gebhart/patrepeval huggingface dataset:
Chiral recognition by cyclic oligosaccharides. Enantioselective complexation of binaphthyl derivatives with cyclodextrins (1993)

Abstract Chiral recognition of binaphthyl derivatives, such as 1,1′-bi-2-naphthol (1), 1,1′-binaphthyl-2,2′-diyl hydrogen phosphate (2), and 2,2′-dihydroxy-1,1′-binaphthyl-3,3′-dicarboxylic acid (3), by cyclodextrins (CDxs) has been studied. The S enantiomers of 1 and 2 are bound to heptakis(2,3,6-tri-O-methyl)-β-CDx (TMe-β-CDx) as well as β-CDx more strongly than the R enantiomers. The molecular mechanics and molecular dynamics calculations for the 1:1 complex of 1 and β-CDx suggest that more effective van der Waals contacts and intermolecular hydrogen bonding stabilize the complex of S-1 compared with that of R-1. Meanwhile the R enantiomer of 3 is the preferable guest for β- and TMe-β-CDxs. Circular dichroism spectroscopy suggests that the complex of S-3 is more unstable than that of R-3 because the dihedral angle of the naphthalene planes of S-3 needs to be reduced for forming the inclusion complex. The enantiomers of the guest binaphthyls are completely separated by means of capillary zone electrophoresis (CZE) when TMe-β-CDx is used as a separating agent. The results of the CZE correspond well with those of the binding constants of the inclusion complexes.
A Solvolysis Model for 2-Chloro-2-methyladamantane Based on the Linear Solvation Energy Approach (2004)

Solvolysis/dehydrohalogenation rates of 2-chloro-2-methyladamantane (CMA) in 15 hydrogen-bond acidic and/or basic solvents are studied. The rates of reaction in these solvents have been correlated with the solvation equation developed by Kamlet, Abraham, and Taft. The linear solvation energy relationship (LSER) derived from this study is given by the following equation: log k = -5.409 + 2.219 + 2.505alpha(1) - 1.823beta(1) where , alpha(1), and beta(1) are the solvation parameters that measure the solvent dipolarity/polarizability, hydrogen-bond acidity (electrophilicity), and hydrogen-bond basicity (nucleophilicity). A high correlation coefficient (r = 0.996, SD = 0.191) was achieved. The cavity term, which includes the Hildebrand parameter for solvent cohesive energy density, delta(H), was not found to be statistically significant for this reaction substrate. The resulting equation allows calculated rates of reaction in other solvents and provides insight into the reaction pathway. In a previously reported correlation for another tertiary chloride, tert-butyl chloride (TBC), the coefficients for alpha(1) and are significantly larger and the coefficient for is statistically significant. In addition, the coefficient for beta(1) in the TBC correlation is positive, rather than negative, indicating that the transition states for TBC and CMA are significantly different. These results demonstrate why the uses of simple solvolytic correlation methods may be invalid even for comparisons of similar type substrates, e.g., tertiary chlorides. Also, these results provide confidence in the use of multiple linear regression analysis for predicting solvolytic rates in additional solvents.
Differential Expression in Phanerochaete chrysosporium of Membrane-Associated Proteins Relevant to Lignin Degradation (2008)

Fungal lignin-degrading systems likely include membrane-associated proteins that participate in diverse processes such as uptake and oxidation of lignin fragments, production of ligninolytic secondary metabolites, and defense of the mycelium against ligninolytic oxidants. Little is known about the nature or regulation of these membrane-associated components. We grew the white rot basidiomycete Phanerochaete chrysosporium on cellulose or glucose as the carbon source and monitored the mineralization of a (14)C-labeled synthetic lignin by these cultures to assess their ligninolytic competence. The results showed that the cellulose-grown cultures were ligninolytic, whereas the glucose-grown ones were not. We isolated microsomal membrane fractions from both types of culture and analyzed tryptic digests of their proteins by shotgun liquid chromatography-tandem mass spectrometry. Comparison of the results against the predicted P. chrysosporium proteome showed that a catalase (Joint Genome Institute P. chrysosporium protein identification number [I.D.] 124398), an alcohol oxidase (126879), two transporters (137220 and 132234), and two cytochrome P450s (5011 and 8912) were upregulated under ligninolytic conditions. Quantitative reverse transcription-PCR assays showed that RNA transcripts encoding all of these proteins were also more abundant in ligninolytic cultures. Catalase 124398, alcohol oxidase 126879, and transporter 137220 were found in a proteomic analysis of partially purified plasma membranes from ligninolytic P. chrysosporium and are therefore most likely associated with the outer envelope of the fungus.
Acinetobacter baumannii ventilator-associated pneumonia: epidemiology, clinical characteristics, and prognosis factors (2013)

A. baumannii VAP is associated with a high mortality. Hemodynamic impairment is predictive of a poor outcome.
Catalytic Activity of Polyethylene Glycols in the Reduction of Carbonyl Compounds Under Phase-Transfer Catalyzed Conditions (1982)

Abstract Polyethylene glycols and their dimethyl ethers of different average molecular weight as cheap and on an industrial scale available products can be used as phase-transfer catalysts in anion promoted two-phase borohydride reduction.
A Novel Trans-Scale Precision Positioning Stage Based on the Stick-Slip Effect (2012)

This article focuses on developing a novel trans-scale precision positioning stage based on the stick-slip effect. The stick-slip effect is introduced and the rigid kinematics model of the stick-slip driving is established. The forward and return displacement equations of each step of the stick-slip driving are deduced. The relationship of return displacement and the acceleration produced by friction are obtained according to displacement equations. Combining with LuGre friction model, the flexible dynamics model of the stick-slip driving is established and simulated by using Simulink software. Simulation results show that the backward displacement will reduce with the acceleration of the slider produced by dynamic friction force, the rigid kinematics model is also verified by simulation results which are explained in further detail in the article.
Differences in the developmental patterns of three microtubule- associated proteins in the rat cerebellum (1985)

The developmental distribution patterns of microtubule-associated proteins (MAPs) 1, 2, and 3 were studied using three monoclonal antibodies. Immunochemical staining at the light and electron microscopic levels demonstrated the specific localization of each MAP in different cellular and subcellular compartments. MAP2, which is specifically associated with dendritic microtubules in the adult brain, is strictly associated with growing dendrites from the onset of their formation. MAP3, a recently described MAP of Mr = 180,000, which in the adult brain is associated with neurofilament-rich axons and glial processes, is associated with axons from the beginning of outgrowth. Although MAP3 is not detectable in granule cells and their parallel fiber axons in the mature cerebellum, it does appear transitorily in these axons during development. During neuronal differentiation, MAP1 is found first in axons and only later in dendrites where the highest concentrations are eventually to be found. These results indicate that the combined appearance of MAP1 and MAP2 (dendrites) or MAP1 and MAP3 (axons) correlates with the appearance of morphologically distinct microtubules and provide further evidence that specific MAPs are molecular determinants of dendritic and axonal formation.
Fast multiple reference frame motion estimation for H.264/AVC (2006)

Multiple reference frame motion compensation is a new feature introduced in H.264/MPEG-4 AVC to improve video coding performance. However, the computational cost of multiple reference frame motion estimation (MRF-ME) is very high. In this paper, we propose an algorithm that takes into account the correlation/continuity of motion vectors among different reference frames. We show that the algorithm effectively reduces the computations of MRF-ME, and achieves similar coding gain compared to the motion search approaches in the reference software.
Communication between the Perilymphatic Scalae and Spiral Ligament Visualized by in vivo MRI (2005)

We evaluated the transport of Gadolinium-diethylenetriaminepentaacetate-bismethylamide (Gd-DTPA-BMA) through the round window (RW) membrane into the perilymphatic space with 4.7-T MRI in an animal study and 1.5-T MRI in humans. After administration of Gd-DTPA-BMA onto the intact RW membrane of guinea pig, Gd-DTPA-BMA uptake was observed in the basal turn and part of the second turn within 40 min. The scala tympani, scala vestibuli, the fibrous part of the spiral ligament and semicircular canal all showed uptake of Gd-DTPA-BMA. All turns of the cochlea were filled with Gd within 10 min in the perforated RW membrane administration group and within 30 min in the intravenous administration group. In patients who accepted middle ear injection of Gd-DTPA-BMA, uptake was observed within 2 h in the basal turn and semicircular canal. After 12 h the apex did still not show any uptake. Gd-DTPA-BMA is transported from the RW to the semicircular canal, the scala tympani and scala vestibuli without passing the helicotrema.
ATIM-24. INTERIM RESULTS OF A PHASE II MULTICENTER STUDY OF THE CONDITIONALLY REPLICATIVE ONCOLYTIC ADENOVIRUS DNX-2401 WITH PEMBROLIZUMAB (KEYTRUDA) FOR RECURRENT GLIOBLASTOMA; CAPTIVE STUDY (KEYNOTE-192) (2018)

BACKGROUND
DNX-2401 (tasadenoturev) is a replication-competent, tumor-selective, oncolytic adenovirus. A dose-escalating, Phase II study of a single intratumoral injection of DNX-2401 with pembrolizumab to determine optimal dose, safety and efficacy is ongoing and enrolling up to 48 patients with recurrent glioblastoma. Key inclusion criteria include patients with a single lesion at first or second recurrence for which resection is not possible or planned.
Aptamers as Modular Components of Therapeutic Nucleic Acid Nanotechnology (2019)

Nucleic acids play a central role in all domains of life, either as genetic blueprints or as regulators of various biochemical pathways. The chemical makeup of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), generally represented by a sequence of four monomers, also provides precise instructions for folding and higher-order assembly of these biopolymers that, in turn, dictate biological functions. The sequence-based specific 3D structures of nucleic acids led to the development of the directed evolution of oligonucleotides, SELEX (systematic evolution of ligands by exponential enrichment), against a chosen target molecule. Among the variety of functions, selected oligonucleotides named aptamers also allow targeting of cell-specific receptors with antibody-like precision and can deliver functional RNAs without a transfection agent. The advancements in the field of customizable nucleic acid nanoparticles (NANPs) opened avenues for the design of nanoassemblies utilizing aptamers for triggering or blocking cell signaling pathways or using aptamer-receptor combinations to activate therapeutic functionalities. A recent selection of fluorescent aptamers enables real-time tracking of NANP formation and interactions. The aptamers are anticipated to contribute to the future development of technologies, enabling an efficient assembly of functional NANPs in mammalian cells or <i>in vivo</i>. These research topics are of top importance for the field of therapeutic nucleic acid nanotechnology with the promises to scale up mass production of NANPs suitable for biomedical applications, to control the intracellular organization of biological materials to enhance the efficiency of biochemical pathways, and to enhance the therapeutic potential of NANP-based therapeutics while minimizing undesired side effects and toxicities.
MULTIPLE STATES OF A VISCOUS FREE SURFACE FLOW: TRANSITION FROM PRE‐METERED TO A METERING INFLOW (1997)

In a forward-roll coating gap or nip, steady laminar flow of liquid between counter-rotating cylinders or rolls is used to split the flow into a coated layer on one roll and a rejected layer on the other. Both layers have free surfaces in contact with air. Liquid may be carried into the gap as a layer on one or both rolls. If the arriving layer is not too thick, all of the liquid flows through the gap, a situation called pre-metered. If the arriving layer is too thick, part of the liquid is rejected and runs back down the lower roll. The flow rate through the gap is said to be metered and is not known a priori. The transition from a pre-metered regime to the metered situation was examined by solving the Navier–Stokes system for steady, two-dimensional flow in a domain bounded by free surfaces, two rigid roll surfaces and chosen inflow and outflow surfaces. The free boundary condition, as described by Papanastasiou et al. (Int. j. numer methods fluids, 14, 587 (1992)), was explored and proved to accommodate both the pre-metered and metered regimes. A run-back flow state across the synthetic inlet plane was obtained, provided a condition on the thickness of the arriving layer was replaced by a kinematic condition at a certain stage. The coupled equation system was solved by Galerkin's method with finite element basis functions. The resulting non-linear algebraic system was solved by Newton's method with initialization by pseduo-arc-length continuation and automatic parameter step adjustment. Results show the existence of multiple solutions which can lead to hysteresis. Flow regime maps were constructed to portray the operating parameter range in which a coating bead can exist and the ranges in which a coating gap operates in either the pre-metered or the metering regime. © 1997 by John Wiley & Sons, Ltd. Int. j. numer. methods fluids 24: 813–831, 1997.
A computer-based tool for generation of progress notes. (1993)

IVORY, a computer-based tool that uses clinical findings as the basic unit for composing progress notes, generates progress notes more efficiently than does a character-based word processor. IVORY's clinical findings are contained within a structured vocabulary that we developed to support generation of both prose progress notes and SNOMED III codes. Observational studies of physician participation in the development of IVORY's structured vocabulary have helped us to identify areas where changes are required before IVORY will be acceptable for routine clinical use.
Type I interferon promotes cell-to-cell spread ofListeria monocytogenes (2016)

Type I interferons (IFNs) play a critical role in antiviral immune responses, but can be deleterious to the host during some bacterial infections. Listeria monocytogenes (Lm) induces a type I IFN response by activating cytosolic antiviral surveillance pathways. This is beneficial to the bacteria as mice lacking the type I IFN receptor (IFNAR1<sup>-/-</sup> ) are resistant to systemic infection by Lm. The mechanisms by which type I IFNs promote Lm infection are unclear. Here, we show that IFNAR1 is required for dissemination of Lm within infection foci in livers of infected mice and for efficient cell-to-cell spread in vitro in macrophages. IFNAR1 promotes ActA polarization and actin-based motility in the cytosol of host cells. Our studies suggest type I IFNs directly impact the intracellular life cycle of Lm and provide new insight into the mechanisms used by bacterial pathogens to exploit the type I IFN response.
Comparison of Bacterial Community Composition of Primary and Persistent Endodontic Infections Using Pyrosequencing (2020)

Elucidating the microbial ecology of endodontic infections (EI) is a necessary step in developing effective intra-canal antimicrobials. The aim of the present study was to investigate the bacterial composition of symptomatic and asymptomatic primary and persistent infections in a Greek population, using high throughput sequencing methods.
Software testing research and software engineering education (2010)

Software testing research has not kept up with modern software system designs and applications, and software engineering education falls short of providing students with the type of knowledge and training that other engineering specialties require. Testing researchers should pay more attention to areas that are currently relevant for practicing software developers, such as embedded systems, mobile devices, safety-critical systems and other modern paradigms, in order to provide usable results and techniques for practitioners. We identify a number of skills that every software engineering student and faculty should have learned, and also propose that education for future software engineers should include significant exposure to real systems, preferably through hands-on training via internships at software-producing firms.
Parametric Macromodeling for Tabulated Data Based on Internal Passivity (2010)

We present a new parametric macromodeling technique for admittance and impedance input-output representations parameterized by design variables such as geometric and material parameters. Stability and passivity of the parametric macromodel are guaranteed over a user defined range of design parameter values, while poles and residues are parameterized indirectly. Numerical results validate the proposed parametric macromodeling approach.
Practical Characterization of Quantum Devices without Tomography (2011)

Quantum tomography is the main method used to assess the quality of quantum information processing devices. However, the amount of resources needed for quantum tomography is exponential in the device size. Part of the problem is that tomography generates much more information than is usually sought. Taking a more targeted approach, we develop schemes that enable (i) estimating the fidelity of an experiment to a theoretical ideal description, (ii) learning which description within a reduced subset best matches the experimental data. Both these approaches yield a significant reduction in resources compared to tomography. In particular, we demonstrate that fidelity can be estimated from a number of simple experiments that is independent of the system size, removing an important roadblock for the experimental study of larger quantum information processing units.
FIELD-INDUCED MAGNETIC PHASE TRANSITION IN A SINGLET GROUND STATE DIMER SYSTEM (1988)

AC-susceptibility measurements on the singlet-ground state system Cs3Cr2Br9 are extended to very low temperatures (46 mK) and high applied magnetic fields (12 T). The resulting phase diagram is shown to exhibit features at variance with recent soft-mode and molecular-field models for this system.
Bidirectional cross-kingdom RNAi and spray-induced gene silencing for plant disease control (2017)

Small RNAs (sRNAs) are a class of short non-coding RNAs that mediate gene silencing in a sequence-specific manner. We have demonstrated that some sRNAs from eukaryotic pathogens, such as Botrytis cinerea, the fungal pathogen that causes grey mold disease on more than 1000 plant species, could be translocated into host plant cells and suppress host immunity genes for successful infection. This finding represented the first example of naturally occurring Cross-Kingdom RNAi in host – pathogen interactions. These sRNAs act as a new class of pathogen effectors that translocate into host cells to suppress host immunity. Recently we have found that transgenic plants expressing hairpin RNAs that targeting Botrytis Dicer 1and Dicer 2 genes could effectively block the generation of fungal sRNA effectors and suppress grey mold disease. This strategy can be adapted to simultaneously control multiple fungal diseases. We show that Arabidopsis plants expressing hairpin RNAs that simultaneously target DCL genes of B. cinerea and V. dahliae show enhanced disease resistance to both pathogens. These results also suggest that sRNA trafficking is bi-directional and sRNAs could move from the host cells to the interacting pathogens. Most strikingly, we discovered that Botrytis could take up double-stranded RNAs and sRNAs from the environment. Applying sRNAs or dsRNAs that target Botrytis Dicer genes on the surface of fruits, vegetables and flowers significantly inhibits grey mold disease. Such pathogen gene-targeting RNAs represent a new generation of environmentally friendly fungicides.
Weight and Friction Display by Controlling Slip Condition at the Fingertip (2012)

In this paper, a novel haptic device is proposed that gives weight and friction illusions. Sensing a slip condition at the fignertip plays an important role to estimate the weight and friction of an object. This fact suggests that controlling the contact condition could yield weight and friction illusions. Based on this idea, a prototype device was developed that controls the contact condition between a fingertip and a rigid plate based on a camera-based eccentricity control. The desired eccentricity profile is given from an analytical relationship among the amount of the slip, the deformation of the contact area, and the investigation of human's force control strategy. The performance of the developed device was evaluated through human experiments. The experimental results show statistically significant difference among presented weight and friction conditions.
DEVELOPMENT OF SPOKE CAVITIES FOR HIGH-VELOCITY APPLICATIONS (2012)

In response to recent interest in alternatives to TM-type cavities for low-frequency, high-velocity applications we have initiated a program for the development of multispoke superconducting cavities. We have completed the electromagnetic design for two-spoke cavities operating at 325, 352, 500, and 700 MHz with a design velocity of β0 = 0.82 or β0 = 1. We present the results of the optimization, higher order mode (HOM) analysis, multipacting analysis, and an initial analysis of multipole effects of the fundamental accelerating mode.
Laparoscopy in the Emergency Room (2006)

OBGYN.net Conference Coverage From Society of Laparoscopic Surgeons New York, December, 1999
The 3-D inelastic analysis methods for hot section components: Brief description (1982)

Advanced 3-D inelastic structural/stress analysis methods and solution strategies for more accurate yet more cost-effective analysis of components subjected to severe thermal gradients and loads in the presence of mechanical loads, with steep stress and strain gradients are being developed. Anisotropy, time and temperature dependent plasticity and creep effects are also addressed. The approach is to develop four different theories, one linear and three higher order theories (polynomial function, special function, general function). The theories are progressively more complex from linear to general function in order to provide streamlined analysis capability with increasing accuracy for each hot section component and for different parts of the same component according to the severity of the local stress, strain and temperature gradients associated with hot spots, cooling holes and surface coating cracks. To further enhance the computational effectiveness, the higher order theories will have embedded singularities (cooling passages, for example) in the generic modeling region. Each of the four theories consists of three formulation models derivable from independent theoretical formulations. These formulation models are based on: (1) mechanics of materials; (2) special finite elements; and (3) an advanced formulation to be recommended by the contractor.
Breviarium de Motu Simulato Ad Atomos Pertinenti (2022)

Abstract In this paper I will present a personal recollection of the development of molecular‐dynamics‐based atomistic simulations in the last forty years. The paper is not meant as a historical account but rather a personal and certainly biased view of the ideas that have underpinned the author's research, allowing ever more complex systems to be studied in an ever more realistic way.