Reproducible research (Reproducible research is when data can be reanalysed taking the same steps and producing the same or similar result) is being implemented at different speeds in different disciplines, and Archaeology, as a discipline that sits at the intersection of the sciences and humanities, is at the start of this journey. Enabling reproducibility of your work by others is an important step in ensuring research quality. There are currently many barriers to moving towards reproducible research such as upskilling researchers in the practices, software and infrastructure needed to do reproducible research and also the need to address how we can, as a discipline, deal with issues like sensitive data. In this article, we seek to introduce reproducible research in an understandable manner so that archaeological researchers can learn where and how to start with this approach. We describe what reproducible archaeological research can look like and suggest three different computational skill levels of constructing reproducible research workflows (a research workflow is the different parts of a research lifecycle such as data collection, data analysis, data archiving, etc, and making all stages reproducible by using a history tracking system (version control) and transparent documation). Finally, in an extensive appendix, we address common questions about reproducible research to remove the stigma about these issues and suggest ways to overcome them.
While parents have long received guidance on how to raise children, a relatively new element of this involves explicit references to infant brain development, drawing on brain scans and neuroscientific knowledge. Sometimes called ‘brain-based parenting’, this has been criticised from within sociological and policy circles alike. However, the engagement of parents themselves with neuroscientific concepts is far less researched. Drawing on 22 interviews with parents/carers of children (mostly aged 0–7) living in Scotland, this article examines how they account for their (non-)use of concepts and understandings relating to neuroscience. Three normative tropes were salient: information about children’s processing speed, evidence about deprived Romanian orphans in the 1990s, and ideas relating to whether or not children should ‘self-settle’ when falling asleep. We interrogate how parents reflexively weigh and judge such understandings and ideas. In some cases, neuroscientific knowledge was enrolled by parents in ways that supported biologically reductionist models of childhood agency. This reductionism commonly had generative effects, enjoining new care practices and producing particular parent and infant subjectivities. Notably, parents do not uncritically adopt or accept (sometimes reductionist) neurobiological and/or psychological knowledge; rather, they reflect on whether and when it is applicable to and relevant for raising their children. Thus, our respondents draw on everyday epistemologies of parenting to negotiate brain-based understandings of infant development and behaviour, and invest meaning in these in ways that cannot be fully anticipated (or appreciated) within straightforward celebrations or critiques of the content of parenting programmes drawing on neuropsychological ideas.
The emergence of mobile herding lifeways in Mongolia and eastern Eurasia was one of the most crucial economic and cultural transitions in human prehistory. Understanding the process by which this played out, however, has been impeded by the absence of a precise chronological framework for the prehistoric era in Mongolia. One rare source of empirically dateable material useful for understanding eastern Eurasia’s pastoral tradition comes from the stone burial mounds and monumental constructions that began to appear across the landscape of Mongolia and adjacent regions during the Bronze Age (ca. 3000–700 BCE). Here, along with presenting 28 new radiocarbon dates from Mongolia’s earliest pastoral monumental burials, we synthesise, critically analyse, and model existing dates to present the first precision Bayesian radiocarbon model for the emergence and geographic spread of Bronze Age monument and burial forms. Model results demonstrate a cultural succession between ambiguously dated Afanasievo, Chemurchek, and Munkhkhairkhan traditions. Geographic patterning reveals the existence of important cultural frontiers during the second millennium BCE. This work demonstrates the utility of a Bayesian approach for investigating prehistoric cultural dynamics during the emergence of pastoral economies. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
Zika Preparedness Latin American Network (ZikaPLAN) is a research consortium funded by the European Commission to address the research gaps in combating Zika and to establish a sustainable network with research capacity building in the Americas. Here we present a report on ZikaPLAN`s mid-term achievements since its initiation in October 2016 to June 2019, illustrating the research objectives of the 15 work packages ranging from virology, diagnostics, entomology and vector control, modelling to clinical cohort studies in pregnant women and neonates, as well as studies on the neurological complications of Zika infections in adolescents and adults. For example, the Neuroviruses Emerging in the Americas Study (NEAS) has set up more than 10 clinical sites in Colombia. Through the Butantan Phase 3 dengue vaccine trial, we have access to samples of 17,000 subjects in 14 different geographic locations in Brazil. To address the lack of access to clinical samples for diagnostic evaluation, ZikaPLAN set up a network of quality sites with access to well-characterized clinical specimens and capacity for independent evaluations. The International Committee for Congenital Anomaly Surveillance Tools was formed with global representation from regional networks conducting birth defects surveillance. We have collated a comprehensive inventory of resources and tools for birth defects surveillance, and developed an App for low resource regions facilitating the coding and description of all major externally visible congenital anomalies including congenital Zika syndrome. Research Capacity Network (REDe) is a shared and open resource centre where researchers and health workers can access tools, resources and support, enabling better and more research in the region. Addressing the gap in research capacity in LMICs is pivotal in ensuring broad-based systems to be prepared for the next outbreak. Our shared and open research space through REDe will be used to maximize the transfer of research into practice by summarizing the research output and by hosting the tools, resources, guidance and recommendations generated by these studies. Leveraging on the research from this consortium, we are working towards a research preparedness network. ispartof: GLOBAL HEALTH ACTION vol:12 issue:1 ispartof: location:United States status: published
descriptionPublicationkeyboard_double_arrow_right Article 2019 United States English Nature Publishing Group UK NIH | Vanderbilt University Bio..., NIH | HuBMAP Integration, Visua..., NIH | Comprehensive reference m...
Authors: Michael Snyder; Shin Lin; Amanda Posgai; Mark A. Atkinson; +130 Authors
Michael Snyder; Shin Lin; Amanda Posgai; Mark A. Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; Julia Laskin; Pehr B. Harbury; Nicholas A. Nystrom; Jonathan C. Silverstein; Ziv Bar-Joseph; Kun Zhang; Katy Börner; Yiing Lin; Richard Conroy; Dena Procaccini; Ananda L. Roy; Ajay Pillai; Marishka Brown; Zorina S. Galis; Caltech-UW Tmc; Long Cai; Cole Trapnell; Dana Jackson; Stanford-WashU Tmc; Garry P. Nolan; William J. Greenleaf; Sylvia K. Plevritis; Sara Ahadi; Stephanie A. Nevins; Hayan Lee; Christian Martijn Schuerch; Sarah Black; Vishal G. Venkataraaman; Ed Esplin; Aaron M. Horning; Amir Bahmani; Ucsd Tmc; Xin bSun; Sanjay Jain; James S. Hagood; Gloria S. Pryhuber; Peter V. Kharchenko; Bernd bBodenmiller; Todd M. Brusko; Michael J. Clare-Salzler; Harry S. Nick; Kevin J. Otto; Clive hWasserfall; Marda Jorgensen; Maigan A. Brusko; Sergio Maffioletti; Richard M. Caprioli; Jeffrey M. Spraggins; Danielle cGutierrez; Nathan Heath Patterson; Elizabeth K. Neumann; Raymond C. Harris; Mark P. deCaestecker; Agnes B. Fogo; Raf Van de Plas; Ken S. Lau; Guo-Cheng Yuan; Qian Zhu; Ruben Dries; Harvard Ttd; Peng Yin; Sinem K. Saka; Jocelyn Y. Kishi; Yu Wang; Isabel Goldaracena; Purdue Ttd; DongHye Ye; Kristin E. Burnum-Johnson; Paul D. Piehowski; Charles Ansong; Ying Zhu; Stanford Ttd; Tushar bDesai; Jay Mulye; Peter Chou; Monica Nagendran; Visualization HuBMAP Integration; Sarah A. Teichmann; Benedict aten; Robert F. dMurphy; Jian Ma; Vladimir Yu. Kiselev; Carl Kingsford; Allyson Ricarte; Maria Keays; Sushma A. Akoju; Matthew Ruffalo; Margaret Vella; Chuck McCallum; Leonard E. Cross; Samuel H. Friedman; Randy Heiland; Bruce Herr; Paul Macklin; Ellen M. Quardokus; Lisel Record; James P. Sluka; Griffin M. Weber; Engagement Component; Philip D. Blood; Alexander J. Ropelewski; William E. Shirey; Robin M. Scibek; Paula M. Mabee; W. Christopher Lenhardt; Kimberly Robasky; Stavros Michailidis; John C. Marioni; Andrew Butler; Tim Stuart; Eyal Fisher; Shila Ghazanfar; Gökcen Eraslan; Tommaso Biancalani; Eeshit Dhaval Vaishnav; Ananda L. Roy; Zorina S. Galis; Pothur Srinivas; Aaron Pawlyk; Salvatore Sechi; Elizabeth L. Wilder; James E. Anderson;
Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions. HuBMAP supports technology development, data acquisition, and spatial analyses to generate comprehensive molecular and cellular three-dimensional tissue maps.
descriptionPublicationkeyboard_double_arrow_right Article , Other literature type 2019 Serbia, United Kingdom, Germany, Portugal, Denmark, Netherlands, Lithuania, Turkey, France, Germany, United Kingdom, Italy, France, United Kingdom English EC | Extinction Genomics, FCT | SFRH/BPD/108326/2015, NSF | Doctoral Dissertation Res...
Authors: Laurent A. F. Frantz; James Haile; Audrey T. Lin; Amelie Scheu; +96 Authors
Laurent A. F. Frantz; James Haile; Audrey T. Lin; Amelie Scheu; Christina Geörg; Norbert Benecke; Michelle Alexander; Anna Linderholm; Victoria E. Mullin; Kevin G. Daly; Vincent M. Battista; Max Price; Kurt J. Gron; Panoraia Alexandri; Rose-Marie Arbogast; Benjamin S. Arbuckle; Adrian Bӑlӑşescu; Ross Barnett; László Bartosiewicz; Gennady F. Baryshnikov; Clive Bonsall; Dusan Boric; Adina Boroneanţ; Jelena Bulatović; Canan Çakirlar; José Miguel Carretero; John Chapman; Mike J. Church; Richard P. M. A. Crooijmans; Bea De Cupere; Cleia Detry; Vesna Dimitrijević; Valentin Dumitraşcu; Louis du Plessis; Ceiridwen J. Edwards; Cevdet Merih Erek; Aslı Erim-Özdoğan; Anton Ervynck; Domenico Fulgione; Mihai Gligor; Anders Götherström; Lionel Gourichon; Martien A. M. Groenen; Daniel Helmer; Hitomi Hongo; Liora Kolska Horwitz; Evan K. Irving-Pease; Ophélie Lebrasseur; Joséphine Lesur; Caroline Malone; Ninna Manaseryan; Arkadiusz Marciniak; Holley Martlew; Marjan Mashkour; Roger Matthews; Giedre Motuzaite Matuzeviciute; Sepideh Maziar; Erik Meijaard; Thomas H. McGovern; Hendrik-Jan Megens; Rebecca Miller; Azadeh Fatemeh Mohaseb; Jörg Orschiedt; David Orton; Anastasia Papathanasiou; Mike Parker Pearson; Ron Pinhasi; Darko Radmanovic; François-Xavier Ricaut; Michael P. Richards; Richard Sabin; Lucia Sarti; Wolfram Schier; Shiva Sheikhi; Elisabeth Stephan; John R. Stewart; Simon Stoddart; Antonio Tagliacozzo; Nenad Tasić; Katerina Trantalidou; Anne Tresset; Cristina Valdiosera; Youri van den Hurk; Sophie Van Poucke; Jean-Denis Vigne; Alexander Yanevich; Andrea Zeeb-Lanz; Alexandros Triantafyllidis; M. Thomas P. Gilbert; Jörg Schibler; Peter Rowley-Conwy; Melinda A. Zeder; Joris Peters; Thomas Cucchi; Daniel G. Bradley; Keith Dobney; Joachim Burger; Allowen Evin; Linus Girdland-Flink; Greger Larson;
International audience; Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process. domestication | evolution | gene flow | Neolithic
From the wilderness of Hyrule, the continent of Tamriel, and the geographies of Middle Earth, players of video games are exposed to wondrous, fantastic, but ultimately fake, landscapes. Given the time people may spend in these worlds compared to the time they spend being trained in geoscience, we wondered whether expert geoscientists would differ from non-geoscientists in whether they judge the landscapes in these video games to be “realistic”. Since video games present a great opportunity for tangential learning, it would be a missed opportunity if it turns out that features obviously fake to geoscientists are perceived as plausible by non-geoscientists. To satisfy our curiosity and answer this question, we conducted a survey where we asked people to judge both photos from real landscapes as well as screenshots from the recent The Legend of Zelda: Breath of the Wild video game on how likely they thought the features in the picture were to exist in the real world. Since game world screenshots are easily identified based on their rendered, pixelated nature, we pre-processed all pictures with an artistic “Van Gogh” filter that removed the rendered nature but retained the dominant landscape features. We found that there is a small but significant difference between geoscientists and non-geoscientists, with geoscientists being slightly better at judging which pictures are from the real world versus from the video game world. While significant, the effect is small enough to conclude that fantastical worlds in video games can be used for tangential learning on geoscientific subjects.
Background This research is an investigation into the role of expert quotes in health news, specifically whether news articles containing a quote from an independent expert are less often exaggerated than articles without such a quote. Methods Retrospective quantitative content analysis of journal articles, press releases, and associated news articles was performed. The investigated sample are press releases on peer-reviewed health research and the associated research articles and news stories. Our sample consisted of 462 press releases and 668 news articles from the UK (2011) and 129 press releases and 185 news articles from The Netherlands (2015). We hand-coded all journal articles, press releases and news articles for correlational claims, using a well-tested codebook. The main outcome measures are types of sources that were quoted and exaggeration of correlational claims. We used counts, 2x2 tables and odds ratios to assess the relationship between presence of quotes and exaggeration of the causal claim. Results Overall, 99.1% of the UK press releases and 84.5% of the Dutch press releases contain at least one quote. For the associated news articles these percentages are: 88.6% in the UK and 69.7% in the Netherlands. Authors of the study are most often quoted and only 7.5% of UK and 7.0% of Dutch news articles contained a new quote by an expert source, i.e. one not provided by the press release. The relative odds that an article without an external expert quote contains an exaggeration of causality is 2.6. Conclusions The number of articles containing a quote from an independent expert is low, but articles that cite an external expert do contain less exaggeration.
Historically speaking, scientists have lived and worked in a multilingual world. Given that, in such a world, translation is simply part of (scientific) life, it is all the more remarkable that practices of translation in science have received less attention from historians of science than one might expect. A focus on translation allows historians of science to scrutinize the changes and transformations of scientific knowledge in motion. Instead of presuming that processes of translation are betrayals of the original, and thus asking about the “fidelity” of a translator or the “faithfulness” of a translation, the contributions to this Focus section see those processes as productive of knowledge, part and parcel of the history of science. This Focus section brings together a wide variety of languages and practices of translation in different places and times, from the Ottoman Empire to Japan and from antiquity to the nineteenth century.
descriptionPublicationkeyboard_double_arrow_right Other literature type , Article 2018 France, United Kingdom, Spain English American Association for the Advancement of Science NSERC, ARC | Mechanisms of virulence o..., ARC | Emergence and evolution o...
Authors: Simon J. O’Hanlon; Adrien Rieux; Rhys A. Farrer; Gonçalo M. Rosa; +54 Authors
Simon J. O’Hanlon; Adrien Rieux; Rhys A. Farrer; Gonçalo M. Rosa; Bruce Waldman; Arnaud Bataille; Tiffany A. Kosch; Kris A. Murray; Balázs Brankovics; Matteo Fumagalli; Michael D. Martin; Nathan Wales; Mario Alvarado-Rybak; Kieran A. Bates; Lee Berger; Susanne Böll; Lola Brookes; Frances C. Clare; Elodie A. Courtois; Andrew A. Cunningham; Thomas M. Doherty-Bone; Pria Ghosh; David J. Gower; William E. Hintz; Jacob Höglund; Thomas S. Jenkinson; Chun-Fu Lin; Anssi Laurila; Adeline Loyau; An Martel; Sara Meurling; Claude Miaud; Pete Minting; Frank Pasmans; Dirk S. Schmeller; Benedikt R. Schmidt; Jennifer M. G. Shelton; Lee F. Skerratt; Freya Smith; Claudio Soto-Azat; Matteo Spagnoletti; Giulia Tessa; Luís Felipe Toledo; Andrés Valenzuela-Sánchez; Ruhan Verster; Judit Vörös; Rebecca J. Webb; Claudia Wierzbicki; Emma Wombwell; Kelly R. Zamudio; David M. Aanensen; Timothy Y. James; M. Thomas P. Gilbert; Ché Weldon; Jaime Bosch; Francois Balloux; Trenton W. J. Garner; Matthew C. Fisher;
S.J.O., T.W.J.G., L.Br., A.Lo., A.A.C., D.S.S., E.A.C., C.M., J.B., D.M.A., F.C., and M.C.F. were supported through NERC (standard grant NE/K014455/1). S.J.O. acknowledges a Microsoft Azure for Research Sponsorship (subscription ID: ab7cd695-49cf-4a83-910a-ef71603e708b). T.W.J.G., A.Lo., A.A.C., D.S.S., E.A.C., C.M., J.B., D.M.A., F.C., and M.C.F. were also supported by the EU BiodivERsA scheme (RACE, funded through NERC directed grant NE/G002193/1 and ANR08-Biodiversa-002-03) and NERC (standard grant NE/K012509/1). M.C.F., E.A.C., and C.M. acknowledge the Nouragues Travel Grant Program 2014. R.A.F. was supported by an MIT/Wellcome Trust Fellowship. T.W.J.G. was supported by the People’s Trust for Endangered Species and the Morris Animal Foundation (D12ZO002). J.M.G.S. and M.C.F. were supported by the Leverhulme Trust (RPG-2014-273) and the Morris Animal Foundation (D16ZO-022). F.B. was supported by the ERC (grant ERC 260801–Big_Idea). D.M.A. was funded by Wellcome Trust grant 099202. J.V. was supported by the Hungarian Scientific Research Fund (OTKA K77841) and Bolyai János Research Scholarship, Hungarian Academy of Sciences (BO/00579/14/8). D.J.G. was supported by the Conservation Leadership Programme (grant 0134010) with additional assistance from F. Gebresenbet, R. Kassahun, and S. P. Loader. C.S.-A. was supported by Fondecyt Nº11140902 and 1181758. T.M.D.-B. was supported by the Royal Geographical Society and the Royal Zoological Society of Scotland with assistance from M. Hirschfeld and the Budongo Conservation Field Station. B.W. was supported by the National Research Foundation of Korea (2015R1D1A1A01057282). L.F.T. was supported by FAPESP (#2016/25358-3) and CNPq (#300896/2016-6). L.Be., L.F.S., and R.J.W. were supported by the Australian Research Council (FT100100375, DP120100811). A.A.C. was supported by a Royal Society Wolfson Research Merit award. J.H., A.La., and S.M. were funded by the Swedish Research Council Formas (grant no. 2013- 1389-26445-20). C.W. was funded by the National Research Foundation, South Africa. T.Y.J. and T.S.J. acknowledge NSF grant DEB-1601259. W.E.H. was funded by the NSERC Strategic and Discovery grant programs Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of the most devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis, a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, BdASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide.