gebhart/patrepeval huggingface dataset:
Nucleoside Phosphotransferase front Malt Sprouts. III. Studies on Metal Ion Requirement, Solvent Effects, Kinetics and Reaction Mechanism (1986)

The nucleoside phosphotransferase from malt sprouts contains one Mg2 per dimeric enzyme molecule. This cation can be removed by EDTA, while other chelating agents are less efficient. The metal-free apoenzyme is inactive. Activity can be restored to its initial value by Mg2 or Co2 and to a minor extent by Mn2, Zn2, Cu2, Ni2 and Fe2. Thermal stability is reduced when the metal is removed but can be restored by addition of Mg2. Adenosine 3',5'-phosphate (cAMP) and arsenate, strong competitive inhibitors, reduce the rate of inactivation by EDTA considerably but do not reduce the rate for the reconstitution with Mg2. We therefore conclude that the phosphate group interacts electrostatically with Mg2 and that the inhibitor is not bound to the apoenzyme. The Sp-isomer of adenosine 3',5'-thionophosphate is a hundred times stronger inhibitor than the Rp-isomer and ten times stronger than cAMP; this allowed us to determine the relative position of the Mg2 in the active site. The imidazolium cation, previously detected as an essential part of the active site, obviously forms a salt bridge to the carboxylate group which attacks the phosphorus opposite to the leaving alcohol group. This conclusion is derived from the fact that organic solvents increase the rate of formation of the phospho-intermediate considerably, while higher concentrations of salt decrease it strongly. In addition, the imidazolium cation seems to polarize the P = O bond and to stabilize the negative charge at the phosphoryl oxygen in the pentacoordinate transition state; this is followed from the pH-dependence of the hydrolysis reaction. The kinetic results reveal that Km does not represent a binding equilibrium, but is the ratio of the rates for decay and formation of the covalent intermediate, while kcat/Km is an indicator for the formation step of the acyl phosphate. On the basis of all these informations it should be allowed to formulate a reaction mechanism, in which all steps of the transferase reaction have to be microscopically reversible.
The effect of excision of the radial head and metallic radial head replacement on the tension in the interosseous membrane (2013)

We measured the tension in the interosseous membrane in six cadaveric forearms using an in vitro forearm testing system with the native radial head, after excision of the radial head and after metallic radial head replacement. The tension almost doubled after excision of the radial head during simulated rotation of the forearm (p = 0.007). There was no significant difference in tension in the interosseous membrane between the native and radial head replacement states (p = 0.09). Maximal tension occurred in neutral rotation with both the native and the replaced radial head, but in pronation if the radial head was excised. Under an increasing axial load and with the forearm in a fixed position, the rate of increase in tension in the interosseous membrane was greater when the radial head was excised than for the native radial head or replacement states (p = 0.02). As there was no difference in tension between the native and radial head replacement states, a radial head replacement should provide a normal healing environment for the interosseous membrane after injury or following its reconstruction. Load sharing between the radius and ulna becomes normal after radial head Replacement. As excision of the radial head significantly increased the tension in the interosseous membrane it may potentially lead to its attritional failure over time.
Self-organized Fault-tolerant Routing in Peer-to-Peer Overlays (2009)

In sufficiently large heterogeneous overlays message loss and delays are likely to occur. This has a significant impact on overlay routing, especially on longer paths. The existing solutions to this problem rely on message redundancy to mask the loss and delays. This incurs a significant bandwidth cost. We propose the forward feedback protocol (FFP) which only routes a single copy of the message and detects the message loss and excessive delays while routing. Failures are signaled along the routing paths. Based only on the simple binary signals, each overlay node locally and independently learns to route to avoid failures. The local node interactions lead to the emergence of fast reliable overlay routes. This is a continuous process, the system constantly self-organizes in response to changing delay and loss conditions. We evaluate the protocol in the Internet deployment and in simulation. Our system uses 2-5 times less bandwidth than the existing overlay routing approaches that rely on high message redundancy for fault-tolerance. Despite its marginal bandwidth investment in reliability, FFP achieves up to a 30% higher delivery success rate in comparison to the existing solutions. The protocol is scalable with local state size of O(log <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> N) in terms of the network size and is universally applicable to all recursively routing overlays.
Dynamical Electromechanical Model for Magnetic Bearings (2007)

Magnetic bearings are electromechanical systems. From a mechanical point of view, their modeling is plainly related to general rotor dynamics modeling. But the forces acting between the rotor and the stator are of an electromagnetic nature. This paper presents the analysis of the potentially unstable dynamical behavior of magnetic bearings. It adopts an electromechanical point of view and represents the forces acting on the system by dampers, springs, and an electrical phase shift. The coefficients of the model are found by parameter identification with a finite-element model of the system.
Persistent Hepatitis C Virus Infection Impairs Ribavirin Antiviral Activity through Clathrin-Mediated Trafficking of Equilibrative Nucleoside Transporter 1 (2014)

The results from this work will allow a review of the competing theories of antiviral therapy development in the field of HCV virology. Ribavirin (RBV) remains an important component of interferon-free hepatitis C treatment regimens. The reason why RBV alone does not inhibit HCV replication effectively has not been established. This study provides a potential mechanism for why RBV antiviral activity is impaired in persistently HCV-infected cell cultures and suggests that inhibition of the HCV-induced autophagy response could be used as a strategy to increase RBV antiviral activity against HCV infection. Therefore, it is anticipated that this work would generate a great deal of interest, not only among virologists but also among the general public.
Carbohydrates as Sources of Chiral Inositol Polyphosphates and Their Mimics (1997)

Introduction Synthesis of D-2-deoxy-myo-inositol 1,3,4,5-tetrakisphosphate Improved Preparation of Methyl 4,6-O-Benzylidene-α-D-Glucopyranoside and Methyl 4,6-O-Benzylidene-α-D-Mannopyranoside Benzylation of Methyl 4,6-O-Benzylidene-α-D-Glucopyranoside and Related Reactions Preparation of Methyl 3,4-Di-O-benzoyl-2-O-benzyl-6-deoxy-α-D-xylo-hex-5-enopyranoside 30 Ferrier Carbocyclisation of 30 Attempted Inversion of Stereochemistry at Position 5 of 32 Synthesis of D-2-Deoxy-myo-inositol 1,3,4,5 Tetrakisphosphate 5 Synthesis of Ring-contracted Analogues of Ins(1,4,5)P3 Preparation of Methyl 2-O-Benzyl-3,4-di-O-(p-methoxybenzyl)-α-D-Glucopyranoside 58 Preparation of (1R,2R,3S,4R,5S)-3-Hydroxy-1,2,4-trisphospho-5-vinyl Cyclopentane 53b Preparation of (1R,2R,3S,4R,5S)-3-Hydroxy-5-hydroxymethyl-1,2,4 trisphospho Cyclopentane 75 Synthesis of a Carbohydrate-based Inositol Polyphosphate Mimic Based on Adenophostin A Synthesis of 2,6-Di-O-benzyl-3,4-di-O-(p-methoxybenzyl)-D-Glucopyranose 93 Synthesis of (2-Hydroxyethyl)-2′,3,4-Trisphosphate-α-D-Glucopyranoside 88 Preparation of a Fluorescent Label Based upon (2-Hydroxy-ethyl)-2′,3,4-trisphosphate-α-D-Glucopyranoside Conclusion References
Effects of fixed-rate CT projection data compression on perceived and measured CT image quality (2010)

Compression of computed tomography (CT) projection data reduces CT scanner bandwidth and storage costs. Since fixed-rate compression guarantees predictable bandwidth, fixed-rate compression is preferable to lossless compression, but fixed-rate compression can introduce image artifacts. This research demonstrates clinically acceptable image quality at 3:1 compression as judged by a radiologist and as estimated by an image quality metric called local structural similarity (SSIM). We examine other common, quantitative image quality metrics from image processing, including peak signal-to-noise (PSNR), contrast-to-noise ratio (CNR), and difference image statistics to quantify the magnitude and location of image artifacts caused by fixed-rate compression of CT projection data. Masking effects caused by local contrast, air and bone pixels, and image reconstruction effects at the image's periphery and iso-center explain why artifacts introduced by compression are not noticed by radiologists. SSIM metrics in this study nearly always exceeds 0.98 (even at 4:1 compression ratios), which is considered visually indistinguishable. The excellent correlation of local SSIM and subjective image quality assessment confirms that fixed-rate 3:1 projection data compression on CT images does not affect clinical diagnosis and is rarely noticed. Local SSIM metrics can be used to significantly reduce the number of viewed images in medical image quality studies.
Design and performance of broadly tunable, narrow line-width, high repetition rate 1310nm VCSELs for swept source optical coherence tomography (2012)

MEMS tunable vertical cavity surface emitting laser (MEMS-VCSEL) development, over the past two decades, has primarily focused on communications and spectroscopic applications. Because of the narrow line-width, single-mode operation, monolithic fabrication, and high-speed capability of these devices, MEMS-VCSELs also present an attractive optical source for emerging swept source optical coherence tomography (SSOCT) systems. In this paper, we describe the design and performance of broadly tunable MEMS-VCSELs targeted for SSOCT, emphasizing 1310nm operation for cancer and vascular imaging. We describe the VCSEL structure and fabrication, employing a fully oxidized GaAs/AlxOy mirrors in conjunction with dielectric mirrors and InP-based multi-quantum well active regions. We also describe the optimization of MEMs speed and frequency response for SSOCT. Key results include 1310 nm VCSELs with &gt;120nm dynamic tuning range and imaging rates near 1MHz, representing the widest VCSEL tuning range and some of the fastest swept source imaging rates thus far obtained. We also describe how low-noise semiconductor optical amplification boosts average optical power to the required levels, while maintaining superior OCT imaging quality and state of the art system sensitivity. Finally, we present measured multi-centimeter dynamic coherence length, and discuss the implications of VCSELs for OCT.
Aggregation of squaraine dyes: Structure–property relationships and solvent effects (1995)

In characterizing the UV–visible absorption properties of a series of seven anilino class squaraine dyes in dimethyl sulfoxide (DMSO) – water mixtures, spectral features characteristic of aggregation were observed. These included hypsochromic and hypochromic shifts of the absorption maximum, relative to the nonassociated state of these dyes. Previously aggregation of this class of squaraine dyes had only been reported in studies of Langmuir–Blodgett (LB) films prepared with squaraine dyes. In the present study two distinctly different and novel solution dye aggregates, designated as type A and type B, were identified on the basis of their characteristic absorption properties. The type A aggregate was characterized by an absorption maximum that was hypsochromically and hypochromically shifted, in comparison with that of the nonassociated dyes, and had a secondary absorption occurring at approximately the same wavelength at which nonassociated squaraine dyes absorb. These spectral features are believed to be the result of a "face-to-face" alignment of molecules in the aggregate. The type B aggregate featured a broad absorption typically from 525 to 700 nm. Based on similarities between the spectral features of type B aggregates and LB films of surfactant squaraines, the alignment of molecules in the solution aggregate was believed to be such that the electron-deficient squarylium moieties interacted with the electron-rich dialkylamino phenyl moieties. Certain squaraine dyes that were investigated as part of this study were found to form both type A and type B aggregates, depending upon the composition of the DMSO–water medium. Typically, the type A aggregate formed preferentially in media of intermediate DMSO content (50–70% DMSO) and the type B aggregate in more water-rich media (&lt;20% DMSO). In the intervening region it was possible to monitor spectroscopically a dynamic conversion from the type B aggregate to the type A aggregate. An examination of structure–property relationships indicated that dyes with less hydrophobic N-alkyl substituents formed only type A aggregates. Squaraine dyes with more hydrophobic N-alkyl substituents were found to form type B aggregates in water and type A aggregates in some DMSO–water mixtures. A model of squaraine aggregation was proposed in which the type A squaraine aggregate was "thermodynamically" preferred while the type B aggregate was "kinetically" preferred. The stability of the type B aggregate was proposed to be enhanced by increasing hydrophobicity of the N-alkyl substituents and decreased by increasing amounts of DMSO in the solvent system. Keywords: squaraine dyes, aggregation, crystallochromy, solvent effects.
Observation of the centrally produced φφ system at 800 GeV/c (2000)

We present evidence of the observation of the centrally produced φφ system at 800 GeV/c in the reaction pp→pslow(φφ)pfast. A clear bump is observed over low φK+K− and K+K−K+K− background. Statistics are comparable to those previously obtained in π−p interactions, where three 2++ waves were found to comprise all cross section.
Memory allocation for Huffman coding of multiplesources (1996)

The authors propose an efficient memory allocation method for memory-constrained Huffman coding of multiple sources which employs the iterative bisection algorithm. The proposed method provides better performance over conventional allocation methods and can be applied to many adaptive variable-length coders with memory constraints.
Emergent Decompressive Craniectomy in Patients with Fixed Dilated Pupils Due to Cerebral Venous and Dural Sinus Thrombosis (1999)

Our results provide preliminary evidence that emergent decompressive craniectomy is effective in patients with brain herniation from dural sinus thrombosis, provided that the clinical onset is recent. We therefore recommend consideration of this aggressive surgical technique for such patients, who may survive with good outcomes.
Modulation of pulmonary DC function by vaccine‐encoded GM‐CSF enhances protective immunity against Mycobacterium tuberculosis infection (2009)

The rational design of new vaccines engineered to target key components of the host immune response is crucial to aid control of important infectious diseases such as tuberculosis. In this report, we determined whether modifying the function of pulmonary APC could improve protection against infection with Mycobacterium tuberculosis. Targeted delivery to the lung of the cytokine GM-CSF, expressed by the Mycobacterium bovis BCG vaccine strain, increased pulmonary DC numbers and secretion of the immunoregulatory cytokine IL-12, compared with parental BCG immunization. This impact on APC number by BCG:GM-CSF resulted in accelerated priming of antigen-specific CD4+ T cells in the mediastinal lymph nodes and increased migration of activated CD4+ T cells into the lung. i.n. administration of BCG:GM-CSF resulted in significantly increased protection against M. tuberculosis infection compared with mice vaccinated with BCG alone. BCG:GM-CSF exhibited an improved safety profile, as immunodeficient RAG1-/- mice vaccinated i.n. with BCG:GM-CSF survived significantly longer than control BCG-vaccinated mice. These data demonstrate that manipulating immune cells in the lung by BCG-based delivery of GM-CSF can assist the development of protective mucosal immunity against pulmonary bacterial infection.
A benchmark study of the multiscale and homogenization methods for fully implicit multiphase flow simulations (2020)

Accurate simulation of multiphase flow in subsurface formations is challenging, as the formations span large length scales (km) with high-resolution heterogeneous properties. To deal with this challenge, different multiscale methods have been developed. Such methods construct coarse-scale systems, based on a given high-resolution fine-scale system. Furthermore, they are amenable to parallel computing and allow for a-posteriori error control. The multiscale methods differ from each other in the way the transition between the different scales is made. Multiscale (finite element and finite volume) methods compute local basis functions to map the solutions (e.g. pressure) between coarse and fine scales. Instead, homogenization methods solve local periodic problems to determine effective models and parameters (e.g. permeability) at a coarser scale. It is yet unknown how these two methods compare with each other, especially when applied to complex geological formations, with no clear scale separation in the property fields. This paper develops the first comparison benchmark study of these two methods and extends their applicability to fully implicit simulations using the algebraic dynamic multilevel (ADM) method. At each time step, on the given fine-scale mesh and based on an error analysis, the fully implicit system is solved on a dynamic multilevel grid. The entries of this system are obtained by using multiscale local basis functions (ADM-MS), and, respectively, by homogenization over local domains (ADM-HO). Both sets of local basis functions (ADM-MS) and local effective parameters (ADM-HO) are computed at the beginning of the simulation, with no further updates during the multiphase flow simulation. The two methods are extended and implemented in the same open-source DARSim2 simulator (https://gitlab.com/darsim2simulator), to provide fair quality comparisons. The results reveal insightful understanding of the two approaches, and qualitatively benchmark their performance. It is re-emphasized that the test cases considered here include permeability fields with no clear scale separation. The development of this paper sheds new lights on advanced multiscale methods for simulation of coupled processes in porous media.
Decentralized Learning over Wireless Networks: The Effect of Broadcast with Random Access (2023)

In this work, we focus on the communication aspect of decentralized learning, which involves multiple agents training a shared machine learning model using decentralized stochastic gradient descent (D-SGD) over distributed data. In particular, we investigate the impact of broadcast transmission and probabilistic random access policy on the convergence performance of D-SGD, considering the broadcast nature of wireless channels and the link dynamics in the communication topology. Our results demonstrate that optimizing the access probability to maximize the expected number of successful links is a highly effective strategy for accelerating the system convergence.
The Electrochemistry of Fe3O4/Polypyrrole Composite Electrodes in Lithium-Ion Cells: The Role of Polypyrrole in Capacity Retention (2016)

In two series of magnetite (Fe<sub>3</sub>O4) composite electrodes, one group with and one group without added carbon, containing varying quantities of polypyrrole (PPy), and a non-conductive polyvinylidene difluoride (PVDF) binder were constructed and then analyzed using electrochemical and spectroscopic techniques. Galvanostatic cycling and alternating current (AC) impedance measurements were used in tandem to measure delivered capacity, capacity retention, and the related impedance at various stages of discharge and charge. Further, the reversibility of Fe<sub>3</sub>O<sub>4</sub> to iron metal (Fe0) conversion observed during discharge was quantitatively assessed ex-situ using X-ray Absorption Spectroscopy (XAS). The Fe<sub>3</sub>O<sub>4</sub> composite containing the largest weight fraction of PPy (20 wt%) with added carbon demonstrated reduced irreversible capacity on initial cycles and improved cycling stability over 50 cycles, attributed to decreased reaction with the electrolyte in the presence of PPy. Our study illustrated the beneficial role of PPy addition to Fe<sub>3</sub>O<sub>4</sub> based electrodes was not strongly related to improved electrical conductivity, but rather to improved ion transport related to the formation of a more favorable surface electrolyte interphase (SEI).
Introducing search behavior into browsing based models of page's importance (2013)

BrowseRank algorithm and its modifications are based on analyzing users' browsing trails. Our paper proposes a new method for computing page importance using a more realistic and effective search-aware model of user browsing behavior than the one used in BrowseRank.
A General Asymmetric Synthesis of syn‐ and anti‐β‐Substituted Cysteine and Serine Derivatives. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
Non-mechanical beam steering in the mid-wave infrared (2017)

The mid-wave infrared (MWIR) portion of the electromagnetic spectrum is critically important for a variety of applications such as LIDAR and chemical sensing. Concerning the latter, the MWIR is often referred to as the “molecular fingerprint” region owing to the fact that many molecules display distinctive vibrational absorptions in this region, making it useful for gas detection. To date, steering MWIR radiation typically required the use of mechanical devices such as gimbals, which are bulky, slow, power-hungry, and subject to mechanical failure. We present the first non-mechanical beam steerer capable of continuous angular tuning in the MWIR. These devices, based on refractive, electro-optic waveguides, provide angular steering in two dimensions without relying on moving parts. Previous work has demonstrated non-mechanical beam steering (NMBS) in the short-wave infrared (SWIR) and near infrared (NIR) using a waveguide in which a portion of the propagating light is evanescently coupled to a liquid crystal (LC) layer in which the refractive index is voltage-tuned. We have extended this NMBS technology into the MWIR by employing chalcogenide glass waveguides and LC materials that exhibit high MWIR transparency. As a result, we have observed continuous, 2D MWIR steering for the first time with a magnitude of 2.74&deg; in-plane and 0.3&deg; out-of-plane.