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Accurate determination of DNA yield from individual mosquitoes for population genomic applications

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Insect Science 2009年第4期16卷 361-363页

作者： Craig S. Wilding D. Weetman K. steen M.J. Donnelly Vector Group Liverpool School of Tropical Medicine Pembroke Place Liverpool L3 5QA UK

Accurate estimates of DNA quantity are likely to become increasingly important for successful genomic screening of insect populations via recently developed, highly multiplexed genotyping assays and high-throughput sequencing methods. Here we show that genomic DNA extractions from single Anopheles gambiae Giles using a standard commercial kit-based methodology yield extracts with concentrations below the linear range of spectrophotometric absorbance at 260 nm. Concentrations determined by spectropho- tometry were not reproducible, and are therefore neither accurate nor reliable. However, DNA quantification using a fluorescent nucleic acid stain （PicoGreen） gave highly reproducible concentration estimates, and indicated that, on average, single mosquitoes yielded approximately 300 ng of DNA. Such a total yield is currently insufficient for many highthroughput genome screening applications, necessitating whole genome amplification of all or most individuals in a population prior to genotyping.

关键词： Anopheles gambiae DNA quantification mosquito picogreen spectrophotometry

Calibration of a Confidence Interval for a Classification Accuracy

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Open Journal of Forestry 2021年第1期11卷 14-36页

作者： steen Magnussen Natural Resources Canada Canadian Forest Service Victoria British Columbia Canada

Coverage of nominal 95% confidence intervals of a proportion estimated from a sample obtained under a complex survey design, or a proportion estimated from a ratio of two random variables, can depart significantly from its target. Effective calibration methods exist for intervals for a proportion derived from a single binary study variable, but not for estimates of thematic classification accuracy. To promote a calibration of confidence intervals within the context of land-cover mapping, this study first illustrates a common problem of under and over-coverage with standard confidence intervals, and then proposes a simple and fast calibration that more often than not will improve coverage. The demonstration is with simulated sampling from a classified map with four classes, and a reference class known for every unit in a population of 160,000 units arranged in a square array. The simulations include four common probability sampling designs for accuracy assessment, and three sample sizes. Statistically significant over- and under-coverage was present in estimates of user’s (UA) and producer’s accuracy (PA) as well as in estimates of class area proportion. A calibration with Bayes intervals for UA and PA was most efficient with smaller sample sizes and two cluster sampling designs.

关键词： Overall Accuracy Producer’s Accuracy User’s Accuracy Area Proportions Semi-Systematic Sampling Post-Stratification Stratified Random Sampling One-Stage Cluster Sampling Two-Stage Cluster Sampling

Comparison of estimators of variance for forest inventories with systematic sampling-results from artificial populations

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Forest Ecosystems 2020年第2期7卷 215-233页

作者： steen Magnussen Ronald EMcRoberts Johannes Breidenbach Thomas Nord-Larsen Göran Ståhl Lutz Fehrmann Sebastian Schnell 506 West Burnside Road VictoriaBC V8Z 1M5Canada Raspberry Ridge Analytics 15111 Elmcrest Avenue NorthHugoMN 55038USA Norwegian Institute of Bioeconomy Research Høgskolevegen 81431ÅsNorway Department of Geosciences and Natural Resource Management University of CopenhagenRolighedsvej 23DK-1958 Frederiksberg CDenmark Department of Forest Resource Management Swedish University of Agricultural SciencesUmeåSweden Forest Inventory and Remote Sensing Faculty of Forest SciencesUniversity of GöttingenBüsgenweg 5D37077GöttingenGermany Alfred-Möller-Straße 1 Haus 41-4216225 EberswaldeGermany.

Background:Large area forest inventories often use regular grids(with a single random start)of sample locations to ensure a uniform sampling intensity across the space of the surveyed populations.A design-unbiased estimator of variance does not exist for this ***,a quasi-default estimator applicable to simple random sampling(SRS)is used,even if it carries with it the likely risk of overestimating the variance by a practically important *** better exploit the precision of systematic sampling we assess the performance of five estimators of variance,including the quasi *** this study,simulated systematic sampling was applied to artificial populations with contrasting covariance structures and with or without linear *** compared the results obtained with the SRS,Matern’s,successive difference replication,Ripley’s,and D’Orazio’s variance ***:The variances obtained with the four alternatives to the SRS estimator of variance were strongly correlated,and in all study settings consistently closer to the target design variance than the estimator for *** latter always produced the greatest *** populations with a near zero spatial autocorrelation,all estimators,performed equally,and delivered estimates close to the actual design ***:Without a linear trend,the SDR and DOR estimators were best with variance estimates more narrowly distributed around the benchmark;yet in terms of the least average absolute deviation,Matern’s estimator held a narrow *** a strong or moderate linear trend,Matern’s estimator is *** large populations,and a low sampling intensity,the performance of the investigated estimators becomes more similar.

关键词： Spatial autocorrelation Linear trend Model based Design biased Matern variance Successive difference replication variance Geary contiguity coefficient Random site effects

Hypoxia in the pulmonary vein increases pulmonary vascular resistance independently of oxygen in the pulmonary artery

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Animal Models and Experimental Medicine 2024年第2期7卷 156-165页

作者： Sigridur Olga Magnusdottir Carsten Simonsen Dan Stieper Karbing Bodil steen Rasmussen Benedict Kjaergaard Biomedical Research Laboratory Aalborg University HospitalAalborgDenmark Department of Clinical Medicine Aalborg UniversityAalborgDenmark Department of Cardiothoracic Surgery Aalborg University HospitalAalborgDenmark Department of Health Science and Technology Aalborg UniversityAalborgDenmark Department of Anesthesia and Intensive Care Aalborg University HospitalAalborgDenmark

Introduction:Hypoxic pulmonary vasoconstriction(HPV)can be a challenging clinical *** is not fully elucidated where in the circulation the regulation of resistance takes *** is often referred to as if it is in the arteries,but we hypothesized that it is in the venous side of the pulmonary ***:In an open thorax model,pigs were treated with a veno-venous extra corporeal membrane oxygenator to either oxygenate or deoxygenate blood passing through the pulmonary *** the same time the lungs were ventilated with extreme variations of inspired air from 5%to 100%oxygen,making it possible to make combinations of high and low oxygen content through the pulmonary circulation.A flow probe was inserted around the main pulmonary artery and catheters in the pulmonary artery and in the left atrium were used for pressure monitoring and blood *** different combinations of oxygenation,pulmonary vascular resistance(PVR)was ***:With unchanged level of oxygen in the pulmonary artery and reduced inspired oxygen fraction lowering oxygen tension from 29 to 6.7 kPa in the pulmonary vein,PVR was *** more extreme hypoxia PVR suddenly *** with low oxygenation in the pulmonary artery did not systematic influence PVR if there was enough oxygen in the inspired air and in the pulmonary ***:The impact of hypoxia occurs from the alveolar level and forward with the blood *** experiments indicated that the regulation of PVR is mediated from the venous side.

关键词： animal models cardiopulmonary support Hypoxic pulmonary vasoconstriction pulmonary circulation

Midwives’views and experiences of providing healthy eating advice to pregnant women:a qualitative content analysis of semi-structured interviews

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Frontiers of Nursing 2020年第4期7卷 345-358页

作者： Shwikar Mahmoud Etman Othman Julie-Anne Fleet Mary steen Rasika Jayasekara Obstetrics and Gynaecology Nursing Department Faculty of NursingSouth Valley University EgyptQena 83523Egypt UniSA Clinical&Health Sciences University of South AustraliaAdelaideSouth Australia 5001Australia

Objective:To explore midwives’views on how they provide healthy eating education to pregnant women after attending a healthy eating education workshop/***:A qualitative descriptive approach was ***-structured interviews were conducted to explore the views and experiences of midwives on providing healthy eating education for pregnant women.A purposive sample of six midwives was interviewed face-to-face,and one was conducted by telephone *** were analyzed through qualitative conventional content ***:Midwives described their views and experiences of factors that impacted their role in providing healthy eating *** identified three categories:perceived role of midwi ves,health literacy,and model of ***:Knowledge and confidence of midwives improved after attending the workshop/webinar on healthy eating *** suggested that midwives perceived their role as important in providing nutrition ***,time and resources were highlighted as challenges when providing healthy eating education for pregnant *** availability of health literacy and model of care were significant factors in enabling midwives to adequately provide this *** acknowledged a need for further education in areas of vegan diet,cultural food preferences for ethnic minority groups,and regular updates on national healthy eating guidelines.

关键词： midwives healthy eating guidelines nutrition policy qualitative content analysis education maternity health services

Mass Spectrometry-based Quantitative Proteomic Profiling of Human Pancreatic and Hepatic Stellate Cell Lines

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Genomics, Proteomics & Bioinformatics 2013年第2期11卷 105-113页

作者： Joao A.Paulo Vivek Kadiyala Peter A.Banks Darwin L.Conwell Hanno steen Department of Pathology Boston Children's Hospital Proteomics Center at Boston Children's Hospital Center for Pancreatic Disease Division of GastroenterologyHepatology and EndoscopyBrigham and Women's Hospital and Department of MedicineHarvard Medical School

The functions of the liver and the pancreas differ; however, chronic inflammation in both organs is associated with fibrosis. Evidence suggests that fibrosis in both organs is partially regu- lated by organ-specific stellate cells. We explore the proteome of human hepatic stellate cells （hHSC） and human pancreatic stellate cells （hPaSC） using mass spectrometry （MS）-based quanti- tative proteomics to investigate pathophysiologic mechanisms. Proteins were isolated from whole cell lysates of immortalized hHSC and hPaSC. These proteins were tryptically digested, labeled with tandem mass tags （TMT）, fractionated by OFFGEL, and subjected to MS. Proteins significantly different in abundance （P 〈 0.05） were classified via gene ontology （GO） analysis. We identified 1223 proteins and among them, 1222 proteins were quantifiable. Statistical analysis determined that 177 proteins were of higher abundance in hHSC, while 157 were of higher abundance in hPaSC. GO classification revealed that proteins of relatively higher abundance in hHSC were associated with protein production, while those of relatively higher abundance in hPaSC were involved in cell structure. Future studies using the methodologies established herein, but with further upstream fractionation and/or use of enhanced MS instrumentation will allow greater proteome coverage, achieving a comprehensive proteomic analysis of hHSC and hPaSC.

关键词： Fibrosis Proteomics Pancreas Tandem mass tag

Improving precision of field inventory estimation of aboveground biomass through an alternative view on plot biomass

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Forest Ecosystems 2020年第4期7卷 760-769页

作者： Christoph Kleinn steen Magnussen Nils Nölke Paul Magdon Juan GabrielÁlvarez-González Lutz Fehrmann César Pérez-Cruzado Forest Inventory and Remote Sensing Georg-August-Universität Göttingen37077 GöttingenGermany. Canadian Forest Service Natural Resources CanadaVictoriaBC V8Z 1M5Canada. Department of Agroforestry Engineering University of Santiago de CompostelaE-27002 LugoSpain

We contrast a new continuous approach(CA)for estimating plot-level above-ground biomass(AGB)in forest inventories with the current approach of estimating AGB exclusively from the tree-level AGB predicted for each tree in a plot,henceforth called DA(discrete approach).With the CA,the AGB in a forest is modelled as a continuous surface and the AGB estimate for a fixed-area plot is computed as the integral of the AGB surface taken over the plot *** with the CA,the portion of the biomass of in-plot trees that extends across the plot perimeter is ignored while the biomass from trees outside of the plot reaching inside the plot is *** use a sampling simulation with data from a fully mapped two hectare area to illustrate that important differences in plot-level AGB estimates can *** CA-based estimates of mean AGB should be less variable than those derived from the *** realized,this difference translates to a higher precision from field sampling,or a lower required sample *** our case study with a target precision of 5%(*** standard error of the estimated mean AGB),the CA required a 27.1%lower sample size for small plots of 100 m2 and a 10.4%lower sample size for larger plots of 1700 *** examined sampling induced errors only and did not yet consider model *** discuss practical issues in implementing the CA in field inventories and the potential in applications that model biomass with remote sensing *** CA is a variation on a plot design for above-ground forest biomass;as such it can be applied in combination with any forest inventory sampling design.

关键词： Branch biomass Foliage biomass Stem biomass Biomass surface plots Sampling surfaces Standard error of estimation

Focus characteristics of long distance flying optics

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Science China Mathematics 2000年第9期43卷 980-987页

作者：程兆谷蒋金波李现勤许国良夏金安 W.M.steen G.Dearden Shanghai Institute of Optics and Fine Mechanics Chinese Academy of Sciences Shanghai 201800 China Department of Mechanical Engineering University of Liverpool Liverpool L69.3BX UK

The ABCD law for the complex parameter q of the TEM00 Gaussian beam is generally not valid for high-order modes. It can be used for the high-order modes or their superposition when the spot size w in the virtual part of the parameter q is substituted by the Rayleigh range ZR of a certain resonator. The focus characteristics of long distance flying optics are studied in this paper theoretically and experimentally for the TEMmn Gaussian beams between the two types of resonators without and with distortion. It is very important for the applications of the flying optical processing, the laser space craft and the spatial filter in the large laser project.

关键词： flying optics Rayleigh range ABCD law focus characteristics

Periprocedural complications and one-year outcomes after catheter ablation for treatment of atrial fibrillation in elderly patients:a nationwide Danish cohort study

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Journal of Geriatric Cardiology 2021年第11期18卷 897-907页

作者： Jesper Nielsen Kristian Hay Kragholm Sofie Brix Christensen Arne Johannessen Christian Torp-Pedersen steen Buus Kristiansen Peter Karl Jacobsen Peter steen Hansen Mogens Stig Djurhus Christoffer Polcwiartek Peter Søgaard Anna Margrethe Thøgersen Uffe Jakob Ortved Gang Ole Dan Jørgensen Filip Lyng Lindgren Sam Riahi Department of Cardiology Aalborg University HospitalDenmark Department of Cardiology Gentofte HospitalCopenhagen University HospitalDenmark Department of Clinical Research and Cardiology Nordsjaellands HospitalHillerødDenmark Department of Cardiology Skejby University HospitalDenmark Department of Cardiology RigshospitaletCopenhagen University HospitalDenmark Mølholm Clinic VejleDenmark Department of Cardiology Odense University hospitalDenmark Department of Cardiology Roskilde University HospitalDenmark Department of Thoracic Surgery Odense University HospitalDenmark AF-Study group Aalborg University Hospital Denmark Clinical Institute Aalborg UniversityDenmark

OBJECTIVES To investigate complications within 30-days following first-time ablation for atrial fibrillation(AF),including a composite of cardiac tamponade,hematoma requiring intervention,stroke or death,in patients≥75 years of age,compared to pa-tients aged 65−74 *** addition,one-year all-cause mortality and AF relapse were ***&RESULTS All patients receiving their first catheter ablation for AF between 2012 and 2016 were identified us-ing Danish nationwide *** aged 65−74 years served as the reference group for patients≥75 *** of AF within one year was defined as cardioversion following a three-month blanking period,re-ablation or confirmed relapse within *** composite complication outcome did not differ between the two age groups,with 39/1554(2.8%)in patients 65−74 years of age,versus 5/199(2.5%)in older patients(adjusted HR=0.94),95%CI:0.37−2.39,P=0.896).Patients≥75 years or older had no increased hazard of death within 30 days after the procedure,with an incidence of 3/1554(0.2%)in younger pa-tients and 2/199(1.0%)in patients≥75 years of age(adjusted HR=4.71,95%CI:0.78−28.40,P=0.091).There was no difference in relapse of AF after one year between age groups(≥75 years adjusted HR=1.00,95%CI:0.78-1.26,P=0.969).CONCLUSION In patients≥75 years of age selected for catheter ablation for AF,the incidence of periprocedural complica-tions,as well as one-year freedom from AF showed no statistical difference,when compared to patients 65−74 years of age.

关键词： patients fibrillation atrial