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This study pushes our understanding of research reliability by reproducing and replicating claims from 110 papers in leading economic and political science journals. The analysis involves computational reproducibility checks and robustness assessments. It reveals several patterns. First, we uncover a high rate of fully computationally reproducible results (over 85%). Second, excluding minor issues like missing packages or broken pathways, we uncover coding errors for about 25% of studies, with some studies containing multiple errors. Third, we test the robustness of the results to 5,511 re-analyses. We find a robustness reproducibility of about 70%. Robustness reproducibility rates are relatively higher for re-analyses that introduce new data and lower for re-analyses that change the sample or the definition of the dependent variable. Fourth, 52% of re-analysis effect size estimates are smaller than the original published estimates and the average statistical significance of a re-analysis is 77% of the original. Lastly, we rely on six teams of researchers working independently to answer eight additional research questions on the determinants of robustness reproducibility. Most teams find a negative relationship between replicators' experience and reproducibility, while finding no relationship between reproducibility and the provision of intermediate or even raw data combined with the necessary cleaning codes.
We present the analysis of Very Large Telescope Multi Unit Spectroscopic Explorer (MUSE) observations of the planetary nebula (PN) IC 4406. MUSE images in key emission lines are used to unveil the presence of at least five ring-like structures north and south of the main nebula of IC4406. MUSE spectra are extracted from the rings to unambiguously assess for the first time in a PN their physical conditions, electron density (n(e)), and temperature (T-e). The rings are found to have similar T-e as the rim of the main nebula, but smaller n(e). Ratios between different ionic species suggest that the rings of IC4406 have a lower ionization state than the main cavity, in contrast to what was suggested for the rings in NGC 6543, the Cat's Eye Nebula.
Jurisdiction
(2022)
Domestic cattle were brought to Spain by early settlers and agricultural societies. Due to missing Neolithic sites in the Spanish region of Galicia, very little is known about this process in this region. We sampled 18 cattle subfossils from different ages and different mountain caves in Galicia, of which 11 were subject to sequencing of the mitochondrial genome and phylogenetic analysis, to provide insight into the introduction of cattle to this region. We detected high similarity between samples from different time periods and were able to compare the time frame of the first domesticated cattle in Galicia to data from the connecting region of Cantabria to show a plausible connection between the Neolithization of these two regions. Our data shows a close relationship of the early domesticated cattle of Galicia and modern cow breeds and gives a general insight into cattle phylogeny. We conclude that settlers migrated to this region of Spain from Europe and introduced common European breeds to Galicia.
Domestic cattle were brought to Spain by early settlers and agricultural societies. Due to missing Neolithic sites in the Spanish region of Galicia, very little is known about this process in this region. We sampled 18 cattle subfossils from different ages and different mountain caves in Galicia, of which 11 were subject to sequencing of the mitochondrial genome and phylogenetic analysis, to provide insight into the introduction of cattle to this region. We detected high similarity between samples from different time periods and were able to compare the time frame of the first domesticated cattle in Galicia to data from the connecting region of Cantabria to show a plausible connection between the Neolithization of these two regions. Our data shows a close relationship of the early domesticated cattle of Galicia and modern cow breeds and gives a general insight into cattle phylogeny. We conclude that settlers migrated to this region of Spain from Europe and introduced common European breeds to Galicia.
Consensify
(2020)
A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.
Consensify
(2020)
A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.
Studies on the “uses of the past” have steadily and consistently advanced over the past twenty years. Following the seminal studies by Hobsbawm and Ranger and Benedict Anderson on the role of narratives of the past in constructing (national) identities, and thanks the always more widespread practice of reception studies, the attention for cultural memory and lieux de mémoire, and following, many publications have investigated the role of nearer and further time layers in defining and determining structures of identity and senses of belonging across the world. Didactics of history has also contributed a great deal to this field of studies, also thanks to the always more refined methodologies of school book analysis. Classical Antiquity has obviously not been neglected, and multiple studies have been dedicated to its role in the development and reinforcement of modern identities. Yet, not only some areas of the world have remained less considered than others, but most attention has been dedicated to national identities, nationalistic discourses, and their activation through historical narratives. This special issues of thersites wants to contribute further to research on the role of Classical Antiquity within modern identities, asking scholars to focus especially on areas that have been less strongly represented in scholarship until now.
X-ray free-electron lasers have, over the past decade, opened up the possibility of understanding the ultrafast response of matter to intense X-ray pulses. In earlier research on atoms and small molecules, new aspects of this response were uncovered, such as rapid sequences of inner-shell photoionization and Auger ionization. Here, we studied a larger molecule, buckminsterfullerene (C-60), exposed to 640 eV X-rays, and examined the role of chemical effects, such as chemical bonds and charge transfer, on the fragmentation following multiple ionization of the molecule. To provide time resolution, we performed femtosecond-resolved X-ray pump/X-ray probe measurements, which were accompanied by advanced simulations. The simulations and experiment reveal that despite substantial ionization induced by the ultrashort (20 fs) X-ray pump pulse, the fragmentation of C-60 is considerably delayed. This work uncovers the persistence of the molecular structure of C-60, which hinders fragmentation over a timescale of hundreds of femtoseconds. Furthermore, we demonstrate that a substantial fraction of the ejected fragments are neutral carbon atoms. These findings provide insights into X-ray free-electron laser-induced radiation damage in large molecules, including biomolecules.
Soil degradation by water is a serious environmental problem worldwide, with specific climatic factors being the major causes. We investigated the relationships between synoptic atmospheric patterns (i.e. weather types, WTs) and runoff, erosion and sediment yield throughout the Mediterranean basin by analyzing a large database of natural rainfall events at 68 research sites in 9 countries. Principal Component Analysis (PCA) was used to identify spatial relationships of the different WTs including three hydro-sedimentary variables: rainfall, runoff, and sediment yield (SY, used to refer to both soil erosion measured at plot scale and sediment yield registered at catchment scale). The results indicated 4 spatial classes of rainfall and runoff: (a) northern sites dependent on North (N) and North West (NW) flows; (b) eastern sites dependent on E and NE flows; (c) southern sites dependent on S and SE flows; and, finally, (d) western sites dependent on W and SW flows. Conversely, three spatial classes are identified for SY characterized by: (a) N and NE flows in northern sites (b) E flows in eastern sites, and (c) W and SW flows in western sites. Most of the rainfall, runoff and SY occurred during a small number of daily events, and just a few WTs accounted for large percentages of the total. Our results confirm that characterization by WT improves understanding of the general conditions under which runoff and SY occur, and provides useful information for understanding the spatial variability of runoff, and SY throughout the Mediterranean basin. The approach used here could be useful to aid of the design of regional water management and soil conservation measures.