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We present an excerpt of the document "Quantum Information Processing and Communication: Strategic report on current status, visions and goals for research in Europe", which has been recently published in electronic form at the website of FET (the Future and Emerging Technologies Unit of the Directorate General Information Society of the European Commission, http://www.cordis.lu/ist/fet/qipc-sr.htm). This document has been elaborated, following a former suggestion by FET, by a committee of QIPC scientists to provide input towards the European Commission for the preparation of the Seventh Framework Program. Besides being a document addressed to policy makers and funding agencies (both at the European and national level), the document contains a detailed scientific assessment of the state-of-the-art, main research goals, challenges, strengths, weaknesses, visions and perspectives of all the most relevant QIPC sub-fields, that we report here
This thesis aims to investigate the visualization approaches in the field of annotated discourse relations and to find a solution that meets the requirements best by comparing different programming tools. The subject of this research are coherence relations, which have several properties that can be challenging for many visualization methods. The thesis presents five different visualization options from both the application and the development perspective. The initially tested simple HTML approaches as well as the software package displaCy show the insufficient level for the visualization purposes of this work. The alternative implementation with D3 would optimally meet the requirements but goes beyond the scope of the project. The main method chosen in this thesis was implemented as a single web application and uses the brat annotation tool, which fulfills most of the defined requirements for the representation of the coherence relations. The application graphically displays the coherence relations annotated in the text and offers a filter function for different relation types.
The morphological features in the deviations of the total electron content (TEC) of the ionosphere from the background undisturbed state as possible precursors of the earthquake of January 12, 2010 (21:53 UT (16:53 LT), 18.46A degrees N, 72.5A degrees W, 7.0 M) in Haiti are analyzed. To identify these features, global and regional differential TEC maps based on global 2-h TEC maps provided by NASA in the IONEX format were plotted. For the considered earthquake, long-lived disturbances, presumably of seismic origin, were localized in the near-epicenter area and were accompanied by similar effects in the magnetoconjugate region. Both decreases and increases in the local TEC over the period from 22 UT of January 10 to 08 UT of January 12, 2010 were observed. The horizontal dimensions of the anomalies were similar to 40A degrees in longitude and similar to 20A degrees in latitude, with the magnitude of TEC disturbances reaching similar to 40% relative to the background near the epicenter and more than 50% in the magnetoconjugate area. No significant geomagnetic disturbances within January 1-12, 2010 were observed, i.e., the detected TEC anomalies were manifestations of interplay between processes in the lithosphere-atmosphere-ionosphere system.
The main morphological features of variations of the total electron content (TEC) of the ionosphere before the earthquakes on March 11, 2011 (Japan) and October 23, 2011 (Turkey) are examined. The revealed features are compared to those of ionospheric TEC disturbances observed prior to several other large seismic events, as well as to those included in a list of the most frequently observed ionospheric TEC disturbances interpreted as possible ionospheric precursors of earthquakes. It is shown that, in the periods of preparation of the earthquakes under consideration, on March 8-11 and October 20-23, abnormal ionospheric TEC disturbances were observed as long-lived structures in a near-epicentral region and in the region magnetically conjugated to it.
Aims. Sunspot distribution in the northern and southern solar hemispheres exibit striking synchronous behaviour on the scale of a Schwabe cycle. However, sometimes the bilateral symmetry of the Butterfly diagram relative to the solar equatorial plane breaks down. The investigation of this phenomenon is important to explaining the almost-periodic behaviour of solar cycles. Methods. We use cross-recurrence plots for the study of the time-varying phase asymmetry of the northern and southern hemisphere and compare our results with the latitudinal distribution of the sunspots. Results. We observe a long-term persistence of phase leading in one of the hemispheres, which lasts almost 4 solar cycles and probably corresponds to the Gleissberg cycle. Long-term variations in the hemispheric-leading do not demonstrate clear periodicity but are strongly anti-correlated with the long-term variations in the magnetic equator.
This dissertation examines the integration of incongruent visual-scene and morphological-case information (“cues”) in building thematic-role representations of spoken relative clauses in German.
Addressing the mutual influence of visual and linguistic processing, the Coordinated Interplay Account (CIA) describes a mechanism in two steps supporting visuo-linguistic integration (Knoeferle & Crocker, 2006, Cog Sci). However, the outcomes and dynamics of integrating incongruent thematic-role representations from distinct sources have been investigated scarcely. Further, there is evidence that both second-language (L2) and older speakers may rely on non-syntactic cues relatively more than first-language (L1)/young speakers. Yet, the role of visual information for thematic-role comprehension has not been measured in L2 speakers, and only limitedly across the adult lifespan.
Thematically unambiguous canonically ordered (subject-extracted) and noncanonically ordered (object-extracted) spoken relative clauses in German (see 1a-b) were presented in isolation and alongside visual scenes conveying either the same (congruent) or the opposite (incongruent) thematic relations as the sentence did.
1 a Das ist der Koch, der die Braut verfolgt.
This is the.NOM cook who.NOM the.ACC bride follows
This is the cook who is following the bride.
b Das ist der Koch, den die Braut verfolgt.
This is the.NOM cook whom.ACC the.NOM bride follows
This is the cook whom the bride is following.
The relative contribution of each cue to thematic-role representations was assessed with agent identification. Accuracy and latency data were collected post-sentence from a sample of L1 and L2 speakers (Zona & Felser, 2023), and from a sample of L1 speakers from across the adult lifespan (Zona & Reifegerste, under review). In addition, the moment-by-moment dynamics of thematic-role assignment were investigated with mouse tracking in a young L1 sample (Zona, under review).
The following questions were addressed: (1) How do visual scenes influence thematic-role representations of canonical and noncanonical sentences? (2) How does reliance on visual-scene, case, and word-order cues vary in L1 and L2 speakers? (3) How does reliance on visual-scene, case, and word-order cues change across the lifespan?
The results showed reliable effects of incongruence of visually and linguistically conveyed thematic relations on thematic-role representations. Incongruent (vs. congruent) scenes yielded slower and less accurate responses to agent-identification probes presented post-sentence. The recently inspected agent was considered as the most likely agent ~300ms after trial onset, and the convergence of visual scenes and word order enabled comprehenders to assign thematic roles predictively.
L2 (vs. L1) participants relied more on word order overall. In response to noncanonical clauses presented with incongruent visual scenes, sensitivity to case predicted the size of incongruence effects better than L1-L2 grouping. These results suggest that the individual’s ability to exploit specific cues might predict their weighting.
Sensitivity to case was stable throughout the lifespan, while visual effects increased with increasing age and were modulated by individual interference-inhibition levels. Thus, age-related changes in comprehension may stem from stronger reliance on visually (vs. linguistically) conveyed meaning.
These patterns represent evidence for a recent-role preference – i.e., a tendency to re-assign visually conveyed thematic roles to the same referents in temporally coordinated utterances. The findings (i) extend the generalizability of CIA predictions across stimuli, tasks, populations, and measures of interest, (ii) contribute to specifying the outcomes and mechanisms of detecting and indexing incongruent representations within the CIA, and (iii) speak to current efforts to understand the sources of variability in sentence comprehension.
Downscaling of microfluidic cell culture and detection devices for electrochemical monitoring has mostly focused on miniaturization of the microfluidic chips which are often designed for specific applications and therefore lack functional flexibility. We present a compact microfluidic cell culture and electrochemical analysis platform with in-built fluid handling and detection, enabling complete cell based assays comprising on-line electrode cleaning, sterilization, surface functionalization, cell seeding, cultivation and electrochemical real-time monitoring of cellular dynamics. To demonstrate the versatility and multifunctionality of the platform, we explored amperometric monitoring of intracellular redox activity in yeast (Saccharomyces cerevisiae) and detection of exocytotically released dopamine from rat pheochromocytoma cells (PC12). Electrochemical impedance spectroscopy was used in both applications for monitoring cell sedimentation and adhesion as well as proliferation in the case of PC12 cells. The influence of flow rate on the signal amplitude in the detection of redox metabolism as well as the effect of mechanical stimulation on dopamine release were demonstrated using the programmable fluid handling capability. The here presented platform is aimed at applications utilizing cell based assays, ranging from e.g. monitoring of drug effects in pharmacological studies, characterization of neural stem cell differentiation, and screening of genetically modified microorganisms to environmental monitoring.
Lava domes are severely hazardous, mound-shaped extrusions of highly viscous lava and commonly erupt at many active stratovolcanoes around the world. Due to gradual growth and flank oversteepening, such lava domes regularly experience partial or full collapses, resulting in destructive and far-reaching pyroclastic density currents. They are also associated with cyclic explosive activity as the complex interplay of cooling, degassing, and solidification of dome lavas regularly causes gas pressurizations on the dome or the underlying volcano conduit. Lava dome extrusions can last from days to decades, further highlighting the need for accurate and reliable monitoring data.
This thesis aims to improve our understanding of lava dome processes and to contribute to the monitoring and prediction of hazards posed by these domes. The recent rise and sophistication of photogrammetric techniques allows for the extraction of observational data in unprecedented detail and creates ideal tools for accomplishing this purpose. Here, I study natural lava dome extrusions as well as laboratory-based analogue models of lava dome extrusions and employ photogrammetric monitoring by Structure-from-Motion (SfM) and Particle-Image-Velocimetry (PIV) techniques. I primarily use aerial photography data obtained by helicopter, airplanes, Unoccupied Aircraft Systems (UAS) or ground-based timelapse cameras. Firstly, by combining a long time-series of overflight data at Volcán de Colima, México, with seismic and satellite radar data, I construct a detailed timeline of lava dome and crater evolution. Using numerical model, the impact of the extrusion on dome morphology and loading stress is further evaluated and an impact on the growth direction is identified, bearing important implications for the location of collapse hazards. Secondly, sequential overflight surveys at the Santiaguito lava dome, Guatemala, reveal surface motion data in high detail. I quantify the growth of the lava dome and the movement of a lava flow, showing complex motions that occur on different timescales and I provide insight into rock properties relevant for hazard assessment inferred purely by photogrammetric processing of remote sensing data. Lastly, I recreate artificial lava dome and spine growth using analogue modelling under controlled conditions, providing new insights into lava extrusion processes and structures as well as the conditions in which they form.
These findings demonstrate the capabilities of photogrammetric data analyses to successfully monitor lava dome growth and evolution while highlighting the advantages of complementary modelling methods to explain the observed phenomena. The results presented herein further bear important new insights and implications for the hazards posed by lava domes.
During eruptive activity of andesitic stratovolcanoes, the extrusion of lava domes, their collapse and intermittent explosions are common volcanic hazards. Many lava domes grow in a preferred direction, in turn affecting the direction of lava flows and pyroclastic density currents. Access to active lava domes is difficult and hazardous, so detailed data characterizing lava dome growth are typically limited, keeping the processes controlling the directionality of extrusions unclear. Here we combine TerraSAR-X satellite radar observations with high-resolution airborne photogrammetry to assess morphological changes, and perform finite element modeling to investigate the impact of loading stress on shallow magma ascent directions associated with lava dome extrusion and crater formation at Volcan de Colima, Mexico. The TerraSAR-X data, acquired in similar to 1-m resolution spotlight mode, enable us to derive a chronology of the eruptive processes from intensity-based time-lapse observations of the general crater and dome evolution. The satellite images are complemented by close-range airborne photos, processed by the Structure-from-Motion workflow. This allows the derivation of high-resolution digital elevation models, providing insight into detailed loading and unloading features. During the observation period from Jan-2013 to Feb-2016, we identify a dominantly W-directed dome growth and lava flow production until Jan-2015. In Feb-2015, following the removal of the active summit dome, the surface crater widened and elongated along a NE-SW axis. Later in May-2015, a new dome grew toward the SW of the crater while a separate vent developed in the NE of the crater, reflecting a change in the direction of magma ascent and possible conduit bifurcation. Finite element models show a significant stress change in agreement with the observed magma ascent direction changes in response to the changing surface loads, both for loading (dome growth) and unloading (crater forming excavation) cases. These results allow insight into shallow dome growth dynamics and the migration of magma ascent in response to changing volcano summit morphology. They further highlight the importance of detailed volcano summit morphology surveillance, as changes in direction or location of dome extrusion may have major implications regarding the directions of potential volcanic hazards, such as pyroclastic density currents generated by dome collapse.
This article presents a simple and facile method to fabricate thermoresponsive polymer-grafted silica particles by direct surface-initiated photopolymerization of N-isopropylacrylamide (NIPAM). This method is based on silica particles bearing thiol functionalities, which are transformed into thiyl radicals by irradiation with UV light to initiate the polymerization of NIPAM in aqueous media at room temperature. The photopolymerization of NIPAM could be applied to smaller thiol-functionalized particles (approximate to 48 nm) as well as to larger particles (approximate to 692 nm). Hollow poly(NIPAM) capsules could be formed after etching away the silica cores from the composite particles. It is possible to produce tailor-made composite particles or capsules for particular applications by extending this approach to other vinyl monomers. (c) 2015 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 2015, 53, 1260-1267
Polymeric matrices mimicking multiple functions of the ECM are expected to enable a material induced regeneration of tissues. Here, we investigated the adipogenic differentiation of human adipose derived mesenchymal stem cells (hADSCs) in a 3D architectured gelatin based hydrogel (ArcGel) prepared from gelatin and L-lysine diisocyanate ethyl ester (LDI) in an one-step process, in which the formation of an open porous morphology and the chemical network formation were integrated. The ArcGel was designed to support adipose tissue regeneration with its 3D porous structure, high cell biocompatibility, and mechanical properties compatible with human subcutaneous adipose tissue. The ArcGel could support initial cell adhesion and survival of hADSCs. Under static culture condition, the cells could migrate into the inner part of the scaffold with a depth of 840 +/- 120 mu m after 4 days, and distributed in the whole scaffold (2mm in thickness) within 14 days. The cells proliferated in the scaffold and the fold increase of cell number after 7 days of culture was 2.55 +/- 0.08. The apoptotic rate of hADSCs in the scaffold was similar to that of cells maintained on tissue culture plates. When cultured in adipogenic induction medium, the hADSCs in the scaffold differentiated into adipocytes with a high efficiency (93 +/- 1%). Conclusively, this gelatin based 3D scaffold presented high cell compatibility for hADSC cultivation and differentiation, which could serve as a potential implant material in clinical applications for adipose tissue reparation and regeneration.
In this work, some new results to exploit the recurrence properties of quasiperiodic dynamical systems are presented by means of a two dimensional visualization technique, Recurrence Plots(RPs). Quasiperiodicity is the simplest form of dynamics exhibiting nontrivial recurrences, which are common in many nonlinear systems. The concept of recurrence was introduced to study the restricted three body problem and it is very useful for the characterization of nonlinear systems. I have analyzed in detail the recurrence patterns of systems with quasiperiodic dynamics both analytically and numerically. Based on a theoretical analysis, I have proposed a new procedure to distinguish quasiperiodic dynamics from chaos. This algorithm is particular useful in the analysis of short time series. Furthermore, this approach demonstrates to be efficient in recognizing regular and chaotic trajectories of dynamical systems with mixed phase space. Regarding the application to real situations, I have shown the capability and validity of this method by analyzing time series from fluid experiments.
We investigate the bifurcation structures in a two-dimensional parameter space (PS) of a parametrically excited system with two degrees of freedom both analytically and numerically. By means of the Renyi entropy of second order K-2, which is estimated from recurrence plots, we uncover that regions of chaotic behavior are intermingled with many complex periodic windows, such as shrimp structures in the PS. A detailed numerical analysis shows that, the stable solutions lose stability either via period doubling, or via intermittency when the parameters leave these shrimps in different directions, indicating different bifurcation properties of the boundaries. The shrimps of different sizes offer promising ways to control the dynamics of such a complex system.
Background: Agility in general and change-of-direction speed (CoD) in particular represent important performance determinants in elite soccer.
Objectives: The objectives of this study were to determine the effects of a 6-week neuromuscular training program on agility performance, and to determine differences in movement times between the slower and faster turning directions in elite soccer players. Materials and Methods: Twenty male elite soccer players from the Stade Rennais Football Club (Ligue 1, France) participated in this study. The players were randomly assigned to a neuromuscular training group (NTG, n = 10) or an active control (CG, n = 10) according to their playing position. NTG participated in a 6-week, twice per week neuromuscular training program that included CoD, plyometric and dynamic stability exercises. Neuromuscular training replaced the regular warm-up program. Each training session lasted 30 min. CG continued their regular training program. Training volume was similar between groups. Before and after the intervention, the two groups performed a reactive agility test that included 180° left and right body rotations followed by a 5-m linear sprint. The weak side was defined as the left/right turning direction that produced slower overall movement times (MT). Reaction time (RT) was assessed and defined as the time from the first appearance of a visual stimulus until the athlete’s first movement. MT corresponded to the time from the first movement until the athlete reached the arrival gate (5 m distance).
Results: No significant between-group baseline differences were observed for RT or MT. Significant group x time interactions were found for MT (p = 0.012, effect size = 0.332, small) for the slower and faster directions (p = 0.011, effect size = 0.627, moderate). Significant pre-to post improvements in MT were observed for NTG but not CG (p = 0.011, effect size = 0.877, moderate). For NTG, post hoc analyses revealed significant MT improvements for the slower (p = 0.012, effect size = 0.897, moderate) and faster directions (p = 0.017, effect size = 0.968, moderate).
Conclusion: Our results illustrate that 6 weeks of neuromuscular training with two sessions per week included in the warm-up program, significantly enhanced agility performance in elite soccer players. Moreover, improvements were found on both sides during body rotations. Thus, practitioners are advised to focus their training programs on both turning directions.
Background: Agility in general and change-of-direction speed (CoD) in particular represent important performance determinants in elite soccer.
Objectives: The objectives of this study were to determine the effects of a 6-week neuromuscular training program on agility performance, and to determine differences in movement times between the slower and faster turning directions in elite soccer players. Materials and Methods: Twenty male elite soccer players from the Stade Rennais Football Club (Ligue 1, France) participated in this study. The players were randomly assigned to a neuromuscular training group (NTG, n = 10) or an active control (CG, n = 10) according to their playing position. NTG participated in a 6-week, twice per week neuromuscular training program that included CoD, plyometric and dynamic stability exercises. Neuromuscular training replaced the regular warm-up program. Each training session lasted 30 min. CG continued their regular training program. Training volume was similar between groups. Before and after the intervention, the two groups performed a reactive agility test that included 180° left and right body rotations followed by a 5-m linear sprint. The weak side was defined as the left/right turning direction that produced slower overall movement times (MT). Reaction time (RT) was assessed and defined as the time from the first appearance of a visual stimulus until the athlete’s first movement. MT corresponded to the time from the first movement until the athlete reached the arrival gate (5 m distance).
Results: No significant between-group baseline differences were observed for RT or MT. Significant group x time interactions were found for MT (p = 0.012, effect size = 0.332, small) for the slower and faster directions (p = 0.011, effect size = 0.627, moderate). Significant pre-to post improvements in MT were observed for NTG but not CG (p = 0.011, effect size = 0.877, moderate). For NTG, post hoc analyses revealed significant MT improvements for the slower (p = 0.012, effect size = 0.897, moderate) and faster directions (p = 0.017, effect size = 0.968, moderate).
Conclusion: Our results illustrate that 6 weeks of neuromuscular training with two sessions per week included in the warm-up program, significantly enhanced agility performance in elite soccer players. Moreover, improvements were found on both sides during body rotations. Thus, practitioners are advised to focus their training programs on both turning directions.
Coated vesicles provide a major mechanism for the transport of proteins through the endomembrane system of plants. Transport between the endoplasmic reticulum and the Golgi involves vesicles with COPI and COPII coats, whereas clathrin is the predominant coat in endocytosis and post-Golgi trafficking. Sorting of cargo, coat assembly, budding, and fission are all complex and tightly regulated processes that involve many proteins. The mechanisms and responsible factors are largely conserved in eukaryotes, and increasing organismal complexity tends to be associated with a greater numbers of individual family members. Among the key factors is the class of ENTH/ANTH/VHS domain-containing proteins, which link membrane subdomains, clathrin, and other adapter proteins involved in early steps of clathrin coated vesicle formation. More than 30 Arabidopsis thaliana proteins contain this domain, but their generally low sequence conservation has made functional classification difficult. Reports from the last two years have greatly expanded our knowledge of these proteins and suggest that ENTH/ANTH/VHS domain proteins are involved in various instances of clathrin-related endomembrane trafficking in plants. This review aims to summarize these new findings and discuss the broader context of clathrin-dependent plant vesicular transport.
Objective: We investigated the effects of combined balance and strength training on measures of balance and muscle strength in older women with a history of falls.
Methods: Twenty-seven older women aged 70.4 ± 4.1 years (age range: 65 to 75 years) were randomly allocated to either an intervention (IG, n = 12) or an active control (CG, n = 15) group. The IG completed 8 weeks combined balance and strength training program with three sessions per week including visual biofeedback using force plates. The CG received physical therapy and gait training at a rehabilitation center. Training volumes were similar between the groups. Pre and post training, tests were applied for the assessment of muscle strength (weight-bearing squat [WBS] by measuring the percentage of body mass borne by each leg at different knee flexions [0°, 30°, 60°, and 90°], sit-to-stand test [STS]), and balance. Balance tests used the modified clinical test of sensory interaction (mCTSIB) with eyes closed (EC) and opened (EO), on stable (firm) and unstable (foam) surfaces as well as spatial parameters of gait such as step width and length (cm) and walking speed (cm/s).
Results: Significant group × time interactions were found for different degrees of knee flexion during WBS (0.0001 < p < 0.013, 0.441 < d < 0.762). Post hoc tests revealed significant pre-to-post improvements for both legs and for all degrees of flexion (0.0001 < p < 0.002, 0.697 < d < 1.875) for IG compared to CG. Significant group × time interactions were found for firm EO, foam EO, firm EC, and foam EC (0.006 < p < 0.029; 0.302 < d < 0.518). Post hoc tests showed significant pre-to-post improvements for both legs and for all degrees of oscillations (0.0001 < p < 0.004, 0.753 < d < 2.097) for IG compared to CG. This study indicates that combined balance and strength training improved percentage distribution of body weight between legs at different conditions of knee flexion (0°, 30°, 60°, and 90°) and also decreased the sway oscillation on a firm surface with eyes closed, and on foam surface (with eyes opened or closed) in the IG.
Conclusion: The higher positive effects of training seen in standing balance tests, compared with dynamic tests, suggests that balance training exercises including lateral, forward, and backward exercises improved static balance to a greater extent in older women.
Objective: We investigated the effects of combined balance and strength training on measures of balance and muscle strength in older women with a history of falls.
Methods: Twenty-seven older women aged 70.4 ± 4.1 years (age range: 65 to 75 years) were randomly allocated to either an intervention (IG, n = 12) or an active control (CG, n = 15) group. The IG completed 8 weeks combined balance and strength training program with three sessions per week including visual biofeedback using force plates. The CG received physical therapy and gait training at a rehabilitation center. Training volumes were similar between the groups. Pre and post training, tests were applied for the assessment of muscle strength (weight-bearing squat [WBS] by measuring the percentage of body mass borne by each leg at different knee flexions [0°, 30°, 60°, and 90°], sit-to-stand test [STS]), and balance. Balance tests used the modified clinical test of sensory interaction (mCTSIB) with eyes closed (EC) and opened (EO), on stable (firm) and unstable (foam) surfaces as well as spatial parameters of gait such as step width and length (cm) and walking speed (cm/s).
Results: Significant group × time interactions were found for different degrees of knee flexion during WBS (0.0001 < p < 0.013, 0.441 < d < 0.762). Post hoc tests revealed significant pre-to-post improvements for both legs and for all degrees of flexion (0.0001 < p < 0.002, 0.697 < d < 1.875) for IG compared to CG. Significant group × time interactions were found for firm EO, foam EO, firm EC, and foam EC (0.006 < p < 0.029; 0.302 < d < 0.518). Post hoc tests showed significant pre-to-post improvements for both legs and for all degrees of oscillations (0.0001 < p < 0.004, 0.753 < d < 2.097) for IG compared to CG. This study indicates that combined balance and strength training improved percentage distribution of body weight between legs at different conditions of knee flexion (0°, 30°, 60°, and 90°) and also decreased the sway oscillation on a firm surface with eyes closed, and on foam surface (with eyes opened or closed) in the IG.
Conclusion: The higher positive effects of training seen in standing balance tests, compared with dynamic tests, suggests that balance training exercises including lateral, forward, and backward exercises improved static balance to a greater extent in older women.
During the period 750-600 Ma ago, prior to the final break-up of the supercontinent Rodinia, the crust of both the North American Craton and Baltica was intruded by significant amounts of rift-related magmas originating from the mantle. In the Proterozoic crust of Southern Norway, the 580 Ma old Fen carbonatite-ultramafic complex is a representative of this type of rocks. In this paper, we report the occurrence of an ultramafic lamprophyre dyke which possibly is linked to the Fen complex, although Ar-40/Ar-39 data from phenocrystic phlogopite from the dyke gave an age of 686 +/- 9 Ma. The lamprophyre dyke was recently discovered in one of the Kongsberg silver mines at Vinoren, Norway. Whole rock geochemistry, geochronological and mineralogical data from the ultramafic lamprophyre dyke are presented aiming to elucidate its origin and possible geodynamic setting. From the whole-rock composition of the Vinoren dyke, the rock could be recognized as transitional between carbonatite and kimberlite-II (orangeite). From its diagnostic mineralogy, the rock is classified as aillikite. The compositions and xenocrystic nature of several of the major and accessory minerals from the Vinoren aillikite are characteristic for diamondiferous rocks (kimberlites/lamproites/UML): Phlogopite with kinoshitalite-rich rims, chromite-spinel-ulvospinel series, Mg- and Mn-rich ilmenites, rutile and lucasite-(Ce). We suggest that the aillikite melt formed during partial melting of a MARID (mica-amphibole-rutile-ilmenite-diopside)-like source under CO2 fluxing. The pre-rifting geodynamic setting of the Vinoren aillikite before the Rodinia supercontinent breakup suggests a relatively thick SCLM (Subcontinental Lithospheric Mantle) during this stage and might indicate a diamond-bearing source for the parental melt. This is in contrast to the about 100 Ma younger Fen complex, which were derived from a thin SCLM.
Photovoltaic cells based on halide perovskites, possessing remarkably high power conversion efficiencies have been reported. To push the development of such devices further, a comprehensive and reliable understanding of their electronic properties is essential but presently not available. To provide a solid foundation for understanding the electronic properties of polycrystalline thin films, we employ single-crystal band structure data from angle-resolved photoemission measurements. For two prototypical perovskites (CH3NH3PbBr3 and CH3NH3PbI3), we reveal the band dispersion in two high-symmetry directions and identify the global valence band maxima. With these benchmark data, we construct "standard" photoemission spectra from polycrystalline thin film samples and resolve challenges discussed in the literature for determining the valence band onset with high reliability. Within the framework laid out here, the consistency of relating the energy level alignment in perovskite-based photovoltaic and optoelectronic devices with their functional parameters is substantially enhanced.
The remarkable progress of metal halide perovskites in photovoltaics has led to the power conversion efficiency approaching 26%. However, practical applications of perovskite-based solar cells are challenged by the stability issues, of which the most critical one is photo-induced degradation. Bare CH3NH3PbI3 perovskite films are known to decompose rapidly, with methylammonium and iodine as volatile species and residual solid PbI2 and metallic Pb, under vacuum under white light illumination, on the timescale of minutes. We find, in agreement with previous work, that the degradation is non-uniform and proceeds predominantly from the surface, and that illumination under N-2 and ambient air (relative humidity 20%) does not induce substantial degradation even after several hours. Yet, in all cases the release of iodine from the perovskite surface is directly identified by X-ray photoelectron spectroscopy. This goes in hand with a loss of organic cations and the formation of metallic Pb. When CH3NH3PbI3 films are covered with a few nm thick organic capping layer, either charge selective or non-selective, the rapid photodecomposition process under ultrahigh vacuum is reduced by more than one order of magnitude, and becomes similar in timescale to that under N-2 or air. We conclude that the light-induced decomposition reaction of CH3NH3PbI3, leading to volatile methylammonium and iodine, is largely reversible as long as these products are restrained from leaving the surface. This is readily achieved by ambient atmospheric pressure, as well as a thin organic capping layer even under ultrahigh vacuum. In addition to explaining the impact of gas pressure on the stability of this perovskite, our results indicate that covalently "locking" the position of perovskite components at the surface or an interface should enhance the overall photostability.
In contrast to the common conception that the interfacial energy-level alignment is affixed once the interface is formed, we demonstrate that heterojunctions between organic semiconductors and metal-halide perovskites exhibit huge energy-level realignment during photoexcitation. Importantly, the photoinduced level shifts occur in the organic component, including the first molecular layer in direct contact with the perovskite. This is caused by charge-carrier accumulation within the organic semiconductor under illumination and the weak electronic coupling between the junction components.
The tremendous success of metal-halide perovskites, especially in the field of photovoltaics, has triggered a substantial number of studies in understanding their optoelectronic properties. However, consensus regarding the electronic properties of these perovskites is lacking due to a huge scatter in the reported key parameters, such as work function (Φ) and valence band maximum (VBM) values. Here, we demonstrate that the surface photovoltage (SPV) is a key phenomenon occurring at the perovskite surfaces that feature a non-negligible density of surface states, which is more the rule than an exception for most materials under study. With ultraviolet photoelectron spectroscopy (UPS) and Kelvin probe, we evidence that even minute UV photon fluxes (500 times lower than that used in typical UPS experiments) are sufficient to induce SPV and shift the perovskite Φ and VBM by several 100 meV compared to dark. By combining UV and visible light, we establish flat band conditions (i.e., compensate the surface-state-induced surface band bending) at the surface of four important perovskites, and find that all are p-type in the bulk, despite a pronounced n-type surface character in the dark. The present findings highlight that SPV effects must be considered in all surface studies to fully understand perovskites’ photophysical properties.
Anti-fat bias is widespread and is linked to the internalization of weight bias and psychosocial problems. The purpose of this study was to examine the internalization of weight bias among children across weight categories and to evaluate the psychometric properties of the Weight Bias Internalization Scale for Children (WBIS-C). Data were collected from 1484 primary school children and their parents. WBIS-C demonstrated good internal consistency (alpha = .86) after exclusion of Item 1. The unitary factor structure was supported using exploratory and confirmatory factor analyses (factorial validity). Girls and overweight children reported higher WBIS-C scores in comparison to boys and non-overweight peers (known-groups validity). Convergent validity was shown by significant correlations with psychosocial problems. Internalization of weight bias explained additional variance in different indicators of psychosocial well-being. The results suggest that the WBIS-C is a psychometrically sound and informative tool to assess weight bias internalization among children.
Weight-related teasing is a widespread phenomenon in childhood, and might foster the internalization of weight bias. The goal of this study was to examine the role of weight teasing and weight bias internalization as mediators between weight status and negative psychological sequelae, such as restrained eating and emotional and conduct problems in childhood. Participants included 546 female (52%) and 501 (48%) male children aged 7-11 and their parents, who completed surveys assessing weight teasing, weight bias internalization, restrained eating behaviors, and emotional and conduct problems at two points of measurement, approximately 2 years apart. To examine the hypothesized mediation, a prospective design using structural equation modeling was applied. As expected, the experience of weight teasing and the internalization of weight bias were mediators in the relationship between weight status and psychosocial problems. This pattern was observed independently of gender or weight status. Our findings suggest that the experience of weight teasing and internalization of weight bias is more important than weight status in explaining psychological functioning among children and indicate a need for appropriate prevention and intervention approaches.
The Lombok Island is part of the Lesser Sunda Islands (LSI) region – Indonesia, situated along the Sunda-Banda Arcs transition. It lies between zones characterized by the highest intensity geomagnetic anomalies of this region, remarkable as one of the eight most important features provided on the 1st edition of World Digital Magnetic Anomaly Map. The seismicity of this region during the last years is high, while the geological and tectonic structures of this region are still not known in detail. Some local magnetic surveys have been conducted previously during 2004–2005. However, due to the lower accuracy of the used equipment and a limited number of stations, the qualities of the previous measurements are questionable for more interpretations. Thus a more detailed study to better characterize the geomagnetic anomaly -spatially and temporally- over this region and to deeply explore the related regional geology, tectonic and seismicity is needed. The intriguing geomagnetic anomalies over this island region vis-à-vis the socio-cultural situations lead to a study with a special aim to contribute to the assessment of the potential of natural hazards (earthquakes) as well as a new natural resource of energy (geothermal potential).
This study is intended to discuss several crucial questions, including:
i. The real values and the general pattern of magnetic anomalies over the island, as well as their relation to the regional one.
ii. Any temporal changes of regional anomalies over the recent time.
iii. The relationships between the anomalies and the geology and tectonic of this region, especially new insights that can be gained from the geomagnetic observations.
iv. The relationships between the anomalies and the high seismicity of this region, especially some possible links between their variations to the earthquake occurrence.
First, all available geomagnetic data of this region and results of the previous measurements are evaluated. The new geomagnetic surveys carried out in 2006 and 2007/2008 are then presented in detail, followed by the general description of data processing and data quality evaluation. The new results show the general pattern of contiguous negative-positive anomalies, revealing an active arc related subduction region. They agree with earlier results obtained by satellite, aeromagnetic, and marine platforms; and provide a much more detailed picture of the strong anomalies on this island. The temporal characteristics of regional anomalies show a decreasing strength of the dipolar structure, where decreasing of the field intensities is faster than the regional secular variations as defined by the global model (the 10th generation of IGRF). However, some exceptions (increasing of anomalies) have to be noted and further analyzed for several locations.
Thereafter, simultaneous magnetic anomalies and gravity models are generated and interpreted in detail. Three profiles are investigated, providing new insights into the tectonics and geological evolution of the Lombok Island. Geological structure of this island can be divided as two main parts with different consecutive ages: an old part (from late Oligocene to late Miocene) in the South and a younger one (from Pliocene to Holocene) in the North. A new subduction in the back arc region (the Flores Thrust zone) is considered mature and active, showing a tendency of progressive subduction during 2005–2008. Geothermal potential in the northern part of this island can be mapped in more detail using these geomagnetic regional survey data. The earlier estimates of reservoir depth can be confirmed further to a depth of about 800 m. Evaluation of temporal changes of the anomalies gives some possible explanations related to the evolution of the back arc region, large stress accumulations over the LSI region, a specific electrical characteristic of the crust of the Lombok Island region, and a structural discontinuity over this island.
Based on the results, several possible advanced studies involving geomagnetic data and anomaly investigations over the Lombok Island region can be suggested for the future:
i. Monitoring the subduction activity of the back arc region (the Flores Thrust zone) and the accumulated stress over the LSI, that could contribute to middle term hazard assessment with a special attention to the earthquake occurrence in this region. Continuous geomagnetic field measurements from a geomagnetic observatory which can be established in the northern part of the Lombok Island and systematic measurements at several repeat stations can be useful in this regards.
ii. Investigating the specific electrical characteristic (high conductivity) of the crust, that is probably related to some aquifer layers or metal mineralization. It needs other complementary geophysical methods, such as magnetotelluric (MT) or preferably DC resistivity measurements.
iii. Determining the existence of an active structural fault over the Lombok Island, that could be related to long term hazard assessment over the LSI region. This needs an extension of geomagnetic investigations over the neighbouring islands (the Bali Island in the West and the Sumbawa Island in the East; probably also the Sumba and the Flores islands). This seems possible because the regional magnetic lineations might be used to delineate some structural discontinuities, based on the modelling of contrasts in crustal magnetizations.
In high-value sweet cherry (Prunus avium), the red coloration - determined by the anthocyanins content - is correlated with the fruit ripeness stage and market value. Non-destructive spectroscopy has been introduced in practice and may be utilized as a tool to assess the fruit pigments in the supply chain processes. From the fruit spectrum in the visible (Vis) wavelength range, the pigment contents are analyzed separately at their specific absorbance wavelengths.
A drawback of the method is the need for re-calibration due to varying optical properties of the fruit tissue. In order to correct for the scattering differences, most often the spectral intensity in the visible spectrum is normalized by wavelengths in the near infrared (NIR) range, or pre-processing methods are applied in multivariate calibrations.
In the present study, the influence of the fruit scattering properties on the Vis/NIR fruit spectrum were corrected by the effective pathlength in the fruit tissue obtained from time-resolved readings of the distribution of time-of-flight (DTOF). Pigment analysis was carried out according to Lambert-Beer law, considering fruit spectral intensities, effective pathlength, and refractive index. Results were compared to commonly applied linear color and multivariate partial least squares (PLS) regression analysis. The approaches were validated on fruits at different ripeness stages, providing variation in the scattering coefficient and refractive index exceeding the calibration sample set.
In the validation, the measuring uncertainty of non-destructively analyzing fruits with Vis/NIR spectra by means of PLS or Lambert-Beer in comparison with combined application of Vis/NIR spectroscopy and DTOF measurements showed a dramatic bias reduction as well as enhanced coefficients of determination when using both, the spectral intensities and apparent information on the scattering influence by means of DTOF readings. Corrections for the refractive index did not render improved results.
Decoupling of optical properties appears challenging, but vital to get better insight of the relationship between light and fruit attributes. In this study, nine solid phantoms capturing the ranges of absorption (μa) and reduced scattering (μs’) coefficients in fruit were analysed non-destructively using laser-induced backscattering imaging (LLBI) at 1060 nm. Data analysis of LLBI was carried out on the diffuse reflectance, attenuation profile obtained by means of Farrell’s diffusion theory either calculating μa [cm−1] and μs’ [cm−1] in one fitting step or fitting only one optical variable and providing the other one from a destructive analysis. The nondestructive approach was approved when calculating one unknown coefficient non-destructively, while no ability of the method was found to analysis both, μa and μs’, non-destructively. Setting μs’ according to destructive photon density wave (PDW) spectroscopy and fitting μa resulted in root mean square error (rmse) of 18.7% in comparison to fitting μs’ resulting in rmse of 2.6%, pointing to decreased measuring uncertainty, when the highly variable μa was known.
The approach was tested on European pear, utilizing destructive PDW spectroscopy for setting one variable, while LLBI was applied for calculating the remaining coefficient. Results indicated that the optical properties of pear obtained from PDW spectroscopy as well as LLBI changed concurrently in correspondence to water content mainly. A destructive batch-wise analysis of μs’ and online analysis of μa may be considered in future developments for improved fruit sorting results, when considering fruit with high variability of μs’.
Throughout the last ~3 million years, the Earth's climate system was characterised by cycles of glacial and interglacial periods. The current warm period, the Holocene, is comparably stable and stands out from this long-term cyclicality. However, since the industrial revolution, the climate has been increasingly affected by a human-induced increase in greenhouse gas concentrations. While instrumental observations are used to describe changes over the past ~200 years, indirect observations via proxy data are the main source of information beyond this instrumental era. These data are indicators of past climatic conditions, stored in palaeoclimate archives around the Earth. The proxy signal is affected by processes independent of the prevailing climatic conditions. In particular, for sedimentary archives such as marine sediments and polar ice sheets, material may be redistributed during or after the initial deposition and subsequent formation of the archive. This leads to noise in the records challenging reliable reconstructions on local or short time scales. This dissertation characterises the initial deposition of the climatic signal and quantifies the resulting archive-internal heterogeneity and its influence on the observed proxy signal to improve the representativity and interpretation of climate reconstructions from marine sediments and ice cores.
To this end, the horizontal and vertical variation in radiocarbon content of a box-core from the South China Sea is investigated. The three-dimensional resolution is used to quantify the true uncertainty in radiocarbon age estimates from planktonic foraminifera with an extensive sampling scheme, including different sample volumes and replicated measurements of batches of small and large numbers of specimen. An assessment on the variability stemming from sediment mixing by benthic organisms reveals strong internal heterogeneity. Hence, sediment mixing leads to substantial time uncertainty of proxy-based reconstructions with error terms two to five times larger than previously assumed.
A second three-dimensional analysis of the upper snowpack provides insights into the heterogeneous signal deposition and imprint in snow and firn. A new study design which combines a structure-from-motion photogrammetry approach with two-dimensional isotopic data is performed at a study site in the accumulation zone of the Greenland Ice Sheet. The photogrammetry method reveals an intermittent character of snowfall, a layer-wise snow deposition with substantial contributions by wind-driven erosion and redistribution to the final spatially variable accumulation and illustrated the evolution of stratigraphic noise at the surface. The isotopic data show the preservation of stratigraphic noise within the upper firn column, leading to a spatially variable climate signal imprint and heterogeneous layer thicknesses. Additional post-depositional modifications due to snow-air exchange are also investigated, but without a conclusive quantification of the contribution to the final isotopic signature.
Finally, this characterisation and quantification of the complex signal formation in marine sediments and polar ice contributes to a better understanding of the signal content in proxy data which is needed to assess the natural climate variability during the Holocene.
Marine sedimentary archives are routinely used to reconstruct past environmental changes. In many cases, bioturbation and sedimentary mixing affect the proxy time-series and the age-depth relationship. While idealized models of bioturbation exist, they usually assume homogeneous mixing, thus that a single sample is representative for the sediment layer it is sampled from.
However, it is largely unknown to which extent this assumption holds for sediments used for paleoclimate reconstructions.
To shed light on
1) the age-depth relationship and its full uncertainty,
2) the magnitude of mixing processes affecting the downcore proxy variations, and
3) the representativity of the discrete sample for the sediment layer, we designed and performed a case study on South China Sea sediment material which was collected using a box corer and which covers the last glacial cycle.
Using the radiocarbon content of foraminiferal tests as a tracer of time, we characterize the spatial age-heterogeneity of sediments in a three-dimensional setup. In total, 118 radiocarbon measurements were performed on defined small- and large-volume bulk samples ( similar to 200 specimens each) to investigate the horizontal heterogeneity of the sediment. Additionally, replicated measurements on small numbers of specimens (10 x 5 specimens) were performed to assess the heterogeneity within a sample volume. Visual assessment of X-ray images and a quantitative assessment of the mixing strength show typical mixing from bioturbation corresponding to around 10 cm mixing depth.
Notably, our 3D radiocarbon distribution reveals that the horizontal heterogeneity (up to 1,250 years), contributing to the age uncertainty, is several times larger than the typically assumed radiocarbon based age-model error (single errors up to 250 years). Furthermore, the assumption of a perfectly bioturbated layer with no mixing underneath is not met.
Our analysis further demonstrates that the age-heterogeneity might be a function of sample size; smaller samples might contain single features from the incomplete mixing and are thus less representative than larger samples.
We provide suggestions for future studies, optimal sampling strategies for quantitative paleoclimate reconstructions and realistic uncertainty in age models, as well as discuss possible implications for the interpretation of paleoclimate records.
The Arabidopsis Kinome
(2014)
Background
Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication.
Results
The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases.
Conclusions
The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.
Background: Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication.
Results: The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases.
Conclusions: The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.
Explicit solution of the Lindblad equation for nearly isotropic boundary driven XY spin 1/2 chain
(2010)
Explicit solution for the two-point correlation function in a non-equilibrium steady state of a nearly isotropic boundary driven open XY spin 1/2 chain in the Lindblad formulation is provided. A non-equilibrium quantum phase transition from exponentially decaying correlations to long range order is discussed analytically. In the regime of long range order a new phenomenon of correlation resonances is reported, where the correlation response of the system is unusually high for certain discrete values of the external bulk parameter, e.g. the magnetic field.
State-of-the-art organic solar cells exhibit power conversion efficiencies of 18% and above. These devices benefit from the suppression of free charge recombination with regard to the Langevin limit of charge encounter in a homogeneous medium. It is recognized that the main cause of suppressed free charge recombination is the reformation and resplitting of charge-transfer (CT) states at the interface between donor and acceptor domains. Here, we use kinetic Monte Carlo simulations to understand the interplay between free charge motion and recombination in an energetically disordered phase-separated donor-acceptor blend. We identify conditions for encounter-dominated and resplitting-dominated recombination. In the former regime, recombination is proportional to mobility for all parameters tested and only slightly reduced with respect to the Langevin limit. In contrast, mobility is not the decisive parameter that determines the nongeminate recombination coefficient, k(2), in the latter case, where k2 is a sole function of the morphology, CT and charge-separated (CS) energetics, and CT-state decay properties. Our simulations also show that free charge encounter in the phase-separated disordered blend is determined by the average mobility of all carriers, while CT reformation and resplitting involves mostly states near the transport energy. Therefore, charge encounter is more affected by increased disorder than the resplitting of the CT state. As a consequence, for a given mobility, larger energetic disorder, in combination with a higher hopping rate, is preferred. These findings have implications for the understanding of suppressed recombination in solar cells with nonfullerene acceptors, which are known to exhibit lower energetic disorder than that of fullerenes.
With recent advances in the area of information extraction, automatically extracting structured information from a vast amount of unstructured textual data becomes an important task, which is infeasible for humans to capture all information manually. Named entities (e.g., persons, organizations, and locations), which are crucial components in texts, are usually the subjects of structured information from textual documents. Therefore, the task of named entity mining receives much attention. It consists of three major subtasks, which are named entity recognition, named entity linking, and relation extraction.
These three tasks build up an entire pipeline of a named entity mining system, where each of them has its challenges and can be employed for further applications. As a fundamental task in the natural language processing domain, studies on named entity recognition have a long history, and many existing approaches produce reliable results. The task is aiming to extract mentions of named entities in text and identify their types. Named entity linking recently received much attention with the development of knowledge bases that contain rich information about entities. The goal is to disambiguate mentions of named entities and to link them to the corresponding entries in a knowledge base. Relation extraction, as the final step of named entity mining, is a highly challenging task, which is to extract semantic relations between named entities, e.g., the ownership relation between two companies.
In this thesis, we review the state-of-the-art of named entity mining domain in detail, including valuable features, techniques, evaluation methodologies, and so on. Furthermore, we present two of our approaches that focus on the named entity linking and relation extraction tasks separately.
To solve the named entity linking task, we propose the entity linking technique, BEL, which operates on a textual range of relevant terms and aggregates decisions from an ensemble of simple classifiers. Each of the classifiers operates on a randomly sampled subset of the above range. In extensive experiments on hand-labeled and benchmark datasets, our approach outperformed state-of-the-art entity linking techniques, both in terms of quality and efficiency.
For the task of relation extraction, we focus on extracting a specific group of difficult relation types, business relations between companies. These relations can be used to gain valuable insight into the interactions between companies and perform complex analytics, such as predicting risk or valuating companies. Our semi-supervised strategy can extract business relations between companies based on only a few user-provided seed company pairs. By doing so, we also provide a solution for the problem of determining the direction of asymmetric relations, such as the ownership_of relation. We improve the reliability of the extraction process by using a holistic pattern identification method, which classifies the generated extraction patterns. Our experiments show that we can accurately and reliably extract new entity pairs occurring in the target relation by using as few as five labeled seed pairs.
The c-Fosc-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.
Molybdenum cofactor (Moco) biosynthesis is a complex process that involves the coordinated function of several proteins. In recent years it has become obvious that the availability of iron plays an important role in the biosynthesis of Moco. First, the MoaA protein binds two (4Fe-4S] clusters per monomer. Second, the expression of the moaABCDE and moeAB operons is regulated by FNR, which senses the availability of oxygen via a functional NFe-4S) cluster. Finally, the conversion of cyclic pyranopterin monophosphate to molybdopterin requires the availability of the L-cysteine desulfurase IscS, which is a shared protein with a main role in the assembly of Fe-S clusters. In this report, we investigated the transcriptional regulation of the moaABCDE operon by focusing on its dependence on cellular iron availability. While the abundance of selected molybdoenzymes is largely decreased under iron-limiting conditions, our data show that the regulation of the moaABCDE operon at the level of transcription is only marginally influenced by the availability of iron. Nevertheless, intracellular levels of Moco were decreased under iron-limiting conditions, likely based on an inactive MoaA protein in addition to lower levels of the L-cysteine desulfurase IscS, which simultaneously reduces the sulfur availability for Moco production. IMPORTANCE FNR is a very important transcriptional factor that represents the master switch for the expression of target genes in response to anaerobiosis. Among the FNR-regulated operons in Escherichia coli is the moaABCDE operon, involved in Moco biosynthesis. Molybdoenzymes have essential roles in eukaryotic and prokaryotic organisms. In bacteria, molybdoenzymes are crucial for anaerobic respiration using alternative electron acceptors. This work investigates the connection of iron availability to the biosynthesis of Moco and the production of active molybdoenzymes.
Bacterial molybdoenzymes are key enzymes involved in the global sulphur, nitrogen and carbon cycles. These enzymes require the insertion of the molybdenum cofactor (Moco) into their active sites and are able to catalyse a large range of redox-reactions. Escherichia coli harbours nineteen different molybdoenzymes that require a tight regulation of their synthesis according to substrate availability, oxygen availability and the cellular concentration of molybdenum and iron. The synthesis and assembly of active molybdoenzymes are regulated at the level of transcription of the structural genes and of translation in addition to the genes involved in Moco biosynthesis. The action of global transcriptional regulators like FNR, NarXL/QP, Fur and ArcA and their roles on the expression of these genes is described in detail. In this review we focus on what is known about the molybdenum- and iron-dependent regulation of molybdoenzyme and Moco biosynthesis genes in the model organism E. coli. The gene regulation in E. coli is compared to two other well studied model organisms Rhodobacter capsulatus and Shewanella oneidensis.
The ability of some plant species to dominate communities in new biogeographical ranges has been attributed to an innate higher competitive ability and release from co-evolved specialist enemies. Specifically, invasive success in the new range might be explained by release from biotic negative soil-feedbacks, which control potentially dominant species in their native range. To test this hypothesis, we grew individuals from sixteen phylogenetically paired European grassland species that became either invasive or naturalized in new ranges, in either sterilized soil or in sterilized soil with unsterilized soil inoculum from their native home range. We found that although the native members of invasive species generally performed better than those of naturalized species, these native members of invasive species also responded more negatively to native soil inoculum than did the native members of naturalized species. This supports our hypothesis that potentially invasive species in their native range are held in check by negative soil-feedbacks. However, contrary to expectation, negative soil-feedbacks in potentially invasive species were not much increased by interspecific competition. There was no significant variation among families between invasive and naturalized species regarding their feedback response (negative vs. neutral). Therefore, we conclude that the observed negative soil feedbacks in potentially invasive species may be quite widespread in European families of typical grassland species.
Species respond to environmental change by dynamically adjusting their geographical ranges. Robust predictions of these changes are prerequisites to inform dynamic and sustainable conservation strategies. Correlative species distribution models (SDMs) relate species’ occurrence records to prevailing environmental factors to describe the environmental niche. They have been widely applied in global change context as they have comparably low data requirements and allow for rapid assessments of potential future species’ distributions. However, due to their static nature, transient responses to environmental change are essentially ignored in SDMs. Furthermore, neither dispersal nor demographic processes and biotic interactions are explicitly incorporated. Therefore, it has often been suggested to link statistical and mechanistic modelling approaches in order to make more realistic predictions of species’ distributions for scenarios of environmental change. In this thesis, I present two different ways of such linkage. (i) Mechanistic modelling can act as virtual playground for testing statistical models and allows extensive exploration of specific questions. I promote this ‘virtual ecologist’ approach as a powerful evaluation framework for testing sampling protocols, analyses and modelling tools. Also, I employ such an approach to systematically assess the effects of transient dynamics and ecological properties and processes on the prediction accuracy of SDMs for climate change projections. That way, relevant mechanisms are identified that shape the species’ response to altered environmental conditions and which should hence be considered when trying to project species’ distribution through time. (ii) I supplement SDM projections of potential future habitat for black grouse in Switzerland with an individual-based population model. By explicitly considering complex interactions between habitat availability and demographic processes, this allows for a more direct assessment of expected population response to environmental change and associated extinction risks. However, predictions were highly variable across simulations emphasising the need for principal evaluation tools like sensitivity analysis to assess uncertainty and robustness in dynamic range predictions. Furthermore, I identify data coverage of the environmental niche as a likely cause for contrasted range predictions between SDM algorithms. SDMs may fail to make reliable predictions for truncated and edge niches, meaning that portions of the niche are not represented in the data or niche edges coincide with data limits. Overall, my thesis contributes to an improved understanding of uncertainty factors in predictions of range dynamics and presents ways how to deal with these. Finally I provide preliminary guidelines for predictive modelling of dynamic species’ response to environmental change, identify key challenges for future research and discuss emerging developments.
Ecologists carry a well-stocked toolbox with a great variety of sampling methods, statistical analyses and modelling tools, and new methods are constantly appearing. Evaluation and optimisation of these methods is crucial to guide methodological choices. Simulating error-free data or taking high-quality data to qualify methods is common practice. Here, we emphasise the methodology of the 'virtual ecologist' (VE) approach where simulated data and observer models are used to mimic real species and how they are 'virtually' observed. This virtual data is then subjected to statistical analyses and modelling, and the results are evaluated against the 'true' simulated data. The VE approach is an intuitive and powerful evaluation framework that allows a quality assessment of sampling protocols, analyses and modelling tools. It works under controlled conditions as well as under consideration of confounding factors such as animal movement and biased observer behaviour. In this review, we promote the approach as a rigorous research tool, and demonstrate its capabilities and practical relevance. We explore past uses of VE in different ecological research fields, where it mainly has been used to test and improve sampling regimes as well as for testing and comparing models, for example species distribution models. We discuss its benefits as well as potential limitations, and provide some practical considerations for designing VE studies. Finally, research fields are identified for which the approach could be useful in the future. We conclude that VE could foster the integration of theoretical and empirical work and stimulate work that goes far beyond sampling methods, leading to new questions, theories, and better mechanistic understanding of ecological systems.
Density regulation influences population dynamics through its effects on demographic rates and consequently constitutes a key mechanism explaining the response of organisms to environmental changes. Yet, it is difficult to establish the exact form of density dependence from empirical data. Here, we developed an individual-based model to explore how resource limitation and behavioural processes determine the spatial structure of white stork Ciconia ciconia populations and regulate reproductive rates. We found that the form of density dependence differed considerably between landscapes with the same overall resource availability and between home range selection strategies, highlighting the importance of fine-scale resource distribution in interaction with behaviour. In accordance with theories of density dependence, breeding output generally decreased with density but this effect was highly variable and strongly affected by optimal foraging strategy, resource detection probability and colonial behaviour. Moreover, our results uncovered an overlooked consequence of density dependence by showing that high early nestling mortality in storks, assumed to be the outcome of harsh weather, may actually result from density dependent effects on food provision. Our findings emphasize that accounting for interactive effects of individual behaviour and local environmental factors is crucial for understanding density-dependent processes within spatially structured populations. Enhanced understanding of the ways animal populations are regulated in general, and how habitat conditions and behaviour may dictate spatial population structure and demographic rates is critically needed for predicting the dynamics of populations, communities and ecosystems under changing environmental conditions.
Data limitations can lead to unrealistic fits of predictive species distribution models (SDMs) and spurious extrapolation to novel environments. Here, we want to draw attention to novel combinations of environmental predictors that are within the sampled range of individual predictors but are nevertheless outside the sample space. These tend to be overlooked when visualizing model behaviour. They may be a cause of differing model transferability and environmental change predictions between methods, a problem described in some studies but generally not well understood. We here use a simple simulated data example to illustrate the problem and provide new and complementary visualization techniques to explore model behaviour and predictions to novel environments. We then apply these in a more complex real-world example. Our results underscore the necessity of scrutinizing model fits, ecological theory and environmental novelty.