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    A CRISPR-Cas9-Based Toolkit for Fast and Precise In Vivo Genetic Engineering of Bacillus subtilis Phages 

    Schilling, Tobias; Dietrich, Sascha; Hoppert, Michael; Hertel, Robert
    Viruses 2018; 10(5): Art. 241
    Phages are currently under discussion as a solution for the antibiotic crisis, as they may cure diseases caused by multi-drug-resistant pathogens. However, knowledge of phage biology and genetics is limited, which impedes risk assessment of therapeutic applications. In order to enable advances in phage genetic research, the aim of this work was to create a toolkit for simple and fast genetic engineering of phages recruiting Bacillus subtilis as host system. The model organism B. subtilis represents a non-pathogenic surrogate of its harmful relatives, such as Bacillus anthracis or Bacillus cereus. This toolkit comprises the application CutSPR, a bioinformatic tool for rapid primer design, and facilitates the cloning of specific CRISPR-Cas9-based mutagenesis plasmids. The employment of the prophage-free and super-competent B. subtilis TS01 strain enables an easy and fast introduction of specific constructs for in vivo phage mutagenesis. Clean gene deletions and a functional clean gene insertion into the genome of the model phage vB_BsuP-Goe1 served as proof of concept and demonstrate reliability and high efficiency. The here presented toolkit allows comprehensive investigation of the diverse phage genetic pool, a better understanding of phage biology, and safe phage applications.
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    Avoiding the Use of Exhausted Drinking Water Filters: A Filter-Clock Based on Rusting Iron 

    Ndé-Tchoupé, Arnaud; Lufingo, Mesia; Hu, Rui; Gwenzi, Willis; Ntwampe, Seteno; Noubactep, Chicgoua; Njau, Karoli
    Water 2018; 10(5): Art. 591
    Efficient but affordable water treatment technologies are currently sought to solve the prevalent shortage of safe drinking water. Adsorption-based technologies are in the front-line of these efforts. Upon proper design, universally applied materials (e.g., activated carbons, bone chars, metal oxides) are able to quantitatively remove inorganic and organic pollutants as well as pathogens from water. Each water filter has a defined removal capacity and must be replaced when this capacity is exhausted. Operational experience has shown that it may be difficult to convince some low-skilled users to buy new filters after a predicted service life. This communication describes the quest to develop a filter-clock to encourage all users to change their filters after the designed service life. A brief discussion on such a filter-clock based on rusting of metallic iron (Fe0) is presented. Integrating such filter-clocks in the design of water filters is regarded as essential for safeguarding public health.
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    Extended Object Tracking: Introduction, Overview, and Applications 

    Granström, Karl; Baum, Marcus; Reuter, Stephan
    Journal of Advances in Information Fusion 2017; 12(2)
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    Time- and frequency-resolved fluorescence with a single TCSPC detector via a Fourier-transform approach 

    Perri, Antonio; Gaida, John H.; Farina, Andrea; Preda, Fabrizio; Viola, Daniele; Ballottari, Matteo; Hauer, Jürgen; De Silvestri, Sandro; D’Andrea, Cosimo; Cerullo, Giulio; et al.
    Polli, Dario
    Optics Express 2018; 26(3): Art. 2270
    We introduce a broadband single-pixel spectro-temporal fluorescence detector, combining time-correlated single photon counting (TCSPC) with Fourier transform (FT) spectroscopy. A birefringent common-path interferometer (CPI) generates two time-delayed replicas of the sample's fluorescence. Via FT of their interference signal at the detector, we obtain a two-dimensional map of the fluorescence as a function of detection wavelength and emission time, with high temporal and spectral resolution. Our instrument is remarkably simple, as it only requires the addition of a CPI to a standard single-pixel TCSPC system, and it shows a readily adjustable spectral resolution with inherently broad bandwidth coverage.
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    Topology determines force distributions in one-dimensional random spring networks 

    Heidemann, Knut M.; Sageman-Furnas, Andrew O.; Sharma, Abhinav; Rehfeldt, Florian; Schmidt, Christoph F.; Wardetzky, Max
    Physical Review E 2018; 97(2): Art. 022306
    etworks of elastic fibers are ubiquitous in biological systems and often provide mechanical stability to cells and tissues. Fiber-reinforced materials are also common in technology. An important characteristic of such materials is their resistance to failure under load. Rupture occurs when fibers break under excessive force and when that failure propagates. Therefore, it is crucial to understand force distributions. Force distributions within such networks are typically highly inhomogeneous and are not well understood. Here we construct a simple one-dimensional model system with periodic boundary conditions by randomly placing linear springs on a circle. We consider ensembles of such networks that consist of N nodes and have an average degree of connectivity z but vary in topology. Using a graph-theoretical approach that accounts for the full topology of each network in the ensemble, we show that, surprisingly, the force distributions can be fully characterized in terms of the parameters (N,z). Despite the universal properties of such (N,z) ensembles, our analysis further reveals that a classical mean-field approach fails to capture force distributions correctly. We demonstrate that network topology is a crucial determinant of force distributions in elastic spring networks.
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    Reconstructing geographical parthenogenesis: effects of niche differentiation and reproductive mode on Holocene range expansion of an alpine plant. 

    Kirchheimer, Bernhard; Wessely, Johannes; Gattringer, Andreas; Hülber, Karl; Moser, Dietmar; Schinkel, Christoph C. F.; Appelhans, Marc; Klatt, Simone; Caccianiga, Marco; Dellinger, Agnes; et al.
    Guisan, AntoineKuttner, MichaelLenoir, JonathanMaiorano, LuigiNieto-Lugilde, DiegoPlutzar, ChristophSvenning, Jens-ChristianWillner, WolfgangHörandl, ElviraDullinger, Stefan
    Ecology Letters 2018; 21(3) p.392-401
    Asexual taxa often have larger ranges than their sexual progenitors, particularly in areas affected by Pleistocene glaciations. The reasons given for this 'geographical parthenogenesis' are contentious, with expansion of the ecological niche or colonisation advantages of uniparental reproduction assumed most important in case of plants. Here, we parameterized a spread model for the alpine buttercup Ranunculus kuepferi and reconstructed the joint Holocene range expansion of its sexual and apomictic cytotype across the European Alps under different simulation settings. We found that, rather than niche broadening or a higher migration rate, a shift of the apomict's niche towards colder conditions per se was crucial as it facilitated overcoming of topographical barriers, a factor likely relevant for many alpine apomicts. More generally, our simulations suggest potentially strong interacting effects of niche differentiation and reproductive modes on range formation of related sexual and asexual taxa arising from their differential sensitivity to minority cytotype disadvantage.
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    The Effects of Diversification Activities on the Technical Efficiency of Organic Farms in Switzerland, Austria, and Southern Germany 

    Lakner, Sebastian; Kirchweger, Stefan; Hoop, Daniel; Brümmer, Bernhard; Kantelhardt, Jochen
    Sustainability 2018; 10(4): Art. 1304
    The diversification of farms can be a result of multifunctional farming, however, in some cases at the cost of lower farm efficiency. In our paper we investigate the influence of para-agricultural diversification on productivity and the technical efficiency of organic farms in Austria, Switzerland, and Southern Germany. We show the benefits and drawbacks of diversification for organic farms, which go beyond the core agricultural production (para-agriculture). We do this by estimating a Stochastic Frontier (SF) combined with a metafrontier model. The data-set consists of bookkeeping data with 1704 observations in the years 2003 to 2005. Para-agricultural diversification activities have a significant effect on both productivity and technical efficiency of organic farms: The farm output in Austria and Switzerland is positively influenced by diversification, whereas we observe a rather small effect in Southern Germany. On the other hand, diversification can reduce farms’ technical efficiency, as it is the case in Switzerland and Germany. Furthermore, our study confirms previous results that agricultural subsidies significantly influence the technical efficiency of organic farms. We also show expected changes of input use driven by increased farm diversification. View Full-Text
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    A toolkit for Nannochloropsis oceanica CCMP1779 enables gene stacking and genetic engineering of the eicosapentaenoic acid pathway for enhanced long-chain polyunsaturated fatty acid production 

    Poliner, Eric; Pulman, Jane A.; Zienkiewicz, Krzysztof; Childs, Kevin; Benning, Christoph; Farré, Eva M.
    Plant Biotechnology Journal 2018; 16(1) p.298-309
    Nannochloropsis oceanica is an oleaginous microalga rich in ω3 long-chain polyunsaturated fatty acids (LC-PUFAs) content, in the form of eicosapentaenoic acid (EPA). We identified the enzymes involved in LC-PUFA biosynthesis in N. oceanica CCMP1779 and generated multigene expression vectors aiming at increasing LC-PUFA content in vivo. We isolated the cDNAs encoding four fatty acid desaturases (FAD) and determined their function by heterologous expression in S. cerevisiae. To increase the expression of multiple fatty acid desaturases in N. oceanica CCMP1779, we developed a genetic engineering toolkit that includes an endogenous bidirectional promoter and optimized peptide bond skipping 2A peptides. The toolkit also includes multiple epitopes for tagged fusion protein production and two antibiotic resistance genes. We applied this toolkit, towards building a gene stacking system for N. oceanica that consists of two vector series, pNOC-OX and pNOC-stacked. These tools for genetic engineering were employed to test the effects of the overproduction of one, two or three desaturase-encoding cDNAs in N. oceanica CCMP1779 and prove the feasibility of gene stacking in this genetically tractable oleaginous microalga. All FAD overexpressing lines had considerable increases in the proportion of LC-PUFAs, with the overexpression of Δ12 and Δ5 FAD encoding sequences leading to an increase in the final ω3 product, EPA.
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    Combined Forward-Backward Asymmetry Measurements in Top-Antitop Quark Production at the Tevatron 

    Aaltonen, T.; Abazov, V. M.; Abbott, B.; Acharya, B. S.; Adams, M.; Adams, T.; Agnew, J. P.; Alexeev, G. D.; Alkhazov, G.; Alton, A.; et al.
    Amerio, S.Amidei, D.Anastassov, A.Annovi, A.Antos, J.Apollinari, G.Appel, J. A.Arisawa, T.Artikov, A.Asaadi, J.Ashmanskas, W.Askew, A.Atkins, S.Auerbach, B.Augsten, K.Aurisano, A.Aushev, V.Aushev, Y.Avila, C.Azfar, F.Badaud, F.Badgett, W.Bae, T.Bagby, L.Baldin, B.Bandurin, D. V.Banerjee, S.Barbaro-Galtieri, A.Barberis, E.Baringer, P.Barnes, V. E.Barnett, B. A.Barria, P.Bartlett, J. F.Bartos, P.Bassler, U.Bauce, M.Bazterra, V.Bean, A.Bedeschi, F.Begalli, M.Behari, S.Bellantoni, L.Bellettini, G.Bellinger, J.Benjamin, D.Beretvas, A.Beri, S. B.Bernardi, G.Bernhard, R.Bertram, I.Besançon, M.Beuselinck, R.Bhat, P. C.Bhatia, S.Bhatnagar, V.Bhatti, A.Bland, K. R.Blazey, G.Blessing, S.Bloom, K.Blumenfeld, B.Bocci, A.Bodek, A.Boehnlein, A.Boline, D.Boos, E. E.Borissov, G.Bortoletto, D.Borysova, M.Boudreau, J.Boveia, A.Brandt, A.Brandt, O.Brigliadori, L.Brochmann, M.Brock, R.Bromberg, C.Bross, A.Brown, D.Brucken, E.Bu, X. B.Budagov, J.Budd, H. S.Buehler, M.Buescher, V.Bunichev, V.Burdin, S.Burkett, K.Busetto, G.Bussey, P.Buszello, C. P.Butti, P.Buzatu, A.Calamba, A.Camacho-Pérez, E.Camarda, S.Campanelli, M.Canelli, F.Carls, B.Carlsmith, D.Carosi, R.Carrillo, S.Casal, B.Casarsa, M.Casey, B. C. K.Castilla-Valdez, H.Castro, A.Catastini, P.Caughron, S.Cauz, D.Cavaliere, V.Cerri, A.Cerrito, L.Chakrabarti, S.Chan, K. M.Chandra, A.Chapelain, A.Chapon, E.Chen, G.Chen, Y. C.Chertok, M.Chiarelli, G.Chlachidze, G.Cho, K.Cho, S. W.Choi, S.Chokheli, D.Choudhary, B.Cihangir, S.Claes, D.Clark, A.Clarke, C.Clutter, J.Convery, M. E.Conway, J.Cooke, M.Cooper, W. E.Corbo, M.Corcoran, M.Cordelli, M.Couderc, F.Cousinou, M.-C.Cox, C. A.Cox, D. J.Cremonesi, M.Cruz, D.Cuevas, J.Culbertson, R.Cuth, J.Cutts, D.Das, A.d'Ascenzo, N.Datta, M.Davies, G.de Barbaro, P.de Jong, S. J.De La Cruz-Burelo, E.Déliot, F.Demina, R.Demortier, L.Deninno, M.Denisov, D.Denisov, S. P.D'Errico, M.Desai, S.Deterre, C.DeVaughan, K.Devoto, F.Di Canto, A.Di Ruzza, B.Diehl, H. T.Diesburg, M.Ding, P. F.Dittmann, J. R.Dominguez, A.Donati, S.D'Onofrio, M.Dorigo, M.Driutti, A.Drutskoy, A.Dubey, A.Dudko, L. V.Duperrin, A.Dutt, S.Eads, M.Ebina, K.Edgar, R.Edmunds, D.Elagin, A.Ellison, J.Elvira, V. D.Enari, Y.Erbacher, R.Errede, S.Esham, B.Evans, H.Evdokimov, A.Evdokimov, V. N.Farrington, S.Fauré, A.Feng, L.Ferbel, T.Fernández Ramos, J. P.Fiedler, F.Field, R.Filthaut, F.Fisher, W.Fisk, H. E.Flanagan, G.Forrest, R.Fortner, M.Fox, H.Franc, J.Franklin, M.Freeman, J. C.Frisch, H.Fuess, S.Funakoshi, Y.Galloni, C.Garbincius, P. H.Garcia-Bellido, A.García-González, J. A.Garfinkel, A. F.Garosi, P.Gavrilov, V.Geng, W.Gerber, C. E.Gerberich, H.Gerchtein, E.Gershtein, Y.Giagu, S.Giakoumopoulou, V.Gibson, K.Ginsburg, C. M.Ginther, G.Giokaris, N.Giromini, P.Glagolev, V.Glenzinski, D.Gogota, O.Gold, M.Goldin, D.Golossanov, A.Golovanov, G.Gomez, G.Gomez-Ceballos, G.Goncharov, M.González López, O.Gorelov, I.Goshaw, A. T.Goulianos, K.Gramellini, E.Grannis, P. D.Greder, S.Greenlee, H.Grenier, G.Gris, Ph.Grivaz, J.-F.Grohsjean, A.Grosso-Pilcher, C.Grünendahl, S.Grünewald, M. W.Guillemin, T.Guimaraes da Costa, J.Gutierrez, G.Gutierrez, P.Hahn, S. R.Haley, J.Han, J. Y.Han, L.Happacher, F.Hara, K.Harder, K.Hare, M.Harel, A.Harr, R. F.Harrington-Taber, T.Hatakeyama, K.Hauptman, J. M.Hays, C.Hays, J.Head, T.Hebbeker, T.Hedin, D.Hegab, H.Heinrich, J.Heinson, A. P.Heintz, U.Hensel, C.Heredia-De La Cruz, I.Herndon, M.Herner, K.Hesketh, G.Hildreth, M. D.Hirosky, R.Hoang, T.Hobbs, J. D.Hocker, A.Hoeneisen, B.Hogan, J.Hohlfeld, M.Holzbauer, J. L.Hong, Z.Hopkins, W.Hou, SHowley, I.Hubacek, Z.Hughes, R. E.Husemann, U.Hussein, M.Huston, J.Hynek, V.Iashvili, I.Ilchenko, Y.Illingworth, R.Introzzi, G.Iori, M.Ito, A. S.Ivanov, A.Jabeen, S.Jaffré, M.James, E.Jang, D.Jayasinghe, A.Jayatilaka, B.Jeon, E. J.Jeong, M. S.Jesik, R.Jiang, P.Jindariani, S.Johns, K.Johnson, E.Johnson, M.Jonckheere, A.Jones, M.Jonsson, P.Joo, K. K.Joshi, J.Jun, S. Y.Jung, A. W.Junk, T. R.Juste, A.Kajfasz, E.Kambeitz, M.Kamon, T.Karchin, P. E.Karmanov, D.Kasmi, A.Kato, Y.Katsanos, I.Kaur, M.Kehoe, R.Kermiche, S.Ketchum, W.Keung, J.Khalatyan, N.Khanov, A.Kharchilava, A.Kharzheev, Y. N.Kilminster, B.Kim, D. H.Kim, H. S.Kim, J. E.Kim, M. J.Kim, S. H.Kim, S. B.Kim, Y. J.Kim, Y. K.Kimura, N.Kirby, M.Kiselevich, I.Kohli, J. M.Kondo, K.Kong, D. J.Konigsberg, J.Kotwal, A. V.Kozelov, A. V.Kraus, J.Kreps, M.Kroll, J.Kruse, M.Kuhr, T.Kumar, A.Kupco, A.Kurata, M.Kurča, T.Kuzmin, V. A.Laasanen, A. T.Lammel, S.Lammers, S.Lancaster, M.Lannon, K.Latino, G.Lebrun, P.Lee, H. S.Lee, H. S.Lee, J. S.Lee, S. W.Lee, W. M.Lei, X.Lellouch, J.Leo, S.Leone, S.Lewis, J. D.Li, D.Li, H.Li, L.Li, Q. Z.Lim, J. K.Limosani, A.Lincoln, D.Linnemann, J.Lipaev, V. V.Lipeles, E.Lipton, R.Lister, A.Liu, H.Liu, Q.Liu, T.Liu, Y.Lobodenko, A.Lockwitz, S.Loginov, A.Lokajicek, M.Lopes de Sa, R.Lucchesi, D.Lucà, A.Lueck, J.Lujan, P.Lukens, P.Luna-Garcia, R.Lungu, G.Lyon, A. L.Lys, J.Lysak, R.Maciel, A. K. A.Madar, R.Madrak, R.Maestro, P.Magaña-Villalba, R.Malik, S.Malik, S.Malyshev, V. L.Manca, G.Manousakis-Katsikakis, A.Mansour, J.Marchese, L.Margaroli, F.Marino, P.Martínez-Ortega, J.Matera, K.Mattson, M. E.Mazzacane, A.Mazzanti, P.McCarthy, R.McGivern, C. L.McNulty, R.Mehta, A.Mehtala, P.Meijer, M. M.Melnitchouk, A.Menezes, D.Mercadante, P. G.Merkin, M.Mesropian, C.Meyer, A.Meyer, J.Miao, T.Miconi, F.Mietlicki, D.Mitra, A.Miyake, H.Moed, S.Moggi, N.Mondal, N. K.Moon, C. S.Moore, R.Morello, M. J.Mukherjee, A.Mulhearn, M.Muller, Th.Murat, P.Mussini, M.Nachtman, J.Nagai, Y.Naganoma, J.Nagy, E.Nakano, I.Napier, A.Narain, M.Nayyar, R.Neal, H. A.Negret, J. P.Nett, J.Neustroev, P.Nguyen, H. T.Nigmanov, T.Nodulman, L.Noh, S. Y.Norniella, O.Nunnemann, T.Oakes, L.Oh, S. H.Oh, Y. D.Okusawa, T.Orava, R.Orduna, J.Ortolan, L.Osman, N.Pagliarone, C.Pal, A.Palencia, E.Palni, P.Papadimitriou, V.Parashar, N.Parihar, V.Park, S. K.Parker, W.Partridge, R.Parua, N.Patwa, A.Pauletta, G.Paulini, M.Paus, C.Penning, B.Perfilov, M.Peters, Y.Petridis, K.Petrillo, G.Pétroff, P.Phillips, T. J.Piacentino, G.Pianori, E.Pilot, J.Pitts, K.Plager, C.Pleier, M.-A.Podstavkov, V. M.Pondrom, L.Popov, A. V.Poprocki, S.Potamianos, K.Pranko, A.Prewitt, M.Price, D.Prokopenko, N.Prokoshin, F.Ptohos, F.Punzi, G.Qian, J.Quadt, A.Quinn, B.Ratoff, P. N.Razumov, I.Redondo Fernández, I.Renton, P.Rescigno, M.Rimondi, F.Ripp-Baudot, I.Ristori, L.Rizatdinova, F.Robson, A.Rodriguez, T.Rolli, S.Rominsky, M.Ronzani, M.Roser, R.Rosner, J. L.Ross, A.Royon, C.Rubinov, P.Ruchti, R.Ruffini, F.Ruiz, A.Russ, J.Rusu, V.Sajot, G.Sakumoto, W. K.Sakurai, Y.Sánchez-Hernández, A.Sanders, M. P.Santi, L.Santos, A. S.Sato, K.Savage, G.Saveliev, V.Savitskyi, M.Savoy-Navarro, A.Sawyer, L.Scanlon, T.Schamberger, R. D.Scheglov, Y.Schellman, H.Schlabach, P.Schmidt, E. E.Schott, M.Schwanenberger, C.Schwarz, T.Schwienhorst, R.Scodellaro, L.Scuri, F.Seidel, S.Seiya, Y.Sekaric, J.Semenov, A.Severini, HSforza, F.Shabalina, E.Shalhout, S. Z.Shary, V.Shaw, S.Shchukin, A. A.Shears, T.Shepard, P. F.Shimojima, M.Shkola, O.Shochet, M.Shreyber-Tecker, I.Simak, V.Simonenko, A.Skubic, P.Slattery, P.Sliwa, K.Smith, J. R.Snider, .F D.Snow, G. R.Snow, J.Snyder, S.Söldner-Rembold, S.Song, H.Sonnenschein, L.Sorin, V.Soustruznik, K.St Denis, R.Stancari, M.Stark, J.Stefaniuk, N.Stentz, D.Stoyanova, D. A.Strauss, M.Strologas, J.Sudo, Y.Sukhanov, A.Suslov, I.Suter, L.Svoisky, P.Takemasa, K.Takeuchi, Y.Tang, J.Tecchio, M.Teng, P. K.Thom, J.Thomson, E.Thukral, V.Titov, M.Toback, D.Tokar, S.Tokmenin, V. V.Tollefson, K.Tomura, T.Tonelli, D.Torre, S.Torretta, D.Totaro, P.Trovato, M.Tsai, Y.-T.Tsybychev, D.Tuchming, B.Tully, C.Ukegawa, F.Uozumi, S.Uvarov, L.Uvarov, S.Uzunyan, S.Van Kooten, R.van Leeuwen, W. M.Varelas, N.Varnes, E. W.Vasilyev, I. A.Vázquez, F.Velev, G.Vellidis, C.Verkheev, A. Y.Vernieri, C.Vertogradov, L. S.Verzocchi, M.Vesterinen, M.Vidal, M.Vilanova, D.Vilar, R.Vizán, J.Vogel, M.Vokac, P.Volpi, G.Wagner, P.Wahl, H. D.Wallny, R.Wang, M. H. L. S.Wang, S. M.Warchol, J.Waters, D.Watts, G.Wayne, M.Weichert, J.Welty-Rieger, L.Wester, W. C.Whiteson, D.Wicklund, A. B.Wilbur, S.Williams, H. H.Williams, M. R. J.Wilson, G. W.Wilson, J. S.Wilson, P.Winer, B. L.Wittich, P.Wobisch, M.Wolbers, S.Wolfmeister, H.Wood, D. R.Wright, T.Wu, X.Wu, Z.Wyatt, T. R.Xie, Y.Yamada, R.Yamamoto, K.Yamato, D.Yang, S.Yang, T.Yang, U. K.Yang, Y. C.Yao, W.-M.Yasuda, T.Yatsunenko, Y. A.Ye, W.Ye, Z.Yeh, G. P.Yi, K.Yin, H.Yip, K.Yoh, J.Yorita, K.Yoshida, T.Youn, S. W.Yu, G. B.Yu, I.Yu, J. M.Zanetti, A. M.Zeng, Y.Zennamo, J.Zhao, T. G.Zhou, B.Zhou, C.Zhu, J.Zielinski, M.Zieminska, D.Zivkovic, L.Zucchelli, S.
    Physical Review Retters 2018; 120(4): Art. 042001
    The CDF and D0 experiments at the Fermilab Tevatron have measured the asymmetry between yields of forward- and backward-produced top and antitop quarks based on their rapidity difference and the asymmetry between their decay leptons. These measurements use the full data sets collected in proton-antiproton collisions at a center-of-mass energy of sqrt[s]=1.96  TeV. We report the results of combinations of the inclusive asymmetries and their differential dependencies on relevant kinematic quantities. The combined inclusive asymmetry is A_{FB}^{tt[over ¯]}=0.128±0.025. The combined inclusive and differential asymmetries are consistent with recent standard model predictions.
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    Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function 

    Roitman, Sheila; Hornung, Ellen; Flores-Uribe, José; Sharon, Itai; Feussner, Ivo; Béjà, Oded
    The ISME Journal 2018; 12(2) p.343-355
    Cyanobacteria are among the most abundant photosynthetic organisms in the oceans; viruses infecting cyanobacteria (cyanophages) can alter cyanobacterial populations, and therefore affect the local food web and global biochemical cycles. These phages carry auxiliary metabolic genes (AMGs), which rewire various metabolic pathways in the infected host cell, resulting in increased phage fitness. Coping with stress resulting from photodamage appears to be a central necessity of cyanophages, yet the overall mechanism is poorly understood. Here we report a novel, widespread cyanophage AMG, encoding a fatty acid desaturase (FAD), found in two genotypes with distinct geographical distribution. FADs are capable of modulating the fluidity of the host's membrane, a fundamental stress response in living cells. We show that both viral FAD (vFAD) families are Δ9 lipid desaturases, catalyzing the desaturation at carbon 9 in C16 fatty acid chains. In addition, we present a comprehensive fatty acid profiling for marine cyanobacteria, which suggests a unique desaturation pathway of medium- to long-chain fatty acids no longer than C16, in accordance with the vFAD activity. Our findings suggest that cyanophages are capable of fiddling with the infected host's membranes, possibly leading to increased photoprotection and potentially enhancing viral-encoded photosynthetic proteins, resulting in a new viral metabolic network.
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    Photodissociation of aligned CH3I and C6H3F2I molecules probed with time-resolved Coulomb explosion imaging by site-selective extreme ultraviolet ionization. 

    Amini, Kasra; Savelyev, Evgeny; Brauße, Felix; Berrah, Nora; Bomme, Cédric; Brouard, Mark; Burt, Michael; Christensen, Lauge; Düsterer, Stefan; Erk, Benjamin; et al.
    Höppner, HaukeKierspel, ThomasKrecinic, FarukLauer, AlexandraLee, Jason W. L.Müller, MariaMüller, ErlandMullins, TerenceRedlin, HaraldSchirmel, NoraThøgersen, JanTechert, SimoneToleikis, SvenTreusch, RolfTrippel, SebastianUlmer, AnatoliVallance, ClaireWiese, JossJohnsson, PerKüpper, JochenRudenko, ArtemRouzée, ArnaudStapelfeldt, HenrikRolles, DanielBoll, Rebecca
    Structural Dynamics 2018; 5(1): Art. 014301
    We explore time-resolved Coulomb explosion induced by intense, extreme ultraviolet (XUV) femtosecond pulses from a free-electron laser as a method to image photo-induced molecular dynamics in two molecules, iodomethane and 2,6-difluoroiodobenzene. At an excitation wavelength of 267 nm, the dominant reaction pathway in both molecules is neutral dissociation via cleavage of the carbon-iodine bond. This allows investigating the influence of the molecular environment on the absorption of an intense, femtosecond XUV pulse and the subsequent Coulomb explosion process. We find that the XUV probe pulse induces local inner-shell ionization of atomic iodine in dissociating iodomethane, in contrast to non-selective ionization of all photofragments in difluoroiodobenzene. The results reveal evidence of electron transfer from methyl and phenyl moieties to a multiply charged iodine ion. In addition, indications for ultrafast charge rearrangement on the phenyl radical are found, suggesting that time-resolved Coulomb explosion imaging is sensitive to the localization of charge in extended molecules.
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    Constraining scalar resonances with top-quark pair production at the LHC 

    Franzosi, Diogo Buarque; Fabbri, Federica; Schumann, Steffen
    Journal of High Energy Physics 2018; 2018(3): Art. 22
    Constraints on models which predict resonant top-quark pair production at the LHC are provided via a reinterpretation of the Standard Model (SM) particle level measurement of the top-anti-top invariant mass distribution, m(t t). We make use of stateof- the-art Monte Carlo event simulation to perform a direct comparison with measurements of m(t t) in the semi-leptonic channels, considering both the boosted and the resolved regime of the hadronic top decays. A simpli ed model to describe various scalar resonances decaying into top-quarks is considered, including CP-even and CP-odd, color-singlet and color-octet states, and the excluded regions in the respective parameter spaces are provided.
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    An ensemble framework for time delay synchronization 

    Pinheiro, Flavia R.; van Leeuwen, Peter Jan; Parlitz, Ulrich
    Quarterly Journal of the Royal Meteorological Society 2018; 144(711) p.305-316
    Synchronization based state estimation tries to synchronize a model with the true evolution of a system via the observations. In practice, an extra term is added to the model equations which hampers growth of instabilities transversal to the synchronization manifold. Therefore, there is a very close connection between synchronization and data assimilation. Recently, synchronization with time-delayed observations has been proposed, in which observations at future times are used to help synchronize a system that does not synchronize using only present observations, with remarkable successes. Unfortunately, these schemes are limited to small-dimensional problems. In this article, we lift that restriction by proposing an ensemble-based synchronization scheme. Tests were performed using the Lorenz’96 model for 20-, 100- and 1000-dimension systems. Results show global synchronization errors stabilizing at values of at least an order of magnitude lower than the observation errors, suggesting that the scheme is a promising tool to steer model states to the truth. While this framework is not a complete data assimilation method, we develop this methodology as a potential choice for a proposal density in a more comprehensive data assimilation method, like a fully nonlinear particle filter.
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    Land Surface Temperature Variation Due to Changes in Elevation in Northwest Vietnam 

    Phan, Thanh; Kappas, Martin; Tran, Trong
    Climate 2018; 6(2): Art. 28
    Land surface temperature (LST) is one of the most important variables for applications relating to the physics of land surface processes. LST rapidly changes in both space and time, and knowledge of LST and its spatiotemporal variation is essential to understand the interactions between human activity and the environment. This study investigates the spatiotemporal variation of LST according to changes in elevation. The newest version (version 6) of MODIS LST data for 2015 was used. An area of 40,000 km2 (200 × 200 km2) in northwest Vietnam with elevations ranging from 8 m to 3165 m was chosen as a case study. Our results showed that the drop in LST with increased elevation varied throughout the year during both the daytime and nighttime. The monthly averages in 2015 and an altitude increase of 1000 m resulted in a decrease in LST ranging from 3.8 °C to 6.1 °C and 1.5 °C to 5.8 °C for the daytime and nighttime, respectively. This suggests that in any study relating to the spatial distribution of LST, the effect of elevation on LST should be considered. In addition, the effects of land use/cover and elevation distribution on the relationship between LST and elevation are discussed.
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    Dendrochronologically dated pine stumps document phase-wise bog expansion at a northwest German site between ca. 6700 and ca. 3400 BC 

    Achterberg, Inke Elisabeth Maike; Eckstein, Jan; Birkholz, Bernhard; Bauerochse, Andreas; Leuschner, Hanns Hubert
    Climate of the Past 2018; 14(1) p.85-100
    The investigated northwest German mire site at "Totes Moor" is densely covered with subfossil pine stumps (Pinus sylvestris L.) from the fen–bog transition. This facilitates the spatio-temporal reconstruction of mire development, which is based on 212 in situ tree stumps in the case study presented here. Six dendrochronologically dated site chronologies together cover 2345 years between 6703 and 3403 BC. The gaps in between are 6 to 550 years long. Additionally, a floating chronology of 309 years, containing 30 trees, was radiocarbon-dated to the beginning of the 7th millennium cal BC. Peat-stratigraphical survey was carried out additionally, and elevations a.s.l. were determined at several locations. Tree dying-off phases, which indicate water level rise at the site, mostly in context of the local fen–bog transition, are evident for ca. 6600–6450, ca. 6350–5750, ca. 5300–4900, ca. 4700–4550, ca. 3900–3850, ca. 3700–3600, ca. 3500–3450 and ca. 3400 BC. The spatial distribution of the dated in situ trees illustrates the phase-wise expansion of raised bog over fen peat at the site. The documented bog expansion pulses likely correspond to climatic wet sifts.
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    Climate effects on vegetation vitality at the treeline of boreal forests of Mongolia 

    Klinge, Michael; Dulamsuren, Choimaa; Erasmi, Stefan; Karger, Dirk Nikolaus; Hauck, Markus
    Biogeosciences 2018; 15(5) p.1319-1333
    In northern Mongolia, at the southern boundary of the Siberian boreal forest belt, the distribution of steppe and forest is generally linked to climate and topography, making this region highly sensitive to climate change and human impact. Detailed investigations on the limiting parameters of forest and steppe in different biomes provide necessary information for paleoenvironmental reconstruction and prognosis of potential landscape change. In this study, remote sensing data and gridded climate data were analyzed in order to identify main distribution patterns of forest and steppe in Mongolia and to detect environmental factors driving forest development. Forest distribution and vegetation vitality derived from the normalized differentiated vegetation index (NDVI) were investigated for the three types of boreal forest present in Mongolia (taiga, subtaiga and forest–steppe), which cover a total area of 73 818 km2. In addition to the forest type areas, the analysis focused on subunits of forest and nonforested areas at the upper and lower treeline, which represent ecological borders between vegetation types. Climate and NDVI data were analyzed for a reference period of 15 years from 1999 to 2013. The presented approach for treeline delineation by identifying representative sites mostly bridges local forest disturbances like fire or tree cutting. Moreover, this procedure provides a valuable tool to distinguish the potential forested area. The upper treeline generally rises from 1800 m above sea level (a.s.l.) in the northeast to 2700 m a.s.l. in the south. The lower treeline locally emerges at 1000 m a.s.l. in the northern taiga and rises southward to 2500 m a.s.l. The latitudinal gradient of both treelines turns into a longitudinal one on the eastern flank of mountain ranges due to higher aridity caused by rain-shadow effects. Less productive trees in terms of NDVI were identified at both the upper and lower treeline in relation to the respective total boreal forest type area. The mean growing season temperature (MGST) of 7.9–8.9 °C and a minimum MGST of 6 °C are limiting parameters at the upper treeline but are negligible for the lower treeline. The minimum of the mean annual precipitation (MAP) of 230–290 mm yr−1 is a limiting parameter at the lower treeline but also at the upper treeline in the forest–steppe ecotone. In general, NDVI and MAP are lower in grassland, and MGST is higher compared to the corresponding boreal forest. One exception occurs at the upper treeline of the subtaiga and taiga, where the alpine vegetation consists of mountain meadow mixed with shrubs. The relation between NDVI and climate data corroborates that more precipitation and higher temperatures generally lead to higher greenness in all ecological subunits. MGST is positively correlated with MAP of the total area of forest–steppe, but this correlation turns negative in the taiga. The limiting factor in the forest–steppe is the relative humidity and in the taiga it is the snow cover distribution. The subtaiga represents an ecological transition zone of approximately 300 mm yr−1 precipitation, which occurs independently from the MGST. Since the treelines are mainly determined by climatic parameters, the rapid climate change in inner Asia will lead to a spatial relocation of tree communities, treelines and boreal forest types. However, a direct deduction of future tree vitality, forest composition and biomass trends from the recent relationships between NDVI and climate parameters is challenging. Besides human impact, it must consider bio- and geoecological issues like, for example, tree rejuvenation, temporal lag of climate adaptation and disappearing permafrost.
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    Ideas and perspectives: hydrothermally driven redistribution and sequestration of early Archaean biomass – the “hydrothermal pump hypothesis” 

    Duda, Jan-Peter; Thiel, Volker; Bauersachs, Thorsten; Mißbach, Helge; Reinhardt, Manuel; Schäfer, Nadine; Van Kranendonk, Martin J.; Reitner, Joachim
    Biogeosciences 2018; 15(5) p.1535-1548
    Archaean hydrothermal chert veins commonly contain abundant organic carbon of uncertain origin (abiotic vs. biotic). In this study, we analysed kerogen contained in a hydrothermal chert vein from the ca. 3.5 Ga Dresser Formation (Pilbara Craton, Western Australia). Catalytic hydropyrolysis (HyPy) of this kerogen yielded n-alkanes up to n-C22, with a sharp decrease in abundance beyond n-C18. This distribution ( n-C18) is very similar to that observed in HyPy products of recent bacterial biomass, which was used as reference material, whereas it differs markedly from the unimodal distribution of abiotic compounds experimentally formed via Fischer–Tropsch-type synthesis. We therefore propose that the organic matter in the Archaean chert veins has a primarily microbial origin. The microbially derived organic matter accumulated in anoxic aquatic (surface and/or subsurface) environments and was then assimilated, redistributed and sequestered by the hydrothermal fluids (“hydrothermal pump hypothesis”)
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    Polyethylene-Grafted Gold and Silver Nanoparticles Using Catalyzed Chain Growth (CCG) 

    Wagner, Jannik; Peng, Wentao; Vana, Philipp
    Polymers 2018; 10(4): Art. 407
    We report an efficient synthesis route for the formation of gold/silver-core–PE-shell nanohybrids in a simple self-assembly approach using PE with strong aurophilicity and argentophilicity, via thiol- and trithiocarbonate terminated moieties. This united the unique properties of polyethylene (PE) with gold and silver nanoparticles, using the well-defined end-group design of PE. These nanocomposites showed a similar solubility as PE, as confirmed by dynamic light scattering, and could be fully incorporated into a polyethylene matrix with different particle contents, as visualized by transmission electron microscopy. Using UV/vis-spectroscopy, we observed reversible, thermoresponsive aggregation/deaggregation properties in the nanohybrids, validating the strong and effective anchoring of PE on gold/silver surfaces.
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    Adapting Chinese Forest Operations to Socio-Economic Developments: What is the Potential of Plantations for Strengthening Domestic Wood Supply? 

    Hoffmann, Stephan; Jaeger, Dirk; Shuirong, Wu
    Sustainability 2018; 10(4) p.1-19: Art. 1042
    Over recent decades, China’s forestry sector went through a transition phase characterized by a management and institutional reform process, with a constant rethinking of the ecological and societal role of forests within a unique political system. Nevertheless, despite impressive achievements in forest restoration and conservation efforts, the enhancement of ecosystem services and forest area expansion through plantation development, China was not able to improve its domestic timber supply capacities according to its demands. Consequently, the continually growing wood processing industry is facing a severe demand-and-supply gap, causing high dependencies on timber imports. Outdated forest operations practices, dominated by manual labour, are not able to meet supply demands or to implement new silvicultural strategies for enhancing forest quality and productivity and are a widely unnoted disruption of a sustainable development. Therefore, this review presents the status quo of China’s forest operations sector, how it is shaped by forest policy reforms and recent socio-economic developments. In addition, suggestions are developed how the sector can progress through policy adaptations in order to develop sustainable timber supply capacities based on a domestic plantation sector.
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    The Suitability of Pozzolan as Admixing Aggregate for Fe0-Based Filters 

    Ndé-Tchoupé, Arnaud; Makota, Suzanne; Nassi, Achille; Hu, Rui; Noubactep, Chicgoua
    Water 2018; 10(4) p.1-17: Art. 417
    Continuous gravity-fed column experiments using the methylene blue (MB) discoloration method were performed to characterize the suitability of a pozzolan (PZ) specimen as alternative admixing aggregate for metallic iron filters (Fe0-filters). Investigated systems were: (i) pure sand, (ii) pure PZ, (iii) pure Fe0, (iv) Fe0/sand, (v) Fe0/PZ, and (vi) Fe0/sand/PZ. The volumetric proportion of Fe0 was 25%. The volumetric proportions of the Fe0/sand/PZ system was 25/45/30. The initial MB concentration was 2.0 mg L􀀀1, 6.0 g of Fe0 was used, and the experiments lasted for 46 days. The individual systems were fed with 3.9 to 8.4 L (7.80 to 16.69 mg of MB) and were characterized by the time-dependent changes of: (i) the pH value, (ii) the iron breakthrough, (iii) the MB breakthrough, and (iv) the hydraulic conductivity. Results showed that the Fe0/sand/PZ system was the most efficient. This ternary system was also the most permeable and therefore the most sustainable. The suitability of MB as a powerful operative indicator for the characterization of processes in the Fe0/H2O system was confirmed. The tested PZ is recommended as an alternative material for efficient but sustainable Fe0 filters.
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