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MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis

Molecular Plant 2019年第6期12卷 879-892页

作者： Rainer Schwacke Gabriel Y.Ponce-Soto Kirsten Krause Anthony M.bolger Borjana Arsova Asis Hallab Kristina Gruden Mark Stitt marie e.bolger Bjorn Usadel Institute for Bio- and Geosciences (IBG-2: Plant Sciences) Forschungszentrum Julich Wilhelm Johnen StraBe Jiilich Germany Department of Arctic and Marine Biology The Arctic University of Norway Biology Building 9037 Tromso Norway Institute for Botany and Molecular Genetics BioEconomy Science Center Worringer Weg RWTH Aachen University 52074 Aachen Germany National Institute of Biology Department of Biotechnology and Systems Biology Vedna Pot 111 1000 Ljubljana Slovenia Max Planck Institute for Molecular Plant Physiology Department of Systems Regulation 14476 Potsdam-Golm Germany

Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.

关键词： Plant genomes Functional annotation MapMan Mercator Transcriptomes

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Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity

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Molecular Plant 2022年第3期15卷 520-536页

作者： Genevieve Hoopes Xiaoxi Meng John P.Hamilton Sai Reddy Achakkagari Fernanda de Alves Freitas Guesdes marie e.bolger Joseph J.Coombs Danny esselink Natalie R.Kaiser Linda Kodde Maria Kyriakidou Brian Lavrijssen Natascha van Lieshout Rachel Shereda Heather K.Tuttle Brieanne Vaillancourt Joshua C.Wood Jan Mde Boer Nolan Bornowski Peter Bourke David Douches Herman Jvan eck Dave ellis Max J.Feldman Kyle M.Gardner Johannes C.P.Hopman Jiming Jiang Walter S.De Jong Joseph C.Kuhl Richard G.Novy Stan Oome Vidyasagar Sathuvalli ek Han Tan Remco A.Ursum M.Isabel Vales Kelly Vining Richard G.F.Visser Jack Vossen G.Craig Yencho Noelle L.Anglin Christian W.B.Bachem Jeffrey B.endelman Laura M.Shannon Martina V.Stromvik Helen H.Tai Bjorn Usadel C.Robin Buell Richard Finkers Department of Plant Biology Michigan State UniversityEast LansingMI 48824USA Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Department of Plant Science McGill UniversitySainte-Anne-de-BellevueQC H9X 3V9Canada Plant Breeding Wageningen University&ResearchPlant Breeding6708 PB Wageningenthe Netherlands IBG-4 Bioinformatics Forschungszentrum JülichWilhelm Johnen Str52428 JülichGermany Department of Plant Soiland Microbial SciencesMichigan State UniversityEast LansingMI 48824USA Bayer Crop Science WoodlandCA 95695USA Averis Seeds B.V. 9640 AA Veendamthe Netherlands International Potato Center 1895 Avenida La MolinaLimaPeru USDA-ARS ProsserWA 99350USA Agriculture and Agri-Food Canada Fredericton Research and Development Centre FrederictonNB E3B 4Z7Canada School of Integrative Plant Science Cornell UniversityIthacaNY 14853-1901USA Department of Plant Sciences University of IdahoMoscowID 83844USA USDA-ARS Small Grains and Potato Germplasm ResearchAberdeenID 83210USA HZPC Research B.V. Edisonweg 58501 XG Jourethe Netherlands Department of Crop and Soil Science Oregon State UniversityHermistonOR 97838USA School of Biology and ecology University of Maine5735 Hitchner Hall OronoME 04469USA Department of Horticultural Sciences Texas A&M UniversityCollege StationTX 77843-2133USA Department of Horticulture Oregon State UniversityCorvallisOR 97331USA Department of Horticultural Science North Carolina State UniversityRaleighNC 27695-7609USA Department of Horticulture University of Wisconsin-MadisonMadisonWI 53706USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Institute for Biological Data Science Heinrich Heine UniversityDusseldorf40225 DusseldorfGermany Plant Resilience Institute Michigan State UniversityEast LansingMI 48824USA Present address:GenNovation B.V. Wageningenthe Netherlands

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous *** assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity,including altered coding and transcript sequences,preferential allele expression,and structural variation that collectively result in a highly complex transcriptome and predicted proteome,which are distributed across the homologous *** species contribute to the extensive allelic diversity in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding *** a clonally propagated autotetraploid that undergoes limited meiosis,dysfunctional and deleterious alleles are not purged in tetraploid *** a quarter of the loci bore mutations are predicted to have a high negative impact on protein function,complicating breeder’s efforts to reduce genetic *** StCDF1 locus controls maturity,and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent *** of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous,diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

关键词： potato allele diversity phased assembly polyploid pan-genome wild introgressions

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Impacts of climate change on the ecotoxicology of chemical contaminants in estuarine organisms

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Current Zoology 2015年第4期61卷 641-652页

作者： marie e. DeLOReNZO NOAA National Ocean Service National Centers for Coastal Ocean Science Center for Coastal Environmental Health andBiomolecular Research 219 Fort Johnson Rd. Charleston SC 29412 USA

Global climate change effects will vary geographically, and effects on estuaries should be independently considered. This review of the impacts of climate change on the ecotoxicology of chemical contaminants aims to summarize responses that are specific to estuafine species. estuarine organisms are uniquely adapted to large fluctuations in temperature, salinity, oxygen, and pH, and yet future changes in climate may make them more susceptible to chemical contaminants. Recent research has hig- hlighted the interactive effects of chemical and nonchemical stressors on chemical uptake, metabolism, and organism survival. Assessments have revealed that the nature of the interaction between climate variables and chemical pollution will depend on es- tuarine species and life stage, duration and timing of exposure, prior stressor exposure, and contaminant class. A need for further research to elucidate mechanisms of toxicity under different abiotic conditions and to incorporate climate change factors into toxicity testing was identified. These efforts will improve environmental risk assessment of chemical contaminants and manage- ment capabilities under changing climate conditions [Current Zoology 61 （4）： 641-652, 2015].

关键词： Climate Toxicity Metals Pesticides Oil esmarine

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Deteriorated function of cutaneous microcirculation in chronic congestive heart failure

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Journal of Geriatric Cardiology 2011年第2期8卷 82-87页

作者： marie-Louise edvinsson erik Uddman Sven e Andersson Department of emergency Medicine Lund University Hospital SE- 221 85 LUND Sweden

Background Chronic congestive heart failure is a complex condition that leads to dysfunction in the peripheral microcirculation. We have previously shown that vascular reactivity is reduced with increasing age. In this study, we examined a group of very old patients with severe chronic heart failure to test the hypothesis that vascular function is further compromised by a combination of heart failure and aging. Methods Cutaneous forearm blood flow was measured by laser Doppler flowmetry and compared among three groups： Group 1 （n = 20, mean ±Se： 85.5 ±4 years）, heart failure patients with New York Heart Association class Ⅳ （NYHA Ⅳ） and with a NT-proBNP level ≥5000 ng/L; Group 2 （n = 15, mean ±Se： 76.5 ±2 years）, heart failure patients with NYHA II and NT-proBNP ≤2000 ng/L, and Group 3 （n = 10, mean ±Se： 67.6 ±3.0 years）, healthy controls with no clinical signs of heart failure. The vasodilator response to the iontophoretic administration of acetylcholine （ACh）, acting via an endothelial mechanism, and sodium nitroprusside （SNP）, acting via a smooth muscle cell mechanism, were studied. Results All patients with heart failure had significantly reduced vascular reactivity independent of the mode of stimulation （ACh, SNP or heat） when compared to healthy controls. However, the responses did not differ between the two groups of heart failure patients. Conclusions Cutaneous vascular reactivity is reduced in heart failure patients and does not correlate with the severity of the condition or age of patients.

关键词： heart failure cutaneous microcirculation endothelial responses acetylcholine smooth muscle responses

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Brain natriuretic peptide is a potent vasodilator in aged human microcircula- tion and shows a blunted response in heart failure patients

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Journal of Geriatric Cardiology 2014年第1期11卷 50-56页

作者： marie-Louise edvinsson erik Uddman Lars edvinsson Sven e. Andersson Department of emergency and Internal Medicine Institute of Clinical Sciences Lund University Lund University Hospital SE- 221 85 Lund Sweden

Background Brain natriuretic peptide （BNP） is normally present in low levels in the circulation, but it is elevated in parallel with the degree of congestion in heart failure subjects （CHF）. BNP has natriuretic effects and is a potent vasodilator. It is suggested that BNP could be a therapeutic alternative in CHF. However, we postulated that the high levels of circulating BNP in CHF may downregulate the response of microvascular natriuretic receptors. This was tested by comparing 15 CHF patients （BNP 〉 3000 ng/L） with 10 matched, healthy controls. Methods Cutaneous microvascular blood flow in the forearm was measured by laser Doppler Flowmetry. Local heating （＋44°C, 10 min） was used to evoke a maximum local dilator response. Results Non-invasive iontophoretic administration of either BNP or acetylcholine （ACh）, a known endothelium-dependent dilator, elicited an increase in local flow. The nitric oxide synthase inhibitor, l-N-Arginine- methyl-ester （L-NAMe）, blocked the BNP response （in controls）. Interestingly, responses to BNP in CHF patients were reduced to about one third of those seen in healthy controls （increase in flow： 251% in CHF vs. 908% in controls; P 〈 0.001）. In contrast, the vasodilator responses to ACh and to local heating were only somewhat attenuated in CHF patients. Thus, dilator capacity and nitric oxide signalling were not af- fected to the same extent as BNP-mediated dilation, indicating a specific downregulation of the latter response. Conclusions The findings show for the first time that microvascular responses to BNP are markedly reduced in CHF patients. This is consistent with the hypothesis of BNP receptor function is downregulated in CHF.

关键词： Heart failure Cutaneous microcirculation endothelial responses Acetylcholine, Brain natriuretic peptide Nitric oxide

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Nitric oxide activation of a potassium channel (BK_(Ca)) in feline lower esophageal sphincter

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World Journal of Gastroenterology 2010年第46期16卷 5852-5860页

作者： marie-Claude L'Heureux Ahmad Muinuddin Herbert Y Gaisano Nicholas e Diamant Department of Physiology University of Toronto Ahmad Muinuddin Nicholas E DiamantToronto Western Research InstituteUniversity Health Network Department of Medicine University of Toronto

AIM:To assess the effect of nitric oxide (NO) on the large conductance potassium channel (BKCa) in isolated circular (CM) and sling (SM) muscle cells and muscle strips from the cat lower esophageal sphincter (LeS) to determine its regulation of resting tone and ***:Freshly enzymatically-digested and isolated circular smooth muscle cells were prepared from each LeS *** study outward K + currents,the perforated patch clamp technique was *** assess LeS resting tone and relaxation,muscle strips were mounted in perfused organ ***:(1) electrophysiological recordings from isolated cells:(a) CM was more depolarized than SM (-39.7 ± 0.8mV vs-48.1 ± 1.6 mV,P ent was similar (27.1 ± 1.5 pA/pF vs 25.7 ± 2.0 pA/pF,P > 0.05);(b) The NO donor sodium nitroprusside (SNP) increased outward currents only in CM (25.9 ± 1.9 to 46.7 ± 4.2 pA/pF,P 0.05);(c) SNP added in the presence of the BK Ca antagonist iberiotoxin (IbTX) produced no increase in the outward current in CM (17.0 ± 2.8 vs 13.7 ± 2.2,P > 0.05);and (d) L-NNA caused a small insignificant inhibition of outward K + currents in both muscles;and (2) Muscle strip studies:(a) Blockade of the nerves with tetrodotoxin (TTX),or BK Ca with IbTX had no significant effect on resting tone of either muscle;and (b) SNP reduced tone in both muscles,and was unaffected by the presence of TTX or ***:exogenous NO activates BK Ca only in CM of the ***,as opposed to other species,exogenous NO-induced relaxation is predominantly by a non-BK Ca mechanism,and endogenous NO has minimal effect on resting tone.

关键词： Circular smooth muscle Feline K+ channel Lower esophageal sphincter Nitric oxide Sling Tone

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exploratory Study of Intolerance of Uncertainty and Its Cognitive Processes by the Stroop Task among Parents of a Childhood Cancer Survivor

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Psycho-Oncologie 2023年第4期17卷 257-266页

作者： marie Vander Haegen Anne-marie Service de Psychologie de la santé/Unitéde Research Unit for a Life-Course Perspective on Health and education-(RUCHe ULiège)University of LiègeLiège4000Belgium

*** study has examined the relationship between the factor of intolerance of uncertainty and its effects on the cognitive processes among parents of a childhood cancer *** of uncertainty is a central factor in generalized anxiety disorder;an anxiety disorder in which impaired processing of cognitive information in the form of cognitive biases is also *** aim of the study was to measure,via a classical Stroop test and an emotional Stroop test,the orientation of selective attention in relation to the uncertainty intolerance ***.61 parents of a childhood cancer survivor(aged 4 to 6 years)were recruited from hospitals in the Province of Liege(Belgium).Parents completed questionnaires on intolerance of uncertainty and its associated factors(i.e.,usefulness of worry,cognitive avoidance,problem-solving attitude,and ruminations)and performed a Stroop test and an emotional Stroop *** correlations and multiple linear regressions were *** results indicated positive and significant correlations between the emotional Stroop(negative interference index)and intolerance to uncertainty but also with repetitive thoughts(ruminations)and *** regressions showed that depressive symptoms seem to contribute to explaining longer latencies for the interference condition(color word written in another color).*** have been published to improve the management of parents of a childhood cancer survivor,but parent-centered neuropsychological studies are still needed and should be developed to improve prevention and detection initiatives for these families.

关键词： Parents childhood cancer survivor Stroop intolerance of uncertainty

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Bone tissue engineering via growth factor delivery:from scaffolds to complex matrices

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Regenerative Biomaterials 2018年第4期5卷 197-211页

作者： Tinke-marie De Witte Lidy e.Fratila-Apachitei Amir A.Zadpoor Nicholas A.Peppas Department of Biomedical engineering The University of Texas at AustinAustinTX 78712USA Additive Manufacturing Laboratory Department of Biomechanical EngineeringDelft University of Technology(TU Delft)2628 CD DelftThe Netherlands McKetta Department of Chemical engineering The University of Texas at AustinAustinTX 78712USA Institute for Biomaterials Drug Delivery and Regenerative MedicineThe University of Texas at AustinAustinTX 78712USA Department of Pediatrics and Department of Surgery and Perioperative CareDell Medical SchoolThe University of Texas at AustinAustinTX 78712USA Division of Molecular Pharmaceutics and Drug Delivery College of PharmacyThe University of Texas at AustinAustinTX 78712USA

In recent years,bone tissue engineering has emerged as a promising solution to the limitations of current gold standard treatment options for bone related-disorders such as bone *** tissue engineering provides a scaffold design that mimics the extracellular matrix,providing an architecture that guides the natural bone regeneration *** this period,a new generation of bone tissue engineering scaffolds has been designed and characterized that explores the incorporation of signaling molecules in order to enhance cell recruitment and ingress into the scaffold,as well as osteogenic differentiation and angiogenesis,each of which is crucial to successful bone ***,we outline and critically analyze key characteristics of successful bone tissue engineering *** also explore candidate materials used to fabricate these *** growth factors involved in the highly coordinated process of bone repair are discussed,and the key requirements of a growth factor delivery system are ***,we concentrate on an analysis of scaffold-based growth factor delivery strategies found in the recent *** particular,the incorporation of two-phase systems consisting of growth factor-loaded nanoparticles embedded into scaffolds shows great promise,both by providing sustained release over a therapeutically relevant timeframe and the potential to sequentially deliver multiple growth factors.

关键词： scaffolds bone growth tissue engineering growth factor delivery

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Comparison between visual clinical examination and the replica method for assessments of sealant retention over a 2-year period

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International Journal of Oral Science 2014年第2期6卷 111-115页

作者： Xuan Hu Xi Chen Lu Ye Ming-Wen Fan marie-Charlotte Huysmans Jo e Frencken State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of education School and Hospital of Stomatology Wuhan University Department of Preventive Dentistry School and Hospital of Stomatology Wuhan University Private Practitioner Department of Preventive and Restorative Dentistry College of Dental Sciences Radboud University Nijmegen Medical Centre Nijmegen The Netherlands Department of Global Oral Health College of Dental Sciences Radboud University Nijmegen Medical Centre Nijmegen The Netherlands

To compare the levels of agreement and the survival rates of sealant retention for different sealing materials over a 2-year period assessed using the visual clinical examination and replica methods, sealant retention data were obtained by visual clinical examination and from replicas of the same sealed tooth at baseline and at 0.5-, 1- and 2-year evaluation points in 407 children and were compared for agreement using kappa coefficients. Survival curves of retained sealants on occlusal surfaces were created using modified categorisation （fully retained sealants and those having all pits and fissures partly covered with the sealant material versus completely lost sealants that included pit and fissure systems that had /〉 1 pit re-exposed） according to the Kaplan-Meier method. The kappa coefficient for the agreement between both assessment methods over the three evaluation time points combined was 0.38 （95% confidence interval （CI）： 0.35-0.41）. More sealant retention was observed from replicas than through visual clinical examination. Cumulative survival curves at the three evaluation times were not statistically significantly higher when assessed from replicas （P=0.47）. Using the replica method, more retained sealant material was observed than through visual clinical examination during the 2-year period. This finding did not result in a difference in the survival rates of sealants assessed by the two assessment methods. When replicas cast in die stone are used for assessing sealant retention, the level of reliability of the data is higher than that of data obtained through the commonly used visual clinical examination, particularly if such assessments are conducted over time.

关键词： clinical examination replica method sealant retention sealant

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Impurity profiling and in-process testing of drugs for injection by fast liquid chromatography

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Journal of Pharmaceutical Analysis 2012年第5期2卷 372-377页

作者： marie-Josée Rocheleau elaine Larouche Cristina Salamu Mihaela Curca Omega Laboratories Ltd. 11177 HamonMontréalQC H3M 3E4Canada

Liquid chromatography （LC） is considered by many as a mature technique. Nonetheless, LC technology continues to evolve driven by the need for high-throughput and high-resolution analyses. Over the past several years, small particle size packing materials have been introduced by several column manufacturers to enable fast and efficient LC separations. Several examples of pharmaceutical analyses, including impurity profiling of taxanes and atracurium besylate, in-process testing of peptides in injectable dosage form, using sub-2 um column technology are presented in this paper, demonstrating some of the capabilities and limitations of the technology.

关键词： Liquid chromatography UPLC Pharmaceutical Taxane Atracurium besylate Peptides

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