Effects of Endotoxin and Catecholamines on Hepatic Mitochondrial Respiration

Catecholamines are frequently used in sepsis, but their interaction with mitochondrial function is controversial. We incubated isolated native and endotoxin-exposed swine liver mitochondria with either dopamine, dobutamine, noradrenaline or placebo for 1h. Mitochondrial State 3 and 4 respiration and their ratio (RCR) were determined for respiratory chain complexes I, II and IV. All catecholamines impaired glutamate-dependent RCR (p = 0.046), predominantly in native mitochondria. Endotoxin incubation alone induced a decrease in glutamate-dependent RCR compared to control samples (p = 0.002). We conclude that catecholamines and endotoxin impair the efficiency of mitochondrial complex I respiration in vitr

Effects of prolonged endotoxemia on liver, skeletal muscle and kidney mitochondrial function

INTRODUCTION: Sepsis may impair mitochondrial utilization of oxygen. Since hepatic dysfunction is a hallmark of sepsis, we hypothesized that the liver is more susceptible to mitochondrial dysfunction than the peripheral tissues, such as the skeletal muscle. We studied the effect of prolonged endotoxin infusion on liver, muscle and kidney mitochondrial respiration and on hepatosplanchnic oxygen transport and microcirculation in pigs. METHODS: Twenty anesthetized pigs were randomized to receive either endotoxin or saline infusion for 24 hours. Muscle, liver and kidney mitochondrial respiration was assessed. The cardiac output (thermodilution) and the carotid, superior mesenteric and kidney arterial, portal venous (ultrasound Doppler) and microcirculatory blood flow (laser Doppler) were measured, and systemic and regional oxygen transport and lactate exchange were calculated. RESULTS: Endotoxin infusion induced hyperdynamic shock and impaired the glutamate-dependent and succinate-dependent mitochondrial respiratory control ratio in the liver (glutamate, median (range) endotoxemia 2.8 (2.3–3.8) vs controls 5.3 (3.8–7.0); P < 0.001; succinate, endotoxemia 2.9 (1.9–4.3) vs controls 3.9 (2.6–6.3), P = 0.003). While the ADP added/oxygen consumed ratio was reduced with both substrates, the maximal ATP production was impaired only in the succinate-dependent respiration. Hepatic oxygen consumption and extraction, and the liver surface laser Doppler blood flow remained unchanged. Glutamate-dependent respiration in the muscle and kidney was unaffected. CONCLUSION: Endotoxemia reduces the efficiency of hepatic mitochondrial respiration but neither skeletal muscle nor kidney mitochondrial respiration, independent of regional and microcirculatory blood flow changes

Two-photon excitation with finite pulses unlocks pure dephasing-induced degradation of entangled photons emitted by quantum dots

Semiconductor quantum dots have emerged as an especially promising platform for the generation of polarization-entangled photon pairs. However, it was demonstrated recently that the two-photon excitation scheme employed in state-of-the-art experiments limits the achievable degree of entanglement by introducing which-path information. In this work, the combined impact of two-photon excitation and longitudinal acoustic phonons on photon pairs emitted by strongly-confining quantum dots is investigated. It is found that phonons further reduce the achievable degree of entanglement even in the limit of vanishing temperature due to phonon-induced pure dephasing and phonon-assisted one-photon processes, which increase the reexcitation probability. In addition, the degree of entanglement, as measured by the concurrence, decreases with rising temperature and/or pulse duration, even if the excitonic fine-structure splitting is absent and when higher electronic states are out of reach. Furthermore, in the case of finite fine-structure splittings, phonons enlarge the discrepancy in concurrence for different laser polarizations.Comment: 10 pages, 3 figure

Evaluation of the biomarker candidate MFAP4 for non-invasive assessment of hepatic fibrosis in hepatitis C patients

$\textbf {Background:}$ The human microfibrillar-associated protein 4 (MFAP4) is located to extracellular matrix fibers and plays a role in disease-related tissue remodeling. Previously, we identified MFAP4 as a serum biomarker candidate for hepatic fibrosis and cirrhosis in hepatitis C patients. The aim of the present study was to elucidate the potential of MFAP4 as biomarker for hepatic fibrosis with a focus on the differentiation of no to moderate (F0–F2) and severe fibrosis stages and cirrhosis (F3 and F4, Desmet-Scheuer scoring system). $\textbf {Methods:}$ MFAP4 levels were measured using an AlphaLISA immunoassay in a retrospective study including $\it n$ = 542 hepatitis C patients. We applied a univariate logistic regression model based on MFAP4 serum levels and furthermore derived a multivariate model including also age and gender. Youden-optimal cutoffs for binary classification were determined for both models without restrictions and considering a lower limit of 80% sensitivity (correct classification of F3 and F4), respectively. To assess the generalization error, leave-one-out cross validation (LOOCV ) was performed. $\textbf {Results:}$ MFAP4 levels were shown to differ between no to moderate fibrosis stages F0–F2 and severe stages (F3 and F4) with high statistical significance ($\it t$ test on log scale, $\it p$ value $<2.2·10^{-16}$). In the LOOCV, the univariate classification resulted in 85.8% sensitivity and 54.9% specificity while the multivariate model yielded 81.3% sensitivity and 61.5% specificity (restricted approaches). $\textbf {Conclusions:}$ We confirmed the applicability of MFAP4 as a novel serum biomarker for assessment of hepatic fibrosis and identification of high-risk patients with severe fibrosis stages in hepatitis C. The combination of MFAP4 with existing tests might lead to a more accurate non-invasive diagnosis of hepatic fibrosis and allow a cost-effective disease management in the era of new direct acting antivirals

Antimicrobial stewardship, therapeutic drug monitoring and infection management in the ICU: results from the international A- TEAMICU survey

Abstract: Background: Severe infections and multidrug-resistant pathogens are common in critically ill patients. Antimicrobial stewardship (AMS) and therapeutic drug monitoring (TDM) are contemporary tools to optimize the use of antimicrobials. The A-TEAMICU survey was initiated to gain contemporary insights into dissemination and structure of AMS programs and TDM practices in intensive care units. Methods: This study involved online survey of members of ESICM and six national professional intensive care societies. Results: Data of 812 respondents from mostly European high- and middle-income countries were available for analysis. 63% had AMS rounds available in their ICU, where 78% performed rounds weekly or more often. While 82% had local guidelines for treatment of infections, only 70% had cumulative antimicrobial susceptibility reports and 56% monitored the quantity of antimicrobials administered. A restriction of antimicrobials was reported by 62%. TDM of antimicrobial agents was used in 61% of ICUs, mostly glycopeptides (89%), aminoglycosides (77%), carbapenems (32%), penicillins (30%), azole antifungals (27%), cephalosporins (17%), and linezolid (16%). 76% of respondents used prolonged/continuous infusion of antimicrobials. The availability of an AMS had a significant association with the use of TDM. Conclusions: Many respondents of the survey have AMS in their ICUs. TDM of antimicrobials and optimized administration of antibiotics are broadly used among respondents. The availability of antimicrobial susceptibility reports and a surveillance of antimicrobial use should be actively sought by intensivists where unavailable. Results of this survey may inform further research and educational activities

Sektionskonzept Meta(daten), Terminologien und Provenienz zur Einrichtung einer Sektion im Verein Nationale Forschungsdateninfrastruktur (NFDI) e.V

Die Sektion befasst sich mit den Themenbereichen (Meta)daten, Terminologien und Provenienz. Aufgabenfelder der Sektion umfassen organisatorische Aspekte (Kollaboration, Wissenstransfer), inhaltliche Aspekte (z.B. Modellierung/Ontologien) und infrastrukturelle Perspektiven (Entwicklung von Standards / Basisdiensten). Eine der wesentlichen Aufgaben der Sektion wird sein, die Arbeit der NFDI-Konsortien im Bereich (Meta)daten, Terminologien und Provenienz entlang der FAIR Kriterien wechselseitig sichtbar zu machen, zu harmonisieren und nachnutzbar zu machen. Hierbei wird die Sektion in enger Rückkopplung mit den Sektionen “Common Infrastructures” sowie “Ethical, Social and Legal Aspects” insbesondere die Themenbereiche Terminologien und Provenienz bearbeiten. (1) Im Themenbereich Metadaten und Forschungsdaten - im Folgenden kurz (Meta)daten - beschäftigt sich die Sektion mit Fragen zur (Meta-)daten-Harmonisierung, Auffindbarkeit von Daten, allgemeine Daten- und Metadaten-Standards mit Blick auf ein mögliches NFDI-Kernmetadatenformat sowie Formatumwandlungen und Persistent-Identifier-Systemen. (2) Im Themenbereich Terminologien beschäftigt sich die Sektion mit community- und disziplinenübergreifenden Definitionen von Top-Level Ontologien und Mappings von Ontologien sowie Best Practices zur Modellierung von Terminologien, Vokabularen und Ontologien sowie darauf aufbauenden Diensten zur Datenintegration (z.B. Terminology Service, Knowledge Graphs etc.). (3) Im Themenbereich Provenienz befasst sich die Sektion mit rechtlichen, technischen und kulturellen Aspekten des Entstehungskontextes von (Meta)daten (z.B. im Rahmen von Experimenten, Laborbüchern, Digitalisierungsprozessen etc.) und entwirft Vorschläge für einheitliche und nachvollziehbare Dokumentationsverfahren zur Beantwortung der Fragen nach dem was, wo, wann, wer, wie und warum der Datenerzeugung und Datenprozessierung. Hierbei entwickelt die Sektion Empfehlungen für die Abbildung der Provenienz in einem möglichen NFDI-Kernmetadatenformat

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs

The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3-prime untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3-prime polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and 3-prime UTR re-annotation (including extension of one 3-prime UTR by 5.9 kb); (2) disentangling of gene expression in complex regions; (3) clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental dataComment: 44 pages, 9 figure

NFDI4Culture - Consortium for research data on material and immaterial cultural heritage

Digital data on tangible and intangible cultural assets is an essential part of daily life, communication and experience. It has a lasting influence on the perception of cultural identity as well as on the interactions between research, the cultural economy and society. Throughout the last three decades, many cultural heritage institutions have contributed a wealth of digital representations of cultural assets (2D digital reproductions of paintings, sheet music, 3D digital models of sculptures, monuments, rooms, buildings), audio-visual data (music, film, stage performances), and procedural research data such as encoding and annotation formats. The long-term preservation and FAIR availability of research data from the cultural heritage domain is fundamentally important, not only for future academic success in the humanities but also for the cultural identity of individuals and society as a whole. Up to now, no coordinated effort for professional research data management on a national level exists in Germany. NFDI4Culture aims to fill this gap and create a usercentered, research-driven infrastructure that will cover a broad range of research domains from musicology, art history and architecture to performance, theatre, film, and media studies. The research landscape addressed by the consortium is characterized by strong institutional differentiation. Research units in the consortium's community of interest comprise university institutes, art colleges, academies, galleries, libraries, archives and museums. This diverse landscape is also characterized by an abundance of research objects, methodologies and a great potential for data-driven research. In a unique effort carried out by the applicant and co-applicants of this proposal and ten academic societies, this community is interconnected for the first time through a federated approach that is ideally suited to the needs of the participating researchers. To promote collaboration within the NFDI, to share knowledge and technology and to provide extensive support for its users have been the guiding principles of the consortium from the beginning and will be at the heart of all workflows and decision-making processes. Thanks to these principles, NFDI4Culture has gathered strong support ranging from individual researchers to highlevel cultural heritage organizations such as the UNESCO, the International Council of Museums, the Open Knowledge Foundation and Wikimedia. On this basis, NFDI4Culture will take innovative measures that promote a cultural change towards a more reflective and sustainable handling of research data and at the same time boost qualification and professionalization in data-driven research in the domain of cultural heritage. This will create a long-lasting impact on science, cultural economy and society as a whole