gebhart/patrepeval huggingface dataset:
CRM1-Dependent Function of a cis-Acting RNA Export Element (2002)

Viruses often contain cis-acting RNA elements, which facilitate the posttranscriptional processing and export of their messages. These elements fall into two classes distinguished by the presence of either viral or cellular RNA binding proteins. To date, studies have indicated that the viral proteins utilize the CRM1-dependent export pathway, while the cellular factors generally function in a CRM1-independent manner. The cis-acting element found in the woodchuck hepatitis virus (WHV) (the WHV posttranscriptional regulatory element [WPRE]) has the ability to posttranscriptionally stimulate transgene expression and requires no viral proteins to function. Conventional wisdom suggests that the WPRE would function in a CRM1-independent manner. However, our studies on this element reveal that its efficient function is sensitive to the overexpression of the C terminus of CAN/Nup214 and treatment with the antimicrobial agent leptomycin B. Furthermore, the overexpression of CRM1 stimulates WPRE activity. These results suggest a direct role for CRM1 in the export function of the WPRE. This observation suggests that the WPRE is directing messages into a CRM1-dependent mRNA export pathway in somatic mammalian cells.
Laplace Entropy and its Application to Time Delay Estimation for Speech Signals (2007)

Time delay estimation (TDE) is a basic technique for numerous applications where there is a need to localize and track a radiating source. It is particularly challenging in the presence of noise and reverberation, and when the source signal is speech which is inherently nonstationary and random. The most important TDE algorithms for two sensors are based on the generalized cross-correlation (GCC) method. These algorithms perform reasonably well when reverberation or noise is not too high. In an earlier study of the authors, a more sophisticated approach was proposed. It employs more sensors and takes advantage of their delay redundancy to improve the precision of the TDOA (time difference of arrival) estimate between the first two sensors. The approach is based on the multichannel cross-correlation coefficient (MCCC) and was found more robust to noise and reverberation. In this paper, we show that this approach can also be developed on a basis of joint entropy. For Gaussian signals, we show that, in the search of the TDOA estimate, maximizing MCCC is equivalent to minimizing joint entropy. But with the generalization of the idea to non-Gaussian speech signals, the joint entropy based new multichannel TDE algorithm manifests a potential to outperform the MCCC-based method. Since there is no rigorous mathematical formula for speech entropy, we use the assumption that speech can be plausibly modeled by a Laplace distribution and develop a practical approximation of Laplace entropy for TDE of speech signals. The performance of the proposed new algorithm is investigated via simulations.
Pulse arrival time is not an adequate surrogate for pulse transit time in terms of tracking diastolic pressure (2011)

We compared pulse arrival time (PAT) and pulse transit time (PTT) in terms of their ability to track diastolic pressure (DP). We performed the comparison using high fidelity, invasive arterial waveforms recorded from six dogs during multiple interventions. On average, DP ranged from 40 to 106 mmHg and therefore varied widely. PAT and PTT were able to predict DP with average root-mean-squared-errors of 9.8 ± 5.8 mmHg and 5.7 ± 2.0 mmHg (p = 0.02). Thus, even though PAT is simpler to measure, we can only recommend using PTT for tracking DP.
Dual‐Function Cobalt–Nickel Nanoparticles Tailored for High‐Temperature Induction‐Heated Steam Methane Reforming (2018)

Abstract The tailored chemical synthesis of binary and ternary alloy nanoparticles with a uniform elemental composition is presented. Their dual use as magnetic susceptors for induction heating and catalytic agent for steam reforming of methane to produce hydrogen at temperatures near and above 800 °C is demonstrated. The heating and catalytic performance of two chemically synthesized samples of CoNi and Cu ⊂ CoNi are compared and held against a traditional Ni‐based reforming catalyst. The structural, magnetic, and catalytic properties of the samples were characterized by X‐ray diffraction, elemental analysis, magnetometry, and reactivity measurements. For induction‐heated catalysts, the conversion rate of methane is limited by chemical reactivity, as opposed to the case of traditional externally heated reformers where heat transport limitations are the limiting factor. Catalyst production by the synthetic route allows controlled doping with miniscule concentrations of auxiliary metals.
In Situ, Fast, High‐Temperature Synthesis of Nickel Nanoparticles in Reduced Graphene Oxide Matrix (2017)

For the first time, a fast heating–cooling process is reported for the synthesis of carbon‐coated nickel (Ni) nanoparticles on a reduced graphene oxide (RGO) matrix (nano‐Ni@C/RGO) as a high‐performance H 2 O 2 fuel catalyst. The Joule heating temperature can reach up to ≈2400 K and the heating time can be less than 0.1 s. Ni microparticles with an average diameter of 2 µm can be directly converted into nanoparticles with an average diameter of 75 nm. The Ni nanoparticles embedded in RGO are evaluated for electro‐oxidation performance as a H 2 O 2 fuel in a direct peroxide–peroxide fuel cell, which exhibits an electro‐oxidation current density of 602 mA cm −2 at 0.2 V (vs Ag/AgCl), ≈150 times higher than the original Ni microparticles embedded in the RGO matrix (micro‐Ni/RGO). The high‐temperature, fast Joule heating process also leads to a 4–5 nm conformal carbon coating on the surface of the Ni nanoparticles, which anchors them to the RGO nanosheets and leads to an excellent catalytic stability. The newly developed nano‐Ni@C/RGO composites by Joule heating hold great promise for a range of emerging energy applications, including the advanced anode materials of fuel cells.
ChemInform Abstract: Stereoselective Oxidation of an Eleven‐Membered Heterocycle. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Non-covalent ligand-oxide interaction promotes oxygen evolution (2023)

Strategies to generate high-valence metal species capable of oxidizing water often employ composition and coordination tuning of oxide-based catalysts, where strong covalent interactions with metal sites are crucial. However, it remains unexplored whether a relatively weak "non-bonding" interaction between ligands and oxides can mediate the electronic states of metal sites in oxides. Here we present an unusual non-covalent phenanthroline-CoO<sub>2</sub> interaction that substantially elevates the population of Co<sup>4+</sup> sites for improved water oxidation. We find that phenanthroline only coordinates with Co<sup>2+</sup> forming soluble Co(phenanthroline)<sub>2</sub>(OH)<sub>2</sub> complex in alkaline electrolytes, which can be deposited as amorphous CoO<sub>x</sub>H<sub>y</sub> film containing non-bonding phenanthroline upon oxidation of Co<sup>2+</sup> to Co<sup>3+/4+</sup>. This in situ deposited catalyst demonstrates a low overpotential of 216 mV at 10 mA cm<sup>-2</sup> and sustainable activity over 1600 h with Faradaic efficiency above 97%. Density functional theory calculations reveal that the presence of phenanthroline can stabilize CoO<sub>2</sub> through the non-covalent interaction and generate polaron-like electronic states at the Co-Co center.
Improving Efficacy of Inhaled Technosphere Insulin (Afrezza) by Postmeal Dosing: In-silico Clinical Trial with the University of Virginia/Padova Type 1 Diabetes Simulator (2016)

In-silico clinical trials comparing the treatment effect of different dosing regimens with TI and of insulin lispro suggest that postmeal dosing or split dosing of TI, in combination with an appropriate titration rule, can achieve a superior postprandial glucose control while providing a lower risk for hypoglycemic events than conventional treatment with subcutaneously administered rapid-acting insulin products.
Molecular nature of voltage‐gated calcium channels: structure and species comparison (2013)

The progression from one to three to 10, and in some instances more, voltage‐gated calcium channels within living organisms during the course of evolution has paralleled the development of complex neuronal and signaling pathway development. Over time, the core structural elements allowing movement of calcium across the cellular membrane in a voltage‐dependent manner have been built upon through the modification of the intra‐ and extracellular regions of the calcium channel protein structure. This has allowed the flow of calcium ions to be coupled to a broad spectrum of signaling and modulatory mechanisms that interact at both the intra‐ and extracellular surfaces. Changes in splice‐variant composition also provide another layer of complexity to the repertoire of possible calcium channels. From next generation sequencing techniques it is becoming clear that much more work remains towards furthering our understanding of the regulation and complexity of splice variation within single channel subtypes. Careful analysis needs to be undertaken within specific target tissues and cell types together with temporal aspects of development and disease pathophysiology in order to confirm that the correct splice‐variant context is considered. Subfamily‐specific calcium channel variations in both vertebrates and invertebrates provide the opportunity to identify both subfamily and organism specific blockers. WIREs Membr Transp Signal 2013, 2:181–206. doi: 10.1002/wmts.91 Conflict of interest: The authors have declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website .
Search for a Standard Model Higgs boson in the mass range 200–600 GeV in the H→ZZ→ℓ+ℓ−qq¯ decay channel with the ATLAS detector (2012)

A search for a heavy Standard Model Higgs boson decaying via H Z Z + -q q, where = e or , is presented. The search uses a data set of pp collisions at s = 7 TeV, corresponding to an integrated luminosity of 4.7 fb -1 collected in 2011 by the ATLAS detector at the CERN LHC. No significant excess of events above the estimated background is found. Upper limits at 95% confidence level on the production cross section of a Higgs boson with a mass in the range between 200 and 600 GeV are derived. A Standard Model Higgs boson with a mass in the range 300 GeV m H 322 GeV or 353 GeV m H 410 GeV is excluded at 95% CL. The corresponding expected exclusion range is 351 GeV m H 404 GeV at 95% CL.
Humoral and T helper cell responses elicited by immunization with dendritic cells genetically modified with an adenoviral vector expressing HCV NS3 protein in HLA-A2.1 transgenic mice (2006)

Dendritic cells (DC) are potent antigen-presenting cells that play a critical role in the initiation of T lymphocyte response. The recombinant adenovirus (rAd) has widely been employed in gene therapy and for delivering genes into primary cell types. DCs and rAd are two highly promising vaccine components against hepatitis C virus (HCV) infection. There has been little information, however, on the advantageous immuno-stimulatory capacity by their combination into one vaccine correlating with clearance of HCV infection in animal models. Aims The present study is to investigate the potential of adenovirus for HCV nonstructural protein NS3 transduced DCs (Ad-NS3 transduced DCs) in priming HCV antigen specific T helper (Th) cell and antibody responses in mice so as to define a optimal strategy of antigen loaded DCs for the successful immunotherapy. To evaluate the potential efficacy of Ad-NS3 transduced DCs, bone marrow cells harvested from HLA-A2.1 transgenic mice were transduced with adenovirus encoding either an antigen gene or a control gene after 7 day co-cultured with granulocyte/macrophage colony-stimulating factor and interleukin–4. DC phenotypic cell surface markers were tested by FACS analysis. HLA-A2.1 transgenic mice were immunized subcutaneously with 3×105 Ad-NS3 transduced DCs twice at the 10 days interval by comparing with recombinant HCV NS3 protein pulsed DCs(rNS3 pulsed DCs) treatment. The antigen specific antibody levels and subclass types, IL–2, IL–10 cytokine secretion and IFN-gamma secreting T cells were evaluated by ELISA and ELISPOT techniques. We found that strong anti-NS3 antibody response which dominated by IgG1 was developed 10 days after the last immunization, NS3-specific CD4+ T cell responses in Ad-NS3 transduced DCs immunized mice peaked at day 7 as measured by higher level of IL–2 production, IFN-γsecreted T cells and contrarily significantly decreased IL–10 secretion. Comparatively, the vigor of these responses was much less in mice challenged with rNS3-DCs. Furthermore, we demonstrated that the previous Ad-NS3 transduced DCs immunization does not influence the subsequent use for boosting. Our results clearly indicate that Ad-NS3 transduced DCs is superior to protein pulsed DCs in inducing vigorous humoral and Th1 cell immune responses in HLA.A2.1 transgenic mice, which suggests that this approach has important implications in initiating specific immune responses against HCV infection.
Beta 3 integrin-mediated fibrin clot retraction by nucleated cells: differing behavior of alpha IIb beta 3 and alpha v beta 3 (1995)

Abstract Fibrin clot retraction may be important in resolution of thrombi and, in platelets, is mediated by integrin alpha IIb beta 3 (GPIIb-IIIa). Nucleated cells that lack alpha IIb beta 3 can retract fibrin clots, and we now report that integrin alpha v beta 3 can support this process. In addition, we compared the capacities of recombinant beta 3 integrins to mediate clot retraction in Chinese hamster ovary and M21 melanoma cells. We found that alpha v beta 3, but not alpha IIb beta 3, could spontaneously support retraction. Transferring the cytoplasmic domain of alpha v to alpha IIb enabled the resulting chimeric alpha IIb beta 3 to support clot retraction. The capacity of the alpha v cytoplasmic domain to support clot retraction was not caused by activation of the ligand binding function of alpha IIb beta 3 or by enhancement of alpha IIb beta 32s capacity to stimulate the formation of focal adhesions or the tyrosine phosphorylation of pp125FAK. These experiments define requirements for alpha IIb beta 3-mediating clot retraction, establish the capacity of alpha v beta 3 to mediate this process, and suggest differing functional roles of the alpha v and alpha IIb cytoplasmic domains.
Method of polymerizing exo-methylene cyclic organic compounds using homogeneous ring-opening catalysts (2023)

The regiospecific (1,2-Me.sub.2 C.sub.5 H.sub.3).sub.2 ZrMe.sup.+ MeB(C.sub.6 F.sub.5).sub.3.sup.- mediated ring-opening polymerization of methylenecyclobutane and its copolymerization with ethylene to polyolefins of microstructure--{CH.sub.2 CH.sub.2 CH.sub.2 C(CH.sub.2)]--.sub.n and {--[CH.sub.2 CHR]--.sub.x [CH.sub.2 CH.sub.2 CH.sub.2 C(CH.sub.2)]--.sub.y }.sub.n' respectively, is disclosed.
A new optical-based technique for real-time measurements of mineral dust concentration in PM10 using a virtual impactor (2020)

Abstract. Atmospheric mineral dust influences Earth’s radiative budget, cloud formation and lifetime, has adverse health effects, and affects the air quality through the increase of regulatory PM10 concentrations, making strategic its real-time quantification in the atmosphere. Only few near-real-time techniques can discriminate dust aerosol in PM10 samples and they are based on the dust chemical composition. The on-line determination of mineral dust using aerosol absorption photometers offers an interesting and competitive alternative, but remains a difficult task to achieve. This is particularly challenging when dust is mixed with black carbon, which features a much higher mass absorption cross-section. We present here for the first time a highly time resolved on-line detection technique of dust absorption by coupling a high flow virtual impactor (VI) sampler that concentrates coarse particles with an aerosol absorption photometer (Aethalometer, model AE33). The absorption of concentrated dust particles is obtained by subtracting the absorption of the submicron (PM1) aerosol fraction from the absorption of the virtual impactor sample (VI-PM1 method). This real-time method for detecting desert dust was tested in the field for a period of two months (April and May 2016) at a regional background site of Cyprus, in the Eastern Mediterranean. Several intense desert mineral dust events were observed during the field campaign with dust concentration in PM10 up to 45 μg m−3. Mineral dust was present most of the time during the campaign with an average PM10 of about 8 μg m−3. Mineral dust absorption was most prominent at short wavelengths, yielding an average mass absorption cross-section (MAC) of 0.24 ± 0.01 m2 g−1 at 370 nm and an absorption Ångström exponent of 1.41 ± 0.29. This MAC value can be used as site specific parameter for on-line determination of mineral dust concentration. The uncertainty of the proposed method is discussed by comparing and validating it with different methods.
Simulations of head-related transfer functions in wideband acoustics (2006)

Head-related transfer functions (HRTFs) have been simulated in three dimensions for a head-and-torso model for the entire audio frequency range, from 20 Hz to 20 kHz. As opposed to data acquired through measurements, the results derived from computer simulations are free from the effects of noise and imperfections in the electro-acoustic chain. In addition, the spatial resolution can easily be made better than in any practical experiment. The simulations have been performed using an ultraweak variational formulation method for solving Helmholtz equation. The numerical method with its parallel computing capability is efficient, enabling numerical calculations of large physical systems, e.g., of size 0.4×0.5×0.8 m, at high frequencies. The method uses plane-wave basis functions instead of polynomial basis as in standard finite-element methods (FEM), resulting in the need of much sparser volume mesh than in FEM. For HRTF calculations, a so-called perfectly matched layer has been utilized and the solutions are derived in the far field. Thus, exterior problems often solved using boundary-element method are dealt with. The specific HRTF simulations have been performed using fully reflecting, sound hard, boundaries on the head and torso, and also with complex impedance boundaries on the torso such as clothing.
The Use of Real-Time and Time-Lapse Logging-While-Drilling Images for Geosteering and Formation Evaluation in the Breitbrunn Field, Bavaria, Germany (2004)

Summary Six horizontal wells were drilled into the Tertiary Chatt Sand reservoir of the Breitbrunn gas field in Bavaria, Germany. The purpose of this campaign was to develop part of the depleted reservoir into a gas-storage sand. A detailed geological and petro-physical study was prepared before drilling and resulted in the identification of high-quality reservoir layers that were targeted by the horizontal wells. Despite the simple anticline structure of the field, geometric drilling was ruled out because of remaining geological and directional uncertainties. The geosteering approach adopted relies on real-time resistivity-at-bit images, which were used for the first time during this drilling campaign. The image data are compressed downhole and transmitted to the acquisition computer on the rig, where they are decompressed and analyzed. The images allow the precise placement of the borehole relative to the geology. Layer heterogeneity such as tight streaks, concretions, or patchy porosity can be identified as such and is not interpreted as a different layer entered by the hole, which would lead to a wrong geosteering decision. Logging-while-drilling (LWD) azimuthal data are acquired during drilling and during washdown passes that follow a bit change. A comparison of these time-lapse data sets can provide invasion profiles through time and around the borehole.
A Red Algal Bourbonane Sesquiterpene Synthase Defined by Microgram-Scale NMR-Coupled Crystalline Sponge X-ray Diffraction Analysis (2017)

Sesquiterpene scaffolds are the core backbones of many medicinally and industrially important natural products. A plethora of sesquiterpene synthases, widely present in bacteria, fungi, and plants, catalyze the formation of these intricate structures often with multiple stereocenters starting from linear farnesyl diphosphate substrates. Recent advances in next-generation sequencing and metabolomics technologies have greatly facilitated gene discovery for sesquiterpene synthases. However, a major bottleneck limits biochemical characterization of recombinant sesquiterpene synthases: the absolute structural elucidation of the derived sesquiterpene products. Here, we report the identification and biochemical characterization of LphTPS-A, a sesquiterpene synthase from the red macroalga Laurencia pacifica. Using the combination of transcriptomics, sesquiterpene synthase expression in yeast, and microgram-scale nuclear magnetic resonance-coupled crystalline sponge X-ray diffraction analysis, we resolved the absolute stereochemistry of prespatane, the major sesquiterpene product of LphTPS-A, and thereby functionally define LphTPS-A as the first bourbonane-producing sesquiterpene synthase and the first biochemically characterized sesquiterpene synthase from red algae. Our study showcases a workflow integrating multiomics approaches, synthetic biology, and the crystalline sponge method, which is generally applicable for uncovering new terpene chemistry and biochemistry from source-limited living organisms.
Functionalized Mesoporous Silicas Direct Structural Polymorphism of Amyloid-β Fibrils (2020)

The aggregation of amyloid-β (Aβ) is associated with the onset of Alzheimer's disease (AD) and involves a complex kinetic pathway as monomers self-assemble into fibrils. A central feature of amyloid fibrils is the existence of multiple structural polymorphs, which complicates the development of disease-relevant structure-function relationships. Developing these relationships requires new methods to control fibril structure. In this work, we evaluated the effect that mesoporous silicas (SBA-15) functionalized with hydrophobic (SBA-PFDTS) and hydrophilic groups (SBA-PEG) have on the aggregation kinetics and resulting structure of Aβ<sub>1-40</sub> fibrils. The hydrophilic SBA-PEG had little effect on amyloid kinetics, while as-synthesized and hydrophobic SBA-PFDTS accelerated aggregation kinetics. Subsequently, we quantified the relative population of fibril structures formed in the presence of each material using electron microscopy. Fibrils formed from Aβ<sub>1-40</sub> exposed to SBA-PEG were structurally similar to control fibrils. In contrast, Aβ<sub>1-40</sub> incubated with SBA-15 or SBA-PFDTS formed fibrils with shorter crossover distances that were more structurally representative of fibrils found in AD patient derived samples. Overall, our results suggest that mesoporous silicas and other exogenous materials are promising scaffolds for the <i>de novo</i> production of specific fibril polymorphs of Aβ<sub>1-40</sub> and other amyloidogenic proteins.