bluuebunny/crossref_metadata_2025_split huggingface dataset:
Historical overview of research on the tobacco mosaic virus genome: genome organization, infectivity and gene manipulation
Authors: Okada Y. 
Published: July 2002

Early in the development of molecular biology, TMV RNA was widely used as a mitochondrial RNA that could be purified easily, and it contributed much to research on protein synthesis. Also, in the early stages of elucidation of the genetic code, artificially produced TMV mutants were widely used and provided the first proof that the genetic code was non–overlapping. In 1982, Goeletet al.determined the complete TMV RNA base sequence of 6395 nucleotides. The four genes (130K, 180K, 30K and coat protein) could then be mapped at precise locations in the TMV genome. Furthermore it had become clear, a little earlier, that genes located internally in the genome were expressed via subgenomic mRNAs. The initiation site for assembly of TMV particles was also determined.However, although TMV contributed so much at the beginning of the development of molecular biology, its influence was replaced by that ofEscherichia coliand its phages in the next phase. As recombinant DNA technology developed in the 1980s, RNA virus research became more detached from the frontier of molecular biology. To recover from this setback, a gene–manipulation system was needed for RNA viruses. In 1986, two such systems were developed for TMV, using full–length cDNA clones, by Dawson's group and by Okada's group. Thus, reverse genetics could be used to elucidate the basic functions of all proteins encoded by the TMV genome. Identification of the function of the 30K protein was especially important because it was the first evidence that a plant virus possesses a cell–to–cell movement function. Many other plant viruses have since been found to encode comparable ‘movement proteins’. TMV thus became the first plant virus for which structures and functions were known for all its genes. At the birth of molecular plant pathology, TMV became a leader again.TMV has also played pioneering roles in many other fields. TMV was the first virus for which the amino acid sequence of the coat protein was determined and first virus for which cotranslational disassembly was demonstrated bothin vivoandin vitro. It was the first virus for which activation of a resistance gene in a host plant was related to the molecular specificity of a product of a viral gene. Also, in the field of plant biotechnology, TMV vectors are among the most promising. Thus, for the 100 years since Beijerinck's work, TMV research has consistently played a leading role in opening up new areas of study, not only in plant pathology, but also in virology, biochemistry, molecular biology, RNA genetics and biotechnology.
Advanced database methodology for the Collation of Connectivity data on the Macaque brain (CoCoMac)
Authors: Stephan Klass E. , Kamper Lars , Bozkurt Ahmet , Burns Gully A. P. C. , Young Malcolm P. , Kötter Rolf 
Published: July 2002

The need to integrate massively increasing amounts of data on the mammalian brain has driven several ambitious neuroscientific database projects that were started during the last decade. Databasing the brain's anatomical connectivity as delivered by tracing studies is of particular importance as these data characterize fundamental structural constraints of the complex and poorly understood functional interactions between the components of real neural systems. Previous connectivity databases have been crucial for analysing anatomical brain circuitry in various species and have opened exciting new ways to interpret functional data, both from electrophysiological and from functional imaging studies. The eventual impact and success of connectivity databases, however, will require the resolution of several methodological problems that currently limit their use. These problems comprise four main points: (i) objective representation of coordinate–free, parcellation–based data, (ii) assessment of the reliability and precision of individual data, especially in the presence of contradictory reports, (iii) data mining and integration of large sets of partially redundant and contradictory data, and (iv) automatic and reproducible transformation of data between incongruent brain maps.
Here, we present the specific implementation of the ‘collation of connectivity data on the macaque brain’ (CoCoMac) database (http://www.cocomac.org). The design of this database addresses the methodological challenges listed above, and focuses on experimental and computational neuroscientists' needs to flexibly analyse and process the large amount of published experimental data from tracing studies. In this article, we explain step–by–step the conceptual rationale and methodology of CoCoMac and demonstrate its practical use by an analysis of connectivity in the prefrontal cortex.
Structural investigations of the active‐site mutant Asn156Ala of outer membrane phospholipase A: Function of the Asn–His interaction in the catalytic triad
Authors: Snijder H.J. , Van Eerde J.H. , Kingma R.L. , Kalk K.H. , Dekker N. , Egmond M.R. , Dijkstra B.W. 
Published: July 2002

AbstractOuter membrane phospholipase A (OMPLA) from Escherichia coli is an integral‐membrane enzyme with a unique His–Ser–Asn catalytic triad. In serine proteases and serine esterases usually an Asp occurs in the catalytic triad; its role has been the subject of much debate. Here the role of the uncharged asparagine in the active site of OMPLA is investigated by structural characterization of the Asn156Ala mutant. Asparagine 156 is not involved in maintaining the overall active‐site configuration and does not contribute significantly to the thermal stability of OMPLA. The active‐site histidine retains an active conformation in the mutant notwithstanding the loss of the hydrogen bond to the asparagine side chain. Instead, stabilization of the correct tautomeric form of the histidine can account for the observed decrease in activity of the Asn156Ala mutant.
Detection of Nonglaucomatous Macula Findings With Ganglion Cell Analysis Printouts vs Full Macular Cube Scans
Authors: Yamane Maya , Ferreyra Henry , Xu Benjamin Y. , Weinreb Robert N. , Camp Andrew S. 
Published: September 2022

ImportanceGanglion cell analysis (GCA) of ocular coherence tomography (OCT) imaging is routinely used to detect and monitor glaucomatous damage of the ganglion cell complex in the macula. The GCA printout provides qualitative and quantitative data about the macular ganglion cell–inner plexiform layer and a single B-scan of the retina through the fovea. However, the full macular cube scan, including all 128 B-scans, is available for review. The macular cube scan provides considerable information about nonglaucomatous ocular pathology that may be missed if clinicians review only the GCA printout.ObjectiveTo determine the frequency and type of nonglaucomatous macular findings that are observable in the full macular cube scan but not the GCA printout.Design, Setting, and ParticipantsA retrospective cross-sectional analysis of GCA printouts and full macular cube scans to detect nonglaucomatous macular pathology at a tertiary care academic center. Consecutive patients undergoing ganglion cell complex imaging during routine glaucoma evaluations over a 1-week period in a multi-clinician glaucoma clinic.Main Outcomes and MeasuresThe prevalence and type of nonglaucomatous macular pathology visible on the GCA printout or macular cube scan.ResultsAmong 105 patients (mean (SD) age, 67 (15.46) years; 63 [60%] female and 42 [40%] male) 201 eyes were imaged (64 [31.7%] with suspected glaucoma, 126 [62.4%] with open-angle glaucoma, 6 [3.0%] with closed-angle glaucoma, and 6 [3.0%] with other glaucoma). GCA printouts and macular cube scans revealed nonglaucomatous macular pathology in 65 eyes (32.2%). Of these, 25 eyes (38.5%) included findings that were not visible on the GCA printout. Of the cases not visible on the printout, 16 eyes (64.0% ) included macular pathology that required further evaluation.Conclusions and RelevanceThe findings indicate that nonglaucomatous macular pathology may be missed based on GCA printouts alone. While it may be beneficial to review the full macular cube to detect potentially vision-threatening disease and ensure proper patient care, this study cannot determine if this missed pathology affects clinical outcomes.
Visualizing In‐Plane Junctions in Nitrogen‐Doped Graphene
Authors: Bouatou Mehdi , Chacon Cyril , Lorentzen Aleksander Bach , Ngo Huu Thoai , Girard Yann , Repain Vincent , Bellec Amandine , Rousset Sylvie , Brandbyge Mads , Dappe Yannick J. , Lagoute Jérôme 
Published: September 2022

AbstractControlling the spatial distribution of dopants in graphene is the gateway to the realization of graphene‐based electronic components. Here, it is shown that a submonolayer of self‐assembled physisorbed molecules can be used as a resist during a post‐synthesis nitrogen doping process to realize a nanopatterning of nitrogen dopants in graphene. The resulting formation of domains with different nitrogen concentrations allows obtaining n–n’ and p–n junctions in graphene. A scanning tunneling microscopy is used to measure the electronic properties of the junctions at the atomic scale and reveal their intrinsic width that is found to be ≈7 nm corresponding to a sharp junction regime.
Interfacial Engineering towards Enhanced Photovoltaic Performance of Sb2Se3 Solar Cell
Authors: Cai Huiling , Cao Rui , Gao Jinxiang , Qian Chen , Che Bo , Tang Rongfeng , Zhu Changfei , Chen Tao 
Published: September 2022

AbstractAntimony selenide (Sb2Se3) is a kind of emerging candidate for the application in low‐cost and high‐efficiency thin film solar cells owing to its non‐toxicity, earth‐abundance, and unique quasi‐1D crystal structure. In this photovoltaic material, quasi‐vertically oriented Sb2Se3 thin films can transfer photocarriers efficiently along the [hk1]‐orientation. However, the crystal orientation control in thin films is still the main obstacle to improve the efficiency of Sb2Se3 solar cells. Herein, an interfacial engineering method is developed by antimony chloride (SbCl3) on CdS films with post‐annealing treatment to improve the quality of both interface and absorber thin film. It is found that the SbCl3 treatment resulted in 1) transformation of the CdS/Sb2Se3 interface from “cliff” to “spike” like energy band alignments; 2) improved surface morphology of CdS surface, and 3) suppressed cubic structure of CdS structure and thus generating improved [hk1]‐oriented Sb2Se3 film on the high‐purity hexagonal CdS. As a result, the Sb2Se3 solar cell treated with SbCl3 achieves a top efficiency of 6.89% in superstrate planar heterojunction Sb2Se3 solar cell. This study provides a new interfacial post‐treatment method for the preparation of high‐performance Sb2Se3 planar heterojunction solar cells.
Modeling Biochemical Gradients In Vitro to Control Cell Compartmentalization in a Microengineered 3D Model of the Intestinal Epithelium
Authors: Altay Gizem , Abad‐Lázaro Aina , Gualda Emilio J. , Folch Jordi , Insa Claudia , Tosi Sébastien , Hernando‐Momblona Xavier , Batlle Eduard , Loza‐Álvarez Pablo , Fernández‐Majada Vanesa , Martinez Elena 
Published: September 2022

AbstractGradients of signaling pathways within the intestinal stem cell (ISC) niche are instrumental for cellular compartmentalization and tissue function, yet how are they sensed by the epithelium is still not fully understood. Here a new in vitro model of the small intestine based on primary epithelial cells (i), apically accessible (ii), with native tissue mechanical properties and controlled mesh size (iii), 3D villus‐like architecture (iv), and precisely controlled biomolecular gradients of the ISC niche (v) is presented. Biochemical gradients are formed through hydrogel‐based scaffolds by free diffusion from a source to a sink chamber. To confirm the establishment of spatiotemporally controlled gradients, light‐sheet fluorescence microscopy and in‐silico modeling are employed. The ISC niche biochemical gradients coming from the stroma and applied along the villus axis lead to the in vivo‐like compartmentalization of the proliferative and differentiated cells, while changing the composition and concentration of the biochemical factors affects the cellular organization along the villus axis. This novel 3D in vitro intestinal model derived from organoids recapitulates both the villus‐like architecture and the gradients of ISC biochemical factors, thus opening the possibility to study in vitro the nature of such gradients and the resulting cellular response.
Electron‐Selective Contacts ATO/LiF/Al‐Based High‐Performance N‐Type Silicon Solar Cells
Authors: Liu Ying , Zhang Lijuan , Cheng Hao , Song Xiaomin , Zhong Sihua , Shi Linxing , Huang Zengguang 
Published: September 2022

AbstractDue to its excellent passivation and low contact resistivity, Al‐doped TiO2(ATO) has become one of the most promising candidates for dopant‐free carriers‐selective contacts (CSCs). This work prepares the ATO/LiF/Al electron‐selective contacts and applies them to the n‐type silicon solar cells as full‐area rear CSCs. It is found that 6 nm‐thickness ATO thin film possesses the highest minority carrier lifetime of 253.0 µs on solar‐grade Cz n‐type wafers, revealing the ultra‐low saturated current densityJ0of 120.7 fA cm−2. Meanwhile, the 6 nm‐ATO/LiF/Al electron‐selective contact has a significantly low contact resistivity ρcof 19.7 mΩ cm2, suggesting a sound electronic transport property of the ATO/LiF/Al stack. Finally, a highest solar cell efficiency of 19.9% is obtained for an n‐type crystalline silicon device with a full‐area rear ATO/LiF/Al contact. The calculated selectivityS10of 13.0 enables the maximum efficiency of 27.3% for the ATO/LiF/Al‐based n‐type solar cell, demonstrating the great potential of applying this passivating contact in high‐efficiency silicon solar cells.
Diastereodivergent Synthesis of Syn‐ and Anti‐9‐Hydroxyhomoisoflavanone and its Application to the Total Syntheses of (±)‐Homoferrugenone and (±)‐Portulacanone F
Authors: Lee Sanha , Kwon Sangil , Hur Joonseong , Seo Seung‐Yong 
Published: September 2022

AbstractThe diastereodivergent synthesis of syn‐ and anti‐9‐hydroxyhomoisoflavanone from various chromones and carbaldehydes is described. The synthetic approaches involving the reductive aldol reaction or the Morita‐Baylis‐Hillman reaction followed by syn‐selective 1,4‐reduction provide both diastereomers of β‐hydroxy chroman‐4‐ones in 51–98% yield with anti (2 : 1–16 : 1 anti/syn) or 22–80% yield with syn (5 : 1–48 : 1 syn/anti) diastereoselectivity. The ambiguity surrounding the stereochemistry of two 9‐hydroxyhomoisoflavanones, homoferrugenone and portulacanone F was elucidated via the first total syntheses.magnified image
Triethyamine‐promoted [5+3] Cycloadditions for Regio‐ and Diastereoselective Synthesis of Functionalized aza‐Bicyclo[3.3.1]alkenones
Authors: Huang Jing , Jiang Bo , Zhang Xiyuan , Gao Yanfeng , Xu Xiufang , Miao Zhiwei 
Published: September 2022

AbstractWe have developed a synthetic strategy for Et3N‐promoted [5+3] cycloaddition reactions between acetoxypyranones and azomethine imines to access functionalized azabicyclo[3.3.1]alkenones with three tertiary stereocenters (31 examples, 36% to 87% yield, 5.5:1 to >20:1 dr). The method was scalable, and the products could be transformed to various eight‐membered‐ring bridged heterocyclic molecules.magnified image
An Atypical Acyl‐CoA Synthetase Enables Efficient Biosynthesis of Extender Units for Engineering a Polyketide Carbon Scaffold
Authors: Zheng Mengmeng , Zhang Jun , Zhang Wan , Yang Lu , Yan Xiaoli , Tian Wenya , Liu Zhihao , Lin Zhi , Deng Zixin , Qu Xudong 
Published: September 2022

AbstractAcyl‐CoAs are key precursors of primary and secondary metabolism. Their efficient biosynthesis is often impeded by the limited substrate specificity and low in vivo activity of acyl‐CoA synthetases (ACSs) due to regulatory acylation of the catalytically important lysine residue in motif A10 (Lys‐A10). In this study, we identified an unusual ACS (UkaQ) from the UK‐2A biosynthetic pathway that naturally lacks the Lys‐A10 residue and exhibits extraordinarily broad substrate specificity. Protein engineering significantly improved its stability and catalytic activity, enabling it to synthesize a large variety of acyl‐CoAs with highly robust activity. By combining it with permissive carboxylases, we produced a large array of polyketide extender units and obtained six novel halobenzyl‐containing antimycin analogues through an engineered biosynthetic pathway. This study significantly expands the catalytic mode of ACSs and provides a potent tool for the biosynthesis of acyl‐CoA‐derived natural products.
Endohedrally Functionalized Heteroleptic Coordination Cages for Phosphate Ester Binding
Authors: Platzek André , Juber Selina , Yurtseven Cem , Hasegawa Shota , Schneider Laura , Drechsler Christoph , Ebbert Kristina E. , Rudolf Robin , Yan Qian‐Qian , Holstein Julian J. , Schäfer Lars V. , Clever Guido H. 
Published: September 2022

AbstractMetallosupramolecular hosts of nanoscopic dimensions, which are able to serve as selective receptors and catalysts, are usually composed of only one type of organic ligand, restricting diversity in terms of cavity shape and functional group decoration. We report a series of heteroleptic [Pd2A2B2] coordination cages that self‐assemble from a library of shape complementary bis‐monodentate ligands in a non‐statistical fashion. Ligands A feature an inward pointing NH function, able to engage in hydrogen bonding and amenable to being functionalized with amide and alkyl substituents. Ligands B comprise tricyclic aromatic backbones of different shape and electronic situation. The obtained heteroleptic coordination cages were investigated for their ability to bind phosphate diesters as guests. All‐atom molecular dynamics (MD) simulations in explicit solvent were conducted to understand the mechanistic relationships behind the experimentally determined guest affinities.
Morphology and Light‐Dependent Spatial Distribution of Spin Defects in Carbon Nitride
Authors: Actis Arianna , Melchionna Michele , Filippini Giacomo , Fornasiero Paolo , Prato Maurizio , Salvadori Enrico , Chiesa Mario 
Published: September 2022

AbstractCarbon nitride (CN) is a heterogeneous photocatalyst that combines good structural properties and a broad scope. The photocatalytic efficiency of CN is associated with the presence of defective and radical species. An accurate description of defective states—both at a local and extended level—is key to develop a thorough mechanistic understanding of the photophysics of CN. In turn, this will maximise the generation and usage of photogenerated charge carriers and minimise wasteful charge recombination. Here the influence of morphology and light‐excitation on the number and chemical nature of radical defects is assessed. By exploiting the magnetic dipole‐dipole coupling, the spatial distribution of native radicals in CN is derived with high precision. From the analysis an average distance in the range 1.99–2.34 nm is determined, which corresponds to pairs of radicals located approximately four tri‐s‐triazine units apart.
Closed‐Loop Recycling of Poly(Imine‐Carbonate) Derived from Plastic Waste and Bio‐based Resources
Authors: Saito Keita , Eisenreich Fabian , Türel Tankut , Tomović Željko 
Published: September 2022

AbstractClosed‐loop recycling of polymers represents the key technology to convert plastic waste in a sustainable fashion. Efficient chemical recycling and upcycling strategies are thus highly sought‐after to establish a circular plastic economy. Here, we present the selective chemical depolymerization of polycarbonate by employing a vanillin derivative as bio‐based feedstock. The resulting di‐vanillin carbonate monomer was used in combination with various amines to construct a library of reprocessable poly(imine‐carbonate)s, which show tailor‐made thermal and mechanical properties. These novel poly(imine‐carbonate)s exhibit excellent recyclability under acidic and energy‐efficient conditions. This allows the recovery of monomers in high yields and purity for immediate reuse, even when mixed with various commodity plastics. This work provides exciting new insights in the design of bio‐based circular polymers produced by upcycling of plastic waste with minimal environmental impact.
Synergistic Interfacial Bonding in Reduced Graphene Oxide Fiber Cathodes Containing Polypyrrole@sulfur Nanospheres for Flexible Energy Storage
Authors: Huang Lei , Guan Tuxiang , Su Han , Zhong Yu , Cao Feng , Zhang Yongqi , Xia Xinhui , Wang Xiuli , Bao Ningzhong , Tu Jiangping 
Published: September 2022

AbstractFlexible lithium sulfur batteries with high energy density and good mechanical flexibility are highly desirable. Here, we report a synergistic interface bonding enhancement strategy to construct flexible fiber‐shaped composite cathodes, in which polypyrrole@sulfur (PPy@S) nanospheres are homogeneously implanted into the built‐in cavity of self‐assembled reduced graphene oxide fibers (rGOFs) by a facile microfluidic assembly method. In this architecture, sulfur nanospheres and lithium polysulfides are synergistically hosted by carbon and polymer interface, which work together to provide enhanced interface chemical bonding to endow the cathode with good adsorption ability, fast reaction kinetics, and excellent mechanical flexibility. Consequently, the PPy@S/rGOFs cathode shows enhanced electrochemical performance and high‐rate capability. COMSOL Multiphysics simulations and density functional theory (DFT) calculations are conducted to elucidate the enhanced electrochemical performance. In addition, a flexible Li−S pouch cell is assembled and delivers a high areal capacity of 5.8 mAh cm−2 at 0.2 A g−1. Our work offers a new strategy for preparation of advanced cathodes for flexible batteries.
Determination of mean activity coefficients and prediction of phase equilibria of the NaCl‐SrCl2‐H2O solution at 318.15 K
Authors: Sang Shi‐Hua , Fu Yang‐Xiao , Ge Qi , Liu Jia , Cui Rui‐Zhi 
Published: September 2022

AbstractIn this work, the cell potential method is used to measure activity coefficients of NaCl‐SrCl2‐H2O mixed solution at 318.15 K. The potential values of NaCl in NaCl‐H2O single salt solution were measured, and the standard cell potential E0 and electrode response slope k were fitted with linear regression. Subsequently, the results show that the ion‐selective electrode has a good Nernst response. The mean activity coefficients NaCl in NaCl‐SrCl2‐H2O solution are also determined with Nernst equation, and the total ionic strength in the mixed solution range is from 0.1000 ~ 0.8000 mol·kg−1, the ionic strength fraction of SrCl2 with yb = (0.0, 0.2, 0.4, 0.6, 0.8). Using the mean activity coefficients data and Pitzer model, the Pitzer ion interaction parameters
and
of Pitzer equations at 318.15 K are fitted. Furthermore, the mean activity coefficients of SrCl2, permeability coefficient Φ, water activity aw, and excess Gibbs free energy GE were also calculated by Pitzer's equations. The phase equilibria of the NaCl‐SrCl2‐H2O solution at 318.15 K are predicted, and corresponding phase diagram of the ternary solution is plotted according to the calculated solubilities in this work, and comparison of phase equilibria at different temperatures is also presented. The results show that the ion interaction parameters of Pitzer equations obtained in this work can be used for calculation of thermodynamic parameters and prediction of phase equilibria of salt‐water solutions containing strontium.