Autor: Bradley, Benjamin - Prolib Integro

Skocz do pozycji: 1.

Tytuł:: 2D cocrystallization from H-bonded organic ferroelectrics
Autorzy:: Rasmussen, Tom
Zurek, Eva
Bradley, Benjamin
Paulo, Costa
Ducharme, Stephen
Beniwal, Sumit
Schlueter, Lisa
Enders, Axel
Kunkel, Donna A.
Hooper, James
Dostawca treści:: Repozytorium Uniwersytetu Jagiellońskiego

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Skocz do pozycji: 2.

Artykuł

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Skocz do pozycji: 3.

Tytuł:: Validating a target‐enrichment design for capturing uniparental haplotypes in ancient domesticated animals
Autorzy:: Larson, Greger
Rødsrud, Christian Løchsen
Bayarsaikhan, Jamsranjav
Charliquart, Léa
Vila, Emmanuelle
Orlando, Ludovic
Bălășescu, Adrian
Dobrescu, Roxana
Zhumatayev, Rinat
Chauvey, Loreleï
Discamps, Emmanuel
Vahdati, Ali A.
More, Kuldeep D.
Fernández, Pablo M.
Buric, Marcel
Daly, Kevin G.
Benecke, Norbert
Taylor, William
Garrido, Jaime Lira
Nikgoftar, Ahmad
Burgos, Nohemi Sala
de Noblet, Thibault
Chiavazza, Horacio
Moskal‐del Hoyo, Magdalena
Bradley, Daniel G.
Steadman, Sharon
Robbe, Emilie
Frantz, Laurent
Guardia, Nicolás M.
Nowak, Marek
Berthon, Rémi
Star, Bastiaan
Padula, Horacio
Allccarima‐Crisóstomo, Diana
Kosintsev, Pavel
Borges, Caroline
Contreras‐Mancilla, Juan
Vukičević, Tajana Trbojević
Post‐Melbye, Julian Robert
Mullin, Victoria E.
Dalen, Love
Wilczynski, Jaroslaw
Lebrasseur, Ophélie
Schiavinato, Stéphanie
Tressières, Gaëtan
Stanton, David W. G.
Boudadi‐Maligne, Myriam
Arbuckle, Benjamin
Shakenov, Samat
Castel, Jean‐Christophe
Houle, Jean‐Luc
Charlton, Sophy
Seguin‐Orlando, Andaine
Šikanjić, Petra Rajić
Mashkour, Marjan
McMahon, Gregory
Bertani, Stéphane
Barrey, Eric
Gibert, Morgane
Estrada, Oscar
Pablos, Adrian
Alvarez, Nadir
Fhon, Miguel
Tonasso‐Calvière, Laure
Khazaeli, Roya
Opis:: In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost‐effective genetic analysis. Here, we develop an in‐solution target‐enrichment approach, based on 80‐mer species‐specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y‐chromosomal diversity within Equus caballus. By applying our target‐enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth‐of‐coverage of 19.4 to 2003.7‐fold. Our assay further retrieved horse mitogenome and Y‐chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.
Dostawca treści:: Repozytorium Uniwersytetu Jagiellońskiego

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Skocz do pozycji: 4.

Tytuł:: Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations
Autorzy:: Reina, Borja
Krupa, Bartosz
Lasinio, Giovanna Jona
Ullrich, Alexander
Montero-Manso, Pablo
Priesemann, Viola
Bejar, Benjamin
Bracher, Johannes
Tucek, Vit
Smid, Martin
Perez Alvarez, Cesar
Fuhrmann, Jan
Kraus, David
Rodiah, Isti
Kraus, Andrea
Nowosielski, Jedrzej
Redlarski, Grzegorz
Filinski, Maciej
Kisielewski, Jan
Michaud, Isaac
Pennoni, Fulvia
Gurung, Heidi
Leithauser, Neele
Venkatramanan, Srinivasan
Lopez, Daniel
Hurt, Benjamin
Pribylova, Lenka
Zibert, Janez
Schneider, Johanna
Stage, Steven
Bartczuk, Rafal P
Szczurek, Ewa
Holger, Kirsten
Hotz, Thomas
Wattanachit, Nutcha
Farcomeni, Alessio
Lewis, Bryan
Wang, Lijing
Castro, Lauren
Bodych, Marcin
Dehning, Jonas
Villanueva, Inmaculada
Mohr, Sebastian
Alaimo Di Loro, Pierfrancesco
Parolini, Nicola
Deuschel, Jannik
Suchoski, Bradley
Grah, Rok
Giudici, Paolo
Catala, Marti
Budzinski, Jozef
Alonso, Sergio
Marathe, Madhav
Morina, David
Idzikowski, Radoslaw
Sun, Tao
Sherratt, Katharine
Meinke, Jan H
Kuhlmann, Alexander
Walraven, Robert
Abbott, Sam
Saksham, Soni
Porebski, Przemyslaw
Zimmermann, Tom
Bartolucci, Francesco
Obozinski, Guillaume
Gogolewski, Krzysztof
Zielinski, Jakub
Rakowski, Franciszek
Pottier, Loic
Tarantino, Barbara
Moszyński, Antoni
Gruson, Hugo
Wang, Yijin
Ardenghi, Giovanni
Biecek, Przemyslaw
Alvarez, Enric
Funk, Sebastian
Mingione, Marco
Bock, Wolfgang
Bosse, Nikos I
Guzman- Merino, Miguel
Dreger, Filip
Ray, Evan L
Wolffram, Daniel
Aznarte, Jose L
Burgard, Jan Pablo
Barbarossa, Maria Vittoria
Singh, David E
Gambin, Anna
Dimitris, Bertsimas
Pabjan, Barbara
Gruziel-Slomka, Magdalena
Kheifetz, Yuri
Divino, Fabio
Zajicek, Milan
Srivastava, Ajitesh
Niehus, Rene
Lovison, Gianfranco
Adiga, Aniruddha
Mohring, Jan
Prats, Clara
Johnson, Helen
Krueger, Tyll
Osthus, Dave
Baccam, Prasith
Prasse, Bastian
Radwan, Maciej
Semeniuk, Marcin
Maruotti, Antonello
Eclerova, Veronika
Scholz, Markus
Krymova, Ekaterina
Trnka, Jan
Thanou, Dorina
Niedzielewski, Karol
Reich, Nicholas G
Meakin, Sophie R
Wlazlo, Jaroslaw
Sheldon, Daniel
Ozanski, Tomasz
Ziarelli, Giovanni
Gibson, Graham
Heyder, Stefan
Rodloff, Arne
Li, Michael Lingzhi
Fairchild, Geoffrey
Sandmann, Frank
Lange, Berit
Wydawca:: eLife Sciences Publications Ltd.
Cytata wydawnicza:: Sherratt K, Gruson H, Grah R, Johnson H, Niehus R, Prasse B, Sandmann F, Deuschel J, Wolffram D, Abbott S, Ullrich A, Gibson G, Ray EL, Reich NG, Sheldon D, Wang Y, Wattanachit N, Wang L, Trnka J, Obozinski G, Sun T, Thanou D, Pottier L, Krymova E, Meinke JH, Barbarossa MV, Leithauser N, Mohring J, Schneider J, Wlazlo J, Fuhrmann J, Lange B, Rodiah I, Baccam P, Gurung H, Stage S, Suchoski B, Budzinski J, Walraven R, Villanueva I, Tucek V, Smid M, Zajicek M, Perez Alvarez C, Reina B, Bosse NI, Meakin SR, Castro L, Fairchild G, Michaud I, Osthus D, Alaimo Di Loro P, Maruotti A, Eclerova V, Kraus A, Kraus D, Pribylova L, Dimitris B, Li ML, Saksham S, Dehning J, Mohr S, Priesemann V, Redlarski G, Bejar B, Ardenghi G, Parolini N, Ziarelli G, Bock W, Heyder S, Hotz T, Singh DE, Guzman-Merino M, Aznarte JL, Morina D, Alonso S, Alvarez E, Lopez D, Prats C, Burgard JP, Rodloff A, Zimmermann T, Kuhlmann A, Zibert J, Pennoni F, Divino F, Catala M, Lovison G, Giudici P, Tarantino B, Bartolucci F, Jona Lasinio G, Mingione M, Farcomeni A, Srivastava A, Montero-Manso P, Adiga A, Hurt B, Lewis B, Marathe M, Porebski P, Venkatramanan S, Bartczuk RP, Dreger F, Gambin A, Gogolewski K, Gruziel-Slomka M, Krupa B, Moszyński A, Niedzielewski K, Nowosielski J, Radwan M, Rakowski F, Semeniuk M, Szczurek E, Zielinski J, Kisielewski J, Pabjan B, Holger K, Kheifetz Y, Scholz M, Przemyslaw B, Bodych M, Filinski M, Idzikowski R, Krueger T, Ozanski T, Bracher J, Funk S. Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations. Elife. 2023 Apr 21;12:e81916. doi: 10.7554/eLife.81916.
Opis:: Wellcome Trust (Grant number 221003/Z/20/Z) in collaboration with the Foreign, Commonwealth, and Development Office, United Kingdom. AA, BH, BL, LWa, MMa, PP, SV funded by National Institutes of Health (NIH) Grant 1R01GM109718, NSF BIG DATA Grant IIS-1633028, NSF Grant No.: OAC-1916805, NSF Expeditions in Computing Grant CCF-1918656, CCF-1917819, NSF RAPID CNS-2028004, NSF RAPID OAC-2027541, US Centers for Disease Control and Prevention 75D30119C05935, a grant from Google, University of Virginia Strategic Investment Fund award number SIF160, Defense Threat Reduction Agency (DTRA) under Contract No. HDTRA1-19-D- 0007, and respectively Virginia Dept of Health Grant VDH- 21- 501- 0141, VDH- 21- 501- 0143, VDH- 21- 501- 0147, VDH- 21- 501- 0145, VDH- 21- 501- 0146, VDH- 21-501-0142, VDH-21-501-0148. AF, AMa, GL funded by SMIGE - Modelli statistici inferenziali per governare l'epidemia, FISR 2020-Covid-19 I Fase, FISR2020IP-00156, Codice Progetto: PRJ-0695. AM, BK, FD, FR, JK, JN, JZ, KN, MG, MR, MS, RB funded by Ministry of Science and Higher Education of Poland with grant 28/WFSN/2021 to the University of Warsaw. BRe, CPe, JLAz funded by Ministerio de Sanidad/ISCIII. BT, PG funded by PERISCOPE European H2020 project, contract number 101016233. CP, DL, EA, MC, SA funded by European Commission - Directorate-General for Communications Networks, Content and Technology through the contract LC-01485746, and Ministerio de Ciencia, Innovacion y Universidades and FEDER, with the project PGC2018- 095456-B- I00. DE., MGu funded by Spanish Ministry of Health / REACT-UE (FEDER). DO, GF, IMi, LC funded by Laboratory Directed Research and Development program of Los Alamos National Laboratory (LANL) under project number 20200700ER. DS, ELR, GG, NGR, NW, YW funded by National Institutes of General Medical Sciences (R35GM119582; the content is solely the responsibility of the authors and does not necessarily represent the official views of NIGMS or the National Institutes of Health). FB, FP funded by InPresa, Lombardy Region, Italy. HG, KS funded by European Centre for Disease Prevention and Control. IV funded by Agencia de Qualitat i Avaluacio Sanitaries de Catalunya (AQuAS) through contract 2021-021OE. JDe, SMo, VP funded by Netzwerk Universitatsmedizin (NUM) project egePan (01KX2021). JPB, SH, TH funded by Federal Ministry of Education and Research (BMBF; grant 05M18SIA). KH, MSc, YKh funded by Project SaxoCOV, funded by the German Free State of Saxony. Presentation of data, model results and simulations also funded by the NFDI4Health Task Force COVID-19 (https://www.nfdi4health.de/task-force-covid-19-2) within the framework of a DFG-project (LO-342/17-1). LP, VE funded by Mathematical and Statistical modelling project (MUNI/A/1615/2020), Online platform for real-time monitoring, analysis and management of epidemic situations (MUNI/11/02202001/2020); VE also supported by RECETOX research infrastructure (Ministry of Education, Youth and Sports of the Czech Republic: LM2018121), the CETOCOEN EXCELLENCE (CZ.02.1.01/0.0/0.0/17-043/0009632), RECETOX RI project (CZ.02.1.01/0.0/0.0/16-013/0001761). NIB funded by Health Protection Research Unit (grant code NIHR200908). SAb, SF funded by Wellcome Trust (210758/Z/18/Z).
Background: Short-term forecasts of infectious disease burden can contribute to situational awareness and aid capacity planning. Based on best practice in other fields and recent insights in infectious disease epidemiology, one can maximise the predictive performance of such forecasts if multiple models are combined into an ensemble. Here, we report on the performance of ensembles in predicting COVID-19 cases and deaths across Europe between 08 March 2021 and 07 March 2022. Methods: We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1–4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models’ predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models’ forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models’ past predictive performance. Results: Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models’ forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models’ forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models’ forecasts of deaths (N=763 predictions from 20 models). Across a 1–4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast models. Conclusions: Our results support the use of combining forecasts from individual models into an ensemble in order to improve predictive performance across epidemiological targets and populations during infectious disease epidemics. Our findings further suggest that median ensemble methods yield better predictive performance more than ones based on means. Our findings also highlight that forecast consumers should place more weight on incident death forecasts than incident case forecasts at forecast horizons greater than 2 weeks.
Dostawca treści:: Repozytorium Centrum Otwartej Nauki