| 1. |
- Petersen, Julian, et al.
(author)
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A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology
- 2023
-
In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
-
Journal article (peer-reviewed)abstract
- In this study we use comparative genomics to uncover a gene with uncharacterized function (1700011H14Rik/C14orf105/CCDC198), which we hereby name FAME (Factor Associated with Metabolism and Energy). We observe that FAME shows an unusually high evolutionary divergence in birds and mammals. Through the comparison of single nucleotide polymorphisms, we identify gene flow of FAME from Neandertals into modern humans. We conduct knockout experiments on animals and observe altered body weight and decreased energy expenditure in Fame knockout animals, corresponding to genome-wide association studies linking FAME with higher body mass index in humans. Gene expression and subcellular localization analyses reveal that FAME is a membrane-bound protein enriched in the kidneys. Although the gene knockout results in structurally normal kidneys, we detect higher albumin in urine and lowered ferritin in the blood. Through experimental validation, we confirm interactions between FAME and ferritin and show co-localization in vesicular and plasma membranes.
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| 2. |
- Abbasi, Rasha, et al.
(author)
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IceCube search for neutrinos from GRB 221009A
- 2023
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In: Proceedings of 38th International Cosmic Ray Conference (ICRC 2023). - : Sissa Medialab Srl.
-
Conference paper (peer-reviewed)abstract
- GRB 221009A is the brightest Gamma Ray Burst (GRB) ever observed. The observed extremelyhigh flux of high and very-high-energy photons provide a unique opportunity to probe the predictedneutrino counterpart to the electromagnetic emission. We have used a variety of methods to searchfor neutrinos in coincidence with the GRB over several time windows during the precursor, promptand afterglow phases of the GRB. MeV scale neutrinos are studied using photo-multiplier ratescalers which are normally used to search for galactic core-collapse supernovae neutrinos. GeVneutrinos are searched starting with DeepCore triggers. These events don’t have directionallocalization, but instead can indicate an excess in the rate of events. 10 GeV - 1 TeV and >TeVneutrinos are searched using traditional neutrino point source methods which take into accountthe direction and time of events with DeepCore and the entire IceCube detector respectively. The>TeV results include both a fast-response analysis conducted by IceCube in real-time with timewindows of T0 − 1 to T0 + 2 hours and T0 ± 1 day around the time of GRB 221009A, as well asan offline analysis with 3 new time windows up to a time window of T0 − 1 to T0 + 14 days, thelongest time period we consider. The combination of observations by IceCube covers 9 ordersof magnitude in neutrino energy, from MeV to PeV, placing upper limits across the range forpredicted neutrino emission.
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| 3. |
- Menkveld, Albert J., et al.
(author)
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Nonstandard Errors
- 2024
-
In: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
-
Journal article (peer-reviewed)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
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| 4. |
- Testor, Pierre, et al.
(author)
-
OceanGliders: A component of the integrated GOOS
- 2019
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In: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 6
-
Research review (peer-reviewed)abstract
- The OceanGliders program started in 2016 to support active coordination and enhancement of global glider activity. OceanGliders contributes to the international efforts of the Global Ocean Observation System (GOOS) for Climate, Ocean Health and Operational Services. It brings together marine scientists and engineers operating gliders around the world: (1) to observe the long-term physical, biogeochemical, and biological ocean processes and phenomena that are relevant for societal applications; and, (2) to contribute to the GOOS through real-time and delayed mode data dissemination. The OceanGliders program is distributed across national and regional observing systems and significantly contributes to integrated, multi-scale and multi-platform sampling strategies. OceanGliders shares best practices, requirements, and scientific knowledge needed for glider operations, data collection and analysis. It also monitors global glider activity and supports the dissemination of glider data through regional and global databases, in real-time and delayed modes, facilitating data access to the wider community. OceanGliders currently supports national, regional and global initiatives to maintian and expand the capabilities and application of gliders to meet key global challenges such as improved measurement of ocean boundary currents, water transformation and storm forecast.
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| 5. |
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| 6. |
- Abellán, C., et al.
(author)
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Challenging Local Realism with Human Choices
- 2018
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In: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 557, s. 212-216
-
Journal article (peer-reviewed)abstract
- A Bell test is a randomized trial that compares experimental observations against the philosophical worldview of local realism , in which the properties of the physical world are independent of our observation of them and no signal travels faster than light. A Bell test requires spatially distributed entanglement, fast and high-efficiency detection and unpredictable measurement settings. Although technology can satisfy the first two of these requirements, the use of physical devices to choose settings in a Bell test involves making assumptions about the physics that one aims to test. Bell himself noted this weakness in using physical setting choices and argued that human 'free will' could be used rigorously to ensure unpredictability in Bell tests. Here we report a set of local-realism tests using human choices, which avoids assumptions about predictability in physics. We recruited about 100,000 human participants to play an online video game that incentivizes fast, sustained input of unpredictable selections and illustrates Bell-test methodology. The participants generated 97,347,490 binary choices, which were directed via a scalable web platform to 12 laboratories on five continents, where 13 experiments tested local realism using photons, single atoms, atomic ensembles and superconducting devices. Over a 12-hour period on 30 November 2016, participants worldwide provided a sustained data flow of over 1,000 bits per second to the experiments, which used different human-generated data to choose each measurement setting. The observed correlations strongly contradict local realism and other realistic positions in bi-partite and tri-partite 12 scenarios. Project outcomes include closing the 'freedom-of-choice loophole' (the possibility that the setting choices are influenced by 'hidden variables' to correlate with the particle properties), the utilization of video-game methods for rapid collection of human-generated randomness, and the use of networking techniques for global participation in experimental science.
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| 7. |
- Alonso-Mori, Roberto, et al.
(author)
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Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode
- 2012
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:47, s. 19103-19107
-
Journal article (peer-reviewed)abstract
- The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this probe-before-destroy approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as well as the ligand environment, critical for understanding the functional role of redox-active metal sites. K beta(1,3) XES spectra of Mn-II and Mn-2(III,IV) complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to > 100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. The technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II.
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| 8. |
- Arndt, D. S., et al.
(author)
-
State of the Climate in 2016
- 2017
-
In: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 98:8, s. S1-S280
-
Journal article (peer-reviewed)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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| 9. |
- Arndt, D. S., et al.
(author)
-
STATE OF THE CLIMATE IN 2017
- 2018
-
In: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 99:8, s. S1-S310
-
Research review (peer-reviewed)
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| 10. |
- Balmer, R. S., et al.
(author)
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Unlocking diamond's potential as an electronic material
- 2008
-
In: Philosophical Transactions. Series A. - London : Royal Society of London. - 1364-503X .- 1471-2962. ; 366:1863, s. 251-265
-
Journal article (peer-reviewed)abstract
- In this paper, we review the suitability of diamond as a semiconductor material for high-performance electronic applications. The current status of the manufacture of synthetic diamond is reviewed and assessed. In particular, we consider the quality of intrinsic material now available and the challenges in making doped structures suitable for practical devices. Two practical applications are considered in detail. First, the development of high-voltage switches capable of switching voltages in excess of 10kV. Second, the development of diamond MESFETs for high-frequency and high-power applications. Here device data are reported showing a current density of more than 30mAmm -1 along with small-signal RF measurements demonstrating gigahertz operation. We conclude by considering the remaining challenges which will need to be overcome if commercially attractive diamond electronic devices are to be manufactured.
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| 11. |
- Björkman, Mats P., 1978, et al.
(author)
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Nitrate postdeposition processes in Svalbard surface snow
- 2014
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In: Journal of Geophysical Research - Atmospheres. - 0148-0227 .- 2156-2202 .- 2169-897X .- 2169-8996. ; 119:22
-
Journal article (peer-reviewed)abstract
- The snowpack acts as a sink for atmospheric reactive nitrogen, but several postdeposition pathways have been reported to alter the concentration and isotopic composition of snow nitrate with implications for atmospheric boundary layer chemistry, ice core records, and terrestrial ecology following snow melt. Careful daily sampling of surface snow during winter (11-15 February 2010) and springtime (9 April to 5 May 2010) near Ny-Ålesund, Svalbard reveals a complex pattern of processes within the snowpack. Dry deposition was found to dominate over postdeposition losses, with a net nitrate deposition rate of (0.6+/-0.2) (my) molm 2 d 1 to homogeneous surface snow. At Ny-Ålesund, such surface dry deposition can either solely result from long-range atmospheric transport of oxidized nitrogen or include the redeposition of photolytic/bacterial emission originating from deeper snow layers. Our data further confirm that polar basin air masses bring 15 N-depleted nitrate to Svalbard, while high nitrate (delta) (18O) values only occur in connection with ozone-depleted air, and show that these signatures are reflected in the deposited nitrate. Such ozone-depleted air is attributed to active halogen chemistry in the air masses advected to the site. However, here the Ny-Ålesund surface snow was shown to have an active role in the halogen dynamics for this region, as indicated by declining bromide concentrations and increasing nitrate (delta) (18O), during high BrO (low-ozone) events. The data also indicate that the snowpack BrO-NO x cycling continued in postevent periods, when ambient ozone and BrO levels recovered.
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| 12. |
- Blunden, Jessica, et al.
(author)
-
State of the Climate in 2012
- 2013
-
In: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 94:8, s. S1-S258
-
Journal article (peer-reviewed)abstract
- For the first time in serveral years, the El Nino-Southern Oscillation did not dominate regional climate conditions around the globe. A weak La Ni a dissipated to ENSOneutral conditions by spring, and while El Nino appeared to be emerging during summer, this phase never fully developed as sea surface temperatures in the eastern conditions. Nevertheless, other large-scale climate patterns and extreme weather events impacted various regions during the year. A negative phase of the Arctic Oscillation from mid-January to early February contributed to frigid conditions in parts of northern Africa, eastern Europe, and western Asia. A lack of rain during the 2012 wet season led to the worst drought in at least the past three decades for northeastern Brazil. Central North America also experienced one of its most severe droughts on record. The Caribbean observed a very wet dry season and it was the Sahel's wettest rainy season in 50 years. Overall, the 2012 average temperature across global land and ocean surfaces ranked among the 10 warmest years on record. The global land surface temperature alone was also among the 10 warmest on record. In the upper atmosphere, the average stratospheric temperature was record or near-record cold, depending on the dataset. After a 30-year warming trend from 1970 to 1999 for global sea surface temperatures, the period 2000-12 had little further trend. This may be linked to the prevalence of La Ni a-like conditions during the 21st century. Heat content in the upper 700 m of the ocean remained near record high levels in 2012. Net increases from 2011 to 2012 were observed at 700-m to 2000-m depth and even in the abyssal ocean below. Following sharp decreases in to the effects of La Ni a, sea levels rebounded to reach records highs in 2012. The increased hydrological cycle seen in recent years continued, with more evaporation in drier locations and more precipitation in rainy areas. In a pattern that has held since 2004, salty areas of the ocean surfaces and subsurfaces were anomalously salty on average, while fresher areas were anomalously fresh. Global tropical cyclone activity during 2012 was near average, with a total of 84 storms compared with the 1981-2010 average of 89. Similar to 2010 and 2011, the North Atlantic was the only hurricane basin that experienced above-normal activity. In this basin, Sandy brought devastation to Cuba and parts of the eastern North American seaboard. All other basins experienced either near-or below-normal tropical cyclone activity. Only three tropical cyclones reached Category 5 intensity-all in Bopha became the only storm in the historical record to produce winds greater than 130 kt south of 7 N. It was also the costliest storm to affect the Philippines and killed more than 1000 residents. Minimum Arctic sea ice extent in September and Northern Hemisphere snow cover extent in June both reached new record lows. June snow cover extent is now declining at a faster rate (-17.6% per decade) than September sea ice extent (-13.0% per decade). Permafrost temperatures reached record high values in northernmost Alaska. A new melt extent record occurred on 11-12 July on the Greenland ice sheet; 97% of the ice sheet showed some form of melt, four times greater than the average melt for this time of year. The climate in Antarctica was relatively stable overall. The largest maximum sea ice extent since records begain in 1978 was observed in September 2012. In the stratosphere, warm air led to the second smallest ozone hole in the past two decades. Even so, the springtime ozone layer above Antarctica likely will not return to its early 1980s state until about 2060. Following a slight decline associated with the global 2 emissions from fossil fuel combustion and cement production reached a record 9.5 +/- 0.5 Pg C in 2011 and a new record of 9.7 +/- 0.5 Pg C is estimated for 2012. Atmospheric CO2 concentrations increased by 2.1 ppm in 2012, to 392.6 ppm. In spring 2012, 2 concentration exceeded 400 ppm at 7 of the 13 Arctic observation sites. Globally, other greenhouse gases including methane and nitrous oxide also continued to rise in concentration and the combined effect now represents a 32% increase in radiative forcing over a 1990 baseline. Concentrations of most ozone depleting substances continued to fall.
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| 13. |
- Brannigan, Liam, et al.
(author)
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Submesoscale Instabilities in Mesoscale Eddies
- 2017
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In: Journal of Physical Oceanography. - 0022-3670 .- 1520-0485. ; 47:12, s. 3061-3085
-
Journal article (peer-reviewed)abstract
- Submesoscale processes have been extensively studied in observations and simulations of fronts. Recent idealized simulations show that submesoscale instabilities also occur in baroclinic mesoscale cyclones and anticyclones. The instabilities in the anticyclone grow faster and at coarser grid resolution than in the cyclone. The instabilities lead to larger restratification in the anticyclone than in the cyclone. The instabilities also lead to changes in the mean azimuthal jet around the anticyclone from 2-km resolution, but a similar effect only occurs in the cyclone at 0.25-km resolution. A numerical passive tracer experiment shows that submesoscale instabilities lead to deeper subduction in the interior of anticyclonic than cyclonic eddies because of outcropping isopycnals extending deeper into the thermocline in anticyclones. An energetic analysis suggests that both vertical shear production and vertical buoyancy fluxes are important in anticyclones but primarily vertical buoyancy fluxes occur in cyclones at these resolutions. The energy sources and sinks vary azimuthally around the eddies caused by the asymmetric effects of the Ekman buoyancy flux. Glider transects of a mesoscale anticyclone in the Tasman Sea show that water with low stratification and high oxygen concentrations is found in an anticyclone, in a manner that may be consistent with the model predictions for submesoscale subduction in mesoscale eddies.
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| 14. |
- Bronge, Mattias, et al.
(author)
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Identification of four novel T cell autoantigens and personal autoreactive profiles in multiple sclerosis
- 2022
-
In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:17
-
Journal article (peer-reviewed)abstract
- Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS), in which pathological T cells, likely autoimmune, play a key role. Despite its central importance, the autoantigen repertoire remains largely uncharacterized. Using a novel in vitro antigen delivery method combined with the Human Protein Atlas library, we screened for T cell autoreactivity against 63 CNS-expressed proteins. We identified four previously unreported autoantigens in MS: fatty acid-binding protein 7, prokineticin-2, reticulon-3, and synaptosomal-associated protein 91, which were verified to induce interferon-gamma responses in MS in two cohorts. Autoreactive profiles were heterogeneous, and reactivity to several autoantigens was MS-selective. Autoreactive T cells were predominantly CD4(+) and human leukocyte antigen-DR restricted. Mouse immunization induced antigen-specific responses and CNS leukocyte infiltration. This represents one of the largest systematic efforts to date in the search for MS autoantigens, demonstrates the heterogeneity of autoreactive profiles, and highlights promising targets for future diagnostic tools and immunomodulatory therapies in MS.
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| 15. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
-
In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 16. |
- Concepcion Gil-Rodriguez, Maria, et al.
(author)
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De Novo Heterozygous Mutations in SMC3 Cause a Range of Cornelia de Lange Syndrome-Overlapping Phenotypes
- 2015
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In: Human Mutation. - : Wiley: 12 months. - 1059-7794 .- 1098-1004. ; 36:4, s. 454-462
-
Journal article (peer-reviewed)abstract
- Cornelia de Lange syndrome (CdLS) is characterized by facial dysmorphism, growth failure, intellectual disability, limb malformations, and multiple organ involvement. Mutations in five genes, encoding subunits of the cohesin complex (SMC1A, SMC3, RAD21) and its regulators (NIPBL, HDAC8), account for at least 70% of patients with CdLS or CdLS-like phenotypes. To date, only the clinical features from a single CdLS patient with SMC3 mutation has been published. Here, we report the efforts of an international research and clinical collaboration to provide clinical comparison of 16 patients with CdLS-like features caused by mutations in SMC3. Modeling of the mutation effects on protein structure suggests a dominant-negative effect on the multimeric cohesin complex. When compared with typical CdLS, many SMC3-associated phenotypes are also characterized by postnatal microcephaly but with a less distinctive craniofacial appearance, a milder prenatal growth retardation that worsens in childhood, few congenital heart defects, and an absence of limb deficiencies. While most mutations are unique, two unrelated affected individuals shared the same mutation but presented with different phenotypes. This work confirms that de novo SMC3 mutations account for approximate to 1%-2% of CdLS-like phenotypes.
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| 17. |
- Dev, Apurba, et al.
(author)
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Electrokinetic effect for molecular recognition : A label-free approach for real-time biosensing
- 2016
-
In: Biosensors & bioelectronics. - : Elsevier. - 0956-5663 .- 1873-4235. ; 82, s. 55-63
-
Journal article (peer-reviewed)abstract
- We present a simple and inexpensive method for label-free detection of biomolecules. The method monitors the changes in streaming current in a fused silica capillary as target biomolecules bind to immobilized receptors on the inner surface of the capillary. To validate the concept, we show detection and time response of different protein-ligand and protein-protein systems: biotin-avidin and biotin-streptavidin, barstar-dibarnase and Z domain-immunoglobulin G (IgG). We show that specific binding of these biomolecules can be reliably monitored using a very simple setup. Using sequential injections of various proteins at a diverse concentration range and as well as diluted human serum we further investigate the capacity of the proposed technique to perform specific target detection from a complex sample. We also investigate the time for the signal to reach equilibrium and its dependence on analyte concentration and demonstrate that the current setup can be used to detect biomolecules at a concentration as low as 100 pM without requiring any advanced device fabrication procedures. Finally, an analytical model based on diffusion theory has been presented to explain the dependence of the saturation time on the analyte concentration and capillary dimensions and how reducing length and inner diameter of the capillary is predicted to give faster detection and in practice also lower limit of detection.
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| 18. |
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| 19. |
- Farrell, W. M., et al.
(author)
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Electron density dropout near Enceladus in the context of water-vapor and water-ice
- 2009
-
In: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 36:10, s. L10203-
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Journal article (peer-reviewed)abstract
- On 12 March 2008, the Cassini spacecraft made a close encounter with the Saturnian moon Enceladus, passing within 52 km of the moon. The spacecraft trajectory was intentionally-oriented in a southerly direction to create a close alignment with the intense water-dominated plumes emitted from the south polar region. During the passage, the Cassini Radio and Plasma Wave System (RPWS) detected two distinct radio signatures: 1) Impulses associated with small water-ice dust grain impacts and 2) an upper hybrid (UH) resonance emission that both intensified and displayed a sharp frequency decrease in the near-vicinity of the moon. The frequency decrease of the UH emission is associated with an unexpectedly sharp decrease in electron density from similar to 90 cl/cm(3) to below 20 cl/cm(3) that occurs on a time scale of a minute near the closest encounter with the moon. In this work, we consider a number of scenarios to explain this sharp electron dropout, but surmise that electron absorption by ice grains is the most likely process.
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| 20. |
- Farrell, W. M., et al.
(author)
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Mass unloading along the inner edge of the Enceladus plasma torus
- 2008
-
In: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 35:2, s. L02203-
-
Journal article (peer-reviewed)abstract
- A major discovery made by the Cassini spacecraft at Saturn was the substantial mass ejection from the south pole of Enceladus. Previous studies show that this ejected gas can become ionized and subsequently load mass onto the connecting magnetic field lines near the moon. Radial diffusion then allows the mass-loaded field lines to move outward to similar to 15 R-s and inward to similar to 2 R-s, forming a plasma torus. We demonstrate herein that the mass is also '' unloaded '' along the inner edge of this plasma torus the edge incident with the plasma-absorbing A-ring. Interpreting down-drifting z-mode tones from active sites along the inner edge of the ion torus as emission near the local electron plasma frequency, f(pe), we can remotely-monitor this reduction in plasma density along the torus inner edge as a function time. We find that the down-drift of the z-mode tones corresponds typically to a plasma density change dn/dt similar to - 5x10(-4)/cm(3)-s and when integrated over an annulus defined by the outer edge of the A-ring, corresponds to a mass loss of similar to 40 kg/s. Using the z-mode tones, we also find locations where plasma mass from the ring-ionosphere is possibly loaded at 1 - 2 kg/s onto field lines near the Cassini gap.
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| 21. |
- Ferrari, S., et al.
(author)
-
Visualizing Vortex Clusters in the Wake of a High-Speed Train
- 2017
-
In: 2017 IEEE INTERNATIONAL CONFERENCE ON SYSTEMS, MAN, AND CYBERNETICS (SMC). - 1062-922X. - 9781538616451 ; 2017-January, s. 683-688
-
Conference paper (peer-reviewed)abstract
- Visualization of fluid flows at a high-Reynolds number (Re similar to 10(5)) presents difficulties for user comprehension due to density and ambiguous interactions between vortices. Prior work has used cluster-based reduced-order modelling (CROM) to analyze the wake of a High-Speed Train (HST) with Re = 86,000. In this paper, we present a novel surface visualization to convey the spatiotemporal changes undergone by clustered vortices in the HST wake. This visualization is accomplished through dimensional reduction of 3D volumetric vortices into 1D ridges, and physics-based feature tracking. The result is 3D surfaces visualizing the behavior of the vortices in the HST wake. Compared to conventional still-image representations, these surfaces allow the user to quickly compare and analyze the two shedding cycles identified via CROM. The spatiotemporal differences of the primary vortices in these shedding cycles provide analytic insight to influence the aerodynamics of the HST.
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| 22. |
- Grossmann, Igor, et al.
(author)
-
Insights into the accuracy of social scientists' forecasts of societal change
- 2023
-
In: Nature Human Behaviour. - : Springer Nature. - 2397-3374. ; 7, s. 484-501
-
Journal article (peer-reviewed)abstract
- How well can social scientists predict societal change, and what processes underlie their predictions? To answer these questions, we ran two forecasting tournaments testing the accuracy of predictions of societal change in domains commonly studied in the social sciences: ideological preferences, political polarization, life satisfaction, sentiment on social media, and gender-career and racial bias. After we provided them with historical trend data on the relevant domain, social scientists submitted pre-registered monthly forecasts for a year (Tournament 1; N = 86 teams and 359 forecasts), with an opportunity to update forecasts on the basis of new data six months later (Tournament 2; N = 120 teams and 546 forecasts). Benchmarking forecasting accuracy revealed that social scientists' forecasts were on average no more accurate than those of simple statistical models (historical means, random walks or linear regressions) or the aggregate forecasts of a sample from the general public (N = 802). However, scientists were more accurate if they had scientific expertise in a prediction domain, were interdisciplinary, used simpler models and based predictions on prior data. How accurate are social scientists in predicting societal change, and what processes underlie their predictions? Grossmann et al. report the findings of two forecasting tournaments. Social scientists' forecasts were on average no more accurate than those of simple statistical models.
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| 23. |
- Grunewald, Johan, et al.
(author)
-
T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis
- 2016
-
In: European Respiratory Journal. - : European Respiratory Society (ERS). - 0903-1936 .- 1399-3003. ; 47:3, s. 898-909
-
Journal article (peer-reviewed)abstract
- In pulmonary sarcoidosis, CD4(+) T-cells expressing T-cell receptor V alpha 2.3 accumulate in the lungs of HLA-DRB1*03(+) patients. To investigate T-cell receptor-HLA-DRB1*03 interactions underlying recognition of hitherto unknown antigens, we performed detailed analyses of T-cell receptor expression on bronchoalveolar lavage fluid CD4(+) T-cells from sarcoidosis patients. Pulmonary sarcoidosis patients (n=43) underwent bronchoscopy with bronchoalveolar lavage. T-cell receptor alpha and beta chains of CD4(+) T-cells were analysed by flow cytometry, DNA-sequenced, and three-dimensional molecular models of T-cell receptor-HLA-DRB1*03 complexes generated. Simultaneous expression of V alpha 2.3 with the V beta 22 chain was identified in the lungs of all HLA-DRB1*03(+) patients. Accumulated V alpha 2.3/V beta 22-expressing T-cells were highly clonal, with identical or near-identical V alpha 2.3 chain sequences and inter-patient similarities in V beta 22 chain amino acid distribution. Molecular modelling revealed specific T-cell receptor-HLA-DRB1*03-peptide interactions, with a previously identified, sarcoidosis-associated vimentin peptide, (Vim)(429-443) DSLPLVDTHSKRTLL, matching both the HLA peptide-binding cleft and distinct T-cell receptor features perfectly. We demonstrate, for the first time, the accumulation of large clonal populations of specific V alpha 2.3/V beta 22 T-cell receptor-expressing CD4(+) T-cells in the lungs of HLA-DRB1*03(+) sarcoidosis patients. Several distinct contact points between V alpha 2.3/V beta 22 receptors and HLA-DRB1*03 molecules suggest presentation of prototypic vimentin-derived peptides.
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| 24. |
- Gyoeroek, Michael, et al.
(author)
-
Surface binding energies of beryllium/tungsten alloys
- 2016
-
In: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 472, s. 76-81
-
Journal article (peer-reviewed)abstract
- Binding energies of beryllium and tungsten atoms on surfaces of the alloys Be2W and Be12W were obtained from density functional theory calculations. Values of 4.08–5.63 eV for beryllium and 6.81–10.04 eV for tungsten were obtained. An analytical force field agrees for beryllium, but its tungsten surface atoms are too strongly bound. The surface binding energies of Be and W on Be12W surfaces is slightly smaller than on the pure Be and W surfaces, respectively. For higher tungsten content, i.e. for Be2W, the situation is more complicated. For some surfaces of this alloy the surface binding energies are enhanced while for others they are diminished, compared to the pure metal surfaces. The dependency of the cohesive energy on the mole fraction follows a linear relationship.
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| 25. |
- Hattne, Johan, et al.
(author)
-
Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
- 2014
-
In: Nature Methods. - 1548-7091 .- 1548-7105. ; 11:5, s. 545-548
-
Journal article (peer-reviewed)abstract
- X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.
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| 26. |
- Hattne, Johan, et al.
(author)
-
Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
- 2014
-
In: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 11:5, s. 545-548
-
Journal article (peer-reviewed)abstract
- X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.
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| 27. |
- Hellgren, Mikko, 1972-, et al.
(author)
-
A hydrogen-bonding network in mammalian sorbitol dehydrogenase stabilizes the tetrameric state and is essential for the catalytic power
- 2007
-
In: Cellular and Molecular Life Sciences (CMLS). - : Springer. - 1420-682X .- 1420-9071. ; 64:23, s. 3129-3138
-
Journal article (peer-reviewed)abstract
- Subunit interaction in sorbitol dehydrogenase (SDH) has been studied with in vitro and in silico methods identifying a vital hydrogen-bonding network, which is strictly conserved among mammalian SDH proteins. Mutation of one of the residues in the hydrogen-bonding network, Tyr110Phe, abolished the enzymatic activity and destabilized the protein into tetramers, dimers and monomers as judged from gel filtration experiments at different temperatures compared to only tetramers for the wild-type protein below 307 K. The determined equilibrium constants revealed a large difference in Gibbs energy (8 kJ/mol) for the tetramer stability between wild-type SDH and the mutated form Tyr110Phe SDH. The results focus on a network of coupled hydrogen bonds in wild-type SDH that uphold the protein interface, which is specific and favorable to electrostatic, van der Waals and hydrogen-bond interactions between subunits, interactions that are crucial for the catalytic power of SDH.
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| 28. |
- Kaiser, Brooks A., et al.
(author)
-
Spatial issues in Arctic marine resource governance workshop summary and comment
- 2015
-
In: Marine Policy. - : Elsevier BV. - 0308-597X .- 1872-9460. ; 58, s. 1-5
-
Journal article (peer-reviewed)abstract
- The rapidly changing Arctic marine ecosystems face new challenges and opportunities that are increasing and shifting governance needs in the region. A group of economists, ecologists, biologists, political scientists and resource managers met in Stockholm, SE, Sept 4-6, 2014 to discuss the governance of Arctic marine resources in a spatial context. We report on the findings here.
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| 29. |
- Kaiser, Eurika, et al.
(author)
-
Cluster-based reduced-order modelling of a mixing layer
- 2014
-
In: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 754, s. 365-414
-
Journal article (peer-reviewed)abstract
- We propose a novel cluster-based reduced-order modelling (CROM) strategy for unsteady flows. CROM combines the cluster analysis pioneered in Gunzburger’s group (Burkardt, Gunzburger & Lee, Comput. Meth. Appl. Mech. Engng, vol. 196, 2006a, pp. 337–355) and transition matrix models introduced in fluid dynamics in Eckhardt’s group (Schneider, Eckhardt & Vollmer, Phys. Rev. E, vol. 75, 2007, art. 066313). CROM constitutes a potential alternative to POD models and generalises the Ulam–Galerkin method classically used in dynamical systems to determine a finite-rank approximation of the Perron–Frobenius operator. The proposed strategy processes a time-resolved sequence of flow snapshots in two steps. First, the snapshot data are clustered into a small number of representative states, called centroids, in the state space. These centroids partition the state space in complementary non-overlapping regions (centroidal Voronoi cells). Departing from the standard algorithm, the probabilities of the clusters are determined, and the states are sorted by analysis of the transition matrix. Second, the transitions between the states are dynamically modelled using a Markov process. Physical mechanisms are then distilled by a refined analysis of the Markov process, e.g. using finite-time Lyapunov exponent (FTLE) and entropic methods. This CROM framework is applied to the Lorenz attractor (as illustrative example), to velocity fields of the spatially evolving incompressible mixing layer and the three-dimensional turbulent wake of a bluff body. For these examples, CROM is shown to identify non-trivial quasi-attractors and transition processes in an unsupervised manner. CROM has numerous potential applications for the systematic identification of physical mechanisms of complex dynamics, for comparison of flow evolution models, for the identification of precursors to desirable and undesirable events, and for flow control applications exploiting nonlinear actuation dynamics.
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| 30. |
- Kaiser, Karol, et al.
(author)
-
MEIS-WNT5A axis regulates development of fourth ventricle choroid plexus
- 2021
-
In: Development. - : The Company of Biologists. - 0950-1991 .- 1477-9129. ; 148:10
-
Journal article (peer-reviewed)abstract
- The choroid plexus (ChP) produces cerebrospinal fluid and forms an essential brain barrier. ChP tissues form in each brain ventricle, each one adopting a distinct shape, but remarkably little is known about the mechanisms underlying ChP development. Here, we show that epithelial WNT5A is crucial for determining fourth ventricle (4V) ChP morphogenesis and size in mouse. Systemic Wnt5a knockout, or forced Wnt5a overexpression beginning at embryonic day 10.5, profoundly reduced ChP size and development. However, Wnt5a expression was enriched in Foxj1-positive epithelial cells of 4V ChP plexus, and its conditional deletion in these cells affected the branched, villous morphology of the 4V ChP. We found that WNT5A was enriched in epithelial cells localized to the distal tips of 4V ChP villi, where WNT5A acted locally to activate non-canonical WNT signaling via ROR1 and ROR2 receptors. During 4V ChP development, MEIS1 bound to the proximal Wnt5a promoter, and gain- and loss-of-function approaches demonstrated that MEIS1 regulated Wnt5a expression. Collectively, our findings demonstrate a dual function of WNT5A in ChP development and identify MEIS transcription factors as upstream regulators of Wnt5a in the 4V ChP epithelium.
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| 31. |
- Kern, Jan, et al.
(author)
-
Room temperature femtosecond X-ray diffraction of photosystem II microcrystals
- 2012
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:25, s. 9721-9726
-
Journal article (peer-reviewed)abstract
- Most of the dioxygen on earth is generated by the oxidation of water by photosystem II (PS II) using light from the sun. This lightdriven, four-photon reaction is catalyzed by the Mn4CaO5 cluster located at the lumenal side of PS II. Various X-ray studies have been carried out at cryogenic temperatures to understand the intermediate steps involved in the water oxidation mechanism. However, the necessity for collecting data at room temperature, especially for studying the transient steps during the O-O bond formation, requires the development of new methodologies. In this paper we report room temperature X-ray diffraction data of PS II microcrystals obtained using ultrashort (<50 fs) 9 keV X-ray pulses from a hard X-ray free electron laser, namely the Linac Coherent Light Source. The results presented here demonstrate that the probe before destroy approach using an X-ray free electron laser works even for the highly-sensitive Mn4CaO5 cluster in PS II at room temperature. We show that these data are comparable to those obtained in synchrotron radiation studies as seen by the similarities in the overall structure of the helices, the protein subunits and the location of the various cofactors. This work is, therefore, an important step toward future studies for resolving the structure of the Mn4CaO5 cluster without any damage at room temperature, and of the reaction intermediates of PS II during O-O bond formation.
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| 32. |
- Kern, Jan, et al.
(author)
-
Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature
- 2013
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 340:6131, s. 491-495
-
Journal article (peer-reviewed)abstract
- Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S-1) and the first illuminated state (S-2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.
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| 33. |
- Kern, Jan, et al.
(author)
-
Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy
- 2014
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 4371-
-
Journal article (peer-reviewed)abstract
- The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O-2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 mu s after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 mu s after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 angstrom. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.
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| 34. |
- Klein, Andreas, et al.
(author)
-
The Fermi energy as common parameter to describe charge compensation mechanisms: A path to Fermi level engineering of oxide electroceramics
- 2023
-
In: Journal of Electroceramics. - 1573-8663 .- 1385-3449. ; 51
-
Journal article (peer-reviewed)abstract
- Chemical substitution, which can be iso- or heterovalent, is the primary strategy to tailor material properties. There are various ways how a material can react to substitution. Isovalent substitution changes the density of states while heterovalent substitution, i.e. doping, can induce electronic compensation, ionic compensation, valence changes of cations or anions, or result in the segregation or neutralization of the dopant. While all these can, in principle, occur simultaneously, it is often desirable to select a certain mechanism in order to determine material properties. Being able to predict and control the individual compensation mechanism should therefore be a key target of materials science. This contribution outlines the perspective that this could be achieved by taking the Fermi energy as a common descriptor for the different compensation mechanisms. This generalization becomes possible since the formation enthalpies of the defects involved in the various compensation mechanisms do all depend on the Fermi energy. In order to control material properties, it is then necessary to adjust the formation enthalpies and charge transition levels of the involved defects. Understanding how these depend on material composition will open up a new path for the design of materials by Fermi level engineering.
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| 35. |
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| 36. |
- Kubin, Markus, et al.
(author)
-
Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers
- 2017
-
In: Structural Dynamics. - : AMER INST PHYSICS. - 2329-7778. ; 4:5
-
Journal article (peer-reviewed)abstract
- X-ray absorption spectroscopy at the L-edge of 3d transition metals provides unique information on the local metal charge and spin states by directly probing 3d-derived molecular orbitals through 2p-3d transitions. However, this soft x-ray technique has been rarely used at synchrotron facilities for mechanistic studies of metalloenzymes due to the difficulties of x-ray-induced sample damage and strong background signals from light elements that can dominate the low metal signal. Here, we combine femtosecond soft x-ray pulses from a free-electron laser with a novel x-ray fluorescence-yield spectrometer to overcome these difficulties. We present L-edge absorption spectra of inorganic high-valent Mn complexes (Mn similar to 6-15 mmol/l) with no visible effects of radiation damage. We also present the first L-edge absorption spectra of the oxygen evolving complex (Mn4CaO5) in Photosystem II (Mn < 1 mmol/l) at room temperature, measured under similar conditions. Our approach opens new ways to study metalloenzymes under functional conditions. (C) 2017 Author(s).
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| 37. |
- Lekberg, Ylva, et al.
(author)
-
Fatty acid 16:1ω5 as a proxy for arbuscular mycorrhizal fungal biomass : current challenges and ways forward
- 2022
-
In: Biology and Fertility of Soils. - : Springer Science and Business Media LLC. - 0178-2762 .- 1432-0789. ; 58:8, s. 835-842
-
Journal article (peer-reviewed)abstract
- Fatty acid biomarkers have emerged as a useful tool to quantify biomass of various microbial groups. Here we focus on the frequent use of the fatty acid 16:1ω5 as a biomarker for arbuscular mycorrhizal (AM) fungi in soils. We highlight some issues with current applications of this method and use several examples from the literature to show that the phospholipid fatty acid (PLFA) 16:1ω5 can occur in high concentrations in soils where actively growing AM fungi are absent. Unless the study includes a control where the contribution of other microbes can be estimated, we advocate for the use of the neutral lipid fatty acid (NLFA) 16:1ω5. This biomarker has higher specificity, is more responsive to shifts in AM fungal biomass, and quantification can be conducted along with PLFA analysis without doubling analytical efforts. We conclude by contrasting various methods used to measure AM fungal biomass in soil and highlight future research needs to optimize fatty acid analyses.
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| 38. |
- Loveday, Benjamin R., et al.
(author)
-
Application of a new net primary production methodology: a daily to annual-scale data set for the North Sea, derived from autonomous underwater gliders and satellite Earth observation
- 2022
-
In: EARTH SYSTEM SCIENCE DATA. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 14:9, s. 3997-4016
-
Journal article (peer-reviewed)abstract
- Shelf seas play a key role in both the global carbon cycle and coastal marine ecosystems through the draw-down and fixing of carbon, as measured through phytoplankton net primary production (NPP). Measuring NPP in situ and extrapolating this to the local, regional, and global scale presents challenges however because of limitations with the techniques utilised (e.g. radiocarbon isotopes), data sparsity, and the inherent biogeochemical heterogeneity of coastal and open-shelf waters. Here, we introduce a new data set generated using a technique based on the synergistic use of in situ glider profiles and satellite Earth observation measurements which can be implemented in a real-time or delayedmode system (haps://doi.org/10.5285/e6974644-2026-0f94-e053-6c86abc00109; Loveday and Smyth, 2022). We apply this system to a fleet of gliders successively deployed over a 19-month time frame in the North Sea, generating an unprecedented fine-scale time series of NPP in the region. At a large scale, this time series gives close agreement with existing satellite-based estimates of NPP for the region and previous in situ estimates. What has not been elucidated before is the high-frequency, small-scale, depth-resolved variability associated with bloom phenology, mesoscale phenomena, and mixed layer dynamics.
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| 39. |
- Mattsson, Niklas, 1979, et al.
(author)
-
Age and diagnostic performance of Alzheimer disease CSF biomarkers.
- 2012
-
In: Neurology. - : American Academy of Neurology (AAN). - 1526-632X .- 0028-3878. ; 78:7, s. 468-76
-
Journal article (peer-reviewed)abstract
- Core CSF changes in Alzheimer disease (AD) are decreased amyloid β(1-42), increased total tau, and increased phospho-tau, probably indicating amyloid plaque accumulation, axonal degeneration, and tangle pathology, respectively. These biomarkers identify AD already at the predementia stage, but their diagnostic performance might be affected by age-dependent increase of AD-type brain pathology in cognitively unaffected elderly.
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| 40. |
- Mattsson, Niklas, 1979, et al.
(author)
-
CSF biomarkers and incipient Alzheimer disease in patients with mild cognitive impairment.
- 2009
-
In: JAMA : the journal of the American Medical Association. - : American Medical Association (AMA). - 1538-3598 .- 0098-7484. ; 302:4, s. 385-93
-
Journal article (peer-reviewed)abstract
- CONTEXT: Small single-center studies have shown that cerebrospinal fluid (CSF) biomarkers may be useful to identify incipient Alzheimer disease (AD) in patients with mild cognitive impairment (MCI), but large-scale multicenter studies have not been conducted. OBJECTIVE: To determine the diagnostic accuracy of CSF beta-amyloid(1-42) (Abeta42), total tau protein (T-tau), and tau phosphorylated at position threonine 181 (P-tau) for predicting incipient AD in patients with MCI. DESIGN, SETTING, AND PARTICIPANTS: The study had 2 parts: a cross-sectional study involving patients with AD and controls to identify cut points, followed by a prospective cohort study involving patients with MCI, conducted 1990-2007. A total of 750 individuals with MCI, 529 with AD, and 304 controls were recruited by 12 centers in Europe and the United States. Individuals with MCI were followed up for at least 2 years or until symptoms had progressed to clinical dementia. MAIN OUTCOME MEASURES: Sensitivity, specificity, positive and negative likelihood ratios (LRs) of CSF Abeta42, T-tau, and P-tau for identifying incipient AD. RESULTS: During follow-up, 271 participants with MCI were diagnosed with AD and 59 with other dementias. The Abeta42 assay in particular had considerable intersite variability. Patients who developed AD had lower median Abeta42 (356; range, 96-1075 ng/L) and higher P-tau (81; range, 15-183 ng/L) and T-tau (582; range, 83-2174 ng/L) levels than MCI patients who did not develop AD during follow-up (579; range, 121-1420 ng/L for Abeta42; 53; range, 15-163 ng/L for P-tau; and 294; range, 31-2483 ng/L for T-tau, P < .001). The area under the receiver operating characteristic curve was 0.78 (95% confidence interval [CI], 0.75-0.82) for Abeta42, 0.76 (95% CI, 0.72-0.80) for P-tau, and 0.79 (95% CI, 0.76-0.83) for T-tau. Cut-offs with sensitivity set to 85% were defined in the AD and control groups and tested in the MCI group, where the combination of Abeta42/P-tau ratio and T-tau identified incipient AD with a sensitivity of 83% (95% CI, 78%-88%), specificity 72% (95% CI, 68%-76%), positive LR, 3.0 (95% CI, 2.5-3.4), and negative LR, 0.24 (95% CI, 0.21-0.28). The positive predictive value was 62% and the negative predictive value was 88%. CONCLUSIONS: This multicenter study found that CSF Abeta42, T-tau, and P-tau identify incipient AD with good accuracy, but less accurately than reported from single-center studies. Intersite assay variability highlights a need for standardization of analytical techniques and clinical procedures.
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| 41. |
- Mitzner, Rolf, et al.
(author)
-
L-Edge X-ray Absorption Spectroscopy of Dilute Systems Relevant to Metalloproteins Using an X-ray Free-Electron Laser
- 2013
-
In: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 4:21, s. 3641-3647
-
Journal article (peer-reviewed)abstract
- L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming 0 K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples.
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| 42. |
- Prokopiou, Markella, et al.
(author)
-
Constraining N2O emissions since 1940 using firn air isotope measurements in both hemispheres
- 2017
-
In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 17:7, s. 4539-4564
-
Journal article (peer-reviewed)abstract
- N2O is currently the third most important anthropogenic greenhouse gas in terms of radiative forcing and its atmospheric mole fraction is rising steadily. To quantify the growth rate and its causes over the past decades, we performed a multi-site reconstruction of the atmospheric N2O mole fraction and isotopic composition using new and previously published firn air data collected from Greenland and Antarctica in combination with a firn diffusion and densification model. The multi-site reconstruction showed that while the global mean N2O mole fraction increased from (290±1)nmolmol-1 in 1940 to (322±1)nmolmol-1 in 2008, the isotopic composition of atmospheric N2O decreased by (-2.2±0.2)% for δ15Nav, (-1.0±0.3)% for δ18O, (-1.3±0.6)% for δ15Nα, and (-2.8±0.6)% for δ15Nβ over the same period. The detailed temporal evolution of the mole fraction and isotopic composition derived from the firn air model was then used in a two-box atmospheric model (comprising a stratospheric box and a tropospheric box) to infer changes in the isotopic source signature over time. The precise value of the source strength depends on the choice of the N2O lifetime, which we choose to fix at 123 years. The average isotopic composition over the investigated period is δ15Nav Combining double low line (-7.6±0.8)% (vs. air-N2), δ18O Combining double low line (32.2±0.2)% (vs. Vienna Standard Mean Ocean Water-VSMOW) for δ18O, δ15Nα Combining double low line (-3.0±1.9)% and δ15Nβ Combining double low line (-11.7±2.3)%. δ15Nav, and δ15Nβ show some temporal variability, while for the other signatures the error bars of the reconstruction are too large to retrieve reliable temporal changes. Possible processes that may explain trends in 15N are discussed. The 15N site preference (Combining double low line δ15Nα-δ15Nβ) provides evidence of a shift in emissions from denitrification to nitrification, although the uncertainty envelopes are large.
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| 43. |
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| 44. |
- Sierra, Raymond G., et al.
(author)
-
Nanoflow electrospinning serial femtosecond crystallography
- 2012
-
In: Acta Crystallographica Section D. - : Wiley-Blackwell. - 0907-4449 .- 1399-0047. ; 68, s. 1584-1587
-
Journal article (peer-reviewed)abstract
- An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14-3.1 mu l min(-1) to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 mu l min(-1) and diffracted to beyond 4 angstrom resolution, producing 14 000 indexable diffraction patterns, or four per second, from 140 mu g of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption.
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| 45. |
- Townhill, Bryony L., et al.
(author)
-
Pollution in the Arctic Ocean : An overview of multiple pressures and implications for ecosystem services
- 2022
-
In: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 51:2, s. 471-483
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Journal article (peer-reviewed)abstract
- The Arctic is undergoing unprecedented change. Observations and models demonstrate significant perturbations to the physical and biological systems. Arctic species and ecosystems, particularly in the marine environment, are subject to a wide range of pressures from human activities, including exposure to a complex mixture of pollutants, climate change and fishing activity. These pressures affect the ecosystem services that the Arctic provides. Current international policies are attempting to support sustainable exploitation of Arctic resources with a view to balancing human wellbeing and environmental protection. However, assessments of the potential combined impacts of human activities are limited by data, particularly related to pollutants, a limited understanding of physical and biological processes, and single policies that are limited to ecosystem-level actions. This manuscript considers how, when combined, a suite of existing tools can be used to assess the impacts of pollutants in combination with other anthropogenic pressures on Arctic ecosystems, and on the services that these ecosystems provide. Recommendations are made for the advancement of targeted Arctic research to inform environmental practices and regulatory decisions.
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| 46. |
- Vega, Carmen P., et al.
(author)
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Composition, isotopic fingerprint and source attribution of nitrate deposition from rain and fog at a Sub-Arctic Mountain site in Central Sweden (Mt Åreskutan)
- 2019
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In: Tellus. Series B, Chemical and physical meteorology. - : Stockholm University Press. - 0280-6509 .- 1600-0889. ; 71
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Journal article (peer-reviewed)abstract
- While dry and rain deposition of nitrate (NO3-) and ammonium (NH4+) are regularly assessed, fog deposition is often overlooked. This work assesses summer fog events contribution to nitrogen deposition and availability for forest ecosystems. Rain and fog samples were collected at Mt Areskutan, Sweden, during CAEsAR (Cloud and Aerosol Characterization Experiment), in 2014. NH4+ + NO3- represent (31 +/- 25) % of total rain ion amount, and (31 +/- 42) % in fog. Based on ion concentrations and the nitrate stable isotope signatures delta(N-15) and delta(O-18), it was possible to detect the plume generated by the Vastmanland forest fire; NOx emissions from oil rigs and Kola Peninsula; and the plume of Bardarbunga volcano, Iceland. Scavenging of ions by fog was more efficient than by rain. Rain NH4+ and NO3- deposition was (26 +/- 36) mu mol m(-2) d(-1) and (23 +/- 27) mu mol m(-2) d(-1), respectively. Fog NH4+ and NO3- contributed (77 +/- 80) % to total wet deposition of these species. Upscaling rain deposition fluxes to 1 year gave an inorganic nitrogen deposition of (18 +/- 16) mmol m(-2) a(-1) ((252 +/- 224) mg m(-2) a(-1) N equivalents), whereas fog deposition was estimated as (59 +/- 47) mmol m(-2) a(-1) ((826 +/- 658) mg m(-2) a(-1) N equivalents). Annual fog deposition was four times higher than previously reported for the area which only considered rain deposition. However, great uncertainty on the calculation of fog deposition need to be bear in mind. These findings suggest that fog should be considered in deposition estimates of inorganic nitrogen and major ions. If fog deposition is not accounted for, ion wet deposition may be greatly underestimated. Further sampling of wet and dry deposition is important for understanding the influence of nitrogen deposition on forest and vegetation development, as well as soil major ion loads.
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| 47. |
- Åkesson, Susanne, et al.
(author)
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Evolution of chain migration in an aerial insectivorous bird, the common swift Apus apus
- 2020
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In: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 74:10, s. 2377-2391
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Journal article (peer-reviewed)abstract
- Spectacular long-distance migration has evolved repeatedly in animals enabling exploration of resources separated in time and space. In birds, these patterns are largely driven by seasonality, cost of migration, and asymmetries in competition leading most often to leapfrog migration, where northern breeding populations winter furthest to the south. Here, we show that the highly aerial common swift Apus apus, spending the nonbreeding period on the wing, instead exhibits a rarely found chain migration pattern, where the most southern breeding populations in Europe migrate to wintering areas furthest to the south in Africa, whereas the northern populations winter to the north. The swifts concentrated in three major areas in sub-Saharan Africa during the nonbreeding period, with substantial overlap of nearby breeding populations. We found that the southern breeding swifts were larger, raised more young, and arrived to the wintering areas with higher seasonal variation in greenness (Normalized Difference Vegetation Index) earlier than the northern breeding swifts. This unusual chain migration pattern in common swifts is largely driven by differential annual timing and we suggest it evolves by prior occupancy and dominance by size in the breeding quarters and by prior occupancy combined with diffuse competition in the winter.
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| 48. |
- Östh, Jan, 1985, et al.
(author)
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Cluster-based reduced-order modelling of the flow in the wake of a high speed train
- 2015
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In: Journal of Wind Engineering and Industrial Aerodynamics. - : Elsevier BV. - 0167-6105. ; 145, s. 327-338
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Journal article (peer-reviewed)abstract
- The flow field in the wake of a high-speed train is studied by cluster analysis and a cluster-based reduced-order model (CROM) is derived. The CROM strategy is a generalization of the Ulam-Galerkin method for the approximation of the finite-rank Perron-Frobenius operator and constitutes a data-driven approach to extract physical mechanisms in an unsupervised manner. Time-resolved data is first clustered into groups by using the k-means clustering algorithm to yield a small number of representative flow states, the cluster centroids. Then, the cluster transitions are modelled as a Markov process. A further analysis of the derived dynamic model provides information on the interaction of the dominant structures in the flow. The flow field around a generic high-speed train model, here the Aerodynamic Train Model, is obtained from a large-eddy simulation. This train model is designed to reproduce the geometrical features of the ICE2 train. The extracted flow structures can be associated with longitudinal vortices and vortex shedding. Furthermore, these structures are found to be associated with either states of low or high drag of the train.
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| 49. |
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