Hyperedge bundling : A practical solution to spurious interactions in MEG/EEG source connectivity analyses

Inter-areal functional connectivity (FC), neuronal synchronization in particular, is thought to constitute a key systems-level mechanism for coordination of neuronal processing and communication between brain regions. Evidence to support this hypothesis has been gained largely using invasive electrophysiological approaches. In humans, neuronal activity can be non-invasively recorded only with magneto-and electroencephalography (MEG/EEG), which have been used to assess FC networks with high temporal resolution and whole-scalp coverage. However, even in source-reconstructed MEG/EEG data, signal mixing, or "source leakage", is a significant confounder for FC analyses and network localization. Signal mixing leads to two distinct kinds of false-positive observations: artificial interactions (AI) caused directly by mixing and spurious interactions (SI) arising indirectly from the spread of signals from true interacting sources to nearby false loci. To date, several interaction metrics have been developed to solve the AI problem, but the SI problem has remained largely intractable in MEG/EEG all-to-all source connectivity studies. Here, we advance a novel approach for correcting SIs in FC analyses using source-reconstructed MEG/EEG data. Our approach is to bundle observed FC connections into hyperedges by their adjacency in signal mixing. Using realistic simulations, we show here that bundling yields hyperedges with good separability of true positives and little loss in the true positive rate. Hyperedge bundling thus significantly decreases graph noise by minimizing the false-positive to true-positive ratio. Finally, we demonstrate the advantage of edge bundling in the visualization of large-scale cortical networks with real MEG data. We propose that hypergraphs yielded by bundling represent well the set of true cortical interactions that are detectable and dissociable in MEG/EEG connectivity analysis.Peer reviewe

Genome Sequence of Lactobacillus brevis Strain D6, Isolated from Smoked Fresh Cheese

Peer reviewe

Validation of an Accelerometer Based BCG Method for Sleep Analysis

Sleep problems are one of the most common medical complaints today. Polysomnography (PSG) as the current standard for sleep analysis is expensive, intrusive and complex. Thus, finding a reliable and unobtrusive method for longer-term home use is important. Ballistocardiography (BCG) based methods have shown potential in sleep analysis recently. The usability and performance of a BCG based method in qualitative and quantitative analysis of sleep was evaluated. The method was validated in a clinical test on 20 subjects using PSG as a reference. Heart rate (HR), heart rate variability (HRV), respiratory rate (RR), respiratory rate variability (RRV), respiratory depth (Rdepth) and movement were utilized for sleep stage detection. The BCG parameter accuracy was presented as the mean error from PSG with 95% confidence interval. The errors were -0.1 ± 4.4 beats per minute for HR, -0.9 ± 14.7 ms for high frequency (HF) HRV, -3.0 ± 29.9 ms for low frequency (LF) HRV, 0.3 ± 4.5 breaths per minute for RR and -40 ± 424 ms for RRV respectively. Correlation coefficient was 0.97 for HR, 0.67 for HF HRV, 0.71 for LF HRV, 0.54 for RR and 0.49 for RRV. HR, RRV and Rdepth were typically at an increased level in REM sleep and wakefulness and decreased in deep sleep. RRV was at its highest during wakefulness. HRV was at a decreased level in REM and wakefulness and increased in deep sleep. Movement was higher during wakefulness than in sleep

Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin

Corrigendum: Douillard, F. P., Kant, R., Ritari, J., Paulin, L., Palva, A. & de Vos, W. M. Microbial Biotechnology 2014, 7, 1, p. 85, DOI: 10.1111/1751-7915.12095Peer reviewe

Defense-related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis

Peer reviewe

Short oligogalacturonides induce pathogen resistance-associated gene expression in Arabidopsis thaliana

Background Oligogalacturonides (OGs) are important components of damage-associated molecular pattern (DAMP) signaling and influence growth regulation in plants. Recent studies have focused on the impact of long OGs (degree of polymerization (DP) from 10–15), demonstrating the induction of plant defense signaling resulting in enhanced defenses to necrotrophic pathogens. To clarify the role of trimers (trimeric OGs, DP3) in DAMP signaling and their impact on plant growth regulation, we performed a transcriptomic analysis through the RNA sequencing of Arabidopsis thaliana exposed to trimers. Results The transcriptomic data from trimer-treated Arabidopsis seedlings indicate a clear activation of genes involved in defense signaling, phytohormone signaling and a down-regulation of genes involved in processes related to growth regulation and development. This is further accompanied with improved defenses against necrotrophic pathogens triggered by the trimer treatment, indicating that short OGs have a clear impact on plant responses, similar to those described for long OGs. Conclusions Our results demonstrate that trimers are indeed active elicitors of plant defenses. This is clearly indicated by the up-regulation of genes associated with plant defense signaling, accompanied with improved defenses against necrotrophic pathogens. Moreover, trimers simultaneously trigger a clear down-regulation of genes and gene sets associated with growth and development, leading to stunted seedling growth in Arabidopsis. Keywords Plant signaling Arabidopsis thaliana Oligogalacturonides OG Trimers Transcriptomics Defense induction Growth inhibition Disease resistance Pectobacterium carotovorum Botrytis cinereaPeer reviewe

Vegetable Oils as Diesel Engine Fuel

Öljykasveista voidaan maassamme viljellä lähinnä rypsiä tai rapsia. Eniten viljelty on rypsi. Rypsiöljyä voidaan käyttää suoraruiskutusdieseleissä dieselöljyn kanssa seoksena. Sekoittamalla 1/3-rypsiöljyä ja 2/3 dieselöljyä saadaan lähes -18° C asti toimiva polttoaineseos. Kylmemmässä polttoaineen viskositeetti tulee liian suureksi. Dieselmoottorissa voidaan käyttää pelkästään rypsiöljyä vain tilapäisesti. Pitempiaikainen käyttö karstoittaa moottorin, lukitsee männänrenkaat ja laimentaa vioteluöljyn. Kylmässä pelkkä rypsiöljy ei toimi, sen viskositeetti on liian korkea ja suotimet tukkeutuvat nopeasti. Rypsiöljyn käyttö ei vaikuta moottorin suoritusarvoihin mainittavasti. Teho ja moottorin käyttäytyminen on lähes sama kuin dieselöljyllä. Moottorille ei tarvitse myöskään tehdä mitään muutostöitä tai säätöjä. Rypsiöljyn hinta on polttoöljyyn verrattuna kolmikertainen ja dieselöljyyn verattuna kaksikertainen. Tämän takia sen käyttö ei ole taloudellisesti kannattavaa.Oilseed crops in Finland are generally rape and turnip rape. Mostly cultivated oilseed crop is spring turnip rape. Fuel mixtures of turnip rape oil and diesel oil can be used as fuel for direct injected diesel engines. A blend of 1/3 turnip rape oil and 2/3 diesel oil turned out to be a useful fuel till -18°C.vokMyynti MTT/VAKOLA puh. (09) 224 25

Identification and characterization of domains responsible for self-assembly and cell wall binding of the surface layer protein of Lactobacillus brevis ATCC 8287

Background: Lactobacillus brevis ATCC 8287 is covered by a regular surface (S-) layer consisting of a 435 amino acid protein SlpA. This protein is completely unrelated in sequence to the previously characterized S-layer proteins of Lactobacillus acidophilus group. Results: In this work, the self-assembly and cell wall binding domains of SlpA were characterized. The C-terminal self-assembly domain encompassed residues 179435 of mature SlpA, as demonstrated by the ability of N-terminally truncated recombinant SlpA to form a periodic structure indistinguishable from that formed by full length SlpA. Furthermore, a trypsin degradation analysis indicated the existence of a protease resistant C-terminal domain of 214 amino acids. By producing a set of C-terminally truncated recombinant SlpA (rSlpA) proteins the cell wall binding region was mapped to the N-terminal part of SlpA, where the first 145 amino acids of mature SlpA alone were sufficient for binding to isolated cell wall fragments of L. brevis ATCC 8287. The binding of full length rSlpA to the cell walls was not affected by the treatment of the walls with 5% trichloroacetic acid (TCA), indicating that cell wall structures other than teichoic acids are involved, a feature not shared by the Lactobacillus acidophilus group S-layer proteins characterized so far. Conserved carbohydrate binding motifs were identified in the positively charged N-terminal regions of six Lactobacillus brevis S-layer proteins. Conclusion: This study identifies SlpA as a two-domain protein in which the order of the functional domains is reversed compared to other characterized Lactobacillus S-layer proteins, and emphasizes the diversity of potential cell wall receptors despite similar carbohydrate binding sequence motifs in Lactobacillus S-layer proteins.(VLID)90437