We introduce a novel, large-scale dataset for microscopy cell annotations. The dataset includes 32 whole slide images (WSI) of canine cutaneous mast cell tumors, selected to include both low grade cases as well as high grade cases. The slides have been completely annotated for mitotic figures and we provide secondary annotations for neoplastic mast cells, inflammatory granulocytes, and mitotic figure look-alikes. Additionally to a blinded two-expert manual annotation with consensus, we provide an algorithm-aided dataset, where potentially missed mitotic figures were detected by a deep neural network and subsequently assessed by two human experts. We included 262,481 annotations in total, out of which 44,880 represent mitotic figures. For algorithmic validation, we used a customized RetinaNet approach, followed by a cell classification network. We find F1-Scores of 0.786 and 0.820 for the manually labelled and the algorithm-aided dataset, respectively. The dataset provides, for the first time, WSIs completely annotated for mitotic figures and thus enables assessment of mitosis detection algorithms on complete WSIs as well as region of interest detection algorithms.

A method for characterising the wave-function of freely-propagating particles would provide a useful tool for developing quantum-information technologies with single electronic excitations. Previous continuous-variable quantum tomography techniques developed to analyse electronic excitations in the energy-time domain have been limited to energies close to the Fermi level. We show that a wide-band tomography of single-particle distributions is possible using energy-time filtering and that the Wigner representation of the mixed-state density matrix can be reconstructed for solitary electrons emitted by an on-demand single-electron source. These are highly localised distributions, isolated from the Fermi sea. While we cannot resolve the pure state Wigner function of our excitations due to classical fluctuations, we can partially resolve the chirp and squeezing of the Wigner function imposed by emission conditions and quantify the quantumness of the source. This tomography scheme, when implemented with sufficient experimental resolution, will enable quantum-limited measurements, providing information on electron coherence and entanglement at the individual particle level.

This study describes a novel application of an “onion-peeling” approach to multi-axis differential optical absorption spectroscopy (MAX-DOAS) measurements of shipping emissions aiming at investigating the strong horizontal inhomogeneities in NO2 over a shipping lane. To monitor ship emissions on the main shipping route towards the port of Hamburg, a two-channel (UV and visible) MAX-DOAS instrument was deployed on the island Neuwerk in the German Bight, 6–7 km south of the main shipping lane. Utilizing the fact that the effective light path length in the atmosphere depends systematically on wavelength, simultaneous measurements and DOAS retrievals in the UV and visible spectral ranges are used to probe air masses at different horizontal distances to the instrument to estimate two-dimensional pollutant distributions. Two case studies have been selected to demonstrate the ability to derive the approximate plume positions in the observed area. A situation with northerly wind shows high NO2 concentrations close to the measurement site and low values in the north of the shipping lane. The opposite situation with southerly wind, unfavorable for the on-site in situ instrumentation, demonstrates the ability to detect enhanced NO2 concentrations several kilometers away from the instrument. Using a Gaussian plume model, in-plume NO2 volume mixing ratios can be derived from the MAX-DOAS measurements.

For validation, a comparison to airborne imaging DOAS measurements during the NOSE campaign in July 2013 is performed, showing good agreement between the approximate plume position derived from the onion-peeling MAX-DOAS and the airborne measurements as well as between the derived in-plume NO2 volume mixing ratios (VMRs).

Sociological research into the transregional North–South circulation of knowledge in the social sciences and humanities has tended to have a unidirectional bias to date. The standard assumption is that as a result of globalization, theories and methods are spread from the global North to the global South. Based on this premise, many of the studies of circulation focus on the transfer of knowledge in terms of ideas, traditions, authors and concepts from the North to the South. Thus far, little attention has been paid to the transregional circulation of theoretical approaches from the South to the North and their impact on the transformation of the European social sciences and humanities. Analysing the circulation of the Latin American dependency theories in the Federal Republic of Germany, this article addresses precisely this gap. The focus is on processes of institutional consolidation of area studies, North–South mobility, the translation-process into German, application in empirical research, modification and rejection. Focusing on this little-explored orientation regarding the circulation of knowledge, this article is in keeping with the current attempt to analyse transregional entanglements within European social sciences.

EU scholars have studied mobilization as a cross-level phenomenon. Individuals and organized interests seek preliminary rulings with the Court of Justice of the EU to challenge national rules. Likewise, the Commission takes member states to court where they infringe commonly agreed rules. However, litigation can also run horizontally in the EU system. EU institutions can go to court to annul actions of other EU institutions. Studying this so far neglected phenomenon of litigation, the paper analyses differences in mobilization across European Parliament, Council and Commission. To this aim it conceptualizes litigation decisions as resulting from an interplay of agency and structure. Decision-making within organizations and in the EU political system as well as different motivations of actors are presented to explain differences in horizontal litigation. Methodologically the analysis combines a database covering 160 horizontal annulment conflicts (1957 to 2017) and case studies based on expert interviews.

This chapter explores how transnational media and culture impacts on the identity formation of recent Latvian migrants in Germany. In the context of the EU, Germany opened its labour market to the new EU countries rather late, when compared to other ‘old’ EU countries. This has had an effect on the composition of the group of Latvian migrants going to Germany, and their identities. In the light of this, this chapter examines how Latvian migrants in Germany feel and experience their belonging to Latvia and its culture. It analyses the social and communicative practices crucial for the development of belonging, including the rootedness in the country where they live and the cultural references that are important for them. The evidence for the analysis in this chapter comes from in-depth interviews, open media diaries and network maps of Latvian migrants in Germany. The chapter situates the description of evidence in the framework of cultural identity concepts and discusses the role of culture and media in the process of building migrant identity. The chapter argues that culture is shaping the transnational self-perception of Latvian migrants in Germany – as it provides collective narratives of imagined common frames of references, and confirms feelings of belonging and distinction.

We reviewed six key peer-reviewed publications that assessed the need for one-year studies of pesticide toxicity in dogs. Each of the six papers took a different approach to comparing the value of one-year studies relative to three-month studies, and despite the adoption of different databases and approaches, each study reached the same conclusion: the recommended limit to the testing of pesticide toxicity in dogs should be three months.

Therefore, the present review supports the conclusion that the routine inclusion of a one-year dog study should not be a mandatory requirement for the safety assessment of pesticides, since it is scientifically no longer justifiable. We recommend that the OECD should adapt a harmonized approach that is in line with the legislation in Europe and the USA.

Invasion biology is a thriving ecological research field, and confusingly many hypotheses, concepts, and ideas about biological invasions populate today's literature. Moreover, some of these hypotheses are very similar, whereas others contradict each other. It is not clear whether in such a situation a plausible global relational structure—or map—of these hypotheses emerges in the minds of the involved researchers and, if so, how this map can be reliably reconstructed from the expertise of individuals. Here, we report results of an online survey with 357 experts on invasion biology and several reconstructions of such a map. Using the distance information between hypotheses provided in the survey, the resulting network is essentially random. This finding implies that invasion biologists currently do not have a joint vision how invasion hypotheses are related to each other. However, the pattern of pairwise familiarities between the hypotheses in the survey yields joint‐mentions networks with highly non‐random features. These networks allow us to assign conceptual roles to many of the hypotheses in the field on purely topological grounds. Such hypothesis networks can help everyone interested in research fields to understand their conceptual structure. They can serve as maps of research fields.

This chapter analyses how ethnic transnational identities are manifested and negotiated on the social networking sites used by Latvian migrants. Although migrants as well as other people use various personal media, including Skype, chat apps such as WhatsApp and telephones, social networking sites stand out with the diversity of functions in migrant communication. This includes one-to-one exchanges, group communication and the ability to locate and connect with users who may or may not be familiar offline. We argue that social networking sites and particularly thematic groups on these sites that migrants create and join serve as forums or bulletin boards where they exchange practical information and are able to communicate with other Latvians who live nearby – and that these uses have implications for the communication of identity. The empirical data in the chapter comes from 20 semi-structured interviews with Latvian migrants who live in a variety of countries and were recruited for the study on social networking sites, as well as survey data, all of which were collected within the research project The Emigrant Communities of Latvia: National Identity, Transnational Relations and Diaspora Politics. The results demonstrate that migrant interactions on social networking sites do not necessarily lead to the homogenisation of migrants’ conception of what ‘being a Latvian’ means. The increased ability to maintain associations with diverse online and offline social circles provides a migrant with a variety of identity elements to associate with. As a result, hybrid identities may emerge. A migrant can identify with the host society yet still reject some of its characteristics – and choose Latvian alternatives instead.

Chicken egg yolk is an easily available source for the isolation of sialylglycopeptides (SGP) carrying homogenous biantennary N-glycans. This approach has gained much attention in the last decade since these SGPs can easily be used for the semi-synthesis of glycoconjugates circumventing laborious full-synthetic methodologies. Here we report an optimised, significantly shorter (one day instead of five) and environmentally friendly procedure for the mg scale isolation of SGP using commercially available egg yolk powder. A single chromatographic step following chloroform/methanol precipitation of proteins and lipids yielded desired approximately 200 mg SGP from 250 g egg yolk powder within a day.

•Environmentally friendly procedure for isolation of sialylglycopeptide from Egg yolk powder. •Reduced the protocol from five days down to one.

Understanding the in vivo redox biology of cells is a complex albeit important biological problem. Studying redox processes within living cells without physical disruption or chemical modifications is essential in determining the native redox states of cells. In this study, the previously characterized reduction-oxidation sensitive green fluorescent protein (roGFP2) was used to elucidate the redox changes of the genetically engineered Escherichia coli strain, SHuffle. SHuffle cells were demonstrated to be under constitutive oxidative stress and responding transcriptionally in an OxyR-dependent manner. Using roGFP2 fused to either glutathione (GSH)- or hydrogen peroxide (H2O2)- sensitive proteins (glutaredoxin 1 or Orp1), the cytosolic redox state of both wild type and SHuffle cells based on GSH/GSSG and H2O2 pools was measured. These probes open the path to in vivo studies of redox changes and genetic selections in prokaryotic hosts.

The September 2018, Mw 7.5 Sulawesi earthquake occurring on the Palu-Koro strike-slip fault system was followed by an unexpected localized tsunami. We show that direct earthquake-induced uplift and subsidence could have sourced the observed tsunami within Palu Bay. To this end, we use a physics-based, coupled earthquake–tsunami modeling framework tightly constrained by observations. The model combines rupture dynamics, seismic wave propagation, tsunami propagation and inundation. The earthquake scenario, featuring sustained supershear rupture propagation, matches key observed earthquake characteristics, including the moment magnitude, rupture duration, fault plane solution, teleseismic waveforms and inferred horizontal ground displacements. The remote stress regime reflecting regional transtension applied in the model produces a combination of up to 6 m left-lateral slip and up to 2 m normal slip on the straight fault segment dipping 65∘ East beneath Palu Bay. The time-dependent, 3D seafloor displacements are translated into bathymetry perturbations with a mean vertical offset of 1.5 m across the submarine fault segment. This sources a tsunami with wave amplitudes and periods that match those measured at the Pantoloan wave gauge and inundation that reproduces observations from field surveys. We conclude that a source related to earthquake displacements is probable and that landsliding may not have been the primary source of the tsunami. These results have important implications for submarine strike-slip fault systems worldwide. Physics-based modeling offers rapid response specifically in tectonic settings that are currently underrepresented in operational tsunami hazard assessment.

Background:

The rapidly increasing dissemination of carbapenem-resistant Enterobacteriaceae (CRE) in both humans and animals poses a global threat to public health. However, the transmission of CRE between humans and animals has not yet been well studied.

Objectives:

We investigated the prevalence, risk factors, and drivers of CRE transmission between humans and their backyard animals in rural China.

Methods:

We conducted a comprehensive sampling strategy in 12 villages in Shandong, China. Using the household [residents and their backyard animals (farm and companion animals)] as a single surveillance unit, we assessed the prevalence of CRE at the household level and examined the factors associated with CRE carriage through a detailed questionnaire. Genetic relationships among human- and animal-derived CRE were assessed using whole-genome sequencing–based molecular methods.

Results:

A total of 88 New Delhi metallo-β-lactamases –type carbapenem-resistant Escherichia coli (NDM-EC), including 17 from humans, 44 from pigs, 12 from chickens, 1 from cattle, and 2 from dogs, were isolated from 65 of the 746 households examined. The remaining 12 NDM-EC were from flies in the immediate backyard environment. The NDM-EC colonization in households was significantly associated with a) the number of species of backyard animals raised/kept in the same household, and b) the use of human and/or animal feces as fertilizer. Discriminant analysis of principal components (DAPC) revealed that a large proportion of the core genomes of the NDM-EC belonged to strains from hosts other than their own, and several human isolates shared closely related core single-nucleotide polymorphisms and blaNDM

genetic contexts with isolates from backyard animals.

Conclusions:

To our knowledge, we are the first to report evidence of direct transmission of NDM-EC between humans and animals. Given the rise of NDM-EC in community and hospital infections, combating NDM-EC transmission in backyard farm systems is needed. https://doi.org/10.1289/EHP5251

This study examines paratexts and images in works of primatology. In order to classify generic traits of primatographical publications, all paratexts, images and narrative positions of a large corpus of such monographs were registered. The analysis of these data allows for the determination of three distinct genres: scientific books, illustrated books and autobiographical/popular science books. The paratexts also reveal the strategies employed in the presentation of the books: They address a lay public, underline scientific objectivity or generate authenticity. The form of the texts indicate the audiences that the books address and enact an intimate relationship between non-human primates and human beings. Images showing researchers in close contact with non-human primates as well as paratexts addressing monkeys or calling for their preservation and conservation embed these field studies within a Christian iconography, invoke the life of saints or martyrs and appeal to the empathy of the readership.

The R package emdi enables the estimation of regionally disaggregated indicators using small area estimation methods and includes tools for processing, assessing, and presenting the results. The mean of the target variable, the quantiles of its distribution, the headcount ratio, the poverty gap, the Gini coefficient, the quintile share ratio, and customized indicators are estimated using direct and model-based estimation with the empirical best predictor (Molina and Rao 2010). The user is assisted by automatic estimation of datadriven transformation parameters. Parametric and semi-parametric, wild bootstrap for mean squared error estimation are implemented with the latter offering protection against possible misspecification of the error distribution. Tools for (a) customized parallel computing, (b) model diagnostic analyses, (c) creating high quality maps and (d) exporting the results to Excel and OpenDocument Spreadsheets are included. The functionality of the package is illustrated with example data sets for estimating the Gini coefficient and median income for districts in Austria.

Immunological responses of hibernating mammals are suppressed at low body temperatures, a possible explanation for the devastating effect of the white-nose syndrome on hibernating North American bats. However, European bats seem to cope well with the fungal causative agent of the disease. To better understand the immune response of hibernating bats, especially against fungal pathogens, we challenged European greater mouse-eared bats (Myotis myotis) by inoculating the fungal antigen zymosan. We monitored torpor patterns, immune gene expressions, different aspects of the acute phase response and plasma oxidative status markers, and compared them with sham-injected control animals at 30 min, 48 h and 96 h after inoculation. Torpor patterns, body temperatures, body masses, white blood cell counts, expression of immune genes, reactive oxygen metabolites and non-enzymatic antioxidant capacity did not differ between groups during the experiment. However, zymosan injected bats had significantly higher levels of haptoglobin than the control animals. Our results indicate that hibernating greater mouse-eared bats mount an inflammatory response to a fungal challenge, with only mild to negligible consequences for the energy budget of hibernation. Our study gives a first hint that hibernating European bats may have evolved a hibernation-adjusted immune response in order to balance the trade-off between competent pathogen elimination and a prudent energy-saving regime.

Negative interactions have been suggested as a major barrier for species arriving in a new habitat. More recently, positive interactions drew attention from community assembly theory and invasion science. The invasional meltdown hypothesis (IMH) introduced the idea that positive interactions among non-native species could facilitate one another’s invasion, even increasing their impact upon the native community. Many studies have addressed IMH, but with contrasting results, reflecting various types of evidence on a multitude of scales. Here we use the hierarchy-of-hypotheses (HoH) approach to differentiate key aspects of IMH, organizing and linking empirical studies to sub-hypotheses of IMH. We also assess the level of empirical support for each sub-hypothesis based on the evidence reported in the studies. We identified 150 studies addressing IMH. The majority of studies support IMH, but the evidence comes from studies with different aims and questions. Supporting studies at the community or ecosystem level are currently rare. Evidence is scarce for marine habitats and vertebrates. Few sub-hypotheses are questioned by more than 50% of the evaluated studies, indicating that non-native species do not affect each other’s survival, growth, reproduction, abundance, density or biomass in reciprocal A ↔ B interactions. With the HoH for IMH presented here, we can monitor progress in empirical tests and evidences of IMH. For instance, more tests at the community and ecosystem level are needed, as these are necessary to address the core of this hypothesis.

Climate change and biological invasions are threatening biodiversity and ecosystem services worldwide. It has now been widely acknowledged that climate change will affect biological invasions. A large number of studies have investigated predicted shifts and other changes in the geographic ranges of invasive alien species related to climate change using modeling approaches. Yet these studies have provided contradictory evidence, and no consensus has been reached. We conducted a systematic review of 423 modeling case studies included in 71 publications that have examined the predicted effects of climate change on those species. We differentiate the approaches used in these studies and synthesize their main results. Our results reaffirm the major role of climate change as a driver of invasive alien species distribution in the future. We found biases in the literature both regarding the taxa, toward plants and invertebrates, and the areas of the planet investigated. Despite these biases, we found for the plants and vertebrates studied that climate change will more frequently contribute to a decrease in species range size than an increase in the overall area occupied. This is largely due to oceans preventing terrestrial invaders from spreading poleward. In contrast, we found that the ranges of invertebrates and pathogens studied are more likely to increase following climate change. An important caveat to these findings is that researchers have rarely considered the effects of climate change on transport, introduction success, or the resulting impacts. We recommend closing these research gaps, and propose additional avenues for future investigations, as well as opportunities and challenges for managing invasions under climate change.

Background The Asian bush mosquito Aedes japonicus japonicus is an invasive species native to East Asia and has become established in North America and Europe. On both continents, the species has spread over wide areas. Since it is a potential vector of human and livestock pathogens, distribution and dissemination maps are urgently needed to implement targeted surveillance and control in case of disease outbreaks. Previous distribution models for Europe and Germany in particular focused on climate data. Until now, effects of other environmental variables such as land use and wind remained unconsidered.

Results In order to better explain the distribution pattern of Ae. j. japonicus in Germany at a regional level, we have developed a nested approach that allows for the combination of data derived from (i) a climate model based on a machine-learning approach; (ii) a landscape model developed by means of ecological expert knowledge; and (iii) wind speed data. The approach is based on the fuzzy modelling technique that enables to precisely define the interactions between the three factors and additionally considers uncertainties with regard to the acceptance of certain environmental conditions. The model combines different spatial resolutions of data for Germany and achieves a much higher degree of accuracy than previous published distribution models. Our results reveal that a well-suited landscape structure can even facilitate the occurrence of Ae. j. japonicus in a climatically unsuitable region. Vice versa, unsuitable land use types such as agricultural landscapes and coniferous forests reduce the occurrence probability in climatically suitable regions.

Conclusions The approach has significantly improved existing distribution models of Ae. j. japonicus for the area of Germany. We generated distribution maps with a resolution of 100 × 100 m that can serve as a basis for the design of control measures. All model input data and scripts are open source and freely available, so that the model can easily be applied to other countries or, more generally, to other species.