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Appelshäuser, Harald ; Bächler, Joachim ; Bailey, Stephen John ; Barna, Daniel ; Barnby, Lee Stuart ; Bartke, Jerzy ; Barton, Robert Allan ; Białkowska, Helena ; Billmeier, Anja ; Blyth, Charles O. ; Bock, Rudolf ; Bormann, Christian ; Brady, Franklin Paul ; Brockmann, Robert ; Brun, René ; Bunčić, Predrag ; Caines, Helen Louise ; Carr, Lincoln D. ; Cebra, Daniel A. ; Cooper, Glenn E. ; Cramer, John G. ; Cristinziani, Markus ; Csató, Péter ; Dunn, Jason ; Eckardt, Volker ; Eckhardt, Frank ; Ferguson, M. I. ; Fischer, Hans Gerhard ; Flierl, Dominik Bernhard ; Fodor, Zoltán ; Foka, Panagiota ; Freund, Peter ; Friese, Volker ; Fuchs, Matthias ; Gabler, Frank ; Ganz, Rudolf ; Geist, W. ; Gál, József ; Gaździcki, Marek ; Gładysz-Dziaduś, Ewa ; Grebieszkow, Jaroslaw ; Günther, Jörg ; Harris, John William ; Hegyi, Sándor ; Henkel, Torsten ; Hill, L. A. ; Hümmler, Holm Gero ; Igo, George J. ; Irmscher, Detlef ; Jacobs, Peter Martin ; Jones, Peter Graham ; Kadija, Krešo ; Kolesnikov, Vadim I. ; Konashenok, Anton ; Kowalski, Marek ; Lasiuk, Brian ; Lévai, Péter ; Liu, F. ; Malakhov, Aleksandr I. ; Margetis, Spyridon ; Markert, Christina ; Melkumov, Georgy L. ; Mock, Andreas ; Molnár, József ; Nelson, J. M. ; Oldenburg, Markus D. ; Odyniec, Grazyna Janina ; Pálla, Gabriella ; Panagiotou, Apostolos D. ; Petridis, Athanasios ; Piper, Andreas ; Porter, R. Jefferson ; Poskanzer, Arthur M. ; Prindle, Duncan J. ; Pühlhofer, Falk ; Rauch, Wolfgang Hans ; Reid, Jeffrey G. ; Renfordt, Rainer Arno Ernst ; Retyk, Waldemar ; Ritter, Hans Georg ; Röhrich, Dieter ; Roland, Christof ; Roland, Gunther ; Rudolph, Heinrich ; Rybicki, Andrzej ; Sandoval, Andres ; Sann, Hans ; Semenov, Alexei Yu. ; Schäfer, Erich ; Schmischke, Dirk ; Schmitz, Norbert ; Schönfelder, Stefan ; Seyboth, Peter ; Seyerlein, Jürgen ; Siklér, Ferenc ; Skrzypczak, Ewa ; Snellings, Raimond ; Squier, Gordon Thomas Anderson ; Stock, Reinhard ; Ströbele, Herbert ; Struck, Christof ; Šuša, Tatjana ; Szentpétery, Imre ; Sziklai, János ; Toy, Milton Y. ; Trainor, Thomas A. ; Trentalange, Stephen ; Ullrich, Thomas ; Vassiliou, Maria ; Veres, Gábor I. ; Vesztergombi, György ; Vranić, Danilo ; Wang, Feipeng ; Weerasundara, Dhammika D. ; Wenig, Siegfried ; Whitten, Charles A. ; Wienold, Thomas ; Wood, Lindsay ; Xu, Nu ; Yates, Tim A. ; Zimányi, József ; Zhu, Xue-Zhou ; Zybert, Ryszard
We report measurements of Xi and Xi-bar hyperon absolute yields as a function of rapidity in 158 GeV/c Pb+Pb collisions. At midrapidity, dN/dy = 2.29 +/- 0.12 for Xi, and 0.52 +/- 0.05 for Xi-bar, leading to the ratio of Xi-bar/Xi = 0.23 +/- 0.03. Inverse slope parameters fitted to the measured transverse mass spectra are of the order of 300 MeV near mid-rapidity. The estimated total yield of Xi particles in Pb+Pb central interactions amounts to 7.4 +/- 1.0 per collision. Comparison to Xi production in properly scaled p+p reactions at the same energy reveals a dramatic enhancement (about one order of magnitude) of Xi production in Pb+Pb central collisions over elementary hadron interactions.
Yu, Wei ; Ma, Xueyan ; Xu, Jinjin ; Heumüller, Andreas ; Fei, Zhaoliang ; Feng, Xue ; Wang, Xiaodong ; Liu, Kuo ; Li, Jinhui ; Cui, Guizhong ; Peng, Guangdun ; Ji, Hongbin ; Li, Jinsong ; Jing, Naihe ; Song, Hai ; Lin, Zhiqiang ; Zhao, Yun ; Wang, Zuoyun ; Zhou, Bin ; Zhang, Lei
Heart valve disease is a major clinical problem worldwide. Cardiac valve development and homeostasis need to be precisely controlled. Hippo signaling is essential for organ development and tissue homeostasis, while its role in valve formation and morphology maintenance remains unknown. VGLL4 is a transcription cofactor in vertebrates and we found it was mainly expressed in valve interstitial cells at the post-EMT stage and was maintained till the adult stage. Tissue specific knockout of VGLL4 in different cell lineages revealed that only loss of VGLL4 in endothelial cell lineage led to valve malformation with expanded expression of YAP targets. We further semi-knockout YAP in VGLL4 ablated hearts, and found hyper proliferation of arterial valve interstitial cells was significantly constrained. These findings suggest that VGLL4 is important for valve development and manipulation of Hippo components would be a potential therapy for preventing the progression of congenital valve disease.
Wang, Mingyi ; Kong, Weimeng ; Marten, Ruby ; He, Xu-Cheng ; Chen, Dexian ; Pfeifer, Joschka ; Heitto, Arto ; Kontkanen, Jenni ; Dada, Lubna ; Kürten, Christoph Andreas ; Yli-Juuti, Taina ; Manninen, Hanna Elina ; Amanatidis, Stavros ; Amorim, Antonio ; Baalbaki, Rima ; Baccarini, Andrea ; Bell, David M. ; Bertozzi, Barbara ; Bräkling, Steffen ; Brilke, Sophia ; Murillo, Lucía Caudillo ; Chiu, Randall ; Chu, Biwu ; De Menezes, Louis-Philippe ; Duplissy, Jonathan ; Finkenzeller, Henning ; Gonzalez Carracedo, Loic ; Granzin, Manuel ; Guida, Roberto ; Hansel, Armin ; Hofbauer, Victoria ; Krechmer, Jordan ; Lehtipalo, Katrianne ; Lamkaddam, Houssni ; Lampimäki, Marku ; Lee, Chuan Ping ; Makhmutov, Vladimir ; Marie, Guillaume ; Mathot, Serge ; Mauldin, Roy Lee ; Mentler, Bernhard ; Müller, Tatjana ; Onnela, Antti ; Partoll, Eva ; Petäjä, Tuukka ; Philippov, Maxim ; Pospisilova, Veronika ; Ranjithkumar, Ananth ; Rissanen, Matti P. ; Rörup, Birte ; Scholz, Wiebke ; Shen, Jiali ; Simon, Mario ; Sipilä, Mikko ; Steiner, Gerhard ; Stolzenburg, Dominik ; Tham, Yee Jun ; Tomé, António ; Wagner, Andrea Christine ; Wang, Dongyu S. ; Wang, Yonghong ; Weber, Stefan K. ; Winkler, Paul M. ; Wlasits, Peter J. ; Wu, Yusheng ; Xiao, Mao ; Ye, Qing ; Zauner-Wieczorek, Marcel ; Zhou, Xueqin ; Volkamer, Rainer ; Riipinen, Ilona ; Dommen, Josef ; Curtius, Joachim ; Baltensperger, Urs ; Kulmala, Markku ; Worsnop, Douglas R. ; Kirkby, Jasper ; Seinfeld, John H. ; El Haddad, Imad ; Flagan, Richard C. ; Donahue, Neil McPherson
A list of authors and their affiliations appears at the end of the paper New-particle formation is a major contributor to urban smog, but how it occurs in cities is often puzzling. If the growth rates of urban particles are similar to those found in cleaner environments (1–10 nanometres per hour), then existing understanding suggests that new urban particles should be rapidly scavenged by the high concentration of pre-existing particles. Here we show, through experiments performed under atmospheric conditions in the CLOUD chamber at CERN, that below about +5 degrees Celsius, nitric acid and ammonia vapours can condense onto freshly nucleated particles as small as a few nanometres in diameter. Moreover, when it is cold enough (below −15 degrees Celsius), nitric acid and ammonia can nucleate directly through an acid–base stabilization mechanism to form ammonium nitrate particles. Given that these vapours are often one thousand times more abundant than sulfuric acid, the resulting particle growth rates can be extremely high, reaching well above 100 nanometres per hour. However, these high growth rates require the gas-particle ammonium nitrate system to be out of equilibrium in order to sustain gas-phase supersaturations. In view of the strong temperature dependence that we measure for the gas-phase supersaturations, we expect such transient conditions to occur in inhomogeneous urban settings, especially in wintertime, driven by vertical mixing and by strong local sources such as traffic. Even though rapid growth from nitric acid and ammonia condensation may last for only a few minutes, it is nonetheless fast enough to shepherd freshly nucleated particles through the smallest size range where they are most vulnerable to scavenging loss, thus greatly increasing their survival probability. We also expect nitric acid and ammonia nucleation and rapid growth to be important in the relatively clean and cold upper free troposphere, where ammonia can be convected from the continental boundary layer and nitric acid is abundant from electrical storms.
Öztürk, Fatma Cagla ; Akkuş, Baki ; Atanasov, Dinko ; Beyer, Heinrich F. ; Bosch, Fritz ; Boutin, David ; Brandau, Carsten ; Bühler, Paul ; Çakirli Mutlu, Rabia Burcu ; Chen, Ruijiu ; Chen, Weidong ; Chen, Xiangcheng ; Dillmann, Iris ; Dimopoulou, Christina ; Enders, Wolfgang ; Essel, Hans G. ; Faestermann, Thomas ; Forstner, Oliver ; Gao, Bing-Shui ; Geissel, Hans ; Gernhäuser, Roman ; Grisenti, Robert Evaristo ; Gumberidze, Alexandre ; Hagmann, Siegbert ; Heftrich, Tanja ; Heil, Michael ; Herdrich, Marc Oliver ; Hillenbrand, Pierre-Michel ; Izumikawa, Takuji ; Kienle, Paul ; Klaushofer, Christoph ; Kleffner, Carl-Michael ; Kozhuharov, Christophor ; Knöbel, Ronja ; Kovalenko, Oleksandr ; Kreim, Susanne ; Kühl, Thomas ; Lederer-Woods, Claudia ; Lestinsky, Michael ; Litvinov, Sergey A. ; Litvinov, Yuri A. ; Liu, Zhong ; Ma, Xinwen ; Maier, Ludwig W. ; Mei, Bo ; Miura, Hiroshi ; Mukha, Ivan ; Najafi, Mohammad Ali ; Nagae, Daisuke ; Nishimura, Takuro ; Nociforo, Chiara ; Nolden, Fritz ; Ohtsubo, Takashi ; Öktem, Yeşim ; Omika, Shunichiro ; Ozawa, Akira ; Petridis, Nikolaos ; Piotrowski, Jeremi ; Reifarth, René ; Roßbach, Jörg ; Sánchez Alarcón, Rodolfo Marcelo ; Sanjari, Mohammad Shahab ; Scheidenberger, Christoph ; Sidhu, Ragandeep Singh ; Simon, Haik ; Spillmann, Uwe ; Steck, Markus ; Stöhlker, Thomas ; Sun, Baohua ; Susam, Lidya Amon ; Suzaki, Fumi ; Suzuki, Takeshi ; Torilov, Sergey Yu. ; Trageser, Christian ; Trassinelli, Martino ; Trotsenko, Sergiy ; Tu, Xiaolin ; Walker, Philip M. ; Wang, M. ; Weber, Günter ; Weick, Helmut ; Winckler, Nicolas ; Winters, Danyal Ferdinant Alexander ; Woods, Philip John ; Yamaguchi, Takayuki ; Xu, X.D. ; Yan, X.L. ; Yang, Jiancheng ; Yuan, You-Jin ; Zhang, Yuhu ; Zhou, Xiaohong
An experiment addressing electron capture (EC) decay of hydrogen-like 142Pm60+ions has been conducted at the experimental storage ring (ESR) at GSI. The decay appears to be purely exponential and no modulations were observed. Decay times for about 9000 individual EC decays have been measured by applying the single-ion decay spectroscopy method. Both visually and automatically analysed data can be described by a single exponential decay with decay constants of 0.0126(7)s−1 for automatic analysis and 0.0141(7)s−1 for manual analysis. If a modulation superimposed on the exponential decay curve is assumed, the best fit gives a modulation amplitude of merely 0.019(15), which is compatible with zero and by 4.9 standard deviations smaller than in the original observation which had an amplitude of 0.23(4).
Acera Mateos, Pablo ; Sethi, Aditya J. ; Ravindran, Agin ; Srivastava, Akanksha ; Woodward, Katrina ; Mahmud, Shafi ; Kanchi, Madhu ; Guarnacci, Marco ; Xu, Jiajia ; Yuen, Zaka Wing Sze ; Zhou, You ; Sneddon, Alexandra ; Hamilton, William ; Gao, Jing ; Starrs, Lora M. ; Hayashi, Rippei ; Wickramasinghe, Vihandha ; Zarnack, Katharina ; Preiss, Thomas ; Burgio, Gaetan ; Dehorter, Nathalie ; Shirokikh, Nikolay ; Eyras Jiménez, Eduardo Angel
The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI’s capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.
Acera Mateos, Pablo ; Sethi, Aditya J. ; Ravindran, Agin ; Srivastava, Akanksha ; Kanchi, Madhu ; Mahmud, Shafi ; Guarnacci, Marco ; Woodward, Katrina ; Xu, Jiajia ; Yuen, Zaka Wing Sze ; Zhou, You ; Sneddon, Alexandra ; Hamilton, William ; Gao, Jing ; Starrs, Lora M. ; Hayashi, Rippei ; Wickramasinghe, Vihandha ; Zarnack, Katharina ; Preiss, Thomas ; Burgio, Gaetan ; Dehorter, Nathalie ; Shirokikh, Nikolay ; Eyras Jiménez, Eduardo Angel
The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.
Acera Mateos, Pablo ; Sethi, Aditya J. ; Ravindran, Agin ; Srivastava, Akanksha ; Kanchi, Madhu ; Mahmud, Shafi ; Guarnacci, Marco ; Woodward, Katrina ; Xu, Jiajia ; Yuen, Zaka Wing Sze ; Zhou, You ; Sneddon, Alexandra ; Hamilton, William ; Gao, Jing ; Starrs, Lora M. ; Hayashi, Rippei ; Wickramasinghe, Vihandha ; Zarnack, Katharina ; Preiss, Thomas ; Burgio, Gaetan ; Dehorter, Nathalie ; Shirokikh, Nikolay ; Eyras Jiménez, Eduardo Angel
The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.
Acera Mateos, Pablo ; Sethi, Aditya J. ; Ravindran, Agin ; Guarnacci, Marco ; Srivastava, Akanksha ; Xu, Jiajia ; Woodward, Katrina ; Yuen, Zaka Wing Sze ; Mahmud, Shafi ; Kanchi, Madhu ; Zhou, You ; Sneddon, Alexandra ; Hamilton, William ; Gao, Jing ; Starrs, Lora M. ; Hayashi, Rippei ; Wickramasinghe, Vihandha ; Zarnack, Katharina ; Preiss, Thomas ; Burgio, Gaetan ; Dehorter, Nathalie ; Shirokikh, Nikolay ; Eyras Jiménez, Eduardo Angel
The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.
Acera Mateos, Pablo ; Sethi, Aditya J. ; Ravindran, Agin ; Srivastava, Akanksha ; Kanchi, Madhu ; Mahmud, Shafi ; Guarnacci, Marco ; Woodward, Katrina ; Xu, Jiajia ; Yuen, Zaka Wing Sze ; Zhou, You ; Sneddon, Alexandra ; Hamilton, William ; Gao, Jing ; Starrs, Lora M. ; Hayashi, Rippei ; Wickramasinghe, Vihandha ; Zarnack, Katharina ; Preiss, Thomas ; Burgio, Gaetan ; Dehorter, Nathalie ; Shirokikh, Nikolay ; Eyras Jiménez, Eduardo Angel
The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.