Monitoring of Deep Fluids in the Nankai Subduction Complex, SE offshore Japan

Fluids are of great importance for various geological processes. To improve our understanding of fluid generation and migration in the Nankai Trough subduction complex, SE offshore Japan, this PhD thesis uses different borehole monitoring techniques that were applied in the course of the Integrated Ocean Drilling Program Nankai Trough Seismogenic Zone Experiment. Long-term monitoring with a SmartPlug borehole observatory was conducted at a splay fault system cutting through the accretionary prism. Further landward, beneath the Kumano forearc basin, information about in situ composition of fluids was obtained by drilling mud gas monitoring and sampling during riser drilling with drilling vessel Chikyu. Long-term pressure data revealed that the fluid pressure data is affected by a wide range of natural signals. Tidal noise was used to estimate hydrogeological fault zone properties. Beneath the Kumano forearc basin, fluid migration and mixing in the accretionary prism is supported by analyses of drilling mud gas focusing on noble gas isotopes and hydrocarbon gas composition. Fluid pathways and mechanisms of fluid migration remain unclear

Micro RNAs of Epstein-Barr Virus Promote Cell Cycle Progression and Prevent Apoptosis of Primary Human B Cells

Cellular and viral microRNAs (miRNAs) are involved in many different processes of key importance and more than 10,000 miRNAs have been identified so far. In general, relatively little is known about their biological functions in mammalian cells because their phenotypic effects are often mild and many of their targets still await identification. The recent discovery that Epstein-Barr virus (EBV) and other herpesviruses produce their own, barely conserved sets of miRNAs suggests that these viruses usurp the host RNA silencing machinery to their advantage in contrast to the antiviral roles of RNA silencing in plants and insects. We have systematically introduced mutations in EBV's precursor miRNA transcripts to prevent their subsequent processing into mature viral miRNAs. Phenotypic analyses of these mutant derivatives of EBV revealed that the viral miRNAs of the BHRF1 locus inhibit apoptosis and favor cell cycle progression and proliferation during the early phase of infected human primary B cells. Our findings also indicate that EBV's miRNAs are not needed to control the exit from latency. The phenotypes of viral miRNAs uncovered by this genetic analysis indicate that they contribute to EBV-associated cellular transformation rather than regulate viral genes of EBV's lytic phase

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Beobachtung tiefer Fluide im Nankai Subduktionskomplex, südöstlich vor der Küste Japans

Fluids are of great importance for various geological processes. To improve our understanding of fluid generation and migration in the Nankai Trough subduction complex, SE offshore Japan, this PhD thesis uses different borehole monitoring techniques that were applied in the course of the Integrated Ocean Drilling Program Nankai Trough Seismogenic Zone Experiment. Long-term monitoring with a SmartPlug borehole observatory was conducted at a splay fault system cutting through the accretionary prism. Further landward, beneath the Kumano forearc basin, information about in situ composition of fluids was obtained by drilling mud gas monitoring and sampling during riser drilling with drilling vessel Chikyu. Long-term pressure data revealed that the fluid pressure data is affected by a wide range of natural signals. Tidal noise was used to estimate hydrogeological fault zone properties. Beneath the Kumano forearc basin, fluid migration and mixing in the accretionary prism is supported by analyses of drilling mud gas focusing on noble gas isotopes and hydrocarbon gas composition. Fluid pathways and mechanisms of fluid migration remain unclear

Mantle-derived fluids in the Nankai Trough Kumano forearc basin

Abstract Noble gas abundance and isotope data from 12 drilling mud gas samples obtained during IODP Expeditions 338 and 348 provide new insights on fluid origin and fluid migration in the inner accretionary prism below the Kumano forearc basin offshore SE Japan. The samples originate from three adjoining boreholes (C0002F, C0002N and C0002P) spanning depths between 950 and 3050 meters below sea floor (mbsf) and are composed of air and variable contributions of mantle-derived and crustal fluids. Air-corrected 3He/4He ratios of samples from Exp. 338 fall between 0.44 ± 0.24 Ra and 3.26 ± 0.28 Ra. Samples #1400 and #1800 (sample number denotes depth in mbsf) are more influenced by radiogenic helium (1.33 ± 0.34 Ra resp. 0.44 ± 0.24 Ra), whereas the air-free helium isotopic composition of sample #950 is clearly higher (3.26 ± 0.28 Ra). Enhanced radon activity around 950 mbsf, 1100 mbsf, 1400 mbsf, and 1800 mbsf suggests active flow of fluids at these depths. The helium isotopic composition of two other samples (#1700 and #1850) collected during Exp. 338 and of all samples obtained during the 1-year-later Exp. 348 are less variable (1.74–2.46 Ra with a mean 3He/4He ratio of ~ 2.4 Ra) and no radon anomalies were observed during sampling. For these samples, we assume migration by diffusive flow of helium-bearing fluids through sediments of the accretionary prism. In contrast, elevated radon activities and the more variable helium isotopic composition of fluids from 950, 1400, and 1800 mbsf from Exp. 338 are better explained by channelized and active fluid flow through temporarily permeable strata, maybe as a short-term episodic flow event caused by reactivation of buried trust faults. The helium isotopic composition of #950 is in good agreement with estimated helium isotope values of the subducting Philippine Sea Plate (PSP) at present (~ 3.4 Ra), whereas fluids from 1400 and 1800 mbsf demonstrate the input of radiogenic helium from a crustal, probably terrestrial source

Adenosine Triphosphate Neutralizes Pneumolysin-induced Neutrophil Activation.

Background: In tissue infections, adenosine triphosphate (ATP) is released into extracellular space and contributes to purinergic chemotaxis. Neutrophils are important players in bacterial clearance and recruited to the site of tissue infections. Pneumococcal infections can lead to uncontrolled hyper-inflammation of the tissue along with substantial tissue damage through excessive neutrophil activation and uncontrolled granule release. We aimed to investigate the role of ATP in neutrophil response to pneumococcal infections. Methods: Primary human neutrophils were exposed to the pneumococcal strain TIGR4 and its pneumolysin deficient mutant or directly to different concentrations of recombinant pneumolysin. Neutrophil activation was assessed by measurement of secreted azurophilic granule protein resistin and profiling of the secretome, using mass spectrometry. Results: Pneumococci are potent inducers of neutrophil degranulation. Pneumolysin was identified as a major trigger of neutrophil activation. This process is partially lysis independent and inhibited by ATP. Pneumolysin and ATP interact with each other in the extracellular space leading to reduced neutrophil activation. Proteome analyses of the neutrophil secretome confirmed that ATP inhibits pneumolysin-dependent neutrophil activation. Conclusions: Our findings suggest that despite its cytolytic activity, pneumolysin serves as a potent neutrophil activating factor. Extracellular ATP mitigates pneumolysin induced neutrophil activation

Bioactive lipid screening during respiratory tract infections with bacterial and viral pathogens in mice

Introduction Respiratory tract infections are a worldwide health problem for humans and animals. Different cell types produce lipid mediators in response to infections, which consist of eicosanoids like hydroxyeicosatetraenoic acids (HETEs) or oxylipins like hydroxydocosahexaenoic acids (HDHAs). Both substance classes possess immunomodulatory functions. However, little is known about their role in respiratory infections. Objectives Here, we aimed to analyze the lipid mediator imprint of different organs of C57BL/6J mice after intranasal mono-infections with Streptococcus pneumoniae (pneumococcus), Staphylococcus aureus or Influenza A virus (IAV) as wells as pneumococcal-IAV co-infection. Methods C57BL/6J mice were infected with different pathogens and lungs, spleen, and plasma were collected. Lipid mediators were analyzed using HPLC-MS/MS. In addition, spatial-distribution of sphingosine 1-phosphate (S1P) and ceramide 1-phosphates (C1P) in tissue samples was examined using MALDI-MS-Imaging. The presence of bacterial pathogens in the lung was confirmed via immunofluorescence staining. Results We found IAV specific changes for different HDHAs and HETEs in mouse lungs as well as enhanced levels of 20-HETE in severe S. aureus infection. Moreover, MALDI-MS-Imaging analysis showed an accumulation of C1P and a decrease of S1P during co-infection in lung and spleen. Long chain C1P was enriched in the red and not in the white pulp of the spleen. Conclusions Lipid mediator analysis showed that host synthesis of bioactive lipids is in part specific for a certain pathogen, in particular for IAV infection. Furthermore, MS-Imaging displayed great potential to study infections and revealed changes of S1P and C1P in lungs and spleen of co-infected animals, which was not described before

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press