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An integrative bioinformatics pipeline shows that honeybee-associated microbiomes are driven primarily by pollen composition

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Insect Science 2023年第2期30卷 555-568页

作者： Douglas chesters Xiuwei Liu Karen L.Bell michael c.orr Tingting Xie Qingsong Zhou chaodong Zhu Key Laboratory ofZoological Systematics andEvolution Institute ofZoologyChinese Academy of SciencesBejingChina International college University of Chinese Academy of SciencesBejingChina Institute of Agro-Products Processing Yunnan Province Academy of Agricultural ScienceKunmingChina School of Biological Sciences University of Western AustraliaCrawleyWAAustralia cSIRO Health&Biosecurity FloreatWAAustralia college of Life Sciences Anhui Normal UniversityWuhuAnhui ProvinceChina State Key Laboratory of Integrated Pest Management Institute of ZoologyChinese Academy of SciencesBeijingChina college of Biological Sciences University of Chinese Academy of SciencesBeijingChina

The microbiomes associated with bee nests influence colony health through various mechanisms,although it is not yet clear how honeybee congeners differ in microbiome assembly processes,in particular the degrees to which floral visitations and the environment contribute to different aspects of *** used DNA metabarcoding to sequence bacterial 16S rRNA from honey and stored pollen from nests of 4 honeybee species(Apis cerana,***,***,and ***)sampled throughout Yunnan,china,a global biodiversity *** developed a computational pipeline integrating multiple databases for quantifying key facets of diversity,including compositional,taxonomic,phylogenetic,and functional ***,we assessed candidate drivers of observed microbiome dissimilarity,particularly differences in floral visitations,habitat disturbance,and other key environmental *** revealed that microbiome alpha diversity was broadly equivalent across the study sites and between bee species,apart from functional diversity which was very low in nests of the reclusive *** in microbiome composition across Yunnan was driven predominantly by pollen *** disturbance negatively impacted both compositional and phylogenetic alpha diversity of nest microbiomes,but did not correlate with microbial *** herein make progress in understanding microbiome diversity associated with key pollinators in a biodiversity hotspot,and provide a model for the use of a comprehensive informatics framework in assessing pattern and drivers of diversity,which enables the inclusion of explanatory variables both subtly and fundamentally different and enables elucidation of emergent or unexpected drivers.

关键词： Apis biodiversity hotspot honeybee informatics metabarcoding microbiome

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Future directions in Systematics: A report from the 4th Systematic Biology Forum in china

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Zoological Systematics 2020年第2期45卷 78-80页

作者： michael c.orr Arong Luo Douglas chesters Qingsong Zhou Feng Zhang chaodong Zhu Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing 100101P.R.China Department of Entomology College of Plant ProtectionNanjing Agricultural UniversityNanjing 210095P.R.China State Key Laboratory of Integrated Pest Management Institute of ZoologyChinese Academy of SciencesBeijing 100101P.R.China college of Biological Sciences University of Chinese Academy of SciencesBeijing 100049P.R.China

The 4 th Systematic Biology Forum,china took place in December 2019,covering a vast array of topics across animals,bacteria,fungi,plants,and viruses in the fields of systematics and evolutionary ***,we discuss the emergent themes of this meeting and how these and other interdisciplinary research programs can be synthesized to better understand evolution in a systematic framework.

关键词： Taxonomy phylogenomics phylogenetics evolution

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Testing the systematic status of Homalictus and Rostrohalictus with weakened cross-vein groups within Halictini(Hymenoptera:Halictidae)using low-coverage whole-genome sequencing

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Insect Science 2022年第6期29卷 1819-1833页

作者： Dan Zhang Ze-Qing Niu A-Rong Luo michael c.orr Rafael R.Ferrari Jian-Feng Jin Qing-Tao Wu Feng Zhang chao-Dong Zhu Key Laboratory of Zoological Systematics and Evolution Insttute of ZoologyChinese Academy of SciencesBejingChina college of Biological Sciences University of Chinese Academy of SciencesBejingChina International college University of Chinese Academy of SciencesBejingChina Department of Entomology College of Plant ProtectionNanjing Agricultural UniversityNanjingChina State Key Laboratory of Integrated Pest Management Institute of ZoologyChinese Academy of SciencesBejingChina

The halictid genus Lasioglossum,as one of the most species-rich bee groups with persistently contentious subgeneric boundaries,is one of the most challenging bee groups from a systematic *** enduring question is the relationship of La-sioglossum and Homalictus,whether all halictine bees with weakened distal wing ve-nation comprise one or multiple ***,we analyzed the phylogenetic relation-ships among the subgroups within Lasioglossum *** on thousands of single-copy orthologs and ultraconserved elements,which were extracted from 23 newly sequenced low-coverage whole genomes alongside a published genome(22 ingroups plus 2 out-groups).Both marker sets provided consistent results across maximum likelihood and coalescent-based species tree *** phylogenetic and topology test results show that the Lasioglossum and Hemihalictus series are reciprocally monophyletic and Homa-lictus and Rostrohalictus are valid subgenera of ***,we lower Homalictus to subgenus status within Lasioglossum again,and we also raise Rostrohalic-tus to subgenus status from its prior synonymy with subgenus *** przewalskyi is also transferred to the subgenus ***,we redefine La-sioglossum to include all halictine bees with weakened distal wing venation.

关键词： Apoidea Lasioglossum phylogenomics systematics ultraconserved ele-ment universal single-copy ortholog

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Six steps for building a technological knowledge base for future taxonomic work

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National Science Review 2022年第12期9卷 19-21页

作者： michael c.orr Anderson Feijó Douglas chesters Alfried P.Vogler Silas Bossert Rafael R.Ferrari Mark John costello Alice c.Hughes Lars Krogmann John S.Ascher Xin Zhou De-Zhu Li Ming Bai Jun chen Deyan Ge Arong Luo Gexia Qiao Paul H.Williams Ai-bing Zhang Keping Ma Feng Zhang chao-Dong Zhu Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Entomologie Staatliches Museum für Naturkunde Stuttgart Department of Life Sciences Silwood Park Campus Imperial College London Natural History Museum Department of Entomology Washington State University Department of Entomology National Museum of Natural History Smithsonian Institution Faculty of Biosciences and Aquaculture Nord University School of Biological Sciences University of Hong Kong Department of Biological Sciences National University of Singapore Department of Entomology China Agricultural University Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences college of Life Sciences Capital Normal University Institute of Botany Chinese Academy of Sciences Department of Entomology College of Plant Protection Nanjing Agricultural University State Key Laboratory of Integrated Pest Management Institute of Zoology Chinese Academy of Sciences college of Life Sciences University of Chinese Academy of Sciences

Species are the principal category we use to study,understand,and conserve the natural world,so how we define species has a cascading impact across fields,well beyond biology [1].Despite such importance,debate on species concepts continues to this day ([2] 2020),with consequences for what organisms we recognize,study and *** the wealth of life forms on our planet,

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comparisons of oxbow lake fish assemblages in relation to bigheaded carp establishment in the lower White River, Arkansas

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Ecological Processes 2024年第1期13卷 188-205页

作者： michael A.Eggleton cody J.Salzmann Joseph E.Kaiser Shannon c.F.Smith Department of Aquaculture and Fisheries University of Arkansas at Pine Bluff Arkansas Game and Fish commission Virginia Institute of Marine Science

Background Since the late 1990s, bigheaded carps(largely silver carp [Hypophthalmichthys molitrix] but also bighead carp [H. nobilis]) have established throughout the lower Mississippi River basin. Using previously studied oxbow lakes in the lower White River basin, Arkansas, we compared current(2017, “post-carp” establishment) fish assemblages to historical(2002, “pre-carp” establishment) fish assemblages. Fish assemblages were comprehensively assessed using multiple gears, including boat electrofishing, mini-fyke nets, and experimental small-mesh gill *** T-tests suggested that fish assemblage indices of richness, diversity, evenness, and dominance were often greater(P carp period as reflected by boat electrofishing and experimental gill nets. However, all indices were generally similar(P > 0.05) between the pre-carp and post-carp period with fish assemblages depicted using mini-fyke nets. Nonmetric multidimensional scaling analyses indicated that fish assemblages differed structurally between pre-carp and post-carp periods. Assemblage differences were linked to both small and large abundance changes for more than 20 species. Abundances of gizzard shad(Dorosoma cepedianum), emerald shiner(Notropis atherinoides), pugnose minnow(Opsopoeodus emiliae), crappies(Pomoxis spp.), bluegill(Lepomis macrochirus), orangespotted sunfish(L. humilis), and yellow bass(Morone mississippiensis) declined between the pre-carp and postcarp periods. conversely, abundances of weed shiner(N. texanus), pallid shiner(Hybopsis amnis), longear sunfish(L. megalotis), buffalofishes(Ictiobus spp.), and gars(Lepisosteus spp.) generally increased during the same *** Although not possible to conclude assemblage shifts were entirely related to bigheaded carps due to the absence of an appropriate reference system where carps did not establish, the wide establishment of these carps is one of the most pervasive changes to have occurred in the lower White

关键词： Bigheaded carp Silver carp Aquatic nuisance species Fish assemblage Oxbow lake Large river

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Assessment of clinical depression metrics in cardiac patients using the patient health Questionnaire-9 before and after phase-II cardiac rehabilitation

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Sports Medicine and Health Science 2024年第3期6卷 240-245页

作者： John c.Quindry michael McNamara carrie Oser crystelle Fogle Integrative Physiology and Athletic Training University of MontanaMissoulaMTUSA St.Patrick's Hospital MissoulaMTUSA cardiovascular Health Program–Montana Department of Public Health and Human Services HelenaMTUSA

cardiovascular disease remains a leading cause of morbidity and mortality,a fact that is commonly associated with co-morbidities such as clinical *** phase II cardiac rehabilitation is an established intervention for those with cardiovascular disease,its effect on patients who also suffer from depression are under ***:To quantify Pre-and Post-cardiac rehabilitation questionnaire scores collected from a large patient data *** this investigation,27670 patients completed Patient Health Questionnaire-9 questionnaires both Pre-and Post-rehabilitation(averaging[28.08.7]phase II sessions).Findings reveal that questionnaire scores decreased by 40%–48%across all groups,a finding that was independent of assigned sex,race,and ***,when data were stratified for questionnaire scores that may indicate major and minor depressive disorder,phase II cardiac rehabilitation outcomes were lower by 61%and 49%*** all groups exhibited lower questionnaire scores following cardiac rehabilitation participation,numerical differences at Preand Post-rehabilitation time points indicate that males and White patients have more favorable *** latter observation,while not confirmed currently,appears to be linked to referral rates to phase II cardiac rehabilitation,which remain poor for females,racial and ethnic minorities.

关键词： clinical depression Exercise Psychological health

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Macroalgal deep genomics illuminate multiple paths to aquatic,photosynthetic multicellularity

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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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Single carbon metabolism–A new paradigm for microbial bioprocesses?

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Synthetic and Systems Biotechnology 2024年第2期9卷 322-329页

作者： michael Baumschabl Özge Ata Diethard Mattanovich Austrian centre of Industrial Biotechnology(AcIB) Vienna1190Austria University of Natural Resources and Life Sciences Department of BiotechnologyInstitute of Microbiology and Microbial BiotechnologyViennaAustria

Increasing atmospheric carbon dioxide levels,a reduction of arable land area and the dependence of first and second generation biotechnology feedstocks on agricultural products,call for alternative,sustainable feedstock sources for industrial *** direct use of cO_(2)or conversion of cO_(2)into other single carbon(c1)sources have great potential as they might help to reduce carbon emissions and do not compete with agricultural land *** we discuss the microbial use of c1 carbon sources,their potential applications in biotechnology,and challenges towards sustainable c1-based industrial biotechnology *** focus on methanol,formic acid,methane,syngas,and cO_(2)as feedstocks for bioprocesses,their assimilation pathways,current and emerging applications,and limitations of their *** mini-review is intended as a first introduction for researchers who are new to the field of c1 biotechnology.

关键词： Sustainability Bioeconomycarbon dioxide Methanol Formate Methane

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Potential of photodynamic therapy in the management of infectious oral diseases

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World Journal of Experimental Medicine 2024年第1期14卷 1-5页

作者： cinzia casu Germano orrù Department of Surgical Science Oral Biotechnology LaboratoryUniversity of CagliariCagliari 09124Italy

Photodynamic therapy(PDT)can take place in the presence of three elements:Light with an appropriate wavelength;a photosensitizer;and the presence of *** type of treatment is very effective overall against bacterial,viral and mycotic *** the last 10 years many papers have been published on PDT with different types of photosensitizers(e.g.,methylene blue,toluidine blue,indocyanine green,curcumin-based photosensitizers),different wavelengths(e.g.,460 nm,630 nm,660 nm,810 nm)and various parameters(e.g.,power of the light,time of illumination,number of sessions).In the scientific literature all types of PDT seem very effective,even if it is difficult to find a standard protocol for each oral *** could be an interesting way to treat some dangerous oral infections refractory to common pharmacological therapies,such as candidiasis from multidrug-resistant candida spp.

关键词： Photodynamic therapy oral infections Photodynamic therapy vs candidiasis Blue light 460 nm Streptococcus mutans

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Stability and Generalization of Hypergraph collaborative Networks

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Machine Intelligence Research 2024年第1期21卷 184-196页

作者： michael K.Ng Hanrui Wu Andy Yip Institute of Data Science The University of Hong KongHong KongChina Department of Mathematics The University of Hong KongHong KongChina college of Information Science and Technology Jinan UniversityGuangzhou 510006China

Graph neural networks have been shown to be very effective in utilizing pairwise relationships across ***,there have been several successful proposals to generalize graph neural networks to hypergraph neural networks to exploit more com-plex *** particular,the hypergraph collaborative networks yield superior results compared to other hypergraph neural net-works for various semi-supervised learning *** collaborative network can provide high quality vertex embeddings and hyperedge embeddings together by formulating them as a joint optimization problem and by using their consistency in reconstructing the given *** this paper,we aim to establish the algorithmic stability of the core layer of the collaborative network and provide generaliz--ation *** analysis sheds light on the design of hypergraph filters in collaborative networks,for instance,how the data and hypergraph filters should be scaled to achieve uniform stability of the learning *** experimental results on real-world datasets are presented to illustrate the theory.

关键词： Hypergraphs vertices hyperedges collaborative networks graph convolutional neural networks(cNNs) stability generalization guarantees

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