Application of the weight-of-evidence approach to assess the decline of brown trout ( Salmotrutta ) in Swiss rivers

Abstract.: To assess potential causes for the decline in catch of brown trout and their impaired health status in Switzerland, a 5-year multidisciplinary research project was conducted. Multiple causal hypotheses were postulated and investigated in a variety of laboratory and field studies. We present here the application of a weight-of-evidence analysis to evaluate the results of these studies and to assess the causes for decline in brown trout abundance. Based on human health epidemiological criteria, the method considers the exposure situation, the correlation between causes and effects, specificity of effects, and amelioration due to removal. For our evaluation, we concentrated on four test rivers and included data on fish health and population density, water quality, and habitat parameters. Our results showed that proliferative kidney disease (PKD) caused by a parasite and clinical outbreak supported by other factors is a very probable single parameter for the decline of brown trout abundance at the sites of the test rivers where it occurs. Elevated levels of nitrogen compounds may also be posing a serious risk at several sites, in particular those downstream of sewage treatment plants. Several habitat parameters, such as large width, low percentage of riffles or elevated winter temperatures, were identified as factors likely contributing to impaired health, recruitment, and abundance at single sites. At most sites, more than one factor must be acting jointly to cause the observed decline in brown trout abundanc

Climate and land-use changes affecting river sediment and brown trout in alpine countries—a review

Background, aim, and scope: Catch decline of freshwater fish has been recorded in several countries. Among the possible causes, habitat change is discussed. This article focuses on potentially increased levels of fine sediments going to rivers and their effects on gravel-spawning brown trout. Indications of increased erosion rates are evident from land-use change in agriculture, changes in forest management practices, and from climate change. The latter induces an increase in air and river water temperatures, reduction in permafrost, changes in snow dynamics and an increase in heavy rain events. As a result, an increase in river sediment is likely. Suspended sediment may affect fish health and behaviour directly. Furthermore, sediment loads may clog gravel beds impeding fish such as brown trout from spawning and reducing recruitment rates. To assess the potential impact on fine sediments, knowledge of brown trout reproductive needs and the effects of sediment on brown trout health were evaluated. Approach: We critically reviewed the literature and included results from ongoing studies to answer the following questions, focusing on recent decades and rivers in alpine countries. Have climate change and land-use change increased erosion and sediment loads in rivers? Do we have indications of an increase in riverbed clogging? Are there indications of direct or indirect effects on brown trout from increased suspended sediment concentrations in rivers or from an increase in riverbed clogging? Results: Rising air temperatures have led to more intensive precipitation in winter months, earlier snow melt in spring, and rising snow lines and hence to increased erosion. Intensification of land use has supported erosion in lowland and pre-alpine areas in the second half of the twentieth century. In the Alps, however, reforestation of abandoned land at high altitudes might reduce the erosion risk while intensification on the lower, more easily accessible slopes increases erosion risk. Data from laboratory experiments show that suspended sediments affect the health and behaviour of fish when available in high amounts. Point measurements in large rivers indicate no common lethal threat and suspended sediment is rarely measured continuously in small rivers. However, effects on fish can be expected under environmentally relevant conditions. River bed clogging impairs the reproductive performance of gravel-spawning fish. Discussion: Overall, higher erosion and increased levels of fine sediment going into rivers are expected in future. Additionally, sediment loads in rivers are suspected to have considerably impaired gravel bed structure and brown trout spawning is impeded. Timing of discharge is put forward and is now more likely to affect brown trout spawning than in previous decades. Conclusions: Reports on riverbed clogging from changes in erosion and fine sediment deposition patterns, caused by climate change and land-use change are rare. This review identifies both a risk of increases in climate erosive forces and fine sediment loads in rivers of alpine countries. Increased river discharge and sediment loads in winter and early spring could be especially harmful for brown trout reproduction and development of young life stages. Recently published studies indicate a decline in trout reproduction from riverbed clogging in many rivers in lowlands and alpine regions. However, the multitude of factors in natural complex ecosystems makes it difficult to address a single causative factor. Recommendations and perspectives: Further investigations into the consequences of climate change and land-use change on river systems are needed. Small rivers, of high importance for the recruitment of gravel-spawning fish, are often neglected. Studies on river bed clogging are rare and the few existing studies are not comparable. Thus, there is a strong need for the development of methods to assess sediment input and river bed clogging. As well, studies on the effects to fish from suspended sediments and consequences of gravel beds clogging under natural conditions are urgently neede

Multilingual Workflows in Bullinger Digital: Data Curation for Latin and Early New High German

This paper presents how we enhanced the accessibility and utility of historical linguistic data in the project Bullinger Digital. The project involved the transformation of 3,100 letters, primarily available as scanned PDFs, into a dynamic, fully digital format. The expanded digital collection now includes 12,000 letters, 3,100 edited, 5,400 transcribed, and 3,500 represented through detailed metadata and results from handwritten text recognition. Central to our discussion is the innovative workflow developed for this multilingual corpus. This includes strategies for text normalisation, machine translation, and handwritten text recognition, particularly focusing on the challenges of code-switching within historical documents. The resulting digital platform features an advanced search system, offering users various filtering options such as correspondent names, time periods, languages, and locations. It also incorporates fuzzy and exact search capabilities, with the ability to focus searches within specific text parts, like summaries or footnotes. Beyond detailing the technical process, this paper underscores the project’s contribution to historical research and digital humanities. While the Bullinger Digital platform serves as a model for similar projects, the corpus behind it demonstrates the vast potential for data reuse in historical linguistics. The project exemplifies how digital humanities methodologies can revitalise historical text collections, offering researchers access to and interaction with historical data. This paper aims to provide readers with a comprehensive understanding of our project’s scope and broader implications for the field of digital humanities, highlighting the transformative potential of such digital endeavours in historical linguistic research

Bullingers Briefwechsel zugänglich machen: Stand der Handschriftenerkennung

"Anhand des Briefwechsels Heinrich Bullingers (1504-1575), das rund 10'000 Briefe umfasst, demonstrieren wir den Stand der Forschung in automatisierter Handschriftenerkennung. Es finden sich mehr als hundert unterschiedliche Schreiberhände in den Briefen mit sehr unterschiedlicher Verteilung. Das Korpus ist zweisprachig (Latein/Deutsch) und teilweise findet der Sprachwechsel innerhalb von Abschnitten oder gar Sätzen statt. Auf Grund dieser Vielfalt eignet sich der Briefwechsel optimal als Testumgebung für entsprechende Algorithmen und ist aufschlussreiche für Forschungsprojekte und Erinnerungsinstitutionen mit ähnlichen Problemstellungen. Im Paper werden drei Verfahren gegeneinander gestellt und abgewogen. Im folgenden werde drei Ansätze an dem Korpus getestet, die Aufschlüsse zum Stand und möglichen Entwicklungen im Bereich der Handschriftenerkennung versprechen. Erstens wird mit Transkribus eine etablierte Plattform genutzt, die zwei Engines (HTR+ und PyLaia) anbietet. Zweitens wird mit Hilfe von Data Augmentation versucht die Erkennung mit der state-of-the-art Engine HTRFlor zu verbessern und drittens werden neue Transformer-basierte Modelle (TrOCR) eingesetzt." Ein Beitrag zur 9. Tagung des Verbands "Digital Humanities im deutschsprachigen Raum" - DHd 2023 Open Humanities Open Culture

Inherited variation in immune genes and pathways and glioblastoma risk

To determine whether inherited variations in immune function single-nucleotide polymorphisms (SNPs), genes or pathways affect glioblastoma risk, we analyzed data from recent genome-wide association studies in conjunction with predefined immune function genes and pathways. Gene and pathway analyses were conducted on two independent data sets using 6629 SNPs in 911 genes on 17 immune pathways from 525 glioblastoma cases and 602 controls from the University of California, San Francisco (UCSF) and a subset of 6029 SNPs in 893 genes from 531 cases and 1782 controls from MD Anderson (MDA). To further assess consistency of SNP-level associations, we also compared data from the UK (266 cases and 2482 controls) and the Mayo Clinic (114 cases and 111 controls). Although three correlated epidermal growth factor receptor (EGFR) SNPs were consistently associated with glioblastoma in all four data sets (Mantel–Haenzel P values = 1 × 10−5 to 4 × 10−3), independent replication is required as genome-wide significance was not attained. In gene-level analyses, eight immune function genes were significantly (minP < 0.05) associated with glioblastoma; the IL-2RA (CD25) cytokine gene had the smallest minP values in both UCSF (minP = 0.01) and MDA (minP = 0.001) data sets. The IL-2RA receptor is found on the surface of regulatory T cells potentially contributing to immunosuppression characteristic of the glioblastoma microenvironment. In pathway correlation analyses, cytokine signaling and adhesion–extravasation–migration pathways showed similar associations with glioblastoma risk in both MDA and UCSF data sets. Our findings represent the first systematic description of immune genes and pathways that characterize glioblastoma risk

Measurement of the top quark forward-backward production asymmetry and the anomalous chromoelectric and chromomagnetic moments in pp collisions at √s = 13 TeV

Abstract The parton-level top quark (t) forward-backward asymmetry and the anomalous chromoelectric (d̂ t) and chromomagnetic (μ̂ t) moments have been measured using LHC pp collisions at a center-of-mass energy of 13 TeV, collected in the CMS detector in a data sample corresponding to an integrated luminosity of 35.9 fb−1. The linearized variable AFB(1) is used to approximate the asymmetry. Candidate t t ¯ events decaying to a muon or electron and jets in final states with low and high Lorentz boosts are selected and reconstructed using a fit of the kinematic distributions of the decay products to those expected for t t ¯ final states. The values found for the parameters are AFB(1)=0.048−0.087+0.095(stat)−0.029+0.020(syst),μ̂t=−0.024−0.009+0.013(stat)−0.011+0.016(syst), and a limit is placed on the magnitude of | d̂ t| &lt; 0.03 at 95% confidence level. [Figure not available: see fulltext.

MUSiC : a model-unspecific search for new physics in proton-proton collisions at root s=13TeV

Results of the Model Unspecific Search in CMS (MUSiC), using proton-proton collision data recorded at the LHC at a centre-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 35.9 fb(-1), are presented. The MUSiC analysis searches for anomalies that could be signatures of physics beyond the standard model. The analysis is based on the comparison of observed data with the standard model prediction, as determined from simulation, in several hundred final states and multiple kinematic distributions. Events containing at least one electron or muon are classified based on their final state topology, and an automated search algorithm surveys the observed data for deviations from the prediction. The sensitivity of the search is validated using multiple methods. No significant deviations from the predictions have been observed. For a wide range of final state topologies, agreement is found between the data and the standard model simulation. This analysis complements dedicated search analyses by significantly expanding the range of final states covered using a model independent approach with the largest data set to date to probe phase space regions beyond the reach of previous general searches.Peer reviewe