gebhart/patrepeval huggingface dataset:
Abstract C68: Suppression of AKT/mTOR antiapoptotic signaling by a novel drug candidate results in growth arrest and apoptosis of hepatocellular carcinoma-derived cell lines. (2011)

Abstract Hepatocellular carcinoma (HCC) is the fourth most common cause of cancer fatalities worldwide, with chronic hepatitis B infection accounting for 60% of cases. In the majority of new diagnoses, primary tumor size contraindicates surgical resection, limiting available treatment options to rarely-curative interventions that generally have severe side effects. Overall, advanced HCC is largely incurable, with a five year survival rate of &amp;lt;5%. To expand the treatment pipeline, we conducted a high-throughput screening campaign of our 85,000-compound small molecule library to identify agents that would exhibit selective cytotoxicity for HCC-derived cell lines, as compared to immortalized non-transformed human hepatocytes. A disubstituted aminothiazole, termed HBF-0079, emerged as a potent and selective inhibitor of cell growth and viability in the HCC lines Huh7, Hep3b, HepaRG, MHCC97H and MHCC97L, and the hepatoblastoma line HepG2, with EC50 values from 0.7 to 33 μM. Conversely, growth and viability in the non-tumorigenic hepatocyte lines THLE2 and PH5CH, and several other non-HCC cancer lines, showed only moderate to no sensitivity. Subsequent structure-activity relationship studies have identified relevant features of the molecule, and resulted in two compounds that retain selectivity and improve EC50 to &amp;lt; 0.1 μM in Huh7. In a murine xenograft model, growth of Hep3B-derived tumors was significantly delayed by either systemic or intratumoral administration of HBF-0079. As determined in cell culture withdrawal experiments, incubation of Huh7 cells with HBF-0079 resulted in irreversible onset of growth arrest and apoptosis. Cell cycle analysis indicated arrest in G1/G0, with subsequent entry of cells into a sub-G0 population consistent with apoptotic cell death. While a putative molecular target is currently being confirmed, we have determined that treated Huh7 cells undergo loss of AKT phosphorylation at the mTORC2-targeted residue S473, with subsequent loss of phosphorylation of the mTORC1 targets SK6 and 4EBP1; these observations are consistent with cell cycle arrest and onset of apoptosis, ostensibly through loss of AKT survival signaling and global translational shutoff. Conversely, phosphorylation of Akt or mTORC1 targets is not affected in the non-sensitive PH5CH line. Thus, we have identified a cytotoxic molecule with in vitro selectivity for liver-derived cancer cells. In vivo efficacy studies and chemical hit-to-lead optimization are currently ongoing. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr C68.
Site‐specific delivery of dexamethasone from biodegradable implants reduces formation of pericardial adhesions in rabbits (2006)

Repeated sternotomy often leads to serious complications in patients due to the formation of cardiac adhesions. In this study we characterized dexamethasone-loaded biodegradable poly(lactide)-poly(ethyleneglycol) copolymer films for site-specific drug delivery and examined their efficacy in the rabbit model of postoperative cardiac adhesions. Tritiated dexamethasone-loaded films were used to determine the in vitro release and in vivo drug distribution. Dexamethasone release in serum was biphasic with 69% drug released after 72 hr. The implants produced sustained drug levels at the implantation site with low distribution into the peripheral tissues. The matrices were implanted in rabbits between the epicardium and the sternum following sternotomy, pericardiectomy and epicardium abrasion, with the drug-releasing surface facing the epicardium. The tenacity and density of the adhesions was examined 21 days post procedure in comparison to both groups of untreated and rabbits implanted with blank matrices. Similarly tenacious and dense adhesions were observed in both control groups. In contrast, epicardial adhesions' formation was significantly reduced and the anatomy was preserved in the treated animals. It is concluded that local delivery of dexamethasone from biodegradable implants provides a promising approach for the prevention of pericardial adhesions while potentially minimizing the systemic adverse effects inherent to systemic therapy or high blood levels of the drug.
Spatial Correlations in Physical Unclonable Functions (2016)

Physical Unclonable Functions (PUFs) are circuits which extract a device dependent secret from inherently available manufacturing variations. This work focuses on evaluating the quality of such circuits regarding intra-die correlations, because canonical quality metrics for PUFs do not sufficiently cover them. Correlations reduce the effort for an attacker to guess the secret with the same severity as biases, yet canonical tests focus only on the latter. Three tests which are used to consider topological properties along with the secret are introduced and adapted to quality evaluation of PUFs. To show the efficiency and effectiveness but also the limitations of the tests, we apply them to three real-world measurement datasets from ring-oscillator PUFs on FPGAs, standard SRAM and Two-Stage PUFs on ASICs. The results show that the presented statistical tests are ideal candidates to complement state-of-the-art metrics for PUF quality.
Automated discovery of scoped memory regions for real-time Java (2002)

Advances in operating systems and languages have brought the ideal of reasonably-bounded execution time closer to developers who need such assurances for real-time and embedded systems applications. Recently, extensions to the Java libraries and virtual machine have been proposed in an emerging standard, which provides for specification of release times, execution costs, and deadlines for a restricted class of threads. To use such features, the code executing in the thread must never reference storage that could be subject to garbage collection. The new standard provides for region-like, stack-allocated areas (scopes) of storage that are ignored by garbage collection and deallocated en masse. It now falls to the developer to adapt ordinary Java code to use the real-time Java scoped memory regions.Unfortunately, it is difficult to determine manually how to map object instantiations to scopes. Moreover, if ordinary Java code is modified to effect instantiations in scopes, the resulting code is difficult to read, maintain, and reuse. Static analysis can yield scopes that are correct across all program executions, but such analysis is necessarily conservative in nature. If too many objects appear to live forever under such analysis, then developers cannot rely on static analysis alone to form reasonable scopes.In this paper we present an approach for automatically determining appropriate storage scopes for Java objects, based on dynamic analysis---observed object lifetimes and object referencing behavior. While such analysis is perhaps unsafe across all program executions, our analysis can be coupled with static analysis to bracket object lifetimes, with the truth lying somewhere in between. We provide experimental results that show the memory regions discovered by our technique.
Improved Sensitivity Mass Spectrometric Detection of Eicosanoids by Charge Reversal Derivatization (2010)

Combined liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) is a powerful method for the analysis of oxygenated metabolites of polyunsaturated fatty acids including eicosanoids. Here we describe the synthesis of a new derivatization reagent N-(4-aminomethylphenyl)pyridinium (AMPP) that can be coupled to eicosanoids via an amide linkage in quantitative yield. Conversion of the carboxylic acid of eicosanoids to a cationic AMPP amide improves sensitivity of detection by 10- to 20-fold compared to negative mode electrospray ionization detection of underivatized analytes. This charge reversal derivatization allows detection of cations rather than anions in the electrospray ionization mass spectrometer, which enhances sensitivity. Another factor is that AMPP amides undergo considerable collision-induced dissociation in the analyte portion rather than exclusively in the cationic tag portion, which allows isobaric derivatives to be distinguished by tandem mass spectrometry, and this further enhances sensitivity and specificity. This simple derivatization method allows prostaglandins, thromboxane B(2), leukotriene B(4), hydroxyeicosatetraenoic acid isomers, and arachidonic acid to be quantified in complex biological samples with limits of quantification in the 200-900 fg range. One can anticipate that the AMPP derivatization method can be extended to other carboxylic acid analytes for enhanced sensitivity detection.
THE POTENTIAL FOR IMPROVED ENERGY EFFICIENCY TO HELP MEET FUTURE ENERGY NEEDS (1981)

The estimated technical potential for cost-effective energy conservation is summarized for both the__lL~S_._and_Calif.ornia.--These-esMoma-~es--------shouldbe viewed as theoretical opportunities for improving energy efficiency; they are not necessarily forecasts of the actual savings that might result from government policies and the market's response to higher energy prices.Detailed analyses are offered for residential buildings, using "supply curves of conserved energy."This technique allows the quantity and cost of energy "supplied" through improved efficiency to be readily compared with the production potential and unit cost of new conventional energy supplies.By the year 2000, there is a potential for the u.s. to reduce i~ annual resource energy consumption from a projected 103 Quads (10 Btu's) to about 62-65 Quads.This savings potential is the energy equivalent of about 18 million barrels per day CMBD) of oil production.Annual savings in the buildings sector alone could be as high as 8 MBD oil-equivalent, or more than the total amount of u.s.oil imports, for all sectors, in 1980.California's proportional share of this technical potential appears to be of the same order of magnitude as USGS estimates of California's OCS resources, but any more precise comparison may be premature.To achieve these efficiency gains will require investments of hundreds of billions of dollars over the next two decades, but the savings for businesses and consumers would be even larger.The average cost to save this energy would be about $10/barrel, _in today' s dollars.The conservation technical potential for California has not been fully evaluated, but estimates have been made for some end-use sectors.A future "low-energy scenario" for the State, while not specifying the full technical potential, identifies some possible goals for conservation and renewable energy use.-iii-* At 5c/kWh, this costs more than $10 billion a.year, or twice.theentire nonmilitary, non-strategic petroleum.reserve budget of DOE~'.
Synaptojanin Forms Two Separate Complexes in the Nerve Terminal (1997)

Endophilin is a recently discovered src homology 3 domain-containing protein that is a major in vitro binding partner for synaptojanin. To further characterize endophilin, we generated an antipeptide antibody. Endophilin is enriched in the brain, and immunofluorescence analysis reveals a high concentration of the protein in synaptic terminals, where it colocalizes with synaptojanin. In vitro binding assays demonstrate that endophilin binds through its src homology 3 domain to synaptojanin, and immunoprecipitation analysis with the antiendophilin antibody reveals that endophilin is stably associated with synaptojanin in the nerve terminal. Immunoprecipitation with an antibody against amphiphysin I and II, which interact through their src homology 3 domains with dynamin and synaptojanin at sites distinct from those for endophilin, reveals a second stable complex, which includes dynamin and synaptojanin but excludes endophilin. These data demonstrate that synaptojanin is present in two separate complexes in the nerve terminal and support an important role for endophilin in the regulation of synaptojanin function.
MOF‐derived/zeolite hybrid catalyst for the production of light olefins from CO2 (2020)

Abstract In this contribution we propose an alternative catalytic system based on MOF derivatives and small pore zeolites for the selective conversion of CO 2 into light olefins, using the lowest metal loadings and highest GHSV reported in literature. The catalyst synthesis involves deriving In−Zr oxides from MOFs containing these metals in their structure, i. e. (Zr)UiO‐67‐bipy‐In, via direct calcination in the presence of the zeolite, avoiding co‐precipitation, washing and mixing steps. This effectively creates a truly bifunctional In−Zr zeolite catalyst, opposed to physical mixtures of two catalysts using different precursors. The good dispersion and low loadings of the MOF‐derived In−Zr oxide supplemented with the strong acidity of chabazite‐type zeolites allows to couple the activation of CO 2 with C−C coupling, obtaining space time yields of 0.1 mol of CO 2 converted to light olefins per gram of In per hour at 375 °C, under the GHSV conditions employed.
The role of legumes in bioenergy poduction (2007)

We are investigating the role of legumes as components of bioenergy production. Two separate experiments, one with annual species and other with perennials, were established at Viikki in 2007. Selected grasses, legumes (or nitrogen fertilizer) and additional species were sown singly or in blends of two or three species.
Additive Manufacturing of Polyolefins (2022)

Polyolefins are semi-crystalline thermoplastic polymers known for their good mechanical properties, low production cost, and chemical resistance. They are amongst the most commonly used plastics, and many polyolefin grades are regarded as engineering polymers. The two main additive manufacturing techniques that can be used to fabricate 3D-printed parts are fused filament fabrication and selective laser sintering. Polyolefins, like polypropylene and polyethylene, can, in principle, be processed with both these techniques. However, the semi-crystalline nature of polyolefins adds complexity to the use of additive manufacturing methods compared to amorphous polymers. First, the crystallization process results in severe shrinkage upon cooling, while the processing temperature and cooling rate affect the mechanical properties and mesoscopic structure of the fabricated parts. In addition, for ultra-high-molecular weight polyolefins, limited chain diffusion is a major obstacle to achieving proper adhesion between adjunct layers. Finally, polyolefins are typically apolar polymers, which reduces the adhesion of the 3D-printed part to the substrate. Notwithstanding these difficulties, it is clear that the successful processing of polyolefins via additive manufacturing techniques would enable the fabrication of high-end engineering products with enormous design flexibility. In addition, additive manufacturing could be utilized for the increased recycling of plastics. This manuscript reviews the work that has been conducted in developing experimental protocols for the additive manufacturing of polyolefins, presenting a comparison between the different approaches with a focus on the use of polyethylene and polypropylene grades. This review is concluded with an outlook for future research to overcome the current challenges that impede the addition of polyolefins to the standard palette of materials processed through additive manufacturing.
Subharmonic emissions of a cavitating bubble (1984)

The nonlinear oscillations of a gas bubble pulsating in a liquid are critically dependent on the damping of these oscillations. We have used an accurate numerical formulation of the problem to investigate the subharmonic emissions from forced oscillations of the bubble. A systematic approach to chaotic behavior will be shown through successive bifurcation of the subharmonic emissions as the driving pressure is increased. [Work supported in part by the NSF and the ONR.]
An evaluation of hourly average wind-speed estimation techniques (1998)

Wind speed time series are often used in computer models to estimate the performance of a wind turbine or an array of wind turbines. In such modeling applications, it is desirable to have complete data for an annual period. However, equipment failure or extreme weather events can result in incomplete data. For certain models to run properly and achieve the best results, it is necessary to estimate the missing data. The estimated wind speed values should replicate, as closely as possible, the time scale properties and statistical characteristics of the missing data. One complete year of data from three sites in different wind regimes was used to test three different data estimation techniques by creating a sufficient number of gaps (sequences of missing values) of various durations to simulate annual data recovery rates of 90% and 80%. Then three modeling techniques were used to estimate the missing data. The accuracy of the estimated data was determined by comparing the statistical characteristics (average, standard deviation, and root mean square error) of the estimated data to those derived from the corresponding original data values. The estimated data were compared to the original wind speed data, and also used as input to the Wind Power Simulator (WIPS) model. The model results from the time series with the estimated data were compared to those from the original, complete time series. The results showed that all three estimation techniques did quite well in replicating the data in the original time series and each worked best at one of the three sites. Errors in the estimated average wind speed were rather small, mostly within about 5%. The errors in theoretical energy from the WIPS model for the entire year of data were mostly on the order of 2% or less. Errors tended to increase with gap length but there was no significant difference in results for the two simulated recovery rates.
Communication LEDs (2006)

LEDs can be used for either free-space communication or for fiber communication applications. Free-space communication applications include the remote control of appliances such as television sets and stereos, and data communication between a computer and peripheral devices. LEDs used in optical fiber communication applications are suited for distances of a few km and bit rates up to about 1 Gbit/s. Most fibers used with LEDs are multimode (step-index and graded-index) fibers. However, some applications employ single-mode fibers.
Organic acid production from food wastes using Gluconobacter oxydans: A possible source of cheaper lixiviants for leaching REE from end-of-life products (2017)

Gluconobacter oxydans is an acidophilic bacterium that is used in industry for producing organic acids, such as gluconic acid, from sugars such as glucose. Recently it has been discovered that the organic acids produced by G. oxydans has potential to be used in the recovery of rare earth elements (REE), especially gluconic acid. Producing gluconic acid from pure glucose has been deemed costly and so research has been conducted to find more economically friendly feedstock. In this work corn stover, potato peel waste, market rejected fruits, and apple processing and holding pond waters were investigated for their ability to provide G. oxydans sufficient sugar to grow and produce organic acid for bioleaching. Substrates such as the corn stover and fruits provided more than 20 g/L of glucose, and the bacterium grew well on all but the apple processing and holding pond water.
Mechanisms of lesion formation in high intensity focused ultrasound therapy (2003)

The lesions generated by high-intensity ultrasound were studied in transparent tissue phantoms premixed with and without Optison ultrasound contrast agents (UCA) at 1.1 and 3.5 MHz acoustic frequencies. Generation of small bubbles was observed at the very beginning of exposure, while cigar-shaped thermal lesions began to form at the focus after a delay. After further heating, boiling occurred and changed the lesion from cigar-shape to tadpole-shape, with advancement toward the transducer. Broadband noise was detected in phantoms with UCA initially. UCA also lowered the pressure threshold and enlarged the lesion. However, the lesion was formed centimeters in front of the focus at 1.1 MHz. While thermal and cavitation effects are believed to be both important in lesion formation, tadpole-shaped transformation results from boiling activity.
All‐Dielectric Fabry–Pérot Cavity Design for Spectrally Selective Mid‐Infrared Absorption (2021)

All‐dielectric metamaterials that exhibit broadband absorption of infrared (IR) radiation are promising platforms for the development of modern and applied nanophotonic technologies ranging from precise biosensing to high‐resolution imaging and high photon‐yield light detection. Herein, bulk meta‐absorbers comprising dielectric layers to provide broadband absorption of mid‐IR light are structured and studied. Through computational investigations and experimental assessments, the geometric parameters of the metastructure are judiciously selected and the peak of absorption is tuned to encompass the mid‐wave IR (MWIR) to long‐wave IR (LWIR) wavelengths, where absorbance of over ≈95% is achieved in the conducted analyses. These results are obtained using numerical optimization to achieve the highest absorption peak values. Thus, based on the mechanistic understanding of the conducted study, the reported percentage is the highest possible absorption efficiency obtained by the absorber metastructure. Importantly, the projected meta‐absorber is polarization insensitive and performs consistently over a wide range of incidence angles. The engineered multilayer architecture based on artificial media provides new possibilities for the broadband manipulation and control of the IR light.
Antithrombogenicity of hydrophilic polyurethane-hydrophobic polystyrene IPNs. II. In vitro and ex vivo studies (1995)

To investigate the effect of hydrophilic and hydrophobic surfaces with phase separated structure on their blood responses, interpenetrating polymer networks (IPNs) composed of hydrophilic polyurethane (PU) and hydrophobic polystyrene (PS) were prepared by simultaneous polymerization. In vitro protein adsorption, in vitro platelet adhesion, and ex vivo A-A shunt test were carried out to evaluate the blood compatibility of the PU/PS IPNs. The results of protein adsorption on the PU/PS IPN surfaces indicated that albumin preferentially adsorbed on the hydrophilic surface (PU), while fibrinogen preferentially adsorbed on the hydrophobic surface (PS). The PU/PS IPNs exhibited suppressive properties for both platelet adhesion and activation. The occlusion time of U50S50 IPN containing 50 wt% of PS was twice as long as that of the PU control (50 min), indicating enhanced blood compatibility, presumably due to the selective adsorption of plasma proteins and the suppression of the adhesion and activation of platelets.
The Transgenic Arabidopsis Plant System, pER8-GFP, as a Powerful Tool in Searching for Natural Product Estrogen-Agonists/Antagonists (2005)

The transgenic Arabidopsis plant system, pER8-GFP, may be used as a powerful tool in searching for natural estrogen-agonists/antagonists. Among selected plant extracts and natural products, the method was able to distinguish active extracts (e.g., Glycine max and Pueraria lobata) and pure compounds (e.g., 17beta-estradiol (1), genistein (10), and daidzein (11)) and also to distinguish effects of structural changes on activity. Thus, this rapid sensitive system was proven to be suitable for the discovery of natural products with estrogenic activity.