gebhart/patrepeval huggingface dataset:
A Spatially Resolved Physical Model for Dynamic Modeling of a Novel Hybrid Reformer-Electrolyzer-Purifier (REP) for Production of Hydrogen (2017)

A molten carbonate electrolysis cell (MCEC) is capable of separating carbon dioxide from methane reformate while simultaneously electrolyzing water. Methane reformate, for this study, primarily consists of carbon dioxide, hydrogen, methane, and a high percentage of water. Carbon dioxide is required for the operation of a MCEC since a carbonate ion is formed and travels from the reformate channel to the sweep gas channel. In this study, a spatially resolved physical model was developed to simulate an MCEC in a novel hybrid reformer electrolyzer purifier (REP) configuration for high purity hydrogen production from methane and water. REP effectively acts as an electrochemical CO2 purifier of hydrogen. In order to evaluate the performance of REP, a dynamic MCEC stack model was developed based upon previous high temperature molten carbonate fuel cell modeling studies carried out at the National Fuel Cell Research Center at the University of California, Irvine. The current model is capable of capturing both steady state performance and transient behavior of an MCEC stack using established physical models originating from first principals. The model was first verified with REP experimental data at steady state which included spatial temperature profiles. Preliminary results show good agreement with experimental data in terms of spatial distribution of temperature, current density, voltage, and power. The combined effect of steam methane reformation (SMR) and water electrolysis with electrochemical CO2 removal results in 96% dry-basis hydrogen at the cathode outlet of the MCEC. Experimental measurements reported 98% dry-basis hydrogen at the cathode outlet.
Acute-Phase Protein α1-Antitrypsin—A Novel Regulator of Angiopoietin-like Protein 4 Transcription and Secretion (2014)

The angiopoietin-like protein 4 (angptl4, also known as peroxisome proliferator-activated receptor [PPAR]γ-induced angiopoietin-related protein) is a multifunctional protein associated with acute-phase response. The mechanisms accounting for the increase in angptl4 expression are largely unknown. This study shows that human α1-antitrypsin (A1AT) upregulates expression and release of angplt4 in human blood adherent mononuclear cells and in primary human lung microvascular endothelial cells in a concentration- and time-dependent manner. Mononuclear cells treated for 1 h with A1AT (from 0.1 to 4 mg/ml) increased mRNA of angptl4 from 2- to 174-fold, respectively, relative to controls. In endothelial cells, the maximal effect on angptl4 expression was achieved at 8 h with 2 mg/ml A1AT (11-fold induction versus controls). In 10 emphysema patients receiving A1AT therapy (Prolastin), plasma angptl4 levels were higher relative to patients without therapy (nanograms per milliliter, mean [95% confidence interval] 127.1 [99.5-154.6] versus 76.8 [54.8-98.8], respectively, p = 0.045) and correlated with A1AT levels. The effect of A1AT on angptl4 expression was significantly diminished in cells pretreated with a specific inhibitor of ERK1/2 activation (UO126), irreversible and selective PPARγ antagonist (GW9662), or genistein, a ligand for PPARγ. GW9662 did not alter the ability of A1AT to induce ERK1/2 phosphorylation, suggesting that PPARγ is a critical mediator in the A1AT-driven angptl4 expression. In contrast, the forced accumulation of HIF-1α, an upregulator of angptl4 expression, enhanced the effect of A1AT. Thus, acute-phase protein A1AT is a physiological regulator of angptl4, another acute-phase protein.
Discovery of a Potent Degrader for Fibroblast Growth Factor Receptor 1/2 (2021)

Abstract Aberrant activation of FGFR signaling occurs in many cancers, and ATP‐competitive FGFR inhibitors have received regulatory approval. Despite demonstrating clinical efficacy, these inhibitors exhibit dose‐limiting toxicity, potentially due to a lack of selectivity amongst the FGFR family and are poorly tolerated. Here, we report the discovery and characterization of DGY‐09‐192, a bivalent degrader that couples the pan‐FGFR inhibitor BGJ398 to a CRL2 VHL E3 ligase recruiting ligand, which preferentially induces FGFR1&amp;2 degradation while largely sparing FGFR3&amp;4. DGY‐09‐192 exhibited two‐digit nanomolar DC 50 s for both wildtype FGFR2 and several FGFR2‐fusions, resulting in degradation‐dependent antiproliferative activity in representative gastric cancer and cholangiocarcinoma cells. Importantly, DGY‐09‐192 induced degradation of a clinically relevant FGFR2 fusion protein in a xenograft model. Taken together, we demonstrate that DGY‐09‐192 has potential as a prototype FGFR degrader.
Hitting two oncogenic machineries in cancer cells: cooperative effects of the multi-kinase inhibitor ponatinib and the BET bromodomain blockers JQ1 or dBET1 on human carcinoma cells (2018)

In recent years, numerous new targeted drugs, including multi-kinase inhibitors and epigenetic modulators have been developed for cancer treatment. Ponatinib blocks a variety of tyrosine kinases including ABL and fibroblast growth factor receptor (FGFR), and the BET bromodomain (BRD) antagonists JQ1 and dBET1 impede MYC oncogene expression. Both drugs have demonstrated substantial anti-cancer efficacy against several hematological malignancies. Solid tumors, on the other hand, although frequently driven by FGFR and/or MYC, are often unresponsive to these drugs. This is due, at least in part, to compensatory feedback-loops in the kinome and transcription network of these tumors, which are activated in response to drug exposure. Therefore, we hypothesized that the combination of the multi-kinase inhibitor ponatinib with transcription modulators such as JQ1 or dBET1 might overcome this therapeutic recalcitrance. Using <sup>3</sup>H-thymidine uptake, cell cycle analysis, and caspase-3 or Annexin V labeling, we demonstrate that single drugs induce moderate dose-dependent growth-inhibition and/or apoptosis in colon (HCT116, HT29), breast (MCF-7, SKBR3) and ovarian (A2780, SKOV3) cancer cells. Ponatinib elicited primarily apoptosis, while JQ1 and dBET1 caused G0/G1 cell cycle arrest and very mild cell death. Phospho-FGFR and MYC, major targets of ponatinib and BET inhibitors, were downregulated after treatment with single drugs. Remarkably, ponatinib was found to sensitize cells to BET antagonists by enhancing apoptotic cell death, and this effect was associated with downregulation of MYC. In summary, our data shows that ponatinib sensitizes colon, breast, and ovarian cancer cells to BET bromodomain inhibitors. Further studies are warranted to determine the clinical value of this phenomenon.
Biological determinants of photobioreactor design. 6. quarterly report, February 1--July 31, 1995 (1995)

Interest has developed in using algae to fix CO{sub 2} to produce oxygen and biomass for life-support in space, and for reducing CO{sub 2} emissions from power plants. A novel photobioreactor (PBR) system using light-emitting diodes (LEDs) as a sole light source was constructed and operated with continuous medium perfusion. Direct internal illumination by 680 nm LEDs could deliver as high as 50 mW/cm{sup 2} of light into the culture medium. Gas transfer by internal sparging had the capacity to transfer 250 mmol O{sub 2}/L culture/h. Nutritional limitations could be overcome by continuous perfusion, supplying the medium components to the culture without increasing osmolarity, while removing potentially inhibitory cellular wastes. When the PBR operated in a continuous perfusion mode with a perfusion rate of 6 reactor volumes a day (6 VVD), it could support ultra high-density algal cultures up to cell concentrations of 4 {times} 10{sup 9} cells/mL and total cell volume fractions of 9.4% v/v (about 25 g dry weight/L). The oxygen production rate at its peak was 13 to 15 mmol/L culture/h. This performance represents the highest reported cell densities attained in photoautotrophic cultures. Continuous perfusion allowed for long-term stable oxygen production, while oxygen production in batch mode ceased when stationary phase was reached. The results presented suggest that PBR technology can still be significantly improved.
A pilot study of intrahepatic yttrium‐90 microsphere radioembolization in combination with intravenous cisplatin for uveal melanoma liver‐only metastases (2019)

The combination of cisplatin with yttrium-90 microspheres was well tolerated; however, it was associated with intrahepatic disease control of relatively short duration. No responses were seen in patients treated with immune checkpoint inhibitors post radioembolization.
Analysis of the normal stress extruder (1974)

Abstract A theoretical and experimental investigation of the pumping characteristics of the normal stress extruder was made. The theoretical model requires only material property data and extruder dimensions and rotation speed to evaluate the main velocity field, flow rate, and pressure. The flow from the extruder was measured for two viscoelastic polymer solutions and a polymer melt as a function of gap setting and angular velocity. These measurements were in reasonable agreement with the proposed model.
Mouse Mammary Tumor Virus Integration Site Selection in Human and Mouse Genomes (2007)

Based on integration site preferences, retroviruses can be placed into three groups. Viruses that comprise the first group, murine leukemia virus and foamy virus, integrate preferentially near transcription start sites. The second group, notably human immunodeficiency virus and simian immunodeficiency virus, preferentially targets transcription units. Avian sarcoma-leukosis virus (ASLV) and human T-cell leukemia virus (HTLV), forming the third group, show little preference for any genomic feature. We have previously shown that some human cells sustain mouse mammary tumor virus (MMTV) infection; therefore, we infected a susceptible human breast cell line, Hs578T, and, without introducing a species-specific bias, compared the MMTV integration profile to those of other retroviruses. Additionally, we infected a mouse cell line, NMuMG, and thus we could compare MMTV integration site selection in human and mouse cells. In total, we examined 468 unique MMTV integration sites. Irrespective of whether human or mouse cells were infected, no integration bias favoring transcription start sites was detected, a profile that is reminiscent of that of ASLV and HTLV. However, in contrast to ASLV and HTLV, not even a modest tendency in favor of integration within genes was observed. Similarly, repetitive sequences and genes that are frequently tagged by MMTV in mammary tumors were not preferentially targeted in cell culture either in mouse or in human cells; hence, we conclude that MMTV displays the most random dispersion of integration sites among retroviruses determined so far.
Abdominal surgery inhibits circulating acyl ghrelin and ghrelin-O-acyltransferase levels in rats: role of the somatostatin receptor subtype 2 (2011)

Clinical studies are evaluating the efficacy of synthetic ghrelin agonists in postoperative ileus management. However, the control of ghrelin secretion under conditions of postoperative gastric ileus is largely unknown. Peripheral somatostatin inhibits ghrelin secretion in animals and humans. We investigated the time course of ghrelin changes postsurgery in fasted rats and whether somatostatin receptor subtype 2 (sst 2 ) signaling is involved. Abdominal surgery (laparotomy and 1-min cecal palpation) induced a rapid and long-lasting decrease in plasma acyl ghrelin levels as shown by the 64, 67, and 59% reduction at 0.5, 2, and 5 h postsurgery, respectively, compared with sham (anesthesia alone for 10 min, P &lt; 0.05). Levels were partly recovered at 7 h and fully restored at 24 h. The percentage of acyl ghrelin reduction was significantly higher than that of desacyl ghrelin at 2 h postsurgery and not at any other time point. This was associated with a 48 and 23% decrease in gastric and plasma ghrelin- O-acyltransferase protein concentrations, respectively ( P &lt; 0.001). Ghrelin-positive cells in the oxyntic mucosa expressed sst 2a receptor and the sst 2 agonist S-346-011 inhibited fasting acyl ghrelin levels by 64 and 77% at 0.5 and 2 h, respectively. The sst 2 antagonist S-406-028 prevented the abdominal surgery-induced decreased circulating acyl ghrelin but not the delayed gastric emptying assessed 0.5 h postinjection. These data show that activation of sst 2 receptor located on gastric X/A-like cells plays a key role in the rapid inhibition of circulating acyl ghrelin induced by abdominal surgery while not being primarily involved in the early phase of postoperative gastric ileus.
A stochastic global net-length distribution for a three-dimensional system-on-a-chip (3D-SoC) (2002)

A global net-length distribution for three-dimensional system-on-a-chip architectures is derived to quantify the impact of the number of strata, or active layers, on the length of the long global interconnects. Model projections indicate a reduction in the global net length as the square root of the number of strata, thus enabling a significant reduction in chip footprint area, power dissipation, and global cycle time in comparison to a two-dimensional system-on-a-chip. Unlike its homogeneous counterpart, the vertical integration of a heterogeneous system is not limited by the density of interstratal interconnects. The size of the large megacells, especially memory, may restrict the effectiveness of a large number of strata.
Interaction of structure-specific and promiscuous G-protein–coupled receptors mediates small-molecule signaling in Caenorhabditis elegans (2012)

A chemically diverse family of small-molecule signals, the ascarosides, control developmental diapause (dauer), olfactory learning, and social behaviors of the nematode model organism, Caenorhabditis elegans. The ascarosides act upstream of conserved signaling pathways, including the insulin, TGF-β, serotonin, and guanylyl cyclase pathways; however, the sensory processes underlying ascaroside function are poorly understood. Because ascarosides often are multifunctional and show strongly synergistic effects, characterization of their receptors will be essential for understanding ascaroside biology and may provide insight into molecular mechanisms that produce synergistic outcomes in small-molecule sensing. Based on DAF-8 immunoprecipitation, we here identify two G-protein-coupled receptors, DAF-37 and DAF-38, which cooperatively mediate ascaroside perception. daf-37 mutants are defective in all responses to ascr#2, one of the most potent dauer-inducing ascarosides, although this mutant responds normally to other ascarosides. In contrast, daf-38 mutants are partially defective in responses to several different ascarosides. Through cell-specific overexpression, we show that DAF-37 regulates dauer when expressed in ASI neurons and adult behavior when expressed in ASK neurons. Using a photoaffinity-labeled ascr#2 probe and amplified luminescence assays (AlphaScreen), we demonstrate that ascr#2 binds to DAF-37. Photobleaching fluorescent energy transfer assays revealed that DAF-37 and DAF-38 form heterodimers, and we show that heterodimerization strongly increases cAMP inhibition in response to ascr#2. These results suggest that that the ascarosides' intricate signaling properties result in part from the interaction of highly structure-specific G-protein-coupled receptors such as DAF-37 with more promiscuous G-protein-coupled receptors such as DAF-38.
All-carbon hybrids for high performance supercapacitors (2018)

A hybrid nanostructure with partially reduced graphene oxide (rGO) and carbon nanofibers (CNFs) was fabricated and used as supercapacitor electrodes. A straightforward, environmentally friendly, and low-cost microwave-assisted reduction process was developed for the synthesis of rGO/CNF hybrid structures. The fabricated supercapacitor devices showed a specific capacitance of 95.3 F g−1 and a superior long-term cycling stability. A capacitance retention of more than 97% after 11 000 galvanostatic charge discharge cycles was obtained. These and other results reported in this paper indicate that high-rate, all-carbon, rGO/CNF hybrid nanostructures are highly promising supercapacitor electrode materials.
Functional magnetic resonance imaging of the human lumbar spinal cord (2005)

FLAIR-HASTE was useful for removing artifact in the spinal cord signal induced by variability in the CSF signal. However, with the techniques used in this study, we were not able to confirm the presence of a consistent fMRI response in the lumbar spinal cord because of the signal enhancement by extravascular protons (SEEP) effect during thermal stimulation of the hindlimb.
Fabrication of Si and Ge vertical nanowire for transistor applications (2014)

One–dimensional nanostructures, such as nanowhisker, nanorod, nanowire, nanopillar, nanocone, nanotip, nanoneedle, have attracted significant attentions in the past decades owing to their numerous applications in electronics, photonics, energy conversion and storage, and interfacing with biomolecules and living cells. Such one–dimensional nanostructures are potential alternatives to planar metal–oxide–semiconductor field–effect transistors (MOSFETs) owing, for example, to their unique electronic structure and reduced carrier scattering caused by one–dimensional quantum confinement effects. Yet whether nanowire field effect transistors (NWFETs) can indeed outperform their planar counterparts is still unclear [1]. Three–dimensional integration and the combination of different material systems are central themes of electronics research. The manufacturing of nanostructured devices relies on either bottom–up approaches such as synthesis or growth process or top–down approaches such as lithography or etching process. Here, vertical Si nanowire and hetero–structure integration of Ge nanowire will be firstly fabricated for the first time to demonstrate the top–down etching process, which is applicable to fabricate vertical transistors. The key step in fabricating 3D vertical devices is the construction of the insulating layer between the contact electrodes. An isolation process without chemical or mechanical polishing steps was also developed to control layer engineering at this length scale.
A Defect in Influenza A Virus Particle Assembly Specific to Primary Human Macrophages (2018)

Influenza A virus (IAV) propagates efficiently in epithelial cells, its primary target in the respiratory tract. In contrast, productive infection of most IAV strains is either blocked or highly inefficient in macrophages. The exact nature of the defect in IAV replication in human macrophages remains unknown. In this study, we showed that even compared to a monocytic cell line differentiated to macrophage-like cells, primary human monocyte-derived macrophages (MDM) are inefficient in IAV production, despite comparable levels of expression of viral glycoproteins at the plasma membrane. Correlative fluorescence scanning electron microscopy revealed that formation of budding structures at the cell surface is inefficient in MDM even though clustering of a viral glycoprotein, hemagglutinin (HA), is observed, suggesting that a step in IAV particle assembly is blocked in MDM. Using an <i>in situ</i> proximity ligation assay, we further determined that HA associates with neuraminidase (NA) but fails to associate with another viral transmembrane protein, M2, at the MDM plasma membrane. Notably, the defects in HA-M2 association and particle assembly in MDM were reversed upon cytochalasin D treatment that inhibits actin polymerization. These results suggest that HA-M2 association on the plasma membrane is a discrete step in IAV production, which is susceptible to suppression by actin cytoskeleton in MDM. Virus release remained inefficient in MDM upon cytochalasin D treatment, suggesting the presence of an additional defect(s) in virus release in this cell type. Overall, our study revealed the presence of multiple cell-type-specific mechanisms negatively regulating IAV production at the plasma membrane in MDM.<b>IMPORTANCE</b> Identification of host cell determinants promoting or suppressing replication of viruses has been aided by analyses of host cells that impose inherent blocks on viral replication. In this study, we show that primary human MDM, which are not permissive to IAV replication, fail to support virus particle formation. This defect is specific to primary human macrophages, since a human monocytic cell line differentiated to macrophage-like cells supports IAV particle formation. We further identified association between two viral transmembrane proteins, HA and M2, on the cell surface as a discrete assembly step, which is defective in MDM. Defective HA-M2 association and particle budding, but not virus release, in MDM are rescued by disruption of actin cytoskeleton, revealing a previously unknown, negative role for actin, which specifically targets an early step in the multistep IAV production. Overall, our study uncovered a host-mediated restriction of association between viral transmembrane components during IAV assembly.
Pressure- and photoinduced transformation into a metastable phase inRbMn[Fe(CN)6] (2003)

Pressure and photoirradiation effects on the structural properties were investigated for a transition metal cyanide, $\mathrm{RbMn}[\mathrm{Fe}(\mathrm{CN}{)}_{6}],$ with perovskitelike structure by means of high-angle resolved synchrotron-radiation x-ray powder diffraction. We have found that (1) photoirradiation by a 532-nm pulse laser at 91 K and (2) application of hydrostatic pressure to about 2 GPa at 300 K change the system from the tetragonal low-temperature phase $(I4\ifmmode\bar\else\textasciimacron\fi{}m2;$ $Z=2)$ to a metastable state with different crystal symmetry $(P4\ifmmode\bar\else\textasciimacron\fi{}n2;$ $Z=2).$ We discuss the difference between the photoinduced and pressure-induced processes and suggest possible origin for the photoinduced demagnetization.
Modeling of Droplet Generation in a Microfluidic Flow-Focusing Junction for Droplet Size Control (2021)

In this paper, we study the parameters that affect the generation of droplets in a microfluidic flow-focusing junction. Droplets are evaluated based on the size and frequency of generation. Droplet size control is essential for microfluidic lab-on-a-chip applications in biology, chemistry, and medicine. We developed a three-dimensional numerical model that can emulate the performance of the physical system. A numerical model can help design droplet-generation chips with new junction geometries, different dispersed and continuous phase types, and different flow rates. Our model uses a conservative level-set method (LSM) to track the interface between two immiscible fluids using a fixed mesh. Water was used for the dispersed phase and mineral oil for the continuous phase. The effects of the continuous-to-dispersed flow rate ratio (Qo/Qw) and the surfactant concentration on the droplet generation were studied both using the numerical model and experimentally. The numerical model was found to render results that are in good agreement with the experimental ones, which validates the LSM model. The validated numerical model was used to study the time effect of changing Qo/Qw on the generated droplet size. Properly timing when the flow rates are changed enables control over the size of the next generated droplet, which is useful for single-droplet size modulation applications.