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The Effect of Attractive Interactions and Macromolecular Crowding on Crystallins Association.
In living systems proteins are typically found in crowded environments where their effective interactions strongly depend on the surrounding medium. Yet, their association and dissociation needs to be robustly controlled in...
A framework to assess the quality and impact of bioinformatics training across ELIXIR.
Kim T Gurwitz, Prakash Singh Gaur, Louisa J Bellis, Lee Larcombe, Eva Alloza, Balint Laszlo Balint, Alexander Botzki, Jure Dimec, Victoria Dominguez Del Angel, Pedro L Fernandes, Eija Korpelainen, Roland Krause, Mateusz Kuzak, Loredana Le Pera, Brane Leskošek, Jessica M Lindvall, Diana Marek, Paula A Martinez, Tuur Muyldermans, Ståle Nygård, Patricia M Palagi, Hedi Peterson, Fotis Psomopoulos, Vojtech Spiwok, Celia WG van Gelder, Allegra Via, Marko Vidak, Daniel Wibberg, Sarah L Morgan, Gabriella Rustici
Jul 23, 2020
ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims...
The Lennard-Jones potential
The Lennard-Jones 12-6 potential (LJ) is arguably the most widely used pair potential in molecular simulations. In fact, it is so popular that the question is rarely asked whether it is fit for purpose. In this paper, we argue...
Emergence of complex behavior in pili-based motility in early stages of P. aeruginosa surface adaptation.
Pseudomonas aeruginosa move across surfaces by using multiple Type IV Pili (TFP), motorized appendages capable of force generation via linear extension/retraction cycles, to generate surface motions collectively known as...
What experiments on pinned nanobubbles can tell about the critical nucleus for bubble nucleation.
Qianxiang Xiao, Yawei Liu, Zhenjiang Guo, Zhiping Liu, Daan Frenkel, Jure Dobnikar, Xianren Zhang
Feb 23, 2018
The process of homogeneous bubble nucleation is almost impossible to probe experimentally, except near the critical point or for liquids under large negative tension. Elsewhere in the phase diagram, the bubble nucleation barrier...
Nanoparticle organization in sandwiched polymer brushes.
The organization of nanoparticles inside grafted polymer layers is governed by the interplay of polymer-induced entropic interactions and the action of externally applied fields. Earlier work had shown that strong external...
Crystallinity of Double-Stranded RNA-Antimicrobial Peptide Complexes Modulates Toll-Like Receptor 3-Mediated Inflammation.
Ernest Y Lee, Toshiya Takahashi, Tine Curk, Jure Dobnikar, Richard L Gallo, Gerard CL Wong
Jan 22, 2018
Double-stranded RNA (dsRNA) induces production of pro-inflammatory cytokines in normal human epidermal keratinocytes (NHEK) by specific binding to endosomal Toll-like receptor-3 (TLR3). Recently, it has been shown that...
Designing stimulus-sensitive colloidal walkers.
Francisco J Martinez-Veracoechea, Bortolo M Mognetti, Stefano Angioletti-Uberti, Patrick Varilly, Daan Frenkel, Jure Dobnikar
Jan 09, 2018
Colloidal particles with DNA "legs" that can bind reversibly to receptors on a surface can be made to 'walk' if there is a gradient in receptor concentration. We use a combination of theory and Monte Carlo simulations to explore...
Computational design of probes to detect bacterial genomes by multivalent binding.
Tine Curk, Chris A Brackley, James D Farrell, Zhongyang Xing, Darshana Joshi, Susana Direito, Urban Bren, Stefano Angioletti-Uberti, Jure Dobnikar, Erika Eiser, Daan Frenkel, Rosalind J Allen
Oct 06, 2020
Rapid methods for diagnosis of bacterial infections are urgently needed to reduce inappropriate use of antibiotics, which contributes to antimicrobial resistance. In many rapid diagnostic methods, DNA oligonucleotide probes...
DNA-based detection computer simulations multivalent binding polymer physics superselectivity Computational Biology Computer Simulation Computer-Aided Design DNA Probes DNA Bacterial Genome Bacterial Oligonucleotide Array Sequence Analysis Oligonucleotide Probes Sensitivity and Specificity Sequence Analysis DNA
Liquid-crystalline ordering of antimicrobial peptide-DNA complexes controls TLR9 activation.
Nathan W Schmidt, Fan Jin, Roberto Lande, Tine Curk, Wujing Xian, Calvin Lee, Loredana Frasca, Daan Frenkel, Jure Dobnikar, Michel Gilliet, Gerard CL Wong
Jul 13, 2015
Patterns of alternative access
Olga Löblová, Marcell Csanádi, Piotr Ozierański, Zoltán Kaló, Lawrence King, Martin McKee
Aug 31, 2019
Many countries employ "alternative access schemes" (e.g. compassionate use, early access programs, off-label use) that seek to provide patients with access to drugs not included on a positive drug list. These schemes offer...
Patterns of alternative access
Olga Löblová, Marcell Csanádi, Piotr Ozierański, Zoltán Kaló, Lawrence King, Martin McKee
Aug 21, 2019
Many countries employ "alternative access schemes" (e.g. compassionate use, early access programs, off-label use) that seek to provide patients with access to drugs not included on a positive drug list. These schemes offer...
Patterns of alternative access
Olga Löblová, Marcell Csanádi, Piotr Ozierański, Zoltán Kaló, Lawrence King, Martin McKee
Aug 31, 2019
Many countries employ "alternative access schemes" (e.g. compassionate use, early access programs, off-label use) that seek to provide patients with access to drugs not included on a positive drug list. These schemes offer...
Thermal WIMPs and the scale of new physics
Peter Athron, Neal Avis Kozar, Csaba Balázs, Ankit Beniwal, Sanjay Bloor, Torsten Bringmann, Joachim Brod, Christopher Chang, Jonathan M. Cornell, Ben Farmer, Andrew Fowlie, Tomás E. Gonzalo, Will Handley, Felix Kahlhoefer, Anders Kvellestad, Farvah Mahmoudi, Markus T. Prim, Are Raklev, Janina J. Renk, Andre Scaffidi, Pat Scott, Patrick Stöcker, Aaron C. Vincent, Martin White, Sebastian Wild, Jure Zupan
Nov 22, 2021
Abstract: We assess the status of a wide class of WIMP dark matter (DM) models in light of the latest experimental results using the global fitting framework GAMBIT. We perform a global analysis of effective field theory (EFT)...
AEDGE
Yousef Abou El-Neaj, Cristiano Alpigiani, Sana Amairi-Pyka, Henrique Araújo, Antun Balaž, Angelo Bassi, Lars Bathe-Peters, Baptiste Battelier, Aleksandar Belić, Elliot Bentine, José Bernabeu, Andrea Bertoldi, Robert Bingham, Diego Blas, Vasiliki Bolpasi, Kai Bongs, Sougato Bose, Philippe Bouyer, Themis Bowcock, William Bowden, Oliver Buchmueller, Clare Burrage, Xavier Calmet, Benjamin Canuel, Laurentiu-Ioan Caramete, Andrew Carroll, Giancarlo Cella, Vassilis Charmandaris, Swapan Chattopadhyay, Xuzong Chen, Maria Luisa Chiofalo, Jonathon Coleman, Joseph Cotter, Yanou Cui, Andrei Derevianko, Albert De Roeck, Goran S. Djordjevic, Peter Dornan, Michael Doser, Ioannis Drougkakis, Jacob Dunningham, Ioana Dutan, Sajan Easo, Gedminas Elertas, John Ellis, Mai El Sawy, Farida Fassi, Daniel Felea, Chen-Hao Feng, Robert Flack, Chris Foot, Ivette Fuentes, Naceur Gaaloul, Alexandre Gauguet, Remi Geiger, Valerie Gibson, Gian Giudice, Jon Goldwin, Oleg Grachov, Peter W. Graham, Dario Grasso, Maurits van der Grinten, Mustafa Gündogan, Martin G. Haehnelt, Tiffany Harte, Aurélien Hees, Richard Hobson, Jason Hogan, Bodil Holst, Michael Holynski, Mark Kasevich, Bradley J. Kavanagh, Wolf von Klitzing, Tim Kovachy, Benjamin Krikler, Markus Krutzik, Marek Lewicki, Yu-Hung Lien, Miaoyuan Liu, Giuseppe Gaetano Luciano, Alain Magnon, Mohammed Attia Mahmoud, Sarah Malik, Christopher McCabe, Jeremiah Mitchell, Julia Pahl, Debapriya Pal, Saurabh Pandey, Dimitris Papazoglou, Mauro Paternostro, Bjoern Penning, Achim Peters, Marco Prevedelli, Vishnupriya Puthiya-Veettil, John Quenby, Ernst Rasel, Sean Ravenhall, Jack Ringwood, Albert Roura, Dylan Sabulsky, Muhammed Sameed, Ben Sauer, Stefan Alaric Schäffer, Stephan Schiller, Vladimir Schkolnik, Dennis Schlippert, Christian Schubert, Haifa Rejeb Sfar, Armin Shayeghi, Ian Shipsey, Carla Signorini, Yeshpal Singh, Marcelle Soares-Santos, Fiodor Sorrentino, Timothy Sumner, Konstantinos Tassis, Silvia Tentindo, Guglielmo Maria Tino, Jonathan N. Tinsley, James Unwin, Tristan Valenzuela, Georgios Vasilakis, Ville Vaskonen, Christian Vogt, Alex Webber-Date, André Wenzlawski, Patrick Windpassinger, Marian Woltmann, Efe Yazgan, Ming-Sheng Zhan, Xinhao Zou, Jure Zupan
Jun 06, 2020
Abstract: We propose in this White Paper a concept for a space experiment using cold atoms to search for ultra-light dark matter, and to detect gravitational waves in the frequency range between the most sensitive ranges of LISA...
AEDGE
Yousef Abou El-Neaj, Cristiano Alpigiani, Sana Amairi-Pyka, Henrique Araújo, Antun Balaž, Angelo Bassi, Lars Bathe-Peters, Baptiste Battelier, Aleksandar Belić, Elliot Bentine, José Bernabeu, Andrea Bertoldi, Robert Bingham, Diego Blas, Vasiliki Bolpasi, Kai Bongs, Sougato Bose, Philippe Bouyer, Themis Bowcock, William Bowden, Oliver Buchmueller, Clare Burrage, Xavier Calmet, Benjamin Canuel, Laurentiu-Ioan Caramete, Andrew Carroll, Giancarlo Cella, Vassilis Charmandaris, Swapan Chattopadhyay, Xuzong Chen, Maria Luisa Chiofalo, Jonathon Coleman, Joseph Cotter, Yanou Cui, Andrei Derevianko, Albert De Roeck, Goran S. Djordjevic, Peter Dornan, Michael Doser, Ioannis Drougkakis, Jacob Dunningham, Ioana Dutan, Sajan Easo, Gedminas Elertas, John Ellis, Mai El Sawy, Farida Fassi, Daniel Felea, Chen-Hao Feng, Robert Flack, Chris Foot, Ivette Fuentes, Naceur Gaaloul, Alexandre Gauguet, Remi Geiger, Valerie Gibson, Gian Giudice, Jon Goldwin, Oleg Grachov, Peter W. Graham, Dario Grasso, Maurits van der Grinten, Mustafa Gündogan, Martin G. Haehnelt, Tiffany Harte, Aurélien Hees, Richard Hobson, Jason Hogan, Bodil Holst, Michael Holynski, Mark Kasevich, Bradley J. Kavanagh, Wolf von Klitzing, Tim Kovachy, Benjamin Krikler, Markus Krutzik, Marek Lewicki, Yu-Hung Lien, Miaoyuan Liu, Giuseppe Gaetano Luciano, Alain Magnon, Mohammed Attia Mahmoud, Sarah Malik, Christopher McCabe, Jeremiah Mitchell, Julia Pahl, Debapriya Pal, Saurabh Pandey, Dimitris Papazoglou, Mauro Paternostro, Bjoern Penning, Achim Peters, Marco Prevedelli, Vishnupriya Puthiya-Veettil, John Quenby, Ernst Rasel, Sean Ravenhall, Jack Ringwood, Albert Roura, Dylan Sabulsky, Muhammed Sameed, Ben Sauer, Stefan Alaric Schäffer, Stephan Schiller, Vladimir Schkolnik, Dennis Schlippert, Christian Schubert, Haifa Rejeb Sfar, Armin Shayeghi, Ian Shipsey, Carla Signorini, Yeshpal Singh, Marcelle Soares-Santos, Fiodor Sorrentino, Timothy Sumner, Konstantinos Tassis, Silvia Tentindo, Guglielmo Maria Tino, Jonathan N. Tinsley, James Unwin, Tristan Valenzuela, Georgios Vasilakis, Ville Vaskonen, Christian Vogt, Alex Webber-Date, André Wenzlawski, Patrick Windpassinger, Marian Woltmann, Efe Yazgan, Ming-Sheng Zhan, Xinhao Zou, Jure Zupan
Mar 04, 2021
Abstract: We propose in this White Paper a concept for a space experiment using cold atoms to search for ultra-light dark matter, and to detect gravitational waves in the frequency range between the most sensitive ranges of LISA...
The ChoCO-W prospective observational global study
Belinda De Simone, Fikri M Abu-Zidan, Elie Chouillard, Salomone Di Saverio, Massimo Sartelli, Mauro Podda, Carlos Augusto Gomes, Ernest E Moore, Susan J Moug, Luca Ansaloni, Yoram Kluger, Federico Coccolini, Aitor Landaluce-Olavarria, Begoña Estraviz-Mateos, Ana Uriguen-Etxeberria, Alessio Giordano, Alfonso Palmieri Luna, Luz Adriana Hernández Amín, Adriana María Palmieri Hernández, Amanda Shabana, Zakaria Andee Dzulkarnaen, Muhammad Asyraf Othman, Mohamad Ikhwan Sani, Andrea Balla, Rosa Scaramuzzo, Pasquale Lepiane, Andrea Bottari, Fabio Staderini, Fabio Cianchi, Andrea Cavallaro, Antonio Zanghì, Alessandro Cappellani, Roberto Campagnacci, Angela Maurizi, Mario Martinotti, Annamaria Ruggieri, Asri Che Jusoh, Karim Abdul Rahman, Anis Suraya M Zulkifli, Barbara Petronio, Belén Matías-García, Ana Quiroga-Valcárcel, Fernando Mendoza-Moreno, Boyko Atanasov, Fabio Cesare Campanile, Ilaria Vecchioni, Luca Cardinali, Grazia Travaglini, Elisa Sebastiani, Serge Chooklin, Serhii Chuklin, Pasquale Cianci, Enrico Restini, Sabino Capuzzolo, Giuseppe Currò, Rosalinda Filippo, Michele Rispoli, Daniel Aparicio-Sánchez, Virginia Durán Muñóz-Cruzado, Sandra Dios Barbeito, Samir Delibegovic, Amar Kesetovic, Diego Sasia, Felice Borghi, Giorgio Giraudo, Diego Visconti, Emanuele Doria, Mauro Santarelli, Davide Luppi, Stefano Bonilauri, Ugo Grossi, Giacomo Zanus, Alberto Sartori, Giacomo Piatto, Maurizio De Luca, Domenico Vita, Luigi Conti, Patrizio Capelli, Gaetano Maria Cattaneo, Athanasios Marinis, Styliani-Aikaterini Vederaki, Mehmet Bayrak, Yasemin Altıntas, Mustafa Yener Uzunoglu, Iskender Eren Demirbas, Yuksel Altinel, Serhat Meric, Yunus Emre Aktimur, Derya Salim Uymaz, Nail Omarov, Ibrahim Azamat, Eftychios Lostoridis, Eleni-Aikaterini Nagorni, Antonio Pujante, Gabriele Anania, Cristina Bombardini, Francesco Bagolini, Emre Gonullu, Baris Mantoglu, Recayi Capoglu, Stefano Cappato, Elena Muzio, Elif Colak, Suleyman Polat, Zehra Alan Koylu, Fatih Altintoprak, Zülfü Bayhan, Emrah Akin, Enrico Andolfi, Sulce Rezart, Jae Il Kim, Sung Won Jung, Yong Chan Shin, Octavian Enciu, Elena Adelina Toma, Fabio Medas, Gian Luigi Canu, Federico Cappellacci, Fabrizio D'Acapito, Giorgio Ercolani, Leonardo Solaini, Francesco Roscio, Federico Clerici, Roberta Gelmini, Francesco Serra, Elena Giulia Rossi, Francesco Fleres, Guglielmo Clarizia, Alessandro Spolini, Francesco Ferrara, Gabriela Nita, Jlenia Sarnari, Mahir Gachabayov, Abakar Abdullaev, Gaetano Poillucci, Gian Marco Palini, Simone Veneroni, Gianluca Garulli, Micaela Piccoli, Gianmaria Casoni Pattacini, Francesca Pecchini, Giulio Argenio, Mariano Fortunato Armellino, Giuseppe Brisinda, Silvia Tedesco, Pietro Fransvea, Giuseppe Ietto, Caterina Franchi, Giulio Carcano, Gennaro Martines, Giuseppe Trigiante, Giulia Negro, Gustavo Machain Vega, Agustín Rodríguez González, Leonardo Ojeda, Gaetano Piccolo, Andrea Bondurri, Anna Maffioli, Claudio Guerci, Boo Han Sin, Zamri Zuhdi, Azlanudin Azman, Hussam Mousa, Shadi Al Bahri, Goran Augustin, Ivan Romic, Trpimir Moric, Ioannis Nikolopoulos, Jacopo Andreuccetti, Giusto Pignata, Rossella D'Alessio, Jakub Kenig, Urszula Skorus, Gustavo Pereira Fraga, Elcio Shiyoiti Hirano, Jackson Vinícius de Lima Bertuol, Arda Isik, Eray Kurnaz, Mohammad Sohail Asghar, Ameer Afzal, Ali Akbar, Taxiarchis Konstantinos Nikolouzakis, Konstantinos Lasithiotakis, Emmanuel Chrysos, Koray Das, Nazmi Özer, Ahmet Seker, Mohamed Ibrahim, Hytham KS Hamid, Ahmed Babiker, Konstantinos Bouliaris, George Koukoulis, Chrysoula-Christina Kolla, Andrea Lucchi, Laura Agostinelli, Antonio Taddei, Laura Fortuna, Carlotta Agostini, Leo Licari, Simona Viola, Cosimo Callari, Letizia Laface, Emmanuele Abate, Massimiliano Casati, Alessandro Anastasi, Giuseppe Canonico, Linda Gabellini, Lorenzo Tosi, Anna Guariniello, Federico Zanzi, Lovenish Bains, Larysa Sydorchuk, Oksana Iftoda, Andrii Sydorchuk, Michele Malerba, Federico Costanzo, Raffaele Galleano, Michela Monteleone, Andrea Costanzi, Carlo Riva, Maciej Walędziak, Andrzej Kwiatkowski, Łukasz Czyżykowski, Piotr Major, Marcin Strzałka, Maciej Matyja, Michal Natkaniec, Maria Rosaria Valenti, Maria Domenica Pia Di Vita, Maria Sotiropoulou, Stylianos Kapiris, Damien Massalou, Massimiliano Veroux, Alessio Volpicelli, Rossella Gioco, Matteo Uccelli, Marta Bonaldi, Stefano Olmi, Matteo Nardi, Giada Livadoti, Cristian Mesina, Theodor Viorel Dumitrescu, Mihai Calin Ciorbagiu, Michele Ammendola, Giorgio Ammerata, Roberto Romano, Mihail Slavchev, Evangelos P Misiakos, Emmanouil Pikoulis, Dimitrios Papaconstantinou, Mohamed Elbahnasawy, Sherief Abdel-Elsalam, Daniel M Felsenreich, Julia Jedamzik, Nikolaos V Michalopoulos, Theodoros A Sidiropoulos, Maria Papadoliopoulou, Nicola Cillara, Antonello Deserra, Alessandro Cannavera, Ionuţ Negoi, Dimitrios Schizas, Athanasios Syllaios, Ilias Vagios, Stavros Gourgiotis, Nick Dai, Rekha Gurung, Marcus Norrey, Antonio Pesce, Carlo Vittorio Feo, Nicolo' Fabbri, Nikolaos Machairas, Panagiotis Dorovinis, Myrto D Keramida, Francesk Mulita, Georgios Ioannis Verras, Michail Vailas, Omer Yalkin, Nidal Iflazoglu, Direnc Yigit, Oussama Baraket, Karim Ayed, Mohamed Hedi Ghalloussi, Parmenion Patias, Georgios Ntokos, Razrim Rahim, Miklosh Bala, Asaf Kedar, Robert G Sawyer, Anna Trinh, Kelsey Miller, Ruslan Sydorchuk, Ruslan Knut, Oleksandr Plehutsa, Rumeysa Kevser Liman, Zeynep Ozkan, Saleh Abdel Kader, Sanjay Gupta, Monika Gureh, Sara Saeidi, Mohsen Aliakbarian, Amin Dalili, Tomohisa Shoko, Mitsuaki Kojima, Raira Nakamoto, Semra Demirli Atici, Gizem Kilinc Tuncer, Tayfun Kaya, Spiros G Delis, Stefano Rossi, Biagio Picardi, Simone Rossi Del Monte, Tania Triantafyllou, Dimitrios Theodorou, Tadeja Pintar, Jure Salobir, Dimitrios K Manatakis, Nikolaos Tasis, Vasileios Acheimastos, Orestis Ioannidis, Lydia Loutzidou, Savvas Symeonidis, Tiago Correia de Sá, Mónica Rocha, Tommaso Guagni, Desiré Pantalone, Gherardo Maltinti, Vladimir Khokha, Wafaa Abdel-Elsalam, Basma Ghoneim, José Antonio López-Ruiz, Yasin Kara, Syaza Zainudin, Firdaus Hayati, Nornazirah Azizan, Victoria Tan Phooi Khei, Rebecca Choy Xin Yi, Harivinthan Sellappan, Zaza Demetrashvili, Nika Lekiashvili, Ana Tvaladze, Caterina Froiio, Daniele Bernardi, Luigi Bonavina, Angeles Gil-Olarte, Sebastiano Grassia, Estela Romero-Vargas, Francesco Bianco, Andrew A Gumbs, Agron Dogjani, Ferdinando Agresta, Andrey Litvin, Zsolt J Balogh, George Gendrikson, Costanza Martino, Dimitrios Damaskos, Nikolaos Pararas, Andrew Kirkpatrick, Mikhail Kurtenkov, Felipe Couto Gomes, Adolfo Pisanu, Oreste Nardello, Fabrizio Gambarini, Hager Aref, Nicola De' Angelis, Vanni Agnoletti, Antonio Biondi, Marco Vacante, Giulia Griggio, Roberta Tutino, Marco Massani, Giovanni Bisetto, Savino Occhionorelli, Dario Andreotti, Domenico Lacavalla, Walter L Biffl, Fausto Catena
Dec 16, 2022
BACKGROUND: The incidence of the highly morbid and potentially lethal gangrenous cholecystitis was reportedly increased during the COVID-19 pandemic. The aim of the ChoCO-W study was to compare the clinical findings and outcomes...