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ABSTRACT Nanopore direct RNA sequencing (DRS) enables the capture and full-length sequencing of native RNAs, without recoding or amplification bias. Resulting data sets may be interrogated to define the identity and location of chemically modified ribonucleotides, as well as the length of poly(A) tails, on individual RNA molecules. The success of these analyses is highly dependent on the provision of high-resolution transcriptome annotations in combination with workflows that minimize misalignments and other analysis artifacts. Existing software solutions for generating high-resolution transcriptome annotations are poorly suited to small gene-dense genomes of viruses due to the challenge of identifying distinct transcript isoforms where alternative splicing and overlapping RNAs are prevalent. To resolve this, we identified key characteristics of DRS data sets that inform resulting read alignments and developed the nanopore guided annotation of transcriptome architectures (NAGATA) software package (https://github.com/DepledgeLab/NAGATA). We demonstrate, using a combination of synthetic and original DRS data sets derived from adenoviruses, herpesviruses, coronaviruses, and human cells, that NAGATA outperforms existing transcriptome annotation software and yields a consistently high level of precision and recall when reconstructing both gene sparse and gene-dense transcriptomes. Finally, we apply NAGATA to generate the first high-resolution transcriptome annotation of the neglected pathogen human adenovirus type F41 (HAdV-41) for which we identify 77 distinct transcripts encoding at least 23 different proteins.IMPORTANCEThe transcriptome of an organism denotes the full repertoire of encoded RNAs that may be expressed. This is critical to understanding the biology of an organism and for accurate transcriptomic and epitranscriptomic-based analyses. Annotating transcriptomes remains a complex task, particularly in small gene-dense organisms such as viruses which maximize their coding capacity through overlapping RNAs. To resolve this, we have developed a new software nanopore guided annotation of transcriptome architectures (NAGATA) which utilizes nanopore direct RNA sequencing (DRS) datasets to rapidly produce high-resolution transcriptome annotations for diverse viruses and other organisms.

Abstract Extreme environments on Earth host a large diversity of microbial life. Bacteria, archaea, and fungi are able to survive under one or several extreme conditions including extreme ranges of temperature, pressure, pH or salinity. Despite extensive research on extremophilic microorganisms, a relatively unexplored frontier within the study of the deep biosphere is the survey of the diversity of microorganisms inhabiting deep geothermal reservoirs used for energy production. These sites offer unique access to investigate life in the deep biosphere. The conditions in these reservoirs are often within the range of the known limits of life, which makes them a suitable habitat for various extremophilic microorganisms. Moreover, microbial-driven processes such as microbially induced scaling or corrosion can decrease the efficacy of geothermal power plant systems. The present review summarizes the current knowledge and uncertainties surrounding microbial life in deep geothermal reservoirs. As the knowledge in deep geothermal fluids is still scarce, the microbial diversity in analogous environments, such as surface geothermal springs, deep-sea hydrothermal vents or deep subsurface environments, is also summarized here. The high diversity of microorganisms inhabiting these analogous environments suggests that deep geothermal fluids may host an unsuspected microbial diversity. Moreover, the challenges associated to the study of microorganisms in geothermal fluids are reviewed. These include notably challenges linked to sampling, DNA extraction from low biomass samples, DNA amplification and sequencing of unknown communities, and biases induced by comparison of the sequences obtained to reference databases. Such biases are even stronger concerning fungi and archaea, as specific databases are less extensive than those for bacteria. A broader knowledge on microorganisms in deep geothermal fluids may not only allow to reduce the negative impact of microbial activity in geothermal power plants, but could also provide new insights into the evolution of microorganisms and their survival in extreme environments.

IntroductionRecent reports have questioned the blood impermeability of the novel frozen elephant trunk (FET) device E-vita Open NEO© (EO-NEO). Therefore, standardized in vitro bleeding tests using porcine heparinized blood were performed, as well as stress testing on the blood tightness of the collar suture line, to investigate this observation.Material and methodsEO-NEO prostheses were examined in vitro for blood permeability in three test series. Initially, antegrade perfusion with heparinized porcine blood [activated clotting time (ACT) of 500 s, with a 60 min duration] was performed, followed by ante/retrograde testing via the EO-NEO side port. Testing of the collar suture line under a tension of 10 Newton (N) within a suspension device (blood pressure 120 mmHg, ACT of 560 s, 1 min duration) was carried out with the suture material force fiber white (FFWs) yarn, using standard fixation (5 stitches/cm), FFWh yarn in hemostatic fixation (15 stitches/cm), and flow weave yarn (FWYh).ResultsBlood permeability testing of EO-NEO through the prosthetic lumen or via the side port demonstrated minor leakage without statistical difference between the standard and hemostatic suture lines or suture materials used, or positioning on the crimped or tapered portion (p > 0.05). The specific collar anastomosis testing demonstrated leakage volumes of 140 ml/min for FFWs vs. 16 ml/min for FFWh (p = 0.02), vs. 9 ml/min with the FWYh (p = 0.01).ConclusionDifferent blood leakage tests showed minimal oozing and no difference in blood loss through the fabric and different collar suture lines, but unphysiological pressurized retrograde perfusion of the collar region showed significantly less leakage using FWYh and FFWh, prompting production modification of EO-NEO. Clinical results confirmed low blood loss using this novel FET device.

This study explored the decision-making processes of soldiers as they evaluated scenarios containing information offering various levels of certainty. Soldiers with different levels of experience read scenarios that presented potential threats and then identified the priority threat, their confidence in this identification, and the cues they used to identify priority threats. Soldiers then searched for additional scenario-relevant information and modified their reports if their assessments changed. Compared with inexperienced soldiers, experienced soldiers reported a greater number of priority threats and informative cues and were more likely to search additional topics that matched details in their initial assessments. High certainty scenarios yielded more identified threats, more cues, and higher confidence in initial reports. Soldiers' initial assessments rarely changed after additional information searches, but when they did, they were associated with low initial confidence.

Die Evolution der Lebewesen (biologische Evolution) ist geprägt von einem ewigen Kampf mit zerstörerischen Folgen, ohne die es keinen Fortschritt gäbe. Es ist der kanalisierende Evolutionsfaktor der Selektion, der, geprägt vom Ökonomischen Prinzip (bzw. Optimierungsprinzip), vor dessen Hintergrund durch den Konkurrenzkampf vielfach ein Massensterben der weniger fitten (d.h. der weniger passenden) Nachkommen resultiert. Kriegsschauplätze im Kampf ums Dasein sind beispielsweise bei Blütenpflanzen die Narben und Griffel eines oder mehrerer Fruchtknoten in einer Blüte (Pollenschlauchkonkurrenz) sowie später die Keimplätze der Samen (Keimlingskonkurrenz), bei Tieren sind es die Balz- und Paarungsplätze und manchmal auch die Brutplätze. An Hand einiger Beispiele werden auf die Kampf-„Strategien“ bei Pflanzen und Tieren eingegangen. Dabei stellen die Autoren ihre neuesten Ergebnisse über das Paarungs- und Brutverhalten zweier Hautflügler- (Hymenopteren-) Arten auf Sizilien vor, nämlich einer Schneckenhausbiene sowie einer besonders großen Dolchwespe. Ähnlich unserem menschlichen Dasein haben sich, natürlich lange zuvor, während der Evolution zwischen Organismen „friedliche Koexistenzen“, Gildenbildung (beispielsweise zur Steigerung einer Bestäubungseffizienz), Mutualismen (gegenseitiges Geben und Nehmen) und enge Symbiosen eingestellt. Aber auch bei Mutualismen kann es zu kriegerischen Auseinandersetzungen kommen: gewisse Pflanzen-Arten der Tropen können sich ein „Söldnerheer“ von Ameisen „leisten“, die beispielsweise die Aufgabe übernehmen, umgebende beschattende Bäume zu entblättern. Im Gegenzug erhalten die Ameisen von den sehr lichtbedürftigen Pflanzen Wohnraum und Futter. Ein abschließendes Kapitel stellt Fragen zu einem dauerhaften Frieden, dem Traum einer friedliebenden menschlichen Gesellschaft.

BackgroundDysregulation of the immune system in amyotrophic lateral sclerosis (ALS) includes changes in T-cells composition and infiltration of T cells in the brain and spinal cord. Recent studies have shown that cytotoxic T cells can directly induce motor neuron death in a mouse model of ALS and that T cells from ALS patients are cytotoxic to iPSC-derived motor neurons from ALS patients. Furthermore, a clonal expansion to unknown epitope(s) was recently found in familial ALS and increased peripheral and intrathecal activation of cytotoxic CD8+ T cells in sporadic ALS.ResultsHere, we show an increased activation of peripheral T cells from patients with sporadic ALS by IL-2 treatment, suggesting an increase of antigen-experienced T cells in ALS blood. However, a putative antigen for T-cell activation in ALS has not yet been identified. Therefore, we investigated if peptides derived from TDP-43, a key protein in ALS pathogenesis, can act as epitopes for antigen-mediated activation of human T cells by ELISPOT and flow cytometry. We found that TDP-43 peptides induced only a weak MHCI or MHCII-restricted activation of both naïve and antigen-experienced T cells from healthy controls and ALS patients. Interestingly, we found less activation in T cells from ALS patients to TDP-43 and control stimuli. Furthermore, we found no change in the levels of naturally occurring auto-antibodies against full-length TDP-43 in ALS.ConclusionOur data suggests a general increase in antigen-experienced T cells in ALS blood, measured by in-vitro culture with IL-2 for 14 days. Furthermore, it suggests that TDP-43 is a weak autoantigen.

This paper presents a critical review of key ethical issues raised by the emergence of mental health chatbots. Chatbots use varying degrees of artificial intelligence and are increasingly deployed in many different domains including mental health. The technology may sometimes be beneficial, such as when it promotes access to mental health information and services. Yet, chatbots raise a variety of ethical concerns that are often magnified in people experiencing mental ill-health. These ethical challenges need to be appreciated and addressed throughout the technology pipeline. After identifying and examining four important ethical issues by means of a recognised ethical framework comprised of five key principles, the paper offers recommendations to guide chatbot designers, purveyers, researchers and mental health practitioners in the ethical creation and deployment of chatbots for mental health.

Abstract Dissolved organic matter (DOM) can be found in a variety of deep subsurface environments such as sedimentary basins, oil fields and mines. However, the origin, composition and fate of DOM within deep geothermal reservoirs used for energy production is relatively unknown. With well depths reaching a few kilometers, these sites give access to investigate deep subsurface environments. Natural DOM as well as artificial DOM (e.g., from chemical scaling inhibitors) might serve as nutrients for microorganisms or affect chemical properties of the fluids by complexation. Its composition might reveal hydraulic connections to organic-rich strata, giving insights to the fluid flow within the reservoir. This review presents an overview of a total of 143 fluid samples from 22 geothermal sites (mainly central Europe), from the literature and compiling data to address the importance of DOM in geothermal fluids and how it might affect geothermal operation. The environmental conditions of the sites included varied greatly. Temperatures range from 34 to $$200\,^{\circ }\hbox {C}$$ 200 ∘ C , depths from 850 to 5000 m, chloride content from 0.1 to $$160\,{\hbox {g}\,\hbox {L}^{-1}}$$ 160 g L - 1 , and dissolved organic carbon (DOC) concentrations from 0.1 to $$30.1\,{\hbox {g}\,\hbox {L}^{-1}}$$ 30.1 g L - 1 . The DOC concentrations were found to be generally lower in the fluids with temperatures below $$80\,{}^{\circ }\hbox {C}$$ 80 ∘ C . DOC concentrations were higher in fluids with temperatures above $$80\,{}^{\circ }\hbox {C}$$ 80 ∘ C and showed a decrease towards $$200\,{}^{\circ }\hbox {C}$$ 200 ∘ C . Microbial degradation might be the main driver for low DOC concentrations in the lower temperature range (below $$80\,{}^{\circ }\hbox {C}$$ 80 ∘ C ), while thermal degradation likely accounts for the decline in DOC in the temperature region between $$80\,{}^{\circ }\hbox {C}$$ 80 ∘ C and $$200\,{}^{\circ }\hbox {C}$$ 200 ∘ C . This review shows that DOM can be found in a variety of geothermal reservoirs and that it could be an additional essential tool to better understand fluid chemistry and reservoir conditions, and to optimize geothermal operation.

Es sind die klassischen vier Elemente der großen griechischen Philosophen, die – entmythologisiert – sich in heutiger Sicht als Schauplätze organismischer Evolution präsentieren. Mit ihren unterschiedlichen physikalischen und chemischen Qualitäten bilden sie die abiotischen Umweltfaktoren, an die sich Organismen durch zufällige genetische Veränderungen im Laufe der Evolution anpassen können. Andererseits können die ständig sich ändernden Umweltfaktoren immer wieder Organismenarten zum Aussterben zwingen. Wasser ist das Element, in dem das Leben entstand und sehr lange Zeit auch das alleinige Substrat für Pflanzen war. Die ältesten Landpflanzen-Fossilien kennen wir aus dem Oberen Silur, sind also mehr als 400 Millionen Jahre alt. Sie hatten allgemein dasselbe Bauprinzip, nämlich im Querschnitt runde Stiele, die sich mehrfach räumlich-gabelig verzweigen und einen sog. Telomstand bilden, von dem sich im Verlauf des Devons durch unterschiedliche Formveränderungen (sogenannte Elementarprozesse) u.a. die Bärlappe und Wedelfarne ableiten lassen, die im Karbon ihren Höhepunkt erreichten. Mit dem Landgang der Pflanzen erobern sie gleichzeitig das Element Luft. Unterschiedliche Feuchtigkeitsgrade und Temperaturen dieses Elements „zwingen“ die Pflanzen (aufgrund zufälliger Erbänderungen und anschließender dem Optimierungsprinzip gehorchender Selektion) zu unterschiedlichsten Anpassungen. Kompromisse zwischen „Hungern“ und „Dursten“ finden sich vielfach an ariden Wuchsorten. Das meist zerstörerische Element Feuer bildet als „Feuerball“ Sonne eine für das Pflanzenleben unabdingbare Lichtquelle. Sogar das offene Feuer kann von Pflanzen in Gebieten regelmäßig auftretender Buschbrände zur Samenausbreitung in genialer Weise genutzt werden. Die „Verschmutzung“ der genannten Elemente, insbesondere des Wassers, der Luft und des Bodens, oft verursacht von ethisch entkernten Großkonzernen, stellt uns heutzutage vor fast unüberwindbare Probleme (Klimawandel, Insektensterben, Rückgang der Biodiversität insgesamt, „versaute“ Nahrungsmittel).

Gleichgültig, ob als aus der Organismischen Evolution hervorgegangenes oder vom Menschen hergestelltes Produkt, wenn es den Anspruch optimaler Funktionalität bei gleichzeitiger Sparsamkeit erhebt, wird ihm im Sprachgebrauch vielfach das Adjektiv „intelligent“ verliehen. Mit „intelligent“ ist natürlich nur der Urheber gemeint: Im einen Fall die Evolution mit ihrem intelligenten Spiel mit den Zufällen und der Auslese, im anderen die Kreativität des „Säugetiers“ Homo sapiens. Bemerkenswert ist eine gewisse Parallelität in Bau und Funktionalität unabhängig voneinander entstandener Geräte und Systeme. Oder aber von der Natur vorgegebene Konstruktionen dienen als Vorbild, was zur Bionik als eigene Wissenschaftsdisziplin geführt hat. Aus der unüberschaubaren Fülle intelligenter Problemlösungen sind in diesem Artikel einige wenige herausgegriffen. Sie betreffen zunächst Gebrauchsgegenstände aus dem Alltag. Es sind z. B. Salzstreuer, die fürs Frühstücksei geeignet sind, Haftvorrichtungen wie Saugnäpfe, klebende Haftscheiben und – allen voran – Klettverschlüsse. Im Hinblick auf die Stabilität von Oberflächen, besonders was die Kratzfestigkeit betrifft, können verschiedene Möglichkeiten bei Pflanzen aufgezeigt werden. Eine mechanische Stabilität bei starker Krafteinwirkung z. B. durch Wind oder Gewichtsbelastung liefert statt einer ebenen Fläche eine gefaltete, wie sie uns bei den Palmblättern begegnet. Faltstrukturen zu einem Zylinder geschlossen ermöglichen eine beträchtliche Volumenveränderung bei gleichbleibender Oberfläche; ein solcher Blasebalg- bzw. Ziehharmonika-Effekt gestattet Rippenkakteen eine Wasseraufnahme (bei Regen) bzw. einen Wasserverlust (durch Verdunstung), ohne dass es zu Gewebespannungen kommt. Leichtbauweise und doch Stabilität zeigen uns die riesigen Schwimmblätter der Victoria-Seerose auf. Mehr Sicherheit bei einer Havarie eines Schiffes durch eine möglichst hohe Anzahl dicht verschlossener Schotten können Techniker von schwimmenden Samen lernen. Mehr Sicherheit beim Hausbau in Erdbebengebieten lernen Architekten von Bäumen mit Brettwurzeln und von Grashalmen. Tarnungen zum Schutz oder Angriff reichen bei Insekten und Spinnen bis zur höchsten Perfektion. Selbst Blumen täuschen und betrügen durch raffinierte (= intelligente) Angepasstheiten an bestimmte Verhaltensmuster von Insekten zum Zwecke der Bestäubung. Fazit: Evolution ist intelligent, kennt aber keine Ethik!

Abstract In many species, dispersal is decisive for survival in a changing climate. Simulation models for population dynamics under climate change thus need to account for this factor. Moreover, large numbers of species inhabiting agricultural landscapes are subject to disturbances induced by human land use. We included dispersal in the HiLEG model that we previously developed to study the interaction between climate change and agricultural land use in single populations. Here, the model was parameterized for the large marsh grasshopper (LMG) in cultivated grasslands of North Germany to analyze (1) the species development and dispersal success depending on the severity of climate change in subregions, (2) the additional effect of grassland cover on dispersal success, and (3) the role of dispersal in compensating for detrimental grassland mowing. Our model simulated population dynamics in 60‐year periods (2020–2079) on a fine temporal (daily) and high spatial (250 × 250 m2) scale in 107 subregions, altogether encompassing a range of different grassland cover, climate change projections, and mowing schedules. We show that climate change alone would allow the LMG to thrive and expand, while grassland cover played a minor role. Some mowing schedules that were harmful to the LMG nevertheless allowed the species to moderately expand its range. Especially under minor climate change, in many subregions dispersal allowed for mowing early in the year, which is economically beneficial for farmers. More severe climate change could facilitate LMG expansion to uninhabited regions but would require suitable mowing schedules along the path. These insights can be transferred to other species, given that the LMG is considered a representative of grassland communities. For more specific predictions on the dynamics of other species affected by climate change and land use, the publicly available HiLEG model can be easily adapted to the characteristics of their life cycle.

Striving for more robust and natural control of multi-fingered hand prostheses, we are studying electrical impedance tomography (EIT) as a method to monitor residual muscle activations. Previous work has shown promising results for hand gesture recognition, but also lacks generalization across multiple sessions and users. Thus, the present paper aims for a detailed analysis of an existing EIT dataset acquired with a 16-electrode wrist band as a prerequisite for further improvements of machine learning results on this type of signal. The performed t-SNE analysis confirms a much stronger inter-session and inter-user variance compared to the expected in-class variance. Additionally, we observe a strong drift of signals within a session. To handle these challenging problems, we propose new machine learning architectures based on deep learning, which allow to separate undesired from desired variation and thus significantly improve the classification accuracy. With these new architectures we increased cross-session classification accuracy on 12 gestures from 19.55 to 30.45%. Based on a fundamental data analysis we developed three calibration methods and thus were able to further increase cross-session classification accuracy to 39.01, 55.37, and 56.34%, respectively.