gebhart/patrepeval huggingface dataset:
A Depletable Pool of Adenosine in Area CA1 of the Rat Hippocampus (2001)

Adenosine plays a major modulatory and neuroprotective role in the mammalian CNS. During cerebral metabolic stress, such as hypoxia or ischemia, the increase in extracellular adenosine inhibits excitatory synaptic transmission onto vulnerable neurons via presynaptic adenosine A(1) receptors, thereby reducing the activation of postsynaptic glutamate receptors. Using a combination of extracellular and whole-cell recordings in the CA1 region of hippocampal slices from 12- to 24-d-old rats, we have found that this protective depression of synaptic transmission weakens with repeated exposure to hypoxia, thereby allowing potentially damaging excitation to both persist for longer during oxygen deprivation and recover more rapidly on reoxygenation. This phenomenon is unlikely to involve A(1) receptor desensitization or impaired nucleoside transport. Instead, by using the selective A(1) antagonist 8-cyclopentyl-1,3-dipropylxanthine and a novel adenosine sensor, we demonstrate that adenosine production is reduced with repeated episodes of hypoxia. Furthermore, this adenosine depletion can be reversed at least partially either by the application of exogenous adenosine, but not by a stable A(1) agonist, N(6)-cyclopentyladenosine, or by endogenous means by prolonged (2 hr) recovery between hypoxic episodes. Given the vital neuroprotective role of adenosine, these findings suggest that depletion of adenosine may underlie the increased neuronal vulnerability to repetitive or secondary hypoxia/ischemia in cerebrovascular disease and head injury.
Decreased DNA repair but normal apoptosis in ultraviolet-irradiated skin of p53-transgenic mice. (1996)

p53 tumor suppressor plays a vital role in the cellular responses to genotoxic stress. It is believed that p53 regulates the cell cycle by activating the G1 checkpoint after exposure to agents like ionizing radiation, ultraviolet (UV) radiation, or genotoxic chemicals. Recently, it is conjectured that p53 may have additional functions in DNA repair and apoptosis. Previously, we demonstrated that p53-transgenic mice that carry mutant alleles of a p53 gene developed twice as many skin tumors as control mice after UV exposure. To elucidate the molecular mechanisms of mutant p53 in skin cancers, we studied DNA repair efficiency and the rate of apoptosis in murine keratinocytes after UV irradiation. In this report, we show that mutant p53-transgenic mouse skin has reduced repair of UV-induced DNA damage in both in vivo and in vitro radioimmunoassays. In control mice, DNA repair is associated with increased amounts of wild-type P53 protein. Unexpectedly, mutant p53-transgenic mice had slightly increased apoptosis after UV irradiation, suggesting that the wild-type p53 protein in the cells still functions in inducing apoptosis, or that this cell death results from p53-independent mechanisms. These results suggest that mutant p53 interferes with wild-type p53 in the repair of UV-induced DNA damage but not in apoptosis.
Back-of-the-Envelope Computation of Throughput Distributions in CSMA Wireless Networks (2010)

This work started out with our discovery of a pattern of throughput distributions among links in IEEE 802.11 networks from experimental results. This pattern gives rise to an easy computation method, which we term back-of-the-envelop (BoE) computation. For many network configurations, very accurate results can be obtained by BoE within minutes, if not seconds, by simple hand computation. This allows us to make shortcuts in performance evaluation, bypassing complicated stochastic analysis. To explain BoE, we construct a theory based on the model of an “ideal CSMA network” (ICN). The BoE computation method emerges from ICN when we take the limit c \to 0, where c is the ratio of the mean backoff countdown time to the mean transmission time in the CSMA protocol. Importantly, we derive a new mathematical result: the link throughputs of ICN are insensitive to the distributions of the backoff countdown time and transmission time (packet duration) given the ratio of their means c. This insensitivity result explains why BoE works so well for practical 802.11 networks, in which the backoff countdown process is one that has memory, and in which the packet size can be arbitrarily distributed. Our results indicate that BoE is a good approximation technique for modest-size networks such as those typically seen in 802.11 deployments. Beyond explaining BoE, the theoretical framework of ICN is also a foundation for fundamental understanding of very-large-scale CSMA networks. In particular, ICN is similar to the Ising model in statistical physics used to explain phenomena arising out of the interactions of a large number of entities. Many new research directions arise out of the ICN model.
Semipolar GaN growth on patterned sapphire substrates by hydride vapor phase epitaxy (2013)

This paper presents the growth of thick semipolar {10-11}, {11-22}, and {20-21} GaN layers on <i>n</i>, <i>r</i>, and {22-43} patterned sapphire substrates (PSSs), respectively, by hydride vapor phase epitaxy. The reduction rate of the dislocation density varied with growth planes. For {10-11} GaN layers, the dislocation density drastically decreased at over 100 &mu;m, which was as fast the reduction rate as in the case of the <i>c</i>-plane. It was revealed that the reduction rate of the dislocation density could be controlled by the proper selection of the growth plane. We obtained a freestanding GaN of 2 inch diameter. Thick GaN growth led to the self-separation of the GaN layer from the PSS during cooling process. The separation plane formed at the interface between GaN and PSS, which is different from the case of a conventional <i>c</i>-plane GaN/sapphire. The separationability of the GaN layer from the PSS depended on the selective growth area of the sapphire sidewall.
Microstructure and mechanical properties of NbC matrix cermets using Ni containing metal binder (2015)

The current study reports on the effect of the addition of Al metal and secondary refractory carbides on the microstructure and mechanical properties of Ni bonded NbC matrix cermets. Powder mixtures were pressurelessly sintered for 1 h at 1420°C in vacuum. Microstructural and elemental mapping of the sintered cermets were performed by electron probe microanalysis (EPMA) to reveal the effect of the additions on the NbC grain morphology, grain growth and binder composition. Results indicated that NbC grain growth was suppressed and a homogeneous NbC grain size distribution was obtained in the cermets with the addition of Al and secondary carbides, i.e. Mo2C + VC + WC, as compared to the pure Ni binder. The liquid phase sintered NbC-12 vol% Ni cermet had a Vickers hardness (HV₁₀) of 1130 ± 22 kg/mm2 and indentation toughness of 11.8 ± 0.4 MPa m½. With the addition of 4 vol% WC-4 vol% VC-4 vol% Mo₂C, the hardness increased to 1490 ± 15 kg/mm², whereas the corresponding toughness decreased to 9.2 ± 0.4 MPa m½. Addition of 4 vol% Mo₂C into WC-13.8 vol% Ni-52.3 vol% NbC mixture further increased the hardness to 1620 ± 19 kg/mm² in combination with a moderate fracture toughness of 7.7 ± 0.2 MPa m½.
Plasmid segregation and accumulation (2017)

The segregation of plasmids in a bacterial population is investigated. Hereby, a dynamical model is formulated in terms of a size-structured population using a hyperbolic partial differential equation incorporating non-local terms (the fragmentation equation). For a large class of parameter functions this PDE can be re-written as an infinite system of ordinary differential equations for the moments of its solution. We investigate the influence of different plasmid production modes, kinetic parameters, and plasmid segregation modes on the equilibrium plasmid distribution. In particular, at small plasmid numbers the distribution is strongly influenced by the production mode, while the kinetic parameters (cell growth rate resp. basic plasmid reproduction rate) influence the distribution mainly at large plasmid numbers. The plasmid transmission characteristics only gradually influence the distribution, but may become of importance for biologically relevant cases. We compare the theoretical findings with experimental results.
Dynamics of absorption, metabolism, and excretion of 5-aminolevulinic acid in human intestinal Caco-2 cells (2017)

5-Aminolevulinic acid (ALA) is a precursor for the biosynthesis of porphyrins and heme. Although the oral administration of ALA has been widely applied in clinical settings, the dynamics of its absorption, metabolism, and excretion within enterocytes remain unknown. In this study, after enterocytic differentiation, Caco-2 cells were incubated with 200 µM ALA and/or 100 µM sodium ferrous citrate (SFC) for up to 72 h. Both ALA and the combination of ALA and SFC promoted the synthesis of heme, without affecting the expression of genes involved in intestinal iron transport, such as <i>DMT1</i> and <i>FPN</i>. The enhanced heme synthesis in Caco-2 cells was more pronounced under the effect of the combination of ALA and SFC than under the effect of ALA alone, as reflected by the induced expression of heme oxygenase 1 (HO-1), as well as a reduced protein level of the transcriptional corepressor Bach1. Chromatin immunoprecipitation analysis confirmed Bach1 chromatin occupancy at the enhancer regions of HO-1, which were significantly decreased by the addition of ALA and SFC. Finally, Transwell culture of Caco-2 cells suggested that the administered ALA to the intestinal lumen was partially transported into vasolateral space. These findings enhance our understanding of the absorption and metabolism of ALA in enterocytes, which could aid in the development of a treatment strategy for various conditions such as anemia.
Ivermectin inhibits HSP27 and potentiates efficacy of oncogene targeting in tumor models (2019)

HSP27 is highly expressed in, and supports oncogene addiction of, many cancers. HSP27 phosphorylation is a limiting step for activation of this protein and a target for inhibition, but its highly disordered structure challenges rational structure-guided drug discovery. We performed multistep biochemical, structural, and computational experiments to define a spherical 24-monomer complex composed of 12 HSP27 dimers with a phosphorylation pocket flanked by serine residues between their N-terminal domains. Ivermectin directly binds this pocket to inhibit MAPKAP2-mediated HSP27 phosphorylation and depolymerization, thereby blocking HSP27-regulated survival signaling and client-oncoprotein interactions. Ivermectin potentiated activity of anti-androgen receptor and anti-EGFR drugs in prostate and EGFR/HER2-driven tumor models, respectively, identifying a repurposing approach for cotargeting stress-adaptive responses to overcome resistance to inhibitors of oncogenic pathway signaling.
Adding sentence boundaries to conversational speech transcriptions using noisily labelled examples (2007)

This paper presents a technique for adding sentence boundaries to text obtained by Automatic Speech Recognition (ASR) of conversational speech audio. We show that starting with imprecise boundary information added by using only silence information from an ASR system, we can improve boundary detection using head and tail phrases. The main purpose for the insertion of sentence boundaries to ASR conversational text is to improve linguistic analysis, namely Information Extraction, for text mining systems that handle huge volumes of textual data and analyze trends and specific features of concepts described in document sets. Hence, we also show how the addition of boundaries improves two basic natural language processing tasks viz. POS label assignment and NP extraction. 1
The heterogeneous generation of N2O from exhaust gases of combustion: A laboratory study (1995)

The heterogeneous reaction of NO, SO 2 and O 2 in the presence of condensed or adsorbed H 2 O results in high yields of N 2 O under conditions mimicking flue gas from fossil fuel combustion. We observed a strong influence of the nature of the substrate surface on the rate of N 2 O formation. The maximum rate of N 2 O formation of 350 ppm h −1 occurred on soot and fly ash at relative humidities approaching 100% at 368K final yields of 80–100% N 2 O. The mechanism corresponds to a complex multiphase system in which NO 2 seems to be a key species. The observed abundance of NO 2 does not correspond to the one predicted by the simple mechanism by Lyon and Cole (1988).
Linkage mapping of the human CSF2 and IL3 genes. (1991)

Interleukin 3 (encoded by the IL3 gene) and granulocyte-macrophage colony-stimulating factor (encoded by the CSF2 gene) are small secreted polypeptides that bind to specific cell surface receptors and regulate the growth, gene expression, and differentiation of many of the hematopoietic cell lineages, particularly nonlymphoid cells. The IL3 and CSF2 genes have been cloned and mapped to human chromosome bands 5q23-31. Only 10 kilobases of DNA separates the two genes, suggesting that they have a common origin and/or regulation. We have cloned 70 kilobases of genomic DNA that includes the IL3 and CSF2 genes, as well as flanking sequences, and report a physical map of this region. Several unique-sequence DNA segments have been identified in this region, and one of these fragments detects two restriction fragment length polymorphisms in DNA from unrelated Caucasians. Segregation of these DNA polymorphisms was followed in the Centre Etudé du Polymorphisme Humaine (CEPH) panel of 40 large three-generation pedigrees, and linkage was detected with 17 genetic markers previously typed in these families. Multipoint linkage analysis permits the placement of the region containing the IL3 and CSF2 structural genes on the recombination-genetic linkage map of chromosome 5q and thereby allows the role of these genes in leukemogenesis to be more critically examined.
Dimpled/grooved face on a fuel injection nozzle body for flame stabilization and related method (2023)

A fuel injection head for a fuel nozzle used in a gas turbine combustor includes a substantially hollow body formed with an upstream end face, a downstream end face and a peripheral wall extending therebetween. A plurality of pre-mix tubes or passages extend axially through the hollow body with inlets at the upstream end face and outlets at the downstream end face. An exterior surface of the downstream end face is formed with three-dimensional surface features that increase a total surface area of the exterior surface as compared to a substantially flat, planar downstream end face.
Type I nitroreductases in soil enterobacteria (2000)

Many enteric bacteria express a type I oxygen-insensitive nitroreductase, which reduces nitro groups on many different nitroaromatic compounds under aerobic conditions. Enzymatic reduction of nitramines was also docu­ mented in enteric bacteria under anaerobic conditions. This study indicates that nitramine reduction in enteric bacteria is carried out by the type I, or oxygen-insensitive nitroreductase, rather than a type II enzyme. The enteric bacterium Morganella morganii strain B2 with documented hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) nitroreductase activity, and Enterobacter cloacae strain 96-3 with documented 2,4,6-trinitrotoluene (TNT) nitroreductase activity, were used here to show that the explosives TNT and RDX were both reduced by a type I nitroreductase. Morganella morganii and E. cloacae exhibited RDX and TNT nitroreductase activities in whole cell assays. Type I nitroreductase, purified from E. cloacae, oxidized NADPH with TNT or RDX as substrate. When expression of the E. cloacae type I nitroreductase gene was induced in an Escherichia coli strain carrying a plasmid, a simultaneous increase in TNT and RDX nitroreductase activities was observed. In addition, neither TNT nor RDX nitroreductase activity was detected in nitrofurazone-resistant mutants of M. morganii. We conclude that a type I nitroreductase present in these two enteric bacteria was responsible for the nitroreduction of both types of explosive.
Demonstration of femtosecond X-ray pump X-ray probe diffraction on protein crystals (2018)

The development of X-ray free-electron lasers (XFELs) has opened the possibility to investigate the ultrafast dynamics of biomacromolecules using X-ray diffraction. Whereas an increasing number of structures solved by means of serial femtosecond crystallography at XFELs is available, the effect of radiation damage on protein crystals during ultrafast exposures has remained an open question. We used a split-and-delay line based on diffractive X-ray optics at the Linac Coherent Light Source XFEL to investigate the time dependence of X-ray radiation damage to lysozyme crystals. For these tests, crystals were delivered to the X-ray beam using a fixed-target approach. The presented experiments provide probe signals at eight different delay times between 19 and 213 femtoseconds after a single pump event, thereby covering the time-scales relevant for femtosecond serial crystallography. Even though significant impact on the crystals was observed at long time scales after exposure with a single X-ray pulse, the collected diffraction data did not show significant signal reduction that could be assigned to beam damage on the crystals in the sampled time window and resolution range. This observation is in agreement with estimations of the applied radiation dose, which in our experiment was clearly below the values expected to cause damage on the femtosecond time scale. The experiments presented here demonstrate the feasibility of time-resolved pump-multiprobe X-ray diffraction experiments on protein crystals.
Histopathologic diagnosis of endometrial precancers: Updates and future directions (2021)

Early detection of endometrial cancer, especially its precancers, remains a critical and evolving issue in patient management and the quest to decrease mortality due to endometrial cancer. Due to many factors such as specimen fragmentation, the confounding influence of endogenous or exogenous hormones, and variable or overlapping histologic features, identification of bona fide endometrial precancers and their reliable discrimination from benign mimics remains one of the most challenging areas in diagnostic pathology. At the same time, the diagnosis of endometrial precancer, or the presence of suspicious but subdiagnostic features in an endometrial biopsy, can lead to long clinical follow-up with multiple patient visits and serial endometrial sampling, emphasizing the need for accurate diagnosis. Our understanding of endometrial precancers and their diagnosis has improved due to systematic investigations into morphologic criteria, the molecular genetics of endometrial cancer and their precursors, the validation of novel biomarkers and their use in panels, and more recent methods such digital image analysis. Although precancers for both endometrioid and non-endometrioid carcinomas will be reviewed, emphasis will be placed on the former. We review these advances and their relevance to the histopathologic diagnosis of endometrial precancers, and the recently updated 2020 World Health Organization (WHO) Classification of Female Genital Tumors.
CMUT design equations for optimizing noise figure and source pressure (2016)

The key parameters for the design of a capacitive micromachined ultrasonic transducer (CMUT) cell are the dimensions of the vibrating plate, i.e. plate diameter and thickness, and the gap height. These dimensions together with the magnitude of the dc bias voltage determine the transducer's center frequency, bandwidth, and transmit and receive sensitivity. For a given center frequency, choosing the plate dimensions typically requires a tradeoff between bandwidth and sensitivity. The expected magnitude of the ac excitation and dc bias voltage guides selection of the gap height. Finite element modeling and simulation of the equivalent circuit model help examine these design tradeoffs. However, analytical expressions give better design insight and aid quick evaluation of designs for given specifications. In this work, we develop expressions for transmit pressure and receive noise figure for a circular CMUT cell with bending plate and an ideal parallel-plate CMUT cell. In order to simplify the analysis, we neglect atmospheric pressure, assume a linear spring constant for the plate stiffness, and assume the dc bias voltage to be close to the pull-in voltage. These assumptions are typically valid for CMUTs similar to those designed for medical imaging.
Investigation of Human Blood Plasma Sample Preparation for Performing Metabolomics Using Ultrahigh Performance Liquid Chromatography/Mass Spectrometry (2009)

The following study investigates the preparation of human blood plasma for metabolomic profiling analysis by ultrahigh performance liquid chromatography coupled to time-of-flight mass spectrometry (UPLC/TOFMS) in a novel two-step design study. Four different organic solvents (acetonitrile, acetone, methanol, and ethanol) were used to assess human blood plasma preparation via protein precipitation. The optimal conditions for sample preparation were investigated, with consideration to the number of extracted markers, data quality/reproducibility, and column lifetime prolongation. Isotopically labeled internal standards were used to monitor data quality/reproducibility. Gel electrophoresis was also used to measure the protein content in the supernatant of the "first design step" allowing assessment of the amount of protein that would be injected/accumulate onto the column after many injections that would be apparent in a global metabolic profiling study. The second design step followed on from the results obtained in step one, with four of the best conditions selected and further investigated, looking at the effects of vortex time and temperature on precipitation/extraction. Two choices of solvent compositions were found to be "optimal" for preparation of plasma for global metabolic profiling analysis; these were "methanol/ethanol" (1:1, v/v) and "methanol/acetonitrile/acetone" (1:1:1, v/v/v) added to plasma (4:1 ratio, 400 microL total volume).