gebhart/patrepeval huggingface dataset:
ChemInform Abstract: DERIVATIVES OF 2‐AMINO‐1,2,3,4‐TETRAHYDRONAPHTHALENE. VII. AROYL ESTERS OF CIS‐ AND TRANS‐2‐DIMETHYLAMINO‐3‐HYDROXY‐5,8‐DIMETHOXY‐1,2,3,4‐TETRAHYDRONAPHTHALENES (1983)

Abstract Die Umsetzung des Aminohydroxytetralins (I) mit den Benzoylchloriden (II) liefert die Aminoaroyloxytetraline (III) als Hydrochloride.
Inference of surfaces, 3-D curves, and junctions from sparse 3-D data (2002)

Addresses the problem of obtaining surface information from a sparse set of 3-D data in the presence of spurious noise samples. The input can be in the form of points, or points with an associated normal, allowing for both position and direction to be corrupted by noise. This is the typical input obtained from matching sparse features in stereo or motion, assuming that the observed scene is rigid. Most approaches treat the problem as an interpolation problem, solved by fitting a surface such as a membrane or thin plate which minimizes some functional. The authors argue that these physical constraints are not sufficient and propose to impose additional perceptual constraints such as good continuation and "co-surfacity". These constraints allow the authors to not only infer surfaces, but also detect surface discontinuities at the same time. The method imposes no restriction on genus, number of discontinuities, number of objects, and is non-iterative. The result is in the form of three dense saliency maps for surfaces, intersections between surfaces, and 3-D junctions. These saliency maps can then be used to guide a 'marching' process to generate a description (e.g. a triangulated mesh) making information about surfaces, space curves, and 3-D junctions explicit. The authors present results on computer-generated and real data having multiple objects, varying curvature, and of different genus.
A Hydrostatically Actuated Piston and Hydraulic System for Deep-Sea Free Vehicle Applications (1978)

A piston actuated by hydrostatic pressure at ocean depths up to 6 km is used to provide a controlled source of hydraulic fluid at above-ambient pressure. This fluid energy is used to collect box cores of deep-sea sediment and ferromanganese nodules from a free-vehicle instrument platform. At the completion of the coring operation, the same hydrostatically actuated piston is used to release ballast and to extract the vehicle and its cores from the sediment.
Learning to Give Checkable Answers with Prover-Verifier Games (2021)

Our ability to know when to trust the decisions made by machine learning systems has not kept up with the staggering improvements in their performance, limiting their applicability in high-stakes domains. We introduce Prover-Verifier Games (PVGs), a game-theoretic framework to encourage learning agents to solve decision problems in a verifiable manner. The PVG consists of two learners with competing objectives: a trusted verifier network tries to choose the correct answer, and a more powerful but untrusted prover network attempts to persuade the verifier of a particular answer, regardless of its correctness. The goal is for a reliable justification protocol to emerge from this game. We analyze variants of the framework, including simultaneous and sequential games, and narrow the space down to a subset of games which provably have the desired equilibria. We develop instantiations of the PVG for two algorithmic tasks, and show that in practice, the verifier learns a robust decision rule that is able to receive useful and reliable information from an untrusted prover. Importantly, the protocol still works even when the verifier is frozen and the prover's messages are directly optimized to convince the verifier.
Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period (2018)

Abstract The Vibrio cholerae biotype ‘El Tor’ is responsible for all current epidemic and endemic cholera outbreaks worldwide. These outbreaks are clonal and are hypothesized to originate from the coastal areas near the Bay of Bengal where the lytic bacteriophage ICP1 specifically preys upon these pathogenic outbreak strains. ICP1 has also been the dominant bacteriophage found in cholera patient stool since 2001. However, little is known about its genomic differences between ICP1 strains collected over time. Here we elucidate the pan-genome and phylogeny of ICP1 strains by aligning, annotating and analyzing the genomes of 19 distinct isolates collected between 2001 and 2012. Our results reveal that ICP1 isolates are highly conserved and possess a large core-genome as well as a smaller, somewhat flexible accessory-genome. Despite its overall conservation, ICP1 strains have managed to acquire a number of unknown genes as well as a CRISPR-Cas system, which is known to be critical for its ongoing struggle for co-evolutionary dominance over its host. This study describes a foundation on which to construct future molecular and bioinformatic studies of this V. cholerae -associated bacteriophages.
Tailoring cavitation nuclei for biomedical applications (2018)

Cavitation, or the creation and oscillation of bubbles, has a pivotal role in a variety of biomedical applications that involve ultrasound. For example, stable oscillating bubbles (stable cavitation) can reversibly permeabilize biological interfaces, including cell membranes and the blood-brain barrier. Bubbles that collapse inertially (inertial cavitation) radiate broadband emissions that can enhance ultrasound-mediated heating and thermal ablation. These cavitation-mediated bioeffects may provide medical benefit provided the location, type, and intensity of cavitation activity can be controlled. Microfluidic devices can be used to produce monodisperse microbubbles coated with viscoelastic shells that promote nonlinear oscillations. Liquid perfluorocarbon nanoemulsions can serve as long-circulating cavitation nuclei capable of extravasating into extravascular tissues. Using these technologies, cavitation nuclei can be tailored to provide a predictable acoustic response in a targeted location, thus providing a desired biological outcome.
Glaucoma Biomarker Discovery (2007)

Purpose: To develop a blood test for predicting susceptibility to primary open angle glaucoma (POAG) and for monitoring the efficacy of POAG therapeutics. Methods: Blood was collected from clinically documented POAG and agematched normal control (CTRL) donors at the Cole Eye Institute, Cleveland Clinic, Louis Stokes Cleveland VA Medical Center and at the Aravind Eye Hospital, Madurai, India. Plasma were fractionated on C18 reverse phase magnetic beads and analyzed by MALDI TOF/TOF mass spectrometry. Bioinformatic cluster analysis for peptidomic patterns and cross validation was performed with GeneSpring software. Results: Plasma from 429 donors was analyzed in this preliminary study. For USA donors (n = 378), MALDI TOF mass spectrometric analyses of 249 POAG and 138 CTRL plasma has allowed correct prediction of 96% as either POAG or normal based on peptidomic profiles. For Indian donors (n = 42), mass spectrometric analyses of 22 POAG and 20 CTRL provided 90% correct prediction as either POAG or normal. The peptide patterns from Indian and US plasma exhibit distinct differences. Relative to normal controls, the mean intensity of peptide m/z 1896 was elevated about 95% in the Indian POAG plasma and 160% in US POAG plasma. Peptide m/z 1896 has been sequenced and determined to be from complement C4B. Conclusions: These preliminary results provide proof of principle that plasma peptidomic patterns offer potential utility in predicting POAG susceptibility and monitoring therapeutic efficacy. Peptidomic pattern differences between USA and Indian plasma may reflect ethnic and environmental differences between the populations. The significance of the elevated complement C4B peptide in POAG plasma remains to be determined. Such findings may provide insights into the mechanism of POAG pathogenesis. LOW HIGH
Unidirectional Liquid Manipulation Via an Integrated Mesh with Orthogonal Anisotropic Slippery Tracks (2019)

Abstract The rational manipulation of fluid behavior by functional interfaces plays an indispensable role in the development of advanced materials and devices involving liquid/solid interactions. Previous examples of the liquid “diode” that allows fluid penetration in only one direction rely mainly on the remarkable wettability gradient/contrast. Inspired by the wetting phenomena of the rice leaf and the Pitcher plant, an integrated mesh with orthogonal anisotropic slippery tracks (IMOAS) is presented here that can realize similar unidirectional droplet penetration using a distinct mechanism. The unidirectional droplet penetration can be conveniently switched via the 90° rotation of the IMOAS, showing a highly controllable liquid manipulation. The droplet tends to slip on the surface, which can maximize the contact area between the liquid and the tracks, and complies with the principle of the lowest surface energy. Based on this unique liquid controlling strategy, droplet manipulation of the IMOAS during fog harvesting and droplet self‐regulation has been conducted to illustrate its potential applications. The current design could aid the understanding of liquid unidirectional penetration and unlock additional possibilities for the optimization of fluid‐related systems.
Biologics for idiopathic inflammatory myopathies (2017)

Further research is required to evaluate the role of newer therapies such as tocilizumab (anti-interleukin-6), abatacept (inhibition of T-cell costimulation), sifalimumab (anti-interferonα) and ruxolitinib, (Janus kinase inhibitor) given their biological plausibility and encouraging recent small case series results. Future clinical trials should consider the targeting of biomarkers implicated in the etiopathogenesis of IIM, predictive factors of treatment response, recent revisions in IIM classification criteria, as well as newly developed data-driven response criteria which employ validated core set measures.
The Influence of Melt Impregnation Parameters on the Degree of Impregnation of a Polypropylene/Glass Fibre Prepreg (1992)

The melt impregnation process to produce a high quality thermoplastic prepreg is studied. Raw materials used in the experimental work are polypropylene and glass fibre. A laboratory scale melt impregnation line is developed with a melt impregna tion die of cross head type. A methodology to determine the degree of impregnation is described. The influence of processing parameters on the degree of impregnation is evalu ated, and the process is developed to produce a well impregnated prepreg. Two different forms of thermoplastic prepreg are produced: a tow and a tape. The influence of the fol lowing processing parameters on the degree of impregnation are studied: impregnation time, polymer temperature, temperature of heated rods inside the die, use of pins inside the impregnation die in different positions, vacuum in the roving infeed stage, prepreg ten sion, MFR-value of the polymer matrix, use of coupling agents with the polypropylene matrix, ultrasonic vibration in the molten polymer and use of two different infeed geome tries of the polymer melt.
Inhibition of Complement by Mouse Serum: Selective Inactivation of the Fourth Component of Human Complement (1977)

Abstract Bound human C4b on EAC4 is rapidly inactivated in the presence of murine serum reagents. The functional characteristics of this inactivation suggest that it is probably caused by factor(s) homologous to human C3bI-C4bI: inactivation is temperature-dependent and occurs without concomitant consumption of the inactivator(s); loss of hemolytic function is associated with the cleavage of the bound C4b into C4c, which is released, and C4d, which is retained on the cell membrane. Murine serum reagents inhibit bound human C4b far more efficiently than C3b and may therefore be employed to selectively inhibit C4b.
Theory of Electrochemical Diodes (1960)

The electric behaviour of electrochemical diodes, consisting of a pair of indifferent electrodes immersed in an electrolytic solution being capable of reversible oxidation-reduction, was investigated theoretically. The general current-voltage relation was obtained by solving the differential equation of diffusion of ions with the proper boundary conditions. The non-ohmic property, the shunting effect for rapidly changing voltage and the rectifying action were deduced.
Abstract 82: CYP3A4 promotes mammary carcinoma angiogenesis in a cell iIntrinsic fashion. (2013)

Abstract Cytochrome P450 3A4 (CYP3A4) has been recently been implicated in breast cancer cell growth and survival, but the role of cell intrinsic CYP3A4 in breast cancer cell engraftment and angiogenesis is unknown. Previously, we have characterized CYP3A4 knock down lines in which CYP3A4 is stably suppressed [J Biol Chem. 2011 May 20;286(20):17543-59]. The CYP3A4 knock down lines exhibit reduced proliferation and clonogenicity in vitro. We therefore tested in an estradiol dependent nude mouse mammary fat pad xenograft model whether the MCF-7 3-18 line (CYP3A4 shRNA), in which CYP3A4 protein levels are suppressed by 60%, exhibits reduced growth compared to a non-target line MCF-7 NT2. Before implantation, the suppression of CYP3A4 mRNA in the shRNA compared to NT2 cells was confirmed by qPCR. After 46 days of monitored tumor growth, the MCF-7 NT2 tumors exhibited a median size of 27±3 mm3 (median±SEM) compared to 2±0.6 mm3 for the MCF-7 CYP3A4 shRNA tumors. Tumor growth was modeled by a Gompertzian method and the difference was statistically significant (P=0.0018). The mammary fat pads were removed after sacrifice at the end of the experiment, inked, oriented and subjected to z-sectioning. All mice exhibited tumors. The CYP3A4 shRNA tumors exhibited necrosis (5 of 6 evaluable mice) whereas the NT2 control tumors did not (0 of 6 evaluable mice) (P=0.0152; two tailed Fisher's exact test). Angiogenesis was measured by CD31 immunohistochemical staining using an automated microvessel image analysis algorithm (Image Analysis Toolbox, Aperio Technologies) allowing measurement of percentage of area occupied by CD31 staining cells at the cortex of tumor nodules. Percent area occupied by CD31 positive cells was 2.69±0.46 vs. 0.67±0.64 (mean±SEM) (P=0.033). Together, these results suggest that cell intrinsic CYP3A4 is important for mammary carcinoma growth and angiogenesis in a xenograft model. Citation Format: Zhijun Guo, Beverly Norris, Jonathan Henriksen, Monique Morgan, Michael Maher, Robert Schumacher, Robin Bliss, Haitao Chu, Kalpna Gupta, Stephen Schmechel, David Potter. CYP3A4 promotes mammary carcinoma angiogenesis in a cell iIntrinsic fashion. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 82. doi:10.1158/1538-7445.AM2013-82
Methicillin-ResistantStaphylococcus aureus: A Community Health Threat (2010)

Methicillin-resistant Staphylococcus aureus (MRSA), one of the most common causes of infections, has been traditionally recognized as a nosocomial pathogen. However, in recent years, its epidemiology has radically changed, being now observed even more frequently in the community, and accounting for > 50% of staphylococcal infections in the US outpatient setting. Community-acquired (CA)-MRSA strains typically cause infections among otherwise healthy individuals, with risk factors differing from those of nosocomial MRSA. The clinical manifestations may range from a furuncle to life-threatening infections, such as necrotizing fasciitis and pneumonia. The antibiotic treatment of these infections may also differ because CA-MRSA strains often retain susceptibility to antimicrobials other than glycopeptides and newer agents. Moreover, the production of toxins, such as the Panton-Valentine leukocidin (PVL), should influence the antibiotic choice because in these cases the use of a combination therapy with antimicrobial agents able to decrease toxin production is suggested. There are still many unanswered key questions regarding the epidemiology, prevention, and treatment of CA-MRSA infections. This article reviews current knowledge of CA-MRSA.
Late Breaking Abstract - MicroRNA signatures in critically ill COVID-19 patients: a bronchial aspirate study (2021)

<bold>Background:</bold> Transcriptomics could provide molecular information on the pathophysiology of COVID-19. <bold>Aims and objectives:</bold> To analyze the host microRNA (miRNA) signature of bronchial aspirates (BAS) from critically ill patients in order to define molecular pathways involved in the disease and identify prognostic biomarkers for fatal outcomes. <bold>Methods:</bold> Two study populations (n=89): 1) critically ill COVID-19 and non-COVID-19 patients; 2) a cohort of COVID-19 patients assisted by invasive mechanical ventilation (IMV). BAS were collected by bronchoaspiration at the ICU. miRNAs were quantified by RT-qPCR. <bold>Results:</bold> The miRNA signature of COVID-19 patients is essentially different from non-COVID-19 patients (five deregulated ratios: miR-122-5p/miR-199a-5p miR-125a-5p/miR-133a-3p, miR-155-5p/miR-486-5p, miR-214-3p/miR-222-3p and miR-221-3p/miR-27a-3p). Five miRNA ratios segregated between survivors and nonsurvivors (miR-1-3p/miR-124-3p, miR-125b-5p/miR-34a-5p, miR-126-3p/miR-16-5p, miR-199a-5p/miR-9-5p and miR-221-3p/miR-491-5p). Functional analyses suggested the implication of miRNAs in fibrosis, coagulation, viral infections, inflammation and immune responses. A prediction model for ICU mortality based on miRNA ratios (miR-125b-5p/miR-34a-5p, miR-199a-5p/miR-9-5p and miR-221-3p/miR-491-5p) showed an optimal discrimination value (AUC 0.85) and outperformed the best clinical predictor (days between first symptoms to IMV initiation, AUC 0.73). Survival analysis confirmed the utility of miRNAs in risk stratification. <bold>Conclusions:</bold> miRNA profiling in respiratory specimens allows risk stratification in COVID-19 patients under IMV and provides information about the factors that mediate the disease and fatal outcomes.
Supplementary Methods from Evolution of the Androgen Receptor Pathway during Progression of Prostate Cancer (2023)

Supplementary Methods from Evolution of the Androgen Receptor Pathway during Progression of Prostate Cancer
Determination of NAPL−Water Interfacial Areas in Well-Characterized Porous Media (2005)

The nonaqueous-phase liquid (NAPL)-water interfacial area is an important parameter which influences the rate of NAPL dissolution in porous media. The aim of this study was to generate a set of baseline data for specific interfacial area for a two-phase-entrapped NAPL-water system in well-characterized porous media and subsequently use these data to evaluate two current theoretical models. The first model tested distributes entrapped NAPL over the pore classes based on Land's algorithm and assumes the resulting blobs to be spherical. The other model is thermodynamically based, assuming that reversible work done on the system results in an increase in interfacial area, such that the area between drainage and imbibition retention curves can be related to the interfacial area. Interfacial tracer tests (IFTT) were used to measure specific entrapped NAPL (hexadecane)-water interfacial areas in columns packed with four grades (12/20, 20/30, 30/40, 40/50) of silica sand. By use of the anionic surfactant dihexylsulfosuccinate (Aerosol MA80), IFTT gave specific interfacial areas between 58 cm(-1) for the finest sand and 16 cm(-1) for the coarsest, compared to values of between 33 and 7 cm(-1) for the first model and between 19 and 5 cm(-1) for the thermodynamic model. Results from the literature suggest that nonspherical blobs shapes occur relatively frequently; hence it is reasonable to suggest that the assumption of spherical NAPL blobs may explain the underprediction by the first model. The thermodynamic model underestimates the interfacial area because it assumes that entrapment occurs only within the largest pores. A modified version of the latter model, allowing entrapment across all pore classes, yielded values between 58 and 13 cm(-1). Of the models tested the modified thermodynamic model best predicts the interfacial area.
Bi‐ISAR sparse imaging algorithm with complex Gaussian scale mixture prior (2019)

The performance of both autofocusing and imaging resolution degrades using the traditional autofocusing and range–Doppler algorithm for bistatic inverse synthetic aperture radar (Bi‐ISAR) with sparse apertures. A Bi‐ISAR sparse imaging algorithm based on complex Gaussian scale mixture (CGSM) prior is proposed to jointly achieve the high‐resolution imaging and autofocusing. First, a sparse basis matrix with the time‐varying bistatic angle is constructed to represent the sparse echo data and the Bi‐ISAR joint with autofocusing imaging model is established based on compressed sensing from sparse apertures. Second, the elements of the target image and the noise are assumed to be a CGSM prior with Gaussian distribution, respectively. Finally, the sparse image reconstruction and phase autofocusing are accomplished by the variational Bayesian expectation maximisation method. The proposed algorithm with the full Bayesian inference can obtain a well‐focused image without manual adjustments of regularisation parameters. Meanwhile, it can avoid the local minimum and structural errors, due to utilising the statistical information of a posterior. Simulated results of electromagnetic numerical data verify the superiority of the algorithm in autofocusing, sparse imaging and noise suppression performance.
Researches on the Noise Models of Valves and DC PLC Filters in UHVDC Transmission Project (2008)

Ultra-high voltage direct current (UHVDC) converter stations produce high levels of carrier frequency noise which can cause harmful interference to power-line carrier and open-wire carrier systems. The noise models of converter valves and converters arranged with two 12-pulse valve groups in series per pole are given. Calculation results of noise interference on dc pole line and electrode line for the Xiangjiaba - Shanghai UHVDC project (plusmn 800 kV 6400 MW) based the noise models are presented and discussed. The PLC filter configuration for the UHVDC project meets the requirements of interference limits calculated by the models.
Interruption of CryAB-Amyloid Oligomer Formation by HSP22 (2006)

An R120G missense mutation in alpha-B-crystallin (CryAB), a small heat-shock protein (HSP), causes a desmin-related cardiomyopathy (DRM) that is characterized by the formation of aggregates containing CryAB and desmin. The mutant CryAB protein leads to the formation of inclusion bodies, which contain amyloid oligomer intermediates (amyloid oligomer) in the cardiomyocytes. To further address the underlying mechanism(s) of amyloid oligomer formation in DRM linked to the CryAB R120G, a recombinant CryAB R120G protein was generated. The purified CryAB R120G protein can form a toxic amyloid oligomer, whereas little immunoreactivity was observed in the wild-type CryAB protein. A native PAGE showed that the oligomerized form was present in the CryAB R120G protein, whereas only a high molecular mass was detected in the wildtype CryAB. The oligomerized CryAB R120G of around 240-480 kDa showed strong positive immunoreactivity against an anti-oligomer antibody. The CryAB R120G amyloid oligomer was unstable and easily lost its conformation by beta-mercaptoethanol and SDS. Recombinant HSP25 or HSP22 proteins can directly interrupt oligomer formation by the CryAB R120G protein, whereas the amyloid oligomer is still present in the mixture of the wild-type CryAB and CryAB R120G proteins. This interruption by HSP25 and HSP22 was confirmed in a cardiomyocyte-based study using an adenoviral transfection system. Blockade of amyloid oligomer formation by HSP25 and HSP22 recovered the ubiquitin proteosomal activity and cellular viability. Blockade of oligomer formation by small HSP may be a new therapeutic strategy for treating DRM as well as other types of amyloid-based degenerative diseases.