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Macroalgal deep genomics illuminate multiple paths to aquatic,photosynthetic multicellularity

Molecular Plant 2024年第5期17卷 747-771页

作者： david R.Nelson Alexandra Mystikou Ashish Jaiswal Cecilia Rad-Menendez Michael J.Preston Frederik De Boever Diana C.El Assal Sarah Daakour Michael W.Lomas Jean-Claude Twizere david h.Green William C.Ratcliff Kourosh Salehi-Ashtiani Division of Science and Math New York University Abu DhabiAbu DhabiUAE Center for Genomics and Systems Biology(CGSB) New York University Abu DhabiAbu DhabiUAE Biotechnology Research Center Technology Innovation InstitutePO Box 9639Masdar CityAbu DhabiUAE Culture Collection of Algae and Protozoa Scottish Association for Marine ScienceObanScotlandUK National Center for Marine Algae and Microbiota Bigelow Laboratory for Ocean SciencesEast BoothbayMEUSA Laboratory of Viral Interactomes GIGA InstituteUniversity of LiegeLiegeBelgium School of Biological Sciences Georgia Institute of TechnologyAtlantaGAUSA

Macroalgae are multicellular,aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering,which are directly linked to their multicellularity ***,their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain *** this study,we sequenced 110 macroalgal genomes from diverse climates and phyla,and identified key genomic features that distinguish them from their microalgal *** for cell adhesion,extracellular matrix formation,cell polarity,transport,and cell differentiation distinguish macroalgae from microalgae across all three major phyla,constituting conserved and unique gene sets supporting multicellular *** genes show phylum-and climate-specific expansions that may facilitate niche ***,our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.

关键词： macroalgae multicellularity comparative genomics evolution adhesome endogenous viral elements

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Construction of a broad-host-range Anderson promoter series and particulate methane monooxygenase promoter variants expand the methanotroph genetic toolbox

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Synthetic and Systems Biotechnology 2024年第2期9卷 250-258页

作者： Etash h.Bhat Jessica M.henard Spencer A.Lee Dustin Mchalffey Mahith S.Ravulapati Elle V.Rogers Logan Yu david Skiles Calvin A.henard Department of Biological Sciences and BioDiscovery Institute University of North TexasDentonTXUSA

Methanotrophic bacteria are currently used industrially for the bioconversion of methane-rich natural gas and anaerobic digestion-derived biogas to valuable *** bacteria may also serve to mitigate the negative effects of climate change by capturing atmospheric greenhouse *** genetic tools have previously been developed for genetic and metabolic engineering of ***,the available tools for use in methanotrophs are significantly underdeveloped compared to many other industrially relevant bacteria,which hinders genetic and metabolic engineering of these *** such,expansion of the methanotroph genetic toolbox is needed to further our understanding of methanotrophy and develop biotechnologies that leverage these unique microbes for mitigation and conversion of methane to valuable ***,we determined the copy number of three broad-host-range plasmids in Methylococcus capsulatus Bath and Methylosinus trichosporium OB3b,representing phylogenetically diverse Gammaproteobacterial and Alphaproteobacterial methanotrophs,***,we show that the commonly used synthetic Anderson series promoters are functional and exhibit similar relative activity in *** and *** OB3b,but the synthetic series had limited ***,we mutagenized the native *** particulate methane monooxygenase promoter and identified variants with activity that expand the activity range of synthetic,constitutive promoters functional not only in ***,but also in Escherichia ***,the tools developed here advance the methanotroph genetic engineering toolbox and represent additional synthetic genetic parts that may have broad applicability in Pseudomonadota bacteria.

关键词： Methanotroph Methane monooxygenase Promoter Metabolic engineering Synthetic biology

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Uncovering the dominant contribution of intermediate volatility compounds in secondary organic aerosol formation from biomass-burning emissions

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National Science Review 2024年第3期11卷 150-158页

作者： Kun Li Jun Zhang david M.Bell Tiantian Wang houssni Lamkaddam Tianqu Cui Lu Qi Mihnea Surdu Dongyu Wang Lin Du Imad El haddad Jay G.Slowik Andre S.h.Prevot Environment Research Institute Shandong University Laboratory of Atmospheric Chemistry Paul Scherrer Institute

Organic vapors from biomass burning are a major source of secondary organic aerosols(SOAs). Previous smog chamber studies found that the SOA contributors in biomass-burning emissions are mainly volatile organic compounds(VOCs). While intermediate volatility organic compounds(IVOCs) are efficient SOA precursors and contribute a considerable fraction of biomass-burning emissions, their contribution to SOA formation has not been directly observed. here, by deploying a newly-developed oxidation flow reactor to study SOA formation from wood burning, we find that IVOCs can contribute ～70% of the formed SOA, i.e.>2 times more than VOCs. This previously missing SOA fraction is interpreted to be due to the high wall losses of semi-volatile oxidation products of IVOCs in smog chambers. The finding in this study reveals that SOA production from biomass burning is much higher than previously thought, and highlights the urgent need for more research on the IVOCs from biomass burning and potentially other emission sources.

关键词： atmospheric chemistry biomass burning secondary organic aerosol intermediate volatility organic compounds

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An AI-empowered indoor digital contact tracing system for COVID-19 outbreaks in residential care homes

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Infectious Disease Modelling 2024年第2期9卷 474-482页

作者： Jiahui Meng Justina Yat Wa Liu Lin Yang Man Sing Wong hilda Tsang Boyu Yu Jincheng Yu Freddy Man-hin Lam Daihai he Lei Yang Yan Li Gilman Kit-hang Siu Stefanos Tyrovolas Yao Jie Xie david Man david h.K.Shum School of Nursing The Hong Kong Polytechnic UniversityHong Kong Special Administrative RegionChina Electronic and Information Engineering The Hong Kong Polytechnic UniversityHong Kong Special Administrative RegionChina Research Centre of Textiles for Future Fashion The Hong Kong Polytechnic UniversityHong Kong Special Administrative RegionChina Department of Land Surveying and Geo-Informatics The Hong Kong Polytechnic UniversityHong Kong Special Administrative RegionChina Department of Applied Mathematics The Hong Kong Polytechnic UniversityHong Kong Special Administrative RegionChina The Jockey Club School of Public health and Primary Care The Chinese University of Hong KongHong Kong Special Administrative RegionChina Department of Rehabilitation Sciences The Hong Kong Polytechnic UniversityHong Kong Special Administrative RegionChina Department of Computing The Hong Kong Polytechnic UniversityHong Kong Special Administrative RegionChina Department of health Technology and Informatics The Hong Kong Polytechnic UniversityHong Kong Special Administrative RegionChina Department of Nutrition and Food Studies George Mason UniversityUSA Tung Wah College Hong Kong Special Administrative RegionChina Mental health Research Centre The Hong Kong Polytechnic UniversityHong Kong Special Administrative RegionChina

An AI-empowered indoor digital contact-tracing system was developed using a centralized architecture and advanced low-energy Bluetooth technologies for indoor positioning,with careful preservation of privacy and data *** analyzed the contact pattern data from two RChs and investigated a COVID-19 outbreak in one study *** evaluate the effectiveness of the system in containing outbreaks with minimal contacts under quarantine,a simulation study was conducted to compare the impact of different quarantine strategies on outbreak containment within *** significant difference in contact hours between weekdays and weekends was observed for some pairs of RCh residents and staff during the two-week data collection *** significant difference between secondary cases and uninfected contacts was observed in a COVID-19 outbreak in terms of their demographics and contact *** results based on the collected contact data indicated that a threshold of accumulative contact hours one or two days prior to diagnosis of the index case could dramatically increase the efficiency of outbreak containment within RChs by targeted isolation of the close *** study demonstrated the feasibility and efficiency of employing an AI-empowered system in indoor digital contact tracing of outbreaks in RChs in the post-pandemic era.

关键词： COVID-19 Indoor contact tracing Contact pattern Outbreak containment Artificial intelligence

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Protective effects of cyclosporine and its analog NIM-811 in a murine model of hepatic ischemia-reperfusion injury

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Liver Research 2024年第1期8卷 46-53页

作者： Joshua hefler Rena Pawlick Braulio A.Marfil-Garza Aducio Thiesen Nerea Cuesta-Gomez Sanaz hatami Darren h.Freed Constantine Karvellas david L.Bigam A.M.James Shapiro Department of Surgery Faculty of Medicine&DentistryUniversity of AlbertaEdmontonABCanada Department of Medicine Faculty of Medicine&DentistryUniversity of AlbertaEdmontonABCanada ChRISTUS-LatAm hub Excellence&Innovation Center MonterreyMexico Alberta Diabetes Institute University of AlbertaEdmontonABCanada Clinical Islet Transplant Program University of AlbertaEdmontonABCanada Department of Laboratory Medicine&Pathology Faculty of Medicine&DentistryUniversity of AlbertaEdmontonABCanada

Background and aim:The liver is susceptible to ischemia-reperfusion injury(IRI)during hepatic surgery,when the vessels are compressed to control bleeding,or liver transplantation,when there is an obligate period of *** hallmark of IRI comprises mitochondrial dysfunction,which generates reactive oxygen species,and cell death through necrosis or ***(CsA),which is a well-known immunosuppressive agent that inhibits calcineurin,has the additional effect of inhibiting the mito-chondrial permeability transition pore(mPTP),thereby,preventing mitochondrial swelling and ***-811,which is the nonimmunosuppressive analog of CsA,has a similar effect on the *** this study,we tested the effect of both agents on mitigating warm hepatic IRI in a murine *** and methods:Before ischemic insult,the mice were administered with intraperitoneal normal saline(control);CsA at 2.5,10,or 25 mg/kg;or NIM-811 at 10 mg/***,the mice were subjected to partial warm hepatic ischemia by selective pedicle clamping for 60 min,followed by 6 h of recovery after *** alanine transaminase(ALT)was measured,and the liver tissue was examined histologically for the presence of apoptosis and the levels of inflammatory ***:Compared with the control mice,the mice treated with 10 and 25 mg/kg of CsA and NIM-811 had significantly lower ALT levels(Phe liver tissue showed reduced histological injury scores after treatment with CsA at 2.5,10,and 25 mg/kg and NIM-811(P=0.041,h CsA at all doses(P=0.012,0.007,andhe pro-inflammatory cyto-kines,particularly interleukin(IL)-1β,IL-2,IL-4,IL-10,and keratinocyte chemoattractant/human growth-regulated oncogene significantly decreased in the mice treated with the highest dose of CsA(25 mg/kg)than those in the control ***

关键词： Cyclosporine(CsA) Cyclosporine analogue Liver surgery Ischemia-reperfusion injury(IRI) Animal model NIM-811

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Learning to bag with a simulation‐free reinforcement learning framework for robots

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IET Cyber-Systems and Robotics 2024年第2期6卷 52-66页

作者： Francisco Munguia-Galeano Jihong Zhu Juan david hernández Ze Ji Cooper Group University of LiverpoolLiverpoolUK School of Physics Engineering and Technology University of YorkYorkUK School of Computer Science and Informatics Cardiff UniversityCardiffUK School of Engineering Cardiff UniversityCardiffUK

Bagging is an essential skill that humans perform in their daily ***,deformable objects,such as bags,are complex for robots to manipulate.A learning-based framework that enables robots to learn bagging is *** novelty of this framework is its ability to learn and perform bagging without relying on *** learning process is accomplished through a reinforcement learning(RL)algorithm introduced and designed to find the best grasping points of the bag based on a set of compact state *** framework utilises a set of primitive actions and represents the task in five *** our experiments,the framework reached 60% and 80% success rates after around 3 h of training in the real world when starting the bagging task from folded and unfolded states,***,the authors test the trained RL model with eight more bags of different sizes to evaluate its generalisability.

关键词： reinforcement learning robot learning robotics

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Amyloid-beta and tau protein beyond Alzheimer's disease

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Neural Regeneration Research 2024年第6期19卷 1262-1276页

作者： Morteza Abyadeh Vivek Gupta Joao A.Paulo Arezoo Gohari Mahmoudabad Sina Shadfar Shahab Mirshahvaladi Veer Gupta Christine T.O.Nguyen david I.Finkelstein Yuyi You Paul A.haynes Ghasem h.Salekdeh Stuart L.Graham Mehdi Mirzaei ProGene Technologies Pty Ltd. SydneyNSWAustralia Department of Clinical Medicine Faculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie ParkNorth RydeSydneyNSWAustralia Department of Cell Biology Harvard Medical SchoolBostonMAUSA School of Medicine Deakin UniversityGeelongVICAustralia Department of Optometry and Vision Sciences School of Health SciencesFaculty of Medicine Dentistry and Health SciencesUniversity of MelbourneParkvilleVICAustralia The Florey Institute of Neuroscience and Mental health The University of MelbourneParkvilleVICAustralia School of Natural Sciences Macquarie UniversityMacquarie ParkNSWAustralia

The aggregation of amyloid-beta peptide and tau protein dysregulation are implicated to play key roles in Alzheimer's disease pathogenesis and are considered the main pathological hallmarks of this devastating ***,these two proteins are produced and expressed within the normal human ***,under pathological conditions,abnormal expression,posttranslational modifications,conformational changes,and truncation can make these proteins prone to aggregation,triggering specific disease-related *** studies have indicated associations between aberrant behavior of amyloid-beta and tau proteins and various neurological diseases,such as Alzheimer's disease,Parkinson's disease,and amyotrophic lateral sclerosis,as well as retinal neurodegenerative diseases like Glaucoma and age-related macular ***,these proteins have been linked to cardiovascular disease,cancer,traumatic brain injury,and diabetes,which are all leading causes of morbidity and *** this comprehensive review,we provide an overview of the connections between amyloid-beta and tau proteins and a spectrum of disorders.

关键词： amyloid-beta cancer cardiovascular diseases diabetes neurodegeneration Tau traumatic brain injury

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Landscape of global urban environmental resistome and its association with local socioeconomic and medical status

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Science China(Life Sciences) 2024年第6期67卷 1292-1301页

作者： Jun Wu Yige hu Michael h Perlin david Danko Jun Lu Manuela Oliveira Johannes Werner Maria M Zambrano Maria A Sierra Olayinka O Osuolale Paweł Łabaj Nicolás Rascovan Nur hazlin hazrin-Chong Soojin Jang haruo Suzuki Marina Nieto-Caballero Bharath Prithiviraj Patrick K h Lee Agnieszka Chmielarczyk Anna Różańska Yongxiang Zhao Lan Wang Christopher E Mason Tieliu Shi Center for Bioinformatics and Computational Biology and the Institute of Biomedical SciencesSchool of Life SciencesEast China Normal UniversityShanghai 200241China Department of Biology Program on Disease EvolutionUniversity of LouisvilleLouisville 40292USA Weill Cornell Medicine New York 10065USA The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine New York 10065USA Department of Pulmonary Medicine Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghai 200025China i3S-Instituto de Investiga玢o e Inova玢o em Saúde Universidade do PortoPorto 4050-290Portugal Ipatimup-Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto 4200-465Portugal Departamento de Biologia Faculdade de CiênciasUniversidade do PortoPorto 4050-290Portugal high Performance and Cloud Computing Group Zentrum für Datenverarbeitung(ZDV)Eberhard Karls University of TübingenW鋍hterstra遝7672074TübingenGermany Corporación Corpogen Research Center Bogotá110311Colombia Applied Environmental Metagenomics and Infectious Diseases Research(AEMIDR) Department of Biological SciencesElizade UniversityIlara-Mokin 340271Nigeria Maopolska Centre of Biotechnology Jagiellonian UniversityKraków 30-005Poland Aix-Marseille Université Mediterranean Institute of OceanologyUniversitéde ToulonCNRSIRDUM 110Marseille 83041France Department of Biological Sciences and Biotechnology Faculty of Science and TechnologyUniversiti Kebangsaan Malaysia43600 UKM BangiSelangor Institut Pasteur Korea Seoul 13488Republic of Korea Faculty of Environment and Information Studies Keio UniversityFujisawaKanagawa 252-0882Japan University of Colorado at Boulder CivilEnvironmental and Architectural DepartmentBoulder 80303USA Brooklyn College of the City University of New York Brooklyn 11210USA School of Energy and Environment City University of Hong KongHong Kong 999077China Department of Microbiology Faculty of MedicineJagiellonian UniversityKraków 30-005Poland Biological Targeting Diagnosis and The

Antimicrobial resistance(AMR)poses a critical threat to global health and development,with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(ARGs).however,most research to date has been conducted at a local level,leaving significant gaps in our understanding of the global status of antibiotic resistance in urban *** address this issue,we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples,which were collected by the Meta SUB International Consortium involving diverse urban environments in 60 cities of 27 countries,utilizing a deep-learning based *** findings demonstrated the strong geographical specificity of urban environmental resistome,and their correlation with various local socioeconomic and medical *** also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters(BGCs)across different countries,and discovered that the urban environment represents a rich source of novel *** study provides a comprehensive overview of the global urban environmental resistome,and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

关键词： urban environment metagenome antibiotic resistance resistance diversity biosynthetic gene clusters

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Long-term effects of gestational diabetes mellitus on the pancreas of female mouse offspring

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World Journal of Diabetes 2024年第4期15卷 758-768页

作者： Enriqueta Muñoz-Islas Edgar david Santiago-SanMartin Eduardo Mendoza-Sánchez héctor Fabián Torres-Rodríguez Laura Yanneth Ramírez-Quintanilla Christopher Michael Peters Juan Miguel Jiménez-Andrade Unidad Académica Multidisciplinaria Reynosa-Aztlán Universidad Autónoma de TamaulipasReynosa 88740TamaulipasMexico Department of Anesthesiology Wake Forest University School of MedicineWinston SalemNC 27101United States

BACKGROUND Prolonged fetal exposure to hyperglycemia may increase the risk of developing abnormal glucose metabolism and type-2 diabetes during childhood,adolescence,and adulthood;however,the mechanisms by which gestational diabetes mellitus(GDM)predisposes offspring to metabolic disorders remain *** To quantify the nerve axons,macrophages,and vasculature in the pancreas from adult offspring born from mouse dams with *** GDM was induced by *** of streptozotocin(STZ)in ICR mouse *** 12 wk old,fasting blood glucose levels were determined in *** 15 wk old,female offspring born from dams with and without GDM were sacrificed and pancreata were processed for *** quantified the density of sensory[calcitonin gene-related peptide(CGRP)]and tyrosine hydroxylase(Th)axons,blood vessels(endomucin),and macro-phages(CD68)in the splenic pancreas using confocal *** Offspring mice born from STZ-treated dams had similar body weight and blood glucose values compared to offspring born from vehicle-treated ***,the density of CGRP+and Th+axons,endomucin+blood vessels,and CD68+macrophages in the exocrine pancreas was significantly greater in offspring from mothers with GDM vs control ***,the microvasculature in the islets was significantly greater,but not the number of macrophages within the islets of offspring born from dams with GDM compared to control *** GDM induces neuronal,vascular,and inflammatory changes in the pancreas of adult progeny,which may partially explain the higher propensity for offspring of mothers with GDM to develop metabolic diseases.

关键词： Gestational diabetes mellitus Immunohistochemistry Confocal microscopy Pancreas Offspring

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Non-pancreatic hyperlipasemia:A puzzling clinical entity

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World Journal of Gastroenterology 2024年第19期30卷 2538-2552页

作者： Krisztina Eszter Feher david Tornai Zsuzsanna Vitalis Laszlo davida Nora Sipeki Maria Papp Division of Gastroenterology Department of Internal MedicineFaculty of MedicineUniversity of DebrecenDebrecen H-4032Hajdu-BiharHungary Kalman Laki Doctoral School of Biomedical and Clinical Sciences Faculty of MedicineUniversity of DebrecenDebrecen H-4032Hungary

BACKGROUND Increased lipase level is a serological hallmark of the diagnosis of acute pancreatitis(AP)but can be detected in various other diseases associated with lipase leakage due to inflammation of organs surrounding the pancreas or reduced renal clearance and/or hepatic *** non-pancreatic hyperlipasemia(NPhL)is puzzling for attending physicians during the diagnostic procedure for *** would be clinically beneficial to identify the clinical and laboratory variables that hinder the accuracy of lipase diagnosis with the aim of improve it.A more precise description of the NPhL condition could potentially provide prognostic factors for adverse outcomes which is currently *** To perform a detailed clinical and laboratory characterization of NPhL in a large prospective patient cohort with an assessment of parameters determining disease *** A hungarian patient cohort with serum lipase levels at least three times higher than the upper limit of normal(ULN)was prospectively evaluated over 31 *** were identified using daily electronic laboratory reports developed to support an ongoing observational,multicenter,prospective cohort study called the EASY trial(ISRCTN10525246)to establish a simple,easy,and accurate clinical scoring system for early prognostication of *** of NPhL was established based on≥3×ULN serum lipase level in the absence of abdominal pain or abdominal imaging results characteristic of *** A total of 808 patients[male,n=420(52%);median age(IQR):65(51-75)years]were diagnosed with≥3×ULN serum lipase levels.A total of 392 patients had AP,whereas 401 had NPhL with more than 20 different *** and acute kidney injury(AKI)were the most prevalent etiologies of NPhL(27.7%and 33.2%,respectively).The best discriminative cut-off value for lipase was≥666 U/L(sensitivity,71.4%;specificity,88.8%).The presence of AKI or sepsis negatively affected the diagnostic performance of *** w

关键词： Non-pancreatic hyperlipasemia Acute pancreatitis Glycoprotein 2 Acute kidney injury Sepsis Mortality

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