bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of ionic liquids supported on silica as a sorbent for fully automated online solid‐phase extraction with LC–MS determination of sulfonamides in bovine milk samples
Authors: da Silva Meire Ribeiro , Mauro Lanças Fernando 
Published: March 2018

AbstractSulfonamides are antibiotics widely used in the treatment of diseases in dairy cattle. However, their indiscriminate use for disease control may lead to their presence in tissues and milk and their determination requires a sample preparation step as part of an analytical approach. Among the several sample preparation techniques available, those based upon the use of sorptive materials have been widely employed. Recently, the application of ionic liquids immobilized on silica surfaces or polymeric materials has been evaluated for such an application. This manuscript addresses the evaluation of silica‐based ionic liquid obtained by a sol–gel synthesis process by basic catalysis as sorbent for online solid‐phase extraction with liquid chromatography and electrospray ionization time‐of‐flight mass spectrometry for sulfonamides determination. Infrared vibrational spectroscopy confirmed the presence of the ionic liquid on the silica surface, suggesting that the ionic liquid was anchored on to the silica surface. Other sorbents varying the ionic liquid alkyl chain were also synthesized and evaluated by off‐line solid‐phase extraction in the sulfonamide extraction. As the length of the alkyl chain increased, the amount of extracted sulfonamides decreased, possibly due to a decrease in the electrostatic interaction caused by the reduction in the polarity, as well as the presence of a hexafluorophosphate anion that increases the hydrophobic character of the material. The use of 1‐butyl‐3‐methylimidazolium hexafluorophosphate as a selective ionic liquid sorbent enabled the isolation and sulfonamide preconcentration in bovine milk by online solid‐phase extraction with liquid chromatography and electrospray ionization time‐of‐flight mass spectrometry. The limit of quantification for the method developed was 5–7, 5 μg/mL, with extraction recoveries ranging between 74 and 93% and intra‐ and interassay between 1.5–12.5 and 2.3–13.1, respectively.
Comparison of MEMS switches and PIN diodes for switched dual tuned RF coils
Authors: Maunder Adam , Rao Madhwesha , Robb Fraser , Wild Jim M. 
Published: March 2018

PurposeTo evaluate the performance of micro‐electromechanical systems (MEMS) switches against PIN diodes for switching a dual‐tuned RF coil between 19F and 1H resonant frequencies for multi‐nuclear lung imaging.MethodsA four‐element fixed‐phase and amplitude transmit–receive RF coil was constructed to provide homogeneous excitation across the lungs, and to serve as a test system for various switching methods. The MR imaging and RF performance of the coil when switched between the 19F and 1H frequencies using MEMS switches, PIN diodes and hardwired configurations were compared.ResultsThe performance of the coil with MEMS or PIN diode switching was comparable in terms of RF measurements, transmit efficiency and image SNR on both 19F and 1H nuclei. When the coil was not switched to the resonance frequency of the respective nucleus being imaged, reductions in the transmit efficiency were observed of 32% at the 19F frequency and 12% at the 1H frequency. The coil provides transmit field homogeneity of ±12.9% at the 1H frequency and ±14.4% at the 19F frequency in phantoms representing the thorax with the air space of the lungs filled with perfluoropropane gas.ConclusionMEMS and PIN diodes were found to provide comparable performance in on‐state configuration, while MEMS were more robust in off‐state high‐powered operation (>1 kW), providing higher isolation and requiring a lower DC switching voltage than is needed for reverse biasing of PIN diodes. In addition, clear benefits of switching between the 19F and 1H resonances were demonstrated, despite the proximity of their Larmor frequencies.
Rapid, theoretically artifact‐free calculation of static magnetic field induced by voxelated susceptibility distribution in an arbitrary volume of interest
Authors: Lee Seung‐Kyun , Hwang Seon‐Ha , Barg Ji‐Seong , Yeo Seok‐Jin 
Published: March 2018

PurposeTo demonstrate a computationally efficient and theoretically artifact‐free method to calculate static field (B0) inhomogeneity in a volume of interest induced by an arbitrary voxelated susceptibility distribution.MethodsOur method computes B0 by circular convolution between a zero‐filled susceptibility matrix and a shifted, voxel‐integrated dipolar field kernel on a grid of size NS+NT – 1 in each dimension, where NS and NT are the sizes of the susceptibility source and B0 target grids, respectively. The computational resource requirement is independent of source‐target separation. The method, called generalized susceptibility voxel convolution, is demonstrated on three susceptibility models: an ellipsoid, MR‐compatible screws, and a dynamic human heartbeat model.ResultsB0 in an ellipsoid calculated by generalized susceptibility voxel convolution matched an analytical solution nearly exactly. The method also calculated screw‐induced B0 in agreement with experimental data. Dynamic simulation demonstrated its computational efficiency for repeated B0 calculations on time‐varying susceptibility. On the contrary, conventional and alias‐subtracted k‐space‐discretized Fourier convolution methods showed nonnegligible aliasing and Gibbs ringing artifacts in the tested models.ConclusionGeneralized susceptibility voxel convolution can be a fast and reliable way to compute susceptibility‐induced B0 when the susceptibility source is not colocated with the B0 target volume of interest, as in modeling B0 variations from motion and foreign objects.
Toward a noninvasive estimate of interstitial fluid pressure by dynamic contrast‐enhanced MRI in a rat model of cerebral tumor
Authors: Elmghirbi Rasha , Nagaraja Tavarekere N. , Brown Stephen L. , Keenan Kelly A. , Panda Swayamprava , Cabral Glauber , Bagher‐Ebadian Hassan , Divine George W. , Lee Ian Y. , Ewing James R. 
Published: March 2018

PurposeThis study demonstrates a DCE‐MRI estimate of tumor interstitial fluid pressure (TIFP) and hydraulic conductivity in a rat model of glioblastoma, with validation against an invasive wick‐in‐needle (WIN) technique. An elevated TIFP is considered a mark of aggressiveness, and a decreased TIFP a predictor of response to therapy.MethodsThe DCE‐MRI studies were conducted in 36 athymic rats (controls and posttreatment animals) with implanted U251 cerebral tumors, and with TIFP measured using a WIN method. Using a model selection paradigm and a novel application of Patlak and Logan plots to DCE‐MRI data, the MRI parameters required for estimating TIFP noninvasively were estimated. Two models, a fluid‐mechanical model and a multivariate empirical model, were used for estimating TIFP, as verified against WIN‐TIFP.ResultsUsing DCE‐MRI, the mean estimated hydraulic conductivity (MRI‐K) in U251 tumors was (2.3 ± 3.1) × 10−5 (mm2/mmHg‐s) in control studies. Significant positive correlations were found between WIN‐TIFP and MRI‐TIFP in both mechanical and empirical models. For instance, in the control group of the fluid‐mechanical model, MRI‐TIFP was a strong predictor of WIN‐TIFP (R2 = 0.76, p < .0001). A similar result was found in the bevacizumab‐treated group of the empirical model (R2 = 0.93, p = .014).ConclusionThis research suggests that MRI dynamic studies contain enough information to noninvasively estimate TIFP in this, and possibly other, tumor models, and thus might be used to assess tumor aggressiveness and response to therapy.
A 2D spiral turbo‐spin‐echo technique
Authors: Li Zhiqiang , Karis John P. , Pipe James G. 
Published: March 2018

Purpose2D turbo‐spin‐echo (TSE) is widely used in the clinic for neuroimaging. However, the long refocusing radiofrequency pulse train leads to high specific absorption rate (SAR) and alters the contrast compared to conventional spin‐echo. The purpose of this work is to develop a robust 2D spiral TSE technique for fast T2‐weighted imaging with low SAR and improved contrast.MethodsA spiral‐in/out readout is incorporated into 2D TSE to fully take advantage of the acquisition efficiency of spiral sampling while avoiding potential off‐resonance‐related artifacts compared to a typical spiral‐out readout. A double encoding strategy and a signal demodulation method are proposed to mitigate the artifacts because of the T2‐decay‐induced signal variation. An adapted prescan phase correction as well as a concomitant phase compensation technique are implemented to minimize the phase errors.ResultsPhantom data demonstrate the efficacy of the proposed double encoding/signal demodulation, as well as the prescan phase correction and concomitant phase compensation. Volunteer data show that the proposed 2D spiral TSE achieves fast scan speed with high SNR, low SAR, and improved contrast compared to conventional Cartesian TSE.ConclusionA robust 2D spiral TSE technique is feasible and provides a potential alternative to conventional 2D Cartesian TSE for T2‐weighted neuroimaging.
Spinal excitability changes do not influence the mechanisms of split‐hand syndrome in amyotrophic lateral sclerosis
Authors: Cengiz Bülent , Mercan Metin , Kuruoğlu Reha 
Published: March 2018

ABSTRACTIntroduction: We studied spinal excitability and its relation to motor unit action potential (MUAP) changes in the thenar and hypothenar muscles in patients with amyotrophic lateral sclerosis (ALS). Methods: Quantitative MUAP and peak ratio interference analyses were performed, and cutaneous silent period (CutSP) was measured in the abductor digiti minimi (ADM) and first dorsal interosseous (FDI) muscles of patients with ALS and controls. Results: Patients with ALS revealed more prominently increased duration (P = 0.002), number of phases (P = 0.02), size index (P = 0.02), and thickness (P = 0.02) in ADM than in FDI. The number of small segments was significantly decreased in ADM (P = 0.036) compared with controls. CutSP latency was prolonged in both ADM and FDI in ALS (P < 0.05). Discussion: Although the reinnervation capacity was notably higher in the ADM of patients with ALS, the lack of a significant difference in CutSP measurements between ADM and FDI argues against spinal excitability changes in the development of split‐hand syndrome. Muscle Nerve 58: 503–508, 2018
Redesign of LAOBP to bind novel l‐amino acid ligands
Authors: Banda‐Vázquez Jesús , Shanmugaratnam Sooruban , Rodríguez‐Sotres Rogelio , Torres‐Larios Alfredo , Höcker Birte , Sosa‐Peinado Alejandro 
Published: March 2018

AbstractComputational protein design is still a challenge for advancing structure‐function relationships. While recent advances in this field are promising, more information for genuine predictions is needed. Here, we discuss different approaches applied to install novel glutamine (Gln) binding into the Lysine/Arginine/Ornithine binding protein (LAOBP) from Salmonella typhimurium. We studied the ligand binding behavior of two mutants: a binding pocket grafting design based on a structural superposition of LAOBP to the Gln binding protein QBP from Escherichia coli and a design based on statistical coupled positions. The latter showed the ability to bind Gln even though the protein was not very stable. Comparison of both approaches highlighted a nonconservative shared point mutation between LAOBP_graft and LAOBP_sca. This context dependent L117K mutation in LAOBP turned out to be sufficient for introducing Gln binding, as confirmed by different experimental techniques. Moreover, the crystal structure of LAOBP_L117K in complex with its ligand is reported.
p53 promotes its own polyubiquitination by enhancing the HDM2 and HDMX interaction
Authors: Medina‐Medina Ixaura , Martínez‐Sánchez Mayra , Hernández‐Monge Jesús , Fahraeus Robin , Muller Petr , Olivares‐Illana Vanesa 
Published: March 2018

AbstractHDM2 and HDMX are two homologs essential for controlling p53 tumor suppressor activity under normal conditions. Both proteins bind different sites on the p53 N‐terminus, and while HDM2 has E3 ubiquitin ligase activity towards p53, HDMX does not. Nevertheless, HDMX is required for p53 polyubiquitination and degradation, but the underlying molecular mechanism remains unclear. Alone, HDMX and HDM2 interact via their respective C‐terminal RING domains but here we show that the presence of p53 induces an N‐terminal interface under normal cellular conditions. This results in an increase in HDM2‐mediated p53 polyubiquitination and degradation. The HDM2 inhibitor Nutlin‐3 binds the N‐terminal p53 binding pocket and is sufficient to induce the HDM2‐HDMX interaction, suggesting that the mechanism depends on allosteric changes that control the multiprotein complex formation. These results demonstrate an allosteric interchange between three different proteins (HDMX‐HDM2‐p53) and help to explain the molecular mechanisms of HDM2‐inhibitory drugs.
A probabilistic network model for structural transitions in biomolecules
Authors: Habeck Michael , Nguyen Thach 
Published: March 2018

AbstractBiological macromolecules often undergo large conformational rearrangements during a functional cycle. To simulate these structural transitions with full atomic detail typically demands extensive computational resources. Moreover, it is unclear how to incorporate, in a principled way, additional experimental information that could guide the structural transition. This article develops a probabilistic model for conformational transitions in biomolecules. The model can be viewed as a network of anharmonic springs that break, if the experimental data support the rupture of bonds. Hamiltonian Monte Carlo in internal coordinates is used to infer structural transitions from experimental data, thereby sampling large conformational transitions without distorting the structure. The model is benchmarked on a large set of conformational transitions. Moreover, we demonstrate the use of the probabilistic network model for integrative modeling of macromolecular complexes based on data from crosslinking followed by mass spectrometry.
Structures of jacalin‐related lectin PPL3 regulating pearl shell biomineralization
Authors: Nakae Setsu , Shionyu Masafumi , Ogawa Tomohisa , Shirai Tsuyoshi 
Published: March 2018

AbstractThe nacreous layer of pearl oysters is one of the major biominerals of commercial and industrial interest. Jacalin‐related lectins, including PPL3 isoforms, are known to regulate biomineralization of the Pteria penguin pearl shell, although the molecular mechanisms are largely unknown. The PPL3 crystal structures were determined partly by utilizing microgravity environments for 3 isoforms, namely, PPL3A, PPL3B, and PPL3C. The structures revealed a tail‐to‐tail dimer structure established by forming a unique inter‐subunit disulfide bond at C‐termini. The N‐terminal residues were found in pyroglutamate form, and this was partly explained by the post‐translational modification of PPL3 isoforms implied from the discrepancy between amino acid and gene sequences. The complex structures with trehalose and isomaltose indicated that the novel specificity originated from the unique α‐helix of PPL3 isoforms. Docking simulations of PPL3B to various calcite crystal faces suggested the edge of a β‐sheet and the carbohydrate‐binding site rich in charged residues were the interface to the biomineral, and implied that the isoforms differed in calcite interactions.
Improved protein model quality assessments by changing the target function
Authors: Uziela Karolis , Menéndez Hurtado David , Shu Nanjiang , Wallner Björn , Elofsson Arne 
Published: March 2018

AbstractProtein modeling quality is an important part of protein structure prediction. We have for more than a decade developed a set of methods for this problem. We have used various types of description of the protein and different machine learning methodologies. However, common to all these methods has been the target function used for training. The target function in ProQ describes the local quality of a residue in a protein model. In all versions of ProQ the target function has been the S‐score. However, other quality estimation functions also exist, which can be divided into superposition‐ and contact‐based methods. The superposition‐based methods, such as S‐score, are based on a rigid body superposition of a protein model and the native structure, while the contact‐based methods compare the local environment of each residue. Here, we examine the effects of retraining our latest predictor, ProQ3D, using identical inputs but different target functions. We find that the contact‐based methods are easier to predict and that predictors trained on these measures provide some advantages when it comes to identifying the best model. One possible reason for this is that contact based methods are better at estimating the quality of multi‐domain targets. However, training on the S‐score gives the best correlation with the GDT_TS score, which is commonly used in CASP to score the global model quality. To take the advantage of both of these features we provide an updated version of ProQ3D that predicts local and global model quality estimates based on different quality estimates.
The modules of trans‐acyltransferase assembly lines redefined with a central acyl carrier protein
Authors: Vander Wood Drew A. , Keatinge‐Clay Adrian T. 
Published: March 2018

AbstractHere, the term “module” is redefined for trans‐acyltransferase (trans‐AT) assembly lines to agree with how its domains cooperate and evolutionarily co‐migrate. The key domain in both the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) modules of assembly lines is the acyl carrier protein (ACP). ACPs not only relay growing acyl chains through the assembly line but also collaborate with enzymes in modules, both in cis and in trans, to add a specific chemical moiety. A ketosynthase (KS) downstream of ACP often plays the role of gatekeeper, ensuring that only a single intermediate generated by the enzymes of a module is passed downstream. Bioinformatic analysis of 526 ACPs from 33 characterized trans‐AT assembly lines reveals ACPs from the same module type generally clade together, reflective of the co‐evolution of these domains with their cognate enzymes. While KSs downstream of ACPs from the same module type generally also clade together, KSs upstream of ACPs do not—in disagreement with the traditional definition of a module. Beyond nomenclature, the presented analysis impacts our understanding of module function, the evolution of assembly lines, pathway prediction, and assembly line engineering.
Quantum information‐theoretic measures for the static screened Coulomb potential
Authors: Isonguyo Cecilia N. , Oyewumi Kayode J. , Oyun Opeyemi S. 
Published: March 2018

AbstractIn this research work, the quantum information‐theoretic analysis of the static screened Coulomb potential has been carried out by studying both analytically and numerically the entropic measures, Fisher information as well as the Onicescu information energy of its wave function. Explicit expressions of these information‐theoretic measures were obtained. Using the Srivastava–Daoust linearization formula in terms of the multivariate Lauricella hypergeometric function, the Rényi entropy, Tsallis entropy, Onicescu information energy were analytically obtained. From the results obtained, it is observed that some of the Shannon entropies are negative, indicating that, negative entropies exists for the probability densities that are highly localized. The trends in the variation of the information‐theoretic measures with the potential screening parameter a for this atomic model are discussed. The Bialynicki‐Birula, Mycielski inequality (BBM), and the Fisher information based uncertainty relation are also verified.
Organolithium complex as a gas sensing material for oxides from ab initio calculations and molecular dynamics simulations
Authors: Ingale Nilesh , Konda Ravinder , Chaudhari Ajay 
Published: March 2018

AbstractGas sensing study of C2H4Li complex toward oxides viz. CO, CO2, NO, NO2, SO, and SO2 gas molecules has been carried out using ab initio method. Different possible configurations of gas molecule adsorption on C2H4Li complex are considered. The structural parameters of most stable configuration of gas molecule adsorbed complexes are thoroughly analysed. Electronic properties are studied using total density of states (DOS) plot. Charge transferred between the gas molecule and the substrate is studied using NBO charge analysis. Gas sensing of all the six gas molecules is possible at ambient conditions. Atom centred density matrix propagation (ADMP) molecular dynamics simulations confirmed that all the gas molecules remain adsorbed on C2H4Li complex at room temperature during the simulation. This study suggests that the C2H4Li complex acts as a novel gas sensing material for CO, CO2, NO, NO2, SO, and SO2 gas molecules at ambient conditions, below room temperature as well as at high pressure.
Mechanisms of phosphine‐catalyzed [4 + 3] annulation of allenoates with C, N‐cyclic azomethine imines: A DFT investigation
Authors: Xu Hao , Zhu Yanyan , Guo Peng , Liu Chunmei , Shan Jiankai , Tang Mingsheng 
Published: March 2018

AbstractIn this article, mechanisms of phosphine‐catalyzed [4 + 3] annulation of allenoates with C, N‐cyclic azomethine imines have been investigated using density functional theory. The catalytic cycle for the title reaction consists of five steps. Namely, the first step is the nucleophilic addition of phosphine catalyst, the second one is the CC bond formation, the third one is the proton transfer process, and the next one is the ring‐closure process, the last one is dissociation of the catalyst and the product generation. The calculated results indicate that the nucleophilic addition of phosphine catalyst is rate‐determining. With the use of Cat as the chiral catalyst, optically active products were obtained in good yields with excellent enantioselectivities while the CC bond formation is stereoselectivity‐determining. Furthermore, the theoretically predicted the main product is SS configuration, which is in good agreement with the experimental results. The special role of the catalysts and origin of stereoselectivity was also identified by NBO, GRI, and FMO analyses. This work might be helpful for understanding the significant roles of phosphine catalyst and thus provide valuable insights on the rational design of potential catalysts for this kind of reactions.