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| 3. |
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| 4. |
- Poyatos, R., et al.
(författare)
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Global transpiration data from sap flow measurements: the SAPFLUXNET database
- 2021
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Ingår i: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 13:6, s. 2607-2649
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Tidskriftsartikel (refereegranskat)abstract
- Plant transpiration links physiological responses of vegetation to water supply and demand with hydrological, energy, and carbon budgets at the land-atmosphere interface. However, despite being the main land evaporative flux at the global scale, transpiration and its response to environmental drivers are currently not well constrained by observations. Here we introduce the first global compilation of whole-plant transpiration data from sap flow measurements (SAPFLUXNET, https://sapfluxnet.creaf.cat/, last access: 8 June 2021). We harmonized and quality-controlled individual datasets supplied by contributors worldwide in a semi-automatic data workflow implemented in the R programming language. Datasets include sub-daily time series of sap flow and hydrometeorological drivers for one or more growing seasons, as well as metadata on the stand characteristics, plant attributes, and technical details of the measurements. SAPFLUXNET contains 202 globally distributed datasets with sap flow time series for 2714 plants, mostly trees, of 174 species. SAPFLUXNET has a broad bioclimatic coverage, with woodland/shrubland and temperate forest biomes especially well represented (80 % of the datasets). The measurements cover a wide variety of stand structural characteristics and plant sizes. The datasets encompass the period between 1995 and 2018, with 50 % of the datasets being at least 3 years long. Accompanying radiation and vapour pressure deficit data are available for most of the datasets, while on-site soil water content is available for 56 % of the datasets. Many datasets contain data for species that make up 90 % or more of the total stand basal area, allowing the estimation of stand transpiration in diverse ecological settings. SAPFLUXNET adds to existing plant trait datasets, ecosystem flux networks, and remote sensing products to help increase our understanding of plant water use, plant responses to drought, and ecohydrological processes. SAPFLUXNET version 0.1.5 is freely available from the Zenodo repository (https://doi.org/10.5281/zenodo.3971689; Poyatos et al., 2020a). The "sapfluxnetr" R package - designed to access, visualize, and process SAPFLUXNET data - is available from CRAN.
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| 7. |
- Ellsworth, D. S., et al.
(författare)
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Convergence in phosphorus constraints to photosynthesis in forests around the world
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Phosphorus (P) limitation is pervasive in tropical forests. Here the authors analyse the dependence of photosynthesis on leaf N and P in tropical forests, and show that incorporating leaf P constraints in a terrestrial biosphere model enhances its predictive power. Tropical forests take up more carbon (C) from the atmosphere per annum by photosynthesis than any other type of vegetation. Phosphorus (P) limitations to C uptake are paramount for tropical and subtropical forests around the globe. Yet the generality of photosynthesis-P relationships underlying these limitations are in question, and hence are not represented well in terrestrial biosphere models. Here we demonstrate the dependence of photosynthesis and underlying processes on both leaf N and P concentrations. The regulation of photosynthetic capacity by P was similar across four continents. Implementing P constraints in the ORCHIDEE-CNP model, gross photosynthesis was reduced by 36% across the tropics and subtropics relative to traditional N constraints and unlimiting leaf P. Our results provide a quantitative relationship for the P dependence for photosynthesis for the front-end of global terrestrial C models that is consistent with canopy leaf measurements.
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| 8. |
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| 10. |
- Unsalan, Ozan, et al.
(författare)
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The Sariçiçek howardite fall in Turkey : Source crater of HED meteorites on Vesta and impact risk of Vestoids
- 2019
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Ingår i: Meteoritics and Planetary Science. - Hoboken : John Wiley & Sons. - 1086-9379 .- 1945-5100. ; 54:5, s. 953-1008
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Tidskriftsartikel (refereegranskat)abstract
- The Sariçiçek howardite meteorite shower consisting of 343 documented stones occurred on September 2, 2015 in Turkey and is the first documented howardite fall. Cosmogenic isotopes show that Sariçiçek experienced a complex cosmic‐ray exposure history, exposed during ~12–14 Ma in a regolith near the surface of a parent asteroid, and that an ~1 m sized meteoroid was launched by an impact 22 ± 2 Ma ago to Earth (as did one‐third of all HED meteorites). SIMS dating of zircon and baddeleyite yielded 4550.4 ± 2.5 Ma and 4553 ± 8.8 Ma crystallization ages for the basaltic magma clasts. The apatite U‐Pb age of 4525 ± 17 Ma, K‐Ar age of ~3.9 Ga, and the U,Th‐He ages of 1.8 ± 0.7 and 2.6 ± 0.3 Ga are interpreted to represent thermal metamorphic and impact‐related resetting ages, respectively. Petrographic; geochemical; and O‐, Cr‐, and Ti‐isotopic studies confirm that Sariçiçek belongs to the normal clan of HED meteorites. Petrographic observations and analysis of organic material indicate a small portion of carbonaceous chondrite material in the Sariçiçek regolith and organic contamination of the meteorite after a few days on soil. Video observations of the fall show an atmospheric entry at 17.3 ± 0.8 km s−1 from NW; fragmentations at 37, 33, 31, and 27 km altitude; and provide a pre‐atmospheric orbit that is the first dynamical link between the normal HED meteorite clan and the inner Main Belt. Spectral data indicate the similarity of Sariçiçek with the Vesta asteroid family (V‐class) spectra, a group of asteroids stretching to delivery resonances, which includes (4) Vesta. Dynamical modeling of meteoroid delivery to Earth shows that the complete disruption of a ~1 km sized Vesta family asteroid or a ~10 km sized impact crater on Vesta is required to provide sufficient meteoroids ≤4 m in size to account for the influx of meteorites from this HED clan. The 16.7 km diameter Antionia impact crater on Vesta was formed on terrain of the same age as given by the 4He retention age of Sariçiçek. Lunar scaling for crater production to crater counts of its ejecta blanket show it was formed ~22 Ma ago.
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| 11. |
- Bruxvoort, K. J., et al.
(författare)
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The Impact of Introducing Malaria Rapid Diagnostic Tests on Fever Case Management: A Synthesis of Ten Studies from the ACT Consortium
- 2017
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Ingår i: Am J Trop Med Hyg. - : American Society of Tropical Medicine and Hygiene. - 0002-9637 .- 1476-1645. ; 97:4, s. 1170-1179
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Tidskriftsartikel (refereegranskat)abstract
- Since 2010, the World Health Organization has been recommending that all suspected cases of malaria be confirmed with parasite-based diagnosis before treatment. These guidelines represent a paradigm shift away from presumptive antimalarial treatment of fever. Malaria rapid diagnostic tests (mRDTs) are central to implementing this policy, intended to target artemisinin-based combination therapies (ACT) to patients with confirmed malaria and to improve management of patients with nonmalarial fevers. The ACT Consortium conducted ten linked studies, eight in sub-Saharan Africa and two in Afghanistan, to evaluate the impact of mRDT introduction on case management across settings that vary in malaria endemicity and healthcare provider type. This synthesis includes 562,368 outpatient encounters (study size range 2,400-432,513). mRDTs were associated with significantly lower ACT prescription (range 8-69% versus 20-100%). Prescribing did not always adhere to malaria test results; in several settings, ACTs were prescribed to more than 30% of test-negative patients or to fewer than 80% of test-positive patients. Either an antimalarial or an antibiotic was prescribed for more than 75% of patients across most settings; lower antimalarial prescription for malaria test-negative patients was partly offset by higher antibiotic prescription. Symptomatic management with antipyretics alone was prescribed for fewer than 25% of patients across all scenarios. In community health worker and private retailer settings, mRDTs increased referral of patients to other providers. This synthesis provides an overview of shifts in case management that may be expected with mRDT introduction and highlights areas of focus to improve design and implementation of future case management programs.
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| 12. |
- Hopkins, H., et al.
(författare)
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Impact of introduction of rapid diagnostic tests for malaria on antibiotic prescribing: analysis of observational and randomised studies in public and private healthcare settings
- 2017
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Ingår i: Bmj-British Medical Journal. - : BMJ. - 1756-1833 .- 0959-8138. ; 356
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES To examine the impact of use of rapid diagnostic tests for malaria on prescribing of antimicrobials, specifically antibiotics, for acute febrile illness in Africa and Asia. Analysis of nine preselected linked and codesigned observational and randomised studies (eight cluster or individually randomised trials and one observational study). Public and private healthcare settings, 2007-13, in Afghanistan, Cameroon, Ghana, Nigeria, Tanzania, and Uganda. Proportions of patients for whom an antibiotic was prescribed in trial groups who had undergone rapid diagnostic testing compared with controls and in patients with negative test results compared with patients with positive results. A secondary aim compared classes of antibiotics prescribed in different settings. Antibiotics were prescribed to 127 052/238 797 (53%) patients in control groups and 167 714/283 683 (59%) patients in intervention groups. Antibiotics were prescribed to 40% (35 505/89 719) of patients with a positive test result for malaria and to 69% (39 400/57 080) of those with a negative result. All but one study showed a trend toward more antibiotic prescribing in groups who underwent rapid diagnostic tests. Random effects meta-analysis of the trials showed that the overall risk of antibiotic prescription was 21% higher (95% confidence interval 7% to 36%) in intervention settings. In most intervention settings, patients with negative test results received more antibiotic prescriptions than patients with positive results for all the most commonly used classes: penicillins, trimethoprim-sulfamethoxazole (one exception), tetracyclines, and metronidazole. Introduction of rapid diagnostic tests for malaria to reduce unnecessary use of antimalarials-a beneficial public health outcome-could drive up untargeted use of antibiotics. That 69% of patients were prescribed antibiotics when test results were negative probably represents overprescription. This included antibiotics from several classes, including those like metronidazole that are seldom appropriate for febrile illness, across varied clinical, health system, and epidemiological settings. It is often assumed that better disease specific diagnostics will reduce antimicrobial overuse, but they might simply shift it from one antimicrobial class to another. Current global implementation of malaria testing might increase untargeted antibiotic use and must be examined.
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| 13. |
- Rifai, Sami W., et al.
(författare)
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ENSO Drives interannual variation of forest woody growth across the tropics
- 2018
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Ingår i: Philosophical Transactions of the Royal Society B: Biological Sciences. - : The Royal Society. - 1471-2970 .- 0962-8436. ; 373:1760
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Tidskriftsartikel (refereegranskat)abstract
- Meteorological extreme events such as El Niño events are expected to affect tropical forest net primary production (NPP) and woody growth, but there has been no large-scale empirical validation of this expectation. We collected a large high-temporal resolution dataset (for 1-13 years depending upon location) of more than 172 000 stem growth measurements using dendrometer bands from across 14 regions spanning Amazonia, Africa and Borneo in order to test how much month-to-month variation in stand-level woody growth of adult tree stems (NPPstem) can be explained by seasonal variation and interannual meteorological anomalies. A key finding is that woody growth responds differently to meteorological variation between tropical forests with a dry season (where monthly rainfall is less than 100 mm), and aseasonal wet forests lacking a consistent dry season. In seasonal tropical forests, a high degree of variation in woody growth can be predicted from seasonal variation in temperature, vapour pressure deficit, in addition to anomalies of soil water deficit and shortwave radiation. The variation of aseasonal wet forest woody growth is best predicted by the anomalies of vapour pressure deficit, water deficit and shortwave radiation. In total, we predict the total live woody production of the global tropical forest biome to be 2.16 Pg C yr-1, with an interannual range 1.96-2.26 Pg C yr-1 between 1996-2016, and with the sharpest declines during the strong El Niño events of 1997/8 and 2015/6. There is high geographical variation in hotspots of El Niño-associated impacts, with weak impacts in Africa, and strongly negative impacts in parts of Southeast Asia and extensive regions across central and eastern Amazonia. Overall, there is high correlation (r = -0.75) between the annual anomaly of tropical forest woody growth and the annual mean of the El Niño 3.4 index, driven mainly by strong correlations with anomalies of soil water deficit, vapour pressure deficit and shortwave radiation.This article is part of the discussion meeting issue 'The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.
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| 14. |
- Rowland, L, et al.
(författare)
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After more than a decade of soil moisture deficit, tropical rainforest trees maintain photosynthetic capacity, despite increased leaf respiration.
- 2015
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 21:12, s. 4662-4672
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Tidskriftsartikel (refereegranskat)abstract
- Determining climate change feedbacks from tropical rainforests requires an understanding of how carbon gain through photosynthesis and loss through respiration will be altered. One of the key changes that tropical rainforests may experience under future climate change scenarios is reduced soil moisture availability. In this study we examine if and how both leaf photosynthesis and leaf dark respiration acclimate following more than 12 years of experimental soil moisture deficit, via a through-fall exclusion experiment (TFE) in an eastern Amazonian rainforest. We find that experimentally drought-stressed trees and taxa maintain the same maximum leaf photosynthetic capacity as trees in corresponding control forest, independent of their susceptibility to drought-induced mortality. We hypothesise that photosynthetic capacity is maintained across all treatments and taxa to take advantage of short-lived periods of high moisture availability, when stomatal conductance (gs ) and photosynthesis can increase rapidly, potentially compensating for reduced assimilate supply at other times. Average leaf dark respiration (Rd ) was elevated in the TFE-treated forest trees relative to the control by 28.2±2.8% (mean ± one standard error). This mean Rd value was dominated by a 48.5±3.6% increase in the Rd of drought-sensitive taxa, and likely reflects the need for additional metabolic support required for stress-related repair, and hydraulic or osmotic maintenance processes. Following soil moisture deficit that is maintained for several years, our data suggest that changes in respiration drive greater shifts in the canopy carbon balance, than changes in photosynthetic capacity. This article is protected by copyright. All rights reserved.
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| 15. |
- Rowland, L, et al.
(författare)
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Death from drought in tropical forests is triggered by hydraulics not carbon starvation.
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 528:7580, s. 119-122
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Tidskriftsartikel (refereegranskat)abstract
- Drought threatens tropical rainforests over seasonal to decadal timescales, but the drivers of tree mortality following drought remain poorly understood. It has been suggested that reduced availability of non-structural carbohydrates (NSC) critically increases mortality risk through insufficient carbon supply to metabolism ('carbon starvation'). However, little is known about how NSC stores are affected by drought, especially over the long term, and whether they are more important than hydraulic processes in determining drought-induced mortality. Using data from the world's longest-running experimental drought study in tropical rainforest (in the Brazilian Amazon), we test whether carbon starvation or deterioration of the water-conducting pathways from soil to leaf trigger tree mortality. Biomass loss from mortality in the experimentally droughted forest increased substantially after >10 years of reduced soil moisture availability. The mortality signal was dominated by the death of large trees, which were at a much greater risk of hydraulic deterioration than smaller trees. However, we find no evidence that the droughted trees suffered carbon starvation, as their NSC concentrations were similar to those of non-droughted trees, and growth rates did not decline in either living or dying trees. Our results indicate that hydraulics, rather than carbon starvation, triggers tree death from drought in tropical rainforest.
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| 16. |
- Esbjörnsson, Joakim, et al.
(författare)
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HIV-2 as a model to identify a functional HIV cure
- 2019
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Ingår i: AIDS Research and Therapy. - : Springer Science and Business Media LLC. - 1742-6405. ; 16:1
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Forskningsöversikt (refereegranskat)abstract
- Two HIV virus types exist: HIV-1 is pandemic and aggressive, whereas HIV-2 is confined mainly to West Africa and less pathogenic. Despite the fact that it has been almost 40 years since the discovery of AIDS, there is still no cure or vaccine against HIV. Consequently, the concepts of functional vaccines and cures that aim to limit HIV disease progression and spread by persistent control of viral replication without life-long treatment have been suggested as more feasible options to control the HIV pandemic. To identify virus-host mechanisms that could be targeted for functional cure development, researchers have focused on a small fraction of HIV-1 infected individuals that control their infection spontaneously, so-called elite controllers. However, these efforts have not been able to unravel the key mechanisms of the infection control. This is partly due to lack in statistical power since only 0.15% of HIV-1 infected individuals are natural elite controllers. The proportion of long-Term viral control is larger in HIV-2 infection compared with HIV-1 infection. We therefore present the idea of using HIV-2 as a model for finding a functional cure against HIV. Understanding the key differences between HIV-1 and HIV-2 infections, and the cross-reactive effects in HIV-1/HIV-2 dual-infection could provide novel insights in developing functional HIV cures and vaccines.
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| 17. |
- Hoencamp, Claire, et al.
(författare)
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3D genomics across the tree of life reveals condensin II as a determinant of architecture type
- 2021
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 372:6545, s. 984-989
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Tidskriftsartikel (refereegranskat)abstract
- We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.
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| 18. |
- James, Katherine L., et al.
(författare)
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Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma
- 2019
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Ingår i: Journal of Virology. - 1098-5514. ; 93:1
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Tidskriftsartikel (refereegranskat)abstract
- Accurate determination of the genetic diversity present in the HIV quasispecies is critical for the development of a preventative vaccine: in particular, little is known about viral genetic diversity for the second type of HIV, HIV-2. A better understanding of HIV-2 biology is relevant to the HIV vaccine field because a substantial proportion of infected people experience long-term viral control, and prior HIV-2 infection has been associated with slower HIV-1 disease progression in coinfected subjects. The majority of traditional and next-generation sequencing methods have relied on target amplification prior to sequencing, introducing biases that may obscure the true signals of diversity in the viral population. Additionally, target enrichment through PCR requires a priori sequence knowledge, which is lacking for HIV-2. Therefore, a target enrichment free method of library preparation would be valuable for the field. We applied an RNA shotgun sequencing (RNA-Seq) method without PCR amplification to cultured viral stocks and patient plasma samples from HIV-2-infected individuals. Libraries generated from total plasma RNA were analyzed with a two-step pipeline: (i) de novo genome assembly, followed by (ii) read remapping. By this approach, whole-genome sequences were generated with a 28× to 67× mean depth of coverage. Assembled reads showed a low level of GC bias, and comparison of the genome diversities at the intrahost level showed low diversity in the accessory gene vpx in all patients. Our study demonstrates that RNA-Seq is a feasible full-genome de novo sequencing method for blood plasma samples collected from HIV-2-infected individuals.IMPORTANCE An accurate picture of viral genetic diversity is critical for the development of a globally effective HIV vaccine. However, sequencing strategies are often complicated by target enrichment prior to sequencing, introducing biases that can distort variant frequencies, which are not easily corrected for in downstream analyses. Additionally, detailed a priori sequence knowledge is needed to inform robust primer design when employing PCR amplification, a factor that is often lacking when working with tropical diseases localized in developing countries. Previous work has demonstrated that direct RNA shotgun sequencing (RNA-Seq) can be used to circumvent these issues for hepatitis C virus (HCV) and norovirus. We applied RNA-Seq to total RNA extracted from HIV-2 blood plasma samples, demonstrating the applicability of this technique to HIV-2 and allowing us to generate a dynamic picture of genetic diversity over the whole genome of HIV-2 in the context of low-bias sequencing.
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| 19. |
- Jenniskens, Peter, et al.
(författare)
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Fall, recovery, and characterization of the Novato L6 chondrite breccia
- 2014
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Ingår i: Meteoritics and Planetary Science. - : Wiley. - 1086-9379. ; 49:8, s. 1388-1425
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Tidskriftsartikel (refereegranskat)abstract
- The Novato L6 chondrite fragmental breccia fell in California on 17 October 2012, and was recovered after the Cameras for Allsky Meteor Surveillance (CAMS) project determined the meteor's trajectory between 95 and 46 km altitude. The final fragmentation from 42 to 22 km altitude was exceptionally well documented by digital photographs. The first sample was recovered before rain hit the area. First results from a consortium study of the meteorite's characterization, cosmogenic and radiogenic nuclides, origin, and conditions of the fall are presented. Some meteorites did not retain fusion crust and show evidence of spallation. Before entry, the meteoroid was 35 +/- 5 cm in diameter (mass 80 +/- 35 kg) with a cosmic-ray exposure age of 9 +/- 1 Ma, if it had a one-stage exposure history. A two-stage exposure history is more likely, with lower shielding in the last few Ma. Thermoluminescence data suggest a collision event within the last similar to 0.1 Ma. Novato probably belonged to the class of shocked L chondrites that have a common shock age of 470 Ma, based on the U, Th-He age of 420 +/- 220 Ma. The measured orbits of Novato, Jesenice, and Innisfree are consistent with a proposed origin of these shocked L chondrites in the Gefion asteroid family, perhaps directly via the 5: 2 mean-motion resonance with Jupiter. Novato experienced a stronger compaction than did other L6 chondrites of shock-stage S4. Despite this, a freshly broken surface shows a wide range of organic compounds.
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| 20. |
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| 21. |
- Stolper, E.M., et al.
(författare)
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The petrochemistry of Jake_M : A martian mugearite
- 2013
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 341:6153
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Tidskriftsartikel (refereegranskat)abstract
- “Jake_M,” the first rock analyzed by the Alpha Particle X-ray Spectrometer instrument on the Curiosity rover, differs substantially in chemical composition from other known martian igneous rocks: It is alkaline (>15% normative nepheline) and relatively fractionated. Jake_M is compositionally similar to terrestrial mugearites, a rock type typically found at ocean islands and continental rifts. By analogy with these comparable terrestrial rocks, Jake_M could have been produced by extensive fractional crystallization of a primary alkaline or transitional magma at elevated pressure, with or without elevated water contents. The discovery of Jake_M suggests that alkaline magmas may be more abundant on Mars than on Earth and that Curiosity could encounter even more fractionated alkaline rocks (for example, phonolites and trachytes).
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| 22. |
- Welsh, Joshua A., et al.
(författare)
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Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches
- 2024
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Ingår i: Journal of Extracellular Vesicles. - : John Wiley and Sons Inc. - 2001-3078. ; 13:2
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Tidskriftsartikel (refereegranskat)abstract
- Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its ‘Minimal Information for Studies of Extracellular Vesicles’, which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly.
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| 23. |
- Andrews, Sophie M., et al.
(författare)
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Analysis of HIV-1 envelope evolution suggests antibody-mediated selection of common epitopes among Chinese former plasma donors from a narrow-source outbreak
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- The HIV-1 envelope mutates rapidly to evade recognition and killing, and is a major target of humoral immune responses and vaccine development. Identification of common epitopes for vaccine development have been complicated by genetic variation on both virus and host levels. We studied HIV-1 envelope gp120 evolution in 12 Chinese former plasma donors infected with a purportedly single founder virus, with the aim of identifying common antibody epitopes under immune selection. We found five amino acid sites under significant positive selection in ≥50% of the study participants, and 22 sites consistent with antibody-mediated selection. Despite strong selection pressure, some sites housed a limited repertoire of amino acids. Structural modelling revealed that most of the variable amino acid sites were located on the exposed distal edge of the Gp120 trimer, whilst invariant sites clustered within the centre of the protein complex. Two sites, flanking the V3 hypervariable loop, represent novel antibody sites. Analysis of HIV-1 evolution in hosts infected with a narrow-source virus may provide insight and novel understanding of common epitopes under antibody-mediated selection. If verified in functional studies, such epitopes could be suitable as targets in vaccine development.
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| 24. |
- Baker, Naomi L., et al.
(författare)
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Molecular consequences of dominant Bethlem myopathy collagen VI mutations
- 2007
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Ingår i: Annals of Neurology. - : Wiley. - 1531-8249 .- 0364-5134. ; 62:4, s. 390-405
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Tidskriftsartikel (refereegranskat)abstract
- Objective: Dominant mutations in the three collagen VI genes cause Bethlem myopathy, a disorder characterized by proximal muscle weakness and commonly contractures of the fingers, wrists, and ankles. Although more than 20 different dominant mutations have been identified in Bethlem myopathy patients, the biosynthetic consequences of only a subset of these have been studied, and in many cases, the pathogenic mechanisms remain unknown. Methods: We have screened fourteen Bethlem myopathy patients for collagen VI mutations and performed detailed analyses of collagen VI biosynthesis and intracellular and extracellular assembly. Results: Collagen VI abnormalities were identified in eight patients. One patient produced around half the normal amount of alpha 1(VI) messenger RNA and reduced amounts of collagen VI protein. Two patients had a previously reported mutation causing skipping of COL6A1 exon 14, and three patients had novel mutations leading to in-frame deletions toward the N-terminal end of the triple-helical domain. These mutations have different and complex effects on collagen VI intracellular and extracellular assembly. Two patients had single amino acid substitutions in the A-domains of COL6A2 and COL6A3. Collagen VI intracellular and extracellular assembly was normal in one of these patients. Interpretation: The key to dissecting the pathogenic mechanisms of collagen VI mutations lies in detailed analysis of collagen VI biosynthesis and assembly. The majority of mutations result in secretion and deposition of structurally abnormal collagen VI. However, one A-domain mutation had no detectable effect on assembly, suggesting that it acts by compromising collagen VI interactions in the extracellular matrix of muscle.
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| 25. |
- Bartholomew, David, et al.
(författare)
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Bornean tropical forests recovering from logging at risk of regeneration failure
- 2024
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Ingår i: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 30:3
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Tidskriftsartikel (refereegranskat)abstract
- Active restoration through silvicultural treatments (enrichment planting, cutting climbers and liberation thinning) is considered an important intervention in logged forests. However, its ability to enhance regeneration is key for long-term recovery of logged forests, which remains poorly understood, particularly for the production and survival of seedlings in subsequent generations. To understand the long-term impacts of logging and restoration we tracked the diversity, survival and traits of seedlings that germinated immediately after a mast fruiting in North Borneo in unlogged and logged forests 30–35 years after logging. We monitored 5119 seedlings from germination for ~1.5 years across a mixed landscape of unlogged forests (ULs), naturally regenerating logged forests (NR) and actively restored logged forests via rehabilitative silvicultural treatments (AR), 15–27 years after restoration. We measured 14 leaf, root and biomass allocation traits on 399 seedlings from 15 species. Soon after fruiting, UL and AR forests had higher seedling densities than NR forest, but survival was the lowest in AR forests in the first 6 months. Community composition differed among forest types; AR and NR forests had lower species richness and lower evenness than UL forests by 5–6 months post-mast but did not differ between them. Differences in community composition altered community-weighted mean trait values across forest types, with higher root biomass allocation in NR relative to UL forest. Traits influenced mortality ~3 months post-mast, with more acquisitive traits and relative aboveground investment favoured in AR forests relative to UL forests. Our findings of reduced seedling survival and diversity suggest long time lags in post-logging recruitment, particularly for some taxa. Active restoration of logged forests recovers initial seedling production, but elevated mortality in AR forests lowers the efficacy of active restoration to enhance recruitment or diversity of seedling communities. This suggests current active restoration practices may fail to overcome barriers to regeneration in logged forests, which may drive long-term changes in future forest plant communities.
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| 26. |
- Bartholomew, David, et al.
(författare)
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Differential nutrient limitation and tree height control leaf physiology, supporting niche partitioning in tropical dipterocarp forests
- 2022
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Ingår i: Functional Ecology. - : John Wiley & Sons. - 0269-8463 .- 1365-2435. ; 36:8, s. 2084-2103
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Tidskriftsartikel (refereegranskat)abstract
- 1. Revealing the mechanisms of environmental niche partitioning within lowland tropical forests is important for understanding the drivers of current species distributions and potential vulnerability to environmental change. Tropical forest structure and species composition change across edaphic gradients in Borneo over short distances. However, our understanding of how edaphic conditions affect tree physiology and whether these relationships drive niche partitioning within Bornean forests remains incomplete.2. This study evaluated how leaf physiological function changes with nutrient availability across a fine-scale edaphic gradient and whether these relationships vary according to tree height. Furthermore, we tested whether intraspecific leaf trait variation allows generalist species to populate a wider range of environments.3. We measured leaf traits of 218 trees ranging in height from 4 to 66 m from 13 dipterocarp species within four tropical forest types (alluvial, mudstone, sandstone and kerangas) occurring along an <5 km edaphic gradient in North Borneo. The traits measured included saturating photosynthesis (Asat), maximum photosynthetic capacity (Vcmax), leaf dark respiration (Rleaf), leaf mass per area (LMA), leaf thickness, minimum stomatal conductance (gdark) and leaf nutrient concentrations (N, P, Ca, K and Mg).4. Across all species, leaf traits varied consistently in response to soil nutrient availability across forest types except Rleaf_mass, [Mg]leaf and [Ca]leaf. Changes in photosynthesis and respiration rates were related to different leaf nutrients across forest types, with greater nutrient-use efficiency in more nutrient-poor environments. Generalist species partially or fully compensated reductions in mass-based photosynthesis through increasing LMA in more nutrient-poor environments.5. Leaf traits also varied with tree height, except Vcmax_mass, but only in response to height-related modifications of leaf morphology (LMA and leaf thickness). These height–trait relationships did not vary across the edaphic gradient, except for Asat, [N]leaf, [P]leaf and [K]leaf.6. Our results highlight that modification of leaf physiological function and morphology act as important adaptations for Bornean dipterocarps in response to edaphic and vertical environmental gradients. Meanwhile, multiple nutrients appear to contribute to niche partitioning and could drive species distributions and high biodiversity within Bornean forest landscapes. Read the free Plain Language Summary for this article on the Journal blog.
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| 27. |
- Boswell, M. T., et al.
(författare)
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Intrahost evolution of the HIV-2 capsid correlates with progression to AIDS
- 2022
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Ingår i: Virus Evolution. - : Oxford University Press (OUP). - 2057-1577. ; 8:2
-
Tidskriftsartikel (refereegranskat)abstract
- HIV-2 infection will progress to AIDS in most patients without treatment, albeit at approximately half the rate of HIV-1 infection. HIV-2 capsid (p26) amino acid polymorphisms are associated with lower viral loads and enhanced processing of T cell epitopes, which may lead to protective Gag-specific T cell responses common in slower progressors. Lower virus evolutionary rates, and positive selection on conserved residues in HIV-2 env have been associated with slower progression to AIDS. In this study we analysed 369 heterochronous HIV-2 p26 sequences from 12 participants with a median age of 30 years at enrolment. CD4% change over time was used to stratify participants into relative faster and slower progressor groups. We analysed p26 sequence diversity evolution, measured site-specific selection pressures and evolutionary rates, and determined if these evolutionary parameters were associated with progression status. Faster progressors had lower CD4% and faster CD4% decline rates. Median pairwise sequence diversity was higher in faster progressors (5.7x10-3 versus 1.4x10-3 base substitutions per site, P<0.001). p26 evolved under negative selection in both groups (dN/dS=0.12). Median virus evolutionary rates were higher in faster than slower progressors – synonymous rates: 4.6x10-3 vs. 2.3x10-3; and nonsynonymous rates: 6.9x10-4 vs. 2.7x10-4 substitutions/site/year, respectively. Virus evolutionary rates correlated negatively with CD4% change rates (ρ = -0.8, P=0.02), but not CD4% level. The signature amino acid at p26 positions 6, 12 and 119 differed between faster (6A, 12I, 119A) and slower (6G, 12V, 119P) progressors. These amino acid positions clustered near to the TRIM5α/p26 hexamer interface surface. p26 evolutionary rates were associated with progression to AIDS and were mostly driven by synonymous substitutions. Nonsynonymous evolutionary rates were an order of magnitude lower than synonymous rates, with limited amino acid sequence evolution over time within hosts. These results indicate HIV-2 p26 may be an attractive therapeutic target.
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| 28. |
- Bray, Lucy, et al.
(författare)
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Developing rights-based standards for children having tests, treatments, examinations and interventions : using a collaborative, multi-phased, multi-method and multi-stakeholder approach to build consensus
- 2023
-
Ingår i: European Journal of Pediatrics. - : Springer Nature. - 0340-6199 .- 1432-1076.
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Tidskriftsartikel (refereegranskat)abstract
- Children continue to experience harm when undergoing clinical procedures despite increased evidence of the need to improve the provision of child-centred care. The international ISupport collaboration aimed to develop standards to outline and explain good procedural practice and the rights of children within the context of a clinical procedure. The rights-based standards for children undergoing tests, treatments, investigations, examinations and interventions were developed using an iterative, multi-phased, multi-method and multi-stakeholder consensus building approach. This consensus approach used a range of online and face to face methods across three phases to ensure ongoing engagement with multiple stakeholders. The views and perspectives of 203 children and young people, 78 parents and 418 multi-disciplinary professionals gathered over a two year period (2020–2022) informed the development of international rights-based standards for the care of children having tests, treatments, examinations and interventions. The standards are the first to reach international multi-stakeholder consensus on definitions of supportive and restraining holds.Conclusion: This is the first study of its kind which outlines international rights-based procedural care standards from multi-stakeholder perspectives. The standards offer health professionals and educators clear evidence-based tools to support discussions and practice changes to challenge prevailing assumptions about holding or restraining children and instead encourage a focus on the interests and rights of the child.What is Known:• Children continue to experience short and long-term harm when undergoing clinical procedures despite increased evidence of the need to improve the provision of child-centred care.• Professionals report uncertainty and tensions in applying evidence-based practice to children’s procedural care. What is New:• This is the first study of its kind which has developed international rights-based procedural care standards from multi-stakeholder perspectives.• The standards are the first to reach international multi-stakeholder consensus on definitions of supportive and restraining holds.
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| 29. |
- Cuthill, Innes C., et al.
(författare)
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The biology of color
- 2017
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 357:6350
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Forskningsöversikt (refereegranskat)abstract
- Coloration mediates the relationship between an organism and its environment in important ways, including social signaling, antipredator defenses, parasitic exploitation, thermoregulation, and protection from ultraviolet light, microbes, and abrasion. Methodological breakthroughs are accelerating knowledge of the processes underlying both the production of animal coloration and its perception, experiments are advancing understanding of mechanism and function, and measurements of color collected noninvasively and at a global scale are opening windows to evolutionary dynamics more generally. Here we provide a roadmap of these advances and identify hitherto unrecognized challenges for this multi- and interdisciplinary field.
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| 30. |
- Esbjörnsson, Joakim, et al.
(författare)
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Long-term follow-up of HIV-2-related AIDS and mortality in Guinea-Bissau : a prospective open cohort study
- 2019
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Ingår i: The Lancet HIV. - : The Lancet Publishing Group. - 2405-4704 .- 2352-3018. ; 6:1, s. E25-E31
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: HIV type 2 (HIV-2) is considered more benign and has fewer pathogenic consequences than HIV type 1 (HIV-1) for most infected individuals. However, reliable estimates of time to AIDS and mortality among those with HIV-2 infection are absent. We therefore aimed to compare the time to AIDS and mortality, and the CD4 T-cell dynamics between those infected with HIV-1 and HIV-2.METHODS: We did a prospective open cohort study. We included all police officers with regular employment from police stations in both urban and rural areas of Guinea-Bissau since Feb 6, 1990. We continued to include participants until Sept 28, 2009, and follow-up of HIV-1-positive and HIV-2-positive individuals continued until Sept 28, 2013. We collected blood samples at enrolment and at scheduled annual follow-up visits at police stations. We analysed longitudinal data from individuals infected with HIV-1 and HIV-2 according to time to AIDS, time to death, and T-cell dynamics. Time of HIV infection was estimated as the mid-timepoint between last HIV-seronegative and first HIV-seropositive sample. Data from an additional 2984 HIV-uninfected individuals from the same population were analysed to assess the effect of natural mortality on HIV-related mortality.FINDINGS: 872 participants tested HIV positive during the 23-year study period: 408 were infected with HIV-1 (183 infected before and 225 infected after enrolment) and 464 were infected with HIV-2 (377 before and 87 after enrolment). The median time from HIV infection to development of AIDS was 6·2 years (95% CI 5·4-7·1) for HIV-1 infection and 14·3 years (10·7-18·0) for HIV-2 infection (p<0·0001). The median survival time after HIV infection was 8·2 years (95% CI 7·5-8·9) for HIV-1 infection and 15·6 years (12·0-19·2) for HIV-2 infection (p<0·0001). Individuals who were infected with HIV-1 or HIV-2 before enrolment showed similar results. Comparison with uninfected individuals indicated limited confounding contribution from natural mortality. Mean CD4 percentages were higher in individuals with HIV-2 than in those with HIV-1 during early infection (28·0% [SE 1·3] vs 22·3% [1·7]; p=0·00094) and declined at a slower rate (0·4% [0·2] vs 0·9% [0·2] per year; p=0·028). HIV-2-infected individuals developed clinical AIDS at higher mean CD4 percentages (18·2%, IQR 7·2-25·4) than HIV-1-infected individuals (8·2%, 3·0-13·8; p<0·0001).INTERPRETATION: Our results show that both HIV-1-infected and HIV-2-infected individuals have a high probability of developing and dying from AIDS without antiretroviral treatment.
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| 31. |
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| 32. |
- Girardin, Cécile A J, et al.
(författare)
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Seasonal trends of Amazonian rainforest phenology, net primary productivity, and carbon allocation
- 2016
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Ingår i: Global Biogeochemical Cycles. - 0886-6236. ; 30:5, s. 700-715
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Tidskriftsartikel (refereegranskat)abstract
- The seasonality of solar irradiance and precipitation may regulate seasonal variations in tropical forests carbon cycling. Controversy remains over their importance as drivers of seasonal dynamics of net primary productivity in tropical forests. We use ground data from nine lowland Amazonian forest plots collected over 3 years to quantify the monthly primary productivity (NPP) of leaves, reproductive material, woody material, and fine roots over an annual cycle. We distinguish between forests that do not experience substantial seasonal moisture stress (“humid sites”) and forests that experience a stronger dry season (“dry sites”). We find that forests from both precipitation regimes maximize leaf NPP over the drier season, with a peak in production in August at both humid (mean 0.39 ± 0.03 Mg C ha−1 month−1 in July, n = 4) and dry sites (mean 0.49 ± 0.03 Mg C ha−1 month−1 in September, n = 8). We identify two distinct seasonal carbon allocation patterns (the allocation of NPP to a specific organ such as wood leaves or fine roots divided by total NPP). The forests monitored in the present study show evidence of either (i) constant allocation to roots and a seasonal trade-off between leaf and woody material or (ii) constant allocation to wood and a seasonal trade-off between roots and leaves. Finally, we find strong evidence of synchronized flowering at the end of the dry season in both precipitation regimes. Flower production reaches a maximum of 0.047 ± 0.013 and 0.031 ± 0.004 Mg C ha−1 month−1 in November, in humid and dry sites, respectively. Fruitfall production was staggered throughout the year, probably reflecting the high variation in varying times to development and loss of fruit among species.
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| 33. |
- Guarin, Jose Rafael, et al.
(författare)
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Impacts of tropospheric ozone and climate change on Mexico wheat production
- 2019
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Ingår i: Climatic Change. - : Springer Science and Business Media LLC. - 1573-1480 .- 0165-0009. ; 155:2, s. 157-174
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Tidskriftsartikel (refereegranskat)abstract
- Wheat is an important staple crop sensitive to negative effects from elevated tropospheric ozone (O 3 ) concentrations, but the impacts of future O 3 concentrations on wheat production in Mexico are unknown. To determine these impacts, the O 3 -modified DSSAT-NWheat crop model was used to simulate wheat production in Mexico using a baseline scenario with pre-industrial O 3 concentrations from 1980 to 2010 and five Global Climate Models (GCMs) under the Representative Concentration Pathway (RCP) 8.5 scenario from 2041 to 2070 paired with future O 3 concentrations from the European Monitoring and Evaluation Programme (EMEP) Meteorological Synthesizing Centre–West (MSC-W) model. Thirty-two representative major wheat-producing locations in Mexico were simulated assuming both irrigated and rainfed conditions for two O 3 sensitivity cultivar classifications. The simulations showed large variability (after averaging over 30 years) in yield loss, ranging from 7 to 26% because of O 3 impact, depending on the location, irrigation, and climate change emissions scenario. After upscaling and aggregating the simulations to the country scale based on observed irrigated and rainfed production, national wheat production for Mexico is expected to decline by 12% under the future RCP 8.5 climate change scenario with additional losses of 7 to 18% because of O 3 impact, depending on the cultivar O 3 sensitivity. This yield loss caused by O 3 is comparable with, or even larger than, the impact from projected future climatic change in temperature, rainfall, and atmospheric CO 2 concentration. Therefore, O 3 impacts should be considered in future agricultural impact assessments.
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| 34. |
- Harper, Anna B., et al.
(författare)
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Improvement of modeling plant responses to low soil moisture in JULESvn4.9 and evaluation against flux tower measurements
- 2021
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Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 14:6, s. 3269-3294
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Tidskriftsartikel (refereegranskat)abstract
- Drought is predicted to increase in the future due to climate change, bringing with it myriad impacts on ecosystems. Plants respond to drier soils by reducing stomatal conductance in order to conserve water and avoid hydraulic damage. Despite the importance of plant drought responses for the global carbon cycle and local and regional climate feedbacks, land surface models are unable to capture observed plant responses to soil moisture stress. We assessed the impact of soil moisture stress on simulated gross primary productivity (GPP) and latent energy flux (LE) in the Joint UK Land Environment Simulator (JULES) vn4.9 on seasonal and annual timescales and evaluated 10 different representations of soil moisture stress in the model. For the default configuration, GPP was more realistic in temperate biome sites than in the tropics or high-latitude (cold-region) sites, while LE was best simulated in temperate and high-latitude (cold) sites. Errors that were not due to soil moisture stress, possibly linked to phenology, contributed to model biases for GPP in tropical savanna and deciduous forest sites. We found that three alternative approaches to calculating soil moisture stress produced more realistic results than the default parameterization for most biomes and climates. All of these involved increasing the number of soil layers from 4 to 14 and the soil depth from 3.0 to 10.8 m. In addition, we found improvements when soil matric potential replaced volumetric water content in the stress equation (the "soil14_psi" experiments), when the critical threshold value for inducing soil moisture stress was reduced ("soil14_p0"), and when plants were able to access soil moisture in deeper soil layers ("soil14_dr&z.ast;2"). For LE, the biases were highest in the default configuration in temperate mixed forests, with overestimation occurring during most of the year. At these sites, reducing soil moisture stress (with the new parameterizations mentioned above) increased LE and increased model biases but improved the simulated seasonal cycle and brought the monthly variance closer to the measured variance of LE. Further evaluation of the reason for the high bias in LE at many of the sites would enable improvements in both carbon and energy fluxes with new parameterizations for soil moisture stress. Increasing the soil depth and plant access to deep soil moisture improved many aspects of the simulations, and we recommend these settings in future work using JULES or as a general way to improve land surface carbon and water fluxes in other models. In addition, using soil matric potential presents the opportunity to include plant functional type-specific parameters to further improve modeled fluxes.
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| 35. |
- James, M. O., et al.
(författare)
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Properties and regional expression of a CYP3A-like protein in channel catfish intestine
- 2005
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Ingår i: Aquatic Toxicology. - : Elsevier BV. - 0166-445X. ; 72:4, s. 361-371
-
Tidskriftsartikel (refereegranskat)abstract
- Biotransformation in the intestine may influence the bioavailability and toxicity of ingested xenobiotics. The objective of this study was to examine the expression and catalytic properties of a constitutive cytochrome P450 (CYP) 3A-like protein along the intestine of channel catfish, Ictalurus punctatus. Fish were maintained on commercial chow or nutritionally complete semi-purified diets. Polyclonal antibodies generated against rainbow trout CYP3A proteins reacted strongly with catfish washed intestinal microsomes on Western blots showing a major protein band with MW of 59 kDa. In catfish maintained on a standard chow diet, the expression of this protein was higher in the proximal segment (0.101 &PLUSMN; 0.031 units/mg protein, mean &PLUSMN; S.D., n = 4) than in the distal part (0.032 &PLUSMN; 0.023 units/mg protein). Microsomal testosterone 6β-hydroxylation activity was monitored as the catalytic indicator of CYP3A, and was higher in proximal than distal catfish intestine (263 &PLUSMN; 80.3 and 88.6 &PLUSMN; 15.6 pmol/min/mg protein for proximal and distal, respectively, mean S.D., n = 4). CYP3A protein levels and testosterone 6β-hydroxylation activities were lower in microsomes from the proximal segment of intestine from catfish maintained on a semi-purified diet, compared with commercial chow, but again the proximal intestine had higher CYP3A and 6β-hydroxylase activities than distal intestine. Testosterone 6β-hydroxylase activities in all samples correlated with the CYP3A protein levels, r(2) = 0.8. Testosterone 6β-hydroxylation was inhibited by specific CYP3A inhibitors, ketoconazole (IC50 = 0.02 μ M) and erythromycin (IC50 = 41 μ M), as well as general CYP inhibitors, metyrapone (IC50 = 2.8 μ M) and SKF-525A (IC50 = 25 μ M). There was evidence for the involvement of CYP3A in the mono-oxygenation of benzo(a)pyrene and of (-)-benzo(a)pyrene-7,8-dihydrodiol in intestinal microsomes from catfish maintained on the semi-purified diet. Mono-oxygenation of both substrates was increased in a concentration-dependent manner by in vitro addition of a-naphthoflavone. Benzo(a)pyrene hydroxylase activities were higher in proximal than in distal intestine; 3.72 &PLUSMN; 0.77 pmol/min/mg protein, mean &PLUSMN; S.D., n = 5 and 1.45 &PLUSMN; 0.42 in these respective segments. The results of this study strongly suggest that CYP3A is important in the first pass metabolism of dietary xenobiotics in untreated fish. © 2005 Elsevier B.V. All rights reserved.
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| 36. |
- Jenniskens, Peter, et al.
(författare)
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The Creston, California, meteorite fall and the origin of L chondrites
- 2019
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Ingår i: Meteoritics and Planetary Science. - : John Wiley & Sons. - 1086-9379 .- 1945-5100. ; 54:4, s. 699-720
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Tidskriftsartikel (refereegranskat)abstract
- It has been proposed that all L chondrites resulted from an ongoing collisional cascade of fragments that originated from the formation of the ~500 Ma old asteroid family Gefion, located near the 5:2 mean‐motion resonance with Jupiter in the middle Main Belt. If so, L chondrite pre‐atmospheric orbits should be distributed as expected for that source region. Here, we present contradictory results from the orbit and collisional history of the October 24, 2015, L6 ordinary chondrite fall at Creston, CA (here reclassified to L5/6). Creston's short 1.30 ± 0.02 AU semimajor axis orbit would imply a long dynamical evolution if it originated from the middle Main Belt. Indeed, Creston has a high cosmic ray exposure age of 40–50 Ma. However, Creston's small meteoroid size and low 4.23 ± 0.07° inclination indicate a short dynamical lifetime against collisions. This suggests, instead, that Creston originated most likely in the inner asteroid belt and was delivered via the ν6 resonance. The U‐Pb systematics of Creston apatite reveals a Pb‐Pb age of 4,497.1 ± 3.7 Ma, and an upper intercept U‐Pb age of 4,496.7 ± 5.8 Ma (2σ), circa 70 Ma after formation of CAI, as found for other L chondrites. The K‐Ar (age ~4.3 Ga) and U,Th‐He (age ~1 Ga) chronometers were not reset at ~500 Ma, while the lower intercept U‐Pb age is poorly defined as 770 ± 320 Ma. So far, the three known L chondrites that impacted on orbits with semimajor axes a <2.0 AU all have high (>3 Ga) K‐Ar ages. This argues for a source of some of our L chondrites in the inner Main Belt. Not all L chondrites originate in a continuous population of Gefion family debris stretching across the 3:1 mean‐motion resonance.
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| 37. |
- Kimberling, W. J., et al.
(författare)
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Linkage of Usher syndrome type I gene (USH1B) to the long arm of chromosome 11
- 1992
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Ingår i: Genomics. - 0888-7543 .- 1089-8646. ; 14:4, s. 988-994
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Tidskriftsartikel (refereegranskat)abstract
- Usher syndrome is the most commonly recognized cause of combined visual and hearing loss in technologically developed countries. There are several different types and all are inherited in an autosomal recessive manner. There may be as many as five different genes responsible for at least two closely related phenotypes. The nature of the gene defects is unknown, and positional cloning strategies are being employed to identify the genes. This is a report of the localization of one gene for Usher syndrome type I to chromosome 11q, probably distal to marker D11S527. Another USH1 gene had been previously localized to chromosome 14q, and this second localization establishes the existence of a new and independent locus for Usher syndrome.
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| 38. |
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| 39. |
- Palm, Angelica A., et al.
(författare)
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Low Postseroconversion CD4+ T-cell Level Is Associated with Faster Disease Progression and Higher Viral Evolutionary Rate in HIV-2 Infection
- 2019
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Ingår i: mBio. - 2161-2129. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- A positive correlation between virus evolutionary rate and disease progression has been shown for human immunodeficiency virus type 1 (HIV-1) infection. Much less is known about HIV-2, the second causative agent of AIDS. We analyzed 528 HIV-2 env V1-C3 sequences generated from longitudinal plasma samples that were collected from 16 study participants during a median observation time of 7.9 years (interquartile range [IQR], 5.2 to 14.0 years). Study participants were classified as faster or slower disease progressors based on longitudinal CD4+ T-cell data. The HIV-2 evolutionary rate was significantly associated with CD4+ T-cell levels and was almost twice as high among the faster progressors as among the slower progressors. Higher evolutionary rates were accounted for by both synonymous and nonsynonymous nucleotide substitutions. Moreover, slow disease progression was associated with stronger positive selection on HIV-2/SIVsm (simian immunodeficiency virus infecting sooty mangabey) surface-exposed conserved residues. This study demonstrated a number of previously unknown characteristics linking HIV-2 disease progression with virus evolution. Some of these findings distinguish HIV-2 from HIV-1 and may contribute to the understanding of differences in pathogenesis.IMPORTANCE The relationship between HIV evolution and disease progression is fundamental to our understanding of HIV immune control and vaccine design. There are no clear definitions for faster and slower HIV-2 disease progression and for the relationship of the rate of progression with HIV-2 evolution. To address the hypothesis that viral evolution is correlated with disease progression in HIV-2 infection, we determined faster and slower disease progression based on follow-up data from a prospective cohort of police officers in Guinea-Bissau. The analysis showed that although the CD4+ T-cell level and the decline in the level were independently associated with progression to AIDS, only the CD4+ T-cell level or a combined CD4+ T-cell level/decline stratification was associated with the rate of HIV-2 evolution. The HIV-2 evolutionary rate was almost twice as high among the faster progressors as among the slower progressors. Importantly, this report defines previously unknown characteristics linking HIV-2 disease progression with virus evolution.
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| 40. |
- Ponticorvo, Adrien, et al.
(författare)
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Quantitative long term measurements of burns in a rat model using spatial frequency domain imaging and laser speckle imaging (Conference Presentation)
- 2016
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Ingår i: Proceedings Volume 9711, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues IX; 971102 (2016). - : SPIE - International Society for Optical Engineering.
-
Konferensbidrag (refereegranskat)abstract
- The ability to accurately assess burn wound severity in a timely manner is a critical component of wound management as it dictates the course of treatment. While full thickness and superficial burns can be easily diagnosed through visual inspection, burns that fall in between these categories are difficult to classify. Additionally, the ability to better quantify different stages of wound healing from a burn of any severity would be important for evaluating the efficacy of different treatment options. Here we present a longitudinal (28 day) study that employs spatial frequency domain imaging (SFDI) and laser speckle imaging (LSI) as non-invasive technologies to characterize in-vivo burn wounds and healing in a murine model. Burn wounds were created using an established technique of a brass comb heated to a given temperature and applied for a set amount of time. They were imaged immediately after the initial injury and then at 2, 4, 7, 14, 21, and 28 days following the injury. Biopsies were taken on the day of the injury in order to verify the extent of the burn damage as well as at different time points after the injury in order to visualize different stages of inflammation and healing. The results of this study suggest that the reduced scattering coefficient measured using SFDI and blood flow as measured using LSI have the potential to provide useful metrics for quantifying the severity of burn injuries as well as track the different stages associated with wound healing progression.
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| 41. |
- Rowland, Lucy, et al.
(författare)
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Shock and stabilisation following long-term drought in tropical forest from 15 years of litterfall dynamics
- 2018
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Ingår i: Journal of Ecology. - : Wiley. - 0022-0477 .- 1365-2745. ; 106:4, s. 1673-1682
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Tidskriftsartikel (refereegranskat)abstract
- Litterfall dynamics in tropical forests are a good indicator of overall tropical forest function, indicative of carbon invested in both photosynthesising tissues and reproductive organs such as flowers and fruits. These dynamics are sensitive to changes in climate, such as drought, but little is known about the long-term responses of tropical forest litterfall dynamics to extended drought stress. We present a 15-year dataset of litterfall (leaf, flower and fruit, and twigs) from the world's only long-running drought experiment in tropical forest. This dataset comprises one of the longest published litterfall time series in natural forest, which allows the long-term effects of drought on forest reproduction and canopy investment to be explored. Over the first 4 years of the experiment, the experimental soil moisture deficit created only a small decline in total litterfall and leaf fall (12% and 13%, respectively), but a very strong initial decline in reproductive litterfall (flowers and fruits) of 54%. This loss of flowering and fruiting was accompanied by a de-coupling of all litterfall patterns from seasonal climate variables. However, following >10 years of the experimental drought, flower and fruiting re-stabilised at levels greater than in the control plot, despite high tree mortality in the drought plot. Litterfall relationships with atmospheric drivers were re-established alongside a strong new apparent trade-off between litterfall and tree growth. Synthesis. We demonstrate that this tropical forest went through an initial shock response during the first 4 years of intense drought, where reproductive effort was arrested and seasonal litterfall patterns were lost. However, following >10 years of experimental drought, this system appears to be re-stabilising at a new functional state where reproduction is substantially elevated on a per tree basis; and there is a new strong trade-off between investment in canopy production and wood production.
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| 42. |
- Saager, Rolf B., 1974-, et al.
(författare)
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Impact of hemoglobin breakdown products in the spectral analysis of burn wounds using spatial frequency domain spectroscopy
- 2019
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Ingår i: Journal of Biomedical Optics. - : SPIE - International Society for Optical Engineering. - 1083-3668 .- 1560-2281. ; 24:2
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Tidskriftsartikel (refereegranskat)abstract
- Burn wounds and wound healing invoke several biological processes that may complicate the interpretation of spectral imaging data. Through analysis of spatial frequency domain spectroscopy data (450 to 1000 nm) obtained from longitudinal investigations using a graded porcine burn wound healing model, we have identified features in the absorption spectrum that appear to suggest the presence of hemoglobin breakdown products, e.g., methemoglobin. Our results show that the calculated concentrations of methemoglobin directly correlate with burn severity, 24 h after the injury. In addition, tissue parameters such as oxygenation (StO2) and water fraction may be underestimated by 20% and 78%, respectively, if methemoglobin is not included in the spectral analysis.
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| 43. |
- Saager, Rolf B., 1974-, et al.
(författare)
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Low-cost tissue simulating phantoms with adjustable wavelength-dependent scattering properties in the visible and infrared ranges
- 2016
-
Ingår i: Journal of Biomedical Optics. - : SPIE - International Society for Optical Engineering. - 1083-3668 .- 1560-2281. ; 21:6
-
Tidskriftsartikel (refereegranskat)abstract
- We present a method for low-cost fabrication of polydimethylsiloxane (PDMS) tissue simulating phantoms with tunable scattering spectra, spanning visible, and near-infrared regimes. These phantoms use optical polishing agents (aluminum oxide powders) at various grit sizes to approximate in vivo tissue scattering particles across multiple size distributions (range: 17 to 3 μm). This class of tunable scattering phantoms is used to mimic distinct changes in wavelength-dependent scattering properties observed in tissue pathologies such as partial thickness burns. Described by a power-law dependence on wavelength, the scattering magnitude of these phantoms scale linearly with particle concentration over a physiologic range [μ's=(0.5 to 2.0 mm−1)] whereas the scattering spectra, specific to each particle size distribution, correlate to distinct exponential coefficients (range: 0.007 to 0.32). Aluminum oxide powders used in this investigation did not detectably contribute to the absorption properties of these phantoms. The optical properties of these phantoms are verified through inverse adding-doubling methods and the tolerances of this fabrication method are discussed.
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| 44. |
- Saager, Rolf B., 1974-, et al.
(författare)
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Low-cost tissue simulating phantoms with tunable, wavelength-dependent scattering properties (Conference Presentation)
- 2016
-
Ingår i: Proceedings Volume 9700, Design and Quality for Biomedical Technologies IX; 970005 (2016). - : SPIE - International Society for Optical Engineering.
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Konferensbidrag (refereegranskat)abstract
- Tissue-simulating phantoms provide the opportunity to evaluate the performance of optical and spectroscopic instruments under controlled experimental conditions. Recent efforts have advanced phantom fabrication methods to provide more tissue realistic phantoms, both in terms of a) incorporating absorbing agents that more faithfully mimic in vivo tissue chromophores spanning visible and near infrared regimes and b) accounting for multi-layer tissue structures with distinct optical properties. The spectral scattering properties in these phantoms, however, are typically based only on a single scattering agent, thereby locking the spectral scattering properties to a single particle size distribution. However, in both healthy tissue as well as pathologic tissue, regions of distinct and differentiated scattering may be present. With differing mean size and distribution of scattering objects in these tissue regions, the relative wavelength-dependent scattering spectra may vary. For example, partial thickness burns exhibit significant cellular damage and collagen denaturation that will significantly alter the wavelength-dependent scattering properties resembling large Mie-like scatterer distributions in both visible and near infrared regimes. We present a low-cost method to fabricate silicone tissue-simulating phantoms with tunable scattering spectra properties that span visible and near infrared wavelengths. We use optical polishing agents (white aluminum oxides powders) at various grit sizes to approximate Mie scattering across multiple mean particle sizes. Mean particle sizes used in this study range from 17-3 micron. The optical properties of these phantoms are verified using an integrating sphere in combination with inverse adding-doubling methods. The tolerances of this fabrication method will be discussed.
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| 45. |
- Saager, Rolf B., 1974-, et al.
(författare)
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Method using in vivo quantitative spectroscopy to guide design and optimization of low-cost, compact clinical imaging devices : emulation and evaluation of multispectral imaging systems
- 2018
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Ingår i: Journal of Biomedical Optics. - : SPIE - International Society for Optical Engineering. - 1083-3668 .- 1560-2281. ; 23:4
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Tidskriftsartikel (refereegranskat)abstract
- With recent proliferation in compact and/or low-cost clinical multispectral imaging approaches and commercially available components, questions remain whether they adequately capture the requisite spectral content of their applications. We present a method to emulate the spectral range and resolution of a variety of multispectral imagers, based on in-vivo data acquired from spatial frequency domain spectroscopy (SFDS). This approach simulates spectral responses over 400 to 1100 nm. Comparing emulated data with full SFDS spectra of in-vivo tissue affords the opportunity to evaluate whether the sparse spectral content of these imagers can (1) account for all sources of optical contrast present (completeness) and (2) robustly separate and quantify sources of optical contrast (crosstalk). We validate the approach over a range of tissue-simulating phantoms, comparing the SFDS-based emulated spectra against measurements from an independently characterized multispectral imager. Emulated results match the imager across all phantoms (<3 % absorption, <1 % reduced scattering). In-vivo test cases (burn wounds and photoaging) illustrate how SFDS can be used to evaluate different multispectral imagers. This approach provides an in-vivo measurement method to evaluate the performance of multispectral imagers specific to their targeted clinical applications and can assist in the design and optimization of new spectral imaging devices.
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| 46. |
- Tavares, Julia, et al.
(författare)
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Basin-wide variation in tree hydraulic safety margins predicts the carbon balance of Amazon forests
- 2023
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 617:7959, s. 111-117
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Tidskriftsartikel (refereegranskat)abstract
- Tropical forests face increasing climate risk(1,2), yet our ability to predict their response to climate change is limited by poor understanding of their resistance to water stress. Although xylem embolism resistance thresholds (for example, ?(50)) and hydraulic safety margins (for example, HSM50) are important predictors of drought-induced mortality risk(3-5), little is known about how these vary across Earth's largest tropical forest. Here, we present a pan-Amazon, fully standardized hydraulic traits dataset and use it to assess regional variation in drought sensitivity and hydraulic trait ability to predict species distributions and long-term forest biomass accumulation. Parameters ?(50) and HSM50 vary markedly across the Amazon and are related to average long-term rainfall characteristics. Both ?(50) and HSM50 influence the biogeographical distribution of Amazon tree species. However, HSM50 was the only significant predictor of observed decadal-scale changes in forest biomass. Old-growth forests with wide HSM50 are gaining more biomass than are low HSM(50 )forests. We propose that this may be associated with a growth-mortality trade-off whereby trees in forests consisting of fast-growing species take greater hydraulic risks and face greater mortality risk. Moreover, in regions of more pronounced climatic change, we find evidence that forests are losing biomass, suggesting that species in these regions may be operating beyond their hydraulic limits. Continued climate change is likely to further reduce HSM50 in the Amazon(6,7), with strong implications for the Amazon carbon sink.
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| 47. |
- Teuten, Emma L, et al.
(författare)
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Transport and release of chemicals from plastics to the environment and to wildlife
- 2009
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Ingår i: PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 364:1526, s. 2027-2045
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Tidskriftsartikel (refereegranskat)abstract
- Plastics debris in the marine environment, including resin pellets, fragments and microscopic plastic fragments, contain organic contaminants, including polychlorinated biphenyls ( PCBs), polycyclic aromatic hydrocarbons, petroleum hydrocarbons, organochlorine pesticides (2,2-bis(p-chlorophenyl)-1,1,1-trichloroethane, hexachlorinated hexanes), polybrominated diphenylethers, alkylphenols and bisphenol A, at concentrations from sub ng g(-1) to mg g(-1). Some of these compounds are added during plastics manufacture, while others adsorb from the surrounding seawater. Concentrations of hydrophobic contaminants adsorbed on plastics showed distinct spatial variations reflecting global pollution patterns. Model calculations and experimental observations consistently show that polyethylene accumulates more organic contaminants than other plastics such as polypropylene and polyvinyl chloride. Both a mathematical model using equilibrium partitioning and experimental data have demonstrated the transfer of contaminants from plastic to organisms. A feeding experiment indicated that PCBs could transfer from contaminated plastics to streaked shearwater chicks. Plasticizers, other plastics additives and constitutional monomers also present potential threats in terrestrial environments because they can leach from waste disposal sites into groundwater and/or surface waters. Leaching and degradation of plasticizers and polymers are complex phenomena dependent on environmental conditions in the landfill and the chemical properties of each additive. Bisphenol A concentrations in leachates from municipal waste disposal sites in tropical Asia ranged from sub mu g l(-1) to mg l(-1) and were correlated with the level of economic development.
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| 48. |
- Watterson, William J., et al.
(författare)
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The roles of an aluminum underlayer in the biocompatibility and mechanical integrity of vertically aligned carbon nanotubes for interfacing with retinal neurons
- 2020
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Ingår i: Micromachines. - 2072-666X. ; 11:6
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Tidskriftsartikel (refereegranskat)abstract
- Retinal implant devices are becoming an increasingly realizable way to improve the vision of patients blinded by photoreceptor degeneration. As an electrode material that can improve restored visual acuity, carbon nanotubes (CNTs) excel due to their nanoscale topography, flexibility, surface chemistry, and double-layer capacitance. If vertically aligned carbon nanotubes (VACNTs) are biocompatible with retinal neurons and mechanically robust, they can further improve visual acuity-most notably in subretinal implants-because they can be patterned into high-aspect-ratio, micrometer-size electrodes. We investigated the role of an aluminum (Al) underlayer beneath an iron (Fe) catalyst layer used in the growth of VACNTs by chemical vapor deposition (CVD). In particular, we cultured dissociated retinal cells for three days in vitro (DIV) on unfunctionalized and oxygen plasma functionalized VACNTs grown from a Fe catalyst (Fe and Fe + Pl preparations, where Pl signifies the plasma functionalization) and an Fe catalyst with an Al underlayer (Al/Fe and Al/Fe + Pl preparations). The addition of the Al layer increased the mechanical integrity of the VACNT interface and enhanced retinal neurite outgrowth over the Fe preparation. Unexpectedly, the extent of neurite outgrowth was significantly greater in the Al/Fe than in the Al/Fe+Pl preparation, suggesting plasma functionalization can negatively impact biocompatibility for some VACNT preparations. Additionally, we show our VACNT growth process for the Al/Fe preparation can support neurite outgrowth for up to 7 DIV. By demonstrating the retinal neuron biocompatibility, mechanical integrity, and pattern control of our VACNTs, this work offers VACNT electrodes as a solution for improving the restored visual acuity provided by modern retinal implants.
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