gebhart/patrepeval huggingface dataset:
Molecular Dynamics of Pyridine Adsorbed on the Silica Surface (2007)

The molecular dynamics of pyridine adsorbed onto dry high-surface-area silica gel was studied using solid-state deuterium NMR spectroscopy. Selectively and totally deuterated pyridine samples were used to identify the spectral signatures associated with each ring location and to identify the dynamical modes present in the surface adsorbed species. Loading levels corresponding to 0.8 and 0.2 monolayer coverage were studied. At 174 K and 0.8 monolayer, the adsorbed pyridine molecules are found in three motional modes: a fraction is found to be static, a larger fraction is found executing fast discontinuous rotation (180° ring flips) about the pyridine Cγ−N axis, and a very small fraction is found in fast continuous rotation (diffusion) about the pyridine Cγ−N axis, all referred to a 5 × 10-6 s time scale. No evidence of O−H−N rotation about the Si−O bond (“swinging arm” motion) is observed. The pyridine flips and rotations permit measurement of the angle between the Cγ−N axis and each of the Cα−D and Cβ−D axes are found to be 55.9 ± 0.3° and 60.4 ± 0.5°, respectively. As the temperature is lowered, the fraction of static pyridine rings increases, while the fractions of flipping and freely rotating pyridine rings decrease. At 78 K and 0.8 monolayer, pyridine ring flip motion is still observed, implying a very low potential barrier to discontinuous rotation for some of the surface population. At 221 K, the flipping rings dominate, rotating rings are a minority, and no static rings remain. Above 221 K, the chemical exchange rate among pyridine molecules becomes significant and further motional averaging is observed. At 221 K and below, the spectra show no contributions corresponding to intermediate-rate motions; the notable absence of intermediate-rate patterns is explained in terms of a previously proposed model based on a broad distribution of motional correlation times. The surface structures and dynamics with 0.2 monolayer are found to be substantially similar to those found at 0.8 monolayer. These dynamical data are interpreted in terms of the structure of the silica surface as probed by pyridine molecules.
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information (2004)

Sequence composition was found to provide sufficient information to predict the probability of its binding to DNA with nearly 69% sensitivity at 64% accuracy for the considered proteins; sequence neighbourhood and solvent accessibility information were sufficient to make binding site predictions with 40% sensitivity at 79% accuracy. Detailed analysis of binding residues shows that some three- and five-residue segments frequently bind to DNA and that solvent accessibility plays a major role in binding. Although, binding behaviour was not associated with any particular secondary structure, there were interesting exceptions at the residue level. Over-representation of some residues in the binding sites was largely lost at the total sequence level, but a different kind of compositional preference was observed in DNA-binding proteins.
Aligned and Graded Type‐II Ruddlesden–Popper Perovskite Films for Efficient Solar Cells (2018)

Abstract Recently, Ruddlesden–Popper perovskites (RPPs) have attracted increasing interests due to their promising stability. However, the efficiency of solar cells based on RPPs is much lower than that based on 3D perovskites, mainly attributed to their poor charge transport. Herein, a simple yet universal method for controlling the quality of RPP films by a synergistic effect of two additives in the precursor solution is presented. RPP films achieved by this method show (a) high quality with uniform morphology, enhanced crystallinity, and reduced density of sub‐bandgap states, (b) vertically oriented perovskite frameworks that facilitate efficient charge transport, and (c) type‐II band alignment that favors self‐driven charge separation. Consequently, a hysteresis‐free RPP solar cell with a power conversion efficiency exceeding 12%, which is much higher than that of the control device (1.5%), is achieved. The findings will spur new developments in the fabrication of high‐quality, aligned, and graded RPP films essential for realizing efficient and stable perovskite solar cells.
Erratum: Nonlinear-resonance line shapes: Dependence on the transverse intensity distribution of a light beam [Phy. Rev. A 69, 024501 (2004)] (2005)

We were recently made aware of an article 1 published some time before our recent paper 2, which addressed much of the same subject matter. In part of their article, Levi et al. analyzed the effects of a nonuniform transverse beam intensity profile on the line shape of coherent population trapping CPT resonances. Specifically, they derived an expression for the line shape of both the emitted rf power in a CPT maser and the fluorescence spectrum in a traditional CPT experiment, when a laser beam with a Gaussian beam profile is used to excite the resonance. In our paper, we derived an expression equivalent to the latter, which does not correspond to the results of 1. Our result Eq. 13 contains a term,
Long‐range millimetre wave wireless links enabled by travelling wave tubes and resonant tunnelling diodes (2020)

High data rate wireless links are an affordable and easily deployable solution to replace or complement fibre. The wide frequency band available at millimetre waves above 100 GHz can support multi‐gigabit per second data rate. However, the high attenuation due to rain and humidity poses a substantial obstacle to long‐range links. This study describes a wireless system being developed for point‐to‐point links at D‐band (DLINK), above 150 GHz, to enable a full fibre‐on‐air link with more than 1 km range and unprecedented data rate up to 45 Gb/s. The upper end of the D‐band spectrum is used (151.5–174.8 GHz) in full frequency division duplex transmission. The DLINK system consists of a transmitter using a directly modulated resonant tunnelling diode oscillator powered by novel travelling wave tubes. The performance and the small footprint of the front end will make the DLINK system highly competitive to the point‐to‐point links presently available in the market at frequencies below 100 GHz. The innovative approach and the design are oriented to large‐scale productions to satisfy the high data traffic demand of the new 5G infrastructure.
1,4-Addition of Alkyl and Aryl-Aluminums to Cyclic Enones (2008)

The authors report the 1,4-addition of organoaluminum reagents to unactivated β-substituted cyclopentenones, which previously comprised a difficult set of substrates for this reaction. A moderate range of compounds bearing quaternary centers in high enantiomeric purity is produced.
Effects of fringe binarization of multiobject joint transform correlation (1989)

A study of the effect of fringe binarization on the joint transform correlator has shown that the interference fringes for multiple targets could produce false alarms and misses.
Pyrazolo[3,4-d)Pyrimidine 2'-Deoxyribo and 2',3'-Dideoxyribo-Furanosides: Synthesis and Application to Oligonucleotide Chemistry (1989)

Abstract The synthesis of pyrazolo[3,4-d]pyrimidine 2′-deoxyribo-nucleosides with various substituents at C-4 and C-6 (1 4) is described employing either liquid-liquid or solid-liquid phase-transfer glycosylation. From 1a (Z8C7Ad) and 2b (Z8C7Gd) the phosphoramidites 12a, b and 15a, b were synthesized. They were used in automated solid-phase synthesis resulting in the oligonucleotides 16 - 25. Deoxygenation (3′-OH) of 1a and 2b yielded pyrazolo[3,4-d]-pyrimidine 2′,3′-dideoxynucleosides isosteric to ddA, ddG, and ddI.
Chemobehavioural phenomics and behaviour-based psychiatric drug discovery in the zebrafish (2008)

Despite their ubiquity and impact, psychiatric illnesses and other disorders of the central nervous system remain among the most poorly treated diseases. Most psychiatric medicines were discovered due to serendipitous observations of behavioural phenotypes in humans, rodents and other mammals. Extensive behaviour-based chemical screens would likely identify novel psychiatric drugs. However, large-scale chemical screens in mammals are inefficient and impractical. In contrast, zebrafish are very well suited for high-throughput behaviour-based drug discovery. Furthermore, the vast amounts of data generated from large-scale behavioural screens in zebrafish will facilitate a systems-level analysis of how chemicals affect behaviour. Unlike serendipitous discoveries in mammals, a comprehensive and integrative analysis of zebrafish chemobehavioural phenomics may identify functional relationships that would be missed by more reductionist approaches. Thus, behaviour-based chemical screens in the zebrafish may improve our understanding of neurobiology and accelerate the pace of psychiatric drug discovery.
Re: the association of viral infection and chronic allograft nephropathy with graft dysfunction after renal transplantation (2003)

CMV disease was a significant cause of early graft dysfunction, whereas the presence of chronic allograft nephropathy was the main determinant of poor long-term graft function. The role of viral infections in chronic allograft nephropathy deserves further investigation.
Direct measurement of the absorption coefficient for the P1(7) transition in HF (1975)

The absorption coefficient for the P1(7) transition in pure HF gas has been measured using resonant radiation from an HF laser. It was found that the Doppler-broadened absorption coefficient is equal to the pressure-broadened absorption coefficient at a pressure of 16 Torr.
Switching Dynamics Between Two Movement Patterns Varies According to Time Interval (2016)

This study investigated the regularity that characterizes the behavior of dissipative dynamical systems excited by external temporal inputs for pointing movements. Right-handed healthy male participants were asked to continuously point their right index finger at two light-emitting diodes (LEDs) located in the oblique left and right directions in front of them. These movements were performed under two conditions: one in which the direction was repeated and one in which the directions were switched on a stochastic basis. These conditions consisted of 12 tempos (30, 36, 42, 48, 51, 54, 57, 60, 63, 66, 69, and 72 beats per minute). Data from the conditions under which the input pattern was repeated revealed two different trajectories in hyper-cylindrical state space [Formula: see text], whereas the conditions under which the inputs were switched induced transitions between the two trajectories, which were considered to be excited attractors. The transitions between the two excited attractors were characterized by a self-similar structure. Moreover, the correlation dimensions increased as the tempos increased. These results suggest a relationship of [Formula: see text] ([Formula: see text] is the switching-time length; i.e. the condition) between temporal input and pointing behavior and that continuous pointing movements are regular rather than random noise.
Modern imaging of cholangitis (2021)

Cholangitis refers to inflammation of the bile ducts with or without accompanying infection. When intermittent or persistent inflammation lasts 6 months or more, the condition is classified as chronic cholangitis. Otherwise, it is considered an acute cholangitis. Cholangitis can also be classified according to the inciting agent, <i>e.g.</i> complete mechanical obstruction, which is the leading cause of acute cholangitis, longstanding partial mechanical blockage, or immune-mediated bile duct damage that results in chronic cholangitis.The work-up for cholangitis is based upon medical history, clinical presentation, and initial laboratory tests. Whereas ultrasound is the first-line imaging modality used to identify bile duct dilatation in patients with colicky abdominal pain, cross-sectional imaging is preferable when symptoms cannot be primarily localised to the hepatobiliary system. CT is very useful in oncologic, trauma, or postoperative patients. Otherwise, magnetic resonance cholangiopancreatography is the method of choice to diagnose acute and chronic biliary disorders, providing an excellent anatomic overview and, if gadoxetic acid is injected, simultaneously delivering morphological and functional information about the hepatobiliary system. If brush cytology, biopsy, assessment of the prepapillary common bile duct, stricture dilatation, or stenting is necessary, then endoscopic ultrasound and/or retrograde cholangiography are performed. Finally, when the pathologic duct is inaccessible from the duodenum or stomach, percutaneous transhepatic cholangiography is an option. The pace of the work-up depends upon the severity of cholestasis on presentation. Whereas sepsis, hypotension, and/or Charcot's triad warrant immediate investigation and management, chronic cholestasis can be electively evaluated.This overview article will cover the common cholangitides, emphasising our clinical experience with the chronic cholestatic liver diseases.
APEX_SCOPE: A graphical user interface for visualization of multi-modal data in inter-disciplinary studies (2017)

In multi-disciplinary studies, different forms of data are often collected for analysis. For example, APEX, a study on the automated prediction of extubation readiness in extremely preterm infants, collects clinical parameters and cardiorespiratory signals. A variety of cardiorespiratory metrics are computed from these signals and used to assign a cardiorespiratory pattern at each time. In such a situation, exploratory analysis requires a visualization tool capable of displaying these different types of acquired and computed signals in an integrated environment. Thus, we developed APEX_SCOPE, a graphical tool for the visualization of multi-modal data comprising cardiorespiratory signals, automated cardiorespiratory metrics, automated respiratory patterns, manually classified respiratory patterns, and manual annotations by clinicians during data acquisition. This MATLAB-based application provides a means for collaborators to view combinations of signals to promote discussion, generate hypotheses and develop features.
Apo(a)-kringle IV-type 6: expression in Escherichia coli, purification and in vitro refolding (2000)

Lipoprotein (a) [Lp(a)] belongs to the class of highly thrombo-atherogenic lipoproteins. The assembly of Lp(a) from LDL and the specific apo(a) glycoprotein takes place extracellularly in a two-step process. First, an unstable complex is formed between LDL and apo(a) due to the interaction of the unique kringle (K) IV-type 6 (T6) in apo(a) with amino groups on LDL, and in the second step this complex is stabilized by a disulfide bond between apo(a) KIV-T9 and apoB(100). In order to understand this process better, we overexpressed and purified apo(a) KIV-T6 in Escherichia coli. Recombinant KIV-T6 was expressed as a His-tag fusion protein under control of the T7 promoter in BL21 (DE3) strain. After one-step purification by affinity chromatography the yield was 7 mg/l of bacterial suspension. Expressed fusion apo(a) KIV-T6 was insoluble in physiological buffers and it also lacked the characteristic kringle structure. After refolding using a specific procedure, high-resolution (1)H-NMR spectroscopy revealed kringle structure-specific signals. Refolded KIV-T6 bound to Lys-Sepharose with a significantly lower affinity than recombinant apo(a) (EC(50) with epsilon-ACA 0.47 mM versus 2-11 mM). In competition experiments a 1000-fold molar excess of KIV-T6 was needed to reach 60% inhibition of Lp(a) assembly.
Feasibility study of an active soft catheter actuated by SMA wires (2018)

This study aims to assess the feasibility of using a combination of thin elastomer tubes and SMA wires to develop an active catheter. Cardiac catheters have been widely used in investigational and interventional procedures such as angiography, angioplasty, electro- physiology, and endocardial ablation. The commercial models manually steer inside the patient’s body via internally installed pull wires. Active catheters, on the other hand, have the potential to revolutionize surgical procedures because of their computer-controlled and enhanced motion. Shape memory alloys have been used for almost a decade as a trustworthy actuator for biomedical applications. In this work, SMA wires were attached to a small pressurized elastomer tube to realize deflection. The tube was pressurized to maintain a constant stress on the SMA wires. The tip motion via actuation of SMA wires was then measured and reported. The results of this study showed that by adopting an appropriate training process for the SMA wires prior to performing the experiments and adopting an appropriate internal pressure for the elastomer tube, less external loads on SMA wires would be needed for a consistent actuation.
New Generalized Method for the TEM Examination of Buried Interfaces with Application to the Copper Bond Wire - Aluminum Pad System (2011)

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.
Comparison of Probabilistic Failure Analysis for Hybrid Wound Composite Ceramic Assembly Tested by Various Methods (2013)

This chapter contains sections titled: Introduction Background Experimental Results and Discussion Conclusion Acknowledgements
New approach to the synthesis of C-glycosides, azasugars, and aza C-glycosides (1996)

Synthesis of sugar analogs in which the ring oxygen atom has been replaced by an-NR-group (azasugars) and/or the anomeric hydroxyl group has been replaced by a carbon atom (C-glycosides) has been a subject of intensive research interest in recent years. Many members of both classes of compounds are specific inhibitors of glycosidases, including enzymes involved in glycoprotein processing, glycogenolysis, and oligo- and disaccharide hydrolysis. In spite of recent developments in the synthesis of C-glycosides and azasugars, the stereospecific formation C-glycosides and aza C-glycosides remains a challenge for synthetic carbohydrate chemistry. A simple way to prepare C-glycosides and aza C-glycosides of D-arabinose and D-lyxose, that can be applied to other aldoses, is reported. The reaction involves oxidation of D-glucose diethyl dithioacetal (with spontaneous cyclization) to the corresponding ($\alpha$-D-arabinopyranosyl)-di(ethyl sufonyl)methane. Reduction to the diethyl dithioacetal of ($\alpha$-D arabinosyl) formaldehyde, and converting it to an aldhehyde provides a compound which can be modified to other desired products. Oxidation of a protected 6-amino-6-deoxy-D-galactose diethyl dithioacetal provided the corresponding azasugars.
Crystallization of Long-Spaced Precision Polyacetals III: Polymorphism and Crystallization Kinetics of Even Polyacetals Spaced by 6 to 26 Methylenes (2021)

In this paper we extend the study of polymorphism and crystallization kinetics of aliphatic polyacetals to include shorter (PA-6) and longer (PA-26) methylene lengths in a series of even long-spaced systems. On a deep quenching to 0 °C, the longest even polyacetals, PA-18 and PA-26, develop mesomorphic-like disordered structures which, on heating, transform progressively to hexagonal, Form I, and Form II crystallites. Shorter polyacetals, such as PA-6 and PA-12 cannot bypass the formation of Form I. In these systems a mixture of this form and disordered structures develops even under fast deep quenching. A prediction from melting points that Form II will not develop in polyacetals with eight or fewer methylene groups between consecutive acetals was further corroborated with data for PA-6. The temperature coefficient of the overall crystallization rate of the two highest temperature polymorphs, Form I and Form II, was analyzed from the differential scanning calorimetry (DSC) peak crystallization times. The crystallization rate of Form II shows a deep inversion at temperatures approaching the polymorphic transition region from above. The new data on PA-26 confirm that at the minimum rate the heat of fusion is so low that crystallization becomes basically extinguished. The rate inversion and dramatic drop in the heat of fusion irrespective of crystallization time are associated with a competition in nucleation between Forms I and II. The latter is due to large differences in nucleation barriers between these two phases. As PA-6 does not develop Form II, the rate data of this polyacetal display a continuous temperature gradient. The data of the extended polyacetal series demonstrate the important role of methylene sequence length on polymorphism and crystallization kinetics.
Metallic Nanoparticle−Carbon Nanotube Composites for Electrochemical Determination of Explosive Nitroaromatic Compounds (2006)

Metal nanoparticles (Pt, Au, or Cu) together with multiwalled and single-walled carbon nanotubes (MWCNT and SWCNT) solubilized in Nafion have been used to form nanocomposites for electrochemical detection of trinitrotoluene (TNT) and several other nitroaromatics. Electrochemical and surface characterization by cyclic voltammetry, AFM, TEM, SEM, and Raman spectroscopy confirmed the presence of metal nanoparticles on CNTs. Among various combinations tested, the most synergistic signal effect was observed for the nanocomposite modified glassy carbon electrode (GC) containing Cu nanoparticles and SWCNT solubilized in Nafion. This combination provided the best sensitivity for detecting TNT and other nitroaromatic compounds. Adsorptive stripping voltammetry for TNT resulted in a detection limit of 1 ppb, with linearity up to 3 orders of magnitude. Selectivity toward the number and position of the nitro groups in different nitroaromatics was very reproducible and distinct. Reproducibility of the TNT signal was within 7% (n = 8) from one electrode preparation to another, and the response signal was stable (+/-3.8% at 95% confidence interval) for 40 repeated analyses with 10 min of preconditioning. The Cu-SWCNT-modified GC electrode was demonstrated for analysis of TNT in tap water, river water, and contaminated soil.
Local Hamiltonians in Quantum Computation (2008)

In this thesis, I investigate aspects of local Hamiltonians in quantum computing. First, I focus on the Adiabatic Quantum Computing model, based on evolution with a time dependent Hamiltonian. I show that to succeed using AQC, the Hamiltonian involved must have local structure, which leads to a result about eigenvalue gaps from information theory. I also improve results about simulating quantum circuits with AQC. Second, I look at classically simulating time evolution with local Hamiltonians and finding their ground state properties. I give a numerical method for finding the ground state of translationally invariant Hamiltonians on an infinite tree. This method is based on imaginary time evolution within the Matrix Product State ansatz, and uses a new method for bringing the state back to the ansatz after each imaginary time step. I then use it to investigate the phase transition in the transverse field Ising model on the Bethe lattice. Third, I focus on locally constrained quantum problems Local Hamiltonian and Quantum Satisfiability and prove several new results about their complexity. Finally, I define a Hamiltonian Quantum Cellular Automaton, a continuous-time model of computation which doesn't require control during the computation process, only preparation of product initial states. I construct two of these, showing that time evolution with a simple, local, translationally invariant and time-independent Hamiltonian can be used to simulate quantum circuits.