@article{12637, abstract = {The performance of glaciohydrological models which simulate catchment response to climate variability depends to a large degree on the data used to force the models. The forcing data become increasingly important in high-elevation, glacierized catchments where the interplay between extreme topography, climate, and the cryosphere is complex. It is challenging to generate a reliable forcing data set that captures this spatial heterogeneity. In this paper, we analyze the results of a 1 year field campaign focusing on air temperature and precipitation observations in the Langtang valley in the Nepalese Himalayas. We use the observed time series to characterize both temperature lapse rates (LRs) and precipitation gradients (PGs). We study their spatial and temporal variability, and we attempt to identify possible controlling factors. We show that very clear LRs exist in the valley and that there are strong seasonal differences related to the water vapor content in the atmosphere. Results also show that the LRs are generally shallower than the commonly used environmental lapse rates. The analysis of the precipitation observations reveals that there is great variability in precipitation over short horizontal distances. A uniform valley wide PG cannot be established, and several scale-dependent mechanisms may explain our observations. We complete our analysis by showing the impact of the observed LRs and PGs on the outputs of the TOPKAPI-ETH glaciohydrological model. We conclude that LRs and PGs have a very large impact on the water balance composition and that short-term monitoring campaigns have the potential to improve model quality considerably.}, author = {Immerzeel, W. W. and Petersen, L. and Ragettli, S. and Pellicciotti, Francesca}, issn = {1944-7973}, journal = {Water Resources Research}, keywords = {Water Science and Technology}, number = {3}, pages = {2212--2226}, publisher = {American Geophysical Union}, title = {{The importance of observed gradients of air temperature and precipitation for modeling runoff from a glacierized watershed in the Nepalese Himalayas}}, doi = {10.1002/2013wr014506}, volume = {50}, year = {2014}, } @article{97, abstract = {The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length (lso < 20 nm), consistent with values extracted in the Coulomb blockade regime (lso < 25 nm).}, author = {Higginbotham, Andrew P and Kuemmeth, Ferdinand and Larsen, Thorvald and Fitzpatrick, Mattias and Yao, Jun and Yan, Hao and Lieber, Charles and Marcus, Charles}, journal = {APS Physics, Physical Review Letters}, number = {21}, publisher = {American Physical Society}, title = {{Antilocalization of coulomb blockade in a Ge/Si nanowire}}, doi = {10.1103/PhysRevLett.112.216806}, volume = {112}, year = {2014}, } @misc{9722, author = {Lovrics, Anna and Gao, Yu and Juhász, Bianka and Bock, István and Byrne, Helen M. and Dinnyés, András and Kovács, Krisztián}, publisher = {Public Library of Science}, title = {{Transition probability between TF expression states when Dbx2 inhibits Nkx2.2}}, doi = {10.1371/journal.pone.0111430.s006}, year = {2014}, } @misc{9739, author = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Adlam, Ben and Novak, Martin}, publisher = {Public Library of Science}, title = {{Detailed proofs for “The time scale of evolutionary innovation”}}, doi = {10.1371/journal.pcbi.1003818.s001}, year = {2014}, } @misc{9740, abstract = {The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens.}, author = {Konrad, Matthias and Grasse, Anna V and Tragust, Simon and Cremer, Sylvia}, publisher = {Dryad}, title = {{Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host}}, doi = {10.5061/dryad.vm0vc}, year = {2014}, } @misc{9741, abstract = {In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.}, author = {Lagator, Mato and Colegrave, Nick and Neve, Paul}, publisher = {Dryad}, title = {{Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses}}, doi = {10.5061/dryad.85dn7}, year = {2014}, } @misc{9747, abstract = {Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.}, author = {Lagator, Mato and Morgan, Andrew and Neve, Paul and Colegrave, Nick}, publisher = {Dryad}, title = {{Data from: Role of sex and migration in adaptation to sink environments}}, doi = {10.5061/dryad.s42n1}, year = {2014}, } @misc{9752, abstract = {Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible.}, author = {Simmons, Kristina and Prentice, Jason and Tkačik, Gašper and Homann, Jan and Yee, Heather and Palmer, Stephanie and Nelson, Philip and Balasubramanian, Vijay}, publisher = {Dryad}, title = {{Data from: Transformation of stimulus correlations by the retina}}, doi = {10.5061/dryad.246qg}, year = {2014}, } @misc{9753, abstract = {Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal - originally described for honeybees as “hygienic behaviour” – is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.}, author = {Tragust, Simon and Ugelvig, Line V and Chapuisat, Michel and Heinze, Jürgen and Cremer, Sylvia}, publisher = {Dryad}, title = {{Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies}}, doi = {10.5061/dryad.nc0gc}, year = {2014}, } @article{977, abstract = {We propose a method for detecting many-body localization (MBL) in disordered spin systems. The method involves pulsed coherent spin manipulations that probe the dephasing of a given spin due to its entanglement with a set of distant spins. It allows one to distinguish the MBL phase from a noninteracting localized phase and a delocalized phase. In particular, we show that for a properly chosen pulse sequence the MBL phase exhibits a characteristic power-law decay reflecting its slow growth of entanglement. We find that this power-law decay is robust with respect to thermal and disorder averaging, provide numerical simulations supporting our results, and discuss possible experimental realizations in solid-state and cold-atom systems.}, author = {Maksym Serbyn and Knap, Michael J and Gopalakrishnan, Sarang and Papić, Zlatko and Yao, Norman Y and Laumann, Chris R and Abanin, Dmitry A and Lukin, Mikhail D and Demler, Eugene A}, journal = {Physical Review Letters}, number = {14}, publisher = {American Physical Society}, title = {{Interferometric probes of many-body localization}}, doi = {10.1103/PhysRevLett.113.147204}, volume = {113}, year = {2014}, } @article{978, abstract = {The newly discovered topological crystalline insulators feature a complex band structure involving multiple Dirac cones, and are potentially highly tunable by external electric field, temperature or strain. Theoretically, it has been predicted that the various Dirac cones, which are offset in energy and momentum, might harbour vastly different orbital character. However, their orbital texture, which is of immense importance in determining a variety of a materialâ €™ s properties remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical topological crystalline insulator. By using Fourier-transform scanning tunnelling spectroscopy we measure the interference patterns produced by the scattering of surface-state electrons. We discover that the intensity and energy dependences of the Fourier transforms show distinct characteristics, which can be directly attributed to orbital effects. Our experiments reveal a complex band topology involving two Lifshitz transitions and establish the orbital nature of the Dirac bands, which could provide an alternative pathway towards future quantum applications.}, author = {Zeljkovic, Ilija and Okada, Yoshinori and Huang, Chengyi and Sankar, Raman and Walkup, Daniel and Zhou, Wenwen and Maksym Serbyn and Chou, Fangcheng and Tsai, Wei-Feng and Lin, Hsin and Bansil, Arun and Fu, Liang and Hasan, Md Z and Madhavan, Vidya}, journal = {Nature Physics}, number = {8}, pages = {572 -- 577}, publisher = {Nature Publishing Group}, title = {{Mapping the unconventional orbital texture in topological crystalline insulators}}, doi = {10.1038/nphys3012}, volume = {10}, year = {2014}, } @article{979, abstract = {In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te, Se), crystal symmetry and electronic topology intertwine to create topological surface states with many interesting features including Lifshitz transition, Van-Hove singularity, and fermion mass generation. These surface states are protected by mirror symmetry with respect to the (110) plane. In this work we present a comprehensive study of the effects of different mirror-symmetry-breaking perturbations on the (001) surface band structure. Pristine (001) surface states have four branches of Dirac fermions at low energy. We show that ferroelectric-type structural distortion generates a mass and gaps out some or all of these Dirac points, while strain shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the surface state gapless, but introduces asymmetry between Dirac points. Finally, an out-of-plane magnetic field leads to discrete Landau levels. We show that the Landau level spectrum has an unusual pattern of degeneracy and interesting features due to the unique underlying band structure. This suggests that Landau level spectroscopy can detect and distinguish between different mechanisms of symmetry breaking in topological crystalline insulators.}, author = {Maksym Serbyn and Fu, Liang}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {3}, publisher = {American Physical Society}, title = {{Symmetry breaking and Landau quantization in topological crystalline insulators}}, doi = {10.1103/PhysRevB.90.035402}, volume = {90}, year = {2014}, } @article{98, abstract = {Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing.}, author = {Higginbotham, Andrew P and Larsen, Thorvald and Yao, Jun and Yan, Hao and Lieber, Charles and Marcus, Charles and Kuemmeth, Ferdinand}, journal = {Nano Letters}, number = {6}, pages = {3582 -- 3586}, publisher = {American Chemical Society}, title = {{Hole spin coherence in a Ge/Si heterostructure nanowire}}, doi = {10.1021/nl501242b}, volume = {14}, year = {2014}, } @article{980, abstract = {Many-body localized (MBL) systems are characterized by the absence of transport and thermalization and, therefore, cannot be described by conventional statistical mechanics. In this paper, using analytic arguments and numerical simulations, we study the behavior of local observables in an isolated MBL system following a quantum quench. For the case of a global quench, we find that the local observables reach stationary, highly nonthermal values at long times as a result of slow dephasing characteristic of the MBL phase. These stationary values retain the local memory of the initial state due to the existence of local integrals of motion in the MBL phase. The temporal fluctuations around stationary values exhibit universal power-law decay in time, with an exponent set by the localization length and the diagonal entropy of the initial state. Such a power-law decay holds for any local observable and is related to the logarithmic in time growth of entanglement in the MBL phase. This behavior distinguishes the MBL phase from both the Anderson insulator (where no stationary state is reached) and from the ergodic phase (where relaxation is expected to be exponential). For the case of a local quench, we also find a power-law approach of local observables to their stationary values when the system is prepared in a mixed state. Quench protocols considered in this paper can be naturally implemented in systems of ultracold atoms in disordered optical lattices, and the behavior of local observables provides a direct experimental signature of many-body localization.}, author = {Maksym Serbyn and Papić, Zlatko and Abanin, Dmitry A}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {17}, publisher = {American Physical Society}, title = {{Quantum quenches in the many-body localized phase}}, doi = {10.1103/PhysRevB.90.174302}, volume = {90}, year = {2014}, } @misc{9888, abstract = {Detailed description of the experimental prodedures, data analyses and additional statistical analyses of the results.}, author = {Wolf, Stephan and Mcmahon, Dino and Lim, Ka and Pull, Christopher and Clark, Suzanne and Paxton, Robert and Osborne, Juliet}, publisher = {Public Library of Science}, title = {{Supporting information}}, doi = {10.1371/journal.pone.0103989.s003}, year = {2014}, } @article{9931, abstract = {Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, subfunctionalization, and neofunctionalization. Little experimental data exist on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region.}, author = {Dhar, Riddhiman and Bergmiller, Tobias and Wagner, Andreas}, issn = {1558-5646}, journal = {Evolution}, number = {6}, pages = {1775--1791}, publisher = {Wiley}, title = {{Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes}}, doi = {10.1111/evo.12373}, volume = {68}, year = {2014}, } @misc{9932, abstract = {Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region.}, author = {Dhar, Riddhiman and Bergmiller, Tobias and Wagner, Andreas}, publisher = {Dryad}, title = {{Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes}}, doi = {10.5061/dryad.jc402}, year = {2014}, } @article{348, abstract = {Bi2S3-xTex bulk nanocomposites with crystal domain sizes in the range from 50 nm to 100 nm were obtained from the reaction of Bi2S3 nanorods with Te powder. The thermoelectric properties of the obtained nanocomposites were analysed in the temperature range from 0°C to 300°C. We observed how the thermoelectric properties of the material improved with the annealing temperature, being a spark plasma sintering process needed to maintain the material nanostructuration while maximising its electrical properties. Finally thermoelectric dimensionless figures of merit ZT up to 0.42 were obtained before any charge carrier concentration optimisation. Copyright © 2014 Inderscience Enterprises Ltd. }, author = {Cadavid, Doris and Ibáñez, Maria and Anselmi Tamburini, Umberto and Durá, Oscar and De La Torre, Marco and Cabot, Andreu}, journal = {International Journal of Nanotechnology}, number = {9-11}, pages = {773 -- 784}, publisher = {Inderscience Enterprises Limited }, title = {{Thermoelectric properties of bottom up assembled Bi2S 3-xTex nanocomposites}}, doi = {10.1504/IJNT.2014.063787}, volume = {11}, year = {2014}, } @article{349, abstract = {Thermoelectricity is a key technology with the potential to improve the efficiency of energy conversion processes, which may strongly benefit from advances in the field of nanotechnology. Nanostructured materials are very appealing for thermoelectric applications, but the full development of their potential requires precise control of their properties at the nanoscale. Bottom-up assembly of nanoparticles provides access to a three-dimensional composition control at the nanoscale not attainable in any other technology. In particular, colloidal nanoheterostructures are especially interesting building blocks for the bottom-up production of functional nanomaterials. In the present work, we use PbTe@PbS core-shell nanoparticles as building blocks for the bottom-up production of PbTe-PbS nanocomposites. We used a ligand exchange strategy and a hot press process to promote the electrical conductivity of the nanocomposite and to increase its density. These two approaches allowed us to improve the performance of bottom-up assembled PbTe-PbS bulk nanostructured materials. }, author = {Ortega, Silvia and Ibáñez, Maria and Cadavid, Doris and Cabot, Andreu}, journal = {International Journal of Nanotechnology}, number = {9-11}, pages = {955 -- 970}, publisher = {Inderscience Enterprises Limited }, title = {{Bottom up processing of PbTe PbS thermoelectric nanocomposites}}, doi = {10.1504/IJNT.2014.063802}, volume = {11}, year = {2014}, } @article{350, abstract = {Herein, a colloidal synthetic route to produce highly monodisperse Cu2HgGeSe4 (CHGSe) nanoparticles (NPs) is presented in detail. The high yield of the developed procedure allowed the production of CHGSe NPs at the gram scale. A thorough analysis of their structural and optical properties is shown. CHGSe NPs displayed poly-tetrahedral morphology and narrow size distributions with average size in the range of 10–40 nm and size dispersions below 10 %. A 1.6 eV optical band gap was measured by mean of UV–Vis. By adjusting the cation ratio, an effective control of their electrical conductivity is achieved. The prepared NPs are used as building blocks for the production of CHGSe bulk nanostructured materials. The thermoelectric properties of CHGSe nanomaterials are studied in the temperature range from 300 to 730 K. CHGSe nanomaterials reached electrical conductivities up to 5 × 104 S m−1, Seebeck coefficients above 100 μV K−1, and thermal conductivities below 1.0 W m−1 K−1 which translated into thermoelectric figures of merit up to 0.34 at 730 K.}, author = {Li, Wenhua and Ibáñez, Maria and Cadavid, Doris and Zamani, Reza and Rubio Garcia, Javier and Gorsse, Stéphane and Morante, Joan and Arbiol, Jordi and Cabot, Andreu}, journal = {Journal of Nanoparticle Research}, number = {3}, publisher = {Kluwer}, title = {{Colloidal synthesis and functional properties of quaternary Cu based semiconductors: Cu2HgGeSe4}}, doi = {10.1007/s11051-014-2297-2}, volume = {16}, year = {2014}, }