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An increasing number of researchers support reproducibility by including pointers to and descriptions of datasets, software and methods in their publications. However, scientific articles may be ambiguous, incomplete and difficult to process by automated systems. In this paper we introduce RO-Crate, an open, community-driven, and lightweight approach to packaging research artefacts along with their metadata in a machine readable manner. RO-Crate is based on Schema$.$org annotations in JSON-LD, aiming to establish best practices to formally describe metadata in an accessible and practical way for their use in a wide variety of situations. An RO-Crate is a structured archive of all the items that contributed to a research outcome, including their identifiers, provenance, relations and annotations. As a general purpose packaging approach for data and their metadata, RO-Crate is used across multiple areas, including bioinformatics, digital humanities and regulatory sciences. By applying "just enough" Linked Data standards, RO-Crate simplifies the process of making research outputs FAIR while also enhancing research reproducibility. An RO-Crate for this article is available at https://www.researchobject.org/2021-packaging-research-artefacts-with-ro-crate/ Comment: 42 pages. Submitted to Data Science

Presentation given during the 2nd ESS-SUSTAIN-2 (#871063) consortium meeting (21/01/2021) for WP 6.

AbstractScientific writings, as one essential part of human culture, have evolved over centuries into their current form. Knowing how scientific writings evolved is particularly helpful in understanding how trends in scientific culture developed. It also allows us to better understand how scientific culture was interwoven with human culture generally. The availability of massive digitized texts and the progress in computational technologies today provide us with a convenient and credible way to discern the evolutionary patterns in scientific writings by examining the diachronic linguistic changes. The linguistic changes in scientific writings reflect the genre shifts that took place with historical changes in science and scientific writings. This study investigates a general evolutionary linguistic pattern in scientific writings. It does so by merging two credible computational methods: relative entropy; word-embedding concreteness and imageability. It thus creates a novel quantitative methodology and applies this to the examination of diachronic changes in the Philosophical Transactions of Royal Society (PTRS, 1665–1869). The data from two computational approaches can be well mapped to support the argument that this journal followed the evolutionary trend of increasing professionalization and specialization. But it also shows that language use in this journal was greatly influenced by historical events and other socio-cultural factors. This study, as a “culturomic” approach, demonstrates that the linguistic evolutionary patterns in scientific discourse have been interrupted by external factors even though this scientific discourse would likely have cumulatively developed into a professional and specialized genre. The approaches proposed by this study can make a great contribution to full-text analysis in scientometrics.

Recently, domain-general recurrent neural networks, without explicit linguistic inductive biases, have been shown to successfully reproduce a range of human language behaviours, such as accurately predicting number agreement between nouns and verbs. We show that such networks will also learn number agreement within unnatural sentence structures, i.e. structures that are not found within any natural languages and which humans struggle to process. These results suggest that the models are learning from their input in a manner that is substantially different from human language acquisition, and we undertake an analysis of how the learned knowledge is stored in the weights of the network. We find that while the model has an effective understanding of singular versus plural for individual sentences, there is a lack of a unified concept of number agreement connecting these processes across the full range of inputs. Moreover, the weights handling natural and unnatural structures overlap substantially, in a way that underlines the non-human-like nature of the knowledge learned by the network.

Marine phytoplankton are believed to account for more than 45% of photosynthetic net primary production on Earth, and hence are at the base of marine food webs and have an enormous impact on the entire Earth system. Their members are found across many of the major clades of the tree of life, including bacteria (cyanobacteria) and multiple eukaryotic lineages that acquired photosynthesis through the process of endosymbiosis. Our understanding of their distribution in marine ecosystems and their contribution to biogeochemical cycles have increased since they were first described in the 18th century. Here, we review historical milestones in marine phytoplankton research and how their roles were gradually understood, with a particular focus on insights derived from large-scale ocean exploration. We start from the first observations made by explorers and naturalists, review the initial identification of the main phytoplankton groups and the appreciation of their function in the influential Kiel and Plymouth schools that established biological oceanography, to finally outline the contribution of modern large-scale initiatives to understand this fundamental biological component of the ocean. Fil: Pierella Karlusich, Juan José. Centre National de la Recherche Scientifique. Ecole Normale Supérieure; Francia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Ibarbalz, Federico Matias. Centre National de la Recherche Scientifique. Ecole Normale Supérieure; Francia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Centro de Investigaciones del Mar y la Atmósfera. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Centro de Investigaciones del Mar y la Atmósfera; Argentina Fil: Bowler, Chris. Centre National de la Recherche Scientifique. Ecole Normale Supérieure; Francia. Centre National de la Recherche Scientifique; Francia

AbstractMany believe that the quality of a scientific publication is as good as the science it cites. However, quantifications of how features of reference lists affect citations remain sparse. We examined seven numerical characteristics of reference lists of 50,878 research articles published in 17 ecological journals between 1997 and 2017. Over this period, significant changes occurred in reference lists’ features. On average, more recent papers have longer reference lists and cite more high Impact Factor papers and fewer non-journal publications. We also show that highly cited articles across the ecological literature have longer reference lists, cite more recent and impactful references, and include more self-citations. Conversely, the proportion of ‘classic’ papers and non-journal publications cited, as well as the temporal span of the reference list, have no significant influence on articles’ citations. From this analysis, we distill a recipe for crafting impactful reference lists, at least in ecology.

Introduction to Women and Photography in Africa: Creative Practices and Feminist Challenges edited by Darren Newbury, Lorena Rizzo and Kylie Thomas. Forthcoming, Routledge, 2020.

­The Eastern Fertile Crescent region of western Iran and eastern Iraq hosted major developments in the transition from hunting and gathering to more sedentary agricultural lifestyles through the Early Neolithic period, 10,000-7000 BC. Within the scope of the Central Zagros Archaeological Project, excavations have been conducted at two Early Neolithic sites in the Kurdistan region of Iraq: Bestansur and Shimshara, as well as survey in the region of the Epipalaeolithic site of Zarzi since 2012. Bestansur represents an early stage in the transition to sedentary, agricultural life, where the inhabitants pursued a biodiverse strategy of hunting, gathering, herding and cultivating, maximising the new opportunities afforded by the warmer climate of the Early Holocene. They also constructed a substantial settlement of mudbrick, including a major building with a minimum of 78 human individuals buried under its floor in association with hundreds of beads. ­ These buildings and human remains provide new insights into social relations, mortuary practices, demography, diet, health and disease during the early stages of sedentarisation. ­ The material culture of Bestansur and Shimshara is rich in imported items such as obsidian, carnelian and sea-shells, indicating the extent to which Early Neolithic communities were networked across the Eastern Fertile Crescent and beyond along routes that later became the Silk Roads. This volume includes final reports by a large-scale interdisciplinary team on a wealth of new data from excavations at Bestansur and Shimshara, through application of state-of-the-art scientific techniques, integrated ecological and social approaches and sustainability studies. ­ The net result is to re-emphasise the enormous significance of the Eastern Fertile Crescent in one of the most important episodes in human history: the Neolithic transition.

The last glacial period is characterized by a number of millennial climate events that have been identified in both Greenland and Antarctic ice cores and that are abrupt in Greenland climate records. The mechanisms governing this climate variability remain a puzzle that requires a precise synchronization of ice cores from the two hemispheres to be resolved. Previously, Greenland and Antarctic ice cores have been synchronized primarily via their common records of gas concentrations or isotopes from the trapped air and via cosmogenic isotopes measured on the ice. In this work, we apply ice core volcanic proxies and annual layer counting to identify large volcanic eruptions that have left a signature in both Greenland and Antarctica. Generally, no tephra is associated with those eruptions in the ice cores, so the source of the eruptions cannot be identified. Instead, we identify and match sequences of volcanic eruptions with bipolar distribution of sulfate, i.e. unique patterns of volcanic events separated by the same number of years at the two poles. Using this approach, we pinpoint 82 large bipolar volcanic eruptions throughout the second half of the last glacial period (12–60 ka). This improved ice core synchronization is applied to determine the bipolar phasing of abrupt climate change events at decadal-scale precision. In response to Greenland abrupt climatic transitions, we find a response in the Antarctic water isotope signals (δ18O and deuterium excess) that is both more immediate and more abrupt than that found with previous gas-based interpolar synchronizations, providing additional support for our volcanic framework. On average, the Antarctic bipolar seesaw climate response lags the midpoint of Greenland abrupt δ18O transitions by 122±24 years. The time difference between Antarctic signals in deuterium excess and δ18O, which likewise informs the time needed to propagate the signal as described by the theory of the bipolar seesaw but is less sensitive to synchronization errors, suggests an Antarctic δ18O lag behind Greenland of 152±37 years. These estimates are shorter than the 200 years suggested by earlier gas-based synchronizations. As before, we find variations in the timing and duration between the response at different sites and for different events suggesting an interaction of oceanic and atmospheric teleconnection patterns as well as internal climate variability.