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Comparison of methods for deriving phenotypes from incomplete observation data with an application to age at puberty in dairy cattle

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Journal of Animal Science and Biotechnology 2024年第2期15卷 535-545页

作者： Melissa A.Stephen Chris R.Burke Jennie E.Pryce Nicole M.Steele Peter R.Amer Susanne Meier Claire V.C.Phyn Dorian J.Garrick DairyNZ Ltd 605 Ruakura RoadHamilton 3240New Zealand AL Rae Centre for Genetics and Breeding-Massey University RuakuraHamilton 3214New Zealand agriculture victoria Research AgriBioCentre for AgriBioscienceBundooraVictoria 3083Australia School of Applied Systems Biology La Trobe UniversityBundooraVictoria 3083Australia AbacusBio DunedinNew Zealand

Background Many phenotypes in animal breeding are derived from incomplete measures,especially if they are challenging or expensive to measure *** include time-dependent traits such as reproductive status,or *** measures for these traits result in phenotypes that are subject to left-,interval-and rightcensoring,where phenotypes are only known to fall below an upper bound,between a lower and upper bound,or above a lower bound *** we compare three methods for deriving phenotypes from incomplete data using age at first elevation(>1 ng/mL)in blood plasma progesterone(AGEP4),which generally coincides with onset of puberty,as an example *** We produced AGEP4 phenotypes from three blood samples collected at about 30-day intervals from approximately 5,000 Holstein–Friesian or Holstein–Friesian×Jersey cross-bred dairy heifers managed in 54 seasonal-calving,pasture-based herds in New *** used these actual data to simulate 7 different visit scenarios,increasing the extent of censoring by disregarding data from one or two of the three *** methods for deriving phenotypes from these data were explored:1)ordinal categorical variables which were analysed using categorical threshold analysis;2)continuous variables,with a penalty of 31 d assigned to right-censored phenotypes;and 3)continuous variables,sampled from within a lower and upper bound using a data augmentation *** Credibility intervals for heritability estimations overlapped across all methods and visit scenarios,but estimated heritabilities tended to be higher when left censoring was *** sires with at least 5 daughters,the correlations between estimated breeding values(EBVs)from our three-visit scenario and each reduced data scenario varied by method,ranging from 0.65 to *** estimated breed effects also varied by method,but breed differences were smaller as phenotype censoring *** Our results indicate that using

关键词： Cattle Gibbs sampler Markov-chain Monte Carlo(MCMC) Puberty

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A novel diagnostic gene region for distinguishing between two pest fruit flies:Bactrocera tryoni(Froggatt)and Bactrocera neohumeralis(Hardy)(Diptera:Tephritidae)

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Insect Science 2024年第4期31卷 1285-1295页

作者： Melissa L.Starkie Elizabeth V.Fowler Alexander M.Piper Xiaocheng Zhu Pauline Wyatt David Gopurenko Matt N.Krosch Francesca Strutt Karen F.Armstrong Hamish Patrick Mark K.Schutze Mark J.Blacket Department of agriculture and Fisheries BiosecurityBrisbaneQueenslandAustralia agriculture victoria AgriBioBundooraVictoriaAustralia Department of Primary Industries Wagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia Forensic Services Group Queensland Police ServiceBrisbaneQueenslandAustralia Department of Pest-management and Conservation Lincoln UniversityLincolnNew Zealand Better Border Biosecurity(B3 B3nz.org.nz)LincolnNew Zealand

Bactrocera tryoni and Bactrocera neohumeralis are morphologically similar sibling pest fruit fly species that possess different biological attributes,geographic distributions,and host *** need to differentiate between the two species is critical for accurate pest status assessment,management,biosecurity,and maintenance of reference *** morphologically similar,adults may be separated based on subtle characters;however,some characters exhibit intraspecific variability,creating overlap between the two ***,there is currently no single molecular marker or rapid diagnostic assay that can reliably distinguish between *** and ***;therefore,ambiguous samples remain *** we report the first molecular marker that can consistently distinguish between *** and *** diagnostic region consists of two adjacent single nucleotide polymorphisms(SNPs)within the pangolin(pan)gene *** confirmed the genotypes of each species are consistent across their distributional range,then developed a tetra-primer amplification refractory mutation system(ARMS)PCR assay for rapid diagnosis of the *** assay utilizes four primers in multiplex,with two outer universal primers,and two internal primers:one designed to target two adjacent SNPs(AA)present in *** and the other targeting adjacent SNPs present in ***(GG).The assay accurately discriminates between the two species,but their SNP genotypes are shared with other nontarget tephritid fruit fly ***,this assay is most suited to adult diagnostics where species confirmation is necessary in determining ambiguous surveillance trap catches;maintaining pure colony lines;and in Sterile Insect Technique management responses.

关键词： ARMS-PCR colony molecular diagnostics pangolin tetra-primer

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Smart mid-infrared metasurface microspectrometer gas sensing system

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Microsystems & Nanoengineering 2024年第3期10卷 273-281页

作者： Jiajun Meng Sivacarendran Balendhran Ylias Sabri Suresh K.Bhargava Kenneth B.Crozier School of Physics University of MelbourneVictoriaAustralia Australian Research Council(ARC)Centre of Excellence for Transformative Meta-Optical Systems(TMOS) University of MelbourneVictoriaAustralia Centre for Advanced Materials&Industrial Chemistry(CAMIC) STEM collegeRMIT UniversityVictoriaAustralia Department of Electrical and Electronic Engineering University of MelbourneVictoriaAustralia

Smart,low-cost and portable gas sensors are highly desired due to the importance of air quality monitoring for environmental and defense-related ***,electrochemical and nondispersive infrared(IR)gas sensors are designed to detect a single specific *** IR spectroscopy-based sensors provide superior performance,their deployment is limited due to their large size and high *** this study,a smart,low-cost,multigas sensing system is demonstrated consisting of a mid-infrared microspectrometer and a machine learning *** microspectrometer is a metasurface filter array integrated with a commercial IR camera that is consumable-free,compact(~1 cm^(3))and lightweight(~1 g).The machine learning algorithm is trained to analyze the data from the microspectrometer and predict the gases *** system detects the greenhouse gases carbon dioxide and methane at concentrations ranging from 10 to 100%with 100%*** also detects hazardous gases at low concentrations with an accuracy of 98.4%.Ammonia can be detected at a concentration of 100 ***,methyl-ethyl-ketone can be detected at its permissible exposure limit(200 ppm);this concentration is considered low and *** study demonstrates the viability of using machine learning with IR spectroscopy to provide a smart and low-cost multigas sensing platform.

关键词： Smart gases system

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Influence of laser parameters on the microstructures and surface properties in laser surface modification of biomedical magnesium alloys

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Journal of Magnesium and Alloys 2024年第1期12卷 72-97页

作者： Chee Ying Tan Cuie Wen Hua Qian Ang School of Engineering RMIT UniversityMelbourneVictoria 3001Australia

Biodegradable implants from magnesium(Mg)alloys have emerged in the biomedical field especially in the orthopedic and cardiovascular stent applications owing to their low density,high specific strength,excellent machinability,good biocompatibility,and *** primary shortcoming of Mg-based implants is their low corrosion resistance in the physiological environment,which results in premature mechanical integrity loss before adequate healing and the production of excessive hydrogen gas,which is harmful to the body tissues and negatively affects the biocompatibility of the *** surface modification has recently received attention because it can improve the surface properties such as surface chemistry,roughness,topography,corrosion resistance,wear resistance,hydrophilicity,and thus cell response to the surface of the *** composition and microstructures including textures and phases of laser-treated surfaces depend largely on the laser processing parameters(input laser power,laser scan velocity,frequency,pulse duration,pressure,gas circulation,working time,spot size,beam focal position,and laser track overlap)and the thermophysical properties of the substrate(solubility,melting point,and boiling point).This review investigates the impacts of various laser surface modification techniques including laser surface melting,laser surface alloying,laser cladding,laser surface texturing,and laser shock peening,and highlights their significance in improving the surface properties of biodegradable Mg alloys for implant ***,we explore how different laser process parameters affect its composition,microstructure,and surface properties in each laser surface modification technique.

关键词： Biocompatibility Biodegradability Corrosion Implant applications Laser surface modification Magnesium alloys

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Excessive manure application stimulates nitrogen cycling but only weakly promotes crop yields in an acidic Ultisol:Results from a 20-year field experiment

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Journal of Integrative agriculture 2024年第7期23卷 2434-2445页

作者： Song Wan Yongxin Lin Hangwei Hu Milin Deng Jianbo Fan Jizheng He Key Laboratory for Humid Subtropical Eco-geographical Processes of Ministry of Education School of Geographical Sciences/School of Carbon Neutrality Future TechnologyFujian Normal UniversityFuzhou 350007China School of agriculture and Food Faculty of ScienceThe University of MelbourneParkvilleVictoria 3010Australia State Key Laboratory of Soil and Sustainable agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China

Population growth and growing demand for livestock products produce large amounts of manure,which can be harnessed to maintain soil sustainability and crop ***,the impacts of excessive manure application on crop yields,nitrogen(N)-cycling processes and microorganisms remain ***,we explored the effects of 20-year of excessive rates(18 and 27 Mg ha^(–1)yr^(–1))of pig manure application on peanut crop yields,soil nutrient contents,N-cycling processes and the abundance of N-cycling microorganisms in an acidic Ultisol in summer and winter,compared with none and a regular rate(9 Mg ha^(–1)yr^(–1))of pig manure ***-term excessive pig manure application,especially at the high-rate,significantly increased soil nutrient contents,the abundance of N-cycling functional genes,potential nitrification and denitrification activity,while it had a weaker effect on peanut yield and plant *** with manure application,seasonality had a much weaker effect on N-cycling gene *** forest analysis showed that available phosphorus(AP)content was the primary predictor for N-cycling gene abundance,with significant and positive associations with all tested N-cycling *** study clearly illustrated that excessive manure application would increase N-cycling gene abundance and potential N loss with relatively weak promotion of crop yields,providing significant implications for sustainable agriculture in the acidic Ultisols.

关键词： denitrification manure amendment nitrification N-cycling functional genes peanut yields

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Treat to target in Crohn’s disease:A practical guide for clinicians

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World Journal of Gastroenterology 2024年第1期30卷 50-69页

作者： Ashish R Srinivasan Department of Gastroenterology Austin HealthVictoriaMelbourne 3083Australia Department of Gastroenterology Eastern HealthVictoriaMelbourne 3128Australia Department of Medicine University of MelbourneVictoriaMelbourne 3052Australia

A treat-to-target(T2T)approach applies the principles of early intervention and tight disease control to optimise long-term outcomes in Crohn's *** Selecting Therapeutic Targets in Inflammatory Bowel Disease(STRIDE)-II guidelines specify short,intermediate,and long-term treatment goals,documenting specific treatment targets to be achieved at each of these *** appraisal of Crohn’s disease activity against pre-defined treatment targets at these timepoints remains central to determining whether current therapy should be continued or *** treatment targets in Crohn’s disease comprise combination clinical and patient-reported outcome remission,in conjunction with biomarker normalisation and endoscopic *** the STRIDE-II guidelines endorse the pursuit of endoscopic healing,clinicians must consider that this may not always be appropriate,acceptable,or achievable in all *** underscores the need to engage patients at the outset in an effort to personalise care and individualise treatment *** use of non-invasive biomarkers such as faecal calprotectin in conjunction with cross-sectional imaging techniques,particularly intestinal ultrasound,holds great promise;as do emerging treatment targets such as transmural *** randomised clinical trials,namely,CALM and STARDUST,have evaluated the efficacy of a T2T approach in achieving endoscopic endpoints in patients with Crohn’s *** from these studies reflect that patient subgroups and Crohn’s disease characteristics likely to benefit most from a T2T approach,remain to be ***,outside of clinical trials,data pertaining to the real-world effectiveness of a T2T approach remains scare,highlighting the need for pragmatic real-world *** the obvious promise of a T2T approach,a lack of guidance to support its integration into real-world clinical practice has the potential to limit its *** highlights the need to describe st

关键词： Treat to target Inflammatory bowel disease Crohn’s disease Treatment targets Endoscopic remission Transmural healing Time to response Intestinal ultrasound

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Aggregation-induced emission polymers via reversible-deactivation radical polymerization Special Collection:Distinguished Australian Researchers

Aggregate

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Aggregate 2024年第1期5卷 16-46页

作者： Nicholas Kai Shiang Teo Bo Fan Aditya Ardana San H.Thang School of Chemistry Monash UniversityClaytonVictoriaAustralia

Aggregation-induced emission(AIE)is a unique phenomenon whereby aggregation of molecules induces fluorescence emission as opposed to the more commonly known aggregation-caused quenching(ACQ).AIE has the potential to be utilized in the large-scale production of AIE-active polymeric materials because of their wide range of practical applications such as stimuli-responsive sensors,biological imaging agents,and drug delivery *** is evident from the increasing number of publications over the years since AIE was first *** addition,the evergrowing interest in this field has led many researchers around the world to develop new and creative methods in the design of monomers,initiators and crosslinkers,with the goal of broadening the scope and utility of AIE *** of the most promising approaches to the design and synthesis of AIE polymers is the use of the reversible-deactivation radical polymerization(RDRP)techniques,which enabled the production of well-controlled AIE materials that are often difficult to achieve by other *** this review,a summary of some recent works that utilize RDRP for AIE polymer design and synthesis is presented,including(i)the design of AIE-related monomers,initiators/crosslinkers;the achievements in preparation of AIE polymers using(ii)reversible addition–fragmentation chain transfer(RAFT)technique;(iii)atom transfer radical polymerization(ATRP)technique;(iv)other techniques such as Cu(0)-RDRP technique and nitroxide-mediated polymerization(NMP)technique;(v)the possible applications of these AIE polymers,and finally(vi)a summary/perspective and the future direction of AIE polymers.

关键词： aggregation-induced emission atom transfer radical polymerization nitroxide-mediated polymerization reversible addition–fragmentation chain transfer reversible-deactivation radical polymerization

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Approach to loss of response to advanced therapies in inflammatory bowel disease

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World Journal of Gastroenterology 2024年第22期30卷 2902-2919页

作者： Nikil Vootukuru Abhinav Vasudevan Department of Gastroenterology and Hepatology Eastern HealthVictoriaBox Hill 3128Australia Eastern Health Clinical School Monash UniversityVictoriaBox Hill 3128Australia

BACKGROUND Remarkable progress over the last decade has equipped clinicians with many options in the treatment of inflammatory bowel *** now have the unique opportunity to provide individualized treatment that can achieve and sustain remission in many ***,issues of primary non-response(PNR)and secondary loss of response(SLOR)to non-tumour necrosis factor inhibitor(TNFi)therapies remains a common *** issues include the choice of optimization of therapy,identifying when dose optimization will recapture response,establishing optimal dose for escalation and when to switch *** To explores the issues of PNR and SLOR to non-TNFi *** This review explores the current evidence and literature to elucidate management options in cases of PNR/*** will also explore potential predictors for response following SLOR/PNR to therapies including the role of therapeutic drug monitoring(TDM).RESULTS In the setting of PNR and loss of response to alpha-beta7-integrin inhibitors and interleukin(IL)-12 and IL-23 inhibitors dose optimization is a reasonable option to capture *** Janus kinase inhibitors dose optimization can be utilized to recapture response with loss of *** The role of TDM in the setting of advanced non-TNFi therapies to identify patients who require dose optimization and as a predictor for clinical remission is not yet established and this remains an area that should be addressed in the future.

关键词： Inflammatory bowel disease Ulcerative colitis Crohn Biologics Interleukin-12 and interleukin-23 inhibitors Alpha-beta7-integrin inhibitors Janus kinase inhibitors Sphingosine-1-phosphate receptor modulators

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Trustworthy semi-supervised anomaly detection for online‐tooffline logistics business in merchant identification

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CAAI Transactions on Intelligence Technology 2024年第3期9卷 544-556页

作者： Yong Li Shuhang Wang Shijie Xu Jiao Yin Business School China University of Political Science and LawBeijingChina JD Logistics BeijingChina Southeast University NanjingChina Institute for Sustainable Industries and Liveable Cities Victoria UniversityMelbourneVictoriaAustralia

The rise of online-to-offline(O2O)e-commerce business has brought tremendous opportunities to the logistics *** the online-to-offline logistics business,it is essential to detect anomaly merchants with fraudulent shipping behaviours,such as sending other merchants'packages for profit with their low *** can help reduce the financial losses of platforms and ensure a healthy *** anomaly detection studies have mainly focused on online fraud behaviour detection,such as fraudulent purchase and comment behaviours in ***,these methods are not suitable for anomaly merchant detection in logistics due to the more complex online and offline operation of package-sending behaviours and the interpretable requirements of offline deployment in ***,a semi-supervised multiview fusion-based Anomaly Detection framework in online-to-offline logistics is proposed,which consists of a basic version SemiDet and an attention-enhanced multi-view fusion *** SemiDet,pair-wise data augmentation is first conducted to promote model robustness and address the challenge of limited labelled anomaly ***,SemiDet calculates the anomaly scoring of each merchant with an auto-encoder *** the multi-relationships among logistics merchants,a multi-view attention fusion-based anomaly detection network is further designed to capture merchants'mutual influences and improve the anomaly merchant detection performance.A post-hoc perturbation-based interpretation model is designed to output the importance of different views and ensure the trustworthiness of end-to-end anomaly *** framework based on an eight-month real-world dataset collected from one of the largest logistics platforms in China is evaluated,involving 6128 merchants and 16 million historical order consignor records in *** results show that the proposed model outperforms other baselines in both AUC-ROC and AUC-PR metrics.

关键词： artificial intelligence techniques data fusion deep learning

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Stand dynamics of old-growth hemlock forests in central Bhutan are shaped by natural disturbances

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Forest Ecosystems 2024年第4期11卷 434-447页

作者： Karma Tenzin Craig R.Nitschke Kathryn J.Allen Raphael Trouve Thiet V.Nguyen Patrick J.Baker School of agriculture Foodand Ecosystem SciencesUniversity of Melbourne500 Yarra BlvdRichmondVictoriaAustralia School of Geography Planningand Spatial SciencesUniversity of TasmaniaSandy BayTasmaniaAustralia Forest Science Institute of South Vietnam 1 Pham Van Hai StreetTan Binh DistrictHo Chi Minh CityViet Nam

Understanding how past disturbances have influenced the development of forests is critical for deciphering their current structure and composition and forecasting future *** this study,dendrochronological methods were applied to uncover the disturbance history of old-growth hemlock-dominated forests in central *** of tree-ring samples from two old-growth hemlock stands,located in two different topographic settings,identified the importance of gap-phase dynamics in facilitating recruitment and growth releases and producing complex,multi-aged structure s over *** site showed evidence of a near stand-replacing disturbance in the late 1700s,while the other showed no evide nce of high-severity disturbance at any time over the last 400 *** both sites low-to medium-severity disturbances,some of which appear to be associated with cyclones originating in the Bay of Bengal,dominated the disturbance *** hemlock stands exhibited a significant positive association between cyclone occurrence and growth release events and between recruitment pulses and growth release *** 1800 to 1970 there was an increase in recruitment of angiosperm tree species at most sites and a corresponding decline in conifer *** the past 50 years there has been little new recruitment;this may be due to light limitation in the understory from shade-tolerant angiosperms and bamboo in the lower strata of these *** variations in disturbance dynamics and recruitment were observed across the study sites,suggesting that other factors,such as topography and climate,may be influencing long-term stand development *** study highlights the complex interplay between historical disturbance regimes and tree recruitment in shaping the age and size structures of old-growth hemlock forests in central *** also provides new insights into the dynamics of these forests that can be used to support effective forest conservation and management i

关键词： Forest structure Hemlock forest Himalaya Natural disturbance

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