ResearchPad - full-papers https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[TASUKE+: a web-based platform for exploring GWAS results and large-scale resequencing data]]> https://www.researchpad.co/article/elastic_article_8842 Recent revolutionary advancements in sequencing technologies have made it possible to obtain mass quantities of genome-scale sequence data in a cost-effective manner and have drastically altered molecular biological studies. To utilize these sequence data, genome-wide association studies (GWASs) have become increasingly important. Hence, there is an urgent need to develop a visualization tool that enables efficient data retrieval, integration of GWAS results with diverse information and rapid public release of such large-scale genotypic and phenotypic data. We developed a web-based genome browser TASUKE+ (https://tasuke.dna.affrc.go.jp/), which is equipped with the following functions: (i) interactive GWAS results visualization with genome resequencing data and annotation information, (ii) PCR primer design, (iii) phylogenetic tree reconstruction and (iv) data sharing via the web. GWAS results can be displayed in parallel with polymorphism data, read depths and annotation information in an interactive and scalable manner. Users can design PCR primers for polymorphic sites of interest. In addition, a molecular phylogenetic tree of any region can be reconstructed so that the overall relationship among the examined genomes can be understood intuitively at a glance. All functions are implemented through user-friendly web-based interfaces so that researchers can easily share data with collaborators in remote places without extensive bioinformatics knowledge.

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<![CDATA[Correcting time‐intensity curves in dynamic contrast‐enhanced breast MRI for inhomogeneous excitation fields at 7T]]> https://www.researchpad.co/article/elastic_article_8294 Inhomogeneous excitation at ultrahigh field strengths (7T and above) compromises the reliability of quantified dynamic contrast‐enhanced breast MRI. This can hamper the introduction of ultrahigh field MRI into the clinic. Compensation for this non‐uniformity effect can consist of both hardware improvements and post‐acquisition corrections. This paper investigated the correctable radiofrequency transmit (B1+) range post‐acquisition in both simulations and patient data for 7T MRI.MethodsSimulations were conducted to determine the minimum B1+ level at which corrections were still beneficial because of noise amplification. Two correction strategies leading to differences in noise amplification were tested. The effect of the corrections on a 7T patient data set (N = 38) with a wide range of B1+ levels was investigated in terms of time‐intensity curve types as well as washin, washout and peak enhancement values.ResultsIn simulations assuming a common amount of T1 saturation, the lowest B1+ level at which the SNR of the corrected images was at least that of the original precontrast image was 43% of the nominal angle. After correction, time‐intensity curve types changed in 24% of included patients, and the distribution of curve types corresponded better to the distribution found in literature. Additionally, the overlap between the distributions of washin, washout, and peak enhancement values for grade 1 and grade 2 tumors was slightly reduced.ConclusionAlthough the correctable range varies with the amount of T1 saturation, post‐acquisition correction for inhomogeneous excitation was feasible down to B1+ levels of 43% of the nominal angle in vivo. ]]> <![CDATA[Continuous Flow Bioamination of Ketones in Organic Solvents at Controlled Water Activity using Immobilized ω‐Transaminases]]> https://www.researchpad.co/article/elastic_article_8234

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<![CDATA[(Electro‐)chemical Splitting of Dinitrogen with a Rhenium Pincer Complex]]> https://www.researchpad.co/article/elastic_article_7144 N2 splitting into terminal nitrides by chemical and electrochemical reduction of [ReCl2{N(CHCHPtBu2)2}] is presented. Comparison of electrochemical data with that of the previously reported, related pincer complex [ReCl2{N(CH2CH2PtBu2)2}] allowed for identifying key parameters that control the efficiency of the reaction sequence, which defines reductive N2 splitting.John Wiley & Sons, Ltd.

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<![CDATA[Synthesis, Modification, and Biological Evaluation of a Library of Novel Water‐Soluble Thiopyridone‐Based Organometallic Complexes and Their Unexpected (Biological) Behavior]]> https://www.researchpad.co/article/elastic_article_7084 A chemical concerto: Thiopyridone‐based piano‐stool complexes undergo dimerization in polar protic solvents. The resulting dimers (featuring a double positive charge) were studied for their effects in cancer cells.

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<![CDATA[Water–fat separation in spiral magnetic resonance fingerprinting for high temporal resolution tissue relaxation time quantification in muscle]]> https://www.researchpad.co/article/elastic_article_7049 To minimize the known biases introduced by fat in rapid T1 and T2 quantification in muscle using a single‐run magnetic resonance fingerprinting (MRF) water–fat separation sequence.MethodsThe single‐run MRF acquisition uses an alternating in‐phase/out‐of‐phase TE pattern to achieve water–fat separation based on a 2‐point DIXON method. Conjugate phase reconstruction and fat deblurring were applied to correct for B 0 inhomogeneities and chemical shift blurring. Water and fat signals were matched to the on‐resonance MRF dictionary. The method was first tested in a multicompartment phantom. To test whether the approach is capable of measuring small in vivo dynamic changes in relaxation times, experiments were run in 9 healthy volunteers; parameter values were compared with and without water–fat separation during muscle recovery after plantar flexion exercise.ResultsPhantom results show the robustness of the water–fat resolving MRF approach to undersampling. Parameter maps in volunteers show a significant (P < .01) increase in T1 (105 ± 94 ms) and decrease in T2 (14 ± 6 ms) when using water–fat‐separated MRF, suggesting improved parameter quantification by reducing the well‐known biases introduced by fat. Exercise results showed smooth T1 and T2 recovery curves.ConclusionWater–fat separation using conjugate phase reconstruction is possible within a single‐run MRF scan. This technique can be used to rapidly map relaxation times in studies requiring dynamic scanning, in which the presence of fat is problematic. ]]> <![CDATA[Exploration of New Biomass‐Derived Solvents: Application to Carboxylation Reactions]]> https://www.researchpad.co/article/elastic_article_7020 Sustainable solvents: The number of biomass‐derived solvents can be expanded. Hitherto unexplored as well as known biomass‐derived solvents can be used for numerous carboxylation reactions with carbon dioxide. Biomass‐derived solvents, such as isosorbide dimethyl ether and acetaldehyde diethyl acetal, are found to be not only as good as but sometimes even better than common organic solvents.

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<![CDATA[Rapid Biophysical Characterization and NMR Spectroscopy Structural Analysis of Small Proteins from Bacteria and Archaea]]> https://www.researchpad.co/article/elastic_article_7019 Reading expands horizons: Structural analysis of small proteins encoded by previously overlooked small open reading frames (sORFs) is achieved by using NMR spectroscopy. A protocol is established for fast NMR spectroscopy structure screening, including optimized sample preparation for systems of this size (14–78 aa), and determination of the structural conformations adopted by the systems.

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<![CDATA[Validation of the Slow Off‐Kinetics of Sirtuin‐Rearranging Ligands (SirReals) by Means of Label‐Free Electrically Switchable Nanolever Technology<a href="#cbic201900527-note-1001">†</a> ]]> https://www.researchpad.co/article/elastic_article_6995 Take your time choosing: Using the novel label‐free switchSENSE® technology, we were able to validate the long residence time of the sirtuin‐rearranging ligands (SirReals) selectively binding to Sirt2. We found that a long residence time as a consequence of an induced‐fit mechanism can be an important driver of pharmacological selectivity.

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<![CDATA[The Multifaceted Inhibitory Effects of an Alkylquinolone on the Diatom <i>Phaeodactylum tricornutum</i> ]]> https://www.researchpad.co/article/elastic_article_6938 Double trouble: In the light, 2‐heptyl‐4‐quinolone (HHQ) primarily blocks photosynthetic electron flow at the cytochrome b 6 f complex in the diatom P. tricornutum. In darkness, HHQ inhibits mitochondrial respiration, resulting in a decreased ATP supply, which ultimately leads to a decreased electric field strength in the thylakoid membranes inside the chloroplast of diatoms.

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<![CDATA[Assessing the Viability of Recovery of Hydroxycinnamic Acids from Lignocellulosic Biorefinery Alkaline Pretreatment Waste Streams]]> https://www.researchpad.co/article/elastic_article_6936 Stream on: A competitive lignocellulosic biorefinery will need to produce multiple product streams that include liquid fuel, solid fuel, and commodity chemicals. In this study, some key parameters are identified for the extraction of the valuable commodity chemicals p‐coumaric acid and ferulic acid from one of the waste streams in an alkaline‐pretreatment‐based biorefinery.

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<![CDATA[Sterically Demanding Ag<sup>I</sup> and Cu<sup>I</sup> N‐Heterocyclic Carbene Complexes: Synthesis, Structures, Steric Parameters, and Catalytic Activity]]> https://www.researchpad.co/article/elastic_article_6909 A unique family of AgI and CuI complexes possessing sterically demanding N‐heterocyclic carbene ligands is described. Their structural and steric profiling reveals the highest buried volumes (%V bur up to 57.5) for any expanded‐ring backbone NHC complex. For the first time, the AgI complexes have been employed as ligand‐transfer reagents while the CuI complexes proved to be efficient candidates for catalysis (see figure).

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<![CDATA[Electrolyte Imbalance Determination of a Vanadium Redox Flow Battery by Potential‐Step Analysis of the Initial Charging]]> https://www.researchpad.co/article/elastic_article_6904 One big step! A new method to quantify electrolyte imbalance in vanadium redox flow batteries is proposed. The key principle is a correlation between the duration of the potential plateaus in the open‐circuit voltage during initial charging and the amount of vanadium ions of a certain oxidation state in the half‐cell electrolytes. By applying this potential‐step analysis, the average oxidation state can be determined with a maximum error of 3.6 %.

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<![CDATA[Luminescent Anion Sensing by Transition‐Metal Dipyridylbenzene Complexes Incorporated into Acyclic, Macrocyclic and Interlocked Hosts]]> https://www.researchpad.co/article/elastic_article_6898 A series of acyclic, macrocyclic and mechanically interlocked luminescent anion sensors have been prepared by incorporation of the isophthalamide motif into dipyridylbenzene to obtain cyclometallated complexes of PtII and RuII. Anion titrations with the ruthenium [2]rotaxane demonstrate a marked increase in chloride binding affinity and indicate the interlocked receptor is capable of chloride recognition even in competitive 30 % aqueous mixtures (see figure).

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<![CDATA[Plasma‐Driven in Situ Production of Hydrogen Peroxide for Biocatalysis]]> https://www.researchpad.co/article/elastic_article_6871 Ride the lightning: Non‐thermal plasma is applied for noninvasive production of hydrogen peroxide to be used in biocatalysis. Side effects of plasma exposure can be alleviated by enzyme immobilization. Enantiomerically pure (R)‐1‐phenylethanol is produced with plasma‐generated H2O2 and AaeUPO.

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<![CDATA[Fibre‐specific regulation of lignin biosynthesis improves biomass quality in <i>Populus</i> ]]> https://www.researchpad.co/article/elastic_article_6856 Lignin is a major component of cell wall biomass and decisively affects biomass utilisation. Engineering of lignin biosynthesis is extensively studied, while lignin modification often causes growth defects.We developed a strategy for cell‐type‐specific modification of lignin to achieve improvements in cell wall property without growth penalty. We targeted a lignin‐related transcription factor, LTF1, for modification of lignin biosynthesis. LTF1 can be engineered to a nonphosphorylation form which is introduced into Populus under the control of either a vessel‐specific or fibre‐specific promoter.The transgenics with lignin suppression in vessels showed severe dwarfism and thin‐walled vessels, while the transgenics with lignin suppression in fibres displayed vigorous growth with normal vessels under phytotron, glasshouse and field conditions. In‐depth lignin structural analyses revealed that such cell‐type‐specific downregulation of lignin biosynthesis led to the alteration of overall lignin composition in xylem tissues reflecting the population of distinctive lignin polymers produced in vessel and fibre cells.This study demonstrates that fibre‐specific suppression of lignin biosynthesis resulted in the improvement of wood biomass quality and saccharification efficiency and presents an effective strategy to precisely regulate lignin biosynthesis with desired growth performance.

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<![CDATA[Photoswitchable Norbornadiene–Quadricyclane Interconversion Mediated by Covalently Linked C<sub>60</sub> ]]> https://www.researchpad.co/article/elastic_article_6851 Switching! The synthesis of several norbornadiene (NBD)–fullerene adducts is herein reported. Within these new hybrid systems, the photochemical isomerization of NBD is combined with the electron affinity of C60. This enables the selective light‐induced isomerization of the NBD derivative to its corresponding quadricyclane (QC) counterpart and the back conversion of the latter mediated by the photochemically excited fullerene core.

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<![CDATA[Structural Peculiarities and Thermoelectric Study of Iron Indium Thiospinel]]> https://www.researchpad.co/article/elastic_article_6844 Iron indium thiospinel: Two different mechanisms for the Fe incorporation into indium thiospinel were investigated, namely the charge‐balanced (A1) and the charge‐unbalanced (A2) series. The Fe content (i.e., vacancy concentration) strongly influences the unit cell parameter, charge carrier concentration, charge carrier mobility, as well as thermal conductivity (κ tot) in both series.

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<![CDATA[Assessment and correction of macroscopic field variations in 2D spoiled gradient‐echo sequences]]> https://www.researchpad.co/article/elastic_article_6835 To model and correct the dephasing effects in the gradient‐echo signal for arbitrary RF excitation pulses with large flip angles in the presence of macroscopic field variations.MethodsThe dephasing of the spoiled 2D gradient‐echo signal was modeled using a numerical solution of the Bloch equations to calculate the magnitude and phase of the transverse magnetization across the slice profile. Additionally, regional variations of the transmit RF field and slice profile scaling due to macroscopic field gradients were included. Simulations, phantom, and in vivo measurements at 3 T were conducted for R2∗ and myelin water fraction (MWF) mapping.ResultsThe influence of macroscopic field gradients on R2∗ and myelin water fraction estimation can be substantially reduced by applying the proposed model. Moreover, it was shown that the dephasing over time for flip angles of 60° or greater also depends on the polarity of the slice‐selection gradient because of phase variation along the slice profile.ConclusionSubstantial improvements in R2∗ accuracy and myelin water fraction mapping coverage can be achieved using the proposed model if higher flip angles are required. In this context, we demonstrated that the phase along the slice profile and the polarity of the slice‐selection gradient are essential for proper modeling of the gradient‐echo signal in the presence of macroscopic field variations. ]]> <![CDATA[Recycling of CO<sub>2</sub> by Hydrogenation of Carbonate Derivatives to Methanol: Tuning Copper–Oxide Promotion Effects in Supported Catalysts]]> https://www.researchpad.co/article/elastic_article_6811 A pillar of support: The Lewis acidity of coordinatively unsaturated centers (cus) on the oxide support tunes promotion effects in oxide‐supported copper nanoparticles as catalysts for selective hydrogenation of propylene carbonate. Intermediate Lewis acidity of the oxide maximizes the selectivity to methanol while preserving the propanediol molecular backbone, as required for cyclic processes of CO2 recycling to methanol via carbonate intermediates.

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