gebhart/patrepeval huggingface dataset:
Oxidant Effects on Epithelial Na,K-ATPase Gene Expression and Promoter Function (1998)

The lung epithelium resorbs alveolar fluid through combined action of sodium channels and the sodium pump, Na,K-ATPase.The lung often is exposed to hyperoxia in disease states and hyperoxia generates a mixture of reactive oxygen species.In vivo and in vitro exposure of rat lung and alveolar type 11 cells, respectively, increases gene expression of both the a-1 and P-1 subunits of the sodium pump.In contrast to the primary type 11 cells, several type 11 cell lines did not increase sodium pump gene expression with hyperoxia, but the renal tubular epithelial MDCK cell line did.Using promoter-reporter constructs transfected into MDCK cells, hyperoxia did not markedly increase transcription of the a-1 subunit but doubled transcription of the ,B-1 subunit gene.Using 5'-deletion constructs, the region required for the ,B-1 increase was localized to a 40- base pair region from -44/-84.The hyperoxic responsiveness of this region was confirmed using constructs with one or two copies of this region placed in minimal promoter-luciferase reporters.This 5' promoter region contains a consensus binding sequence for SP-1, a basal transcription factor but not for binding of other known transcription factors.Thus, hyperoxia induces Na,K-
Open PHACTS computational protocols for <i>in silico</i> target validation of cellular phenotypic screens: knowing the knowns (2016)

Phenotypic screening is in a renaissance phase and is expected by many academic and industry leaders to accelerate the discovery of new drugs for new biology. Given that phenotypic screening is per definition target agnostic, the emphasis of <i>in silico</i> and <i>in vitro</i> follow-up work is on the exploration of possible molecular mechanisms and efficacy targets underlying the biological processes interrogated by the phenotypic screening experiments. Herein, we present six exemplar computational protocols for the interpretation of cellular phenotypic screens based on the integration of compound, target, pathway, and disease data established by the IMI Open PHACTS project. The protocols annotate phenotypic hit lists and allow follow-up experiments and mechanistic conclusions. The annotations included are from ChEMBL, ChEBI, GO, WikiPathways and DisGeNET. Also provided are protocols which select from the IUPHAR/BPS Guide to PHARMACOLOGY interaction file selective compounds to probe potential targets and a correlation robot which systematically aims to identify an overlap of active compounds in both the phenotypic as well as any kinase assay. The protocols are applied to a phenotypic pre-lamin A/C splicing assay selected from the ChEMBL database to illustrate the process. The computational protocols make use of the Open PHACTS API and data and are built within the Pipeline Pilot and KNIME workflow tools.
Validation of an ex vivo human cervical tissue model for optical imaging studies (2012)

We conclude that the proposed cervical tissue model appears to be applicable for ex vivo OCT studies.
Nanoconfined Magnesium Borohydride for Hydrogen Storage Applications Investigated by SANS and SAXS (2010)

Nanoscale hydride systems have recently gained increased attention for their possible energy storage applications. In the present work, nanoscale particles of Mg(11BD4)2 infiltrated into an activated carbon scaffold were studied by small-angle scattering techniques, and their behavior was compared with that of the bulk powders. Upon heating to 400 °C, under dynamic vacuum, the nanoconfined particles maintain their size distribution, and the decomposition affects only the morphology of the particle surface. On the contrary, the bulk powders showed a significant modification of both particle size and surface morphology under the same conditions. The carbon scaffold therefore serves to ensure both the desired nanoscale organization of the magnesium borohydride and stabilization in size of the incorporated material.
Detailed comparison of the da Vinci Xi and S surgical systems for transaxillary thyroidectomy (2021)

Robotic surgical systems have evolved over time. The da Vinci Xi system was developed in 2014 and was expected to solve the shortcomings of the previous S system. Therefore, we conducted this study to compare these 2 systems and identify if the Xi system truly improves surgical outcomes.In this retrospective study, a total of 86 patients with unilateral papillary thyroid carcinoma without central lymph node involvement underwent gasless transaxillary hemithyroidectomy using 2 robotic systems, the da Vinci S and Xi. Forty patients were in the da Vinci S group and 46 patients were in the da Vinci Xi group. All surgeries were performed by 1 surgeon (YWC). All surgery video files were analyzed to compare the duration of each surgical step.The total operation time was significantly shorter in the Xi group than in the S group (153.0 minutes vs 105.7 minutes, P < .01). Time for robot docking was shorter in the Xi group (19.8 minutes vs 10.6 minutes, P < .01), and all procedures performed in the console also required a shorter time in this group. The overall complication rate did not differ significantly (P = .464).The da Vinci Xi system made robotic thyroidectomy easier and faster without increasing the complication rate. It is a safe and valuable system for robotic thyroidectomy.
Reduction of reperfusion injury in the canine preparation by intracoronary adenosine: importance of the endothelium and the no-reflow phenomenon. (1987)

We hypothesized that the endogenous coronary vasodilator adenosine may reduce infarct size by progressively increasing reflow in a preparation of coronary occlusion-reperfusion. After 90 min of proximal left anterior descending artery occlusion, 20 dogs were randomized to blood reperfusion with (n = 10) or without (n = 10) adenosine into the proximal left anterior descending vessel at 3.75 mg/min for 60 min after reperfusion. Regional myocardial blood flow was determined serially with microspheres and regional ventricular function was assessed by a computerized radial shortening method. At 24 hr, the area at risk was defined in vivo with monastral blue dye and area of necrosis was determined after incubation of left ventricular slices in triphenyltetrazolium chloride. Hemodynamic variables were similar in the two groups during the experimental protocol. Infarct size was significantly reduced in treated animals, both when expressed as a percentage of the area at risk (9.9 +/- 2.8% vs 40.9 +/- 6.6%, p less than .001) and as a percentage of the left ventricle (4.6 +/- 1.3% vs 18.0 +/- 3.4%, p = .002). This was associated with significant improvement in radial shortening in the ischemic zone 24 hr after reperfusion (10.1 +/- 2.5 vs -2.8 +/- 2.2%, p less than .01). Regional myocardial blood flow was significantly increased in endocardial and epicardial regions from the lateral ischemic zone 1 hr after reperfusion in adenosine-treated animals. Light microscopy demonstrated decreased neutrophil infiltration in the ischemic zone and electron microscopy showed relative preservation of endothelial structure in the subendocardium with reduced neutrophil and red cell stagnation of capillaries in the treated group. These findings suggest that intracoronary administration of adenosine after reperfusion significantly reduces infarct size and improves regional ventricular function in the ischemic zone in the canine preparation.
Wireless Structural Health Monitoring of Wind Turbine Blades Using an Energy Harvester as a Sensor (2014)

Structural Health Monitoring (SHM) of wind turbine blades is critical to improve the reliability of wind turbines. A health monitoring algorithm was developed that utilizes energy harvesters as sensors. An accumulated energy sensor is described in which an energy harvester mounted on the surface of the wind turbine blade converts low frequency vibrational strain energy from the blade to electrical charge, that is subsequently stored to power an RF transmitter. The premise of this sensing approach is that the timing of data output from the RF transmitter, which is tied to the charging time, is indicative of the structural health. The time between data transmission pulses will be reduced if the blade stiffness decreases. The SHM algorithm compares data transmission time for the three blades to identify the onset of blade damage. To demonstrate the effectiveness of the algorithm, an expected energy harvester signal transmission rate is established from blade strain data from a 2.5 MW wind turbine. The transmission rates for the three blades are compared to establish a threshold for “healthy” blades. Simulated damage corresponding to approximately 20% increase in harvested energy can be detected by the SHM algorithm.
Basic Fibroblast Growth Factor Induces Proteolysis of Secreted and Cell Membrane-Associated Insulin-Like Growth Factor Binding Protein-2 in Human Neuroblastoma Cells* (1999)

Insulin-like growth factor (IGF) action in the brain is modulated by IGF-binding proteins (IGFBPs) whose abundance can be altered by other locally expressed growth factors. However, the mechanisms involved are unclear. We here employed the neuroblastoma cell line SK-N-MC as a model to define the mechanisms involved in modulation of IGFBPs in neuronal cells. Western ligand blotting analysis and immunoprecipitation of conditioned media (CM) from SK-N-MC cells showed that in these cells, as in the brain, the most abundantly expressed IGFBP was IGFBP-2. However, IGFBP-2 was barely detectable in CM from cells treated with basic fibroblast growth factor (bFGF) without a change in IGFBP-2 messenger RNA (mRNA) abundance. These CM contained specific IGFBP-2 proteolytic activity, resulting in two IGFBP-2 fragments of 14 and 22 kDa. The activity was inhibited by EDTA/phenylmethylsulfonyl fluoride or aprotinin. Competitive binding studies indicated that IGFBP-2 fragments had reduced binding affinity for IGF-I. bFGF induced IGFBP-3 mRNA and protein. Affinity cross-linking of [125I]IGF-I to neuroblastoma cell membranes followed by immunoprecipitation revealed a approximately 38 kDa [125I]IGF-I/IGFBP-2 complex. Cell surface-associated IGFBP-2 was also susceptible to bFGF-induced proteolysis, with the appearance of a single cross-linked 21-kDa complex with low affinity for IGF-I. These findings indicate that intact IGFBP-2 and the 14-kDa, but not the 22-kDa fragment, bind to the cell surface. Our data suggest that induction of IGFBP-2 proteolysis on neuronal cell surface is a novel mechanism whereby IGF availability is modulated by the local growth factor bFGF.
Fisher Information Bounds with Applications in Nonlinear Learning, Compression and Inference. (2015)

The problem how to derive a generic lower bound for the Fisher information measure is considered. We review a recent approach by two examples and identify a connection between the construction of strong Fisher information bounds and the sufficient statistics of the underlying system model. In order to present the problem of such information bounds within a broad scope, we discuss the properties of the Fisher information measure for distributions belonging to the exponential family. Under this restriction, we establish an identity connecting Fisher information, the natural parameters and the sufficient statistics of the system model. Replacing an arbitrary system model by an equivalent distribution within the exponential family, we then derive a general lower bound for the Fisher information measure. With the optimum estimation theoretic model matching rule we show how to obtain a strong version of the information bound. We then demonstrate different applications of the proposed conservative likelihood framework and the derived Fisher information bound. In particular, we discuss how to determine the minimum guaranteed inference capability of a memoryless system with unknown statistical output model and show how to achieve this pessimistic performance assessment with a root-n consistent estimator operating on a nonlinear compressed version of the observed data. Finally, we identify that the derived conservative maximum-likelihood algorithm can be formulated as a special version of Hansen’s generalized method of moments.
An Evolutionary Computation Approach for Optimizing Multilevel Data to Predict Patient Outcomes (2018)

Widespread adoption of electronic health records (EHR) and objectives for meaningful use have increased opportunities for data-driven predictive applications in healthcare. These decision support applications are often fueled by large-scale, heterogeneous, and multilevel (i.e., defined at hierarchical levels of specificity) patient data that challenge the development of predictive models. Our objective is to develop and evaluate an approach for optimally specifying multilevel patient data for prediction problems. We present a general evolutionary computational framework to optimally specify multilevel data to predict individual patient outcomes. We evaluate this method for both flattening (single level) and retaining the hierarchical predictor structure (multiple levels) using data collected to predict critical outcomes for emergency department patients across five populations. We find that the performance of both the flattened and hierarchical predictor structures in predicting critical outcomes for emergency department patients improve upon the baseline models for which only a single level of predictor-either more general or more specific-is used (<i>p</i> < 0.001). Our framework for optimizing the specificity of multilevel data improves upon more traditional single-level predictor structures and can readily be adapted to similar problems in healthcare and other domains.
Tolerance to lipopolysaccharide promotes an enhanced neutrophil extracellular traps formation leading to a more efficient bacterial clearance in mice (2012)

Tolerance to lipopolysaccharide (LPS) constitutes a stress adaptation, in which a primary contact with LPS results in a minimal response when a second exposure with the same stimulus occurs. However, active important defence mechanisms are mounted during the tolerant state. Our aim was to assess the contribution of polymorphonuclear neutrophils (PMN) in the clearance of bacterial infection in a mouse model of tolerance to LPS. After tolerance was developed, we investigated in vivo different mechanisms of bacterial clearance. The elimination of a locally induced polymicrobial challenge was more efficient in tolerant mice both in the presence or absence of local macrophages. This was related to a higher number of PMN migrating to the infectious site as a result of an increased number of PMN from the marginal pool with higher chemotactic capacity, not because of differences in their phagocytic activity or reactive species production. In vivo, neutrophils extracellular trap (NET) destruction by nuclease treatment abolished the observed increased clearance in tolerant but not in control mice. In line with this finding, in vitro NETs formation was higher in PMN from tolerant animals. These results indicate that the higher chemotactic response from an increased PMN marginal pool and the NETs enhanced forming capacity are the main mechanisms mediating bacterial clearance in tolerant mice. To sum up, far from being a lack of response, tolerance to LPS causes PMN priming effects which favour distant and local anti-infectious responses.
Facile and scalable patterning of sublithographic scale uniform nanowires by ultra-thin AAO free-standing membrane (2012)

Creating sublithographic scale uniform nanowires for large area is an important issue for nanowire-based various device applications. Although anodic aluminium oxide (AAO) membrane is a promising technique, existing attached AAO membrane mask methods have not been able to fabricate such small nanowires for large areas due to difficulties on transferring a thin membrane. Here we demonstrate a facile and scalable methodology to fabricate sublithographic scale uniform-sized nanowires by introducing ultra-thin AAO free-standing membrane with a rigid Al frame and a hydrophilic contacting method. The present method allows us to fabricate sub 20 nm nanowires with the standard deviations of 1.1 nm via defining the size and spacing of metal catalysts for nanowire growth. We also show the scalability of the present attached AAO membrane mask method for a 4-inch scale wafer.
Galanin-like immunoreactive expression in the central nervous system of the toad. (1995)

The distribution of galanin (GAL)-like immunoreactivity (-LI) was studied in the CNS of the toad (Bufo arenarum Hensel). Tissue sections were incubated with antibodies directed toward rat or porcine GAL and processed either for the avidin-biotin complex, or for the indirect immunofluorescence techniques. In the telencephalon GAL-immunoreactive (-IR) perikarya were observed in the ventral part of the striatum and in the septal accumbens nuclei. Immunopositive neurons were also observed in the medial amigdala with some intermingled cells between the fibers of the anterior commissure. Numerous GAL-IR perikarya were present along the rostrocaudal medial preoptic nucleus. Occasionally lightly immunoreactive cells were detected in the magnocellular region. The most numerous accumulation of GAL-IR cells was present in the ventral hypothalamus around the infundibular region, in the posterior tubercle and in the nucleus of the paraventricular organ. Immunostained cells were also present in the pretectal gray, solitary nucleus, gracil nucleus and in the spinal cord in the intermediate gray and in large motoneurons of the ventral horn. The widespread distribution found of GAL-LI suggests that GAL in the toad, as well as in mammalian species, may serve a variety of functions with a preponderant role in neuroendocrine processes. A role for GAL as a trophic factor in the brain of the toad is also suggested.
Supplementary Data from Expression Analysis and Significance of PD-1, LAG-3, and TIM-3 in Human Non–Small Cell Lung Cancer Using Spatially Resolved and Multiparametric Single-Cell Analysis (2023)

&lt;p&gt;Supplementary Figures and Tables&lt;/p&gt;
Thermoelectric development at Hi-Z technology (2002)

An improved thermoelectric generator (TEG) for the heavy duty class eight diesel trucks is under development at Hi-Z Technology. The current TEG is equipped with the improved HZ-14 thermoelectric module, which features better mechanical properties as well as higher electric power output. Also, the modules are held in place more securely. The TEG is comprised of 72 TE modules, which are capable of producing 1 kW of electrical power at 30 V DC during nominal engine operation. Currently the upgraded generator has completed testing in a test cell and starting from August 2001 will be tested on a diesel truck under typical road and environmental conditions. It is expected that the TEG will be able to supplement the existing shaft driven alternator, resulting in significant fuel saving, generating additional power required by the truck's accessories. The electronic and thermal properties of bulk materials are altered when they are incorporated into quantum wells. Two-dimensional quantum wells have been synthesized by alternating layers of B/sub 4/C and B/sub 9/C in one system and alternating layers of Si and Si/sub 0.8/Ge/sub 0.2/ in another system. Such nanostructures are being investigated as candidate thermoelectric materials with high figures of merit (Z). The predicted enhancement is attributed to the confined motion of charge carriers and phonons in the two dimensions and separating them from the ion scattering centers. Multilayer quantum well materials development continues with the fabrication of thicker films, evaluation of various substrates to minimize bypass heat loss, and bonding techniques to minimize high contact resistance quantum well thermoelectric devices with N-type Si/Si/sub 0.8/Ge/sub 0.2/ and P-type B/sub 4/C/B/sub 9/C have been fabricated from these films. The test results generated continue to indicate that much higher thermoelectric efficiencies can be achieved in the quantum wells compared to the bulk materials.
Hat die Hydrierung von Pflanzenölen noch eine Zukunft? (2013)

Seit über hundert Jahren ist die katalytische Hydrierung ein wichtiges Industrieverfahren zur Prozessierung von Pflanzenöl, hat aber heute stark an Bedeutung verloren. Grund sind die gesundheitsschädlichen trans-Fettsäure-Nebenprodukte. Modernes Katalysatordesign und neue Strategien zur selektiven Abtrennung der trans-Isomere ermöglichen es aber, durch Pflanzenölhydrierung trans-freie Fette mit erwünschter Funktionalität zu synthetisieren.
Epithelial–Mesenchymal Transition (EMT) Induced by TNF-α Requires AKT/GSK-3β-Mediated Stabilization of Snail in Colorectal Cancer (2013)

Chronic inflammation-promoted metastasis has been considered as a major challenge in cancer therapy. Pro-inflammatory cytokine TNFa can induce cancer invasion and metastasis associated with epithelial-mesenchymal transition (EMT). However, the underlying mechanisms are not entirely clear. In this study, we showed that TNFa induces EMT in human HCT116 cells and thereby promotes colorectal cancer (CRC) invasion and metastasis. TNFa-induced EMT was characterized by acquiring mesenchymal spindle-like morphology and increasing the expression of N-cadherin and fibronectin with a concomitant decrease of E-cadherin and Zona occludin-1(ZO-1). TNFa treatment also increased the expression of transcription factor Snail, but not Slug, ZEB1 and Twist. Overexpression of Snail induced a switch from E-cadherin to Ncadherin expression in HCT116 cells, which is a characteristic of EMT. Conversely, knockdown of Snail significantly attenuated TNFa-induced EMT in HCT116 cells, suggesting that Snail plays a crucial role in TNFa-induced EMT. Interestingly, exposure to TNFa rapidly increased Snail protein expression and Snail nuclear localization but not mRNA level upregulation. Finally, we demonstrated that TNFa elevated Snail stability by activating AKT pathway and subsequently repressing GSK-3b activity and decreasing the association of Snail with GSK-3b. Knockdown of GSK-3b further verified our finding. Taken together, these results revealed that AKT/GSK-3b-mediated stabilization of Snail is required for TNFa-induced EMT in CRC cells. Our study provides a better understanding of inflammation-induced CRC metastasis.
Particle Transport Analysis of Sand Ingestion in Gas Turbine Engines (2011)

Significant interest exists in the military and commercial aerospace industry to be able to better predict and improve the durability of gas turbine jet engines that are operating in hostile desert environments, specifically, jet engines that see significant inlet sand or ash ingestion. This paper describes the development of a mixed CFD-empirical software tool that allows a detailed analysis of the kinematic and impact behavior of sand and other particulates in the near-field of turbomachinery blades and impellers. The tool employs a commercially available CFD solver to calculate the machine’s transient flow field and then uses the output to determine a set of non-dimensional coefficients in a set of empirical functions to predict the statistical probability of particles impacting on rotating or stationary surfaces. Based on this tool’s output information, improved inlet air filtering techniques, optimized engine maintenance practices, and component designs can be realized. To determine the empirical coefficient and to validate the method, PIV testing was performed on an airfoil in a wind tunnel, and then particle injection into a simple rotating impeller was tested on SwRI’s high-speed compressor test rig. Results from these tests allowed optimizing of the model to reflect rotating machinery particle impact behavior more accurately.