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Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity

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molecular Plant 2022年第3期15卷 520-536页

作者： Genevieve Hoopes Xiaoxi meng John P.Hamilton Sai Reddy Achakkagari Fernanda de Alves Freitas Guesdes marie E.Bolger Joseph J.Coombs Danny Esselink Natalie R.Kaiser Linda Kodde maria Kyriakidou Brian Lavrijssen Natascha van Lieshout Rachel Shereda Heather K.Tuttle Brieanne Vaillancourt Joshua C.Wood Jan mde Boer Nolan Bornowski Peter Bourke David Douches Herman Jvan Eck Dave Ellis max J.Feldman Kyle m.Gardner Johannes C.P.Hopman Jiming Jiang Walter S.De Jong Joseph C.Kuhl Richard G.Novy Stan Oome Vidyasagar Sathuvalli Ek Han Tan Remco A.Ursum m.Isabel Vales Kelly Vining Richard G.F.Visser Jack Vossen G.Craig Yencho Noelle L.Anglin Christian W.B.Bachem Jeffrey B.Endelman laura m.shannon martina V.Stromvik Helen H.Tai Bjorn Usadel C.Robin Buell Richard Finkers Department of Plant Biology Michigan State UniversityEast LansingMI 48824USA Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Department of Plant Science McGill UniversitySainte-Anne-de-BellevueQC H9X 3V9Canada Plant Breeding Wageningen University&ResearchPlant Breeding6708 PB Wageningenthe Netherlands IBG-4 Bioinformatics Forschungszentrum JülichWilhelm Johnen Str52428 JülichGermany Department of Plant Soiland Microbial SciencesMichigan State UniversityEast LansingMI 48824USA Bayer Crop Science WoodlandCA 95695USA Averis Seeds B.V. 9640 AA Veendamthe Netherlands International Potato Center 1895 Avenida La MolinaLimaPeru USDA-ARS ProsserWA 99350USA Agriculture and Agri-Food Canada Fredericton Research and Development Centre FrederictonNB E3B 4Z7Canada School of Integrative Plant Science Cornell UniversityIthacaNY 14853-1901USA Department of Plant Sciences University of IdahoMoscowID 83844USA USDA-ARS Small Grains and Potato Germplasm ResearchAberdeenID 83210USA HZPC Research B.V. Edisonweg 58501 XG Jourethe Netherlands Department of Crop and Soil Science Oregon State UniversityHermistonOR 97838USA School of Biology and Ecology University of Maine5735 Hitchner Hall OronoME 04469USA Department of Horticultural Sciences Texas A&M UniversityCollege StationTX 77843-2133USA Department of Horticulture Oregon State UniversityCorvallisOR 97331USA Department of Horticultural Science North Carolina State UniversityRaleighNC 27695-7609USA Department of Horticulture University of Wisconsin-MadisonMadisonWI 53706USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Institute for Biological Data Science Heinrich Heine UniversityDusseldorf40225 DusseldorfGermany Plant Resilience Institute Michigan State UniversityEast LansingMI 48824USA Present address:GenNovation B.V. Wageningenthe Netherlands

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous *** assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity,including altered coding and transcript sequences,preferential allele expression,and structural variation that collectively result in a highly complex transcriptome and predicted proteome,which are distributed across the homologous *** species contribute to the extensive allelic diversity in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding *** a clonally propagated autotetraploid that undergoes limited meiosis,dysfunctional and deleterious alleles are not purged in tetraploid *** a quarter of the loci bore mutations are predicted to have a high negative impact on protein function,complicating breeder’s efforts to reduce genetic *** StCDF1 locus controls maturity,and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent *** of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous,diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

关键词： potato allele diversity phased assembly polyploid pan-genome wild introgressions

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Analysis of cerium substitution in Co-Sr based spinel ferrites for high frequency application

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Journal of Rare Earths 2024年第9期42卷 1755-1763,I0005页

作者： laura Khudaysh Inas A.Ahmed Syeda Rabia Ejaz Sajjad Ahmad Khan Yasir A.Haleem mohamed m.Ibrahim mahmood Ali Hafiz muhammad Tahir Farid Zeinhom m.El-Bahy Department of Physics Faculty of ScienceJazan UniversityJazan45142Saudi Arabia Department of Chemistry Faculty of ScienceKing Khalid UniversityAbha62224Saudi Arabia Department of Physics The Government Sadiq College Women UniversityBahawalpur63100Pakistan Institute of Physics Khwaja Fareed University of Engineering and Information TechnologyRahim Yar Khan64200Pakistan Department of Chemistry College of ScienceTaif UniversityP.O.Box 11099Taif21944Saudi Arabia Centre of Excellence in Solid State Physics University of the PunjabLahorePakistan Department of Physics Government CollegeTaunsa Sharif32200Pakistan Department of Chemistry Faculty of ScienceAl-Azhar UniversityNasr City11884CairoEgypt

Spinel ferrites exhibit exceptional magnetic properties,making them a distinctive class of magnetic *** sol-gel technique was utilized for the synthesis of spinel ferrites with the chemical formula Co_(0.6)Sr_(0.4)Ce_(x)Fe_(2-x)O_(4). Following that,a comprehensive X-ray diffraction analysis unveiled the crystalline cubic structure of the synthesized *** the utilization of the m-H loop approach,the ferromagnetic attributes of ferrites were assessed,and the assimilation of rare earth elements led to substantial enhancements in saturation magnetization,remanence,and *** ferrites with a high concentration of rare earth elements have improved direct current resistivity and activation *** logarithm of a material's resistance increased from 5.29 to 8.12 Ω·cm as cerium is *** a change in the amount of cerium,the activation energy goes up from 0.19 to *** changing the frequency from 5.5 to 9.5 GHz,the dielectric characteristics were *** the frequency goes up,the dielectric constant goes *** ferrites that have been made better in every way can be used in high-frequency applications.

关键词： Activation energy DC electrical resistance Remanence magnetization Cobalt strontium spinel ferrites High frequency application Rare earths

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Electrifying Ba_(0.5)Sr_(0.5)Co_(0.8)Fe_(0.2)O_(3-δ) for focalized heating in oxygen transport membranes

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Journal of Energy Chemistry 2024年第4期91卷 99-110页

作者： marwan Laqdiem Julio García-Fayos laura Almar Alfonso J.Carrillo Álvaro Represa Josém.López Nieto Sonia Escolástico David Catalán-martinez Jose m.Serra Instituto de Tecnología Química(Universitat Politècnica de València–Consejo Superior de Investigaciones Científicas) Av.Los Naranjos s/nE-46022 ValenciaSpain

Industry decarbonization requires the development of highly efficient and flexible technologies relying on renewable energy resources,especially biomass and solar/wind *** the case of pure oxygen production,oxygen transport membranes(OTms)appear as an alternative technology for the cryogenic distillation of air,the industrially-established process of producing ***,OTms could provide oxygen from different sources(air,water,CO_(2),etc.),and they are more flexible in adapting to current processes,producing oxygen at 700^(-1)000℃.Furthermore,OTms can be integrated into catalytic membrane reactors,providing new pathways for different *** first part of this study was focused on electrification on a traditional OTm material(Ba_(0.5)Sr_(0.5)Co_(0.8)Fe_(0.2)O_(3-δ)),imposing different electric currents/voltages along a capillary *** to the emerging Joule effect,the membrane-surface temperature and the associated O_(2) permeation flux could be ***,the OTm is electrically and locally heated and reaches 900℃on the surface,whereas the surrounding of the membrane was maintained at 650℃.The O_(2)permeation flux reached for the electrified membranes was~3.7 NmL min^(-1)cm^(-2),corresponding to the flux obtained with an OTm non-electrified at 900℃.The influence of depositing a porous Ce_(0.8)Tb_(0.2)O_(2-δ) catalytic/protective layer on the outer membrane surface revealed that lower surface temperatures(830℃)were detected at the same imposed electric ***,the electrification concept was demonstrated in a catalytic membrane reactor(CmR)where the oxidative dehydrogenation of ethane(ODHE)was carried *** reaction is very sensitive to temperature,and here,we demonstrate an improvement of the ethylene yield by reaching moderate temperatures in the reaction chamber while the O_(2) injection into the reaction can be easily fine-tuned.

关键词： Oxygen permeation Oxidative dehydrogenation of ethane Oxygen transport membranes Joule effect mixed ionic-electronic conductors Catalytic membrane reactors

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Identific tion of quantitative trait loci and associated candidate genes for pregnancy success in Angus–Brahman crossbred heifers

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Journal of Animal Science and Biotechnology 2024年第1期15卷 162-170页

作者： Quinn A.Hoorn Gabriel A.Zayas Eduardo E.Rodriguez laura m.Jensen Raluca G.mateescu Peter J.Hansen Department of Animal Sciences Donald Henry Barron Reproductive and Perinatal Biology Research Programand the Genetics InstituteUniversity of FloridaGainesvilleFLUSA School of Applied Systems Biology La Trobe UniversityBundooraVIC 3083Australia

Background In beef cattle, more than 50% of the energy input to produce a unit of beef is consumed by the female that produced the calf. Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef *** Genome-wide association studies(GWAS) were performed using a single-step genomic best linear unbiased prediction approach on pregnancy outcome traits from a population of Angus–Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another farm. Heifers were genotyped with the Bovine GGP F250 array that contains 221,077 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination(AI) followed by natural mating for 3 months. Two phenotypes were analyzed: pregnancy outcome to first-service AI(PAI;n = 1,481) and pregnancy status at the end of the breeding season(PEBS;n = 1,725). The heritability was estimated as 0.149 and 0.122 for PAI and PEBS, respectively. In the PAI model, one quantitative trait locus(QTL), located between 52.3 and 52.5 mb on BTA7, explained about 3% of the genetic variation, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5% and 1% of the genetic variation were found on BTA12 and 25. In the PEBS model, a large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTLs located on BTA5, 9, 10, 11, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus–Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTLs on BTA10 and 12 were *** In summary, QTLs and candidate SNPs identified were associated with pregnancy outcomes in beef heifers, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations

关键词： Beef cattle Fertility GWAS QTL

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^(15)N tracers and microbial analyses reveal in situ N_(2)O sources in contrasting water regimes of a drained peatland forest

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Pedosphere 2024年第4期34卷 749-758页

作者： mohit mASTA mikk ESPENBERG laura KUUSEmETS Jaan PÄRN Sandeep THAYAmKOTTU Holar SEPP Kalle KIRSImÄE Fotis SGOURIDIS Kuno KASAK Kaido SOOSAAR Ülo mANDER Institute of Ecology and Earth Sciences University of TartuVanemuise Street 46Tartu 51003Estonia School of Geographical Sciences University of BristolUniversity RoadBristol BS81SSUK

managed peatlands are a significant source of nitrous oxide(N_(2)O),a powerful greenhouse gas and stratospheric ozone *** to the complexity and diversity of microbial N_(2)O processes,different methods such as tracer,isotopomer,and microbiological technologies are required to understand these *** combined application of different methods helps to precisely estimate these processes,which is crucial for the future management of drained peatlands,and to mitigate soil degradation and negative atmospheric *** this study,we investigated N_(2)O sources by combining tracer,isotopomer,and microbial analysis in a drained peatland forest under flooded and drained *** average,the nitrification genes showed higher abundances in the drained treatment,and the denitrification genes showed higher abundances in the flooded *** is consistent with the underlying chemistry,as nitrification requires oxygen while denitrification is *** observed significant differences in labelled N_(2)O fluxes between the drained and flooded *** emissions of N_(2)O from the flooded treatment were nearly negligible,whereas the N_(2)O evolved from the nitrogen-15(^(15)N)-labelled ammonium(^(15)NH4+)in the drained treatment peaked at 147μg ^(15)N m^(-2) h^(-1).This initially suggested nitrification as the driving mechanism behind N_(2)O fluxes in drained peatlands,but based on the genetic data,isotopic analysis,and N_(2)O mass enrichment,we conclude that hybrid N_(2)O formation involving ammonia oxidation was the main source of N_(2)O emissions in the drained *** on the ^(15)N-labelled nitrate(^(15)NO3-)tracer addition and gene copy numbers,the low N_(2)O emissions in the flooded treatment came possibly from complete denitrification producing inert *** atomic level,we observed selective enrichment of mass 45 of N_(2)O molecule under ^(15)NH4+amendment in the drained treatment and enrichment of both masses 45 and 46 under

关键词： denitrification nitrification N_(2)O quantitative polymerase chain reaction

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Effect of Turbidity on Semi-Automatic Analysis of Copepod Size and Abundance Distribution in the Water Column

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Advances in Bioscience and Biotechnology 2024年第6期15卷 380-395页

作者： Thiago da Silva matos Carolina Siqueira dos Reis laura de Andrade moura márcio Abreu Ricardo Coutinho Lohengrin Fernandes IEAPm/UFF marine Biotechnology Post-Graduate Program Arraial do Cabo Brazil Instituto de Estudos do mar Almirante Paulo moreira Arraial do Cabo Brazil

Automated image systems to characterize aquatic organisms improve research and enable fast response to environmental risk situations. In November 2015, a dam in mariana City-mG (Brazil) collapsed and led to the disposal of mud tailings from the mining process to the Doce River. The accident resulted in several casualties and incalculable damage to surrounding communities and the environment. The mud increased water turbidity, an essential condition to the functioning of the image analysis systems, and directly affected the characterization of the organisms, making it impossible to distinguish copepods in the mud, due to the blurred outline. To get a quick response evaluating environmental situations, this work aimed to develop and test different algorithms characterizing and classifying copepods by their size (length and area) using in situ images acquired by the Lightframe On-Sight Keyspecies Investigation device. Field tests were carried out under different turbidity levels throughout the gradient observed in the coastal zone adjacent to the Doce River. The best algorithm reduced nearly 50% of the noise in some images when compared with manual treatment and led to 96% accuracy in measurement and counting. Semi-automated devices that perform post-processing corrections are suitable for fast environmental evaluation under high turbidity scenarios.

关键词： Imaging Zooplankton Doce River LOKI Copepod

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Factors associated with decreased compliance after on-site extracorporeal membrane oxygenation cannulation for acute respiratory distress syndrome:A retrospective,observational cohort study

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Journal of Intensive medicine 2024年第2期4卷 194-201页

作者： Sylvain Le Pape Florent Joly François Arrivé Jean-Pierre Frat maeva Rodriguez maïa Joos laura marchasson mathilde Wairy Arnaud WThille Rémi Coudroy Centre Hospitalier Universitaire de Poitiers Service de Médecine Intensive RéanimationPoitiersFrance INSERm Centre d'Investigation Clinique 1402 IS-ALIVE Research GroupUniversitéde PoitiersPoitiersFrance

Background Extracorporeal membrane oxygenation(ECmO)for acute respiratory distress syndrome(ARDS)is systematically associated with decreased respiratory system compliance(CRS).It remains unclear whether transportation to the referral ECmO center,changes in ventilatory mode or settings to achieve ultra-protective ventilation,or the natural evolution of ARDS drives this change in respiratory ***,we assessed the precise moment when CRS decreases after ECmO cannulation and identified factors associated with decreased *** To rule out the effect of transportation and the different modes of ventilation on CRS,we conducted a retrospective,single-center,observational cohort study from January 2013 to may 2020,on 22 patients with severe ARDS requiring on-site ECmO and ventilated in pressure-controlled mode to achieve ultra-protective *** was assessed at different time points ranging from 12 h before ECmO cannulation to 72 h after ECmO *** primary outcome was the relative change in CRS between 3 h before and 3 h after ECmO *** secondary outcomes included variables associated with the relative changes in CRS within the first 3 h after ECmO cannulation and the relative changes in CRS at each time *** CRS decreased within the first 3 h after ECmO cannulation(−28.3%,95%confidence interval[CI]:−38.8 to−17.9,Pmild before and after these first 3 h after ECmO *** achieve ultra-protective ventilation,respiratory rate decreased in the mean by–13 breaths/min(95%CI:−15 to−11)and driving pressure by−8.3 cmH2O(95%CI:−11.2 to−5.3),resulting in decreased tidal volume by−3.3 mL/kg of predicted body weight(95%CI:−3.9 to−2.6)as compared to before ECmO cannulation(Pme reduction were significantly associated with decreased CRS after ECmO cannulation,whereas neither respiratory rate,positive end-expiratory pr

关键词： Acute respiratory distress syndrome Extracorporeal membrane oxygenation Driving pressure Respiratory compliance

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Brain-derived neurotrophic factor signaling in the neuromuscular junction during developmental axonal competition and synapse elimination

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Neural Regeneration Research 2025年第2期20卷 394-401页

作者： Josep Tomàs Víctor Cilleros-mañé Laia Just-Borràs marta Balanyà-Segura Aleksandra Polishchuk laura Nadal marta Tomàs Carolina Silvera-Simón manel m.Santafé maria A.Lanuza Unitat d’Histologia i Neurobiologia(UHNeurob) Facultat de Medicina i Ciències de la SalutUniversitat Rovira i VirgiliReusSpain

During the development of the nervous system,there is an overproduction of neurons and *** competition between neighboring nerve endings and synapses performing different activity levels leads to their elimination or *** have extensively studied the involvement of the brain-derived neurotrophic factor-Tropomyosin-related kinase B receptor neurotrophic retrograde pathway,at the neuromuscular junction,in the axonal development and synapse elimination process versus the synapse *** purpose of this review is to describe the neurotrophic influence on developmental synapse elimination,in relation to other molecular pathways that we and others have found to regulate this *** particular,we summarize our published results based on transmitter release analysis and axonal counts to show the different involvement of the presynaptic acetylcholine muscarinic autoreceptors,coupled to downstream serine-threonine protein kinases A and C(PKA and PKC)and voltage-gated calcium channels,at different nerve endings in developmental *** dynamic changes that occur simultaneously in several nerve terminals and synapses converge across a postsynaptic site,influence each other,and require careful studies to individualize the mechanisms of specific *** describe an activity-dependent balance(related to the extent of transmitter release)between the presynaptic muscarinic subtypes and the neurotrophin-mediated TrkB/p75NTR pathways that can influence the timing and fate of the competitive interactions between the different axon *** downstream displacement of the PKA/PKC activity ratio to lower values,both in competing nerve terminals and at postsynaptic sites,plays a relevant role in controlling the elimination of supernumerary ***,calcium entry through L-and P/Q-subtypes of voltage-gated calcium channels(both channels are present,together with the N-type channel in developing nerve terminals)contributes to red

关键词： acetylcholine release adenosine receptors axonal competition brain-derived neurotrophic factor calcium channels motor end-plate muscarinic acetylcholine receptors postnatal synapse elimination serine kinases tropomyosin-related kinase receptorB

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Clinical and demographic features of patients undergoing videocapsule endoscopy management:A descriptive study

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World Journal of Gastrointestinal Endoscopy 2024年第7期16卷 424-431页

作者： maría C mejía Luis G Piñeros Luis m Pombo laura A León Jenny A Velásquez Aníbal A Teherán Karen P Ayala Research Center Fundación Universitaria Juan N.CorpasBogotá111321Colombia Fundación Universitaria Juan N.Corpas Bogotá111321Colombia Department of Gastroenterology Universidad Militar Nueva GranadaBogotá111711Colombia Department of Gastroenterology Hospital Universitario Clínica San RafaelBogotá111711Colombia

BACKGROUND Video-capsule endoscopy(VCE)is an efficient tool that has proven to be highly useful in approaching several gastrointestinal *** was implemented in Colombia in 2003,however current characterization of patients undergoing VCE in Colombia is limited,and mainly comes from two investigations conducted before the SARS-CoV-2 pandemic *** To describe the characteristics of patients undergoing VCEs and establish the main indications,findings,technical limitations,and other outstanding *** A descriptive study was carried out using data from reports of VCE(PillCam SB3 system)use in a Gastroenterology Unit in Bogotá,Colombia between September 2019 and January *** and clinical variables such as indication for the VCE,gastric and small bowel transit times(GTT,SBTT),endoscopic preparation quality,and limitations were described[n(%),median(IQR)].RESULTS A total of 133 VCE reports were *** were in men with a median age of 70 *** majority had good preparation(96.2%),and there were technical limitations in 15.8%of *** main indications were unexplained anemia(91%)or occult bleeding(23.3%).The median GTT and SBTT were 14 and 30 minutes,*** frequencies of bleeding stigma(3.79%)and active bleeding(9.09%)were low,and the most frequent abnormal findings were red spots(28.3%),erosions(17.6%),and vascular ectasias(12.5%).CONCLUSION VCE showed high-level *** main indication was unexplained *** bleeding was the most frequent *** with artificial intelligence,VCE can improve diagnostic precision and targeted therapeutic interventions.

关键词： Endoscopy Video-capsule endoscopy Capsule endoscopy Gastrointestinal diseases Observational study Gastrointestinal bleeding

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Further Studies of the Cap Pushing Response in Honey Bees (Apis mellifera)

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Natural Science 2024年第5期16卷 45-64页

作者： Riley J. Wincheski Kiri Li N. Stauch laura m. Grossner maya B. Zepeda James W. Grice Charles I. Abramson Department of Psychology Oklahoma State University Stillwater USA Laboratory of Comparative Psychology and Behavioral Biology Oklahoma State University Stillwater USA Department of Earth and Environmental Sciences California State University Fresno USA

The Cap Pushing Response (CPR) is a free-flying technique used to study learning and memory in honey bees (Apis mellifera). The series of experiments outlined in this paper aimed to test whether honey bees exhibit the cognitive concept of “expectancy” utilizing the CPR in a weight differentiation paradigm. Five previous experiments in our laboratory have explored whether the concept of expectancy can account for honey bee performance and have all failed to support the cognitive interpretation. The first experiment examined if bees could differentiate between the two caps in the amount of force they used to push the cap and the distance the cap was pushed when the caps were presented one at a time. The second experiment explored cap weight preference by presenting bees with a choice between the two caps. The third and fourth experiments tested the bee’s ability to expect reward or punishment based on cap weight. Results revealed that bees were found to have a strong preference for the light cap and therefore were not able to expect reward or punishment based on cap weight. These experiments contribute to the debate on whether bees have “cognitive” representations and continue to support the behaviorist interpretation.

关键词： Apis mellifera Cap Pushing Response Cognition Learning

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