Progress in Multi-Disciplinary Data Life Cycle Management

Modern science is most often driven by data. Improvements in state-of-the-art technologies and methods in many scientific disciplines lead not only to increasing data rates, but also to the need to improve or even completely overhaul their data life cycle management. Communities usually face two kinds of challenges: generic ones like federated authorization and authentication infrastructures and data preservation, and ones that are specific to their community and their respective data life cycle. In practice, the specific requirements often hinder the use of generic tools and methods. The German Helmholtz Association project "Large-Scale Data Management and Analysis" (LSDMA) addresses both challenges: its five Data Life Cycle Labs (DLCLs) closely collaborate with communities in joint research and development to optimize the communities data life cycle management, while its Data Services Integration Team (DSIT) provides generic data tools and services. We present most recent developments and results from the DLCLs covering communities ranging from heavy ion physics and photon science to high-throughput microscopy, and from DSIT

Genome-wide association study of borderline personality disorder reveals genetic overlap with bipolar disorder, major depression and schizophrenia

Borderline personality disorder (BOR) is determined by environmental and genetic factors, and characterized by affective instability and impulsivity, diagnostic symptoms also observed in manic phases of bipolar disorder (BIP). Up to 20% of BIP patients show comorbidity with BOR. This report describes the first case–control genome-wide association study (GWAS) of BOR, performed in one of the largest BOR patient samples worldwide. The focus of our analysis was (i) to detect genes and gene sets involved in BOR and (ii) to investigate the genetic overlap with BIP. As there is considerable genetic overlap between BIP, major depression (MDD) and schizophrenia (SCZ) and a high comorbidity of BOR and MDD, we also analyzed the genetic overlap of BOR with SCZ and MDD. GWAS, gene-based tests and gene-set analyses were performed in 998 BOR patients and 1545 controls. Linkage disequilibrium score regression was used to detect the genetic overlap between BOR and these disorders. Single marker analysis revealed no significant association after correction for multiple testing. Gene-based analysis yielded two significant genes: DPYD (P=4.42 × 10−7) and PKP4 (P=8.67 × 10−7); and gene-set analysis yielded a significant finding for exocytosis (GO:0006887, PFDR=0.019; FDR, false discovery rate). Prior studies have implicated DPYD, PKP4 and exocytosis in BIP and SCZ. The most notable finding of the present study was the genetic overlap of BOR with BIP (rg=0.28 [P=2.99 × 10−3]), SCZ (rg=0.34 [P=4.37 × 10−5]) and MDD (rg=0.57 [P=1.04 × 10−3]). We believe our study is the first to demonstrate that BOR overlaps with BIP, MDD and SCZ on the genetic level. Whether this is confined to transdiagnostic clinical symptoms should be examined in future studies

Intersection local times of independent fractional Brownian motions as generalized white noise functionals

In this work we present expansions of intersection local times of fractional Brownian motions in $\R^d$, for any dimension $d\geq 1$, with arbitrary Hurst coefficients in $(0,1)^d$. The expansions are in terms of Wick powers of white noises (corresponding to multiple Wiener integrals), being well-defined in the sense of generalized white noise functionals. As an application of our approach, a sufficient condition on $d$ for the existence of intersection local times in $L^2$ is derived, extending the results of D. Nualart and S. Ortiz-Latorre in "Intersection Local Time for Two Independent Fractional Brownian Motions" (J. Theoret. Probab.,20(4)(2007), 759-767) to different and more general Hurst coefficients.Comment: 28 page

Meeting report : 1st international functional metagenomics workshop May 7–8, 2012, St. Jacobs, Ontario, Canada

This report summarizes the events of the 1st International Functional Metagenomics Workshop. The workshop was held on May 7 and 8 in St. Jacobs, Ontario, Canada and was focused on building a core international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo

Distinct Steps of Neural Induction Revealed by Asterix, Obelix and TrkC, Genes Induced by Different Signals from the Organizer

The amniote organizer (Hensen's node) can induce a complete nervous system when grafted into a peripheral region of a host embryo. Although BMP inhibition has been implicated in neural induction, non-neural cells cannot respond to BMP antagonists unless previously exposed to a node graft for at least 5 hours before BMP inhibitors. To define signals and responses during the first 5 hours of node signals, a differential screen was conducted. Here we describe three early response genes: two of them, Asterix and Obelix, encode previously undescribed proteins of unknown function but Obelix appears to be a nuclear RNA-binding protein. The third is TrkC, a neurotrophin receptor. All three genes are induced by a node graft within 4–5 hours but they differ in the extent to which they are inducible by FGF: FGF is both necessary and sufficient to induce Asterix, sufficient but not necessary to induce Obelix and neither sufficient nor necessary for induction of TrkC. These genes are also not induced by retinoic acid, Noggin, Chordin, Dkk1, Cerberus, HGF/SF, Somatostatin or ionomycin-mediated Calcium entry. Comparison of the expression and regulation of these genes with other early neural markers reveals three distinct “epochs”, or temporal waves, of gene expression accompanying neural induction by a grafted organizer, which are mirrored by specific stages of normal neural plate development. The results are consistent with neural induction being a cascade of responses elicited by different signals, culminating in the formation of a patterned nervous system

Competitiveness and communication for effective inoculation byRhizobium, Bradyrhizobium and vesicular-arbuscular mycorrhiza fungi

After a short summary on the ecology and rhizosphere biology of symbiotic bacteria and vesicular-arbuscular (VA) mycorrhiza fungi and their application as microbial inocula, results on competitiveness and communication are summarized. Stress factors such as high temperature, low soil pH, aluminium concentrations and phytoalexins produced by the host plants were studied withRhizobium leguminosarum bv.phaseoli andRhizobium tropici onPhaseolus beans. Quantitative data for competitiveness were obtained by usinggus + (glucoronidase) labelled strains, which produce blue-coloured nodules. ForPhaseolus-nodulating rhizobia, a group specific DNA probe was also developed, which did not hybridize with more than 20 other common soil and rhizosphere bacteria. Results from several laboratories contributing to knowledge of signal exchange and communication in theRhizobium/Bradyrhizobium legume system are summarized in a new scheme, including also defense reactions at the early stages of legume nodule initiation. Stimulating effects of flavonoids on germination and growth of VA mycorrhiza fungi were also found. A constitutive antifungal compound in pea roots, -isoxazolinonyl-alanine, was characterized

Biochars from animal wastes as alternative materials to treat colored effluents containing Basic Red 9

Bovine bones (BB) and fish scales (FS) were used as alternative precursors to produce biochars, which in turn, were applied for the removal of Basic Red 9 (BR9) from aqueous solutions. BB and FS were pyrolyzed generating a solid (biochars), a liquid (pyrolytic oils) and a gas fraction. All fractions were characterized to evaluate the pyrolysis process. The biochars presented different functional groups and a mesoporous structure with surface areas around 90 m2 g–1. Both biochars demonstrated potential to adsorb BR9, with maximum adsorption capacities of 49.5 (BB–biochar) and 52.3 mg g–1 (FS–biochar). Pyrolytic oils were composed mainly by palmitic acid (BB) and imidazolidinedione (FS), which are compounds with biological and antioxidant activity. Pyrolysis of BB generated CO2 while pyrolysis of FS generated H2. In summary, bovine bones and fish scales are promising precursors to concomitantly produce biochars with great adsorbent potential and oils with interesting characteristics

Magnetic susceptibility of EuTe/PbTe Heisenberg superlattices: experimental and theoretical studies

We report results on the temperature dependence of the susceptibilities of a set of MBE-grown short-period EuTe/PbTe antiferromagnetic superlattices having different EuTe layer thicknesses. In-plane and orthogonal susceptibilities have been measured and display a strong anisotropy at low temperature, confirming the occurrence of a magnetic phase transition in the thicker samples, as seen also in neutron diffraction studies. We suggest that dipolar interactions stabilize antiferromagnetic long-range order in an otherwise isotropic system and we present numerical and analytical results for the low-temperature orthogonal susceptibility.Comment: 30 pages, 8 ps figures, RevTe

Association of Locomotor Activity During Sleep Deprivation Treatment With Response

Disrupted circadian rhythms and sleep patterns are frequently observed features of psychiatric disorders, and especially mood disorders. Sleep deprivation treatment (SD) exerts rapid but transient antidepressant effects in depressed patients and has gained recognition as a model to study quick-acting antidepressant effects. It is of interest how locomotor activity patterns during SD might be associated with and potentially predict treatment response. The present study is an analysis of locomotor activity data, previously collected over a 24 h period, to examine the night of SD (Trautmann et al. 2018) as mood disorder patients suffering from a depressive episode (n = 78; after exclusions n = 59) underwent SD. In this exploratory analysis, the associations between response to SD, locomotor activity, and subjective mood during the 24 h period of SD were explored. Higher levels of activity overall were observed in non-responders (n = 18); in particular, non-responders moved more during the evening of SD until midnight and remained high thereafter. In contrast, activity in responders (n = 41) decreased during the evening and increased in the morning. Subjective mood was not found to be associated with locomotor activity. The window of data available in this analysis being limited, additional data from before and after the intervention are required to fully characterize the results observed. The present results hint at the possible utility of locomotor activity as a predictor and early indicator of treatment response, and suggest that the relationship between SD and locomotor activity patterns should be further investigated