Evidence for heterothermic endothermy and reptile-like eggshell mineralization in Troodon, a non-avian maniraptoran theropod.

The dinosaur-bird transition involved several anatomical, biomechanical, and physiological modifications of the theropod bauplan. Non-avian maniraptoran theropods, such as Troodon, are key to better understand changes in thermophysiology and reproduction occurring during this transition. Here, we applied dual clumped isotope (Δ47 and Δ48) thermometry, a technique that resolves mineralization temperature and other nonthermal information recorded in carbonates, to eggshells from Troodon, modern reptiles, and modern birds. Troodon eggshells show variable temperatures, namely 42 and 29 ± 2 °C, supporting the hypothesis of an endothermic thermophysiology with a heterothermic strategy for this extinct taxon. Dual clumped isotope data also reveal physiological differences in the reproductive systems between Troodon, reptiles, and birds. Troodon and modern reptiles mineralize their eggshells indistinguishable from dual clumped isotope equilibrium, while birds precipitate eggshells characterized by a positive disequilibrium offset in Δ48. Analyses of inorganic calcites suggest that the observed disequilibrium pattern in birds is linked to an amorphous calcium carbonate (ACC) precursor, a carbonate phase known to accelerate eggshell formation in birds. Lack of disequilibrium patterns in reptile and Troodon eggshells implies these vertebrates had not acquired the fast, ACC-based eggshell calcification process characteristic of birds. Observation that Troodon retained a slow reptile-like calcification suggests that it possessed two functional ovaries and was limited in the number of eggs it could produce; thus its large clutches would have been laid by several females. Dual clumped isotope analysis of eggshells of extinct vertebrates sheds light on physiological information otherwise inaccessible in the fossil record.

Accurate measurement of K/Ca in low-[K] carbonate samples using laser-ablation sector-field inductively coupled plasma mass spectrometry.

RATIONALE: Potassium (K) is a major component of several silicate minerals and seawater, and, therefore, constraining past changes in the potassium cycle is a promising way of tracing large-scale geological processes on Earth. However, [K] measurement using inductively coupled plasma mass spectrometry (ICP-MS) is challenging due to an ArH+ interference, which may be of a similar magnitude to the K+ ion beam in samples with <0.1% m/m [K]. METHODS: In this work, we investigated the effect of the ArH+ interference on K/Ca data quality by comparing results from laser-ablation (LA)-ICP-MS measured in medium and high mass resolution modes and validating our LA results via solution ICP-optical emission spectroscopy (OES) and solution ICP-MS measurements. To do so, we used a wide range of geological reference materials, with a particular focus on marine carbonates, which are potential archives of past changes in the K cycle but are typically characterised by [K] < 200 µg/g. In addition, we examine the degree to which trace-element data quality is driven by downhole fractionation during LA-ICP-MS measurements. RESULTS: Our results show that medium mass resolution (MR) mode is sufficiently capable of minimising the effect of the ArH+ interference on K+ . However, the rate of downhole fractionation for Na and K varies between different samples as a result of their differing bulk composition, resulting in matrix-specific inaccuracy. We show how this can be accounted for via downhole fractionation corrections, resulting in an accuracy of better than 1% and a long-term reproducibility (intermediate precision) of <6% (relative standard deviation) in JCp-1NP using LA-ICP-MS in MR mode. CONCLUSION: Our [K] measurement protocol is demonstrably precise and accurate and applicable to a wide range of materials. The measurement of K/Ca in relatively low-[K] marine carbonates is presented here as a key example of a new application opened up by these advances.

Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases.

This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusable) data principles in a large distributed bioinformatics infrastructure. We address the challenge of heterogeneity of wet lab technologies, data, metadata, software, computational workflows and the levels of implementation and monitoring of FAIR principles within the different bioinformatics sub-disciplines joint in de.NBI. On the one hand, this broad service landscape and the excellent network of experts are a strong basis for the development of useful research data management plans. On the other hand, the large number of tools and techniques maintained by distributed teams renders FAIR compliance challenging.

Early life of Neanderthals.

The early onset of weaning in modern humans has been linked to the high nutritional demand of brain development that is intimately connected with infant physiology and growth rate. In Neanderthals, ontogenetic patterns in early life are still debated, with some studies suggesting an accelerated development and others indicating only subtle differences vs. modern humans. Here we report the onset of weaning and rates of enamel growth using an unprecedented sample set of three late (∼70 to 50 ka) Neanderthals and one Upper Paleolithic modern human from northeastern Italy via spatially resolved chemical/isotopic analyses and histomorphometry of deciduous teeth. Our results reveal that the modern human nursing strategy, with onset of weaning at 5 to 6 mo, was present among these Neanderthals. This evidence, combined with dental development akin to modern humans, highlights their similar metabolic constraints during early life and excludes late weaning as a factor contributing to Neanderthals' demise.

PEtab-Interoperable specification of parameter estimation problems in systems biology.

Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been-so far-no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies.

Ministerial Autonomy, Parliamentary Scrutiny and Government Reform Output in Parliamentary Democracies.

One of the most important decisions coalition partners make when forming a government is the division of ministries. Ministerial portfolios provide the party in charge with considerable informational and agenda-setting advantages, which parties can use to shape policies according to their preferences. Oversight mechanisms in parliaments play a central role in mitigating ministerial policy discretion, allowing coalition partners to control each other even though power has been delegated to individual ministers. However, we know relatively little about how such mechanisms influence the agenda-setting and gatekeeping powers of ministers and how much influence minister parties have on policy output relative to the government as a whole in different institutional settings. We fill this gap by analyzing original data on over 2000 important social and economic policy reform measures adopted in nine Western European countries over 20 years, based on a coding of more than 1200 country reports issued by the Economist Intelligence Unit and the Organisation for Economic Co-operation and Development (OECD). We find that parliaments with strong oversight powers constrain the agenda-setting capacity of minister parties but have limited impact on their gatekeeping capacity. Our findings have important implications for our understanding of policy-making and democratic accountability.

How and why party position estimates from manifestos, expert, and party elite surveys diverge: A comparative analysis of the 'left-right' and the 'European integration' dimensions.

This paper examines the validity of three approaches to estimate party positions on the general left-right and EU dimensions. We newly introduce party elite data from the comprehensive IntUne survey and cross-validate it with existing expert survey and manifesto data. The general left-right estimates generated by elites and experts show a higher congruence than those derived from party manifestos; neither measure clearly materializes as more valid regarding EU positions. We identify which factors explain diverging estimates. For instance, disagreement among experts has greater impact than their mere number. The substantial centrist bias of the manifesto estimates persists even when alternative documents are used to substitute manifestos. Low response rates among elites have no systematic detrimental effect on the validity of party position estimates.

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

Sustainable noncommercial bioinformatics infrastructures are a prerequisite to use and take advantage of the potential of big data analysis for research and economy. Consequently, funders, universities and institutes as well as users ask for a transparent value model for the tools and services offered. In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly the total costs of ownership. Five representative scenarios for value estimation from a rough estimation to a detailed breakdown of costs are presented. To account for the diversity in bioinformatics applications and services, the notion of service-specific 'service provision units' is introduced together with the factors influencing them and the main underlying assumptions for these 'value influencing factors'. Special attention is given on how to handle personnel costs and indirect costs such as electricity. Four examples are presented for the calculation of the value of tools and services provided by the German Network for Bioinformatics Infrastructure (de.NBI): one for tool usage, one for (Web-based) database analyses, one for consulting services and one for bioinformatics training events. Finally, from the discussed values, the costs of direct funding and the costs of payment of services by funded projects are calculated and compared.

A PP4 holoenzyme balances physiological and oncogenic nuclear factor-kappa B signaling in T lymphocytes.

Signal transduction to nuclear factor-kappa B (NF-κB) involves multiple kinases and phosphorylated target proteins, but little is known about signal termination by dephosphorylation. By RNAi screening, we have identified protein phosphatase 4 regulatory subunit 1 (PP4R1) as a negative regulator of NF-κB activity in T lymphocytes. PP4R1 formed part of a distinct PP4 holoenzyme and bridged the inhibitor of NF-κB kinase (IKK) complex and the phosphatase PP4c, thereby directing PP4c activity to dephosphorylate and inactivate the IKK complex. PP4R1 expression was triggered upon activation and proliferation of primary human T lymphocytes and deficiency for PP4R1 caused sustained and increased IKK activity, T cell hyperactivation, and aberrant NF-κB signaling in NF-κB-addicted T cell lymphomas. Collectively, our results unravel PP4R1 as a previously unknown activation-associated negative regulator of IKK activity in lymphocytes whose downregulation promotes oncogenic NF-κB signaling in a subgroup of T cell lymphomas.

The Climate Response to Emissions Reductions Due to COVID-19: Initial Results From CovidMIP.

Many nations responded to the corona virus disease-2019 (COVID-19) pandemic by restricting travel and other activities during 2020, resulting in temporarily reduced emissions of CO2, other greenhouse gases and ozone and aerosol precursors. We present the initial results from a coordinated Intercomparison, CovidMIP, of Earth system model simulations which assess the impact on climate of these emissions reductions. 12 models performed multiple initial-condition ensembles to produce over 300 simulations spanning both initial condition and model structural uncertainty. We find model consensus on reduced aerosol amounts (particularly over southern and eastern Asia) and associated increases in surface shortwave radiation levels. However, any impact on near-surface temperature or rainfall during 2020-2024 is extremely small and is not detectable in this initial analysis. Regional analyses on a finer scale, and closer attention to extremes (especially linked to changes in atmospheric composition and air quality) are required to test the impact of COVID-19-related emission reductions on near-term climate.

Eocene greenhouse climate revealed by coupled clumped isotope-Mg/Ca thermometry.

Past greenhouse periods with elevated atmospheric CO2 were characterized by globally warmer sea-surface temperatures (SST). However, the extent to which the high latitudes warmed to a greater degree than the tropics (polar amplification) remains poorly constrained, in particular because there are only a few temperature reconstructions from the tropics. Consequently, the relationship between increased CO2, the degree of tropical warming, and the resulting latitudinal SST gradient is not well known. Here, we present coupled clumped isotope (Δ47)-Mg/Ca measurements of foraminifera from a set of globally distributed sites in the tropics and midlatitudes. Δ47 is insensitive to seawater chemistry and therefore provides a robust constraint on tropical SST. Crucially, coupling these data with Mg/Ca measurements allows the precise reconstruction of Mg/Casw throughout the Eocene, enabling the reinterpretation of all planktonic foraminifera Mg/Ca data. The combined dataset constrains the range in Eocene tropical SST to 30-36 °C (from sites in all basins). We compare these accurate tropical SST to deep-ocean temperatures, serving as a minimum constraint on high-latitude SST. This results in a robust conservative reconstruction of the early Eocene latitudinal gradient, which was reduced by at least 32 ± 10% compared with present day, demonstrating greater polar amplification than captured by most climate models.

Use of a quantitative data report in a hypothetical decision scenario for health policymaking: a computer-assisted laboratory study.

BACKGROUND: Quantitative data reports are widely produced to inform health policy decisions. Policymakers are expected to critically assess provided information in order to incorporate the best available evidence into the decision-making process. Many other factors are known to influence this process, but little is known about how quantitative data reports are actually read. We explored the reading behavior of (future) health policy decision-makers, using innovative methods. METHODS: We conducted a computer-assisted laboratory study, involving starting and advanced students in medicine and health sciences, and professionals as participants. They read a quantitative data report to inform a decision on the use of resources for long-term care in dementia in a hypothetical decision scenario. Data were collected through eye-tracking, questionnaires, and a brief interview. Eye-tracking data were used to generate 'heatmaps' and five measures of reading behavior. The questionnaires provided participants' perceptions of understandability and helpfulness as well as individual characteristics. Interviews documented reasons for attention to specific report sections. The quantitative analysis was largely descriptive, complemented by Pearson correlations. Interviews were analyzed by qualitative content analysis. RESULTS: In total, 46 individuals participated [students (85%), professionals (15%)]. Eye-tracking observations showed that the participants spent equal time and attention for most parts of the presented report, but were less focused when reading the methods section. The qualitative content analysis identified 29 reasons for attention to a report section related to four topics. Eye-tracking measures were largely unrelated to participants' perceptions of understandability and helpfulness of the report. CONCLUSIONS: Eye-tracking data added information on reading behaviors that were not captured by questionnaires or interviews with health decision-makers.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics.

SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions and is not restricted to any organism class. The data are made available to the public by a web-based search interface and by web services for programmatic access. In this update we describe major improvements and extensions of SABIO-RK since our last publication in the database issue of Nucleic Acid Research (2012). (i) The website has been completely revised and (ii) allows now also free text search for kinetics data. (iii) Additional interlinkages with other databases in our field have been established; this enables users to gain directly comprehensive knowledge about the properties of enzymes and kinetics beyond SABIO-RK. (iv) Vice versa, direct access to SABIO-RK data has been implemented in several systems biology tools and workflows. (v) On request of our experimental users, the data can be exported now additionally in spreadsheet formats. (vi) The newly established SABIO-RK Curation Service allows to respond to specific data requirements.

Dose limits for occupational exposure to ionising radiation and genotoxic carcinogens: a German perspective.

This paper summarises the view of the German Commission on Radiological Protection ("Strahlenschutzkommission", SSK) on the rationale behind the currently valid dose limits and dose constraints for workers recommended by the International Commission on Radiological Protection (ICRP). The paper includes a discussion of the reasoning behind current dose limits followed by a discussion of the detriment used by ICRP as a measure for stochastic health effects. Studies on radiation-induced cancer are reviewed because this endpoint represents the most important contribution to detriment. Recent findings on radiation-induced circulatory disease that are currently not included in detriment calculation are also reviewed. It appeared that for detriment calculations the contribution of circulatory diseases plays only a secondary role, although the uncertainties involved in their risk estimates are considerable. These discussions are complemented by a review of the procedures currently in use in Germany, or in discussion elsewhere, to define limits for genotoxic carcinogens. To put these concepts in perspective, actual occupational radiation exposures are exemplified with data from Germany, for the year 2012, and regulations in Germany are compared to the recommendations issued by ICRP. Conclusions include, among others, considerations on radiation protection concepts currently in use and recommendations of the SSK on the limitation of annual effective dose and effective dose cumulated over a whole working life.

Focused ultrasound transiently increases membrane conductance in isolated crayfish axon.

We report a novel phenomenon produced by focused ultrasound (US) that may be important for understanding its effects on cell membranes. When a US burst (2.1 MHz, 1-mm focal diameter, 0.1-1 MPa) was focused on a motor axon of the crayfish neuromuscular junction, it consistently produced a fast hyperpolarization, which was followed or superseded by subthreshold depolarizations or action potentials in a stochastic manner. The depolarization persisted in the presence of voltage-gated channel blockers [1 µM TTX ( INa), 50 µM ZD7288 ( Ih), and 200 µM 4-aminopyridine ( IK)] and typically started shortly after the onset of a 5-ms US burst, with a mean latency of 3.35 ± 0.53 ms (SE). The duration and amplitude of depolarizations averaged 2.13 ± 0.87 s and 10.1 ± 2.09 mV, with a maximum of 200 s and 60 mV, respectively. The US-induced depolarization was always associated with a decrease in membrane resistance. By measuring membrane potential and resistance during the US-induced depolarization, the reversal potential of US-induced conductance ( gus) was estimated to be -8.4 ± 2.3 mV, suggesting a nonselective conductance. The increase in gus was 10-100 times larger than the leak conductance; thus it could significantly influence neuronal activity. This change in conductance may be due to stimulation of mechanoreceptors. Alternatively, US may perturb the lateral motion of phospholipids and produce nanopores, which then increase gus. These results may be important for understanding mechanisms underlying US-mediated modulation of neuronal activity and brain function. NEW & NOTEWORTHY We report a specific increase in membrane conductance produced by ultrasound (US) on neuronal membrane. When a 5-ms US tone burst was focused on a crayfish motor axon, it stochastically triggered either depolarization or a spike train. The depolarization was up to 60 mV in amplitude and 200 s in duration and therefore could significantly influence neuronal activity. Depolarization was still evoked by US burst in the presence of Na+ and Ca2+ channel blockers and had a reversal potential of -8.4 ± 2.3 mV, suggesting a nonselective permeability. US can be applied noninvasively in the form of a focused beam to deep brain areas through the skull and has been shown to modulate brain activity. Understanding the depolarization reported here should be helpful for improving the use of US for noninvasive modulation and stimulation in brain-related disease.

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. It is a web-accessible repository for storing and sharing systems biology research assets. It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations that produced them, and to interrogate them via API interfaces. By using the FAIRDOMHub, researchers can achieve more effective exchange with geographically distributed collaborators during projects, ensure results are sustained and preserved and generate reproducible publications that adhere to the FAIR guiding principles of data stewardship.

Who will attack the competitors? How political parties resolve strategic and collective action dilemmas in negative campaigning.

Negative campaigning presents parties with a collective action problem. While parties would prefer to have their competitors attacked, potential backlash effects from negative messages mean that individual politicians typically lack the incentives to carry out such attacks. We theorize that parties solve this problem by implementing a division of labour that takes into account the incentives of individual office holders, their availability for campaign activity, and media relevance. Drawing on these arguments we expect that holders of high public office and party leaders are less likely to issue attacks, leaving the bulk of the 'dirty work' to be carried out by party floor leaders and general secretaries. Examining almost 8000 press releases issued by over 600 individual politicians during four election campaigns in Austria, we find strong support for our theoretical expectations.

Current knowledge on radon risk: implications for practical radiation protection? radon workshop, 1/2 December 2015, Bonn, BMUB (Bundesministerium für Umwelt, Naturschutz, Bau und Reaktorsicherheit; Federal Ministry for the Environment, Nature Conservation, Building and Nuclear Safety).

ICRP suggested a strategy based on the distinction between a protection approach for dwellings and one for workplaces in the previous recommendations on radon. Now, the Commission recommends an integrated approach for the protection against radon exposure in all buildings irrespective of their purpose and the status of their occupants. The strategy of protection in buildings, implemented through a national action plan, is based on the application of the optimisation principle below a derived reference level in concentration (maximum 300 Bq m(-3)). A problem, however, arises that due to new epidemiological findings and application of dosimetric models, ICRP 115 (Ann ICRP 40, 2010) presents nominal probability coefficients for radon exposure that are approximately by a factor of 2 larger than in the former recommendations of ICRP 65 (Ann ICRP 23, 1993). On the basis of the so-called epidemiological approach and the dosimetric approach, the doubling of risk per unit exposure is represented by a doubling of the dose coefficients, while the risk coefficient of ICRP 103 (2007) remains unchanged. Thus, an identical given radon exposure situation with the new dose coefficients would result in a doubling of dose compared with the former values. This is of serious conceptual implications. A possible solution of this problem was presented during the workshop.

Hare-to-human transmission of Francisella tularensis subsp. holarctica, Germany.

In November 2012, a group of 7 persons who participated in a hare hunt in North Rhine-Westphalia, Germany, acquired tularemia. Two F. tularensis subsp. holarctica isolates were cultivated from human and hare biopsy material. Both isolates belonged to the FTN002-00 genetic subclade (derived for single nucleotide polymorphisms B.10 and B.18), thus indicating likely hare-to-human transmission.