gebhart/patrepeval huggingface dataset:
Glutathione Reductase-Catalyzed Cascade of Redox Reactions To Bioactivate Potent Antimalarial 1,4-Naphthoquinones – A New Strategy to Combat Malarial Parasites (2011)

Our work on targeting redox equilibria of malarial parasites propagating in red blood cells has led to the selection of six 1,4-naphthoquinones, which are active at nanomolar concentrations against the human pathogen Plasmodium falciparum in culture and against Plasmodium berghei in infected mice. With respect to safety, the compounds do not trigger hemolysis or other signs of toxicity in mice. Concerning the antimalarial mode of action, we propose that the lead benzyl naphthoquinones are initially oxidized at the benzylic chain to benzoyl naphthoquinones in a heme-catalyzed reaction within the digestive acidic vesicles of the parasite. The major putative benzoyl metabolites were then found to function as redox cyclers: (i) in their oxidized form, the benzoyl metabolites are reduced by NADPH in glutathione reductase-catalyzed reactions within the cytosols of infected red blood cells; (ii) in their reduced forms, these benzoyl metabolites can convert methemoglobin, the major nutrient of the parasite, to indigestible hemoglobin. Studies on a fluorinated suicide-substrate indicate as well that the glutathione reductase-catalyzed bioactivation of naphthoquinones is essential for the observed antimalarial activity. In conclusion, the antimalarial naphthoquinones are suggested to perturb the major redox equilibria of the targeted infected red blood cells, which might be removed by macrophages. This results in development arrest and death of the malaria parasite at the trophozoite stage.
Reactive Oxygen Species‐Scavenging Nanomedicines for the Treatment of Oxidative Stress Injuries (2014)

This Progress Report describes a development of two types of reactive oxygen species (ROS)-scavenging nanomedicines for the treatment of oxidative stress injuries, referred to as pH-sensitive redox nanoparticle (RNP(N) ) and pH-insensitive redox nanoparticle (RNP(O) ), which are prepared by self-assembling amphiphilic block copolymers possessing nitroxide radicals as a side chain of hydrophobic segment via amine and ether linkages, respectively. Due to a protonation of amino groups in hydrophobic core, RNP(N) disintegrates in low pH environments such as ischemic, inflamed, and tumor tissues, resulting in increased ROS-scavenging activity because of the exposed nitroxide radicals from the core. Utilizing pH-responsiveness of RNP(N) , it shows remarkable therapeutic effects on oxidative stress injuries such as renal and cerebral ischemia-reperfusion injuries after intravenous administration. Moreover, RNP(N) shows an enhancement of the activity of anticancer drugs by suppression of activation of transcription factors in tumor due to the ROS scavenging. On the other hand, orally administered RNP(O) has notable characteristics such as preferential accumulation in mucosa and inflamed area of gastrointestinal tract and no uptake into blood stream. Based on these characters, RNP(O) shows a remarkable therapeutic effect for the gastrointestinal inflammation without any adverse effects. Thus, ROS-scavenging nanomedicines have therapeutic efficacy in numerous oxidative stress diseases.
Abstract 13379: Cause-specific Mortality by Diffuse Coronary Artery Calcium Phenotypes: Results From the Coronary Artery Calcium Consortium (2020)

Objectives: We sought to assess characteristics of diffuse coronary artery calcium (CAC) phenotypes and their associations with cause-specific mortality. Background: CAC is a measure of subclinical atherosclerosis and improves risk stratification. CAC characteristics including vessel involvement, number of vessels, volume, and density have been shown to differentially impact risk. Less is known about clinical predictors of a diffuse CAC phenotype and its impact on cause-specific mortality. Methods: The CAC Consortium is a retrospective, multi-site cohort of 66,636 participants without CHD who underwent CAC scoring. Risk factor data were collected at enrollment or scan. Participants with CAC&gt;0 were included—CAC area, CAC density, and the CAC index of diffusion (the percentage of total CAC in the vessel with the highest CAC score) were calculated and the association between CAC characteristics and CVD- and CHD-specific mortality was assessed. Results: In 28,147 study participants (mean age 58.3 years, 25% female, and 89.6% white), ~66% had ≥2 calcified vessels. Diabetes, hypertension, and hyperlipidemia were predictors of multivessel involvement (p&lt;0.001). After controlling for CAC score, those with 4-vessel CAC had more CAC area involved with less dense calcification compared to those with 1-vessel involvement. After adjustment, those with CAC score 1-299 had a graded increase in CVD- and CHD-specific mortality with increasing vessel number compared with 1-vessel CAC. No difference was seen for individuals with CAC &gt;300. Among those with multivessel CAC involvement, all-cause survival was significantly worse in diffuse compared to other phenotypes. Conclusion: Diffuse CAC involvement was characterized by less dense calcification, more CAC area, multiple coronary vessel involvement, and presence of certain traditional risk factors. Multivessel CAC is associated with increased CVD- and CHD-specific mortality, particularly among CAC scores 1-299.
Optimization spatial multiple coil transmitter structure for wireless power transfer (2013)

The contactless charging system has a wide application range and many advantages for portable consumer electronic products. Wireless power transfer (WPT) includes both the transmitter and the receiver which are in the state of resonance to achieve high efficiency. This paper presents a new multiple overlapping coil transmitter structure which enables the receiver has high efficiency within transmitter center area in a freedom of movement manner. The optimization novel transmitter structure can achieve higher efficiency than the typical single coil. Simulation results show that the axial component of magnetic induction resulting from the overlapping coil structure has a preferable homogeneous distribution. The proposed optimization system achieves the efficiency of 60% for a receiver placed 10 cm away from a 4 coil (four overlapping coil) transmitter.
ChemInform Abstract: New Hepatoprotective Saponins, Bupleurosides III, VI, IX, and XIII, from Chinese Bupleuri Radix: Structure‐Requirements for the Cytoprotective Activity in Primary Cultured Rat Hepatocytes. (1997)

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.
The topography of the anterior surface of the cat's cornea (1984)

The topography of the cornea in nine unanaesthetised domestic cats was studied by the computer analysis of photokeratographs obtained using a Wessley Jessen P.E.K. 2000 photokeratoscope . Mean figures were obtained for: Central corneal radius in the steeper (9.06 mm) and flatter (9.20 mm) corneal meridians. Corneal astigmatism (0. 61D ). Corneal shape factor in the steeper (0.33) and flatter (0.31) corneal meridians and the diameter of the corneal cap in the vertical (6.23 mm) and horizontal (7.08 mm) meridians. The results are discussed and compared with previous such estimates for corneal topography. Dimensions for an hydrophilic contact lens suitable for general therapeutic or research use in the cat are suggested.
Data from Protein Expression Profiling Identifies Subclasses of Breast Cancer and Predicts Prognosis (2023)

&lt;div&gt;Abstract&lt;p&gt;Breast cancer is a heterogeneous disease whose evolution is difficult to predict by using classic histoclinical prognostic factors. Prognostic classification can benefit from molecular analyses such as large-scale expression profiling. Using immunohistochemistry on tissue microarrays, we have monitored the expression of 26 selected proteins in more than 1,600 cancer samples from 552 consecutive patients with early breast cancer. Both an unsupervised approach and a new supervised method were used to analyze these profiles. Hierarchical clustering identified relevant clusters of coexpressed proteins and clusters of tumors. We delineated protein clusters associated with the estrogen receptor and with proliferation. Tumor clusters correlated with several histoclinical features of samples, including 5-year metastasis-free survival (MFS), and with the recently proposed pathophysiologic taxonomy of disease. The supervised method identified a set of 21 proteins whose combined expression significantly correlated to MFS in a learning set of 368 patients (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001) and in a validation set of 184 patients (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001). Among the 552 patients, the 5-year MFS was 90% for patients classified in the “good-prognosis class” and 61% for those classified in the “poor-prognosis class” (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001). This difference remained significant when the molecular grouping was applied according to lymph node or estrogen receptor status, as well as the type of adjuvant systemic therapy. In multivariate analysis, the 21-protein set was the strongest independent predictor of clinical outcome. These results show that protein expression profiling may be a clinically useful approach to assess breast cancer heterogeneity and prognosis in stage I, II, or III disease.&lt;/p&gt;&lt;/div&gt;
Physics of extraordinary transmission through subwavelength hole arrays (2011)

The recent history of the research and development around plasmon surface waves that was initiated by the work published in Nature in 1998 by Ebbesen et al. [1] looks like a ten-fold compressed version of studies initiated more than a century ago by Robert Wood with his discovery of anomalies in the efficiency of metallic diffraction gratings, now known as Wood's anomalies [2]. In 1902, R. Wood wrote: “I was astounded to find that under certain conditions, the drop from maximum illumination to minimum, a drop certainly from 10 to 1, occurred within a range of wavelengths not greater than the distance between the sodium lines,” an observation that marked the discovery of grating anomalies.
Special Synergy between Electrolyte Additives and Positive Electrode Surface Coating to Enhance the Performance of Li[Ni<sub>0.6</sub>Mn<sub>0.2</sub>Co<sub>0.2</sub>]O<sub>2</sub>/Graphite Cells (2016)

Li[Ni0.6Mn0.2Co0.2]O2 (NMC622) is one of the most attractive positive electrode materials for Li-ion cells. Ultra high precision coulometry, impedance spectroscopy, gas evolution and long-term cycling were used to explore the combined impact of several electrolyte additives and an Al2O3 surface coating on NMC622/graphite cells tested to 4.4 V at 40°C. An excellent correlation between the short-term coulombic efficiency measurements and the long-term cycling results was noted. An electrolyte containing 1 M LiPF6 in ethylene carbonate: ethyl methyl carbonate (3:7 by weight) with additives 2 wt% prop-1-ene-1,3 sultone (PES) + 1 wt% methylene methane disulfonate (MMDS) + 1 wt% tris (trimethylsilyl) phosphite (TTSPi) (this electrolyte is called PES 211) was found to give the best performance in both coated and uncoated NMC622/graphite cells. The surface coating was found to improve coulombic efficiency, reduce impedance and improve capacity retention in all cases studied. However, uncoated NMC622/graphite cells with PES211 were found to perform better than coated NMC622/graphite cells which used any other electrolyte. The special synergy between Al2O3-coated NMC622 and PES211 needs to be understood so that even better coatings and electrolyte combinations can be developed.
Maude as a wide-spectrum framework for formal modeling and analysis of active networks (2003)

Modeling and formally analyzing active network systems and protocols is quite challenging, due to their highly dynamic nature and the need for new network models. We propose a wide-spectrum methodology using executable rewriting logic specifications to address this challenge. We also show how, using the Maude rewriting logic language and tools, active network systems, languages, and protocols can be formally specified and analyzed using a wide range of formal methods. Benefits include precise documentation of designs, early discovery of many bugs and omissions, and higher assurance of correct behavior. In this paper we illustrate these methods and their practical usefulness through two case studies: the AER/NCA protocol suite and the PLAN active networks language.
Structural Degradations in the Bulk of Cathode Particles for Li-ion Batteries (2018)

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Bilayer Fibril Formation by Genetically Engineered Polypeptides:  Preparation and Characterization (2006)

A de novo, genetically engineered 687 residue polypeptide expressed in E. coli has been found to form highly rectilinear, β-sheet containing fibrillar structures. Tapping-mode atomic force microscopy, deep-UV Raman spectroscopy, and transmission electron microscopy definitively established the tendency of the fibrils to predominantly display an apparently planar bilayer or ribbon assemblage. The ordered self-assembly of designed, extremely repetitive, high molecular weight peptides is a harbinger of the utility of similar materials in nanoscience and engineering applications.
A copper-loss based design method and verification for a zero-ripple interface for PV/Battery-to-grid applications (2016)

A systematic design of a zero-ripple Ćuk converter for PV/Battery-to-grid dc-dc conversion is presented. This paper derives the copper loss geometrical constant (K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> ) for this kind of integrated magnetic core using a simplified yet intuitive flux-reluctance model. Unlike earlier designs, the design procedure is completely analytical and valid for a range of duty-ratio operation. Verification is done by finite element methods and circuit simulations.
Formation of low-resistance Ohmic contacts to N-face n-GaN for high-power GaN-based vertical light-emitting diodes (2010)

We report on the formation of low-resistance Ohmic contacts to N-face n-GaN for high-power vertical light-emitting diodes using an Al–Ga solid solution (50 nm)/Ti(30 nm)/Al(200 nm) scheme and compare them with Ti(30 nm)/Al(200 nm) contacts. The Al–Ga solid solution layer is introduced to minimize the formation of Ga vacancies near the N-face n-GaN surface. It is shown that, unlike the Ti/Al contacts, the Al–Ga solid solution/Ti/Al contacts exhibit Ohmic behavior with a resistivity of 4.1×10−4 Ω cm2, even after annealing at 250 °C. X-ray photoemission spectroscopy and secondary ion mass spectrometry examinations are performed to understand the temperature dependence of the electrical properties.
The 2014 IODC lens design problem: the Cinderella lens (2014)

The lens design problem for the 2014 IODC is to design a 100 mm focal length lens in which all the components of the lens can be manufactured from ten Schott N-BK7 lens blanks 100 mm in diameter x 30 mm thick. The lens is used monochromatically at 587.56 nm. The goal of the problem is to maximize the product of the entrance pupil diameter and the semi-field of view while holding the RMS wavefront error to &le; 0.070 wave within the field of view. There were 45 entries from 13 different countries. Four different commercial lens design programs were used, along with six custom, in-house programs. The number of lens elements in the entries ranged from 10 to 52. The winning entry from Jon Ehrmann had 25 lens elements, and had an entrance pupil diameter of 33.9 mm and a semi-field of view of 62.5° for a merit function product of 2,119.
Zinc Oxide Nanowire Networks for Macroelectronic Devices (2008)

Zinc oxide (ZnO) nanowire networks have been proposed as an alternative to organic and amorphous semiconductors for plastic electronics. Although the mobility of the ZnO networks is lower than that of individual nanowires, they offer the advantages of high transparency and flexibility. A major drawback of using individual nanowires in nano or microelectronic applications is the lack of a manufacturable process to precisely assemble nanowires into small devices. The use of ZnO networks avoid this issue for relatively large area macroelectronic devices since the devices exhibit the average properties of a large number of random individual nanowires. In this work, we have deposited uniform ZnO thin films using an easy, scalable, stamping method and characterized their electronic and optoelectronic properties. We have also demonstrated the use of ZnO networks as an active material in thin film transistors where mobility values in excess of 20 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs has been achieved. The results presented here simply reveal the potential use of inorganic nanowires for optoelectronic devices.
Continuous Time Level Crossing Sampling ADC for Bio-Potential Recording Systems (2013)

In this paper we present a fixed window level crossing sampling analog to digital convertor for bio-potential recording sensors. This is the first proposed and fully implemented fixed window level crossing ADC without local DACs and clocks. The circuit is designed to reduce data size, power, and silicon area in future wireless neurophysiological sensor systems. We built a testing system to measure bio-potential signals and used it to evaluate the performance of the circuit. The bio-potential amplifier offers a gain of 53 dB within a bandwidth of 200 Hz-20 kHz. The input-referred rms noise is 2.8 µV. In the asynchronous level crossing ADC, the minimum delta resolution is 4 mV. The input signal frequency of the ADC is up to 5 kHz. The system was fabricated using the AMI 0.5 µm CMOS process. The chip size is 1.5 mm by 1.5 mm. The power consumption of the 4-channel system from a 3.3 V supply is 118.8 µW in the static state and 501.6 µW with a 240 kS/s sampling rate. The conversion efficiency is 1.6 nJ/conversion.
Fluorocarbon and PTFE Thermodegradation and Contamination Modeling in a Space Habitat (1993)

&lt;div class="htmlview paragraph"&gt;The products of thermodegradation of fluorocarbon polymers (found in electrical insulation) will be toxic to space habitat crews, and the monitoring and detection of such contaminants are important to space environmental health. Experiments are therefore being performed on the thermodegradation of a liquid perfluoroalkane mixture (consisting of perfluorohexanes, C&lt;sub&gt;6&lt;/sub&gt;F&lt;sub&gt;14&lt;/sub&gt;, and −5% perfluoropentane, C&lt;sub&gt;5&lt;/sub&gt;F&lt;sub&gt;12&lt;/sub&gt;), similar in structure to polytetrafluoroethylene (PTFE - Teflon), in atmospheres of varying oxygen concentration. PTFE is a common material used on space vehicles for insulation of wires. When PTFE is thermally degraded, such as from the overheating of a wire and subsequent smoldering of the insulation, it may produce toxic compounds ranging from carbonyl fluoride and hydrogen fluoride through perfluorinated aromatic compounds to ultrafine particles. The liquid perfluoroalkane (PFA) mixture is vaporized in the presence of helium, which is used as a carrier gas in this experiment and is acting in place of nitrogen as the non-reactive portion of the atmosphere. The helium and perfluoroalkane vapor can then be mixed with oxygen to yield atmospheres of known concentrations. The mixture is fed into a tube reactor furnace where it is thermally degraded. The resulting thermodegradation products are analyzed by combined gas chromatography/mass spectrometry (GC/MS) for composition. This analysis allows the characterization of the reaction products for simulation models and monitoring and detection systems in space habitats.&lt;/div&gt;
Pattern of retinoblastoma pathway inactivation dictates response to CDK4/6 inhibition in GBM (2010)

Glioblastoma multiforme (GBM) is a fatal primary brain tumor harboring myriad genetic and epigenetic alterations. The recent multidimensional analysis of the GBM genome has provided a more complete view of the landscape of such alterations and their linked pathways. This effort has demonstrated that certain pathways are universally altered, but that the specific genetic events altered within each pathway can vary for each particular patient's tumor. With this atlas of genetic and epigenetic events, it now becomes feasible to assess how the patterns of mutations in a pathway influence response to drugs that are targeting such pathways. This issue is particularly important for GBM because, in contrast to other tumor types, molecularly targeted therapies have failed to alter overall survival substantially. Here, we combined functional genetic screens and comprehensive genomic analyses to identify CDK6 as a GBM oncogene that is required for proliferation and viability in a subset of GBM cell lines and tumors. Using an available small molecule targeting cyclin-dependent kinases (CDKs) 4 and 6, we sought to determine if the specific pattern of retinoblastoma pathway inactivation dictated the response to CDK4/6 inhibitor therapy. We showed that codeletion of CDKN2A and CDKN2C serves as a strong predictor of sensitivity to a selective inhibitor of CDK4/6. Thus, genome-informed drug sensitivity studies identify a subset of GBMs likely to respond to CDK4/6 inhibition. More generally, these observations demonstrate that the integration of genomic, functional and pharmacologic data can be exploited to inform the development of targeted therapy directed against specific cancer pathways.
How to Achieve Better Results Using PASS-Based Virtual Screening: Case Study for Kinase Inhibitors (2018)

Discovery of new pharmaceutical substances is currently boosted by the possibility of utilization of the Synthetically Accessible Virtual Inventory (SAVI) library, which includes about 283 million molecules, each annotated with a proposed synthetic one-step route from commercially available starting materials. The SAVI database is well-suited for ligand-based methods of virtual screening to select molecules for experimental testing. In this study, we compare the performance of three approaches for the analysis of structure-activity relationships that differ in their criteria for selecting of "active" and "inactive" compounds included in the training sets. PASS (Prediction of Activity Spectra for Substances), which is based on a modified Naïve Bayes algorithm, was applied since it had been shown to be robust and to provide good predictions of many biological activities based on just the structural formula of a compound even if the information in the training set is incomplete. We used different subsets of kinase inhibitors for this case study because many data are currently available on this important class of drug-like molecules. Based on the subsets of kinase inhibitors extracted from the ChEMBL 20 database we performed the PASS training, and then applied the model to ChEMBL 23 compounds not yet present in ChEMBL 20 to identify novel kinase inhibitors. As one may expect, the best prediction accuracy was obtained if only the experimentally confirmed active and inactive compounds for distinct kinases in the training procedure were used. However, for some kinases, reasonable results were obtained even if we used merged training sets, in which we designated as inactives the compounds not tested against the particular kinase. Thus, depending on the availability of data for a particular biological activity, one may choose the first or the second approach for creating ligand-based computational tools to achieve the best possible results in virtual screening.