| 1. |
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| 2. |
- Aartsen, M. G., et al.
(författare)
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Very high-energy gamma-ray follow-up program using neutrino triggers from IceCube
- 2016
-
Ingår i: Journal of Instrumentation. - 1748-0221. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- We describe and report the status of a neutrino-triggered program in IceCube that generates real-time alerts for gamma-ray follow-up observations by atmospheric-Cherenkov telescopes (MAGIC and VERITAS). While IceCube is capable of monitoring the whole sky continuously, high-energy gamma-ray telescopes have restricted fields of view and in general are unlikely to be observing a potential neutrino-flaring source at the time such neutrinos are recorded. The use of neutrino-triggered alerts thus aims at increasing the availability of simultaneous multi-messenger data during potential neutrino flaring activity, which can increase the discovery potential and constrain the phenomenological interpretation of the high-energy emission of selected source classes (e. g. blazars). The requirements of a fast and stable online analysis of potential neutrino signals and its operation are presented, along with first results of the program operating between 14 March 2012 and 31 December 2015.
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| 3. |
- Arndt, D. S., et al.
(författare)
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STATE OF THE CLIMATE IN 2017
- 2018
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 99:8, s. S1-S310
-
Forskningsöversikt (refereegranskat)
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| 4. |
- Arndt, D. S., et al.
(författare)
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State of the Climate in 2016
- 2017
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 98:8, s. S1-S280
-
Tidskriftsartikel (refereegranskat)abstract
- In 2016, the dominant greenhouse gases released into Earth's atmosphere-carbon dioxide, methane, and nitrous oxide-continued to increase and reach new record highs. The 3.5 +/- 0.1 ppm rise in global annual mean carbon dioxide from 2015 to 2016 was the largest annual increase observed in the 58-year measurement record. The annual global average carbon dioxide concentration at Earth's surface surpassed 400 ppm (402.9 +/- 0.1 ppm) for the first time in the modern atmospheric measurement record and in ice core records dating back as far as 800000 years. One of the strongest El Nino events since at least 1950 dissipated in spring, and a weak La Nina evolved later in the year. Owing at least in part to the combination of El Nino conditions early in the year and a long-term upward trend, Earth's surface observed record warmth for a third consecutive year, albeit by a much slimmer margin than by which that record was set in 2015. Above Earth's surface, the annual lower troposphere temperature was record high according to all datasets analyzed, while the lower stratospheric temperature was record low according to most of the in situ and satellite datasets. Several countries, including Mexico and India, reported record high annual temperatures while many others observed near-record highs. A week-long heat wave at the end of April over the northern and eastern Indian peninsula, with temperatures surpassing 44 degrees C, contributed to a water crisis for 330 million people and to 300 fatalities. In the Arctic the 2016 land surface temperature was 2.0 degrees C above the 1981-2010 average, breaking the previous record of 2007, 2011, and 2015 by 0.8 degrees C, representing a 3.5 degrees C increase since the record began in 1900. The increasing temperatures have led to decreasing Arctic sea ice extent and thickness. On 24 March, the sea ice extent at the end of the growth season saw its lowest maximum in the 37-year satellite record, tying with 2015 at 7.2% below the 1981-2010 average. The September 2016 Arctic sea ice minimum extent tied with 2007 for the second lowest value on record, 33% lower than the 1981-2010 average. Arctic sea ice cover remains relatively young and thin, making it vulnerable to continued extensive melt. The mass of the Greenland Ice Sheet, which has the capacity to contribute similar to 7 m to sea level rise, reached a record low value. The onset of its surface melt was the second earliest, after 2012, in the 37-year satellite record. Sea surface temperature was record high at the global scale, surpassing the previous record of 2015 by about 0.01 degrees C. The global sea surface temperature trend for the 21st century-to-date of +0.162 degrees C decade(-1) is much higher than the longer term 1950-2016 trend of +0.100 degrees C decade(-1). Global annual mean sea level also reached a new record high, marking the sixth consecutive year of increase. Global annual ocean heat content saw a slight drop compared to the record high in 2015. Alpine glacier retreat continued around the globe, and preliminary data indicate that 2016 is the 37th consecutive year of negative annual mass balance. Across the Northern Hemisphere, snow cover for each month from February to June was among its four least extensive in the 47-year satellite record. Continuing a pattern below the surface, record high temperatures at 20-m depth were measured at all permafrost observatories on the North Slope of Alaska and at the Canadian observatory on northernmost Ellesmere Island. In the Antarctic, record low monthly surface pressures were broken at many stations, with the southern annular mode setting record high index values in March and June. Monthly high surface pressure records for August and November were set at several stations. During this period, record low daily and monthly sea ice extents were observed, with the November mean sea ice extent more than 5 standard deviations below the 1981-2010 average. These record low sea ice values contrast sharply with the record high values observed during 2012-14. Over the region, springtime Antarctic stratospheric ozone depletion was less severe relative to the 1991-2006 average, but ozone levels were still low compared to pre-1990 levels. Closer to the equator, 93 named tropical storms were observed during 2016, above the 1981-2010 average of 82, but fewer than the 101 storms recorded in 2015. Three basins-the North Atlantic, and eastern and western North Pacific-experienced above-normal activity in 2016. The Australian basin recorded its least active season since the beginning of the satellite era in 1970. Overall, four tropical cyclones reached the Saffir-Simpson category 5 intensity level. The strong El Nino at the beginning of the year that transitioned to a weak La Nina contributed to enhanced precipitation variability around the world. Wet conditions were observed throughout the year across southern South America, causing repeated heavy flooding in Argentina, Paraguay, and Uruguay. Wetter-than-usual conditions were also observed for eastern Europe and central Asia, alleviating the drought conditions of 2014 and 2015 in southern Russia. In the United States, California had its first wetter-than-average year since 2012, after being plagued by drought for several years. Even so, the area covered by drought in 2016 at the global scale was among the largest in the post-1950 record. For each month, at least 12% of land surfaces experienced severe drought conditions or worse, the longest such stretch in the record. In northeastern Brazil, drought conditions were observed for the fifth consecutive year, making this the longest drought on record in the region. Dry conditions were also observed in western Bolivia and Peru; it was Bolivia's worst drought in the past 25 years. In May, with abnormally warm and dry conditions already prevailing over western Canada for about a year, the human-induced Fort McMurray wildfire burned nearly 590000 hectares and became the costliest disaster in Canadian history, with $3 billion (U.S. dollars) in insured losses.
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| 5. |
- Ades, M., et al.
(författare)
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Global Climate : in State of the climate in 2019
- 2020
-
Ingår i: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 101:8, s. S17-S127
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Tidskriftsartikel (refereegranskat)
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| 6. |
- Ades, M., et al.
(författare)
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GLOBAL CLIMATE
- 2020
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Ingår i: BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY. - 0003-0007 .- 1520-0477. ; 101:8
-
Tidskriftsartikel (refereegranskat)
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| 7. |
- Mayer, Manuel, et al.
(författare)
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Constraints on particle acceleration in SS433/W50 from MAGIC and HESS observations
- 2018
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 612
-
Tidskriftsartikel (refereegranskat)abstract
- Context. The large jet kinetic power and non-thermal processes occurring in the microquasar SS 433 make this source a good candidate for a very high-energy (VHE) gamma-ray emitter. Gamma-ray fluxes above the sensitivity limits of current Cherenkov telescopes have been predicted for both the central X-ray binary system and the interaction regions of SS 433 jets with the surrounding W50 nebula. Non-thermal emission at lower energies has been previously reported, indicating that efficient particle acceleration is taking place in the system. Aims. We explore the capability of SS 433 to emit VHE gamma rays during periods in which the expected flux attenuation due to periodic eclipses (P-orb similar to 13.1 days) and precession of the circumstellar disk (P-pre similar to 162 days) periodically covering the central binary system is expected to be at its minimum. The eastern and western SS 433/W50 interaction regions are also examined using the whole data set available. We aim to constrain some theoretical models previously developed for this system with our observations. Methods. We made use of dedicated observations from the Major Atmospheric Gamma Imaging Cherenkov telescopes (MAGIC) and High Energy Spectroscopic System (H.E.S.S.) of SS 433 taken from 2006 to 2011. These observation were combined for the first time and accounted for a total effective observation time of 16.5 h, which were scheduled considering the expected phases of minimum absorption of the putative VHE emission. Gamma-ray attenuation does not affect the jet/medium interaction regions. In this case, the analysis of a larger data set amounting to similar to 40-80 h, depending on the region, was employed. Results. No evidence of VHE gamma-ray emission either from the central binary system or from the eastern/western interaction regions was found. Upper limits were computed for the combined data set. Differential fluxes from the central system are found to be less than or similar to 10(-12)-10(-13) TeV-1 cm(-2) s(-1) in an energy interval ranging from similar to few x 100 GeV to similar to few TeV. Integral flux limits down to similar to 10(-12)-10(-13) ph cm(-2) s(-1) and similar to 10(-13)-10(-14) ph cm(-2) s(-1) are obtained at 300 and 800 GeV, respectively. Our results are used to place constraints on the particle acceleration fraction at the inner jet regions and on the physics of the jet/medium interactions. Conclusions. Our findings suggest that the fraction of the jet kinetic power that is transferred to relativistic protons must be relatively small in SS 433, q(p) <= 2.5 x 10(-5), to explain the lack of TeV and neutrino emission from the central system. At the SS 433/W50 interface, the presence of magnetic fields greater than or similar to 10 mu G is derived assuming a synchrotron origin for the observed X-ray emission. This also implies the presence of high-energy electrons with E-e up to 50 TeV, preventing an efficient production of gamma-ray fluxes in these interaction regions.
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| 8. |
- Aleksic, J., et al.
(författare)
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Measurement of the Crab Nebula spectrum over three decades in energy with the MAGIC telescopes
- 2015
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Ingår i: Journal of High Energy Astrophysics. - : Elsevier BV. - 2214-4048 .- 2214-4056. ; 5-6, s. 30-38
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Tidskriftsartikel (refereegranskat)abstract
- The MAGIC stereoscopic system collected 69 hours of Crab Nebula data between October 2009 and April 2011. Analysis of this data sample using the latest improvements in the MAGIC stereoscopic software provided an unprecedented precision of spectral and night-by-night light curve determination at gamma rays. We derived a differential spectrum with a single instrument from 50 GeV up to almost 30 TeV with 5 bins per energy decade. At low energies, MAGIC results, combined with Fermi-LAT data, show a flat and broad Inverse Compton peak. The overall fit to the data between 1 GeV and 30 TeV is not well described by a log-parabola function. We find that a modified log-parabola function with an exponent of 2.5 instead of 2 provides a good description of the data (chi(2)(red) = 35/26). Using systematic uncertainties of the MAGIC and Fermi-LAT measurements we determine the position of the Inverse Compton peak to be at (53 +/- 3(stat)+ 31(syst)-13(syst)) GeV, which is the most precise estimation up to date and is dominated by the systematic effects. There is no hint of the integral flux variability on daily scales at energies above 300 GeV when systematic uncertainties are included in the flux measurement. We consider three state-of-the-art theoretical models to describe the overall spectral energy distribution of the Crab Nebula. The constant B-field model cannot satisfactorily reproduce the VHE spectral measurements presented in this work, having particular difficulty reproducing the broadness of the observed IC peak. Most probably this implies that the assumption of the homogeneity of the magnetic field inside the nebula is incorrect. On the other hand, the time-dependent 1D spectral model provides a good fit of the new VHE results when considering a 80 mu G magnetic field. However, it fails to match the data when including the morphology of the nebula at lower wavelengths.
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| 9. |
- Aleksic, J., et al.
(författare)
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MAGIC reveals a complex morphology within the unidentified gamma-ray source HESS J1857+026
- 2014
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 571
-
Tidskriftsartikel (refereegranskat)abstract
- Aims. HESS J1857+026 is an extended TeV gamma-ray source that was discovered by H. E. S. S. as part of its Galactic plane survey. Given its broadband spectral energy distribution and its spatial coincidence with the young energetic pulsar PSR J1856+0245, the source has been put forward as a pulsar wind nebula (PWN) candidate. MAGIC has performed follow-up observations aimed at mapping the source down to energies approaching 100 GeV in order to better understand its complex morphology. Methods. HESS J1857+026 was observed by MAGIC in 2010, yielding 29 h of good quality stereoscopic data that allowed us to map the source region in two separate ranges of energy. Results. We detected very-high-energy gamma-ray emission from HESS J1857+026 with a significance of 12 sigma above 150 GeV. The differential energy spectrum between 100 GeV and 13 TeV is described well by a power law function dN/dE = N-0(E/1TeV)(-Gamma) with N-0 = (5.37 +/- 0.44(stat) +/- 1.5(sys)) X 10(-12) (TeV-1 cm(-2) s(-1)) and Gamma = 2.16 +/- 0.07(stat) +/- 0.15(sys), which bridges the gap between the GeV emission measured by Fermi-LAT and the multi-TeV emission measured by H.E.S.S.. In addition, we present a detailed analysis of the energy-dependent morphology of this region. We couple these results with archival multiwavelength data and outline evidence in favor of a two-source scenario, whereby one source is associated with a PWN, while the other could be linked with a molecular cloud complex containing an HII region and a possible gas cavity.
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| 10. |
- Ahnen, M. L., et al.
(författare)
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Limits to dark matter annihilation cross-section from a combined analysis of MAGIC and Fermi-LAT observations of dwarf satellite galaxies
- 2016
-
Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :2
-
Tidskriftsartikel (refereegranskat)abstract
- We present the first joint analysis of gamma-ray data from the MAGIC Cherenkov telescopes and the Fermi Large Area Telescope (LAT) to search for gamma-ray signals from dark matter annihilation in dwarf satellite galaxies. We combine 158 hours of Segue 1 observations with MAGIC with 6-year observations of 15 dwarf satellite galaxies by the Fermi-LAT. We obtain limits on the annihilation cross-section for dark matter particle masses between 10 GeV and 100 TeV - the widest mass range ever explored by a single gamma-ray analysis. These limits improve on previously published Fermi-LAT and MAGIC results by up to a factor of two at certain masses. Our new inclusive analysis approach is completely generic and can be used to perform a global, sensitivity-optimized dark matter search by combining data from present and future gamma-ray and neutrino detectors.
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| 11. |
- Soranzo, Nicole, et al.
(författare)
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A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 41:11, s. 38-1182
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Tidskriftsartikel (refereegranskat)abstract
- The number and volume of cells in the blood affect a wide range of disorders including cancer and cardiovascular, metabolic, infectious and immune conditions. We consider here the genetic variation in eight clinically relevant hematological parameters, including hemoglobin levels, red and white blood cell counts and platelet counts and volume. We describe common variants within 22 genetic loci reproducibly associated with these hematological parameters in 13,943 samples from six European population-based studies, including 6 associated with red blood cell parameters, 15 associated with platelet parameters and 1 associated with total white blood cell count. We further identified a long-range haplotype at 12q24 associated with coronary artery disease and myocardial infarction in 9,479 cases and 10,527 controls. We show that this haplotype demonstrates extensive disease pleiotropy, as it contains known risk loci for type 1 diabetes, hypertension and celiac disease and has been spread by a selective sweep specific to European and geographically nearby populations.
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| 12. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 13. |
- Coll, M., et al.
(författare)
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Towards Oxide Electronics: a Roadmap
- 2019
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Ingår i: Applied Surface Science. - : Elsevier BV. - 0169-4332 .- 1873-5584. ; 482, s. 1-93
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Tidskriftsartikel (refereegranskat)abstract
- At the end of a rush lasting over half a century, in which CMOS technology has been experiencing a constant and breathtaking increase of device speed and density, Moore’s law is approaching the insurmountable barrier given by the ultimate atomic nature of matter. A major challenge for 21st century scientists is finding novel strategies, concepts and materials for replacing silicon-based CMOS semiconductor technologies and guaranteeing a continued and steady technological progress in next decades. Among the materials classes candidate to contribute to this momentous challenge, oxide films and heterostructures are a particularly appealing hunting ground. The vastity, intended in pure chemical terms, of this class of compounds, the complexity of their correlated behaviour, and the wealth of functional properties they display, has already made these systems the subject of choice, worldwide, of a strongly networked, dynamic and interdisciplinary research community. Oxide science and technology has been the target of a wide four-year project, named Towards Oxide-Based Electronics (TO-BE), that has been recently running in Europe and has involved as participants several hundred scientists from 29 EU countries. In this review and perspective paper, published as a final deliverable of the TO-BE Action, the opportunities of oxides as future electronic materials for Information and Communication Technologies ICT and Energy are discussed. The paper is organized as a set of contributions, all selected and ordered as individual building blocks of a wider general scheme. After a brief preface by the editors and an introductory contribution, two sections follow. The first is mainly devoted to providing a perspective on the latest theoretical and experimental methods that are employed to investigate oxides and to produce oxide-based films, heterostructures and devices. In the second, all contributions are dedicated to different specific fields of applications of oxide thin films and heterostructures, in sectors as data storage and computing, optics and plasmonics, magnonics, energy conversion and harvesting, and power electronics.
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| 14. |
- Berntsson, Oskar, 1989, et al.
(författare)
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Sequential conformational transitions and alpha-helical supercoiling regulate a sensor histidine kinase
- 2017
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Sensor histidine kinases are central to sensing in bacteria and in plants. They usually contain sensor, linker, and kinase modules and the structure of many of these components is known. However, it is unclear how the kinase module is structurally regulated. Here, we use nano- to millisecond time-resolved X-ray scattering to visualize the solution structural changes that occur when the light-sensitive model histidine kinase YF1 is activated by blue light. We find that the coiled coil linker and the attached histidine kinase domains undergo a left handed rotation within microseconds. In a much slower second step, the kinase domains rearrange internally. This structural mechanism presents a template for signal transduction in sensor histidine kinases.
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| 15. |
- Berntsson, Oskar, 1989, et al.
(författare)
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Time-Resolved X-Ray Solution Scattering Reveals the Structural Photoactivation of a Light-Oxygen-Voltage Photoreceptor
- 2017
-
Ingår i: Structure. - : Elsevier BV. - 0969-2126. ; 25:6
-
Tidskriftsartikel (refereegranskat)abstract
- Light-oxygen-voltage (LOV) receptors are sensory proteins controlling a wide range of organismal adaptations in multiple kingdoms of life. Because of their modular nature, LOV domains are also attractive for use as optogenetic actuators. A flavin chromophore absorbs blue light, forms a bond with a proximal cysteine residue, and induces changes in the surroundings. There is a gap of knowledge on how this initial signal is relayed further through the sensor to the effector module. To characterize these conformational changes, we apply time-resolved X-ray scattering to the homodimeric LOV domain from Bacillus subtilis YtvA. We observe a global structural change in the LOV dimer synchronous with the formation of the chromophore photoproduct state. Using molecular modeling, this change is identified as splaying apart and relative rotation of the two monomers, which leads to an increased separation at the anchoring site of the effector modules.
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| 16. |
- Rockstuhl, C., et al.
(författare)
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Large scale simulations in the realm of nanooptics
- 2010
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Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. - 0277-786X .- 1996-756X. - 9780819480002 ; 7604
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The realm of nanooptics is usually characterized by the interaction of light with structures having relevant feature sizes much smaller than the wavelength. To model such problems, a large variety of methods exists. However, most of them either require a periodic arrangement of a unit cell or can handle only single entities. But there exists a great variety of functional devices which may have either a spatial extent much larger than the wavelength and which comprise structural details with sizes in the order of a fraction of the wavelength or they may consist of an amorphous arrangement of strongly scattering entities. Such structures require large scale simulations where the fine details are retained. In this contribution we outline our latest research on such devices and detail the computational peculiarities we have to overcome. Presenting several examples, we show how simulations support the physical understanding of these devices. Examples are randomly textured surfaces used for solar cells, where guided modes excited in the light absorbing layers strongly affect the solar cell efficiency, amorphous metamaterials and stochastically arranged nanoantennas. The usage of computational experiments will be motivated by the unprecedented insight into the functionality of such components. © 2010 Copyright SPIE - The International Society for Optical Engineering.
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| 17. |
- Björling, Alexander, 1983, et al.
(författare)
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Structural photoactivation of a full-length bacterial phytochrome
- 2016
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 2:8
-
Tidskriftsartikel (refereegranskat)abstract
- Phytochromes are light sensor proteins found in plants, bacteria, and fungi. They function by converting a photon absorption event into a conformational signal that propagates from the chromophore through the entire protein. However, the structure of the photoactivated state and the conformational changes that lead to it are not known. We report time-resolved x-ray scattering of the full-length phytochrome from Deinococcus radiodurans on micro-and millisecond time scales. We identify a twist of the histidine kinase output domains with respect to the chromophore-binding domains as the dominant change between the photoactivated and resting states. The time-resolved data further show that the structural changes up to the microsecond time scales are small and localized in the chromophore-binding domains. The global structural change occurs within a few milliseconds, coinciding with the formation of the spectroscopic meta-Rc state. Our findings establish key elements of the signaling mechanism of full-length bacterial phytochromes.
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| 18. |
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| 19. |
- Takala, H., et al.
(författare)
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On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome
- 2018
-
Ingår i: Journal of Biological Chemistry. - 0021-9258. ; 293:21, s. 8161-8172
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Tidskriftsartikel (refereegranskat)abstract
- Phytochromes are photoreceptors in plants, fungi, and various microorganisms and cycle between metastable red light-absorbing (Pr) and far-red light-absorbing (Pfr) states. Their light responses are thought to follow a conserved structural mechanism that is triggered by isomerization of the chromophore. Downstream structural changes involve refolding of the so-called tongue extension of the phytochrome-specific GAF-related (PHY) domain of the photoreceptor. The tongue is connected to the chromophore by conserved DIP and PRXSF motifs and a conserved tyrosine, but the role of these residues in signal transduction is not clear. Here, we examine the tongue interactions and their interplay with the chromophore by substituting the conserved tyrosine (Tyr(263)) in the phytochrome from the extremophile bacterium Deinococcus radiodurans with phenylalanine. Using optical and FTIR spectroscopy, X-ray solution scattering, and crystallography of chromophore-binding domain (CBD) and CBD-PHY fragments, we show that the absence of the Tyr(263) hydroxyl destabilizes the -sheet conformation of the tongue. This allowed the phytochrome to adopt an -helical tongue conformation regardless of the chromophore state, hence distorting the activity state of the protein. Our crystal structures further revealed that water interactions are missing in the Y263F mutant, correlating with a decrease of the photoconversion yield and underpinning the functional role of Tyr(263) in phytochrome conformational changes. We propose a model in which isomerization of the chromophore, refolding of the tongue, and globular conformational changes are represented as weakly coupled equilibria. The results also suggest that the phytochromes have several redundant signaling routes.
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| 20. |
- Andersson, Robin, et al.
(författare)
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A Segmental Maximum A Posteriori Approach to Genome-wide Copy Number Profiling
- 2008
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 24:6, s. 751-758
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- MOTIVATION: Copy number profiling methods aim at assigning DNA copy numbers to chromosomal regions using measurements from microarray-based comparative genomic hybridizations. Among the proposed methods to this end, Hidden Markov Model (HMM)-based approaches seem promising since DNA copy number transitions are naturally captured in the model. Current discrete-index HMM-based approaches do not, however, take into account heterogeneous information regarding the genomic overlap between clones. Moreover, the majority of existing methods are restricted to chromosome-wise analysis. RESULTS: We introduce a novel Segmental Maximum A Posteriori approach, SMAP, for DNA copy number profiling. Our method is based on discrete-index Hidden Markov Modeling and incorporates genomic distance and overlap between clones. We exploit a priori information through user-controllable parameterization that enables the identification of copy number deviations of various lengths and amplitudes. The model parameters may be inferred at a genome-wide scale to avoid overfitting of model parameters often resulting from chromosome-wise model inference. We report superior performances of SMAP on synthetic data when compared with two recent methods. When applied on our new experimental data, SMAP readily recognizes already known genetic aberrations including both large-scale regions with aberrant DNA copy number and changes affecting only single features on the array. We highlight the differences between the prediction of SMAP and the compared methods and show that SMAP accurately determines copy number changes and benefits from overlap consideration.
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| 21. |
- Bartel, T., et al.
(författare)
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Investigations on enhanced Fischer–Burmeister NCP functions : application to a rate-dependent model for ferroelectrics
- 2019
-
Ingår i: Archive of Applied Mechanics. - : Springer Science and Business Media LLC. - 0939-1533 .- 1432-0681. ; 89:6, s. 995-1010
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Tidskriftsartikel (refereegranskat)abstract
- This contribution deals with investigations on enhanced Fischer–Burmeister nonlinear complementarity problem (NCP) functions applied to a rate-dependent laminate-based material model for ferroelectrics. The framework is based on the modelling and parametrisation of the material’s microstructure via laminates together with the respective volume fractions. These volume fractions are treated as internal-state variables and are subject to several inequality constraints which can be treated in terms of Karush–Kuhn–Tucker conditions. The Fischer–Burmeister NCP function provides a sophisticated scheme to incorporate Karush–Kuhn–Tucker-type conditions into calculations of internal-state variables. However, these functions are prone to numerical instabilities in their original form. Therefore, some enhanced formulations of the Fischer–Burmeister ansatz are discussed and compared to each other in this contribution.
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| 22. |
- Baust, A., et al.
(författare)
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Ultrastrong coupling in two-resonator circuit QED
- 2016
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Ingår i: Physical Review B. - 2469-9969 .- 2469-9950. ; 93:21, s. Art. no. 214501-
-
Tidskriftsartikel (refereegranskat)abstract
- We report on ultrastrong coupling between a superconducting flux qubit and a resonant mode of a system comprised of two superconducting coplanar stripline resonators coupled galvanically to the qubit. With a coupling strength as high as 17.5% of the mode frequency, exceeding that of previous circuit quantum electrodynamics experiments, we observe a pronounced Bloch-Siegert shift. The spectroscopic response of our multimode system reveals a clear breakdown of the Jaynes-Cummings approximation. In contrast to earlier experiments, the high coupling strength is achieved without making use of an additional inductance provided by a Josephson junction.
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| 23. |
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| 24. |
- Biermann, D., et al.
(författare)
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Modelling and simulation of thermal effects in internal traverse grinding of hardened bearing steel
- 2016
-
Ingår i: CIRP Annals - Manufacturing Technology. - : Elsevier BV. - 0007-8506. ; 65:1, s. 321-324
-
Tidskriftsartikel (refereegranskat)abstract
- Internal traverse grinding with electro-plated cBN wheels combines the advantages of both internal hard turning and internal grinding, enabling a high material removal rate along with a high surface quality. The drawback, however, is a high thermal load on the workpiece, resulting in shape and dimension errors of the finished part. This paper deals with the compensation of these manufacturing errors with a hybrid simulation system. It combines thermo-mechanically coupled finite element models on both meso- and macro-scale with a scale-bridging kinematic simulation system, enabling the prediction of the resulting temperatures and the development of corresponding simulation-based compensation strategies.
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| 25. |
- Buckley, Patrick G., et al.
(författare)
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Identification of genetic aberrations on chromosome 22 outside the NF2 locus in schwannomatosis and neurofibromatosis type 2
- 2005
-
Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 26:6, s. 540-9
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Tidskriftsartikel (refereegranskat)abstract
- Schwannomatosis is characterized by multiple peripheral and cranial nerve schwannomas that occur in the absence of bilateral 8th cranial nerve schwannomas. The latter is the main diagnostic criterion of neurofibromatosis type 2 (NF2), which is a related but distinct disorder. The genetic factors underlying the differences between schwannomatosis and NF2 are poorly understood, although available evidence implicates chromosome 22 as the primary location of the gene(s) of interest. To investigate this, we comprehensively profiled the DNA copy number in samples from sporadic and familial schwannomatosis, NF2, and a large cohort of normal controls. Using a tiling-path chromosome 22 genomic array, we identified two candidate regions of copy number variation, which were further characterized by a PCR-based array with higher resolution. The latter approach allows the detection of minute alterations in total genomic DNA, with as little as 1.5 kb per measurement point of nonredundant sequence on the array. In DNA derived from peripheral blood from a schwannomatosis patient and a sporadic schwannoma sample, we detected rearrangements of the immunoglobulin lambda (IGL) locus, which is unlikely to be due to a B-cell specific somatic recombination of IGL. Analysis of normal controls indicated that these IGL rearrangements were restricted to schwannomatosis/schwannoma samples. In the second candidate region spanning GSTT1 and CABIN1 genes, we observed a frequent copy number polymorphism at the GSTT1 locus. We further describe missense mutations in the CABIN1 gene that are specific to samples from schwannomatosis and NF2 and make this gene a plausible candidate for contributing to the pathogenesis of these disorders.
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| 26. |
- Böddecker, M., et al.
(författare)
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Effect of uncertainty of material parameters on stress triaxiality and Lode angle in finite elasto-plasticity—A variance-based global sensitivity analysis
- 2023
-
Ingår i: Advances in Industrial and Manufacturing Engineering. - 2666-9129. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- This work establishes a computational framework for the quantification of the effect of uncertainty of material model parameters on extremal stress triaxiality and Lode angle values in plastically deformed devices, whereby stress triaxiality and Lode angle are accepted as key indicators for damage initiation in metal forming processes. Attention is paid to components, the material response of which can be represented as elasto-plastic with proportional hardening as a prototype model, whereby the finite element method is used as a simulation approach generally suitable for complex geometries and loading conditions. Uncertainty about material parameters is characterized resorting to probability theory. The effects of material parameter uncertainty on stress triaxiality and Lode angle are quantified by means of a variance-based global sensitivity analysis. Such sensitivity analysis is most useful for apportioning the variance of the stress triaxiality and Lode angle to the uncertainty on material properties. The practical implementation of this sensitivity analysis is carried out resorting to a Gaussian process regression, Bayesian probabilistic integration and active learning in order to decrease the associated numerical costs. An example illustrates the proposed framework, revealing that parameters governing plasticity affect stress triaxiality and Lode angle the most.
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| 27. |
- Dehghani, H., et al.
(författare)
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The role of microscale solid matrix compressibility on the mechanical behaviour of poroelastic materials
- 2020
-
Ingår i: European Journal of Mechanics, A/Solids. - : Elsevier BV. - 0997-7538. ; 83
-
Tidskriftsartikel (refereegranskat)abstract
- We present the macroscale three-dimensional numerical solution of anisotropic Biot's poroelasticity, with coefficients derived from a micromechanical analysis as prescribed by the asymptotic homogenisation technique. The system of partial differential equations (PDEs) is discretised by finite elements, exploiting a formal analogy with the fully coupled thermal displacement systems of PDEs implemented in the commercial software Abaqus. The robustness of our computational framework is confirmed by comparison with the well-known analytical solution of the one-dimensional Therzaghi's consolidation problem. We then perform three-dimensional numerical simulations of the model in a sphere (representing a biological tissue) by applying a given constant pressure in the cavity. We investigate how the macroscale radial displacements (as well as pressures) profiles are affected by the microscale solid matrix compressibility (MSMC). Our results suggest that the role of the MSMC on the macroscale displacements becomes more and more prominent by increasing the length of the time interval during which the constant pressure is applied. As such, we suggest that parameter estimation based on techniques such as poroelastography (which are commonly used in the context of biological tissues, such as the brain, as well as solid tumours) should allow for a sufficiently long time in order to give a more accurate estimation of the mechanical properties of tissues.
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| 28. |
- Erdogan, F, et al.
(författare)
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Impact of low copy repeats on the generation of balanced and unbalanced chromosomal aberrations in mental retardation
- 2006
-
Ingår i: Cytogenetic and Genome Research. - : S. Karger AG. - 1424-859X .- 1424-8581. ; 115:3-4, s. 247-253
-
Tidskriftsartikel (refereegranskat)abstract
- Low copy repeats (LCRs) are stretches of duplicated DNA that are more than 1 kb in size and share a sequence similarity that exceeds 90%. Non-allelic homologous recombination (NAHR) between highly similar LCRs has been implicated in numerous genomic disorders. This study aimed at defining the impact of LCRs on the generation of balanced and unbalanced chromosomal rearrangements in mentally retarded patients. A cohort of 22 patients, preselected for the presence of submicroscopic imbalances, was analysed using submegabase resolution tiling path array CGH and the results were compared with a set of 41 patients with balanced translocations and breakpoints that were mapped to the BAC level by FISH. Our data indicate an accumulation of LCRs at breakpoints of both balanced and unbalanced rearrangements. LCRs with high sequence similarity in both breakpoint regions, suggesting NAHR as the most likely cause of rearrangement, were observed in 6/22 patients with chromosomal imbalances, but not in any of the balanced translocation cases studied. In case of chromosomal imbalances, the likelihood of NAHR seems to be inversely related to the size of the aberration. Our data also suggest the presence of additional mechanisms coinciding with or dependent on the presence of LCRs that may induce an increased instability at these chromosomal sites.
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| 29. |
- Fellinger, Joris, et al.
(författare)
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Tungsten based divertor development for Wendelstein 7-X
- 2023
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Ingår i: Nuclear Materials and Energy. - 2352-1791. ; 37
-
Tidskriftsartikel (refereegranskat)abstract
- Wendelstein 7-X, the world’s largest superconducting stellarator in Greifswald (Germany), started plasma experiments with a water-cooled plasma-facing wall in 2022, allowing for long pulse operation. In parallel, a project was launched in 2021 to develop a W based divertor, replacing the current CFC divertor, to demonstrate plasma performance of a stellarator with a reactor relevant plasma facing materials with low tritium retention. The project consists of two tasks: Based on experience from the previous experimental campaigns and improved physics modelling, the geometry of the plasma-facing surface of the divertor and baffles is optimized to prevent overloads and to improve exhaust. In parallel, the manufacturing technology for a W based target module is qualified. This paper gives a status update of project. It focusses on the conceptual design of a W based target module, the manufacturing technology and its qualification, which is conducted in the framework of the EUROfusion funded WPDIV program. A flat tile design in which a target module is made of a single target element is pursued. The technology must allow for moderate curvatures of the plasma-facing surface to follow the magnetic field lines. The target element is designed for steady state heat loads of 10 MW/m2 (as for the CFC divertor). Target modules of a similar size and weight as for the CFC divertor are assumed (approx. < 0.25 m2 and < 60 kg) using the existing water cooling infrastructure providing 5 l/s and roughly maximum 15 bar pressure drop per module. The main technology under qualification is based on a CuCrZr heat sink made either by additive manufacturing using laser powder bed fusion (LPBF) or by uniaxial diffusion welding of pre-machined forged CuCrZr plates. After heat treatment, the plasma-facing side of the heat sink is covered by W or if feasible by the more ductile WNiFe, preferably by coating or alternatively by hot isostatic pressing W based tiles with a soft OFE-Cu interlayer. Last step is a final machining of the plasma-exposed surface and the interfaces to the water supply lines and supports to correct manufacturing deformations.
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| 30. |
- Galizia, C. G., et al.
(författare)
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Relationship of visual and olfactory signal parameters in a food-deceptive flower mimicry system
- 2005
-
Ingår i: Behavioral Ecology. - : Oxford University Press (OUP). - 1045-2249 .- 1465-7279. ; 16:1, s. 159-168
-
Tidskriftsartikel (refereegranskat)abstract
- Pollinators such as bees are attracted to flowers by their visual display and their scent. Although most flowers reinforce visits by providing pollen and/or nectar, there are species-notably from the orchid family-that do not but do resemble rewarding species. These mimicry relationships provide ideal opportunities for investigating the evolution of floral signals and their impact on pollinator behavior. Here, we have reanalyzed a case of specialized food mimicry between the orchid Orchis israelitica and its model, the lily Bellevalia flexuosa. Based on current knowledge of insect sensory physiology, we were able to characterize both the visual and olfactory signals of model and mimic, as well as of two phylogenetically related orchids. By using a color vision model, we mapped each species' visual signals to the perceptual space of honeybees and found an apparent shift of the mimic's visual signals towards the model. We confirm that visual mimicry is present. We analyzed the flower odors by using gas chromatography/mass spectroscopy. We related these signals to the perceptual space of the pollinators by testing the scent extracts physiologically, using in vivo brain imaging. We found no evidence of olfactory mimicry. The results indicate that evolutionary pressure acts on the visual, but not olfactory, traits of O. israelitica toward a higher similarity to its model. Apparently, odor mismatch does not prevent a bee from landing on a flower that has the expected visual display. The results therefore argue for the dominance of visual stimuli in short-distance flower choice. The orchid may still depend on long-distance olfactory attraction originating from neighboring model plants.
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| 31. |
- Herlin, G, et al.
(författare)
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Quantitative assessment of 99mTc-depreotide uptake in patients with non-small-cell lung cancer: immunohistochemical correlations
- 2009
-
Ingår i: Acta radiologica (Stockholm, Sweden : 1987). - : SAGE Publications. - 1600-0455 .- 0284-1851. ; 50:8, s. 902-908
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Somatostatin receptor (SSTR) scintigraphy with 99mTc-depreotide is used for differential diagnosis of solitary pulmonary nodules. The method is based on SSTR expression in cancer tissue. Purpose: To estimate the expression of SSTRs in non-small-cell lung cancer (NSCLC) in vitro, and to determine the correlation between 99mTc-depreotide uptake in vivo and different tumor characteristics determined in vitro, such as tumor grade, and presence of SSTR2, MIB-1, and p53. Material and Methods: A total of 127 patients with lung lesions detected on computed tomography (CT) were investigated with SSTR scintigraphy after injection of 740 MBq 99mTc-depreotide. This study includes 19 patients with NSCLC with histologically proven diagnosis. The quantitative evaluation of 99mTc-depreotide was performed using region-of-interest analysis and includes tumor counts/cm3, background counts/cm3, and the ratio between tumor and background counts. Results: 99mTc-depreotide uptake was found in all NSCLC tumors, which expressed SSTR2 defined in vitro by immunochemical methods. SSTR2 expression was negatively correlated to the degree of the tumor's differentiation ( P<0.05). 99mTc-depreotide uptake in tumor cells did not correlate with tumor grade, or SSTR2, MIB-1, or p53 expression. Conclusion: There is an expression of SSTRs in NSCLC. The degree of tumor differentiation correlates negatively with SSTR2 measured in vitro and positively with MIB-1 expression in tumor tissue. No correlation was found between 99mTc-depreotide uptake and possible prognostic factors such as MIB-1 and p53 expression in tumor cells in NSCLC. Lastly, no correlation was found between 99mTc-depreotide uptake and tumor grade or SSTR2 expression.
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| 32. |
- Holtermann, R., et al.
(författare)
-
A Hybrid Approach to the Modelling and Simulation of Grinding Processes
- 2014
-
Ingår i: Proceedings of the 11th World Congress on Computational Mechanics (WCCM XI); 5th European Conference on Computational Mechanics (ECCM V); 6th European Conference on Computational Fluid Dynamics (ECFD VI). - 9788494284472 ; , s. 1932-1937
-
Konferensbidrag (refereegranskat)abstract
- We present recent advances in the modelling and simulation of Internal Traverse Grinding, a high performance grinding process incorporating a high rate of material removal combined with a high surface quality. Due to a special grinding wheel geometry, the latter two goals are achieved in just one pass of the tool through the axisymmetric workpiece. The simulation framework we present generally consists of three components. The first one is a parametric plane strain, h-adaptive finite element model capturing the material penetration of a single cBN grain on a meso-scale during the machining process. Secondly, a topography analysis procedure as well as a kinematic simulation have been developed to measure and analyse the surface topography of an actual grinding wheel. We then use this information to model the grinding wheel surface in the latter kinematic simulation. This enables us to perform an exact calculation of the transient penetration history of every grain intersecting with the workpiece bulk. The superposition of these results is then used in the third component of the simulation framework, namely a process scale workpiece model currently under development which captures the effects of thermo-mechanical loads on the workpiece undergoing material removal and thus, in the near future, shall enable us to predict potential unwanted phase transformations of the bulk surface as well as size and shape errors of the finished part. In this contribution, we will focus on the first two parts of the simulation framework, namely the meso-scale as well as the kinematic simulation and the coupling between the two scales.
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| 33. |
- Holtermann, R., et al.
(författare)
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Numerical Determination of Process Values Influencing the Surface Integrity in Grinding
- 2016
-
Ingår i: 3rd CIRP Conference on Surface Integrity. - : Elsevier BV. - 2212-8271. - 9781510824621 ; 45, s. 39-42
-
Konferensbidrag (refereegranskat)abstract
- Internal traverse grinding with electroplated cBN wheels using high-speed process conditions combines high material removal rates and a high surface quality of the workpiece in one single grinding stroke. In order to capture the macroscopic and mesoscopic thermo-mechanical loads onto the workpiece during internal traverse grinding, numerical simulations are conducted at the two scales. This results in a hybrid approach coupling two finite element models with a geometric kinematic simulation. The article focuses on the influence of multiple grain engagements onto a surface layer region using a two-dimensional chip formation simulation.
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| 34. |
- Junker, Robert R., et al.
(författare)
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Covariation and phenotypic integration in chemical communication displays : Biosynthetic constraints and eco-evolutionary implications
- 2018
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 220:3, s. 739-749
-
Tidskriftsartikel (refereegranskat)abstract
- Chemical communication is ubiquitous. The identification of conserved structural elements in visual and acoustic communication is well established, but comparable information on chemical communication displays (CCDs) is lacking. We assessed the phenotypic integration of CCDs in a meta-analysis to characterize patterns of covariation in CCDs and identified functional or biosynthetically constrained modules. Poorly integrated plant CCDs (i.e. low covariation between scent compounds) support the notion that plants often utilize one or few key compounds to repel antagonists or to attract pollinators and enemies of herbivores. Animal CCDs (mostly insect pheromones) were usually more integrated than those of plants (i.e. stronger covariation), suggesting that animals communicate via fixed proportions among compounds. Both plant and animal CCDs were composed of modules, which are groups of strongly covarying compounds. Biosynthetic similarity of compounds revealed biosynthetic constraints in the covariation patterns of plant CCDs. We provide a novel perspective on chemical communication and a basis for future investigations on structural properties of CCDs. This will facilitate identifying modules and biosynthetic constraints that may affect the outcome of selection and thus provide a predictive framework for evolutionary trajectories of CCDs in plants and animals.
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| 35. |
- Maniprakash, S., et al.
(författare)
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Experimental investigation, modelling and simulation of rate-dependent response of 1-3 ferroelectric composites
- 2016
-
Ingår i: Mechanics of Materials. - : Elsevier BV. - 0167-6636. ; 94, s. 91-105
-
Tidskriftsartikel (refereegranskat)abstract
- Further development and design of piezoelectric composites enhances the improved use of piezoelectric materials and devices by overcoming their brittleness. In order to engineer this class of materials and to predictably simulate its behaviour, a computationally efficient constitutive model is established in this paper. This contribution deals with the development of a model for piezoelectric composites to capture their effective behaviour. We first discuss a three-dimensional fully coupled electromechanical rate-dependent model for the response of ferroelectric ceramics. Secondly, a simple homogenisation approach is applied to capture the behaviour of composites for various volume fractions of PZT fibres under different loading frequencies. Following this, a finite element formulation is applied in order to study the behaviour of composites. Finally, these two approaches are compared with experimental results.
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| 36. |
- Mantripragada, K K, et al.
(författare)
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Identification of novel deletion breakpoints bordered by segmental duplications in the NF1 locus using high resolution array-CGH.
- 2006
-
Ingår i: Journal of medical genetics. - : BMJ. - 1468-6244 .- 0022-2593. ; 43:1, s. 28-38
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Segmental duplications flanking the neurofibromatosis type 1 (NF1) gene locus on 17q11 mediate most gene deletions in NF1 patients. However, the large size of the gene and the complexity of the locus architecture pose difficulties in deletion analysis. We report the construction and application of the first NF1 locus specific microarray, covering 2.24 Mb of 17q11, using a non-redundant approach for array design. The average resolution of analysis for the array is approximately 12 kb per measurement point with an increased average resolution of 6.4 kb for the NF1 gene. METHODS: We performed a comprehensive array-CGH analysis of 161 NF1 derived samples and identified heterozygous deletions of various sizes in 39 cases. The typical deletion was identified in 26 cases, whereas 13 samples showed atypical deletion profiles. RESULTS: The size of the atypical deletions, contained within the segment covered by the array, ranged from 6 kb to 1.6 Mb and their breakpoints could be accurately determined. Moreover, 10 atypical deletions were observed to share a common breakpoint either on the proximal or distal end of the deletion. The deletions identified by array-CGH were independently confirmed using multiplex ligation-dependent probe amplification. Bioinformatic analysis of the entire locus identified 33 segmental duplications. CONCLUSIONS: We show that at least one of these segmental duplications, which borders the proximal breakpoint located within the NF1 intron 1 in five atypical deletions, might represent a novel hot spot for deletions. Our array constitutes a novel and reliable tool offering significantly improved diagnostics for this common disorder.
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| 37. |
- Menzel, Annette, et al.
(författare)
-
European phenological response to climate change matches the warming pattern
- 2006
-
Ingår i: Global Change Biology. - 1354-1013 .- 1365-2486. ; 12:10, s. 1969-1976
-
Tidskriftsartikel (refereegranskat)abstract
- Global climate change impacts can already be tracked in many physical and biological systems; in particular, terrestrial ecosystems provide a consistent picture of observed changes. One of the preferred indicators is phenology, the science of natural recurring events, as their recorded dates provide a high-temporal resolution of ongoing changes. Thus, numerous analyses have demonstrated an earlier onset of spring events for mid and higher latitudes and a lengthening of the growing season. However, published single-site or single-species studies are particularly open to suspicion of being biased towards predominantly reporting climate change-induced impacts. No comprehensive study or meta-analysis has so far examined the possible lack of evidence for changes or shifts at sites where no temperature change is observed. We used an enormous systematic phenological network data set of more than 125000 observational series of 542 plant and 19 animal species in 21 European countries (1971-2000). Our results showed that 78% of all leafing, flowering and fruiting records advanced (30% significantly) and only 3% were significantly delayed, whereas the signal of leaf colouring/fall is ambiguous. We conclude that previously published results of phenological changes were not biased by reporting or publication predisposition: the average advance of spring/summer was 2.5 days decade -1 in Europe. Our analysis of 254 mean national time series undoubtedly demonstrates that species' phenology is responsive to temperature of the preceding months (mean advance of spring/summer by 2.5 days °C -1, delay of leaf colouring and fall by 1.0 day °C -1). The pattern of observed change in spring efficiently matches measured national warming across 19 European countries (correlation coefficient r = -0.69, P < 0.001).
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| 38. |
- Menzel, Andreas, et al.
(författare)
-
On a computational orientation-distribution-function-based remodelling framework
- 2007
-
Ingår i: Proceedings of the 20th Nordic Seminar on Computational Mechanics.
-
Konferensbidrag (refereegranskat)abstract
- In this contribution, we apply the framework of orientation distribution functions (odf) to the modelling of adapting anisotropic biological tissues. Remodelling phenomena are thereby incorporated by means of an evolution equation for a generalised structural tensor so that the underlying odf evolves according to the local loading conditions.
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| 39. |
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| 40. |
- Nasedkin, Alexandr, et al.
(författare)
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Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation
- 2015
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5
-
Tidskriftsartikel (refereegranskat)abstract
- The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un) folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un) folding reaction has often been questioned. One of the most well studied (un) folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un) folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un) folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.
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| 41. |
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| 42. |
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| 43. |
- Schumann, S., et al.
(författare)
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Determination of the Thermal Load Distribution in Internal Traverse Grinding using a Geometric-Kinematic Simulation
- 2015
-
Ingår i: 15th CIRP Conference on Modelling of Machining Operations (15TH CMMO). - : Elsevier BV. - 2212-8271. ; 31, s. 322-327
-
Konferensbidrag (refereegranskat)abstract
- During grinding processes, numerous grains interact with the workpiece material producing mechanical and thermal loads on the surface. In the field of thermal simulation of grinding processes, a widely used approach is to substitute numerous cutting edges by a single moving distributed heat source of a specific geometrical shape referring to the theory of Carslaw and Jaeger. This heat source is then moved across the modelled workpiece according to the specific kinematics of the grinding process. The geometrical shape of the substituted heat source can usually be determined using different approaches, e.g., predefined distribution functions or, more precisely, based on measurements of the shear stress within the contact zone. Referring to the state of the art, it is not possible to measure the shear stress within the contact zone during internal traverse grinding with roughing and finishing zone because of its very complex engagement conditions and the non-rectangular shape of its contact zone. In this work, a novel approach to determining a heat source distribution based on a geometric-kinematic simulation for internal traverse grinding is presented. This simulation identifies the ideal geometrical interaction of workpiece and grinding wheel. For this purpose, the specific material removal rate for each grain is calculated and accumulated with respect to the contact zone resulting in a three-dimensional thermal load distribution. This heat source can be used in finite element simulations to determine the thermal load on the workpiece. (C) 2015 The Authors. Published by Elsevier B.V.
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| 44. |
- Sverrild, A., et al.
(författare)
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Tezepelumab decreases airway epithelial IL-33 and T2-inflammation in response to viral stimulation in patients with asthma
-
Ingår i: Allergy: European Journal of Allergy and Clinical Immunology. - 0105-4538.
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Respiratory virus infections are main triggers of asthma exacerbations. Tezepelumab, an anti-TSLP mAb, reduces exacerbations in patients with asthma, but the effect of blocking TSLP on host epithelial resistance and tolerance to virus infection is not known. Aim: To examine effects of blocking TSLP in patients with asthma on host resistance (IFNβ, IFNλ, and viral load) and on the airway epithelial inflammatory response to viral challenge. Methods: Bronchoalveolar lavage fluid (BALF, n = 39) and bronchial epithelial cells (BECs) were obtained from patients with uncontrolled asthma before and after 12 weeks of tezepelumab treatment (n = 13) or placebo (n = 13). BECs were cultured in vitro and exposed to the viral infection mimic poly(I:C) or infected by rhinovirus (RV). Alarmins, T2- and pro-inflammatory cytokines, IFNβ IFNλ, and viral load were analyzed by RT-qPCR and multiplex ELISA before and after stimulation. Results: IL-33 expression in unstimulated BECs and IL-33 protein levels in BALF were reduced after 12 weeks of tezepelumab. Further, IL-33 gene and protein levels decreased in BECs challenged with poly(I:C) after tezepelumab whereas TSLP gene expression remained unaffected. Poly(I:C)-induced IL-4, IL-13, and IL-17A release from BECs was also reduced with tezepelumab whereas IFNβ and IFNλ expression and viral load were unchanged. Conclusion: Blocking TSLP with tezepelumab in vivo in asthma reduced the airway epithelial inflammatory response including IL-33 and T2 cytokines to viral challenge without affecting anti-viral host resistance. Our results suggest that blocking TSLP stabilizes the bronchial epithelial immune response to respiratory viruses.
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| 45. |
- Takala, Heikki, et al.
(författare)
-
Light-induced structural changes in a monomeric bacteriophytochrome
- 2016
-
Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 3:5
-
Tidskriftsartikel (refereegranskat)abstract
- Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from Deinococcus radiodurans. The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains. Infrared spectroscopy shows the refolding of the PHY tongue. We conclude that a monomer of the phytochrome photosensory core is sufficient to perform the light-induced structural changes. This implies that allosteric cooperation with the other monomer is not needed for structural activation. The dimeric arrangement may instead be intrinsic to the biochemical output domains of bacterial phytochromes. © Author(s) 2016.
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| 46. |
- Takala, Heikki, et al.
(författare)
-
Signal amplification and transduction in phytochrome photosensors
- 2014
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 509:7499, s. 245-248
-
Tidskriftsartikel (refereegranskat)abstract
- Sensory proteins must relay structural signals from the sensory site over large distances to regulatory output domains. Phytochromes are a major family of red-light-sensing kinases that control diverse cellular functions in plants, bacteria and fungi(1-9). Bacterial phytochromes consist of a photosensory core and a carboxy-terminal regulatory domain(10,11). Structures of photosensory cores are reported in the resting state(12-18) and conformational responses to light activation have been proposed in the vicinity of the chromophore(19-23). However, the structure of the signalling state and the mechanism of downstream signal relay through the photosensory core remain elusive. Here we report crystal and solution structures of the resting and activated states of the photosensory core of the bacteriophytochrome from Deinococcus radiodurans. The structures show an open and closed form of the dimeric protein for the activated and resting states, respectively. This nanometre-scale rearrangement is controlled by refolding of an evolutionarily conserved 'tongue', which is in contact with the chromophore. The findings reveal an unusual mechanism in which atomic-scale conformational changes around the chromophore are first amplified into ana angstrom-scale distance change in the tongue, and further grow into a nanometre-scale conformational signal. The structural mechanism is a blueprint for understanding how phytochromes connect to the cellular signalling network.
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| 47. |
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| 48. |
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