Nonmarine Ostracoda as proxies in (geo-)archaeology: a review

Abstract Ostracods as bioindicators are extremely useful for reconstructing palaeoenvironment and palaeoclimate and can also indicate the provenance of sediments and materials, for example, in studies on ancient commercial networks. Ostracods are small crustaceans that live in almost all aquatic habitats, both natural and man-made. Due to their calcitic carapace, they have high fossilization potential, and their use in geoarchaeology has been steadily increasing during the last decades. Their small size needs mean that only small volumes of sediment samples are needed, and species-specific ecological tolerances and preferences allow detailed palaeoenvironmental reconstructions. Typical methods of their application are palaeoecological analyses of associations based on ecological information and taphonomy, morphometric variability and stable isotope and chemistry analyses of their shells. The present paper aims to present an overview of applications of non-marine ostracods in (geo-)archaeological research, recommending sampling and analytical techniques for addressing archaeological research questions on palaeoclimate, habitat and landscape changes, water availability and quality, land use and other anthropogenic impacts, the provenance of materials and commercial networks to promote the application of Ostracoda in geoarchaeology/environmental archaeology.1 Introduction 2 Applications 2.1 short history of ostracod‐based palaeoenvironmental reconstructions 2.2 Palaeoclimate and palaeoenvironmental studies on continental archaeological sites 2.2.1 General palaeoenvironment/landscape reconstructions 2.2.2 Salinity 2.2.3 Temperature 2.2.4 Radiocarbon dating 2.3 Landscape changes by human activity 2.4 Water use and water works 2.5 Provenance studies 3 Methods for sampling and lab analyses 4 Conclusion

SMOKE for Europe – adaptation, modification and evaluation of a comprehensive emission model for Europe

The US EPA regional emission model SMOKE was adopted and modified to create temporally and spatially distributed emission for Europe and surrounding countries based on official reports and public domain data only. The aim is to develop a flexible model capable of creating consistent high resolution emission data for long-term runs of Chemical Transport Models (CTMs). This modified version of SMOKE, called SMOKE for EUROPE (SMOKE-EU) was successfully used to create hourly gridded emissions for the timespan 1970–2010. <br><br> In this paper the SMOKE-EU model and the underlying European datasets are introduced. Emission data created by SMOKE-EU for the year 2000 are evaluated by comparison to data of three different state-of-the-art emission models. SMOKE-EU produced a range of values comparable to the other three datasets. Further, concentrations of criteria pollutants calculated by the CTM CMAQ using the four different emission datasets were compared against EMEP measurements with hourly and daily resolution. Using SMOKE-EU gave the most reliable modelling of O<sub>3</sub>, NO<sub>2</sub> and SO<sub>4</sub><sup>2−</sup>. The amount of simulated concentrations within a factor of 2 (F2) of the observations for these species are: O<sub>3</sub> (F2 = 0.79, <i>N</i> = 329 197), NO<sub>2</sub> (F2 = 0.55, <i>N</i> = 11 465) and SO<sub>4</sub><sup>2−</sup> (F2 = 0.62, <i>N</i> = 17 536). The lowest values were found for NH<sub>4</sub><sup>+</sup> (F2 = 0.34, <i>N</i> = 7400) and NO<sub>3</sub><sup>−</sup> (F2 = 0.25, <i>N</i> = 6184). NH<sub>4</sub><sup>+</sup> concentrations were generally overestimated, leading to a fractional bias (FB) averaged over 22 measurement stations of (FB = 0.83 ± 0.41) while better agreements with observations were found for SO<sub>4</sub><sup>2−</sup> (FB = 0.06 ± 0.38, 51 stations) and NO<sub>3</sub><sup>−</sup> (FB = 0.13 ± 0.75, 18 stations). <br><br> CMAQ simulations using the three other emission datasets were similar to those modelled using SMOKE-EU emissions. Highest differences where found for NH<sub>4</sub><sup>+</sup> while O<sub>3</sub> concentrations were almost identical

Identification of Lineage-Uncommitted, Long-Lived, Label-Retaining Cells in Healthy Human Esophagus and Stomach, and in Metaplastic Esophagus

Background & Aims The existence of slowly cycling, adult stem cells has been challenged by the identification of actively cycling cells. We investigated the existence of uncommitted, slowly cycling cells by tracking 5-iodo-2'-deoxyuridine (IdU) label-retaining cells (LRCs) in normal esophagus, Barrett's esophagus (BE), esophageal dysplasia, adenocarcinoma, and healthy stomach tissues from patients. Methods Four patients (3 undergoing esophagectomy, 1 undergoing esophageal endoscopic mucosal resection for dysplasia and an esophagectomy for esophageal adenocarcinoma) received intravenous infusion of IdU (200 mg/m2 body surface area; maximum dose, 400 mg) over a 30-minute period; the IdU had a circulation half-life of 8 hours. Tissues were collected at 7, 11, 29, and 67 days after infusion, from regions of healthy esophagus, BE, dysplasia, adenocarcinoma, and healthy stomach; they were analyzed by in situ hybridization, flow cytometry, and immunohistochemical analyses. Results No LRCs were found in dysplasias or adenocarcinomas, but there were significant numbers of LRCs in the base of glands from BE tissue, in the papillae of the basal layer of the esophageal squamous epithelium, and in the neck/isthmus region of healthy stomach. These cells cycled slowly because IdU was retained for at least 67 days and co-labeling with Ki-67 was infrequent. In glands from BE tissues, most cells did not express defensin-5, Muc-2, or chromogranin A, indicating that they were not lineage committed. Some cells labeled for endocrine markers and IdU at 67 days; these cells represented a small population (<0.1%) of epithelial cells at this time point. The epithelial turnover time of the healthy esophageal mucosa was approximately 11 days (twice that of the intestine). Conclusions LRCs of human esophagus and stomach have many features of stem cells (long lived, slow cycling, uncommitted, and multipotent), and can be found in a recognized stem cell niche. Further analyses of these cells, in healthy and metaplastic epithelia, is required

SALL4 controls cell fate in response to DNA base composition

Contains fulltext : 232790.pdf (Publisher’s version ) (Open Access

Recent Change—North Sea

This chapter discusses past and ongoing change in the following physical variables within the North Sea: temperature, salinity and stratification; currents and circulation; mean sea level; and extreme sea levels. Also considered are carbon dioxide; pH and nutrients; oxygen; suspended particulate matter and turbidity; coastal erosion, sedimentation and morphology; and sea ice. The distinctive character of the Wadden Sea is addressed, with a particular focus on nutrients and sediments. This chapter covers the past 200 years and focuses on the historical development of evidence (measurements, process understanding and models), the form, duration and accuracy of the evidence available, and what the evidence shows in terms of the state and trends in the respective variables. Much work has focused on detecting long-term change in the North Sea region, either from measurements or with models. Attempts to attribute such changes to, for example, anthropogenic forcing are still missing for the North Sea. Studies are urgently needed to assess consistency between observed changes and current expectations, in order to increase the level of confidence in projections of expected future conditions

Modeling inflammation and oxidative stress in gastrointestinal disease development using novel organotypic culture systems

Gastroesophageal reflux disease (GERD), Barrett's esophagus (BE), graft-versus-host disease (GVHD), and inflammatory bowel diseases such as ulcerative colitis and Crohn's disease are common human gastrointestinal diseases that share inflammation as a key driver for their development. A general outcome resulting from these chronic inflammatory conditions is increased oxidative stress. Oxidative stress is caused by the generation of reactive oxygen and nitrogen species that are part of the normal inflammatory response, but are also capable of damaging cellular DNA, protein, and organelles. Damage to DNA can include DNA strand breaks, point mutations due to DNA adducts, as well as alterations in methylation patterns leading to activation of oncogenes or inactivation of tumor suppressors. There are a number of significant long-term consequences associated with chronic oxidative stress, most notably cancer. Infiltrating immune cells and stromal components of tissue including fibroblasts contribute to dynamic changes occurring in tissue related to disease development. Immune cells can potentiate oxidative stress, and fibroblasts have the capacity to contribute to advanced growth and proliferation of the epithelium and any resultant cancers. Disease models for GERD, BE, GVHD, and ulcerative colitis based on three-dimensional human cell and tissue culture systems that recapitulate in vivo growth and differentiation in inflammatory-associated microphysiological environments would enhance our understanding of disease progression and improve our ability to test for disease-prevention strategies. The development of physiologically relevant, human cell-based culture systems is therefore a major focus of our research. These novel models will be of enormous value, allowing us to test hypotheses and advance our understanding of these disorders, and will have a translational impact allowing us to more rapidly develop therapeutic and chemopreventive agents. In summary, this work to develop advanced human cell-based models of inflammatory conditions will greatly improve our ability to study, prevent, and treat GERD, BE, GVHD, and inflammatory bowel disease. The work will also foster the development of novel therapeutic and preventive strategies that will improve patient care for these important clinical conditions

NAD+ protects against EAE by regulating CD4+ T-cell differentiation

CD4+ T cells are involved in the development of autoimmunity, including multiple sclerosis (MS). Here we show that nicotinamide adenine dinucleotide (NAD+) blocks experimental autoimmune encephalomyelitis (EAE), a mouse model of MS, by inducing immune homeostasis through CD4+IFNγ+IL-10+ T cells and reverses disease progression by restoring tissue integrity via remyelination and neuroregeneration. We show that NAD+ regulates CD4+ T-cell differentiation through tryptophan hydroxylase-1 (Tph1), independently of well-established transcription factors. In the presence of NAD+, the frequency of T-bet−/− CD4+IFNγ+ T cells was twofold higher than wild-type CD4+ T cells cultured in conventional T helper 1 polarizing conditions. Our findings unravel a new pathway orchestrating CD4+ T-cell differentiation and demonstrate that NAD+ may serve as a powerful therapeutic agent for the treatment of autoimmune and other diseases

Effects of ship emissions on air quality in the Baltic Sea region simulated with three different chemistry transport models

The Baltic Sea is a highly frequented shipping area with busy shipping lanes close to densely populated regions. Exhaust emissions from ship traffic into the atmosphere do not only enhance air pollution, they also affect the Baltic Sea environment through acidification and eutrophication of marine waters and surrounding terrestrial ecosystems. As part of the European BONUS project SHEBA (Sustainable Shipping and Environment of the Baltic Sea region), the transport, chemical transformation and fate of atmospheric pollutants in the Baltic Sea region were simulated with three regional chemistry transport model (CTM) systems, CMAQ, EMEP/MSC-W and SILAM, with grid resolutions between 4 and 11&thinsp;km. The main goal was to quantify the effect that shipping emissions have on the regional air quality in the Baltic Sea region when the same shipping emission dataset but different CTMs are used in their typical set-ups. The performance of these models and the shipping contribution to the results of the individual models were evaluated for sulfur dioxide (SO2), nitrogen dioxide (NO2), ozone (O3) and particulate matter (PM2.5). Model results from the three CTMs for total air pollutant concentrations were compared to observations from rural and urban background stations of the AirBase monitoring network in the coastal areas of the Baltic Sea region. Observed PM2.5 in summer was underestimated strongly by CMAQ and to some extent by EMEP/MSC-W. Observed PM2.5 in winter was underestimated by SILAM. In autumn all models were in better agreement with observed PM2.5. The spatial average of the annual mean O3 in the EMEP/MSC-W simulation was ca. 20&thinsp;% higher compared to the other two simulations, which is mainly the consequence of using a different set of boundary conditions for the European model domain. There are significant differences in the calculated ship contributions to the levels of air pollutants among the three models. EMEP/MSC-W, with the coarsest grid, predicted weaker ozone depletion through NO emissions in the proximity of the main shipping routes than the other two models. The average contribution of ships to PM2.5 levels in coastal land areas is in the range of 3.1&thinsp;%–5.7&thinsp;% for the three CTMs. Differences in ship-related PM2.5 between the models are mainly attributed to differences in the schemes for inorganic aerosol formation. Differences in the ship-related elemental carbon (EC) among the CTMs can be explained by differences in the meteorological conditions, atmospheric transport processes and the applied wet-scavenging parameterizations. Overall, results from the present study show the sensitivity of the ship contribution to combined uncertainties in boundary conditions, meteorological data and aerosol formation and deposition schemes. This is an important step towards a more reliable evaluation of policy options regarding emission regulations for ship traffic and the planned introduction of a nitrogen emission control area (NECA) in the Baltic Sea and the North Sea in 2021.</p

Dclk1 Defines Quiescent Pancreatic Progenitors that Promote Injury-Induced Regeneration and Tumorigenesis

The existence of adult pancreatic progenitor cells has been debated. While some favor the concept of facultative progenitors involved in homeostasis and repair, neither a location nor markers for such cells have been defined. Using genetic lineage tracing, we show that Doublecortin-like kinase-1 (Dclk1) labels a rare population of long-lived, quiescent pancreatic cells. In vitro, Dclk1+ cells proliferate readily and sustain pancreatic organoid growth. In vivo, Dclk1+ cells are necessary for pancreatic regeneration following injury and chronic inflammation. Accordingly, their loss has detrimental effects after cerulein-induced pancreatitis. Expression of mutant Kras in Dclk1+ cells does not affect their quiescence or longevity. However, experimental pancreatitis converts Kras mutant Dclk1+ cells into potent cancer-initiating cells. As a potential effector of Kras, Dclk1 contributes functionally to the pathogenesis of pancreatic cancer. Taken together, these observations indicate that Dclk1 marks quiescent pancreatic progenitors that are candidates for the origin of pancreatic cancer

Climate change in the Baltic Sea region : a summary

Based on the Baltic Earth Assessment Reports of this thematic issue in Earth System Dynamics and recent peer-reviewed literature, current knowledge of the effects of global warming on past and future changes in climate of the Baltic Sea region is summarised and assessed. The study is an update of the Second Assessment of Climate Change (BACC II) published in 2015 and focuses on the atmosphere, land, cryosphere, ocean, sediments, and the terrestrial and marine biosphere. Based on the summaries of the recent knowledge gained in palaeo-, historical, and future regional climate research, we find that the main conclusions from earlier assessments still remain valid. However, new long-term, homogenous observational records, for example, for Scandinavian glacier inventories, sea-level-driven saltwater inflows, so-called Major Baltic Inflows, and phytoplankton species distribution, and new scenario simulations with improved models, for example, for glaciers, lake ice, and marine food web, have become available. In many cases, uncertainties can now be better estimated than before because more models were included in the ensembles, especially for the Baltic Sea. With the help of coupled models, feedbacks between several components of the Earth system have been studied, and multiple driver studies were performed, e.g. projections of the food web that include fisheries, eutrophication, and climate change. New datasets and projections have led to a revised understanding of changes in some variables such as salinity. Furthermore, it has become evident that natural variability, in particular for the ocean on multidecadal timescales, is greater than previously estimated, challenging our ability to detect observed and projected changes in climate. In this context, the first palaeoclimate simulations regionalised for the Baltic Sea region are instructive. Hence, estimated uncertainties for the projections of many variables increased. In addition to the well-known influence of the North Atlantic Oscillation, it was found that also other low-frequency modes of internal variability, such as the Atlantic Multidecadal Variability, have profound effects on the climate of the Baltic Sea region. Challenges were also identified, such as the systematic discrepancy between future cloudiness trends in global and regional models and the difficulty of confidently attributing large observed changes in marine ecosystems to climate change. Finally, we compare our results with other coastal sea assessments, such as the North Sea Region Climate Change Assessment (NOSCCA), and find that the effects of climate change on the Baltic Sea differ from those on the North Sea, since Baltic Sea oceanography and ecosystems are very different from other coastal seas such as the North Sea. While the North Sea dynamics are dominated by tides, the Baltic Sea is characterised by brackish water, a perennial vertical stratification in the southern subbasins, and a seasonal sea ice cover in the northern subbasins.Peer reviewe