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FunHoP:Enhanced Visualization and Analysis of Functionally Homologous Proteins in Complex Metabolic Networks

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Genomics, Proteomics & Bioinformatics 2021年第5期19卷 848-859页

作者： kjersti Rise May-Britt Tessem Finn Drablos Morten B.Rye Department of Clinical and Molecular Medicine NTNU-Norwegian University of Science and TechnologyTrondheim NO-7491Norway Department of Circulation and Medical Imaging NTNU-Norwegian University of Science and TechnologyTrondheim NO-7491Norway Clinic of surgery St.Olavs HospitalTrondheim University HospitalTrondheim NO-7491Norway

Cytoscape is often used for visualization and analysis of metabolic *** example,based on KEGG data,a reader for KEGG Markup Language(KGML)is used to load files into ***,although multiple genes can be responsible for the same reaction,the KGMLreader KEGGscape only presents the first listed gene in a network node for a given *** can lead to incorrect interpretations of the *** new method,FunHoP,shows all possible genes in each node,making the pathways more *** collapses all genes in a node into one measurement using read counts from *** that activity for an enzymatic reaction mainly depends upon the gene with the highest number of reads,and weighting the reads on gene length and ratio,a new expression value is calculated for the node as a *** expression at node level is then applied to the *** prostate cancer as model,we integrate RNA-seq data from two patient cohorts with metabolism data from *** we show that FunHoP gives more consistent pathways that are easier to interpret *** and documentation for running FunHoP can be found at https://***/kjerstirise/FunHoP.

关键词： Homologous proteins Metabolic network Pathway visualization and analysis RNA-seq KEGG Cytoscape

Target-Oriented Inversion of Time-Lapse seismic Waveform Data

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Communications in Computational Physics 2020年第6期28卷 249-275页

作者： Xingguo Huang Morten Jakobsen kjersti solberg Eikrem Geir Nævdal Department of Earth science University of BergenP.O.Box 78035020 BergenNorway NORCE Norwegian Research Centre Postboks 225838 BergenNorway

Full waveform inversion of time-lapse seismic data can be used as a means of estimating the reservoir changes due to the *** the repeated computa-tions for the monitor surveys lead to a large computational cost,time-lapse full wave-form inversion is still considered to be a challenging *** address this problem,we present an efficient target-oriented inversion scheme for time-lapse seismic data using an integral equation formulation with Gaussian beam based Green’s function *** proposed time-lapse approach allows one to perform a local inversion within a small region of interest(e.g.a reservoir under production)for the monitor *** have verified that the T-matrix approach is indeed naturally target-oriented,which was mentioned by Jakobsen and Ursin[24]and allows one to reduce the compu-tational cost of time-lapse inversion by focusing the inversion on the target-area *** method is based on a new version of the distorted Born iterative T-matrix inverse scattering *** Gaussian beam and T-matrix are used in this approach to perform the wavefield computation for the time-lapse inversion in the baseline model from the survey surface to the target *** have provided target-oriented inversion results of the synthetic time-lapse waveform data,which shows that the proposed scheme reduces the computational cost significantly.

关键词： Waveform inversion time-lapse seismic seismic inverse scattering target-oriented inversion Gaussian beam based Green’s function

Antenatal corticosteroids in COVID-19 perspective

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World Journal of Experimental Medicine 2021年第4期11卷 37-43页

作者： Alex C Vidaeff kjersti M Aagaard Michael A Belfort Department of Obstetrics and Gynecology Division of Maternal Fetal MedicineTexas Children’s HospitalBaylor College MedicineHoustonTX 77030United States

The aim of this manuscript is to discuss the practice of antenatal corticosteroids administration for fetal maturation in severe acute respiratory syndrome coronavirus 2 positive pregnant *** high-quality evidence supports the use of dexamethasone in the treatment of hospitalized patients with coronavirus disease 2019(COVID-19).Randomized disease outcome data have identified an association between disease stage and treatment *** contrast to patients with more severe forms who benefit from dexamethasone,patients with mild disease do not appear to improve and may even be harmed by this ***,indiscriminate usage of fluorinated corticosteroids for fetal maturation,regardless of disease trajectory,is *** care needs to be adjusted during the COVID-19 pandemic with careful attention paid to candidate selection and risk stratification.

关键词： Antenatal corticosteroids COVID-19 Dexamethasone Pregnancy sARsCoV-2 Preterm delivery

Experiences of staying Healthy in Relationally Demanding Jobs: An Interpretative Phenomenological study of Work-Engaged Nurses in the Hospital

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Open Journal of Nursing 2015年第5期5卷 437-450页

作者： Asgerdur Bjarnadottir kjersti Vik Faculty of Health and social Work S&oslashr-Tr&oslashndelag University College Trondheim Norge

Background: Based on the experience of hospital nurses, the aim of this study is to explore the phenomenon of how work-engaged nurses stay healthy in relationally demanding jobs involving very sick and/or dying patients. Method: In-depth interviews were conducted with ten work-engaged nurses employed at the main hospital in one region in Norway. The interviews were interpreted using the Interpretative Phenomenological Analysis method (IPA). Results: The results indicate the importance of using the personal resources: authenticity and a sense of humour for staying healthy. The nurses’ authenticity, in the sense of having a strong sense of ownership towards their personal life experiences, and a sense of having a meaningful life in line with their own values and interests, was an important element when they considered their own health to be good in spite of repetitive strain injuries and perceived stress. These personal resources seem to be positively related to their well-being and work engagement, which serves as an argument for including them among other personal resources, often conceptualized in terms of Psychological Capital (PsyCap). The results also showed that the nurses worked actively and intentionally with conditions that could contribute to safeguarding their own health. Conclusion: The results indicated the importance of stimulating the nurses’ area of knowledge about caring for themselves in order to enable them to maintain good physical and mental health. A focus on self-care should be part of the agenda as early as during nursing education.

关键词： Health Personal Resources Work Engagement Relationally Demanding Jobs Nurses Interpretative Phenomenological Analysis

Major-effect candidate genes identified in cultivated strawberry(Fragaria×ananassa Duch.)for ellagic acid deoxyhexoside and pelargonidin-3-O-malonylglucoside biosynthesis,key polyphenolic compounds

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Horticulture Research 2020年第1期7卷 1109-1125页

作者： Jahn Davik kjersti Aaby Matteo Buti Muath Alsheikh NadaŠurbanovski stefan Martens Dag Røen Daniel James sargent Division of Biotechnology and Plant Health Norwegian Institute of Bioeconomy ResearchÅs N-1433Norway NOFIMA As Norwegian Institute of Food Fisheries and Aquaculture ResearchÅs N-1433Norway Department of Agriculture FoodEnvironment and ForestryUniversity of FlorenceFlorenceItaly Graminor Breeding Ltd. N-2322 RidabuNorway Department of Plant sciences Norwegian University of Life SciencesRidabu N-1432ÅsNorway NIAB-EMR East MallingME196BJ KentUK Department of Food Quality and Nutrition Fondazione Edmund MachCentro Ricerca e InnovazioneVia E.Mach 138010 San Michele all’AdigeTNItaly Department of Genetics Genomics and BreedingNIAB-EMREast MallingME196BJ KentUK

strawberries are rich in polyphenols which impart health benefits when metabolized by the gut microbiome,including anti-inflammatory,neuroprotective,and antiproliferative *** addition,polyphenolic anthocyanins contribute to the attractive color of strawberry ***,the genetic basis of polyphenol biosynthesis has not been extensively studied in *** this investigation,ripe fruits from three cultivated strawberry populations were characterized for polyphenol content using HPLC-DAD-Msn and genotyped using the istraw35k *** and QTL analyses identified genetic loci controlling polyphenol *** were identified on four chromosomes for pelargonidin-3-O-malonylglucoside,pelargonidin-3-O-acetylglucoside,cinnamoyl glucose,and ellagic acid deoxyhexoside ***/absence of ellagic acid deoxyhexoside and pelargonidin-3-O-malonylglucoside was found to be under the control of major gene loci on LG1X2 and LG6b,respectively,on the F.×ananassa linkage *** of gene predictions in the *** reference genome sequence identified a single candidate gene for ellagic acid deoxyhexoside biosynthesis,while seven malonyltransferase genes were identified as candidates for pelargonidin-3-O-malonylglucoside *** malonyltransferase genes were identified in the F.×ananassa‘Camarosa’genome sequence but the candidate for ellagic acid deoxyhexoside biosynthesis was absent from the‘Camarosa’*** study demonstrated that polyphenol biosynthesis in strawberry is,in some cases,under simple genetic control,supporting previous observations of the presence or absence of these compounds in strawberry *** has also shed light on the mechanisms controlling polyphenol biosynthesis and enhanced the knowledge of these biosynthesis pathways in *** above findings will facilitate breeding for strawberries enriched in compounds with beneficial health effects.

关键词： straw polyphenol breeding

Testing Reliability and Validity of the Oulu Patient Classification Instrument—The First step in Evaluating the RAFAELA system in Norway

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Open Journal of Nursing 2014年第4期4卷 303-311页

作者： Marit Helen Andersen kjersti Lonning Lisbeth Fagerstrom Division of Cancer Medicine Surgery and TransplantationOslo University HospitalOsloNorway Department of Health sciences Buskerud and Vestfold University CollegeBuskerudNorway

Objective: To study reliability and validity of the Finnish Oulu Patient Classification instrument in Norway. Background: The Finnish patient classification system RAFAELA consists of three parts: 1) daily patient classification of nursing intensity using the Oulu Patient Classification instrument, 2) calculation of nursing resources providing bed side care per 24 hours, and 3) Professional Assessment of Optimal Nursing Care Intensity Level. The RAFAELA system has not been tested outside of Finland. Methods: A prospective, descriptive study was performed at 5 clinical units at Oslo University Hospital during 2011-2012. The interrater reliability of the Oulu Patient Classification instrument was tested by parallel classification including 100-167 patient classifications pr. unit, and analyzed by consensus in % and using Cohen’s Kappa. Convergent validity was tested by using the average Oulu Patient Classification instrument value to predict the average Professional Assessment of Optimal Nursing Care Intensity Level for the same calendar day by linear regression analysis. Results: The Oulu Patient Classification instrument consensus of parallel classifications varied between 70.1%-89%. Cohen’s Kappa within patient classes varied between 0.57 and 0.81, representing substantial interrater reliability. The Oulu Patient Classification instrument was valid as the instrument in average explained about 38% of the variation of the Professional Assessment of Optimal Nursing Care Intensity Level. Conclusions: Patient classification systems tested for psychometric properties are needed and this study provides evidence of satisfactory reliability and validity of the Oulu Patient Classification instrument as tested outside Finland, demonstrating that this instrument has international relevance within nursing.

关键词： Nursing Intensity staffing RAFAELA system Oulu Patient Classification Instrument Reliability Validity