, the failure of the composites in mechanical testing changed from extensive debonding without pMDI to progressive rupture of the SBP particles with pMDI.
Photon reconstruction in the ATLAS Inner Detector and Liquid Argon Barrel Calorimeter at the 2004 Combined Test Beam (2011)

The reconstruction of photons in the ATLAS detector is studied with data taken during the 2004 Combined Test Beam, where a full slice of the ATLAS detector was exposed to beams of particles of known energy at the CERN SPS. The results presented show significant differences in the longitudinal development of the electromagnetic shower between converted and unconverted photons as well as in the total measured energy. The potential to use the reconstructed converted photons as a means to precisely map the material of the tracker in front of the electromagnetic calorimeter is also considered. All results obtained are compared with a detailed Monte-Carlo simulation of the test-beam setup which is based on the same simulation and reconstruction tools as those used for the ATLAS detector itself.
Efficiency of data alignment on Maspar (1993)

article Efficiency of data alignment on Maspar Share on Authors: Bill Maniatty View Profile , Boleslaw Szymanski View Profile , Balaram Sinharoy View Profile Authors Info & Claims ACM SIGPLAN NoticesVolume 28Issue 1Jan. 1993 pp 48–51https://doi.org/10.1145/156668.156686Online:01 January 1993Publication History 5citation68DownloadsMetricsTotal Citations5Total Downloads68Last 12 Months1Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Relative Production of IL‐1β and TNFα by Mononuclear Cells After Exposure to Dental Implants (1992)

Interleukin-1 (also known as osteoclast activating factor, OAF) is a cytokine produced primarily by monocytes and macrophages and is thought to mediate many of the immunologic, metabolic, and endocrine alterations seen with microbial infection, tissue injury, inflammatory disease, and bone loss. Stimuli for IL-1 production include microorganisms, endotoxins (LPS), antigen-antibody complexes, clotting components, and other cytokines. The purpose of this study was to determine whether dental implants stimulated peripheral blood mononuclear cells (PBMCs) to produce IL-1β (OAF) as well as tumor necrosis factor (TNFα). This production may lead to bone loss or failure of an implant. Three duplicates of five different implants were incubated with 2 × 106 PBMCs/ ml in 20% autologous serum; the esterase positive PBMCs amounted to 14.5%. Measured by radioimmunoassay techniques and compared to controls, all of the implants except one caused significant in vitro generation of IL-1β and TNFα. The stimulation of IL1β/TNFα production by these materials suggests that they are not physiologically inert and that the IL-1β (OAF) production may contribute to a less favorable osseoadaptation. OAF has a physiologic (homeostatic) role in maintenance and alteration of osseous structures, but the level at which physiologic becomes pathologic is unknown. Although there were statistical differences between the cellular response to these implants, the clinical significance of the differences remains to be determined. J Periodontol 1992; 63:426-430.
Stretchcam: Zooming Using Thin, Elastic Optics (2018)

Stretchcam is a thin camera with a lens capable of zooming with small actuations. In our design, an elastic lens array is placed on top of a sparse, rigid array of pixels. This lens array is then stretched using a small mechanical motion in order to change the field of view of the system. We present in this paper the characterization of such a system and simulations which demonstrate the capabilities of stretchcam. We follow this with the presentation of images captured from a prototype device of the proposed design. Our prototype system is able to achieve 1.5 times zoom when the scene is only 300 mm away with only a 3% change of the lens array's original length.
Effects of macroparticle weighting in axisymmetric particle-in-cell Monte Carlo collision simulations (2023)

Abstract In this paper, the effects of macroparticle (MP) weighting on the plasma discharge, particularly near the centerline, are investigated using a two-dimensional axisymmetric particle-in-cell Monte Carlo collision (PIC/MCC) model. A variable MP weight according to the radial position of the MPs is employed to maintain sufficient number of MPs near the centerline of the plasma source. The plasma density obtained from the PIC/MCC simulations for low-pressure (25–100 mTorr) capacitively coupled plasmas is found to be artificially large when the MP weight near the centerline is not well resolved, demonstrating the need for particle convergence studies for axisymmetric PIC/MCC simulations.
In-flight thrust monitoring: an acoustics-based approach (2019)

Purpose The purpose of this paper is to present an acoustics-based method for measuring turbofan nozzle exhaust thrust, while assessing the potential of scaling the methods for in-flight measurements. Design/methodology/approach Although many methods proposed for achieving in-flight thrust measurements involve complicated, sensitive and expense instruments, an acoustics-based approach is discussed that greatly simplifies the technology development pathway to in-flight applications. Findings Results are provided for a minimum set of sensors applied in the exhaust of a research turbofan engine at Virginia Tech, showing the difference in acoustics-measured thrust and nozzle thrust found by integrating thermocouple and Kiel probe measurements to be less than 6 per cent at the maximum fan speed examined. Practical implications Measuring accurate thrust values in flight will prove immediately valuable for installed thrust validation and engine health monitoring. Acoustics-based methodologies are attractive because of the robustness and low cost of sensors and sources. The value of in-flight thrust measurements, along with the benefits of acoustic approaches, makes the current topic of great interest for further development. Originality/value This paper presents unique applications of a time-of-flight acoustic thrust sensor, while providing an original assessment of technological challenges involved with the progression of the technique for in-flight measurements.
HD iPSC-derived neural progenitors accumulate in culture and are susceptible to BDNF withdrawal due to glutamate toxicity (2015)

Huntington's disease (HD) is a fatal neurodegenerative disease, caused by expansion of polyglutamine repeats in the Huntingtin gene, with longer expansions leading to earlier ages of onset. The HD iPSC Consortium has recently reported a new in vitro model of HD based on the generation of induced pluripotent stem cells (iPSCs) from HD patients and controls. The current study has furthered the disease in a dish model of HD by generating new non-integrating HD and control iPSC lines. Both HD and control iPSC lines can be efficiently differentiated into neurons/glia; however, the HD-derived cells maintained a significantly greater number of nestin-expressing neural progenitor cells compared with control cells. This cell population showed enhanced vulnerability to brain-derived neurotrophic factor (BDNF) withdrawal in the juvenile-onset HD (JHD) lines, which appeared to be CAG repeat-dependent and mediated by the loss of signaling from the TrkB receptor. It was postulated that this increased death following BDNF withdrawal may be due to glutamate toxicity, as the N-methyl-d-aspartate (NMDA) receptor subunit NR2B was up-regulated in the cultures. Indeed, blocking glutamate signaling, not just through the NMDA but also mGlu and AMPA/Kainate receptors, completely reversed the cell death phenotype. This study suggests that the pathogenesis of JHD may involve in part a population of 'persistent' neural progenitors that are selectively vulnerable to BDNF withdrawal. Similar results were seen in adult hippocampal-derived neural progenitors isolated from the BACHD model mouse. Together, these results provide important insight into HD mechanisms at early developmental time points, which may suggest novel approaches to HD therapeutics.
Genetic and epigenetic studies of amyotrophic lateral sclerosis (2013)

The identification of genetic and epigenetic factors that are associated with an increased risk of developing amyotrophic lateral sclerosis (ALS), or that modify the age of onset or rate of progression, requires a multimodal research strategy, facilitated through international collaboration. The discovery of several ALS genes strongly linked to RNA biology, the proteasome pathway, and axonal transport suggest they have an important role in pathogenesis, but the immense complexity of these processes is also apparent. The increasing rate of genetic discoveries brings the hope of designing more targeted and efficacious therapies.