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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.
To identify genetic variants associated with head circumference in infancy, we performed a meta-analysis of seven genome-wide association studies (GWAS) (N = 10,768 individuals of European ancestry enrolled in pregnancy and/or birth cohorts) and followed up three lead signals in six replication studies (combined N = 19,089). rs7980687 on chromosome 12q24 (P = 8.1 x 10(-9)) and rs1042725 on chromosome 12q15 (P = 2.8 x 10(-10)) were robustly associated with head circumference in infancy. Although these loci have previously been associated with adult height(1), their effects on infant head circumference were largely independent of height (P = 3.8 x 10(-7) for rs7980687 and P = 1.3 x 10(-7) for rs1042725 after adjustment for infant height). A third signal, rs11655470 on chromosome 17q21, showed suggestive evidence of association with head circumference (P = 3.9 x 10(-6)). SNPs correlated to the 17q21 signal have shown genome-wide association with adult intracranial volume(2), Parkinson's disease and other neurodegenerative diseases(3-5), indicating that a common genetic variant in this region might link early brain growth with neurological disease in later life.
The genetic integrity of each organism depends on the faithful segregation of its genome during mitosis. To meet this challenge, a cellular surveillance mechanism, termed the spindle assembly checkpoint (SAC), evolved that monitors the correct attachment of chromosomes and blocks progression through mitosis if corrections are needed. While the central role of the SAC for genome integrity is well established, its functional dissection has been hampered by the limited availability of appropriate small molecule inhibitors. Using a fluorescence polarization-based screen, we identify Mad2 inhibitor-1 (M2I-1), the first small molecule inhibitor targeting the binding of Mad2 to Cdc20, an essential protein-protein interaction (PPI) within the SAC. Based on computational and biochemical analyses, we propose that M2I-1 disturbs conformational dynamics of Mad2 critical for complex formation with Cdc20. Cellular studies revealed that M2I-1 weakens the SAC response, indicating that the compound might be active in cells. Thus, our study identifies the SAC specific complex formation between Mad2 and Cdc20 as a protein-protein interaction that can be targeted by small molecules.
Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.
The Low Earth Orbit (LEO) experiment Biology and Mars Experiment (BIOMEX) is an interdisciplinary and international space research project selected by ESA. The experiment will be accommodated on the space exposure facility EXPOSE-R2 on the International Space Station (ISS) and is foreseen to be launched in 2013. The prime objective of BIOMEX is to measure to what extent biomolecules, such as pigments and cellular components, are resistant to and able to maintain their stability under space and Mars-like conditions. The results of BIOMEX will be relevant for space proven biosignature definition and for building a biosignature data base (e.g. the proposed creation of an international Raman library). The library will be highly relevant for future space missions such as the search for life on Mars. The secondary scientific objective is to analyze to what extent terrestrial extremophiles are able to survive in space and to determine which interactions between biological samples and selected minerals (including terrestrial, Moon- and Mars analogs) can be observed under space and Mars-like conditions. In this context, the Moon will be an additional platform for performing similar experiments with negligible magnetic shielding and higher solar and galactic irradiation compared to LEO. Using the Moon as an additional astrobiological exposure platform to complement ongoing astrobiological LEO investigations could thus enhance the chances of detecting organic traces of life on Mars. We present a lunar lander mission with two related objectives: a lunar lander equipped with Raman and PanCam instruments which can analyze the lunar surface and survey an astrobiological exposure platform. This dual use of testing mission technology together with geo- and astrobiological analyses will significantly increase the science return, and support the human preparation objectives. It will provide knowledge about the Moon's surface itself and, in addition, monitor the stability of life-markers, such as cells, cell components and pigments, in an extraterrestrial environment with much closer radiation properties to the surface of Mars. The combination of a Raman data base of these data together with data from LEO and space simulation experiments, will lead to further progress on the analysis and interpretation of data that we will obtain from future Moon and Mars exploration missions.
Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [H-1, N-15]-HSQC-NOESY-[H-1, N-15]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign.
The serine protease thrombin is known as a blood coagulation factor. Through limited cleavage of proteinase- activated receptors it can also control growth and functions in various cell types, including neurons, astrocytes, and microglia ( brain macrophages). A number of previous studies indicated that thrombin induces the release of proinflammatory cytokines and chemokines from microglial cells, suggesting another important role for the protease beyond hemostasis. In the present report, we provide evidence that this effect is not mediated by any proteolytic or non- proteolytic mechanism involving thrombin proper. Inhibition of the enzymatic thrombin activity did not affect the microglial release response. Instead the cyto-/chemokine-inducing activity solely resided in a high molecular weight protein fraction that could be isolated in trace amounts even from apparently homogenous alpha- and gamma-thrombin preparations. High molecular weight material contained thrombin-derived peptides as revealed by mass spectrometry but was devoid of thrombin-like enzymatic activity. Separated from the high molecular weight fraction by fast protein liquid chromatography, enzymatically intact alpha- and gamma-thrombin failed to trigger any release. Our findings may force a revision of the notion that thrombin itself is a direct proinflammatory release signal for microglia. In addition, they could be relevant for the study of other cellular activities and their assignment to this protease
In this work the adsorption of CO2 and CH4 on a series of isoreticular microporous metal-organic frameworks based on 2-substituted imidazolate-4-amide-5-imidates, IFP-1-IFP-6 (IFP Imidazolate Framework Potsdam), is studied firstly by pure gas adsorption at 273 K. All experimental isotherms can be nicely described by using the Toth isotherm model and show the preferred adsorption of CO2 over CH4. At low pressures the Toth isotherm equation exhibits a Henry region, wherefore Henry's law constants for CO2 and CH4 uptake could be determined and ideal selectivity (alpha CO2/CH4) has been calculated. Secondly, selectivities were calculated from mixture data by using nearly equimolar binary mixtures of both gases by a volumetric-chromatographic method to examine the IFPs. Results showed the reliability of the selectivity calculation. Values of (alpha CO2/CH4) around 7.5 for IFP-5 indicate that this material shows much better selectivities than IFP-1, IFP-2, IFP-3, IFP-4 and IFP-6 with slightly lower selectivity (alpha CO2/CH4) = 4-6. The preferred adsorption of CO2 over CH4 especially of IFP-5 and IFP-4 makes these materials suitable for gas separation application.
Fontanes Medien
(2023)
Theodor Fontane war, im durchaus modernen Sinne, ein Medienarbeiter: Als Presse-Agent in London lernte er die innovativste Presselandschaft seiner Zeit kennen; als Redakteur in Berlin leistete er journalistische Kärrnerarbeit; er schrieb Kritiken über das Theater, die bildende Kunst und die Literatur – und auch seine Romane wie seine Reisebücher sind stets Medienprodukte, als Serien in in Zeitungen und Zeitschriften platziert, bevor sie auf dem Buchmarkt erschienen.
Der vorliegende Band dokumentiert die Ergebnisse eines internationalen Kongresses, veranstaltet 2019 vom Theodor-Fontane-Archiv in Potsdam. Die ebenso rasante wie umfassende Medialisierung und Vernetzung der Gesellschaft im Laufe des 19. Jahrhunderts wird dabei als produktive Voraussetzung der schriftstellerischen Tätigkeit Fontanes begriffen. Eingebettet in ein weit verzweigtes Netz der Korrespondenz und der postalischen Textzirkulation, vertraut mit den Routinen und Publika der periodischen Massenpresse, für die er sein Leben lang schrieb, und auf vielfältige Weise geprägt von der visuellen Kultur seiner Zeit wird Theodor Fontane als gleichermaßen journalistisch versierter wie ästhetisch sensibler Grenzgänger erkennbar.
Fontanes Medien
(2022)
Theodor Fontane war, im durchaus modernen Sinne, ein Medienarbeiter: Als Presse-Agent in London lernte er die innovativste Presselandschaft seiner Zeit kennen; als Redakteur in Berlin leistete er journalistische Kärrnerarbeit; er schrieb Kritiken über das Theater, die bildende Kunst und die Literatur – und auch seine Romane wie seine Reisebücher sind stets Medienprodukte, als Serien in in Zeitungen und Zeitschriften platziert, bevor sie auf dem Buchmarkt erschienen.
Der vorliegende Band dokumentiert die Ergebnisse eines internationalen Kongresses, veranstaltet 2019 vom Theodor-Fontane-Archiv in Potsdam. Die ebenso rasante wie umfassende Medialisierung und Vernetzung der Gesellschaft im Laufe des 19. Jahrhunderts wird dabei als produktive Voraussetzung der schriftstellerischen Tätigkeit Fontanes begriffen. Eingebettet in ein weit verzweigtes Netz der Korrespondenz und der postalischen Textzirkulation, vertraut mit den Routinen und Publika der periodischen Massenpresse, für die er sein Leben lang schrieb, und auf vielfältige Weise geprägt von der visuellen Kultur seiner Zeit wird Theodor Fontane als gleichermaßen journalistisch versierter wie ästhetisch sensibler Grenzgänger erkennbar.
For Vibrio cholerae, the coordinated import and export of Na+ is crucial for adaptation to habitats with different osmolarities. We investigated the Na+-extruding branch of the sodium cycle in this human pathogen by in vivo Na-23-NMR spectroscopy. The Na+ extrusion activity of cells was monitored after adding glucose which stimulated respiration via the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR). In a V. cholerae deletion mutant devoid of the Na+-NQR encoding genes (nqrA-F), rates of respiratory Na+ extrusion were decreased by a factor of four, but the cytoplasmic Na+ concentration was essentially unchanged. Furthermore, the mutant was impaired in formation of transmembrane voltage (Delta psi, inside negative) and did not grow under hypoosmotic conditions at pH 8.2 or above. This growth defect could be complemented by transformation with the plasmid encoded nqr operon. In an alkaline environment, Na+/H+ antiporters acidify the cytoplasm at the expense of the transmembrane voltage. It is proposed that, at alkaline pH and limiting Na+ concentrations, the Na+-NQR is crucial for generation of a transmembrane voltage to drive the import of H+ by electrogenic Na+/H+ antiporters. Our study provides the basis to understand the role of the Na+-NQR in pathogenicity of V. cholerae and other pathogens relying on this primary Na+ pump for respiration. (C) 2015 Elsevier B.V. All rights reserved.