gebhart/patrepeval huggingface dataset:
Regioselective C4 and C6 Double Oxidation of Cellulose by Lytic Polysaccharide Monooxygenases (2021)

Lytic polysaccharide monooxygenases (LPMOs) play a key role in enzymatic degradation of hard-to-convert polysaccharides, such as chitin and cellulose. It is widely accepted that LPMOs catalyze a single regioselective oxidation of the C1 or C4 carbon of a glycosidic linkage, after which the destabilized linkage breaks. Here, a series of novel C4/C6 double oxidized cello-oligosaccharides was discovered. Products were characterized, aided by sodium borodeuteride reduction and hydrophilic interaction chromatography coupled to mass spectrometric analysis. The C4/C6 double oxidized products were generated by C4 and C1/C4 oxidizing LPMOs, but not by C1 oxidizing ones. By performing incubation and reduction in H<sub>2</sub> <sup>18</sup> O, it was confirmed that the C6 gem-diol structure resulted from oxygenation, although oxidation to a C6 aldehyde, followed by hydration to the C6 gem-diol, could not be excluded. These findings can be extended to how the reactive LPMO-cosubstrate complex is positioned towards the substrate.
Angiotensin II and NADPH Oxidase Increase ADMA in Vascular Smooth Muscle Cells (2010)

Asymmetrical dimethylarginine inhibits nitric oxide synthase, cationic amino acid transport, and endothelial function. Patients with cardiovascular risk factors often have endothelial dysfunction associated with increased plasma asymmetrical dimethylarginine and markers of reactive oxygen species. We tested the hypothesis that reactive oxygen species, generated by nicotinamide adenine dinucleotide phosphate oxidase, enhance cellular asymmetrical dimethylarginine. Incubation of rat preglomerular vascular smooth muscle cells with angiotensin II doubled the activity of nicotinamide adenine dinucleotide phosphate oxidase but decreased the activities of dimethylarginine dimethylaminohydrolase by 35% and of cationic amino acid transport by 20% and doubled cellular (but not medium) asymmetrical dimethylarginine concentrations (P<0.01). This was blocked by tempol or candesartan. Cells stably transfected with p22(phox) had a 50% decreased protein expression and activity of dimethylarginine dimethylaminohydrolase despite increased promoter activity and mRNA. The decreased DDAH protein expression and the increased asymmetrical dimethylarginine concentration in p22(phox)-transfected cells were prevented by proteosomal inhibition. These cells had enhanced protein arginine methylation, a 2-fold increased expression of protein arginine methyltransferase-3 (P<0.05) and a 30% reduction in cationic amino acid transport activity (P<0.05). Asymmetrical dimethylarginine was increased from 6+/-1 to 16+/-3 micromol/L (P<0.005) in p22(phox)-transfected cells. Thus, angiotensin II increased cellular asymmetrical dimethylarginine via type 1 receptors and reactive oxygen species. Nicotinamide adenine dinucleotide phosphate oxidase increased cellular asymmetrical dimethylarginine by increasing enzymes that generate it, enhancing the degradation of enzymes that metabolize it, and reducing its cellular transport. This could underlie increases in cellular asymmetrical dimethylarginine during oxidative stress.
Nanocrystalline N-doped ceria porous thin films as efficient visible-active photocatalysts (2012)

Nanocrystalline porous N-doped ceria films have been prepared by combining sol–gel chemistry, evaporation-induced self-assembly (EISA), flash crystallization and treatment in NH3 gas between 550 and 700 °C at flow rates of 270 and 670 cm3 min−1. The maximum nitrogen uptake is 0.06 moles per Ce, observed for the sample treated at 600 °C and NH3 flow rate of 670 cm3 min−1. Nitrogen bonding to cerium is proved by XPS, through the observation of the characteristic Ce–N feature at ∼397 eV. Microstructural characterization shows that the mesostructure of the films is lost for treatment temperatures in ammonia higher than 550 °C but the porous fraction remains between 35 and 40% after ammonolysis for all the samples. The nitrided films show photocatalytic activity under visible light in the acetaldehyde decomposition, with the best results obtained for the films treated at 550 °C under NH3 flow rate of 670 cm3 min−1.
SLA-aware Interactive Workflow Assistant for HPC Parameter Sweeping Experiments (2016)

A common workflow in science and engineering is to (i) setup and deploy large experiments with tasks comprising an application and multiple parameter values; (ii) generate intermediate results; (iii) analyze them; and (iv) reprioritize the tasks. These steps are repeated until the desired goal is achieved, which can be the evaluation/simulation of complex systems or model calibration. Due to time and cost constraints, sweeping all possible parameter values of the user application is not always feasible. Experimental Design techniques can help users reorganize submission-execution-analysis workflows to bring a solution in a more timely manner. This paper introduces a novel tool that leverages users' feedback on analyzing intermediate results of parameter sweeping experiments to advise them about their strategies on parameter selections tied to their SLA constraints. We evaluated our tool with three applications of distinct domains and search space shapes. Our main finding is that users with submission-execution-analysis workflows can benefit from their interaction with intermediate results and adapt themselves according to their domain expertise and SLA constraints.
Follicular dendritic cell dysfunction contributes to impaired antigen-specific humoral responses in sepsis-surviving mice (2021)

Sepsis survivors exhibit impaired responsiveness to antigen (Ag) challenge associated with increased mortality from infection. The contribution of follicular dendritic cells (FDCs) in the impaired humoral response in sepsis-surviving mice is investigated in this study. We demonstrated that mice subjected to sepsis from cecal ligation and puncture (CLP mice) have reduced NP-specific high-affinity class-switched Ig antibodies (Abs) compared with sham-operated control mice following immunization with the T cell-dependent Ag, NP-CGG. NP-specific germinal center (GC) B cells in CLP mice exhibited reduced TNF-α and AID mRNA expression compared with sham-operated mice. CLP mice showed a reduction in FDC clusters, a reduced binding of immune complexes on FDCs, and reduced mRNA expression of CR2, ICAM-1, VCAM-1, FcγRIIB, TNFR1, IKK2, and LTβR compared with sham-operated mice. Adoptive transfer studies showed that there was no B cell-intrinsic defect. In summary, our data suggest that the reduced Ag-specific Ab response in CLP mice is secondary to a disruption in FDC and GC B cell function.
Snuff box radial artery access for arteriovenous fistula intervention (2019)

Snuff box radial access was used successfully for radiocephalic fistula intervention with procedure times similar to direct fistula access without major complications.
Room temperature detector array technology for the terahertz to far-infrared. (2011)

Thermal detection has made extensive progress in the last 40 years, however, the speed and detectivity can still be improved. The advancement of silicon photonic microring resonators has made them intriguing for detection devices due to their small size and high quality factors. Implementing silicon photonic microring or microdisk resonators as a means of a thermal detector gives rise to higher speed and detectivity, as well as lower noise compared to conventional devices with electrical readouts. This LDRD effort explored the design and measurements of silicon photonic microdisk resonators used for thermal detection. The characteristic values, consisting of the thermal time constant ({tau} {approx} 2 ms) and noise equivalent power were measured and found to surpass the performance of the best microbolometers. Furthermore the detectivity was found to be D{sub {lambda}} = 2.47 x 10{sup 8} cm {center_dot} {radical}Hz/W at 10.6 {mu}m which is comparable to commercial detectors. Subsequent design modifications should increase the detectivity by another order of magnitude. Thermal detection in the terahertz (THz) remains underdeveloped, opening a door for new innovative technologies such as metamaterial enhanced detectors. This project also explored the use of metamaterials in conjunction with a cantilever design for detection in the THz region and demonstrated the use of metamaterials as custom thin film absorbers for thermal detection. While much work remains to integrate these technologies into a unified platform, the early stages of research show promising futures for use in thermal detection.
Synthesis of Ring‐Substituted 4‐Aminoquinolines and Evaluation of Their Antimalarial Activities. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
ChemInform Abstract: Pyrrolo(2,1‐a)isoindol‐5‐ones, e.g. (V), and Benz(3,4)azocin‐1(2H)‐1,4, 6‐triones, e.g. (VIII). (1994)

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.
Automatic exposure selection for High Dynamic Range photography (2015)

High Dynamic Range photography involves fusing bracket images taken at different exposure values in order to compensate for the low dynamic range of image sensors in digital and smartphone cameras. Bracket images normally consist of an image taken by the auto-exposure setting of a camera as well as two other images at ±n exposure values where n is manually specified or selected. This paper discusses a method to automatically and optimally select exposures by using pixel clustering and local entropy. The results obtained show that the developed automatic exposure selection method provides more scene details compared to the manual or fixed exposure selection.
Production of Ethylene and its Commercial Importance in the Global Market (2016)

Ethylene is the largest of the olefin markets and is also one of the most important petrochemically derived monomers that are used as a feedstock for the production of various commercially useful chemical products (e.g. polyethylene, polymers, fibers etc.). The primary objective of this chapter is to provide a comprehensive overview about olefins particularly ethylene production technologies and its commercial significance in the world market. The content of this chapter is presented as follows: a general overview about olefins production is given. This is followed by introducing the reader to ethylene including its properties importance/applications. The next section describes the production technologies of ethylene and some of its selected derivatives, followed by an overview of the technology, market, costs, capacity, global demand and supply of ethylene technology. Finally, main points and outlook of this highly industrially important commodity chemical are summarized.
Network topologies dictate electromechanical coupling in liquid metal–elastomer composites (2020)

Elastomers embedded with micro- and nanoscale droplets of liquid metal (LM) alloys like eutectic gallium-indium (EGaIn) can exhibit unique combinations of elastic, thermal, and electrical properties that are difficult to achieve using rigid filler. For composites with sufficient concentrations of liquid metal, the LM droplets can form percolating networks that conduct electricity and deform with the surrounding elastomer as the composite is stretched. Surprisingly, experimental measurements performed on LM-embedded elastomers (LMEEs) show that the total electrical resistance of the composite increases only slightly even as the elastomer is stretched to several times its natural length. In contrast, Pouillet's law would predict an exponential increase in resistance (Ω) with stretch (λ) due to the incompressibility of liquid metal and elastomer. In this manuscript, we perform a computational analysis to examine the unique electromechanical properties of conductive LMEE composites. Our analysis suggests that the gauge factor that quantifies electromechanical coupling (i.e. G = {ΔΩ/Ω0}/λ) decreases with increasing tortuosity of the conductive pathways formed by the connected LM droplets. A dimensionless parameter for path tortuosity can be used to estimate G for statistically homogeneous LMEE composites. These results rationalize experimental observations and provide insight into the influence of liquid metal droplet assembly on the functionality of the composite.
Abstract 517: Supraphysiological androgens activate innate immune signaling in prostate cancer (2019)

Castration resistance prostate cancer (CRPC) first manifests as a sustained rise in the androgen-responsive gene, PSA, consistent with reactivation of a functioning androgen receptor (AR) axis. This observation led to the development of “second-line” therapies aimed at further blocking androgen/AR signaling. Unfortunately, resistance to these agents can also develop quickly. Paradoxically, several studies have suggested that the growth of AR-positive human CRPC cell lines may be inhibited by supraphysiologic levels of testosterone (SupT). These studies suggested that the adaptive reliance on AR signaling by CRPC cells becomes a therapeutic liability that can be exploited through the administration of SupT, which we termed as bipolar androgen therapy (BAT). Understanding how BAT works at the molecular and cellular levels might help in rationally combining BAT with other agents to achieve increased efficacy and tumor responses. Our data indicates that SupT induces DNA double strand breaks (DSBs) in prostate cancer (PCa) cells. Unrepaired DSBs induced by SupT are routed for specialized autophagic degradation, termed nucleophagy. We further show that SupT-induced autophagosomal DNA can activate cytoplasmic DNA sensing pathways and downstream innate immune signaling. Based on our findings, we propose that BAT engages the immune system to inhibit tumor growth. Future combination of BAT with existing immunotherapeutics including immune checkpoint blockade may prove beneficial for treatment of CRPC.Citation Format: Janet Mendonca, Olutosin Owoyemi, Marc Rosen, Michael Carducci, Mark Markowski, Emmanuel Antonarakis, Drew Pardoll, Samuel Denmeade, Sushant K. Kachhap. Supraphysiological androgens activate innate immune signaling in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 517.
ChemInform Abstract: SEMICONDUCTOR ELECTRODES. XV. PHOTOELECTROCHEMICAL CELLS WITH MIXED POLYCRYSTALLINE N‐TYPE CADMIUM SULFIDE‐CADMIUM SELENIDE (1978)

Abstract Mischkristalle zwischen CdS und CdSe verschiedener Zusammensetzung werden durch Sintern von Preßlingen oder Aufdampfen im Vakuum hergestellt.
Quantitative Viscoelastic Mapping of Polyolefin Blends with Contact Resonance Atomic Force Microscopy (2012)

The storage modulus (E′) and loss modulus (E″) of polyolefin blends have been mapped on the nanoscale with contact resonance atomic force microscopy (CR-FM), a dynamic contact mode of atomic force microscopy (AFM). Modulus values measured on various components within a blend of polyethylene, polypropylene, and polystyrene compared favorably with expected moduli of individual pure components at the contact resonance frequency that were calculated from bulk dynamic mechanical analysis (DMA) measurement results. Absolute storage modulus values were in good agreement with DMA results, while the loss modulus values obtained from CR-FM were consistently lower than those acquired from DMA. Application of CR-FM to an elastomer-containing blend resulted in moduli map artifacts due to the elastomer’s high adhesion and low storage modulus, illustrating its limitation in quantifying viscoelastic properties of soft elastomers. In spite of this current limitation, the results presented in this paper demonstrate the potential of contact resonance methods for quantifying nanoscale viscoelastic properties of certain thermoplastic polymers.
Conversion of a Carboxylesterase into a Triacylglycerol Lipase by a Random Mutation (2005)

A true convert: The carboxylesterase enzyme R.34 (see picture) can be converted into a triacylglycerol lipase without modification of the shape, size, or hydrophobicity of the substrate binding site. The substitution of Asn33 by Asp results in a salt bridge between the Asp33 and Arg49, which causes a distortion of the enzyme structure that makes the catalytic site more accessible to larger substrates but also more labile. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z502461_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Effects of high heel wear and increased weight on the knee during walking (2014)

ABSTRACT Knee osteoarthritis (OA), a leading cause of disability, is more prevalent in women than men. Wearing high heeled shoes has been implicated as a potential contributing factor for the higher lifetime risk of osteoarthritis in women. This study tests the hypotheses that changes to knee kinematics and kinetics observed during high heeled walking increase in magnitude with increasing heel height and are accentuated by a 20% increase in weight. Fourteen healthy females were tested using marker‐based gait analysis in combinations of footwear (flat athletic shoe, 3.8 cm and 8.3 cm heeled shoes) and weight (with and without 20% bodyweight vest). At preferred walking speed, knee flexion angle at heel‐strike and midstance increased with increasing heel height and weight. Maximum knee extension moment during loading response decreased with added weight; maximum knee extension moment during terminal stance decreased with heel height; maximum adduction moments increased with heel height. Many of the changes observed with increasing heel height and weight were similar to those seen with aging and OA progression. This suggests that high heel use, especially in combination with additional weight, may contribute to increased OA risk in women. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 33:???–???, 2015.
Synthesis and pharmacology of 8-amino-3-[(tetrahydro-2-furanyl)methyl] benzomorphan. (2003)

The relative poor binding affinity of the target compounds did not warrant conducting the in vivo studies to determine if they have the profile(kappa agonist/mu antagonist) that will be potentially useful in the treatment of drug addiction. Further study is in progress.
A Quantitative Study for Hydrothermal Alteration Zones using Short Wavelength Infrared Spectrometry (2017)

열수 광상의 잠두 광체를 예측하는데 중요한 인자로 인식되는 고(산성)점토 변질대, 점토 변질대 및 필릭 변질대의 정량성을 확보하기 위해 명반석-고령석 조합과 일라이트-고령석 조합에 대한 합성 혼합시료를 대상으로 단파장적외선 스펙트럼의 흡광특성과 광물함량의 점이적인 변화추이를 비교하였다. 명반석-고령석 조합에서 명반석은 Hull quotient 반사도가 가장 높은 상관관계(0.99)를 보이며, 고령석은 가우시안 피크가 가장 높은 상관관계(0.92)를 나타내고 있다. 일라이트-고령석 조합은 흡수영역이 중첩하고 있어 가우시안 분해가 필수적이며, 일라이트와 고령석은 각각 0.93과 0.98의 높은 상관도를 보이고 있다. 단파장적외선 분광분석법에서 유도한 명반석-고령석과 일라이트-고령석 조합의 오차범위(8%, 5%)는 리트벨트 X-선 회절정량분석법에서 구한 성분비의 오차범위(29%, 26%)보다 작아 분광분석결과가 상대적으로 정량적 신뢰도가 높다는 것으로 확인되었다. Advanced argillic, argillic, and phyllic zones are the most important alteration patterns to predict the hidden ore body during exploration of hydrothermal deposits. We examined the quantitative relationship between the spectral absorption characteristics and the mineral content of the synthetic mixtures such as alunite-kaolinite and illite-kaolinite using short wavelength infrared (SWIR) spectroscopy. In the alunite-kaolinite mixtures, the spectral absorption characteristics of the alunite was highly correlated with the Hull quotient reflectance(0.99) and the kaolinite had the highest correlation with the Gaussian peak(0.92). Illite-kaolinite mixtures are essential for Gaussian deconvolution because of the overlap of absorption region. Illite and kaolinite mixtures indicate the high correlation of 0.93 and 0.98, respectively. The error ranges in the alunite-kaolinite(8%) and illite-kaolinite mixtures(5%) derived from SWIR were smaller than the ones(29% and 26%) obtained from X-ray diffraction(Rietveld) analysis. These results show that SWIR spectroscopic analysis is more reliable than XRD Rietveld analysis in terms of quantification of allowed minerals.
Hybrid Spin-Exchange Optical Pumping ofHe3 (2003)

We demonstrate spin-exchange optical pumping of 3He using a "hybrid" K-Rb vapor mixture. The Rb atoms absorb light from a standard laser at 795 nm, then collisionally polarize the potassium atoms. Spin-exchange collisions of K and 3He atoms then transfer the angular momentum to the 3He with much greater efficiency than Rb-3He. For a K-rich vapor, the efficiency of the hybrid spin-exchange collisions approaches 1/4, an order of magnitude greater than achieved by pure Rb pumping. We present the first measurements of actual photon efficiencies (polarized nuclei produced per absorbed photon), and show that a new parasitic absorption process limits the total efficiencies for both hybrid and pure Rb pumping.
Molecular mechanism underlying impaired hepatic autophagy in glycogen storage disease type Ib (2022)

Type Ib glycogen storage disease (GSD-Ib) is caused by a deficiency in the glucose-6-phosphate (G6P) transporter (G6PT) that translocates G6P from the cytoplasm into the endoplasmic reticulum lumen, where the intraluminal G6P is hydrolyzed to glucose by glucose-6-phosphatase-α (G6Pase-α). Clinically, GSD-Ib patients manifest a metabolic phenotype of impaired blood glucose homeostasis and a long-term risk of hepatocellular adenoma/carcinoma (HCA/HCC). Studies have shown that autophagy deficiency contributes to hepatocarcinogenesis. In this study, we show that G6PT deficiency leads to impaired hepatic autophagy evident from attenuated expression of many components of the autophagy network, decreased autophagosome formation and reduced autophagy flux. The G6PT-deficient liver displayed impaired sirtuin 1 (SIRT1) and AMP-activated protein kinase (AMPK) signaling, along with reduced expression of SIRT1, forkhead boxO3a (FoxO3a), liver kinase B-1 (LKB1) and the active p-AMPK. Importantly, we show that overexpression of either SIRT1 or LKB1 in G6PT-deficient liver restored autophagy and SIRT1/FoxO3a and LKB1/AMPK signaling. The hepatosteatosis in G6PT-deficient liver decreased SIRT1 expression. LKB1 overexpression reduced hepatic triglyceride levels, providing a potential link between LKB1/AMPK signaling upregulation and the increase in SIRT1 expression. In conclusion, downregulation of SIRT1/FoxO3a and LKB1/AMPK signaling underlies impaired hepatic autophagy which may contribute to HCA/HCC development in GSD-Ib. Understanding this mechanism may guide future therapies.