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Machine Learning Techniques for predicting Crop photosynthetic Capacity from Leaf Reflectance Spectra

Molecular plant 2017年第6期10卷 878-890页

作者： david Heckmann Urte Schluter Andreas p.M. Weber Heinrich-Heine-Universitat Institute for Computer Science Heinrich-Heine-Universitat Institute of Plant Biochemistry Cluster of Excellence on plant Sciences (CEpLAS) 'From Complex Traits towards Synthetic Modules' 40225 Dusseldorf Germany

Harnessing natural variation in photosynthetic capacity is a promising route toward yield increases, but physiological phenotyping is still too laborious for large-scale genetic screens. Here, we evaluate the potential of leaf reflectance spectroscopy to predict parameters of photosynthetic capacity in Brassica oleracea and Zea mays, a C3 and a C4 crop, respectively. To this end, we systematically evaluated properties of reflectance spectra and found that they are surprisingly similar over a wide range of species. We assessed the performance of a wide range of machine learning methods and selected recursive feature elimination on untransformed spectra followed by partial least squares regression as the preferred algorithm that yielded the highest predictive power. Learning curves of this algorithm suggest optimal species-specific sample sizes. Using the Brassica relative Moricandia, we evaluated the model transferability between spe- cies and found that cross-species performance cannot be predicted from phylogenetic proximity. The final intra-species models predict crop photosynthetic capacity with high accuracy. Based on the estimated model accuracy, we simulated the use of the models in selective breeding experiments, and showed that high-throughput photosynthetic phenotyping using our method has the potential to greatly improve breeding success. Our results indicate that leaf reflectance phenotyping is an efficient method for improving crop photosynthetic capacity.

关键词： leaf spectrometry photosynthesis machine learning crops C4 phenotyping

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Simplified seismic performance assessment and implications for seismic design

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Earthquake Engineering and Engineering Vibration 2014年第S1期13卷 95-122页

作者： Timothy J.Sullivan david p.Welch Gian Michele Calvi University of pavia Department of Civil Engineering & ArchitecturePavia 27100Italy European Centre for Training and Research in Earthquake Engineering Pavia 27100Italy UME School ROSE ProgrammeIUSS Pavia phD candidate IUSS pavia professor

The last decade or so has seen the development of refined performance-based earthquake engineering(pBEE) approaches that now provide a framework for estimation of a range of important decision variables,such as repair costs,repair time and number of casualties. This paper reviews current tools for pBEE,including the pACT software,and examines the possibility of extending the innovative displacement-based assessment approach as a simplified structural analysis option for performance assessment. Details of the displacement-based s+eismic assessment method are reviewed and a simple means of quickly assessing multiple hazard levels is proposed. Furthermore,proposals for a simple definition of collapse fragility and relations between equivalent single-degree-of-freedom characteristics and multi-degree-of-freedom story drift and floor acceleration demands are discussed,highlighting needs for future research. To illustrate the potential of the methodology,performance measures obtained from the simplified method are compared with those computed using the results of incremental dynamic analyses within the pEER performance-based earthquake engineering framework,applied to a benchmark building. The comparison illustrates that the simplified method could be a very effective conceptual seismic design tool. The advantages and disadvantages of the simplified approach are discussed and potential implications of advanced seismic performance assessments for conceptual seismic design are highlighted through examination of different case study scenarios including different structural configurations.

关键词： performance-based earthquake engineering displacement-based assessment seismic assessment

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A combined experimental and DEM investigation of grain interlocking in sheared granular assemblies

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particuology 2024年第7期90卷 436-451页

作者： Rui Lu Qiang Luo Tengfei Wang david p.Connolly Tao Xie School of Civil Engineering Southwest Jiaotong UniversityChengdu 610031China Key Laboratory of High-Speed Railway Engineering(Southwest Jiaotong University) Ministry of EducationChengdu 610031China School of Civil Engineering University of LeedsLeeds LS29JTUK Department of Civil Engineering McMaster UniversityHamiltonONCanada

Compacted granular material,integral to geotechnical engineering,undergoes translation,rotation,and interlocking when subject to shear displacements or external *** present study focuses on the interlocking of heterogeneous granular materials,a complex behavior influenced by gradation,compaction,and varying particle geometry,and has consequently received limited attention in existing *** address this research gap,we conducted an analysis on the effect of grain interlocking on the shear resistance of granular assemblies,using a combination of laboratory testing and the discrete element method(DEM).Initially,large-scale direct shear tests were conducted on gravel−sand mixes with varying degrees of compaction and normal *** of the mixes also underwent subsequent shear reversal to explore the differences in grain interlocking between the two shearing processes on the shear *** analyzing the laboratory results,a mesoscopic scale investigation was performed by replicating the test using discrete element *** facilitate this,granular particle geometries were measured using 3D laser scanning based on the physical lab ***,based on these scans,discrete element R-block and ball models were utilized to construct both the coarse and fine particles within the *** vibro-compaction was employed to regulate the degree of *** results indicate that an increase in vertical pressure,coupled with a zero dilatancy angle,results in a rising stress ratio,indicative of grain *** interlocking exhibits a positive correlation with both the coarse content and the degree of compaction,and varies depending on the shear *** interlocking progresses,the shear band,induced by particle movement,expands and is associated with reduced particle rotation near the shear *** study further reveals a consistent positive correlation between interlocking and the principal orientation angle of strong normal c

关键词： Granular material Interlocking Shear resistance Direct shear Discrete element method Vibro-compaction

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Mutifactorial analysis of risk factors for reduced bone mineral density in patients with Crohn’s disease

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World Journal of Gastroenterology 2006年第35期12卷 5680-5686页

作者： Sarah A Bartram Robert T peaston david J Rawlings david Walshaw Roger M Francis Nick p Thompson Musculoskeletal unit Freeman HospitalNewcastle-upon-Tyne United Kingdom Department of Biochemistry Freeman Hospital Newcastle-upon-Tyne United Kingdom Regional Medical physics Department Newcastle General Hospital United Kingdom Dept of Statistics University of Newcastle upon Tyne United Kingdom Musculoskeletal unit Freeman Hospital Newcastle-upon-Tyne United Kingdom Department of Medicine Freeman Hospital Newcastle-upon-Tyne United Kingdom

AIM: To determine the prevalence of osteoporosis in a cohort of patients with Crohn’s disease (CD) and to identify the relative significance of risk factors for osteoporosis. METHODS: Two hundred and fifty-eight unselected patients (92 M, 166 F) with CD were studied. Bone mineral density (BMD) was measured at the lumbar spine and hip by dual X-ray absorptiometry. Bone formation was assessed by measuring bone specific alkaline phosphatase (BSAp) and bone resorption by measuring urinary excretion of deoxypyridinoline (DpD) and N-telopeptide (NTX). RESULTS: Between 11.6%-13.6% patients were osteoporotic (T score pine and/or hip. NTX levels were significantly higher in the patients with osteoporosis (p p and DpD levels were not significantly different. Independent risk factors for osteoporosis at either the lumbar spine or hip were a low body mass index (p p p pine and hip respectively. CONCLUSION: Our results confirm that osteoporosis is common in patients with CD and suggest that increased bone resorption is the mechanism responsible for thebone loss. However, less than half of the reduction in BMD can be attributed to risk factors such as corticosteroid use and low BMI and therefore remains unexplained.

关键词： Crohn's disease Osteoporosis Osteopenia Bone mineral density

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Drag on Hydroid-Fouled Nets – An Experimental Approach

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China Ocean Engineering 2015年第3期29卷 369-389页

作者： pl LADER david W. FREDRIKSSON Jana GUENTHER Zsolt VOLENT Nina BLOCHER david KRISTIANSEN Lars GANSEL Jud DECEW SINTEF Fisheries and Aquaculture United States Naval Academy University of New Hampshire

The present study investigated the drag increase on aquaculture nets due to biofouling of the colonial hydroid Ectopleura larynx. It had two main parts： firstly the growth characteristics of E. larynx were investigated by use of field tests at a Norwegian aquaculture site; secondly the hydrodynamic drag on the fouled twines was studied in a towing tank by using fabricated models of net twines with artificial hydroid fouling. In the field tests, the growth of the hydroids was first measured after three weeks of immersion and then again after six weeks. During this interval, the density of hydroids and the thickness of the hydroid stem were almost constant（1.4 hydroids/mm and 0.29 mm, respectively）, while the average length of the hydroids increased from 6.4 to 11.2 mm. The hydroid length followed a Rayleigh distribution, while the thickness was normal（Gaussian） distributed. Replicas of twines with three different levels of hydroid growth were made（1.5 hydroids/mm twine, hydroid length 9 mm, 16 mm and 20 mm）, and the drag on these twines was measured at different towing velocities（0.1 to 1.4 m/s） and with different twine configurations. For the twine with the shortest hydroids（9 mm）, the drag was from 1.5 times（Re=4000） to 2.2 times（Re=1000） the drag on a clean twine. For the longest hydroids（21 mm）, the drag was 2 times and 3.8 times, respectively.

关键词： hydroid biofouling aquaculture net hydrodynamic drag

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Adjustable muscle plication:a new surgical technique for strabismic patients with high risk for anterior segment ischemia

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International Journal of Ophthalmology(English edition) 2015年第4期8卷 839-842页

作者： Carlos Laria david p.pinero Department of Ophthalmology(OFTALMAR) Vithas Medimar International Hospital Foundation for the Visual Quality(FUNCAVIS Fundación para la Calidad Visual) Department of Optics Pharmacology and AnatomyUniversity of Alicante

INTRODUCTION Anterior ciliary arteries provide 70%of the vascular supply of the anterior segment.A significant interruption of the vascular flow of these arteries increases the risk for anterior *** the frequency of this special condition is low after strabismus surgery(1:13 000)[1],its effects may involve substantial visual problems[2].We report the successful outcome of a new surgical approach for strabismus management in a case of high risk for anterior ***,we show the correction of the horizontal ocular deviation by means of an adjustable muscle

关键词： Figure a new surgical technique for strabismic patients with high risk for anterior segment ischemia high

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Specific serum antibody binding to phosphorylated and non-phosphorylated tau in non-cognitively impaired,mildly cognitively impaired,and Alzheimer’s disease subjects:an exploratory study

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Translational Neurodegeneration 2017年第1期6卷 324-332页

作者： Andrea C.Klaver Mary p.Coffey david A.Bennett david A.Loeffler Department of Neurology Beaumont Research InstituteBeaumont HealthRoyal OakMIUSA Department of Biostatistics Beaumont Research InstituteBeaumont HealthRoyal OakMIUSA Rush Alzheimer’s Disease Center ChicagoIL 60612USA

Background:Tau vaccination and administration of anti-tau antibodies can prevent pathology and cognitive impairment in transgenic mouse models of tauopathy,suggesting that therapies which increase anti-tau antibodies might slow the development and/or progression of Alzheimer’s disease(AD).The extent to which individuals with no cognitive impairment(NCI)possess serum anti-tau antibodies,and whether their concentrations of these antibodies differ from anti-tau antibody levels in persons with mild cognitive impairment(MCI)or AD,are *** studies measuring these antibodies did not account for antibody polyvalent binding,which can be extensive,nor that antibody binding to phosphorylated tau peptides could be due to binding to non-phosphorylated epitopes on those ***:An ELISA controlling for these factors was used to measure the specific binding of serum IgG and IgM to phosphorylated(“pTau;”phosphorylated at Serine-199 and Serine-202)and non-phosphorylated(“non-pTau”)tau 196-207 in subjects with NCI,MCI,or AD(n=10/group).Between-group differences in these antibody levels were evaluated for statistical significance,and correlations were examined in pooled data from all subjects between these antibody levels and subject age,global cognitive functioning,and NFT ***:Specific IgG binding to pTau and non-pTau was detected in all subjects except for one NCI *** IgM binding was detected to pTau in all subjects except for two AD patients,and to non-pTau in all *** pTau IgG was increased in MCI subjects by 53% and 70% *** and NCI subjects respectively(both pps for non-pTau IgG(p=0.052),pTau IgM,or non-pTau ***-pTau IgG was negatively associated with global cognition(Spearman rho=−0.50).Conclusions:Specific binding of serum IgG and IgM to phosphorylated and non-phosphorylated tau may be present in older persons regardless of their cognitive *** IgG

关键词： Alzheimer’s disease Antibodies Elisa ELISA Mild cognitive impairment phosphorylated tau

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Ca^(2+)-induced myelin pathology precedes axonal spheroid formation and is mediated in part by store-operated Ca^(2+)entry after spinal cord injury

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Neural Regeneration Research 2023年第12期18卷 2720-2726页

作者： Spencer Ames Kia Adams Mariah E.Geisen david p.Stirling Kentucky Spinal Cord Injury Research Center Department of Neurological Surgery Anatomical Sciences and Neurobiology Microbiology and Immunology University of LouisvilleSchool of MedicineLouisvilleKYUSA

The formation of axonal spheroid is a common feature following spinal cord *** further understand the source of Ca^(2+)that mediates axonal spheroid formation,we used our previously characterized ex vivo mouse spinal cord model that allows precise perturbation of extracellular Ca^(2+).We performed twophoton excitation imaging of spinal cords isolated from Thy1YFp+transgenic mice and applied the lipophilic dye,Nile red,to record dynamic changes in dorsal column axons and their myelin sheaths *** selectively released Ca^(2+)from internal stores using the Ca^(2+)ionophore ionomycin in the presence or absence of external Ca^(2+).We reported that ionomycin dose-dependently induces pathological changes in myelin and pronounced axonal spheroid formation in the presence of normal 2 m M Ca^(2+)artificial cerebrospinal *** contrast,removal of external Ca^(2+)significantly decreased ionomycin-induced myelin and axonal spheroid formation at 2 hours but not at 1 hour after *** mice that express a neuron-specific Ca^(2+)indicator in spinal cord axons,we confirmed that ionomycin induced significant increases in intra-axonal Ca^(2+),but not in the absence of external Ca^(2+).periaxonal swelling and the resultant disruption in the axo-myelinic interface often precedes and is negatively correlated with axonal spheroid *** with YM58483(500 n M),a well-established blocker of store-operated Ca^(2+)entry,significantly decreased myelin injury and axonal spheroid ***,these data reveal that ionomycin-induced depletion of internal Ca^(2+)stores and subsequent external Ca^(2+)entry through store-operated Ca^(2+)entry contributes to pathological changes in myelin and axonal spheroid formation,providing new targets to protect central myelinated fibers.

关键词： axonal degeneration axonal spheroid formation ionomycin store-operated calcium entry myelin Nile red peri-axonal swelling

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Numerical modelling of resonance mechanisms in jointed rocks using transfer functions

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Journal of Rock Mechanics and Geotechnical Engineering 2023年第5期15卷 1076-1089页

作者： Harry Holmes Chrysothemis paraskevopoulou Mark Hildyard Krishna Neaupane david p.Connolly School of Earth and Environment University of LeedsLeedsLS29JTUK AECOM Ltd. ChesterfieldS417SLUK

Resonance effects in parallel jointed rocks subject to stress waves are investigated using transfer functions,derived from signals generated through numerical *** is important for a range of engineering situations as it identifies the frequency of waves which will be favourably *** different numerical methods are used for this study,adopting the finite difference method and the combined discrete element-finite difference *** numerical models are validated by replicating results from previous *** two methods are found to behave similarly and show the same resonance effects;one operating at low frequency and the other operating at relatively high *** resonance effects are interpreted in terms of simple physical systems and analytical equations are derived to predict the resonant frequencies of complex rock *** frequency resonance is shown to be generated by a system synonymous with masses between springs,described as spring resonance,with an equal number of resonant frequencies as the number of *** frequency resonance is generated through superposition of multiple reflected waves developing standing waves within intact blocks,described as superposition *** resonance through superposition has previously been identified,resonance based on masses between springs has not been previously identified in jointed *** findings of this study have implications for future analysis of multiple jointed rock masses,showing that a wave travelling through such materials can induce other modes of propagation of waves,*** resonance.

关键词： Resonance Jointed rocks Finite difference method Discrete element Transfer functions Wave propagation

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Novel ecosystems in ecological restoration and rehabilitation:Innovative planning or lowering the bar?

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Ecological processes 2014年第1期3卷 186-189页

作者： Michael p perring patrick Audet david Lamb Ecosystem Restoration and Intervention Ecology Research Group School of Plant BiologyThe University of Western Australia35 Stirling HighwayPerth(Crawley)WA 6009Australia Northern Forestry Centre Canadian Forestry ServiceNatural Resources Canada5320-122nd StreetEdmontonABT6H 3S5Canada Centre for Mined Land Rehabilitation Sustainable Minerals InstituteThe University of QueenslandSir James Foots BuildingBrisbane(St Lucia)QLD 4072Australia

Stemming from a special symposium at the 2012 inaugural meeting of the Society for Ecological Restoration Australasia in perth,Western Australia,this special issue editorial addresses novel ecosystems in ecological restoration and the inherent challenges of maintaining the highest standards of environmental stewardship and biological conservation in the face of increasing urbanization,agricultural expansion,and *** others,we(the Guest Editors)view novel ecosystems as offering opportunities for conservation and restoration in the coming years and a pragmatic recognition that it may not always be possible,or desirable,to overcome adverse consequences of environmental degradation to reinstate historical *** mindful of hubris and taking into account difficulties with identification,novel ecosystems may be viewed as a temporary or interim stage on the way towards the evolution of other future ecosystems able to supply a variety of ecosystem services,while attempting to maintain and enhance biodiversity,function and ***,a concise summary of contributions to the special issue and their significance to the field of restoration ecology is provided noting that authors were tasked to answer whether novel ecosystems are innovative planning or lowering the bar in ecological *** themes shared by the manuscripts are elucidated leading to guiding principles and,more importantly,an assessment of how and why restoration priorities are changing in the 21^(st)century.

关键词： ecosystems restoration consequences

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