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1.
  • Arndt, D. S., et al. (författare)
  • STATE OF THE CLIMATE IN 2017
  • 2018
  • Ingår i: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 99:8, s. S1-S310
  • Forskningsöversikt (refereegranskat)
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2.
  • Boccaletti, Anthony, et al. (författare)
  • Fast-moving features in the debris disk around AU Microscopii
  • 2015
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 526:7572, s. 230-
  • Tidskriftsartikel (refereegranskat)abstract
    • In the 1980s, excess infrared emission was discovered around main-sequence stars; subsequent direct-imaging observations revealed orbiting disks of cold dust to be the source(1). These 'debris disks' were thought to be by-products of planet formation because they often exhibited morphological and brightness asymmetries that may result from gravitational perturbation by planets. This was proved to be true for the beta Pictoris system, in which the known planet generates an observable warp in the disk(2-5). The nearby, young, unusually active late-type star AU Microscopii hosts a well-studied edge-on debris disk; earlier observations in the visible and near-infrared found asymmetric localized structures in the form of intensity variations along the midplane of the disk beyond a distance of 20 astronomical units(6-9). Here we report high-contrast imaging that reveals a series of five large-scale features in the southeast side of the disk, at projected separations of 10-60 astronomical units, persisting over intervals of 1-4 years. All these features appear to move away from the star at projected speeds of 4-10 kilometres per second, suggesting highly eccentric or unbound trajectories if they are associated with physical entities. The origin, localization, morphology and rapid evolution of these features are difficult to reconcile with current theories.
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3.
  • Muralidhara, Prathibha, et al. (författare)
  • Perturbations in plant energy homeostasis prime lateral root initiation via SnRK1-bZIP63-ARF19 signaling
  • 2021
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:37
  • Tidskriftsartikel (refereegranskat)abstract
    • Plants adjust their energy metabolism to continuous environmental fluctuations, resulting in a tremendous plasticity in their architecture. The regulatory circuits involved, however, remain largely unresolved. In Arabidopsis, moderate perturbations in photosynthetic activity, administered by short-term low light exposure or unexpected darkness, lead to increased lateral root (LR) initiation. Consistent with expression of low-energy markers, these treatments alter energy homeostasis and reduce sugar availability in roots. Here, we demonstrate that the LR response requires the metabolic stress sensor kinase Snf1-RELATED-KINASE1 (SnRK1), which phosphorylates the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) that directly binds and activates the promoter of AUXIN RESPONSE FACTOR19 (ARF19), a key regulator of LR initiation. Consistently, starvation-induced ARF19 transcription is impaired in bzip63 mutants. This study highlights a positive developmental function of SnRK1. During energy limitation, LRs are initiated and primed for outgrowth upon recovery. Hence, this study provides mechanistic insights into how energy shapes the agronomically important root system.
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4.
  • Ades, M., et al. (författare)
  • Global Climate : in State of the climate in 2019
  • 2020
  • Ingår i: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 101:8, s. S17-S127
  • Tidskriftsartikel (refereegranskat)
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5.
  • Ades, M., et al. (författare)
  • GLOBAL CLIMATE
  • 2020
  • Ingår i: BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY. - 0003-0007 .- 1520-0477. ; 101:8
  • Tidskriftsartikel (refereegranskat)
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6.
  • Arndt, D. S., et al. (författare)
  • State of the Climate in 2016
  • 2017
  • Ingår i: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 98:8, s. S1-S280
  • Tidskriftsartikel (refereegranskat)abstract
    • In 2016, the dominant greenhouse gases released into Earth's atmosphere-carbon dioxide, methane, and nitrous oxide-continued to increase and reach new record highs. The 3.5 +/- 0.1 ppm rise in global annual mean carbon dioxide from 2015 to 2016 was the largest annual increase observed in the 58-year measurement record. The annual global average carbon dioxide concentration at Earth's surface surpassed 400 ppm (402.9 +/- 0.1 ppm) for the first time in the modern atmospheric measurement record and in ice core records dating back as far as 800000 years. One of the strongest El Nino events since at least 1950 dissipated in spring, and a weak La Nina evolved later in the year. Owing at least in part to the combination of El Nino conditions early in the year and a long-term upward trend, Earth's surface observed record warmth for a third consecutive year, albeit by a much slimmer margin than by which that record was set in 2015. Above Earth's surface, the annual lower troposphere temperature was record high according to all datasets analyzed, while the lower stratospheric temperature was record low according to most of the in situ and satellite datasets. Several countries, including Mexico and India, reported record high annual temperatures while many others observed near-record highs. A week-long heat wave at the end of April over the northern and eastern Indian peninsula, with temperatures surpassing 44 degrees C, contributed to a water crisis for 330 million people and to 300 fatalities. In the Arctic the 2016 land surface temperature was 2.0 degrees C above the 1981-2010 average, breaking the previous record of 2007, 2011, and 2015 by 0.8 degrees C, representing a 3.5 degrees C increase since the record began in 1900. The increasing temperatures have led to decreasing Arctic sea ice extent and thickness. On 24 March, the sea ice extent at the end of the growth season saw its lowest maximum in the 37-year satellite record, tying with 2015 at 7.2% below the 1981-2010 average. The September 2016 Arctic sea ice minimum extent tied with 2007 for the second lowest value on record, 33% lower than the 1981-2010 average. Arctic sea ice cover remains relatively young and thin, making it vulnerable to continued extensive melt. The mass of the Greenland Ice Sheet, which has the capacity to contribute similar to 7 m to sea level rise, reached a record low value. The onset of its surface melt was the second earliest, after 2012, in the 37-year satellite record. Sea surface temperature was record high at the global scale, surpassing the previous record of 2015 by about 0.01 degrees C. The global sea surface temperature trend for the 21st century-to-date of +0.162 degrees C decade(-1) is much higher than the longer term 1950-2016 trend of +0.100 degrees C decade(-1). Global annual mean sea level also reached a new record high, marking the sixth consecutive year of increase. Global annual ocean heat content saw a slight drop compared to the record high in 2015. Alpine glacier retreat continued around the globe, and preliminary data indicate that 2016 is the 37th consecutive year of negative annual mass balance. Across the Northern Hemisphere, snow cover for each month from February to June was among its four least extensive in the 47-year satellite record. Continuing a pattern below the surface, record high temperatures at 20-m depth were measured at all permafrost observatories on the North Slope of Alaska and at the Canadian observatory on northernmost Ellesmere Island. In the Antarctic, record low monthly surface pressures were broken at many stations, with the southern annular mode setting record high index values in March and June. Monthly high surface pressure records for August and November were set at several stations. During this period, record low daily and monthly sea ice extents were observed, with the November mean sea ice extent more than 5 standard deviations below the 1981-2010 average. These record low sea ice values contrast sharply with the record high values observed during 2012-14. Over the region, springtime Antarctic stratospheric ozone depletion was less severe relative to the 1991-2006 average, but ozone levels were still low compared to pre-1990 levels. Closer to the equator, 93 named tropical storms were observed during 2016, above the 1981-2010 average of 82, but fewer than the 101 storms recorded in 2015. Three basins-the North Atlantic, and eastern and western North Pacific-experienced above-normal activity in 2016. The Australian basin recorded its least active season since the beginning of the satellite era in 1970. Overall, four tropical cyclones reached the Saffir-Simpson category 5 intensity level. The strong El Nino at the beginning of the year that transitioned to a weak La Nina contributed to enhanced precipitation variability around the world. Wet conditions were observed throughout the year across southern South America, causing repeated heavy flooding in Argentina, Paraguay, and Uruguay. Wetter-than-usual conditions were also observed for eastern Europe and central Asia, alleviating the drought conditions of 2014 and 2015 in southern Russia. In the United States, California had its first wetter-than-average year since 2012, after being plagued by drought for several years. Even so, the area covered by drought in 2016 at the global scale was among the largest in the post-1950 record. For each month, at least 12% of land surfaces experienced severe drought conditions or worse, the longest such stretch in the record. In northeastern Brazil, drought conditions were observed for the fifth consecutive year, making this the longest drought on record in the region. Dry conditions were also observed in western Bolivia and Peru; it was Bolivia's worst drought in the past 25 years. In May, with abnormally warm and dry conditions already prevailing over western Canada for about a year, the human-induced Fort McMurray wildfire burned nearly 590000 hectares and became the costliest disaster in Canadian history, with $3 billion (U.S. dollars) in insured losses.
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7.
  • Jansen, Iris E, et al. (författare)
  • Genome-wide meta-analysis for Alzheimer's disease cerebrospinal fluid biomarkers.
  • 2022
  • Ingår i: Acta neuropathologica. - : Springer Science and Business Media LLC. - 1432-0533 .- 0001-6322. ; 144:5, s. 821-842
  • Tidskriftsartikel (refereegranskat)abstract
    • Amyloid-beta 42 (Aβ42) and phosphorylated tau (pTau) levels in cerebrospinal fluid (CSF) reflect core features of the pathogenesis of Alzheimer's disease (AD) more directly than clinical diagnosis. Initiated by the European Alzheimer & Dementia Biobank (EADB), the largest collaborative effort on genetics underlying CSF biomarkers was established, including 31 cohorts with a total of 13,116 individuals (discovery n=8074; replication n=5042 individuals). Besides the APOE locus, novel associations with two other well-established AD risk loci were observed; CR1 was shown a locus for Aβ42 and BIN1 for pTau. GMNC and C16orf95 were further identified as loci for pTau, of which the latter is novel. Clustering methods exploring the influence of all known AD risk loci on the CSF protein levels, revealed 4 biological categories suggesting multiple Aβ42 and pTau related biological pathways involved in the etiology of AD. In functional follow-up analyses, GMNC and C16orf95 both associated with lateral ventricular volume, implying an overlap in genetic etiology for tau levels and brain ventricular volume.
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8.
  • Kattge, Jens, et al. (författare)
  • TRY plant trait database - enhanced coverage and open access
  • 2020
  • Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
  • Tidskriftsartikel (refereegranskat)abstract
    • Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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9.
  • Kurz, Alexander, et al. (författare)
  • RHAPSODY - Internet-based support for caregivers of people with young onset dementia : program design and methods of a pilot study
  • 2016
  • Ingår i: International psychogeriatrics. - 1041-6102 .- 1741-203X. ; 28:12, s. 2091-2099
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Young Onset Dementia (YOD), defined by first symptoms of cognitive or behavioral decline occurring before the age of 65 years, is relatively rare compared to dementia of later onset, but it is associated with diagnostic difficulty and heavy burden on affected individuals and their informal carers. Existing health and social care structures rarely meet the needs of YOD patients. Internet-based interventions are a novel format of delivering health-related education, counseling, and support to this vulnerable yet underserved group. Methods: The RHAPSODY (Research to Assess Policies and Strategies for Dementia in the Young) project is a European initiative to improve care for people with YOD by providing an internet-based information and skill-building program for family carers. The e-learning program focuses on managing problem behaviors, dealing with role change, obtaining support, and looking after oneself. It will be evaluated in a pilot study in three countries using a randomized unblinded design with a wait-list control group. Participants will be informal carers of people with dementia in Alzheimer's disease or behavioral-variant Frontotemporal degeneration with an onset before the age of 65 years. The primary outcome will be caregiving self-efficacy after 6 weeks of program use. As secondary outcomes, caregivers' stress and burden, carer health-related quality of life, caring-related knowledge, patient problem behaviors, and user satisfaction will be assessed. Program utilization will be monitored and a health-economic evaluation will also be performed. Conclusions: The RHAPSODY project will add to the evidence on the potential and limitations of a conveniently accessible, user-friendly, and comprehensive internet-based intervention as an alternative for traditional forms of counseling and support in healthcare, aiming to optimize care and support for people with YOD and their informal caregivers.
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10.
  • Pfeiffer, Anne, et al. (författare)
  • Integration of light and metabolic signals for stem cell activation at the shoot apical meristem
  • 2016
  • Ingår i: eLIFE. - : eLife Sciences. - 2050-084X. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • A major feature of embryogenesis is the specification of stem cell systems, but in contrast to the situation in most animals, plant stem cells remain quiescent until the postembryonic phase of development. Here, we dissect how light and metabolic signals are integrated to overcome stem cell dormancy at the shoot apical meristem. We show on the one hand that light is able to activate expression of the stem cell inducer WUSCHEL independently of photosynthesis and that this likely involves inter-regional cytokinin signaling. Metabolic signals, on the other hand, are transduced to the meristem through activation of the TARGET OF RAPAMYCIN (TOR) kinase. Surprisingly, TOR is also required for light signal dependent stem cell activation. Thus, the TOR kinase acts as a central integrator of light and metabolic signals and a key regulator of stem cell activation at the shoot apex.
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11.
  • Ademuyiwa, Adesoji O., et al. (författare)
  • Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
  • 2016
  • Ingår i: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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12.
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13.
  • André, Domenique, et al. (författare)
  • FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees
  • 2022
  • Ingår i: Current Biology. - : Cell Press. - 0960-9822 .- 1879-0445. ; 32:13, s. 2988-2996.e4
  • Tidskriftsartikel (refereegranskat)abstract
    • In temperate and boreal regions, perennials adapt their annual growth cycle to the change of seasons. These adaptations ensure survival in harsh environmental conditions, allowing growth at different latitudes and altitudes, and are therefore tightly regulated. Populus tree species cease growth and form terminal buds in autumn when photoperiod falls below a certain threshold.1 This is followed by establishment of dormancy and cold hardiness over the winter. At the center of the photoperiodic pathway in Populus is the gene FLOWERING LOCUS T2 (FT2), which is expressed during summer and harbors significant SNPs in its locus associated with timing of bud set.1–4 The paralogous gene FT1, on the other hand, is hyper-induced in chilling buds during winter.3,5 Even though its function is so far unknown, it has been suggested to be involved in the regulation of flowering and the release of winter dormancy.3,5 In this study, we employ CRISPR-Cas9-mediated gene editing to individually study the function of the FT-like genes in Populus trees. We show that while FT2 is required for vegetative growth during spring and summer and regulates the entry into dormancy, expression of FT1 is absolutely required for bud flush in spring. Gene expression profiling suggests that this function of FT1 is linked to the release of winter dormancy rather than to the regulation of bud flush per se. These data show how FT duplication and sub-functionalization have allowed Populus trees to regulate two completely different and major developmental control points during the yearly growth cycle.
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14.
  • Benstein, Ruben M., et al. (författare)
  • Isolation of nuclei tagged in specific cell types (INTACT) in Arabidopsis
  • 2023. - 2
  • Ingår i: Flower development. - New york : Humana Press. - 9781071632987 - 9781071632994 ; , s. 313-328
  • Bokkapitel (refereegranskat)abstract
    • Many functionally distinct plant tissues have relatively low numbers of cells that are embedded within complex tissues. For example, the shoot apical meristem (SAM) consists of a small population of pluripotent stem cells surrounded by developing leaves and/or flowers at the growing tip of the plant. It is technically challenging to collect enough high-quality SAM samples for molecular analyses. Isolation of Nuclei Tagged in specific Cell Types (INTACT) is an easily reproducible method that allows the enrichment of biotin-tagged cell-type-specific nuclei from the total nuclei pool using biotin-streptavidin affinity purification. Here, we provide a detailed INTACT protocol for isolating nuclei from the Arabidopsis SAM. One can also adapt this protocol to isolate nuclei from other tissues and cell types for investigating tissue/cell-type-specific transcriptome and epigenome and their changes during developmental programs at a high spatiotemporal resolution. Furthermore, due to its low cost and simple procedures, INTACT can be conducted in any standard molecular laboratory.
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15.
  • Bergin, Claudia, et al. (författare)
  • Acquisition of a Novel Sulfur-Oxidizing Symbiont in the Gutless Marine Worm Inanidrilus exumae
  • 2018
  • Ingår i: Applied and Environmental Microbiology. - : AMER SOC MICROBIOLOGY. - 0099-2240 .- 1098-5336. ; 84:7
  • Tidskriftsartikel (refereegranskat)abstract
    • Gutless marine oligochaetes (Annelida, Clitellata) lack a digestive and excretory system, and live in an obligate association with multiple bacterial endosymbionts that supply them with nutrition. In this study, we discovered an unusual symbiont community in the gutless oligochaete Inanidrilus exumae that differs markedly from the microbiome of all other 22 examined host species. Comparative 16S rRNA sequence analysis and fluorescence in situ hybridization revealed that I.exumae harboured co-occurring gamma-, alpha- and deltaproteobacterial symbionts, while all other host species harbour gamma- and either alpha- or deltaproteobacterial symbionts. Surprisingly, the primary chemoautotrophic, sulfur-oxidizer, Ca. Thiosymbion, which occurs in all other gutless oligochaetes, does not appear to be present in I.exumae. Instead, I. exumae harboured a bacterial endosymbiont that resembled Ca. Thiosymbion morphologically and metabolically, but originated from a novel lineage within the Gammaproteobacteria. This endosymbiont, named Gamma 4 symbiont here, had a 16S rRNA sequence that differed by at least 7% from those of other free-living and symbiotic bacteria and by 10% from Ca. Thiosymbion. Sulfur globules in the Gamma 4 symbiont cells, as well as the presence of genes characteristic for autotrophy (cbbL) and sulfur oxidation (aprA), suggest that this symbiont is a chemoautotrophic sulfur oxidizer. Our results indicate that a novel lineage of free-living bacteria was able to establish a stable and specific association with I. exumae, and displace the Ca. Thiosymbion symbionts originally associated with these hosts.
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16.
  • Bogdal, Christian, et al. (författare)
  • Emissions of Polychlorinated Biphenyls, Polychlorinated Dibenzo-p-dioxins, and Polychlorinated Dibenzofurans during 2010 and 2011 in Zurich, Switzerland
  • 2014
  • Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 48:1, s. 482-490
  • Tidskriftsartikel (refereegranskat)abstract
    • Persistent organic pollutants (POPs) are ubiquitous contaminants of environmental and human health relevance, but their emissions into the environment are still poorly known. In this study, concentrations of selected POPs were measured in ambient air in Zurich, Switzerland, and interpreted with a multimedia mass balance model. The aim of the combination of measurements and modeling was to back-calculate atmospheric emission rates of POPs. Measurements were performed in summer 2010 and winter 2011 and target analytes included polychlorinated biphenyls (PCBs) and polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs). Estimated emissions were higher in summer than in winter. Emission estimates for Zurich can be extrapolated to annual averages for Switzerland of 312 kg·a–1 (39 mg·capita–1·a–1), 53 kg·a–1 (7 mg·capita–1·a–1), and 3 kg·a–1 (0.4 mg·capita–1·a–1, 94 g WHO98-TEQ·a–1, 65 g I-TEQ·a–1) for the six indicator PCBs (iPCBs), the twelve coplanar dioxin-like PCBs (dlPCBs), and the 17 2,3,7,8-chlorosubstituted PCDD/Fs, respectively. The emission rates of iPCBs are in agreement with existing emission inventories, whereas for PCDD/Fs the emissions are five times higher than the estimates from the Swiss national emission inventory. Emissions of dlPCBs in Switzerland are presented here for the first time. Our study also provides the first seasonally resolved emission rates of POPs, which were determined with our combined measurement and modeling approach. These findings highlight the relevance of ongoing sources of POPs, even decades after regulations aiming to reduce or eliminate sources were established.
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17.
  • Bonnefoy, M., et al. (författare)
  • First light of the VLT planet finder SPHERE IV. Physical and chemical properties of the planets around HR8799
  • 2016
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 587
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. The system of four planets discovered around the intermediate-mass star HR8799 offers a unique opportunity to test planet formation theories at large orbital radii and to probe the physics and chemistry at play in the atmospheres of self-luminous young (similar to 30 Myr) planets. We recently obtained new photometry of the four planets and low-resolution (R similar to 30) spectra of HR8799 d and e with the SPHERE instrument (Paper III).Aims. In this paper (Paper IV), we aim to use these spectra and available photometry to determine how they compare to known objects, what the planet physical properties are, and how their atmospheres work.Methods. We compare the available spectra, photometry, and spectral energy distribution (SED) of the planets to field dwarfs and young companions. In addition, we use the extinction from corundum, silicate (enstatite and forsterite), or iron grains likely to form in the atmosphere of the planets to try to better understand empirically the peculiarity of their spectrophotometric properties. To conclude, we use three sets of atmospheric models (BT-SETTL14, Cloud-AE60, Exo-REM) to determine which ingredients are critically needed in the models to represent the SED of the objects, and to constrain their atmospheric parameters (T-eff, log g, M/H).Results. We find that HR8799d and e properties are well reproduced by those of L6-L8 dusty dwarfs discovered in the field, among which some are candidate members of young nearby associations. No known object reproduces well the properties of planets b and c. Nevertheless, we find that the spectra and WISE photometry of peculiar and/or young early-T dwarfs reddened by submicron grains made of corundum, iron, enstatite, or forsterite successfully reproduce the SED of these planets. Our analysis confirms that only the Exo-REM models with thick clouds fit (within 2 sigma) the whole set of spectrophotometric datapoints available for HR8799 d and e for T-eff = 1200 K, log g in the range 3.0-4.5, and M/H = +0.5. The models still fail to reproduce the SED of HR8799c and b. The determination of the metallicity, log g, and cloud thickness are degenerate.Conclusions. Our empirical analysis and atmospheric modelling show that an enhanced content in dust and decreased CIA of H-2 is certainly responsible for the deviation of the properties of the planet with respect to field dwarfs. The analysis suggests in addition that HR8799c and b have later spectral types than the two other planets, and therefore could both have lower masses.
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19.
  • Brunoni, Federica, et al. (författare)
  • A bacterial assay for rapid screening of IAA catabolic enzymes
  • 2019
  • Ingår i: Plant Methods. - : BioMed Central (BMC). - 1746-4811. ; 15:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of IAA homeostasis. Free IAA levels can be reduced by inactivation mechanisms, such as conjugation and degradation. IAA can be conjugated via ester linkage to glucose, or via amide linkage to amino acids, and degraded via oxidation. Members of the UDP glucosyl transferase (UGT) family catalyze the conversion of IAA to indole-3-acetyl-1-glucosyl ester (IAGlc); by contrast, IAA is irreversibly converted to indole-3-acetyl-L-aspartic acid (IAAsp) and indole-3-acetyl glutamic acid (IAGlu) by Group II of the GRETCHEN HAGEN3 (GH3) family of acyl amido synthetases. Dioxygenase for auxin oxidation (DAO) irreversibly oxidizes IAA to oxindole-3-acetic acid (oxIAA) and, in turn, oxIAA can be further glucosylated to oxindole-3-acetyl-1-glucosyl ester (oxIAGlc) by UGTs. These metabolic pathways have been identified based on mutant analyses, in vitro activity measurements, and in planta feeding assays. In vitro assays for studying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification. However, the need to extract and purify the recombinant proteins represents a major obstacle when performing in vitro assays.Results: In this work we report a rapid, reproducible and cheap method to screen the enzymatic activity of recombinant proteins that are known to inactivate IAA. The enzymatic reactions are carried out directly in bacteria that produce the recombinant protein. The enzymatic products can be measured by direct injection of a small supernatant fraction from the bacterial culture on ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UHPLC–ESI-MS/MS). Experimental procedures were optimized for testing the activity of different classes of IAA-modifying enzymes without the need to purify recombinant protein.Conclusions: This new method represents an alternative to existing in vitro assays. It can be applied to the analysis of IAA metabolites that are produced upon supplementation of substrate to engineered bacterial cultures and can be used for a rapid screening of orthologous candidate genes from non-model species.
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20.
  • Brunoni, Federica, et al. (författare)
  • Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis
  • 2020
  • Ingår i: New Phytologist. - : John Wiley & Sons. - 0028-646X .- 1469-8137. ; 226:6, s. 1753-1765
  • Tidskriftsartikel (refereegranskat)abstract
    • Dynamic regulation of the concentration of the natural auxin (IAA) is essential to coordinate most of the physiological and developmental processes and responses to environmental changes. Oxidation of IAA is a major pathway to control auxin concentrations in angiosperms and, along with IAA conjugation, to respond to perturbation of IAA homeostasis. However, these regulatory mechanisms remain poorly investigated in conifers. To reduce this knowledge gap, we investigated the different contributions of the IAA inactivation pathways in conifers. MS-based quantification of IAA metabolites under steady-state conditions and after perturbation was investigated to evaluate IAA homeostasis in conifers. Putative Picea abies GH3 genes (PaGH3) were identified based on a comprehensive phylogenetic analysis including angiosperms and basal land plants. Auxin-inducible PaGH3 genes were identified by expression analysis and their IAA-conjugating activity was explored. Compared to Arabidopsis, oxidative and conjugative pathways differentially contribute to reduce IAA concentrations in conifers. We demonstrated that the oxidation pathway plays a marginal role in controlling IAA homeostasis in spruce. By contrast, an excess of IAA rapidly activates GH3-mediated irreversible conjugation pathways. Taken together, these data indicate that a diversification of IAA inactivation mechanisms evolved specifically in conifers.
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21.
  • Bulte, Carolien S. E., et al. (författare)
  • The effects of preoperative moderate to severe anaemia on length of hospital stay : A propensity score-matched analysis in non-cardiac surgery patients
  • 2021
  • Ingår i: European Journal of Anaesthesiology. - : Wolters Kluwer. - 0265-0215 .- 1365-2346. ; 38:6, s. 571-581
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND Anaemia is frequently recorded during preoperative screening and has been suggested to affect outcomes after surgery negatively.OBJECTIVES The objectives were to assess the frequency of moderate to severe anaemia and its association with length of hospital stay.DESIGN Post hoc analysis of the international observational prospective ‘Local ASsessment of VEntilatory management during General Anaesthesia for Surgery’ (LAS VEGAS) study.PATIENTS AND SETTING The current analysis included adult patients requiring general anaesthesia for non-cardiac surgery. Preoperative anaemia was defined as a haemoglobin concentration of 11 g dl−1 or lower, thus including moderate and severe anaemia according to World Health Organisation criteria.MAIN OUTCOME MEASURES The primary outcome was length of hospital stay. Secondary outcomes included hospital mortality, intra-operative adverse events and postoperative pulmonary complications (PPCs).RESULTS Haemoglobin concentrations were available for 8264 of 9864 patients. Preoperative moderate to severe anaemia was present in 7.7% of patients. Multivariable analysis showed that preoperative moderate to severe anaemia was associated with an increased length of hospital stay with a mean difference of 1.3 ((95% CI 0.8 to 1.8) days; P < .001). In the propensity-matched analysis, this association remained present, median 4.0 [IQR 1.0 to 5.0] vs. 2.0 [IQR 0.0 to 5.0] days, P = .001. Multivariable analysis showed an increased in-hospital mortality (OR 2.9 (95% CI 1.1 to 7.5); P = .029), and higher incidences of intra-operative hypotension (36.3 vs. 25.3%; P < .001) and PPCs (17.1 vs. 10.5%; P = .001) in moderately to severely anaemic patients. However, this was not confirmed in the propensity score-matched analysis.CONCLUSIONS In this international cohort of non-cardiac surgical patients, preoperative moderate to severe anaemia was associated with a longer duration of hospital stay but not increased intra-operative complications, PPCs or in-hospital mortality.
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22.
  • Capovilla, Giovanna, et al. (författare)
  • Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana
  • 2017
  • Ingår i: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 68:18, s. 5117-5127
  • Tidskriftsartikel (refereegranskat)abstract
    • FLOWERING LOCUS M (FLM), a component of the thermosensory flowering time pathway in Arabidopsis thaliana, is regulated by temperature-dependent alternative splicing (AS). The main splicing variant, FLM-beta, is a well-documented floral repressor that is down-regulated in response to increasing ambient growth temperature. Two hypotheses have been formulated to explain how flowering time is modulated by AS of FLM. In the first model a second splice variant, FLM-delta, acts as a dominant negative isoform that competes with FLM-beta at elevated ambient temperatures, thereby indirectly promoting flowering. Alternatively, it has been suggested that the induction of flowering at elevated temperatures is caused only by reduced FLM-beta expression. To better understand the role of the two FLM splice forms, we employed CRISPR/Cas9 technology to specifically delete the exons that characterize each splice variant. Lines that produced repressive FLM-beta but were incapable of producing FLM-delta were late flowering. In contrast, FLM-beta knockout lines that still produced FLM-delta flowered early, but not earlier than the flm-3 loss of function mutant, as would be expected if FLM-delta had a dominant-negative effect on flowering. Our data support the role of FLM-beta as a flower repressor and provide evidence that a contribution of FLM-delta to the regulation of flowering time in wild-type A. thaliana seems unlikely.
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23.
  • Capovilla, Giovanna, et al. (författare)
  • Control of flowering by ambient temperature
  • 2015
  • Ingår i: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 66:1, s. 59-69
  • Tidskriftsartikel (refereegranskat)abstract
    • The timing of flowering is a crucial decision in the life cycle of plants since favourable conditions are needed to maximize reproductive success and, hence, the survival of the species. It is therefore not surprising that plants constantly monitor endogenous and environmental signals, such as day length (photoperiod) and temperature, to adjust the timing of the floral transition. Temperature in particular has been shown to have a tremendous effect on the timing of flowering: the effect of prolonged periods of cold, called the vernalization response, has been extensively studied and the underlying epigenetic mechanisms are reasonably well understood in Arabidopsis thaliana. In contrast, the effect of moderate changes in ambient growth temperature on the progression of flowering, the thermosensory pathway, is only starting to be understood on the molecular level. Several genes and molecular mechanisms underlying the thermosensory pathway have already been identified and characterized in detail. At a time when global temperature is rising due to climate change, this knowledge will be pivotal to ensure crop production in the future.
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24.
  • Capovilla, Giovanna, et al. (författare)
  • PORCUPINE regulates development in response to temperature through alternative splicing
  • 2018
  • Ingår i: Nature plants. - : Nature Publishing Group. - 2055-026X .- 2055-0278. ; 4:8, s. 534-539
  • Tidskriftsartikel (refereegranskat)abstract
    • Recent findings suggest that alternative splicing has a critical role in controlling the responses of plants to temperature variations. However, alternative splicing factors in plants are largely uncharacterized. Here we establish the putative splice regulator, PORCUPINE (PCP), as temperature-specific regulator of development in Arabidopsis thaliana. Our findings point to the misregulation of WUSCHEL and CLAVATA3 as the possible cause for the meristem defects affecting the pcp-1 loss-of-function mutants at low temperatures.
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25.
  • Capovilla, Giovanna, et al. (författare)
  • Role of alternative pre-mRNA splicing in temperature signaling
  • 2015
  • Ingår i: Current opinion in plant biology. - : Elsevier BV. - 1369-5266 .- 1879-0356. ; 27, s. 97-103
  • Forskningsöversikt (refereegranskat)abstract
    • Developmental plasticity enables plants to respond rapidly to changing environmental conditions, such as temperature fluctuations. Understanding how plants measure temperature and integrate this information into developmental programs at the molecular level will be essential to breed thermo-tolerant crop varieties. Recent studies identified alternative splicing (AS) as a possible 'molecular thermometer', allowing plants to quickly adjust the abundance of functional transcripts to environmental perturbations. In this review, recent advances regarding the effects of temperature-responsive AS on plant development will be discussed, with emphasis on the circadian clock and flowering time control. The challenge for the near future will be to understand the molecular mechanisms by which temperature can influence AS regulation.
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26.
  • Chauvin, G., et al. (författare)
  • Discovery of a warm, dusty giant planet around HIP 65426
  • 2017
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 605
  • Tidskriftsartikel (refereegranskat)abstract
    • Aims. The SHINE program is a high-contrast near-infrared survey of 600 young, nearby stars aimed at searching for and characterizing new planetary systems using VLT/SPHERE's unprecedented high-contrast and high-angular-resolution imaging capabilities. It is also intended to place statistical constraints on the rate, mass and orbital distributions of the giant planet population at large orbits as a function of the stellar host mass and age to test planet-formation theories.Methods. We used the IRDIS dual-band imager and the IFS integral field spectrograph of SPHERE to acquire high-contrast coronagraphic differential near-infrared images and spectra of the young A2 star HIP 65426. It is a member of the similar to 17 Myr old Lower Centaurus-Crux association. Results. At a separation of 830 mas (92 au projected) from the star, we detect a faint red companion. Multi-epoch observations confirm that it shares common proper motion with HIP 65426. Spectro-photometric measurements extracted with IFS and IRDIS between 0.95 and 2.2 mu m indicate a warm, dusty atmosphere characteristic of young low-surface-gravity L5-L7 dwarfs. Hot-start evolutionary models predict a luminosity consistent with a 6-12 M-Jup, T-eff = 1300-1600K and R = 1.5 +/- 0.1 R-Jup giant planet. Finally, the comparison with Exo-REM and PHOENIX BT-Settl synthetic atmosphere models gives consistent effective temperatures but with slightly higher surface gravity solutions of log(g) = 4.0-5.0 with smaller radii (1.0-1.3 R-Jup).Conclusions. Given its physical and spectral properties, HIP 65426 b occupies a rather unique placement in terms of age, mass, and spectral-type among the currently known imaged planets. It represents a particularly interesting case to study the presence of clouds as a function of particle size, composition, and location in the atmosphere, to search for signatures of non-equilibrium chemistry, and finally to test the theory of planet formation and evolution.
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27.
  • Collani, Silvio, et al. (författare)
  • FT Modulates Genome-Wide DNA-Binding of the bZIP Transcription Factor FD
  • 2019
  • Ingår i: Plant Physiology. - : American Society of Plant Biologists. - 0032-0889 .- 1532-2548. ; 180:1, s. 367-380
  • Tidskriftsartikel (refereegranskat)abstract
    • The transition to flowering is a crucial step in the plant life cycle that is controlled by multiple endogenous and environmental cues, including hormones, sugars, temperature, and photoperiod. Permissive photoperiod induces the expression of FLOWERING LOCUS T (FT) in the phloem companion cells of leaves. The FT protein then acts as a florigen that is transported to the shoot apical meristem, where it physically interacts with the Basic Leucine Zipper Domain transcription factor FD and 14-3-3 proteins. However, despite the importance of FD in promoting flowering, its direct transcriptional targets are largely unknown. Here, we combined chromatin immunoprecipitation sequencing and RNA sequencing to identify targets of FD at the genome scale and assessed the contribution of FT to DNA binding. We further investigated the ability of FD to form protein complexes with FT and TERMINAL FLOWER1 through interaction with 14-3-3 proteins. Importantly, we observed direct binding of FD to targets involved in several aspects of plant development. These target genes were previously unknown to be directly related to the regulation of flowering time. Our results confirm FD as a central regulator of floral transition at the shoot meristem and provide evidence for crosstalk between the regulation of flowering and other signaling pathways, such as pathways involved in hormone signaling.
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28.
  • Conn, Vanessa M., et al. (författare)
  • A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation
  • 2017
  • Ingår i: Nature Plants. - : Nature Publishing Group. - 2055-026X .- 2055-0278. ; 3:5
  • Tidskriftsartikel (refereegranskat)abstract
    • Circular RNAs (circRNAs) are a diverse and abundant class of hyper-stable, non-canonical RNAs that arise through a form of alternative splicing (AS) called back-splicing. These single-stranded, covalently-closed circRNA molecules have been identified in all eukaryotic kingdoms of life(1), yet their functions have remained elusive. Here, we report that circRNAs can be used as bona fide biomarkers of functional, exon-skipped AS variants in Arabidopsis, including in the homeotic MADS-box transcription factor family. Furthermore, we demonstrate that circRNAs derived from exon 6 of the SEPALLATA3 (SEP3) gene increase abundance of the cognate exon-skipped AS variant (SEP3.3 which lacks exon 6), in turn driving floral homeotic phenotypes. Toward demonstrating the underlying mechanism, we show that the SEP3 exon 6 circRNA can bind strongly to its cognate DNA locus, forming an RNA: DNA hybrid, or R-loop, whereas the linear RNA equivalent bound significantly more weakly to DNA. R-loop formation results in transcriptional pausing, which has been shown to coincide with splicing factor recruitment and AS(2-4). This report presents a novel mechanistic insight for how at least a subset of circRNAs probably contribute to increased splicing efficiency of their cognate exon-skipped messenger RNA and provides the first evidence of an organismal-level phenotype mediated by circRNA manipulation.
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29.
  • Cugno, G., et al. (författare)
  • A search for accreting young companions embedded in circumstellar disks High-contrast H alpha imaging with VLT/SPHERE
  • 2019
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 622
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. In recent years, our understanding of giant planet formation progressed substantially. There have even been detections of a few young protoplanet candidates still embedded in the circumstellar disks of their host stars. The exact physics that describes the accretion of material from the circumstellar disk onto the suspected circumplanetary disk and eventually onto the young, forming planet is still an open question.Aims. We seek to detect and quantify observables related to accretion processes occurring locally in circumstellar disks, which could be attributed to young forming planets. We focus on objects known to host protoplanet candidates and/or disk structures thought to be the result of interactions with planets.Methods. We analyzed observations of six young stars (age 3.5-10 Myr) and their surrounding environments with the SPHERE/ZIMPOL instrument on the Very Large Telescope (VLT) in the H alpha filter (656 nm) and a nearby continuum filter (644.9 nm). We applied several point spread function (PSF) subtraction techniques to reach the highest possible contrast near the primary star, specifically investigating regions where forming companions were claimed or have been suggested based on observed disk morphology.Results. We redetect the known accreting M-star companion HD142527 B with the highest published signal to noise to date in both H alpha and the continuum. We derive new astrometry (r = 62.8(-2.7)(+2.1)mas and PA = (98.7 +/- 1.8)degrees) and photometry (Delta N_Ha = 6.3-(+0.2)(0.3) mag, Delta B_Ha = 6.7 +/- 0.2 mag and Delta Cnt_Ha= 7.3(-0.2)(+0.3) mag) for the companion in agreement with previous studies, and estimate its mass accretion rate (M approximate to 1-2 x 10(-10) M-circle dot yr(-1)). A faint point-like source around HD135344 B (SA0206462) is also investigated, but a second deeper observation is required to reveal its nature. No other companions are detected. In the framework of our assumptions we estimate detection limits at the locations of companion candidates around HD100546, HD169142, and MWC 758 and calculate that processes involving Ha fluxes larger than similar to 8 x 10(-14)-10(-15) erg s(-1) cm(-2) (M > 10(-10)-10(-12) M-circle dot yr(-1)) can be excluded. Furthermore, flux upper limits of similar to 10(-14)-10(-15)erg s(-1) cm(-2) (M < 10(-11) -10(-12)M(circle dot )yr(-1)) are estimated within the gaps identified in the disks surrounding HD135344 B and TW Hya. The derived luminosity limits exclude H alpha signatures at levels similar to those previously detected for the accreting planet candidate LkCa15 b.
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30.
  • Desidera, S., et al. (författare)
  • The SPHERE infrared survey for exoplanets (SHINE) I. Sample definition and target characterization
  • 2021
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 651
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. Large surveys with new-generation high-contrast imaging instruments are needed to derive the frequency and properties of exoplanet populations with separations from ~5 to 300 au. A careful assessment of the stellar properties is crucial for a proper understanding of when, where, and how frequently planets form, and how they evolve. The sensitivity of detection limits to stellar age makes this a key parameter for direct imaging surveys.Aims. We describe the SpHere INfrared survey for Exoplanets (SHINE), the largest direct imaging planet-search campaign initiated at the VLT in 2015 in the context of the SPHERE Guaranteed Time Observations of the SPHERE consortium. In this first paper we present the selection and the properties of the complete sample of stars surveyed with SHINE, focusing on the targets observed during the first phase of the survey (from February 2015 to February 2017). This early sample composed of 150 stars is used to perform a preliminary statistical analysis of the SHINE data, deferred to two companion papers presenting the survey performance, main discoveries, and the preliminary statistical constraints set by SHINE.Methods. Based on a large database collecting the stellar properties of all young nearby stars in the solar vicinity (including kinematics, membership to moving groups, isochrones, lithium abundance, rotation, and activity), we selected the original sample of 800 stars that were ranked in order of priority according to their sensitivity for planet detection in direct imaging with SPHERE. The properties of the stars that are part of the early statistical sample wererevisited, including for instance measurements from the Gaia Data Release 2. Rotation periods were derived for the vast majority of the late-type objects exploiting TESS light curves and dedicated photometric observations.Results. The properties of individual targets and of the sample as a whole are presented.
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31.
  • Dikaya, Varvara, et al. (författare)
  • Insights into the role of alternative splicing in plant temperature response
  • 2021
  • Ingår i: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 72:21, s. 7384-7403
  • Forskningsöversikt (refereegranskat)abstract
    • Alternative splicing occurs in all eukaryotic organisms. Since the first description of multiexon genes and the splicing machinery, the field has expanded rapidly, especially in animals and yeast. However, our knowledge about splicing in plants is still quite fragmented. Though eukaryotes show some similarity in the composition and dynamics of their splicing machinery, observations of unique plant traits are only starting to emerge. For instance, plant alternative splicing is closely linked to their ability to perceive various environmental stimuli. Due to their sessile lifestyle, temperature is a central source of information, allowing plants to adjust their development to match current growth conditions. Hence, seasonal temperature fluctuations and day-night cycles can strongly influence plant morphology across developmental stages. Here we discuss available data on temperature-dependent alternative splicing in plants. Given its fragmented state, it is not always possible to fit specific observations into a coherent picture, yet it is sufficient to estimate the complexity of this field and the need for further research. Better understanding of alternative splicing as a part of plant temperature response and adaptation may also prove to be a powerful tool for both fundamental and applied sciences.
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32.
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33.
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34.
  • Egg, David, et al. (författare)
  • Therapeutic options for CTLA-4 insufficiency
  • 2022
  • Ingår i: Journal of Allergy and Clinical Immunology. - : MOSBY-ELSEVIER. - 0091-6749 .- 1097-6825. ; 149:2, s. 736-746
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Heterozygous germline mutations in cytotoxic T lymphocyte-associated antigen-4 (CTLA4) impair the immunomodulatory function of regulatory T cells. Affected individuals are prone to life-threatening autoimmune and lymphoproliferative complications. A number of therapeutic options are currently being used with variable effectiveness. Objective: Our aim was to characterize the responsiveness of patients with CTLA-4 insufficiency to specific therapies and provide recommendations for the diagnostic workup and therapy at an organ-specific level. Methods: Clinical features, laboratory findings, and response to treatment were reviewed retrospectively in an international cohort of 173 carriers of CTLA4 mutation. Patients were followed between 2014 and 2020 for a total of 2624 months from diagnosis. Clinical manifestations were grouped on the basis of organ-specific involvement. Medication use and response were recorded and evaluated. Results: Among the 173 CTLA4 mutation carriers, 123 (71%) had been treated for immune complications. Abatacept, rituximab, sirolimus, and corticosteroids ameliorated disease severity, especially in cases of cytopenias and lymphocytic organ infiltration of the gut, lungs, and central nervous system. Immunoglobulin replacement was effective in prevention of infection. Only 4 of 16 patients (25%) with cytopenia who underwent splenectomy had a sustained clinical response. Cure was achieved with stem cell transplantation in 13 of 18 patients (72%). As a result of the aforementioned methods, organ-specific treatment pathways were developed. Conclusion: Systemic immunosuppressants and abatacept may provide partial control but require ongoing administration. Allogeneic hematopoietic stem cell transplantation offers a possible cure for patients with CTLA-4 insufficiency.
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35.
  • Engelhorn, Julia, et al. (författare)
  • Dynamics of H3K4me3 Chromatin Marks Prevails over H3K27me3 for Gene Regulation during Flower Morphogenesis in Arabidopsis thaliana
  • 2017
  • Ingår i: Epigenomes. - : MDPI. - 2075-4655. ; 1:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine 4 (H3K4me3). However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with expression changes, in a developmental series including Arabidopsis thaliana leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prevail over changes in H3K27me3 and quantitatively correlate with expression changes, while H3K27me3 changes occur later. Notably, we found that H3K4me3 increase during the early activation of PcG target genes while H3K27me3 level remain relatively constant at the locus. Our results reveal that H3K4me3 predicts changes in gene expression better than H3K27me3, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.
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36.
  • Engler, N., et al. (författare)
  • The high-albedo, low polarization disk around HD 114082 that harbors a Jupiter-sized transiting planet Constraints from VLT/SPHERE completed with TESS, Gaia, and radial velocities
  • 2023
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 672
  • Tidskriftsartikel (refereegranskat)abstract
    • Aims. We present new optical and near-infrared images of the debris disk around the F-type star HD 114082 in the Scorpius-Centaurus OB association. We obtained direct imaging observations and analyzed the TESS photometric time series data of this target with the goal of searching for planetary companions to HD 114082 and characterizing the morphology of the debris disk and the scattering properties of dust particles. Methods. HD 114082 was observed with the VLT/SPHERE instrument in different modes - the IRDIS camera in the K band (2.0-2.3 mu m) together with the IFS in the Y, J, and H bands (0.95-1.66 mu m) using the angular differential imaging technique as well as IRDIS in the H band (1.5-1.8 mu m) and ZIMPOL in the I_PRIME band (0.71-0.87 mu m) using the polarimetric differential imaging technique. To constrain the basic geometrical parameters of the disk and the scattering properties of dust grains, scattered light images were fitted with a 3D model for single scattering in an optically thin dust disk using a Markov chain Monte Carlo approach. We performed aperture photometry to derive the scattering and polarized phase functions, the polarization fraction, and the spectral scattering albedo for the dust particles in the disk. This method was also used to obtain the reflectance spectrum of the disk and, in turn, to retrieve the disk color and study the dust reflectivity in comparison to the debris disk HD 117214. We also performed the modeling of the HD 114082 light curve measured by TESS using models for planet transit and stellar activity to put constraints on the radius of the detected planet and its orbit. Last, we searched for additional planets in the system by combining archival radial velocity data, astrometry, and direct imaging. Results. The debris disk HD 114082 appears as an axisymmetric debris belt with a radius of similar to 0.37 '' (35 au), an inclination of similar to 83 degrees, and a wide inner cavity. Dust particles in HD 114082 have a maximum polarization fraction of similar to 17% and a higher reflectivity when compared to the debris disk HD 117214. This high reflectivity results in a spectral scattering albedo of similar to 0.65 for the HD 114082 disk at near-infrared wavelengths. The disk reflectance spectrum exhibits a red color at the position of the planetesimal belt and shows no obvious features, whereas that of HD 117214 might indicate the presence of CO2 ice. The analysis of TESS photometric data reveals a transiting planetary companion to HD 114082 with a radius of similar to 1 R-Jup on an orbit with a semimajor axis of 0.7 +/- 0.4 au. No additional planet was detected in the system when we combined the SPHERE images with constraints from astrometry and radial velocity. We reach deep sensitivity limits down to similar to 5 M-Jup at 50 au and similar to 10 M-Jup at 30 au from the central star.
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37.
  • Engler, N., et al. (författare)
  • The HIP 79977 debris disk in polarized light
  • 2017
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 607
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. Debris disks are observed around 10 to 20% of FGK main-sequence stars as infrared excess emission. They are important signposts for the presence of colliding planetesimals and therefore provide important information about the evolution of planetary systems. Direct imaging of such disks reveals their geometric structure and constrains their dust-particle properties. Aims. We present observations of the known edge-on debris disk around HIP 79977 (HD 146897) taken with the ZIMPOL differential polarimeter of the SPHERE instrument. We measure the observed polarization signal and investigate the diagnostic potential of such data with model simulations. Methods. SPHERE-ZIMPOL polarimetric data of the 15 Myr-old F star HIP 79977 (Upper Sco, 123 pc) were taken in the Very Broad Band (VBB) filter (lambda(c) = 735 nm, Delta lambda = 290 nm) with a spatial resolution of about 25 mas. Imaging polarimetry efficiently suppresses the residual speckle noise from the AO system and provides a differential signal with relatively small systematic measuring uncertainties. We measure the polarization flux along and perpendicular to the disk spine of the highly inclined disk for projected separations between 0 : 200 (25 AU) and 1 : 600 (200 AU). We perform model calculations for the polarized flux of an optically thin debris disk which are used to determine or constrain the disk parameters of HIP 79977. Results. We measure a polarized flux contrast ratio for the disk of (F-pol) disk/F-* = (5 : 5 +/- 0 : 9) x 10(-4) in the VBB filter. The surface brightness of the polarized flux reaches a maximum of SBmax = 16.2 mag arcsec(-2) at a separation of 0 : 200 -0 : 500 along the disk spine with a maximum surface brightness contrast of 7 : 64 mag arcsec(-2). The polarized flux has a minimum near the star < 0 : 200 because no or only little polarization is produced by forward or backward scattering in the disk section lying in front of or behind the star. The width of the disk perpendicular to the spine shows a systematic increase in FWHM from 0 : 1 (12 AU) to 0 : 3 -0.5, when going from a separation of 0 : 2 to > 1. This can be explained by a radial blow-out of small grains. The data are modelled as a circular dust belt with a well defined disk inclination i = 85(+/- 1 : 5)degrees and a radius between r(0) = 60 and 90 AU. The radial density dependence is described by (r/r(0))alpha with a steep (positive) power law index alpha = 5 inside r(0) and a more shallow (negative) index alpha = -2 : 5 outside r(0). The scattering asymmetry factor lies between g = 0.2 and 0.6 (forward scattering) adopting a scattering-angle dependence for the fractional polarization such as that for Rayleigh scattering. Conclusions. Polarimetric imaging with SPHERE-ZIMPOL of the edge-on debris disk around HIP 79977 provides accurate profiles for the polarized flux. Our data are qualitatively very similar to the case of AU Mic and they confirm that edge-on debris disks have a polarization minimum at a position near the star and a maximum near the projected separation of the main debris belt. The comparison of the polarized flux contrast ratio (F-pol)(disk)/F* with the fractional infrared excess provides strong constraints on the scattering albedo of the dust.
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38.
  • Galvao, Vinicius Costa, et al. (författare)
  • Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana
  • 2015
  • Ingår i: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 84:5, s. 949-962
  • Tidskriftsartikel (refereegranskat)abstract
    • Distinct molecular mechanisms integrate changes in ambient temperature into the genetic pathways that govern flowering time in Arabidopsis thaliana. Temperature-dependent eviction of the histone variant H2A.Z from nucleosomes has been suggested to facilitate the expression of FT by PIF4 at elevated ambient temperatures. Here we show that, in addition to PIF4, PIF3 and PIF5, but not PIF1 and PIF6, can promote flowering when expressed specifically in phloem companion cells (PCC), where they can induce FT and its close paralog, TSF. However, despite their strong potential to promote flowering, genetic analyses suggest that the PIF genes seem to have only a minor role in adjusting flowering in response to photoperiod or high ambient temperature. In addition, loss of PIF function only partially suppressed the early flowering phenotype and FT expression of the arp6 mutant, which is defective in H2A.Z deposition. In contrast, the chemical inhibition of gibberellic acid (GA) biosynthesis resulted in a strong attenuation of early flowering and FT expression in arp6. Furthermore, GA was able to induce flowering at low temperature (15 degrees C) independently of FT, TSF, and the PIF genes, probably directly at the shoot apical meristem. Together, our results suggest that the timing of the floral transition in response to ambient temperature is more complex than previously thought and that GA signaling might play a crucial role in this process.
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39.
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40.
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41.
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42.
  • Garufi, A., et al. (författare)
  • The SPHERE view of the planet-forming disk around HD 100546
  • 2016
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 588
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. The mechanisms governing planet formation are not fully understood. A new era of high-resolution imaging of protoplanetary disks has recently started, thanks to new instruments such as SPHERE, GPI, and ALMA. The planet formation process can now be directly studied by imaging both planetary companions embedded in disks and their e ff ect on disk morphology. Aims. We image disk features that could be potential signs of planet-disk interaction with unprecedented spatial resolution and sensitivity. Two companion candidates have been claimed in the disk around the young Herbig Ae /Be star HD 100546. Thus, this object serves as an excellent target for our investigation of the natal environment of giant planets. Methods. We exploit the power of extreme adaptive optics operating in conjunction with the new high-contrast imager SPHERE to image HD 100546 in scattered light. We obtained the first polarized light observations of this source in the visible (with resolution as fine as 2 AU) and new H and K band total intensity images that we analyzed with the p y n p o i n t package. Results. The disk shows a complex azimuthal morphology, where multiple scattering of photons most likely plays an important role. High brightness contrasts and arm-like structures are ubiquitous in the disk. A double-wing structure (partly due to angular di ff erential imaging processing) resembles a morphology newly observed in inclined disks. Given the cavity size in the visible (11 AU), the CO emission associated to the planet candidate c might arise from within the circumstellar disk. We find an extended emission in the K band at the expected location of b. The surrounding large-scale region is the brightest in scattered light. There is no sign of any disk gap associated to b.
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43.
  • Goretti, Daniela, et al. (författare)
  • TERMINAL FLOWER1 Functions as a Mobile Transcriptional Cofactor in the Shoot Apical Meristem
  • 2020
  • Ingår i: Plant Physiology. - : American Society of Plant Biologists. - 0032-0889 .- 1532-2548. ; 182:4, s. 2081-2095
  • Tidskriftsartikel (refereegranskat)abstract
    • TERMINAL FLOWER1 acts in the shoot apical meristem as a mobile cell-non-autonomous transcriptional cofactor that associates with DNA to regulate meristem indeterminacy and flowering. The floral transition is a critical step in the life cycle of flowering plants, and several mechanisms control this finely orchestrated process. TERMINAL FLOWER1 (TFL1) is a floral repressor and close relative of the florigen, FLOWERING LOCUS T (FT). During the floral transition, TFL1 expression is up-regulated in the inflorescence apex to maintain the indeterminate growth of the shoot apical meristem (SAM). Both TFL1 and FT are mobile proteins, but they move in different ways. FT moves from the leaves to the SAM, while TFL1 appears to move within the SAM. The importance of TFL1 movement for its function in the regulation of flowering time and shoot indeterminacy and its molecular function are still largely unclear. Our results using Arabidopsis (Arabidopsis thaliana) indicate that TFL1 moves from its place of expression in the center of the SAM to the meristem layer L1 and that the movement in the SAM is required for the regulation of the floral transition. Chromatin immunoprecipitation sequencing and RNA sequencing demonstrated that TFL1 functions as a cotranscription factor that associates with and regulates the expression of hundreds of genes. These newly identified direct TFL1 targets provide the possibility to discover new roles for TFL1 in the regulation of floral transition and inflorescence development.
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44.
  • Gratton, R., et al. (författare)
  • Investigating three Sirius-like systems with SPHERE
  • 2021
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 646
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. Sirius-like systems are relatively wide binaries with a separation from a few to hundreds of au; they are composed of a white dwarf (WD) and a companion of a spectral type earlier than M0. Here we consider main sequence (MS) companions, where the WD progenitor evolves in isolation, but its wind during the former asymptotic giant branch (AGB) phase pollutes the companion surface and transfers some angular momentum. They are rich laboratories to constrain stellar models and binary evolution.Aims. Within the SpHere INfrared survey for Exoplanet survey that uses the Spectro-Polarimetric High-contrast Exoplanet REsearch (SPHERE) instrument at the Very Large Telescope, our goal is to acquire high contrast multi-epoch observations of three Sirius-like systems, HD 2133, HD 114174, and CD-56 7708 and to combine this data with archive high resolution spectra of the primaries, TESS archive, and literature data.Methods. These WDs are easy targets for SPHERE and were used as spectrophotometric standards. We performed very accurate abundance analyses for the MS stars using methods considered for solar analogs. Whenever possible, WD parameters and orbits were obtained using Monte Carlo Markov chain methods.Results. We found brighter J and K magnitudes for HD 114174B than obtained previously and extended the photometry down to 0.95 μm. Our new data indicate a higher temperature and then shorter cooling age (5.57 ± 0.02 Gyr) and larger mass (0.75 ± 0.03 M⊙) for this WD than previously assumed. Together with the oldest age for the MS star connected to the use of the Gaia DR2 distance, this solved the discrepancy previously found with the age of the MS star. The two other WDs are less massive, indicating progenitors of ∼1.3 M⊙ and 1.5 − 1.8 M⊙ for HD 2133B and CD-56 7708B, respectively. In spite of the rather long periods, we were able to derive useful constraints on the orbit for HD 114174 and CD-56 7708. They are both seen close to edge-on, which is in agreement with the inclination of the MS stars that are obtained coupling the rotational periods, stellar radii, and the projected rotational velocity from spectroscopy. The composition of the MS stars agrees fairly well with expectations from pollution by the AGB progenitors of the WDs: HD 2133A has a small enrichment of n-capture elements, which is as expected for pollution by an AGB star with an initial mass < 1.5 M⊙; CD-56 7708A is a previously unrecognized mild Ba-star, which is also expected due to pollution by an AGB star with an initial mass in the range of 1.5 − 3.0 M⊙; and HD 114174 has a very moderate excess of n-capture elements, which is in agreement with the expectation for a massive AGB star to have an initial mass > 3.0 M⊙.Conclusions. On the other hand, none of these stars show the excesses of C that are expected to go along with those of n-capture elements. This might be related to the fact that these stars are at the edges of the mass range where we expect nucleosynthesis related to thermal pulses. More work, both theoretical and observational, is required to better understand this issue.
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45.
  • Hagleitner, Daniel R., et al. (författare)
  • Bulk and surface characterization of In2O3(001) single crystals
  • 2012
  • Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121. ; 85:11
  • Tidskriftsartikel (refereegranskat)abstract
    • A comprehensive bulk and surface investigation of high-quality In2O3(001) single crystals is reported. The transparent-yellow, cube-shaped single crystals were grown using the flux method. Inductively coupled plasma mass spectrometry (ICP-MS) reveals small residues of Pb, Mg, and Pt in the crystals. Four-point-probe measurements show a resistivity of 2.0 +/- 0.5 x 10(5) Omega cm, which translates into a carrier concentration of approximate to 10(12) cm(-3). The results from x-ray diffraction (XRD) measurements revise the lattice constant to 10.1150(5) angstrom from the previously accepted value of 10.117 angstrom. Scanning tunneling microscopy (STM) images of a reduced (sputtered/annealed) and oxidized (exposure to atomic oxygen at 300 degrees C) surface show a step height of 5 angstrom, which indicates a preference for one type of surface termination. The surfaces stay flat without any evidence for macroscopic faceting under any of these preparation conditions. A combination of low-energy ion scattering (LEIS) and atomically resolved STM indicates an indium-terminated surface with small islands of 2.5 angstrom height under reducing conditions, with a surface structure corresponding to a strongly distorted indium lattice. Scanning tunneling spectroscopy (STS) reveals a pronounced surface state at the Fermi level (E-F). Photoelectron spectroscopy (PES) shows additional, deep-lying band gap states, which can be removed by exposure of the surface to atomic oxygen. Oxidation also results in a shoulder at the O 1s core level at a higher binding energy, possibly indicative of a surface peroxide species. A downward band bending of 0.4 eV is observed for the reduced surface, while the band bending of the oxidized surface is of the order of 0.1 eV or less.
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46.
  • Haider, Susanne, et al. (författare)
  • Raman microspectroscopy reveals long-term extracellular activity of Chlamydiae
  • 2010
  • Ingår i: Molecular Microbiology. - : Blackwell Publishing. - 0950-382X .- 1365-2958. ; 77:3, s. 687-700
  • Tidskriftsartikel (refereegranskat)abstract
    • The phylum Chlamydiae consists exclusively of obligate intracellular bacteria. Some of them are formidable pathogens of humans, while others occur as symbionts of amoebae. These genetically intractable bacteria possess a developmental cycle consisting of replicative reticulate bodies and infectious elementary bodies, which are believed to be physiologically inactive. Confocal Raman microspectroscopy was applied to differentiate between reticulate bodies and elementary bodies of Protochlamydia amoebophila and to demonstrate in situ the labelling of this amoeba symbiont after addition of isotope-labelled phenylalanine. Unexpectedly, uptake of this amino acid was also observed for both developmental stages for up to 3 weeks, if incubated extracellularly with labelled phenylalanine, and P. amoebophila remained infective during this period. Furthermore, P. amoebophila energizes its membrane and performs protein synthesis outside of its host. Importantly, amino acid uptake and protein synthesis after extended extracellular incubation could also be demonstrated for the human pathogen Chlamydia trachomatis, which synthesizes stress-related proteins under these conditions as shown by 2-D gel electrophoresis and MALDI-TOF/TOF mass spectrometry. These findings change our perception of chlamydial biology and reveal that host-free analyses possess a previously not recognized potential for direct experimental access to these elusive microorganisms.
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47.
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48.
  • Hemmes, Sabrine N. T., et al. (författare)
  • Epidemiology, practice of ventilation and outcome for patients at increased risk of postoperative pulmonary complications : LAS VEGAS - an observational study in 29 countries
  • 2017
  • Ingår i: European Journal of Anaesthesiology. - : LIPPINCOTT WILLIAMS & WILKINS. - 0265-0215 .- 1365-2346. ; 34:8, s. 492-507
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND Limited information exists about the epidemiology and outcome of surgical patients at increased risk of postoperative pulmonary complications (PPCs), and how intraoperative ventilation was managed in these patients. OBJECTIVES To determine the incidence of surgical patients at increased risk of PPCs, and to compare the intraoperative ventilation management and postoperative outcomes with patients at low risk of PPCs. DESIGN This was a prospective international 1-week observational study using the ‘Assess Respiratory Risk in Surgical Patients in Catalonia risk score’ (ARISCAT score) for PPC for risk stratification. PATIENTS AND SETTING Adult patients requiring intraoperative ventilation during general anaesthesia for surgery in 146 hospitals across 29 countries. MAIN OUTCOME MEASURES The primary outcome was the incidence of patients at increased risk of PPCs based on the ARISCAT score. Secondary outcomes included intraoperative ventilatory management and clinical outcomes. RESULTS A total of 9864 patients fulfilled the inclusion criteria. The incidence of patients at increased risk was 28.4%. The most frequently chosen tidal volume (VT) size was 500 ml, or 7 to 9 ml kg1 predicted body weight, slightly lower in patients at increased risk of PPCs. Levels of positive end-expiratory pressure (PEEP) were slightly higher in patients at increased risk of PPCs, with 14.3% receiving more than 5 cmH2O PEEP compared with 7.6% in patients at low risk of PPCs (P < 0.001). Patients with a predicted preoperative increased risk of PPCs developed PPCs more frequently: 19 versus 7%, relative risk (RR) 3.16 (95% confidence interval 2.76 to 3.61), P < 0.001) and had longer hospital stays. The only ventilatory factor associated with the occurrence of PPCs was the peak pressure. CONCLUSION The incidence of patients with a predicted increased risk of PPCs is high. A large proportion of patients receive high VT and low PEEP levels. PPCs occur frequently in patients at increased risk, with worse clinical outcome. TRIAL REGISTRATION The study was registered at Clinicaltrials.gov, number NCT01601223.
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49.
  • Hemmes, Sabrine N. T., et al. (författare)
  • High versus low positive end-expiratory pressure during general anaesthesia for open abdominal surgery (PROVHILO trial) : a multicentre randomised controlled trial
  • 2014
  • Ingår i: The Lancet. - 0140-6736 .- 1474-547X. ; 384:9942, s. 495-503
  • Tidskriftsartikel (refereegranskat)abstract
    • Background The role of positive end-expiratory pressure in mechanical ventilation during general anaesthesia for surgery remains uncertain. Levels of pressure higher than 0 cm H2O might protect against postoperative pulmonary complications but could also cause intraoperative circulatory depression and lung injury from overdistension. We tested the hypothesis that a high level of positive end-expiratory pressure with recruitment manoeuvres protects against postoperative pulmonary complications in patients at risk of complications who are receiving mechanical ventilation with low tidal volumes during general anaesthesia for open abdominal surgery. Methods In this randomised controlled trial at 30 centres in Europe and North and South America, we recruited 900 patients at risk for postoperative pulmonary complications who were planned for open abdominal surgery under general anaesthesia and ventilation at tidal volumes of 8 mL/kg. We randomly allocated patients to either a high level of positive end-expiratory pressure (12 cm H2O) with recruitment manoeuvres (higher PEEP group) or a low level of pressure (<= 2 cm H2O) without recruitment manoeuvres (lower PEEP group). We used a centralised computer-generated randomisation system. Patients and outcome assessors were masked to the intervention. Primary endpoint was a composite of postoperative pulmonary complications by postoperative day 5. Analysis was by intention-to-treat. The study is registered at Controlled-Trials. com, number ISRCTN70332574. Findings From February, 2011, to January, 2013, 447 patients were randomly allocated to the higher PEEP group and 453 to the lower PEEP group. Six patients were excluded from the analysis, four because they withdrew consent and two for violation of inclusion criteria. Median levels of positive end-expiratory pressure were 12 cm H2O (IQR 12-12) in the higher PEEP group and 2 cm H2O (0-2) in the lower PEEP group. Postoperative pulmonary complications were reported in 174 (40%) of 445 patients in the higher PEEP group versus 172 (39%) of 449 patients in the lower PEEP group (relative risk 1.01; 95% CI 0.86-1.20; p = 0.86). Compared with patients in the lower PEEP group, those in the higher PEEP group developed intraoperative hypotension and needed more vasoactive drugs. Interpretation A strategy with a high level of positive end-expiratory pressure and recruitment manoeuvres during open abdominal surgery does not protect against postoperative pulmonary complications. An intraoperative protective ventilation strategy should include a low tidal volume and low positive end-expiratory pressure, without recruitment manoeuvres.
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50.
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