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Dominance of transposable element‑related satDNAs results in great complexity of“satDNA library”and invokes the extension towards“repetitive DNA library”

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Marine Life Science & Technology 2024年第2期6卷 236-251页

作者： Monika Tunjić‑Cvitanić Daniel García‑Souto juan j.Pasantes EvaŠatović‑Vukšić Division of Molecular Biology Ruđer BoškovićInstitute10000 ZagrebCroatia Genomes and Disease Centre for Research in Molecular Medicine and Chronic Diseases(CIMUS)Universidade de Santiago de Compostela15706 Santiago de CompostelaSpain Department of Zoology Genetics and Physical AnthropologyUniversidade de Santiago de Compostela15706 Santiago de CompostelaSpain Centro de Investigación Mariña Dpto de BioquímicaXenética e InmunoloxíaUniversidade de Vigo36310 VigoSpain

Research on bivalves is fast-growing,including genome-wide analyses and genome sequencing.Several characteristics qualify oysters as a valuable model to explore repetitive DNA sequences and their genome organization.Here we char-acterize the satellitomes of five species in the family Ostreidae(Crassostrea angulata,C.virginica,C.hongkongensis,C.ariakensis,Ostrea edulis),revealing a substantial number of satellite DNAs(satDNAs)per genome(ranging between 33 and 61)and peculiarities in the composition of their satellitomes.Numerous satDNAs were either associated to or derived from transposable elements,displaying a scarcity of transposable element-unrelated satDNAs in these genomes.Due to the non-conventional satellitome constitution and dominance of Helitron-associated satDNAs,comparative satellitomics demanded more in-depth analyses than standardly employed.Comparative analyses(including C.gigas,the first bivalve species with a defined satellitome)revealed that 13 satDNAs occur in all six oyster genomes,with Cg170/HindIII satDNA being the most abundant in all of them.Evaluating the“satDNA library model”highlighted the necessity to adjust this term when studying tandem repeat evolution in organisms with such satellitomes.When repetitive sequences with potential variation in the organizational form and repeat-type affiliation are examined across related species,the introduction of the terms“TE library”and“repetitive DNA library”becomes essential.

关键词： Satellitome Comparative satellitomics Helitron Bivalves “Dark matter of the genome”

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Management of monogenic diabetes in pregnancy:A narrative review

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World journal of Diabetes 2024年第1期15卷 15-23页

作者： Mohammad Sadiq jeeyavudeen Sarah R Murray Mark W j Strachan Metabolic Unit Western General HospitalEdinburgh EH42XUUnited Kingdom MRC Centre for Reproductive Health University of Edinburgh Queen’s Medical Research InstituteEdinburgh EH164TJUnited Kingdom

Pregnancy in women with monogenic diabetes is potentially complex,with significant implications for both maternal and fetal health.Among these,maturity-onset diabetes of the young(MODY)stands out as a prevalent monogenic diabetes subtype frequently encountered in clinical practice.Each subtype of MODY requires a distinct approach tailored to the pregnancy,diverging from management strategies in non-pregnant individuals.Glucokinase MODY(GCK-MODY)typically does not require treatment outside of pregnancy,but special considerations arise when a woman with GCK-MODY becomes pregnant.The glycemic targets in GCK-MODY pregnancies are not exclusively dictated by the maternal/paternal MODY genotype but are also influenced by the genotype of the developing fetus.During pregnancy,the choice between sulfonylurea or insulin for treating hepatocyte nuclear factor 1-alpha(HNF1A)-MODY and HNF4A-MODY depends on the mother’s specific circumstances and the available expertise.Management of other rarer MODY subtypes is individu-alized,with decisions made on a case-by-case basis.Therefore,a collaborative approach involving expert diabetes and obstetric teams is crucial for the compre-hensive management of MODY pregnancies.

关键词： Diabetes Pregnancy Maturity-onset diabetes of the young Insulin Sulphonylurea Glucokinase Hepatocyte nuclear factor 1-alpha,hepatocyte nuclear factor 1-beta,and hepatocyte nuclear factor 4-alpha

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Superplasticity of fine-grained Mg-10Li alloy prepared by severe plastic deformation and understanding its deformation mechanisms

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journal of Magnesium and Alloys 2024年第1期12卷 316-331页

作者： H.T.jeong S.W.Lee W.j.Kim Department of Materials Science and Engineering Hongik UniversityMapo-guSangsu-dong 72-1Seoul 121-791Republic of Korea

The superplastic behavior and associated deformation mechanisms of a fine-grained Mg-10.1 Li-0.8Al-0.6Zn alloy(LAZ1011)with a grain size of 3.2μm,primarily composed of the BCCβphase and a small amount of the HCPαphase,were examined in a temperature range of 473 K to 623 K.The microstructural refinement of this alloy was achieved by employing high-ratio differential speed rolling.The best superplasticity was achieved at 523 K and at strain rates of 10^(-4)-5×10^(-4)s^(-1),where tensile elongations of 550±600%were obtained.During the heating and holding stage of the tensile samples prior to tensile loading,a significant increase in grain size was observed at temperatures above 573 K.Therefore,it was important to consider this effect when analyzing and understanding the superplastic deformation behavior and mechanisms.In the investigated strain rate range,the superplastic flow at low strain rates was governed by lattice diffusion-controlled grain boundary sliding,while at high strain rates,lattice diffusion-controlled dislocation climb creep was the rate-controlling deformation mechanism.It was concluded that solute drag creep is unlikely to occur.During the late stages of deformation at 523 K,it was observed that grain boundary sliding led to the agglomeration of theαphase,resulting in significant strain hardening.Deformation mechanism maps were constructed forβ-Mg-Li alloys in the form of 2D and 3D formats as a function of strain rate,stress,temperature,and grain size,using the constitutive equations for various deformation mechanisms derived based on the data of the current tests.

关键词： Magnesium-lithium alloy Superplasticity Severe plastic deformation Grain size Grain growth

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Interaction between diet and genetics in patients with inflammatory bowel disease

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World journal of Gastroenterology 2024年第12期30卷 1644-1650页

作者： Daniéla Oliveira Magro Ligia Yukie Sassaki júlio Maria Fonseca Chebli Department of Surgery Faculty of Medical SciencesState University of Campinas(UNICAMP)Campinas 13083-970São PauloBrazil Department of Internal Medicine Medical SchoolSao Paulo State University(UNESP)Botucatu 18618-687São PauloBrazil Department of Medicine University Hospital of the Federal University of Juiz de ForaUniversity of Juiz de Fora School of MedicineJuiz de Fora 36036-247Minas GeraisBrazil

In this editorial,we comment on the article by Marangoni et al,published in the recent issue of the World journal of Gastroenterology 2023;29:5618-5629,about“Diet as an epigenetic factor in inflammatory bowel disease”.The authors emphasized the role of diet,especially the interaction with genetics,in promoting the inflam-matory process in inflammatory bowel disease(IBD)patients,focusing on DNA methylation,histone modifications,and the influence of microRNAs.In this editorial,we explore the interaction between genetics,gut microbiota,and diet,in an only way.Furthermore,we provided dietary recommendations for patients with IBD.The Western diet,characterized by a low fiber content and deficiency the micronutrients,impacts short-chain fatty acids production and may be related to the pathogenesis of IBD.On the other hand,the consumption of the Mediter-ranean diet and dietary fibers are associated with reduced risk of IBD flares,particularly in Crohn’s disease(CD)patients.According to the dietary guidance from the International Organization for the Study of Inflammatory Bowel Diseases(IOIBD),the regular consumption of fruits and vegetables while reducing the consumption of saturated,trans,dairy fat,additives,processed foods rich in maltodextrins,and artificial sweeteners containing sucralose or saccharine is recommended to CD patients.For patients with ulcerative colitis,the IOIBD recommends the increased intake of natural sources of omega-3 fatty acids and follows the same restrictive recommendations aimed at CD patients,with the possible inclusion of red meats.In conclusion,IBD is a complex and hetero-geneous disease,and future studies are needed to elucidate the influence of epigenetics on diet and microbiota in IBD patients.

关键词： Diet Genetics MicroRNAs Gastrointestinal microbiome Inflammatory bowel diseases Crohn’s disease

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Mathematical modelling of ball and plate system with experimental and correlation function-based model validation

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Control Theory and Technology 2024年第2期22卷 326-341页

作者： T.R.Dil Kumar S.j.Mija Department of Electrical Engineering National Institute of Technology CalicutKozhikode673601KeralaIndia

The ball and plate system is an inherently nonlinear under actuated benchmark system used for validating the performance of various control schemes. A mathematical model depicting the dynamics close to that of the system is very much required for such a test bed. In this correspondence, the complete nonlinear model, a simplified nonlinear model, and a linearized model of the ball and plate system are developed. The system comprises a ball and plate mechanism and a rotary servo unit. The ball and plate mechanism is modelled using the Euler–Lagrange method, whereas the rotary servo subsystem is modelled from the first principles. The nonlinear model of the combined system is developed by including the dynamics of the servo motor with gear and rolling resistance between the ball and the plate. The simplified nonlinear model of the system is obtained with suitable assumptions. The model is linearized around the operating point using the jacobian. The validity of the developed models is investigated through correlation function analysis. The open-loop response of the three models, viz., nonlinear, simplified nonlinear, and linearized models, is analyzed in the MATLAB/Simulink platform. Since the open-loop system is unstable, the experimental validation of the model is performed with a double-loop PSO (particle swarm optimization) PID control scheme.

关键词： Ball and plate system Correlation function Model validation Particle swarm optimization(PSO) PSO PID controller

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n-Alkane bound biomarker fingerprints from asphaltenes in the bitumens of Eastern Dahomey Basin,Nigeria:Source and genetic implications

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Petroleum Research 2024年第1期9卷 85-91页

作者： Modupe A.Egbeola Olubunmi C.Adeigbe Olajide j.Adamolekun Department of Geology University of IbadanIbadanNigeria Structural Geology and Tectonics Institute of Applied GeosciencesKIT-Karlsruhe Institute of TechnologyAdenauerring 20a76131KarlsruheGermany

The asphaltene fractions of the bitumens of Eastern Dahomey Basin in Nigeria,were analyzed by flash pyrolysis-gas chromatography(Py-GC)method in order to unravel its geochemical history and properties.The distributions of the initial biomarkers of the original oils from the pyrolysates are related to the assessment of organic matter source,paleo-redox conditions and source environment during deposition.Also,it effectively establishes the genetic relationship of the bitumens.The n-alkane distributions in the pyrolysates reveal nC_(9)-nC_(32)n-alkanes,maximizing at nC_(14),isoprenoids-pristane(Pr)and phytane(Ph),and some n-alkene peaks.High peaks of low to medium-weight nC_(9)-nC20 n-alkanes and low peaks of nC_(21)+n-alkanes characterize the distributions.These reveal that abundant algal organic matter with some terrigenous inputs contributed to the source rock of the bitumens.The high concentration of marine organic matter inputs to the source rock is further confirmed by the nC_(17)/nC27 ratios which range from 5.39 to 19.82 and shows the predominance of nC_(17)alkanes.The general unimodal n-alkane distributions in the bitumens indicate derivation from similar organic matter types showing that they are genetically related.The anoxic to suboxic environmental conditions that prevailed during the deposition of the sediments is revealed by the isoprenoids,Pr/Ph ratios(0.72-1.28).Pristane/nC_(17)and Phytane/nC_(18)range from 0.16 to 0.33 and 0.22 to 0.56,revealing that the bitumens were from predominantly marine organic matter(type II kerogen)preserved in a reducing environment with no evidence of biodegradation.However,the Ph/nC_(18)ratio and the cross plot of Pr+Ph/nC_(17)+nC_(18)allow the classification of the bitumens into two subfamilies/groups(A and B).The bitumen samples have low wax content as indicated by the degree of waxiness ranging from 0.21 to 0.38 which confirms low terrigenous input.Based on the carbon preference index(CPI:0.92 to 1.55)and odd-even predominance(OEP:0.70 to 1.36),it is concluded that t

关键词： Genetic relationship Flash pyrolysis Biomarker Asphaltene Pyrolysates

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High resolution sequence stratigraphy of the Mishrif Formation(Cenomanian-Early Turonian)at zubair oilfield(al-rafdhiah dome),southern Iraq

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Petroleum Research 2024年第1期9卷 61-71页

作者： Aymen A.Lazim Maher j.Ismail Maher M.Mahdi Geoscience Department Zubair Field Operation DivisionBasra Oil CompanyIraq Basrah Oil Company WQ1 FODBasrahIraq University of Basrah College of ScienceGeology Dept.BasrahIraq

The Mishrif Formation(Cenomanian-E Turonian)is one of the most important geological formations in the Middle East and Iraq because it contains enormous petroleum accumulations.It is considered to be the first reservoir in the region,and is still being studied because of its economic significance.The carbonate of the Mishrif Formation derives from a variety of depositional settings,including mid-ramp,shoal,lagoon,and intertidal.The five main microfacies discussed in this paper are wackestone,packstone,grainstone,floatstone,and bindstone.The most frequent fossilised components found in the Mishrif Formation are rudists,benthic foraminifera,echinoderms,burrows molluscs,and algae.According to the microfacies and analysed wireline log data,the sequence stratigraphy of the studied formation is composed of two regression cycles.Five parasequences of transgressive-regressive cycles make up the depositional sequence of the Mishrif Formation.The standard depositional environments seem to demonstrate a gradual regression,beginning with a short period of the outer ramp,then a steady period of the mid-ramp,and ending in the intertidal environment.Additionally,the study recorded two regional maximum flooding surfaces:K-135 and K-140.The former is present in the lowermost part of the formation,while the other lies in the middle.This study shows a close relationship between facies(environments)and hydrocarbon accumulation.The increased accumulation focuses on the lower part of the studied formation,and seems to be lower in the upper part of the formation as a result of changes in the environment of deposition.

关键词： Mishrif formation Cenomanian Sequence stratigraphy Zubair oilfield Iraq

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A detailed comparison of the composition of(RE)-Ba-Cu-O-Ag bulk superconductors

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Superconductivity 2024年第1期9卷 87-94页

作者： j.V.j.Congreve Y.Shi A.R.Dennis H.Druiff N.C.Tutt D.A.Cardwell j.H.Durrell Department of Engineering University of CambridgeCambridgeUK

The homogeneity of the microstructure and composition are critical in determining the properties of rare earthbarium‐cuprate,single grain bulk superconductors[(RE)BCO].The magnitude of the trapped magnetic field achieveable in these technologically important materials,in particular,is influenced heavily by the size and distribution of(RE)_(2)BaCuO_(x)(RE‐211)flux pinning inclusions in the bulk microstructure,whereas the size and distribution of silver agglomerates present within the bulk superconducting matrix correlate directly with improved mechanical properties.With careful engineering,these materials have significant potential for application in range of devices related to energy storage,medicine,electro‐magnetic machinery and microelectronic technology.Fabrication of(RE)BCO bulk superconductors typically involves heating a powder compact above its peritectic decomposition temperature followed by slow cooling to facilitate the growth of a single grain.Each(RE)BCO composition has a different peritectic temperature and growth rate,which,therefore,necessitates different requirements in the heating profile.The fabrication temperature and growth rate,for example,may have an effect on the RE‐211 and silver distribution,which may,in turn,affect the superconducting properties of the resulting single grain.In this work we compare the distributions of silver and RE‐211 in the single grain microstructures of YBCOAg,GdBCO‐Ag,EuBCO‐Ag and SmBCO‐Ag bulk superconductors using optical microscopy,scanning electron microscopy and energy dispersive X‐ray spectroscopy.We observe that the distributions are very similar along both the a/b‐axis and c‐axis of these materials.This suggests that factors other than the maximum temperature used to achieve peritectic decomposition and the rate of single grain growth are particularly influential in determining the properties of the as‐processed samples in the top seeded melt growth process.This observation demonstrates there is freedom to use(RE)materials interchangeably between different

关键词： YBCO‐Ag GdBCO‐Ag SmBCO‐Ag EuBCO‐Ag Composition Bulk superconductor

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A facile strategy for tuning the density of surface-grafted biomolecules for melt extrusion-based additive manufacturing applications

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Bio-Design and Manufacturing 2024年第3期7卷 277-291页

作者： I.A.O.Beeren G.Dos Santos P.j.Dijkstra C.Mota j.Bauer H.Ferreira Rui L.Reis N.Neves S.Camarero-Espinosa M.B.Baker L.Moroni Department of Complex Tissue Regeneration MERLN Institute for Technology-Inspired Regenerative MedicineMaastricht University6229 ER MaastrichtThe Netherlands 3B’s Research Group I3Bs–Research Institute on BiomaterialsBiodegradables and BiomimeticsHeadquarters of the European Institute of Excellence on Tissue Engineering and Regenerative MedicineUniversity of MinhoAveParkZona Industrial da Gandra4805-017 BarcoGuimarãesPortugal ICVS/3B’s-PT Government Associate Laboratory 4806-909 Braga/GuimarãesPortugal POLYMAT University of the Basque Country UPV/EHU20018 Donostia/San SebastiánSpain IKERBASQUE Basque Foundation for Science48009 BilbaoSpain

Melt extrusion-based additive manufacturing(ME-AM)is a promising technique to fabricate porous scaffolds for tissue engi-neering applications.However,most synthetic semicrystalline polymers do not possess the intrinsic biological activity required to control cell fate.Grafting of biomolecules on polymeric surfaces of AM scaffolds enhances the bioactivity of a construct;however,there are limited strategies available to control the surface density.Here,we report a strategy to tune the surface density of bioactive groups by blending a low molecular weight poly(ε-caprolactone)5k(PCL5k)containing orthogonally reactive azide groups with an unfunctionalized high molecular weight PCL75k at different ratios.Stable porous three-dimensional(3D)scaf-folds were then fabricated using a high weight percentage(75 wt.%)of the low molecular weight PCL 5k.As a proof-of-concept test,we prepared films of three different mass ratios of low and high molecular weight polymers with a thermopress and reacted with an alkynated fluorescent model compound on the surface,yielding a density of 201-561 pmol/cm^(2).Subsequently,a bone morphogenetic protein 2(BMP-2)-derived peptide was grafted onto the films comprising different blend compositions,and the effect of peptide surface density on the osteogenic differentiation of human mesenchymal stromal cells(hMSCs)was assessed.After two weeks of culturing in a basic medium,cells expressed higher levels of BMP receptor II(BMPRII)on films with the conjugated peptide.In addition,we found that alkaline phosphatase activity was only significantly enhanced on films contain-ing the highest peptide density(i.e.,561 pmol/cm^(2)),indicating the importance of the surface density.Taken together,these results emphasize that the density of surface peptides on cell differentiation must be considered at the cell-material interface.Moreover,we have presented a viable strategy for ME-AM community that desires to tune the bulk and surface functionality via blending of(modified)polymers.Furthermore,the use of alkyne-a

关键词： Additive manufacturing Blending Surface functionalization Surface density Click chemistry Human

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Adeno-associated virus as a delivery vector for gene therapy of human diseases

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Signal Transduction and Targeted Therapy 2024年第5期9卷 1808-1840页

作者： jiang-Hui Wang Dominic j.Gessler Wei Zhan Thomas L.Gallagher Guangping Gao Horae Gene Therapy Center University of Massachusetts Chan Medical SchoolWorcesterMA01605USA Department of Microbiology and Physiological Systems University of Massachusetts Chan Medical SchoolWorcesterMA01605USA Centre for Eye Research Australia Royal Victorian Eye and Ear HospitalEast MelbourneVIC3002Australia Ophthalmology Department of SurgeryUniversity of MelbourneEast MelbourneVIC3002Australia Department of Neurological Surgery University of Massachusetts Chan Medical SchoolWorcesterMA01605USA Department of Neurosurgery University of MinnesotaMinneapolisMN55455USA Department of Medicine University of Massachusetts Chan Medical SchoolWorcesterMA01605USA Li Weibo Institute for Rare Diseases Research University of Massachusetts Chan Medical SchoolWorcesterMA01605USA

Adeno-associated virus(AAV)has emerged as a pivotal delivery tool in clinical gene therapy owing to its minimal pathogenicity and ability to establish long-term gene expression in different tissues.Recombinant AAV(rAAV)has been engineered for enhanced specificity and developed as a tool for treating various diseases.However,as rAAV is being more widely used as a therapy,the increased demand has created challenges for the existing manufacturing methods.Seven rAAV-based gene therapy products have received regulatory approval,but there continue to be concerns about safely using high-dose viral therapies in humans,including immune responses and adverse effects such as genotoxicity,hepatotoxicity,thrombotic microangiopathy,and neurotoxicity.In this review,we explore AAV biology with an emphasis on current vector engineering strategies and manufacturing technologies.We discuss how rAAVs are being employed in ongoing clinical trials for ocular,neurological,metabolic,hematological,neuromuscular,and cardiovascular diseases as well as cancers.We outline immune responses triggered by rAAV,address associated side effects,and discuss strategies to mitigate these reactions.We hope that discussing recent advancements and current challenges in the field will be a helpful guide for researchers and clinicians navigating the ever-evolving landscape of rAAV-based gene therapy.

关键词： diseases specificity approval

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