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Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology
- Pablo Conesa, Yunior C. Fonseca, Jorge Jiménez de la Morena, Grigory Sharov, Jose Miguel de la Rosa-Trevín, Ana Cuervo, Alberto García Mena, Borja Rodríguez de Francisco, Daniel del Hoyo, David Herreros, Daniel Marchan, David Strelak, Estrella Fernández-Giménez, Erney Ramírez-Aportela, Federico Pedro de Isidro-Gómez, Irene Sánchez, James Krieger, José Luis Vilas, Laura del Cano, Marcos Gragera, Mikel Iceta, Marta Martínez, Patricia Losana, Roberto Melero, Roberto Marabini, José María Carazo, Carlos Oscar Sánchez Sorzano
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- Journal:
- Biological Imaging / Volume 3 / 2023
- Published online by Cambridge University Press:
- 29 June 2023, e13
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Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing.
Reconstruction of a Ross lost Cambrian Series 2 mixed siliciclastic–carbonate platform from carbonate clasts of the Shackleton Range, Antarctica
- Marta RODRÍGUEZ-MARTÍNEZ, Werner BUGGISCH, Silvia MENÉNDEZ, Elena MORENO-EIRIS, Antonio PEREJÓN
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- Journal:
- Earth and Environmental Science Transactions of The Royal Society of Edinburgh / Volume 113 / Issue 3 / September 2022
- Published online by Cambridge University Press:
- 28 July 2022, pp. 175-226
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- September 2022
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The presence of archaeocyath-bearing clasts from Cenozoic tills and Cambrian Mount Wegener Formation reveal erosion of a hidden Cambrian carbonate platform in Shackleton Range, Antarctica. We provide microfacies, paleontological, diagenetic and tectonically induced fabric data from carbonate clasts which, in addition to available geochemical and geochronological data from Shackleton Range, allow the paleoenvironmental reconstruction of a lost Cambrian Series 2 mixed siliciclastic–carbonate platform that was developed and eroded during the Ross orogeny. Carbonate production was dominated by non-skeletal grains in possibly restricted platform-interior and oolitic shoal complex settings, while open subtidal sub-environments (calcimicrobe carpets, calcimicrobe–archaeocyath patch reefs, muddy bottoms) were dominated by a diverse calcimicrobe assemblage and/or by secondary to accessory heterozoan assemblage (archaeocyaths and other sponges, chancelloriids, hyoliths, coralomorphs, trilobites, echinoderms). We describe a Botoman assemblage with 34 archaeocyathan species among 12 existing archaeocyathan genera. A new archaeocyath family Shackletoncyathidae is proposed. New species (Rotundocyathus glacius sp. nov., Buggischicyathus microporus gen. et sp. nov., Paragnaltacyathus hoeflei, Shackletoncyathus buggischi gen. et. sp. nov., Santelmocyathus santelmoi gen. et sp. nov., Wegenercyathus sexangulae gen. et sp. nov.) and Tabulaconus kordae coralomorph are reported from Antarctica for the first time. Archaeocyathan fauna share few species with contemporary fauna of South Australia (9) and even fewer with the Antarctic platforms of the Shackleton Limestone (2) or the Schneider Hills limestone (1). Similarity is greater with Antarctic allochthonous assemblages of Permo-Carboniferous tillites from Ellsworth Mountains (2), Cenozoic deposits from King George Island (4) or Weddell Sea (1). The Shackleton Range lost/hidden platform shows a distinct entity related with its tectonosedimentary evolution, in a possible back-arc basin on the Mozambique seaway during the E and W Gondwana amalgamation, which distinguishes it from those developed on the palaeo-Pacific margin of the E Antarctic craton.
The Mesolithic–Neolithic transition in southern Iberia
- Miguel Cortés Sánchez, Francisco J. Jiménez Espejo, María D. Simón Vallejo, Juan F. Gibaja Bao, António Faustino Carvalho, Francisca Martinez-Ruiz, Marta Rodrigo Gamiz, José-Abel Flores, Adina Paytan, José A. López Sáez, Leonor Peña-Chocarro, José S. Carrión, Arturo Morales Muñiz, Eufrasia Roselló Izquierdo, José A. Riquelme Cantal, Rebecca M. Dean, Emília Salgueiro, Rafael M. Martínez Sánchez, Juan J. De la Rubia de Gracia, María C. Lozano Francisco, José L. Vera Peláez, Laura Llorente Rodríguez, Nuno F. Bicho
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- Journal:
- Quaternary Research / Volume 77 / Issue 2 / March 2012
- Published online by Cambridge University Press:
- 20 January 2017, pp. 221-234
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New data and a review of historiographic information from Neolithic sites of the Malaga and Algarve coasts (southern Iberian Peninsula) and from the Maghreb (North Africa) reveal the existence of a Neolithic settlement at least from 7.5 cal ka BP. The agricultural and pastoralist food producing economy of that population rapidly replaced the coastal economies of the Mesolithic populations. The timing of this population and economic turnover coincided with major changes in the continental and marine ecosystems, including upwelling intensity, sea-level changes and increased aridity in the Sahara and along the Iberian coast. These changes likely impacted the subsistence strategies of the Mesolithic populations along the Iberian seascapes and resulted in abandonments manifested as sedimentary hiatuses in some areas during the Mesolithic–Neolithic transition. The rapid expansion and area of dispersal of the early Neolithic traits suggest the use of marine technology. Different evidences for a Maghrebian origin for the first colonists have been summarized. The recognition of an early North-African Neolithic influence in Southern Iberia and the Maghreb is vital for understanding the appearance and development of the Neolithic in Western Europe. Our review suggests links between climate change, resource allocation, and population turnover.
Millennial- to centennial-scale climate periodicities and forcing mechanisms in the westernmost Mediterranean for the past 20,000 yr
- Marta Rodrigo-Gámiz, Francisca Martínez-Ruiz, Francisco J. Rodríguez-Tovar, Francisco J. Jiménez-Espejo, Eulogio Pardo-Igúzquiza
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- Journal:
- Quaternary Research / Volume 81 / Issue 1 / January 2014
- Published online by Cambridge University Press:
- 20 January 2017, pp. 78-93
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Cyclostratigraphic analysis conducted on a continuous high-resolution marine record from the western most Mediterranean reveals well-identified paleoclimate cycles for the last 20,000 yr. The detrital proxies used (Si/Al, Ti/Al, Zr/Al, Mg/Al, K/Al, Rb/Al) are related to different sediment-transport mechanisms, including eolian dust and fluvial runoff, which involve fluctuations in the atmosphere–hydrosphere systems. These fluctuations are accompanied by changes in marine productivity (supported by Ba/Al) and bottom-water redox conditions (Cu/Al, V/Al, Zn/Al, Fe/Al, Mn/Al, U/Th). Spectral analysis conducted using the Lomb–Scargle periodogram and the achieved significance level implemented with the permutation test allowed us to establish major periodicities at 1300, 1515, 2000, and 5000 yr, and secondary peaks at 650, 1087, and 3000 yr. Some of these cycles also agree with those previously described in the North Atlantic Ocean and circum-Mediterranean records. The periodicities obtained at 2000 and 5000 yr support a global connection with records distributed at high, mid, and low latitudes associated with solar activity, monsoonal regime and orbital forcing. The 1300- and 1515-yr cycles appear to be linked with North Atlantic climate variability and the African monsoon system. Thus, the analyzed record provides evidence of climate cycles and plausible forcing mechanisms coupled with ocean–atmosphere fluctuations.
Use of vitamin D supplements during infancy in an international feeding trial
- Eveliina Lehtonen, Anne Ormisson, Anita Nucci, David Cuthbertson, Susa Sorkio, Mila Hyytinen, Kirsi Alahuhta, Carol Berseth, Marja Salonen, Shayne Taback, Margaret Franciscus, Teba González-Frutos, Tuuli E Korhonen, Margaret L Lawson, Dorothy J Becker, Jeffrey P Krischer, Mikael Knip, Suvi M Virtanen, , Thomas Mandrup-Poulsen, Elias Arjas, Åke Lernmark, Barbara Schmidt, Jeffrey P. Krischer, Hans K. Åkerblom, Mila Hyytinen, Mikael Knip, Katriina Koski, Matti Koski, Eeva Pajakkala, Marja Salonen, David Cuthbertson, Jeffrey P. Krischer, Linda Shanker, Brenda Bradley, Hans-Michael Dosch, John Dupré, William Fraser, Margaret Lawson, Jeffrey L. Mahon, Mathew Sermer, Shayne P. Taback, Dorothy Becker, Margaret Franciscus, Anita Nucci, Jerry Palmer, Minna Pekkala, Suvi M. Virtanen, Jacki Catteau, Neville Howard, Patricia Crock, Maria Craig, Cheril L. Clarson, Lynda Bere, David Thompson, Daniel Metzger, Colleen Marshall, Jennifer Kwan, David K. Stephure, Daniele Pacaud, Wendy Schwarz, Rose Girgis, Marilyn Thompson, Shayne P. Taback, Daniel Catte, Margaret L. Lawson, Brenda Bradley, Denis Daneman, Mathew Sermer, Mary-Jean Martin, Valérie Morin, Lyne Frenette, Suzanne Ferland, Susan Sanderson, Kathy Heath, Céline Huot, Monique Gonthier, Maryse Thibeault, Laurent Legault, Diane Laforte, Elizabeth A. Cummings, Karen Scott, Tracey Bridger, Cheryl Crummell, Robyn Houlden, Adriana Breen, George Carson, Sheila Kelly, Koravangattu Sankaran, Marie Penner, Richard A. White, Nancy King, James Popkin, Laurie Robson, Eva Al Taji, Irena Aldhoon, Pavla Mendlova, Jan Vavrinec, Jan Vosahlo, Ludmila Brazdova, Jitrenka Venhacova, Petra Venhacova, Adam Cipra, Zdenka Tomsikova, Petra Krckova, Pavla Gogelova, Ülle Einberg, Mall-Anne Riikjärv, Anne Ormisson, Vallo Tillmann, Päivi Kleemola, Anna Parkkola, Heli Suomalainen, Anna-Liisa Järvenpää, Anu-Maaria Hämälainen, Hannu Haavisto, Sirpa Tenhola, Pentti Lautala, Pia Salonen, Susanna Aspholm, Heli Siljander, Carita Holm, Samuli Ylitalo, Raisa Lounamaa, Anja Nuuja, Timo Talvitie, Kaija Lindström, Hanna Huopio, Jouni Pesola, Riitta Veijola, Päivi Tapanainen, Abram Alar, Paavo Korpela, Marja-Liisa Käär, Taina Mustila, Ritva Virransalo, Päivi Nykänen, Bärbel Aschemeier, Thomas Danne, Olga Kordonouri, Dóra Krikovszky, László Madácsy, Yeganeh Manon Khazrai, Ernesto Maddaloni, Paolo Pozzilli, Carla Mannu, Marco Songini, Carine de Beaufort, Ulrike Schierloh, Jan Bruining, Margriet Bisschoff, Aleksander Basiak, Renata Wasikowa, Marta Ciechanowska, Grazyna Deja, Przemyslawa Jarosz-Chobot, Agnieszka Szadkowska, Katarzyna Cypryk, Malgorzata Zawodniak-Szalapska, Luis Castano, Teba Gonzalez Frutos, Mirentxu Oyarzabal, Manuel Serrano-Ríos, María Teresa Martínez-Larrad, Federico Gustavo Hawkins, Dolores Rodriguez Arnau, Johnny Ludvigsson, Malgorzata Smolinska Konefal, Ragnar Hanas, Bengt Lindblad, Nils-Osten Nilsson, Hans Fors, Maria Nordwall, Agne Lindh, Hans Edenwall, Jan Aman, Calle Johansson, Margrit Gadient, Eugen Schoenle, Dorothy Becker, Ashi Daftary, Margaret Franciscus, Carol Gilmour, Jerry Palmer, Rachel Taculad, Marilyn Tanner-Blasiar, Neil White, Uday Devaskar, Heather Horowitz, Lisa Rogers, Roxana Colon, Teresa Frazer, Jose Torres, Robin Goland, Ellen Greenberg, Maudene Nelson, Holly Schachner, Barney Softness, Jorma Ilonen, Massimo Trucco, Lynn Nichol, Erkki Savilahti, Taina Härkönen, Mikael Knip, Outi Vaarala, Kristiina Luopajärvi, Hans-Michael Dosch
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- Journal:
- Public Health Nutrition / Volume 17 / Issue 4 / April 2014
- Published online by Cambridge University Press:
- 24 June 2013, pp. 810-822
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Objective
To examine the use of vitamin D supplements during infancy among the participants in an international infant feeding trial.
DesignLongitudinal study.
SettingInformation about vitamin D supplementation was collected through a validated FFQ at the age of 2 weeks and monthly between the ages of 1 month and 6 months.
SubjectsInfants (n 2159) with a biological family member affected by type 1 diabetes and with increased human leucocyte antigen-conferred susceptibility to type 1 diabetes from twelve European countries, the USA, Canada and Australia.
ResultsDaily use of vitamin D supplements was common during the first 6 months of life in Northern and Central Europe (>80 % of the infants), with somewhat lower rates observed in Southern Europe (>60 %). In Canada, vitamin D supplementation was more common among exclusively breast-fed than other infants (e.g. 71 % v. 44 % at 6 months of age). Less than 2 % of infants in the USA and Australia received any vitamin D supplementation. Higher gestational age, older maternal age and longer maternal education were study-wide associated with greater use of vitamin D supplements.
ConclusionsMost of the infants received vitamin D supplements during the first 6 months of life in the European countries, whereas in Canada only half and in the USA and Australia very few were given supplementation.
Efficacy of a Social Cognition Training Program for Schizophrenic Patients: A Pilot Study
- David Gil Sanz, Marián Diego Lorenzo, Rosario Bengochea Seco, Marta Arrieta Rodríguez, Ismael Lastra Martínez, Raúl Sánchez Calleja, Ana Álvarez Soltero
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- The Spanish Journal of Psychology / Volume 12 / Issue 1 / May 2009
- Published online by Cambridge University Press:
- 10 January 2013, pp. 184-191
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Psychosocial functioning impairment is recognized as a core feature of schizophrenia. Numerous studies have assessed the process that may underlie this impairment. In the last years, one of these processes that has been studied more is social cognition, which has been proposed as a mediator variable between neurocognition and functional outcome. Social cognition includes the subdomains of emotion recognition and social perception, and in recent years several authors have developed diverse training programs in these areas.
The purpose of the present article is to assess the efficacy of the Social Cognition Training Program, a program that includes emotion recognition training and social perception training. The sample was made up of 14 outpatients with a diagnosis of schizophrenia according to CIE-10 criteria, randomly divided into two groups: experimental and control. All patients were assessed before and after the training program. Cognitive and psychopathological variables, social functioning, emotion recognition and social perception performance were assessed. Results suggest improvement in social perception and interpretation in the experimental group, in comparison with the control group, but not in emotion recognition. No significant correlations were obtained between social cognition training and other variables tested.
In vitro capacitation of bull spermatozoa by oviductal fluid and its components
- Ann-Sofi Bergqvist, Joan Ballester, Anders Johannisson, Marta Hernandez, Nils Lundeheim, Heriberto Rodríguez-Martínez
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Sperm capacitation is crucial for fertilization. However, debate continues on exactly how, where and when capacitation is elicited in the bovine female genital tract. In this study we used merocyanine-540 and the chlortetracycline (CTC) assay to test how capacitation of bull spermatozoa is affected in vitro by exposure to oviductal fluid (ODF) collected in vivo, various glycosaminoglycans (GAGs) or bicarbonate. Following different durations of exposure, spermatozoa were stained with CTC or merocyanine-540, and evaluated with epifluorescent light microscopy or flow cytometry, respectively. Incubation time did not significantly affect capacitation. Exposure (30–120 min) to ODF capacitated (p < 0.05) bull spermatozoa as measured by either merocyanine-540 or CTC. Hyaluronan was the only GAG that induced a significant increase in B-pattern spermatozoa (capacitated; p = 0.012) compared with controls. Dermatan sulphate also induced capacitation (merocyanine-540 high fluorescence; p = 0.035). Exposure to bicarbonate-enriched media also yielded an increase in merocyanine-540 high fluorescence (p < 0.0001). When bicarbonate was added to the other treatments (ODF or GAGs) an equal increase in merocyanine-540 high fluorescence was noted (p < 0.0001), compared with before addition of bicarbonate and independent of the treatment before exposure. There was no significant difference in the number of B-pattern spermatozoa when bicarbonate was added, but an significant increase in spermatozoa with an acrosome-reacted (AR)-pattern (p < 0.0001) was observed. Exposure of spermatozoa to solubilized zonae pellucidae significantly increased the AR-pattern spermatozoa (p = 0.016). In conclusion, ODF was more potent in inducing capacitation of bull spermatozoa than the individual GAGs. Our results also indicate that bicarbonate is an effector of bull sperm capacitation.