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Novel strategy for disease risk prediction incorporating predicted gene expression and DNA methylation data:a multi-phased study of prostate cancer

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Cancer Communications 2021年第12期41卷 1387-1397页

作者： Chong Wu Jingjing Zhu Austin King Xiaoran Tong Qing Lu Jong Y.Park Liang Wang Guimin Gao Hong-Wen Deng Yaohua Yang karen e.knudsen Timothy R.Rebbeck Jirong Long Wei Zheng Wei Pan David V.Conti Christopher A Haiman Lang Wu Department of Statistics Florida State UniversityTallahasseeFL 32304USA Cancer epidemiology Division Population Sciences in the Pacific ProgramUniversity of Hawaii Cancer CenterUniversity of Hawaii at ManoaHonoluluHI 96813USA Department of epidemiology and Biostatistics Michigan State UniversityEast LansingMI 48824USA Department of Biostatistics University of FloridaGainesvilleFL 32603USA Department of Cancer epidemiology H.Lee Moffitt Cancer Center and Research InstituteTampaFL 33612USA Department of Tumor Biology H.Lee Moffitt Cancer Center and Research InstituteTampaFL 33612USA Department of Public Health Sciences University of ChicagoChicagoIL 60637USA Center of Bioinformatics and Genomics Department of Global Biostatistics and Data ScienceTulane UniversityNew OrleansLA 70112USA Division of epidemiology Department of MedicineVanderbilt Epidemiology CenterVanderbilt-Ingram Cancer CenterVanderbilt University Medical CenterNashvilleTN 37203USA Department of Cancer Biology Sidney Kimmel Cancer CenterThomas Jefferson UniversityPhiladelphiaPA 19107USA Department of Medical Oncology Dana-Farber Cancer InstituteBostonMA 02215USA Department of epidemiology Harvard TH Chan School of Public HealthBostonMA 02115USA Division of Biostatistics University of MinnesotaMinneapolisMN 55455USA Department of Preventive Medicine Keck School of MedicineUniversity of Southern California/Norris Comprehensive Cancer CenterLos AngelesCA 90033USA

Background:DNA methylation and gene expression are known to play important roles in the etiology of human diseases such as prostate cancer(PCa).However,it has not yet been possible to incorporate information of DNA methylation and gene expression into polygenic risk scores(PRSs).Here,we aimed to develop and validate an improved PRS for PCa risk by incorporating genetically predicted gene expression and DNA methylation,and other genomic information using an integrative ***:Using data from the PRACTICAL consortium,we derived multiple sets of genetic scores,including those based on available single-nucleotide polymorphisms through widely used methods of pruning and thresholding,LDpred,LDpred-funt,AnnoPred,and eBPRS,as well as PRS constructed using the genetically predicted gene expression and DNA methylation through a revised pruning and thresholding *** the tuning step,using the UK Biobank data(1458 prevalent cases and 1467 controls),we selected PRSs with the best *** an independent set of data from the UK Biobank,we developed an integrative PRS combining information from individual ***,in the testing step,we tested the performance of the integrative PRS in another independent set of UK Biobank data of incident cases and ***:Our constructed PRS had improved performance(C statistics:76.1%)over PRSs constructed by individual benchmark methods(from 69.6%to 74.7%).Furthermore,our new PRS had much higher risk assessment power than family *** overall net reclassification improvement was 69.0%by adding PRS to the baseline model compared with 12.5%by adding family ***:We developed and validated a new PRS which may improve the utility in predicting the risk of developing *** innovative method can also be applied to other human diseases to improve risk prediction across multiple outcomes.

关键词： risk prediction polygenic risk scores predicted gene expression predicted DNA methylation integrative models prostate cancer

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Prospective cohort study on facial profile changes in infants with Robin sequence and healthy controls

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World Journal of Pediatrics 2024年第6期20卷 581-589页

作者： Cornelia Wiechers Julian Sowula karen Kreutzer Christoph e.Schwarz Christina Weismann Michael Krimmel Christian F.Poets Bernd Koos Department of Neonatology Tuebingen University HospitalCalwerstrasse 772076 TuebingenGermany Center for Cleft Lip Palate and Craniofacial MalformationsTuebingen University HospitalTuebingenGermany Department of Orthodontics Tuebingen University HospitalTuebingenGermany Department of Oral and Maxillofacial Surgery Tuebingen University HospitalTuebingenGermany

Background Various conservative and surgical approaches exist to treat Robin sequence(RS),but their effects on facial profile and mandibular catch-up growth are unclear.A functional treatment concept,used in our centre for 25 years,includes an individualized palatal plate with a velo-pharyngeal extension and intensive feeding *** We performed a prospective study to objectively describe facial profiles in infants with RS treated with the above *** with isolated RS were admitted to our tertiary perinatal and national referral centre for craniofacial malformations between May 2018 and Nov *** with RS received 3D-photographs during clinically indicated *** controls were recruited from Dec 2018 to Sep 2019 and received 3D-photographs every 3 *** digitally measured jaw index(JI),defined as alveolar overjet(O)x maxillary arch(U)/mandibular arch(L),and the soft tissue reference points A’-point,Nasion’,B’-point angle(ANB’),describing the relative position of maxilla to mandible,were *** mixed models were used to examine time trajectories in JI and ANB’.Results A total of 2073D images,obtained in 19 infants with RS and 32 controls,were *** and ANB’decreased over time in both groups[for JI−0.18(95%CI−0.25 to−0.10);for ANB’:−0.40°per month[(95%CI−0.48 to−0.32)]]but remained lower in controls[for JI−2.5(95%CI−3.2 to−1.8);for ANB’-1.7°(95%CI−2.4 to−1.0)].Also,the ANB’model showed a significant effect of the interaction term diagnosis x *** Based on longitudinal 3D images,we describe changes in objective parameters of facial profile in infants with and without RS during the first year of *** findings indicate catch-up growth in infants treated for RS.

关键词： Infant Mandibular catch-up growth Pre-epiglottic Baton Plate Robin sequence Three-dimensional photography

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A new method for precise optical measurements of the sub-micron height of levitation of droplet clusters

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Particuology 2024年第4期87卷 173-178页

作者： Alexander A.Fedorets eduard e.Kolmakov Leonid A.Dombrovsky University of Tyumen 6 Volodarskogo StTyumen625003Russia engineering Faculty Ariel UniversityP0.B.3407000ArielIsrael Joint Institute for High Temperatures 17A Krasnokazarmennaya StMoscow111116Russia

Droplet clusters levitating over the locally heated water surface are considered a very promising phe-nomenon of microfluidics for the potential use of the droplets as unique microreactors for microbio-logical experiments.A new optical method is suggested for precise measurements of the sub-micron levitation height of single *** method is based on the analysis of variable colors of the inter-ference halo around the *** the first time,it is possible to measure the extremely low downward velocity of droplets,which grow due to steam *** velocity was found to be 5-8 nm/*** height of the levitation of various droplets just before their coalescence with a layer of water was also *** measurements might be used for the verification of sophisticated models for the droplet levitation to be developed for a very thin layer of humid air under the droplet when the.knudsen effect should be taken into account.

关键词： Precise measurements Interferometric method Droplet cluster Levitation height

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Summer sea-surface temperatures and climate events on the North Icelandic shelf through the last 3000 years

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Chinese Science Bulletin 2007年第6期52卷 789-796页

作者： JIANG Hui ReN Jian karen Luise.knudsen Jon eIRiKSSON RAN LiHua Key Laboratory of Geographic Information Science East China Normal University Shanghai 200062 China Department of earth Sciences University of Aarhus DK-8000 Arhus C Denmark earth Science Institute University of Iceland Askja IS-101 Reykjavfk Iceland

Diatom data from core MD992271 on the North Icelandic shelf record a cooling trend through the last 3000 years. This is indicated by a general decrease in warm water species and an increase in cold water taxa. The relative abundance of these two diatom groups changed periodically, suggesting that the climate also fluctuated within this time period. The results of diatom-based transfer function calculation show that the summer sea-surface temperatures (SSTs) before 1400 cal. a BP were generally higher than the mean value for the last 3000 years and the summer SSTs fluctuated around the mean between 1400 and 700 cal. a BP, and dropped to the values below the mean after 700 cal. a BP. Four cooling events were distinguished, centered at around 2600, 1900, 1300 and 600 cal. a BP respectively. The results are not only consistent with the data from neighbouring cores HM107-03 and MD992275, but also comparable with those from the GISP2 ice core and from other marine sediment records in the North Atlantic. This suggests that changes in the summer SSTs reflect regional climate variations in the North Atlantic. On the North Icelandic shelf, the summer SST variation is a result of changes in the in-teraction between the cold and the warm currents in the area.

关键词：夏季海面温度气候事件冰岛北部大陆架晚全新世

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Biogenic silica concentration as a marine primary productivity proxy in the Holsteinsborg Dyb, West Greenland, during the last millennium

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Acta Oceanologica Sinica 2020年第9期39卷 78-85页

作者： Longbin Sha Dongling Li Yanguang Liu Bin Wu Yanni Wu karen Luise.knudsen Zhongqiao Li Hao Xu Department of Geography and Spatial Information Techniques Ningbo UniversityNingbo 315211China Laboratory for Marine Geology Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266237China State Key Laboratory of estuarine and Coastal Research East China Normal UniversityShanghai 200062China Key Laboratory of Marine Sedimentology and environmental Geology First Institute of OceanographyMinistry of Natural ResourcesQingdao 266061China Key Laboratory of Marine ecosystem and Biogeochemistry Second Institute of OceanographyMinistry of Natural ResourcesHangzhou 310012China Centre for Past Climate Studies and Arctic Research Centre Department of GeoscienceAarhus UniversityAarhus C DK-8000Denmark

We analyzed the biogenic silica(BSi)content and produced a diatom-based summer sea-surface temperature(SST)reconstruction for sediment core GC4 from the Holsteinsborg Dyb,West *** aim was to reconstruct marine productivity and climatic fluctuations during the last *** BSi content and diatom abundance suggest relatively high marine productively during the interval of AD 1000–1400,corresponding in time to the Medieval Warm Period(MWP).The summer SST reconstruction indicates relatively warm conditions during AD 900–1100,followed by cooling after AD *** extended cooling period during AD 1400–1900 is characterized by prolonged low in reconstructed SST and high sea-ice *** BSi values fluctuated during this period,suggesting varying marine productivity during the Little Ice Age(LIA).There is no significant correlation between the BSi content and SST during the last millennium,suggesting that the summer SST has little influence on marine productively in the Holsteinsborg Dyb.A good correspondence between the BSi content and the element Ti counts in core GC4 suggests that silicate-rich meltwater from the Greenland ice sheet was likely responsible for changes in marine productively in the Holsteinsborg Dyb.

关键词： biogenic silica marine productivity sea-surface temperature sea-ice concentration

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Confirmation of a Sub-Saturn-size Transiting exoplanet Orbiting a G Dwarf:TOI-1194 b and a Very Low Mass Companion Star: TOI-1251 B from TeSS

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Research in Astronomy and Astrophysics 2024年第3期24卷 129-143页

作者： Jia-Qi Wang Xiao-Jun Jiang Jie Zheng Hanna Kellermann Arno Riffeser Liang Wang karen A.Collins Allyson Bieryla Lars A.Buchhave Steve B.Howell elise Furlan eric Girardin Joao Gregorio eric Jensen Felipe Murgas Mesut Yilmaz Sam Quinn Xing Gao Ruo-Yu Zhou Frank Grupp Hui-Juan Wang CAS Key Laboratory of Optical Astronomy National Astronomical ObservatoriesChinese Academy Of SciencesBeijing 10010China University of Chinese Academy of Sciences Beijing 100049China University Observatory Munich Scheinertrsse 1.D-81679 MunichGemany Max Planck Institute for extraterrestrial Physics Giessenbachstr.1D-85748 GarchingGermany National Astronomical Observatories/Nanjing Institute of Astronomical Optics&Technology Chinese Academy of SciencesNanjing210042China CAS Key Laboratory of Astronomical Optics&Technology Nanjing Institute of Astronomical Optics&TechnologyNanjing 210042China Center for Astrophysics Harvard&Smithsonian60 Garden Street.CambridgeMA 02138USA National Space Institute Technical University of DenmarkElektrovejDK-2800 KgsLyngbyDenmark NASA Ames Research Center Moffett FieldCA 94035USA NASA exoplanet Science Institute Caltech/IPACMail Code 100-221200 E.California Blvd.PasadenaCA91125USA Grand Pra Observatory Switzerland Department of Physics Washington UniversitySt.LouisMO 63130.USA Department of Physics and Astronomy Swarthmore CollegeSwarthmorePA 19081USA Instituto de Astrofísica de Canarias(IAC) E-38205 La Laguna.TenerifeSpain Departamento de Astrofísica Universidad de La LagunaSpain Dept.of Astronomy and Space Sciences Ankara UniversityTandogan 06100AnkaraTurkey Xinjiang Astronomical Observatory Chinese Academy of SciencesUrumqi 830011China Urumqi No.1 Senior High School Urumqi 830002China Lijiang Gemini Observatory Lijiang 674199China

We report the confirmation of a sub-Saturn-size exoplanet,TOI-1194 b,with a mass of about 0.456+0.055-0.051M_(J),and a very low mass companion star with a mass of about 96.5±1.5 MJ,TOI-1251 *** candidates provided by the Transiting exoplanet Survey Satellite(TeSS)are suitable for further follow-up observations by ground-based telescopes with small and medium *** analysis is performed based on data from several telescopes worldwide,including telescopes in the Sino-German multiband photometric campaign,which aimed at confirming TeSS Objects of Interest(TOIs)using ground-based small-aperture and medium-aperture telescopes,especially for long-period ***-1194 b is confirmed based on the consistent periodic transit depths from the multiband photometric *** measure an orbital period of 2.310644±0.000001 days,the radius is 0.767+0.045-0.041RJ and the amplitude of the RV curve is 69.4_(-7.3)^(+7.9)m s^(-1).TOI-1251 B is confirmed based on the multiband photometric and high-resolution spectroscopic data,whose orbital period is 5.963054+0.000002-0.000001days,radius is 0.947+0.035-0.033 R_(J) and amplitude of the RV curve is 9849_(-40)^(+42)ms^(-1).

关键词： planets and satellites fundamental parameters-planets and satellites gaseous planets-stars fundamental parameters-stars low-mass-methods data analysis-techniques photometric-techniques spectroscopic

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Outcomes and management of viral hepatitis and human immunodeficiency virus co-infection in liver transplantation

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World Journal of Gastroenterology 2014年第2期20卷 414-424页

作者： Stephen e Congly karen e Doucette Carla S Coffin Liver Unit Division of Gastroenterology and HepatologyUniversity of CalgaryCalgaryAB T2N 4Z6Canada Division of Infectious Diseases University of AlbertaEdmontonAB T6G 2R3Canada

Liver transplantation for human immunodeficiency virus(HIV)positive patients with viral hepatitis co-infection is increasingly offered in many North American and european liver transplant *** studies have demonstrated acceptable post-transplant outcomes and no increased risk of HIV complications in patients coinfected with hepatitis B virus(HBV).However,liver transplantation in HIV positive patients with hepatitis C virus(HCV)has poorer outcomes overall,requiring careful selection of *** review aims to summarize the published literature on outcomes after transplant in HIV patients with HBV or HCV related end-stage liver disease and recommendations for *** particular the pre-transplant factors impacting outcomes in HCV/HIV co-infected candidates and importance of multidisciplinary management will be discussed.

关键词： Hepatitis B virus Human immunodeficiency virus co-infection Hepatitis C virus Co-infection Liver transplantation

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Prediction of protein and amino acid composition and digestibility in individual feedstuffs and mixed diets for pigs using near-infrared spectroscopy

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Animal Nutrition 2021年第4期7卷 1242-1252页

作者： Samantha J.Noel Henry J.Høgh Jørgensen Knud e.Bach knudsen Department of Animal Science AU FoulumAarhus UniversityDK 8830TjeleDenmark

Knowledge of the amounts and digestibility of amino acids in pig feedstuffs is essential for calculating the appropriate inclusion level in a complete *** chemical analysis and in vivo digestibility trials are time-consuming and costly and cannot be used for routine ***-infrared spectroscopy(NIRS)offers a rapid,cost effective and environmentally friendly method for evaluating *** models were developed using NIRS to predict the content of crude protein and 18 amino acids from a wide range of feedstuffs used in pig production(n=607).The samples ranged from single feed ingredients(containing amino acids from 0.3 to 129.8 g/kg of dry matter)to feed mixtures(containing amino acids from 1.2 to 53.2 g/kg of dry matter).The predictive ability of the calibrations was tested with an independent dataset(n=150)and with ***,we compare these calibrations with calibrations developed on more narrowly defined groups of samples and with predictions from regression analysis of crude *** models were able to predict the concentrations of crude protein and 18 amino acids with good levels of precision and high coefficients of determination for calibration(RSQ^(CAL))from 0.91 to 0.99 and validation(RSQ^(VAL))from 0.87 to *** models were able to predict all amino acids except tryptophan and valine with greater accuracy than those from protein *** also developed calibration models to predict the apparent ileal and total tract digestibility of protein and amino *** the exception of tryptophan,RSQ values(>0.7)and standard error of cross validation(SeCV)values(ere obtained for the digestibility of most of the amino *** conclusion,NIRS can be used to predict crude protein and amino acid concentrations from a wide range of single ingredients and feed mixtures used for pig diets without separate models for each *** digestibility of protein and amino acids can be predicted with an

关键词： Near-infrared spectroscopy Amino acids Protein Apparent ileal digestibility Total tract digestibility Swine

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Planning for Community Relocations Due to Climate Change in Fiji

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International Journal of Disaster Risk Science 2015年第3期6卷 315-319页

作者： karen e.Mc Namara Helene Jacot Des Combes School of Geography Planning and Environmental ManagementThe University of Queensland Pacific Centre for environment and Sustainable Development University of the South Pacific

As a consequence of the impacts of climate change, some households and entire communities across the Pacific are making the complex and challenging decision to leave their homelands and relocate to new environments that can sustain their livelihoods. This short article charts how the residents of Vunidogoloa village in Fiji relocated in early 2014 to reduce their vulnerability to encroaching sea level and inundation events that regularly devastated the community. As a consequence of the Vunidogoloa relocation, this article also explores how the Fiji Government is planning for similar resettlement transitions, including vulnerability and adaptation assessments to develop a list of potential community relocations and the development of national relocation guidelines. This study draws from key informant interviews(n = 8) with government officials, as well as representatives from intergovernmental and local nongovernmental organizations,who are involved in the relocation issue. Given the speed at which these national, top-down initiatives are being forged and especially in light of the absence of any mention of relocation in Fiji’s 2012 climate change policy, careful and inclusive engagement across all scales and stakeholders,including communities 'earmarked' for relocation, is paramount.

关键词： Climate change Community relocation Fiji Risk planning Sea level rise

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Identification of a novel population of human cord blood cells with hema-topoietic and chondrocytic potential

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Cell Research 2004年第4期14卷 268-282页

作者： karen e JAY,Anne ROULeAU,T Michael UNDeRHILL,Mickie BHATIA Stem Cell Biology and Regenerative Medicine The John P. Robarts Research Institute 100 Perth Drive London Ontario N6A 5K8 Canada Department of Microbiology and Immunology The University of Western Ontario London Ontario Canada Stem Cell Biology and Regenerative Medicine The John P. Robarts Research Institute 100 Perth Drive London Ontario N6A 5K8 Canada Department of Physiology The University of Western Ontario London Ontario Canada Stem Cell Biology and Regenerative Medicine The John P. Robarts Research Institute 100 Perth Drive London Ontario N6A 5K8 Canada Department of Microbiology and Immunology The University of Western Ontario London Ontario Canada. Department of Physiology The University of Western Ontario London Ontario Canada

With the exception of mature erythrocytes, cells within the human hematopoietic system are characterized by the cell surface expression of the pan-leukocyte receptor CD45. Here, we identify a novel subset among mononuclear cord blood cells depleted of lineage commitment markers (Lin) that are devoid of CD45 expression. Surprisingly, functional examination of Lin"CD45" cells also lacking cell surface CD34 revealed they were capable of multipotential hematopoietic progenitor capacity. Co-culture with mouse embryonic limb bud cells demonstrated that Lin-CD45-CD34- cells were capable of contributing to cartilage nodules and differentiating into human chondrocytes. BMP-4, a mesodermal factor known to promote chondrogenesis, significantly augmented Lin-CD45-CD34- differentiation into chondrocytes. Moreover, unlike CD34+ human hematopoietic stem cells, Lin-CD45-CD34- cells were unable to proliferate or survive in liquid cultures, whereas single Lin-CD45-CD34- cells were able to chimerize the inner cell mass (IC

关键词： hematopoietic chondrocyte CD45 embryonic.

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