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Computing on Phenotypic Descriptions for Candidate Gene Discovery and Crop Improvement

Plant Phenomics 2020年第1期2卷 118-121页

作者： ian r.braun Colleen F.Yanarella Carolyn J.Lawrence-Dill Interdepartmental Bioinformatics and Computational Biology Iowa State UniversityAmesIA 50011USA Department of Genetics Development and Cell BiologyIowa State UniversityAmesIA 50011USA Department of Agronomy Iowa State UniversityAmesIA 50011USA

Many newly observed phenotypes are first described,then experimentally manipulated.These language-based descriptions appear in both the literature and in community datastores.To standardize phenotypic descriptions and enable simple data aggregation and analysis,controlled vocabularies and specific data architectures have been developed.Such simplified descriptions have several advantages over natural language:they can be rigorously defined for a particular context or problem,they can be assigned and interpreted programmatically,and they can be organized in a way that allows for semantic reasoning(inference of implicit facts).Because researchers generally report phenotypes in the literature using natural language,curators have been translating phenotypic descriptions into controlled vocabularies for decades to make the information computable.Unfortunately,this methodology is highly dependent on human curation,which does not scale to the scope of all publications available across all of plant biology.Simultaneously,researchers in other domains have been working to enable computation on natural language.This has resulted in new,automated methods for computing on language that are now available,with early analyses showing great promise.Natural language processing(NLP)coupled with machine learning(ML)allows for the use of unstructured language for direct analysis of phenotypic descriptions.Indeed,we have found that these automated methods can be used to create data structures that perform as well or better than those generated by human curators on tasks such as predicting gene function and biochemical pathway membership.Here,we describe current and ongoing efforts to provide tools for the plant phenomics community to explore novel predictions that can be generated using these techniques.We also describe how these methods could be used along with mobile speech-to-text tools to collect and analyze in-field spoken phenotypic descriptions for association genetics and breeding applications.

关键词： stores translating enable

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Quantum state tomography from observable time traces in closed quantum systems

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Control Theory and Technology 2024年第2期22卷 222-234页

作者： Shuixin Xiao Yuanlong Wang Qi Yu Jun Zhang Daoyi Dong ian r.Petersen University of Michigan–Shanghai Jiao Tong University Joint Institute Shanghai Jiao Tong UniversityShanghai200240China School of Engineering The Australian National UniversityCanberraACT2601Australia Key Laboratory of Systems and Control Academy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing100190China Centre for Quantum Computation and Communication Technology(Australian research Council) Centre for Quantum DynamicsGriffith UniversityBrisbaneQLD4111Australia School of Engineering and Technology University of New South WalesCanberraACT2600Australia

The task to estimate all the parameters of an unknown quantum state, also called quantum state tomography, is essential for characterizing and controlling quantum systems. In this paper, we utilize observable time traces to identify the initial quantum state of a closed quantum system, based on the state space approach in the control theory. In the informationally complete scenario, we show that with a linear regression estimation (LrE), the mean squared error (MSE) scales as , where N is the resource number. In the informationally incomplete scenario, we introduce regularization LrE to perform the state tomography task. We employ PBH test to demonstrate that closed quantum systems with only one observable are informationally incomplete and propose using observables, where d is the dimension of the quantum state, for informational completeness. Numerical examples demonstrate the effectiveness of our method.

关键词： Quantum state tomography Time trace Quantum system identification

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Considerations for exerkine research focusing on the response to exercise training

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Journal of Sport and Health Science 2024年第2期13卷 130-132页

作者： ian A.J.Darragh Brendan Egan School of Health and Human Performance Dublin City UniversityGlasnevinDublin D09 V209Ireland Florida Institute for Human and Machine Cognition PensacolaFL 32502USA

García-Hermoso and colleagues1 recently published a systematic literature review and meta-analysis on exercise training-induced changes in exerkine concentrations in type 2diabetes mellitus patients,providing a contemporary view on how exerkines respond to exercise training.That review prompted us to highlight 2 additional considerations that should be taken into account when studying the response of exerkines to exercise training.Firstly,whether exerkines can exhibit discordant responses to acute exercise compared to exercise training,and secondly,the need to consider the residual effects of the most recent exercise bout.

关键词： acute exercise prompt

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Dual PPAr delta/gamma agonist offer therapeutic potential for Alzheimer's disease

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Neural regeneration research 2024年第6期19卷 1175-1176页

作者： ian Steinke Meenakshi Singh rajesh Amin Department of Drug Discovery and Development Auburn University

The increasing incidence of Alzheimer’s disease(AD) in the aging population, indicates the critical need for the development of novel targeted molecular therapies for ameliorating AD pathology. Moreover, clinical and preclinical evidence demonstrates that peroxisomal proliferator activating receptors(PPAr) agonists regulate energy and lipid homeostasis in models of diabetes, as well as improve spatial memory in animal models of AD(Khan et al., 2019).

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Health economics for intra-capsular hip fractures undertaking fixation

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World Journal of Orthopedics 2024年第1期15卷 30-38页

作者： Anatole Wiik Thomas Ashdown ian Holloway Department of Surgery Trauma and OrthopaedicsLondon North West University HealthcareLondon HA13UJUnited Kingdom Department of Surgery Trauma and OrthopaedicsLondon North West University HospitalLondon HA13UJUnited Kingdom

BACKGrOUND Hip fracture is a common musculoskeletal injury in the elderly requiring surgery worldwide.The operative mainstay of intra-capsular hip fractures is arthroplasty with a smaller proportion for fixation.AIM To determine the most beneficial method of fixation for patients with intracapsular hip fractures.METHODS A registered audit from 2012-2018 was conducted on all intra-capsular hip fractures treated with 2 commonly used fixation methods.Patient notes,electronic records and clinical codes for cost benefit were evaluated.A validated quality of life measure was collected at least 1 year after surgery.rESULTS A total of 83 patients were identified with intra-capsular fractures undergoing fixation during the retrospective period.There were 47 cannulated cancellous screw and 36 sliding hip screw fixations with the case mix comparable for age,gender,co-morbidities and fracture configuration.There was no significant difference in blood loss,tip apex distance,radiation exposure,length of stay,radiological union time,collapse,avascular necrosis or re-operation between fixation methods.Logistic regression analysis demonstrated displaced intracapsular hip fractures correlated significantly with an undesirable outcome conferring a relative odds ratio of 7.25.There were 9(19%)and 4(11%)patients respectively,who required re-operation.There was no significant difference in health resource group tariff and implant cost with comparable EQ-5D and visual CONCLUSION No significant advantage was identified with differing fixation type,but irrespective there were a high number of patients requiring re-operation.This was predicted by initial fracture displacement and patient age.Arthroplasty may need to be carefully considered for health economics and patient benefit.

关键词： Hip fracture Fixation Patient reported outcome measure Cost

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A seed and soil model of loneliness in Alzheimer's disease

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Neural regeneration research 2024年第12期19卷 2575-2576页

作者： Hannah L.Apostolou ian M.McDonough Department of Psychology The University of AlabamaTuscaloosaALUSA Department of Psychology Binghamton UniversityBinghamtonNYUSA

Loneliness is classically defined as a result of perceiving a discrepancy between the desired quantity and quality of one's social life and actual social relationships(Perlman and Peplau,1984).Lifespan research has indicated older adults are among the highest risk for experiencing loneliness because their social network size decreases more frequently than that of younger adults.

关键词： Alzheimer younger soil

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Public health importance of light intensity physical activity

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Journal of Sport and Health Science 2024年第5期13卷 674-675页

作者： robert ross ian Janssen Mark S.Tremblay School of Kinesiology and Health Studies Queen’s UniversityKingstonON K7L 3N6Canada School of Medicine Division of Endocrinology and MetabolismQueen’s UniversityKingstonON K7L 3N6Canada Healthy Active Living and Obesity research Group Children’s Hospital of Eastern Ontario Research InstituteOttawaON K1H 8L1Canada Department of Pediatrics University of OttawaOttawaON K1H 8L1Canada

1.Light intensity physical activity(PA)benefits health PA guidelines worldwide recommend that adults accumulate 150 min of moderate intensity or 75 min of vigorous intensity PA(moderate-to-vigorous PA(MVPA))weekly to achieve health benefits.1-3 Absent from these guidelines are recommendations for light intensity PA(LPA,e.g.,walking at a leisurely pace of 3 km/h or less,equivalent to 1.5-2.9 metabolic equivalents).

关键词： intensity light benefits

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Multi-Timescale Distributed Approach to Generalized-Nash-Equilibrium Seeking in Noncooperative Nonconvex Games

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IEEE/CAA Journal of Automatica Sinica 2024年第3期11卷 791-793页

作者： Banghua Huang Yang Liu Kit ian Kou Weihua Gui the School of Mathematical Sciences Zhejiang Normal UniversityJinhua 321004China IEEE the Key Laboratory of Intelligent Education Technology and Application of Zhejiang Province Jinhua 321004China the Faculty of Science and Technology University of MacaoMacaoChina the School of Automation Central South UniversityChangsha 410083China

Dear Editor,The distributed generalized-Nash-equilibrium(GNE)seeking in noncooperative games with nonconvexity is the topic of this letter.Inspired by the sequential quadratic programming(SQP)method,a multi-timescale multi-agent system(MAS)is developed,and its convergence to a critical point of the game is proven.To illustrate the qualities and efficacy of the theoretical findings,a numerical example is elaborated.

关键词： letter seeking programming

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Isolating higher yielding and more stable rice genotypes in stress environments: fine-tuning a selection method using production and resilience score indices

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Frontiers of Agricultural Science and Engineering 2024年第1期11卷 169-185页

作者： Arnauld THIrY William J.DAVIES ian C.DODD Lancaster Environment Centre Lancaster UniversityLancasterLancashire LA14YWUK

In Asia, the rice crop sustains millions of people. However, growing demand for this crop needs to be met while simultaneously reducing its water consumption to cope with the effects of climate change. Lowland cropping systems are the most common and productive but have particularly high water requirements. High-yielding rice genotypes adapted to drier environments(such as rainfed or aerobic rice ecosystems) are needed to increase the water use efficiency of cropping. Identifying these genotypes requires fast and more accurate selection methods. It is hypothesized that applying a new quantitative selection method(the score index selection method), can usefully compare rice yield responses over different years and stress intensities to select genotypes more rapidly and efficiently. Applying the score index to previously published rice yield data for 39 genotypes grown in no-stress and two stress environments, identified three genotypes(ArB 8, Ir55419-04 and ArB 7) with higher and stable yield under moderate to severe stress conditions. These genotypes are postulated to be better adapted to stress environment such as upland and aerobic environments. Importantly, the score index selection method offers improved precision than the conventional breeding selection method in identifying genotypes that are well-suited to a range of stress levels within the target environment.

关键词： Aerobic rice breeding selection drought resilience production capacity index resilience capacity index stress score index upland

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Supramolecular Manipulation of Intracellular Acidic Vesicles to Improve Cellular Self-repair and Self-Defense

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CCS Chemistry 2024年第6期6卷 1487-1498页

作者： Ziyi Wang Chen Sun Yu Dong Yuan-Fu Ding Chen Zhao ian Wa Ho Jiahong Lu ruibing Wang State Key Laboratory of Quality research in Chinese Medicine Institute of Chinese Medical SciencesUniversity of MacaoTaipaMacao 999078

Lysosomes are the“cell stomach”that digests various species including macromolecules and pathogens for self-repair and self-defense upon fusion with endosomes,autophagosomes,and phagosomes.Therefore,artificially manipulating intracellular vesicles could potentially promote lysosome-mediated intracellular digestion for disease prevention and treatment.Herein,a supramolecular strategy to efficiently tether and fuse acidic vesicles(i.e.,lysosomes,late endosomes,autolysosomes,and phagosomes)has been developed for the first time to enhance the digestion of cellular wastes and foreign matter,including pathogens.A linear polyethylene glycol(PEG)derivative dually tagged with morpholine(MOr)and adamantane(ADA)on the opposite side,namely,MOr-PEG-ADA,was designed to target intracellular acidic vesicles via MOr and to decorate their surfaces with ADA.Subsequently,the addition of cucurbit[7]uril(CB[7])grafted hyaluronic acid(HA)induced supramolecular tethering and fusion of acidic vesicles via strong host-guest interactions between CB[7]of CB[7]-HA and ADA residing on the surface of acidic vesicles.As a proof-ofconcept,the overall cellular metabolism,including endogenous autophagy and the exogenous endocytosis and phagocytosis,was effectively upregulated,demonstrating that supramolecular regulation of the dynamics of intracellular acidic vesicles may promote the lysosome’s digestion to significantly improve cellular self-repair and self-defense.

关键词： supramolecular chemistry organelle regulation intracellular acidic vesicles lysosomes selfdefense self-repair

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