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Half a century after their discovery:Structural insights into exonuclease and annealase proteins catalyzing recombineering

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Engineering Microbiology 2024年第1期4卷 39-54页

作者： Lucy j.Fitschen Timothy p.Newing Nikolas p.j.hnston Charles E.Bell Gökhan Tolun School of Chemistry and Molecular Bioscience and Molecular HorizonsUniversity of WollongongWollongongNSWAustralia The ARC Training Centre for Cryo-electron Microscopy of Membrane proteins University of WollongongWollongongNSWAustralia Faculty of Science University of Technology SydneyUltimoNSW 2007Australia Department of Biological Chemistry and pharmacology The Ohio State University College of MedicineColumbusOH 43210

Recombineering is an essential tool for molecular biologists,allowing for the facile and efficient manipulation of bacterial genomes directly in cells without the need for costly and laborious in vitro manipulations involving restriction *** main workhorses behind recombineering are bacteriophage proteins that promote the single-strand annealing(SSA)homologous recombination pathway to repair double-stranded DNA *** there have been several reviews examining recombineering methods and applications,comparatively few have focused on the mechanisms of the proteins that are the key players in the SSA pathway:a 5′→3′exonuclease and a single-strand annealing protein(SSAp or“annealase”).This review dives into the structures and functions of the two SSA recombination systems that were the first to be developed for recombineering in ***:the RecET system from *** Rac prophage and the𝜆Red system from bacteriophageλ.By comparing the structures of the RecT and Red𝛽annealases,and the RecE and𝜆Exo exonucleases,we provide new insights into how the structures of these proteins dictate their *** the sequence conservation of the𝜆λExo and RecE exonucleases gives more profound insights into their critical functional ***,as recombineering accelerates and evolves in the laboratory,a better understanding of the mechanisms of the proteins behind this powerful technique will drive the development of improved and expanded capabilities in the future.

关键词： Recombineering Redβ λExo RecE RecT protein structure Annealase Exonuclease

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Modelling dynamic pantograph loads with combined numerical analysis

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Railway Engineering Science 2024年第1期32卷 81-94页

作者： F.F.j.ckson R.Mishra j.M.Rebelo j.Santos p.Antunes j.pombo H.Magalhaes L.Wills M.Askill School of Computing and Engineering University of HuddersfieldHuddersfieldUK School of Computing and Engineering Institute of Railway ResearchUniversity of HuddersfieldHuddersfieldUK IDMEC Instituto Superior TecnicoUniversidade de LisboaLisbonPortugal ISEL Instituto Politecnico de LisboaLisbonPortugal Hitachi Rail Newton AycliffeUK Wabtec/Brecknell Willis ChardUK

Appropriate interaction between pantograph and catenary is imperative for smooth operation of electric *** heights of overhead lines to accommodate level crossings,overbridges,and tunnels pose significant challenges in maintaining consistent current collection performance as the pantograph aerodynamic profile,and thus aerodynamic load changes significantly with operational *** research aims to analyse the global flow characteristics and aerodynamic forces acting on individual components of an HSX pantograph operating in different configurations and orientations,such that the results can be combined with multibody simulations to obtain accurate dynamic insight into contact ***,computational fluid dynamics simulations are used to investigate the pantograph component loads in a representative setting,such as that of the recessed cavity on a Class 800 *** an aerodynamic perspective,this study indicates that the total drag force acting on non-fixed components of the pantograph is larger for the knuckle-leading orientation rather than the knuckle-trailing,although the difference between the two is found to reduce with increasing pantograph *** the aerodynamic loads acting on individual components with multibody tools allows for realistic dynamic insight into the pantograph *** results obtained show how considering aerodynamic forces enhance the realism of the models,leading to behaviour of the pantograph-catenary contact forces closely matching that seen in experimental tests.

关键词： pantograph-catenary interaction pantograph aerodynamics Computational fluid dynamics pantograph loads Current collection performance

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The Reality of Baryonic Acoustic Oscillations

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j.urnal of Modern physics 2024年第3期15卷 377-402页

作者： j. C. Botke Ronin Institute Montclair New Jersey USA

The initial idea for baryonic acoustic oscillations (BAO) came about during early efforts to understand the origin of galaxies by studying perturbed versions of the Friedmann-Robertson-Walker (FRW) model. In more recent times, the emphasis has shifted to the idea that 2-point galaxy correlations embedded in the distribution of matter by the BAO could be used as a standard ruler to fix the parameters of cosmological models. In this paper, we first consider the actual business of extracting the correlation length from large data sets of measured galaxy locations. To facilitate this process, we introduce a much-improved method for extracting the correlation peak from the data set. Fundamental to this process in any model is the use of a fiducial cosmological model to transition from redshift space to comoving coordinate space where the correlations actually exist. The belief is that the correlation length so determined can then be reverted to redshift space to fix the parameters of cosmological models. We show, however, that this process is circular and hence of no value whatsoever for fixing model parameters. All one obtains are the parameters of the model used to transition to comoving space in the first place. Finally, we present simple arguments that show that the idea of BAO being responsible for the structure of the universe, i.e. the cosmic web, is unworkable.

关键词： Baryonic Acoustic Oscillations Two-point Correlations CMB Anisotropy Early Universe Time-Varying Curvature

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The Origin of Cosmic Structures part 6: CMB Anisotropy

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j.urnal of High Energy physics, Gravitation and Cosmology 2024年第1期10卷 257-276页

作者： j. C. Botke Ronin Institute Montclair New Jersey USA

In a recent series of papers, we introduced a new model of nucleosynthesis in which the matter content of the universe came into existence at a time of about 4 × 10-5 s. At that time, a small percentage of the vacuum... 详细信息

In a recent series of papers, we introduced a new model of nucleosynthesis in which the matter content of the universe came into existence at a time of about 4 × 10p>-5p> s. At that time, a small percentage of the vacuum energy was converted into neutron/antineutron pairs with a very small excess of neutrons. This process was regulated by an imprint that was established in the vacuum during an initial plank-era inflation. Immediately after their inception, annihilation and charge exchange reactions proceeded at a very high rate and ran to completion after an interval of about 10p>-11p> s. By then, all the antibaryons had disappeared thereby establishing the matter/antimatter asymmetry of the universe. What remained were very high densities of mesons and leptons, somewhat lower densities of protons and neutrons, and finally, the very high density of photons that eventually became the CMB. The density of matter so created varied from one location to another in such a manner as to account for all cosmic structures and because the energy density of the photons varied in proportion to that of the matter, the CMB-to-be came into existence with an anisotropic spectrum already in place. For structures, the size of galaxy clusters, the initial anisotropy magnitudes were on the order of 25%. In this paper, we will follow the subsequent evolution of the photons and show that this model predicts with accuracy the temperature of the warmest anisotropies in the observed CMB spectrum. .

关键词： CMB Anisotropy Dispersion Nucleosynthesis Early Universe Time-Varying Curvature

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Bulking Up the Bay-position Substituents Enables Enhanced Selectivity of C_(s)‑Symmetric Boron Subphthalocyanine−Subnaphthalocyanine Hybrids

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precision Chemistry 2024年第4期2卷 161-181页

作者： Nina F.Farac Alan j.Lough Timothy p.Bender Department of Chemical Engineering and Applied Chemistry University of TorontoTorontoOntario M5S 3E5Canada Department of Chemistry University of TorontoTorontoOntario M5S 3H6Canada Department of Materials Science and Engineering University of TorontoTorontoOntario M5S 3E4Canada Department of Mechanical and Industrial Engineering University of TorontoTorontoOntario M5S 3G8Canada

The precise synthesis of subporphyrinoid hybrids withπ-expanded topologies and unique material properties plays a promising role in the design of functional ***,selective,and controllable routes to boron subphthalocyanine−subnaphthalocyanine hybrids,Bsub(pc_(3‑p)-Nc_(p))s,are desirable for this purpose yet synthetically challenging due to random mixtures of C_(s-),C_(3v-),and,in some cases,C_(1)-symmetric compounds that form during traditional statistical mixed ***,we addressed this issue by developing a sterically driven mixed cyclotrimerization with enhanced selectivity for the targeted C_(s)-symmetric hybrid and complete suppression of sterically crowded macrocyclic *** process,coupled with a rationally designed precursor bearing bulky phenyl substituents,enabled the synthesis and characterization of bay-position phenylated ph_(2)-(R_(p))_(8)Bsub(pc_(2)-Nc_(1))hybrids with halogens(Rp=Cl or F)in their peripheral isoindole *** selectivity ranged between 59 and 72%with remarkable yields,significantly higher than that of conventional mixed *** findings were augmented by theoretical calculations on precursor Lewis basicity as guiding principles into hybrid macrocycle ***,the incorporation of unfused phenyl groups and halogen atoms into the hybrid framework resulted in fine-tuned optical,structural,electronic,and electrochemical *** straightforward approach achieved improved selectivity and controlled narrowing of the product distribution,affording the efficient synthesis of structurally sophisticated Bsub(pc_(2)-Nc_(1))*** then expands the library of 3-dimensionalπ-extended macrocycles for use in a range of applications,such as in optoelectronic devices with precisely tailored optical properties.

关键词： subphthalocyanine hybrids low-symmetry aromatic macrocycle selective cyclotrimerization sterically driven chemistry broad absorption material properties

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Copernicrinus zamorae *** ***.,the oldest thiolliericrinid crinoid(Crinoidea,Echinodermata) from the Baj.cian strata of Algeria,Africa

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j.urnal of palaeogeography 2024年第2期13卷 237-251页

作者： Bartosz j.pιachno Madani Benyoucef Fayc al Mekki Mohammed Adaci Imad Bouchemla Sreepat j.in Marcin Kraj.wski Mariusz A.Salamon Faculty of Biology Institute of BotanyJagiellonian University in KrakowGronostajowa Street 930-387 KrakowPoland Laboratoire de Géomatique Ecologie et EnvironnementMustapha Stambouli University of MascaraDZ-29000 MascaraAlgeria Abou Bekr Belkaid University of Tlemcen TlemcenAlgeria Department of Geological Sciences Faculty of Biological and Agricultural SciencesMouloud Mammeri University of Tizi-OuzouTizi-OuzouAlgeria Adama Science and Technology University School of Applied Natural SciencesDepartment of Applied GeologyP.O.Box 1888AdamaEthiopia Faculty of Geology Geophysics and Environmental ProtectionAGH University of Science and TechnologyAl.A.Mickiewicza 30PL-30-059KrakowPoland Faculty of Natural Sciences University of Silesia in KatowiceBedzinska Street 60PL-41-200 SosnowiecPoland

The thiolliericrinids(Thiolliericrinidae) are comatulids(Comatulida),which retained their stalks as ***,we report a centrodorsal from the Baj.cian strata(Middle j.rassic) of the Dj.bel Kérdacha area,northwestern Algeria(Africa).It is the first thiolliericrinid report from outside of Europe and also the oldest representative of the Thiolliericrinidae whose first occurrence is from the *** crinoid is assigned to Copernicrinus zamorae *** *** reported new taxon shows strong similarities with the stemless ‘true’comatulids,Solanocrinites;the only difference is the presence of a facet to the stem in *** closest comparable thiolliericrinid to Copernicrinus is the Oxfordian Thiolliericrinus,interpreted as a descendant of the *** origin and overview of all thiolliericrinid representatives are also discussed herein.

关键词： Thiolliericrinidae Crinoids Coral facies Baj.cian j.rassic Algeria Southern Tethys margin

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Modeling of Total Dissolved Solids (TDS) and Sodium Absorption Ratio (SAR) in the Edwards-Trinity plateau and Ogallala Aquifers in the Midland-Odessa Region Using Random Forest Regression and eXtreme Gradient Boosting

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j.urnal of Geoscience and Environment protection 2024年第5期12卷 218-241页

作者： Azuka I. Udeh Osayamen j. Imarhiagbe Erepamo j. Omietimi Department of Geoscience University of Texas Permian Basin Odessa Texas USA Department of Geology University of Pretoria Pretoria South Africa

Efficient water quality monitoring and ensuring the safety of drinking water by government agencies in areas where the resource is constantly depleted due to anthropogenic or natural factors cannot be overemphasized. The above statement holds for West Texas, Midland, and Odessa precisely. Two machine learning regression algorithms (Random Forest and XGBoost) were employed to develop models for the prediction of total dissolved solids (TDS) and sodium absorption ratio (SAR) for efficient water quality monitoring of two vital aquifers: Edward-Trinity (plateau), and Ogallala aquifers. These two aquifers have contributed immensely to providing water for different uses ranging from domestic, agricultural, industrial, etc. The data was obtained from the Texas Water Development Board (TWDB). The XGBoost and Random Forest models used in this study gave an accurate prediction of observed data (TDS and SAR) for both the Edward-Trinity (plateau) and Ogallala aquifers with the Rp>2p> values consistently greater than 0.83. The Random Forest model gave a better prediction of TDS and SAR concentration with an average R, MAE, RMSE and MSE of 0.977, 0.015, 0.029 and 0.00, respectively. For the XGBoost, an average R, MAE, RMSE, and MSE of 0.953, 0.016, 0.037 and 0.00, respectively, were achieved. The overall performance of the models produced was impressive. From this study, we can clearly understand that Random Forest and XGBoost are appropriate for water quality prediction and monitoring in an area of high hydrocarbon activities like Midland and Odessa and West Texas at large.

关键词： Water Quality prediction predictive Modeling Aquifers Machine Learning Regression eXtreme Gradient Boosting

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Macroinvertebrate Community Index (MCI) and Quantitative Macroinvertebrate Community Index (QMCI) Analysis: A Comparative Study between Le Afe and Mulivaifagatoloa Rivers, Upolu Island, Samoa

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j.urnal of Geoscience and Environment protection 2024年第8期12卷 149-167页

作者： S. Taupega-Satau p. Amosa A. Leauga j. Nunufolau T. Veni Nun Yan Department of Science National University of Samoa Apia Samoa Office of The Vice Chancellor National University of Samoa Apia Samoa Department of Information Technology and Systems National University of Samoa Apia Samoa

The diversity of Samoa’s freshwater macroinvertebrates remains largely unexplored, with past studies focusing on specific species without comprehensive cataloguing. This research evaluated the health of Upolu Island’s rural rivers through macroinvertebrate analysis, particularly in the Le Afe and Mulivaifagatoloa Rivers. Collaborating with Samoa’s Water Resources Division in the Ministry of Natural Resources and Environment (MNRE), three sites along each river were sampled, representing a gradient from pristine to anthropogenically impacted areas. A total of 2953 macroinvertebrates were collected and classified into five categories using established identification keys. The Macroinvertebrate Community Index (MCI) and Quantitative Macroinvertebrate Community Index (QMCI) were applied for analysis. The results showed no clear pattern of pollutant-sensitive species prevalence or decline in less disturbed rivers. High MCI scores with low QMCI values indicated numerous low-scoring species, while the opposite suggested a richness of high-scoring taxa. Although MCI and QMCI are tools for monitoring freshwater health, this study lays the groundwork for future research to categorize Samoan macroinvertebrates and assign tolerance scores based on their presence in varying river conditions. .

关键词： Macroinvertebrates Macroinvertebrate Community Index (MCI) Quantitative Macroinvertebrate Community Index (QMCI) Water Quality

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Optimization of chemistry and process parameters for control of intermetallic formation in Mg sludges

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j.urnal of Magnesium and Alloys 2024年第4期12卷 1431-1448页

作者： Y.Fu G.G.Wang A.Hu Y.Li K.B.Thacker j.p.Weiler H.Hu Department of Mechanical Automotive and Materials EngineeringUniversity of Windsor401 Sunset AveWindsorOntario N9B 3P4Canada Global Technology Centre Meridian Lightweight Technologies25 MacNab AveStrathroyOntario N7G 4H6Canada

Intermetallic formation in sludge during magnesium(Mg)melting,holding and high pressure die casting practices is a very important ***,very often it is overlooked by academia,original equipment manufacturers(OEM),metal ingot producers and even die *** aim of this study was to minimize the intermetallic formation in Mg sludge via the optimization of the chemistry and process *** Al8Mn5 intermetallic particles were identified by the microstructure analysis based on the Al and Mn *** design of experiment(DOE)technique,Taguchi method,was employed to minimize the intermetallic formation in the sludge of Mg alloys with various chemical compositions of Al,Mn,Fe,and different process parameters,holding temperature and holding *** sludge yield(SY)and intermetallic size(IS)was selected as two *** optimum combination of the levels in terms of minimizing the intermetallic formation were 9 wt.%Al,0.15 wt.%Mn,0.001 wt.%(10 ppm)Fe,690℃ for the holding temperature and holding at 30 mins for the holding time,*** best combination for smallest intermetallic size were 9 wt.%Al,0.15 wt.%Mn,0.001 wt.%(10 ppm)Fe,630℃ for the holding temperature and holding at 60 mins for the holding time,*** groups of sludge factors,Chemical Sludge(CSF),physical Sludge(pSF)and Comprehensive Sludge Factors(and CpSF)were established for prediction of sludge yields and intermetallic sizes in Al-containing Mg *** CpSF with five independent variables including both chemical elements and process parameters gave high accuracy in prediction,as the prediction of the pSF with only the two processing parameters of the melt holding temperature and time showed a relatively large deviation from the experimental *** Chemical Sludge Factor was primarily designed for small ingot producers and die casters with a limited melting and holding capacity,of which process parameters could be fixed *** physical Sludge Factor could be used f

关键词： Magnesium sludge Al-Mn intermetallic Optimization Taguchi method Sludge factor Chemical composition process parameter

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Towards efficient strain engineering of 2D materials:A four-points bending approach for compressive strain

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Nano Research 2024年第6期17卷 5317-5325页

作者： Hao Li Félix Carrascoso Ana Borrás Gloria p.Moreno Francisco j.Aparicio Ángel Barranco Andrés Castellanos Gómez Campus de Cantoblanco Instituto de Ciencia de Materiales de MadridC.Sor Juana Inés de la Cruz328049 MadridSpain Nanotechnology on Surfaces and plasma Lab Instituto de Ciencia de Materiales de Sevilla(CSIC-Universidad de Sevilla).C/Americo Vespucio 49E-41092 SevilleSpain Departamento de Física Aplicada I Escuela Politécnica SuperiorUniversidad de Sevillac/Virgen deÁfrica 7E-41011 SevilleSpain

Strain engineering,as a powerful strategy to tune the optical and electrical properties of two-dimensional(2D)materials by deforming their crystal lattice,has attracted significant interest in recent years.2D materials can sustain ultra-high strains,even up to 10%,due to the lack of dangling bonds on their surface,making them ideal brittle *** remarkable mechanical resilience,together with a strong strain-tunable band structure,endows 2D materials with a broad optical and electrical response upon ***,strain engineering based on 2D materials is restricted by their nanoscale and strain quantification *** this study,we have modified a homebuilt three-points bending apparatus to transform it into a four-points bending apparatus that allows for the application of both compressive and tensile strains on 2D *** approach allows for the efficient and reproducible construction of a strain system and minimizes the buckling effect caused by the van der Waals interaction by adamantane encapsulation *** results demonstrate the feasibility of introducing compressive strain on 2D materials and the potential for tuning their optical and physical properties through this approach.

关键词： uniaxial compressive strain polymer encapsulation differential reflectance spectroscopy exciton tunability

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