gebhart/patrepeval huggingface dataset:
Alcohol and the Pancreas (2001)

This article represents the proceedings of a workshop at the 2000 ISBRA Meeting in Yokohama, Japan. The presentations were (1) Phenotypic alteration of myofibroblast during ethanol-induced pancreatic injury: its relation to bFGF, by Masahiko Nakamura, Kanji Tsuchimoto, and Hiromasa Ishii; (2) Activation of pancreatic stellate cells in pancreatic fibrosis, by Paul S. Haber, Gregory W. Keogh, Minoti V. Apte, Corey S. Moran, Nancy L. Stewart, Darrell H.G. Crawford, Romano C. Pirola, Geoffrey W. McCaughan, Grant A. Ramm, and Jeremy S. Wilson; (3) Pancreatic blood flow and pancreatic enzyme secretion on acute ethanol infusion in anesthetized RAT, by H. Nishino, M. Kohno, R. Aizawa, and N. Tajima; (4) Genotype difference of alcohol-metabolizing enzymes in relation to chronic alcoholic pancreatitis between the alcoholic in the National Institute on Alcoholism and patients in other general hospitals in Japan, by K. Maruyama, H. Takahashi, S. Matsushita, K. Okuyama, A. Yokoyama, Y. Nakamura, K. Shirakura, and H. Ishii; and (5) Alcohol consumption and incidence of type 2 diabetes, by Katherine M. Conigrave, B. Frank Hu, Carlos A. Camargo Jr, Meir J. Stampfer, Walter C. Willett, and Eric B. Rimm.
Parametric Normal-Mode Splitting in Cavity Optomechanics (2008)

Recent experimental progress in cavity optomechanics has allowed cooling of mesoscopic mechanical oscillators via dynamic backaction provided by the parametric coupling to either an optical or an electrical resonator. Here we analyze the occurrence of normal-mode splitting in backaction cooling at high input power. We find that a hybridization of the oscillator's motion with the fluctuations of the driving field occurs and leads to a splitting of the mechanical and optical fluctuation spectra. Moreover, we find that cooling experiences a classical limitation through the cavity lifetime.
Mitigation of Commuter's Air Pollution Exposure Via Personal Choices: Exploring Exposure Metrics (2018)

In the developed world some of the highest air pollution exposures are experienced when commuting on roadways. Choice of route and transit mode have implications for the harmful dose of air pollution received; however, few studies have assessed how these factors influence exposure in real-world settings. In this study, we quantified the differences in cyclists&amp;#8217; and drivers&amp;#8217; air pollution exposure accounting for inhalation and commute duration under realistic conditions and assessed whether pollution intake can be changed by choice of route and mode.Personal exposure to black carbon (BC), carbon monoxide (CO), PM2.5 (the mass of particles &amp;lt; 2.5&amp;#956;m in diameter), and particle number (PN) were measured for 45 commuters over approximately 700 commutes. Each commuter drove and cycled to and from their workplace via direct and alternative routes designed to lower exposure levels. Commuter&amp;#8217;s inhalation was modeled using their measured heart rate and physiological variables.Differences in commuter&amp;#8217;s mean exposure levels (when comparing combinations of various route/mode choices for the four pollutants) ranged from -66% to 96% and were strongly impacted by differences in their minute ventilation rate and trip duration. On comparable direct routes cyclists inhaled: 460% [95% Confidence Interval (CI): 306%, 638%] more BC, 98% [95% CI: 38%, 173%] more CO, 727% [95% CI: 435%, 1073%] more PM2.5, and 552% [95% CI: 263%, 1010%] more PN than when driving. On routes designed to avoid traffic cyclists saw reductions in the amount of pollution they inhaled: -36% [95% CI: -53%, -8%] less BC, -44% [95% CI: -63%, -15%] less CO, -26% [95% CI: -53%, 15%] less PM2.5, and -9% [95% CI: -46%, 62%] less PN compared to cycling directly along larger roads. These results suggest a fraction of the additional air pollution inhaled when cycling compared to driving can be mitigated by choice of route in a mid-sized city.
A receiver-extension approach to robust full-waveform inversion (2020)

We propose a receiver-extension approach to full waveform inversion, which, contrary to source-extension methods, can be used directly with a time-domain formulation. We introduce the receiver position as the extension parameter. We use a nested loop strategy to minimize the resulting misfit function: the inner loop corrects for the receiver position using global optimization while the outer loop corrects for the subsurface velocity using local optimization. First results illustrate the interest of the approach. Presentation Date: Tuesday, October 13, 2020 Session Start Time: 8:30 AM Presentation Time: 8:30 AM Location: 361F Presentation Type: Oral
Terahertz interferometric and synthetic aperture imaging (2006)

Experimental results of homodyne terahertz interferometric 1-D and 2-D imaging are presented. Continuous waves at 0.25-0.3 THz are used to detect a metal object behind a barrier. The performance of an <i>N </i>element detector array is imitated by only one detector placed at <i>N</i> positions. The reconstructed images are in a good agreement with theoretical predictions. The terahertz interferometric imaging method can be used in defense and security applications to detect concealed weapons, explosives as well as chemical and biological agents.
ChemInform Abstract: Coupling Biocatalysis and Click Chemistry: One‐Pot Two‐Step Convergent Synthesis of Enantioenriched 1,2,3‐Triazole‐Derived Diols. (2013)

Abstract A one‐pot synthesis of different enantiopure 1,2,3‐triazole‐derived diols (III) and (V) in high yields and excellent enantio‐ and stereoselectivities is achieved under mild conditions in aqueous medium by combining a single alcohol dehydrogenase with a Cu‐catalyzed “Click”‐reaction.
Ca12InC13–x and Ba12InC18H4: Alkaline-Earth Indium Allenylides Synthesized in AE/Li Flux (AE = Ca, Ba) (2014)

Two new complex main-group metal carbides were synthesized from reactions of indium, carbon, and a metal hydride in metal flux mixtures of an alkaline earth (AE = Ca, Ba) and lithium. Ca(12)InC(13-x) and Ba(12)InC(18)H(4) both crystallize in cubic space group Im3̅ [a = 9.6055(8) and 11.1447(7) Å, respectively]. Their related structures are both built on a body-centered-cubic array of icosahedral clusters comprised of an indium atom and 12 surrounding alkaline-earth cations; these clusters are connected by bridging monatomic anions (either H(-) or C(4-)) and allenylide anions, C(3)(4-). The allenylide anions were characterized by Raman spectroscopy and hydrolysis studies. Density of states and crystal orbital Hamilton population calculations confirm that both compounds are metallic.
Tutorial: RAM-based Circuits and Architectures for Multimedia and Signal Processing SOCs (2006)

In recent years, a growing class of SOCs has emerged for mobile applications, such as portable desktops, digital pens, audio- and video-based multimedia products, wireless communications and imaging systems, personal digital assistants, personal communicators and smart cards. These SOCs demand high-speed, high-throughput computations, complex functionalities and often real-time processing capabilities. The performance of these SOCs is mostly limited by lifetime of batteries. Thus, new design approaches and methodologies that produce more power-efficient and higher throughput designs are greatly desired. In recent years, the use of SIMD (single instruction multiple data) or MIMD (multiple instruction multiple data) architectures is spreading into the general DSP domain due to recent innovations that boost performance and flexibility of the architectures by several orders of magnitude. The Processor-in-Memory (PIM) environment provides a unique prospective because the impact of low-power techniques on performance is more sensitive in PIM than in standard RAM. The performance balancing in PIM architectures plays a critical role. Even though PIM concept is not new, recent breakthroughs pushed the application domain from traditional multimedia use to general signal processing use. This tutorial provides a unique overview and prospective of these recent developments to a much broader audience. The tutorial covers recent developments presented in literature and the most recent advances proposed by the author and his research group.
Definition of EGF-like, closely interacting modules that bear activation epitopes in integrin β subunits (2001)

Integrin beta subunits contain four cysteine-rich repeats in a long extracellular stalk that connects the headpiece to the membrane. Most mAbs to integrin activation epitopes map to these repeats, and they are important in propagating conformational signals from the membrane/cytosol to the ligand-binding headpiece. Sequence analysis of a protein containing only 10 integrin-like, cysteine-rich repeats suggests that these repeats start one cysteine earlier than previously reported. By using the new repeat boundaries, statistically significant sequence homology to epidermal growth factor-like domains is found, and a disulfide bond connectivity of the eight cysteines is predicted that differs in three of four disulfides from a previous prediction of epidermal growth factor-like modules [Berg, R. W., Leung, E., Gough, S., Morris, C., Yao, W.-P., Wang, S.-x., Ni, J. & Krissansen, G. W. (1999) Genomics 56, 169-178]. N-terminally truncated beta2 integrin stalk fragments were well expressed and secreted from 293 T cells when they began at repeat boundaries but not when they began one cysteine earlier or later. Furthermore, peptides that correspond to module 3 or modules 2 + 3 were expressed in bacteria and refolded. The module 2 + 3 fragment was as reactive with three mAbs to activation epitopes as a beta2 fragment expressed in eukaryotic cells, indicating a native fold. Only one residue intervenes between the last cysteine of one module and the first cysteine of the next. This arrangement is consistent with a tight intermodule connection, a prerequisite for signal propagation from the membrane to the ligand binding headpiece.
BIOMOSAIC Film: Artificial Biofilms with Catalytic and Self‐Sealing Properties (2019)

Abstract Biofilms are a self‐organized, self‐structured community of microorganisms that are enclosed in a self‐produced polymeric matrix. Due to the intrinsic complexity of biofilms, their artificial preparation has remained a challenge despite practical usefulness as reservoirs for biocatalysts. Herein, autonomously generated artificial biofilms termed BIOMOSAIC (BioInspired, Oxygen‐induced Microbial Organization through Self‐Assembly at the air/liquid Interface as a Catalyst) films are reported. Similar to bacterial homing, a large number of cells are spontaneously recruited and immobilized into the film, which is autonomously generated at air/liquid interfaces by simple mixing of phenolic polyamine and tyrosinase‐expressing Pseudomonas fluorescens . BIOMOSAIC films are self‐regenerated, portable, reusable, and freestanding. They are multifunctional depending on types of gene expressions from the cells, catalyzing various reactions such as l ‐DOPA production, dephosphorylation, and lipid hydrolysis. Furthermore, BIOMOSAIC film exhibits effective crude oil degradation properties, indicating that it can be a new self‐producing and self‐sustaining platform for bioremediation.
Security problems and way of prevention and recovery to Station System (2004)

It was chiefly described all kinds of problems in the Station System, and brought forward methods to deal with them.
NRG1 fusions in solid tumors. (2023)

3132 Background: NRG1 fusions are rare but actionable genomic drivers that occur across a growing number of tumor types. NRG1 has an EGF-like domain that serves as a ligand for ErbB (HER3) receptors, thereby inducing heterodimerization, usually with HER2, and subsequent activation of relevant downstream signaling pathways. Agents targeting the HER2/HER3 pathway have shown early clinical promise in NRG1 fusion-positive cancers: currently zenocutuzumab has FDA Fast Track Designation for tumors harboring NRG1-fusions. Here, we update the incidence and characterization of NRG1 fusions across tumor types. Methods: Samples were submitted for clinical molecular profiling at Caris Life Sciences via Caris MI Tumor Seek (Phoenix, AZ). Gene fusion detection was performed on mRNA isolated from a formalin-fixed paraffin-embedded tumor sample using the Illumina NovaSeq platform (Illumina, Inc., San Diego, CA) and Agilent SureSelect Human All Exon V7 bait panel (Agilent Technologies, Santa Clara, CA). All NRG1 fusions with ≥ 3 junction reads were identified for manual review and for characterization of fusion class, intact functional domains, domain prediction, breakpoints, frame retention and co-occurring alterations by next-generation sequencing. Results: In an analysis of 169,273 tumor specimens, 261 unique tumors with an NRG1 fusion were identified for an overall incidence of 0.154% across tumors. NRG1 fusions were most frequently detected in NSCLC, breast cancer, ovarian cancer, pancreatic ductal adenocarcinoma, colorectal cancer, cholangiocarcinoma, prostate cancer, bladder and urothelial cancers, esophagogastric cancers and less commonly, prostate cancer, soft tissue sarcoma, anal cancer, salivary gland cancers, head and neck cancer, small intestine cancer, small cell lung cancer, endometrial cancer, thyroid cancer, neuroendocrine cancer, high grade glioma, and melanoma. The highest incidence was in breast cancer (0.301%), followed by cholangiocarcinoma (0.263%), NSCLC (0.232%), carcinoma of unknown primary (0.215%), pancreatic ductal adenocarcinoma (0.190%), ovarian cancer (0.174%), bladder cancer (0.148%), esophageal cancer (0.145%) and vulvar cancers (0.145%). There were 153 unique NRG1 fusion partners. The most common fusion partner was CD74 (12.37%), followed by SLC3A2 (8.13%), ATP1B1 (4.59%), and RBPMS (4.24%). Conclusions: NRG1 fusions are rare but actionable genomic events with significant heterogeneity of tumor type and fusion partner.
A Wolf in Sheep's Clothing: Systemic Immune Activation Post Immunotherapy (2021)

ABSTRACT Introduction Immune checkpoint inhibitors (ICIs) are increasingly a standard of care for many cancers; these agents can result in immune-related adverse events (irAEs) including fever, which is common but can rarely be associated with systemic immune activation (SIA or acquired HLH). Methods All consecutive patients receiving ICIs in the Drug Development Unit of the Royal Marsden Hospital between May 2014 and November 2019 were retrospectively reviewed. Patients with fever ≥ 38°C or chills/rigors (without fever) ≤ 6 weeks of commencing ICIs were identified for clinical data collection. Results Three patients met diagnostic criteria for SIA/HLH with median time to onset of symptoms of 10 days. We describe the clinical evolution, treatment used, and outcomes for these patients. High-dose steroids are used first-line with other treatments, such as tocilizumab, immunoglobulin and therapeutic plasmapheresis can be considered for steroid-refractory SIA/HLH. Conclusion SIA/HLH post ICI is a rare but a potentially fatal irAE that presents with fever and a constellation of nonspecific symptoms. Early recognition and timely treatment are key to improving outcomes.
The MET/Vascular Endothelial Growth Factor Receptor (VEGFR)-targeted Tyrosine Kinase Inhibitor Also Attenuates FMS-dependent Osteoclast Differentiation and Bone Destruction Induced by Prostate Cancer (2016)

The tyrosine kinase inhibitor TAS-115 that blocks VEGF receptor and hepatocyte growth factor receptor MET signaling exhibits antitumor properties in xenografts of human gastric carcinoma. In this study, we have evaluated the efficacy of TAS-115 in preventing prostate cancer metastasis to the bone and bone destruction using the PC3 cell line. When PC3 cells were injected into proximal tibiae in nude mouse, severe trabecular and cortical bone destruction and subsequent tumor growths were detected. Oral administration of TAS-115 almost completely inhibited both PC3-induced bone loss and PC3 cell proliferation by suppressing osteoclastic bone resorption. In an ex vivo bone organ culture, PC3 cells induced osteoclastic bone resorption when co-cultured with calvarial bone, but TAS-115 effectively suppressed the PC3-induced bone destruction. We found that macrophage colony-stimulating factor-dependent macrophage differentiation and subsequent receptor activator of NF-κB ligand-induced osteoclast formation were largely suppressed by adding TAS-115. The phosphorylation of the macrophage colony-stimulating factor receptor FMS and osteoclast related kinases such as ERK and Akt were also suppressed by the presence of TAS-115. Gene expression profiling showed that FMS expression was only seen in macrophage and in the osteoclast cell lineage. Our study indicates that tyrosine kinase signaling in host pre-osteoclasts/osteoclasts is critical for bone destruction induced by tumor cells and that targeting of MET/VEGF receptor/FMS activity makes it a promising therapeutic candidate for the treatment of prostate cancer patients with bone metastasis.
Selective Restoration of the Selenoprotein Population in a Mouse Hepatocyte Selenoproteinless Background with Different Mutant Selenocysteine tRNAs Lacking Um34 (2007)

Novel mouse models were developed in which the hepatic selenoprotein population was targeted for removal by disrupting the selenocysteine (Sec) tRNA([Ser]Sec) gene (trsp), and selenoprotein expression was then restored by introducing wild type or mutant trsp transgenes. The selenoprotein population was partially replaced in liver with mutant transgenes encoding mutations at either position 34 (34T-->A) or 37 (37A-->G) in tRNA([Ser]Sec). The A34 transgene product lacked the highly modified 5-methoxycarbonylmethyl-2'-O-methyluridine, and its mutant base A was converted to I34. The G37 transgene product lacked the highly modified N(6)-isopentenyladenosine. Both mutant tRNAs lacked the 2'-methylribose at position 34 (Um34), and both supported expression of housekeeping selenoproteins (e.g. thioredoxin reductase 1) in liver but not stress-related proteins (e.g. glutathione peroxidase 1). Thus, Um34 is responsible for synthesis of a select group of selenoproteins rather than the entire selenoprotein population. The ICA anticodon in the A34 mutant tRNA decoded Cys codons, UGU and UGC, as well as the Sec codon, UGA. However, metabolic labeling of A34 transgenic mice with (75)Se revealed that selenoproteins incorporated the label from the A34 mutant tRNA, whereas other proteins did not. These results suggest that the A34 mutant tRNA did not randomly insert Sec in place of Cys, but specifically targeted selected selenoproteins. High copy numbers of A34 transgene, but not G37 transgene, were not tolerated in the absence of wild type trsp, further suggesting insertion of Sec in place of Cys in selenoproteins.
Density of High Pressure and Temperature Gas Reservoirs: Effect of Non-hydrocarbon Contaminants on Density of Natural Gas Mixtures (2010)

Abstract New experimental density data are generated in this study for light and heavy dry gas mixtures. The light mixtures consist mostly of methane and small fractions of ethane, propane, and nitrogen. Normal alkanes up to C6, iso-butane and iso-pentane together with carbon dioxide form the heavier gas mixtures. For each mixture, isothermal gas density is measured from 3.45 MPa to 140 MPa at temperatures of 423.15 K and 478.15 K. Effects of CO2 and N2 as two non-hydrocarbon contaminants, on density of gas mixtures are examined in steps of 5 mol%, 10 mol%, and 20 mol%. In addition, water vapor influence on gas phase density of water-saturated gas mixtures is also investigated. Different correlations for sweet and sour gas critical properties are combined with the most widely used equations of state (Hall-Yarborough and Dranchuk-Abou-Kassem) to predict density data for comparison with 450 experimental measurements. The most important results demonstrated from this study are: Among all correlations, the combination of the Hall-Yarborough equation with the pseudo-critical properties correlated by Sutton generates the lowest average absolute deviation (AAD) between predicted and experimental density data. The correction term developed by Wichert and Aziz to modify the pseudo-critical properties due to the presence of non-hydrocarbon compounds in the gas mixture, drastically improves the prediction of density data. At very high pressure and temperature conditions, effect of water vapor becomes more significant on gas phase density and it should be considered in density related correlations.
Mitigation of Transmitter Impairment with 4×2 WL MIMO Equalizer Embedding Preliminary CPR (2022)

Transmitter impairment mitigation for 58-GBaud PM-64QAM with 4×2 WL MIMO embedding preliminary CPR was demonstrated over 100 km SSMF. Q-penalties of 0.1 dB with 14 ps IQ skew and 10 degree phase error were achieved.
Microfluidic pumping, routing and metering by contactless metal-based electro-osmosis (2015)

Over the past decade, many microfluidic platforms for fluid processing have been developed in order to perform on-chip fluidic manipulations. Many of these methods, however, require expensive and bulky external supporting equipment, which are not typically applicable for microsystems requiring portability. We have developed a new type of portable contactless metal electro-osmotic micropump capable of on-chip fluid pumping, routing and metering. The pump operates using two pairs of gallium metal electrodes, which are activated using an external voltage source, and separated from a main flow channel by a thin micron-scale PDMS membrane. The thin contactless membrane allows for field penetration and electro-osmotic (EO) flow within the microchannel, but eliminates electrode damage and sample contamination commonly associated with traditional DC electro-osmotic pumps that utilize electrodes in direct contact with the working fluid. The maximum flow rates and pressures generated by the pump using DI water as a working buffer are 10 nL min(-1) and 30 Pa, respectively. With our current design, the maximum operational conductivity where fluid flow is observed is 0.1 mS cm(-1). Due to the small size and simple fabrication procedure, multiple micropump units can be integrated into a single microfluidic device for automated on-chip routing and sample metering applications. We experimentally demonstrated the ability to quantify micropump electro-osmotic flowrate and pressure as a function of applied voltage, and developed a mathematical model capable of predicting the performance of a contactless micropump for a given external load and internal hydrodynamic microchannel resistance. Finally, we showed that by activating specific pumps within a microchannel network, our micropumps are capable of routing microchannel fluid flow and generating plugs of solute.
Modulation of the immune response to ragweed allergens by peptic fragments (1990)

Fragments of short ragweed extract were prepared by peptic digestion and fractionated by molecular exclusion chromatography. We focused on fragmenting a ragweed fraction that was enriched for Amb aI. Digestion products in the molecular weight range of 5-15 kD (fSRW) were examined for their antigenic, immunogenic and immunosuppressive properties. fSRW was poorly immunogenic and unable to induce ragweed-specific PCA reactions in rat skin or to bind to anti-ragweed IgG antibodies. Intravenous administration of fSRW either prior to or after intraperitoneal immunization with a ragweed preparation resulted in a significant suppression of the immune response. T cells isolated from lymph nodes of mice immunized with ragweed were stimulated by fSRW in a lymphoproliferation assay. Moreover, T cells from mice injected with fSRW were immunosuppressive when transferred into mice immunized with intact ragweed antigens. Our data demonstrate that peptic fragments (fSRW) of ragweed lack B-cell determinants while retaining their T-cell immunoregulatory properties. Potentially these peptides are less likely to cause adverse reactions in allergen sensitive patients and thus offer a new approach to allergen immunotherapy.