Ocean Eddy Identification and Tracking using Neural Networks

Global climate change plays an essential role in our daily life. Mesoscale ocean eddies have a significant impact on global warming, since they affect the ocean dynamics, the energy as well as the mass transports of ocean circulation. From satellite altimetry we can derive high-resolution, global maps containing ocean signals with dominating coherent eddy structures. The aim of this study is the development and evaluation of a deep-learning based approach for the analysis of eddies. In detail, we develop an eddy identification and tracking framework with two different approaches that are mainly based on feature learning with convolutional neural networks. Furthermore, state-of-the-art image processing tools and object tracking methods are used to support the eddy tracking. In contrast to previous methods, our framework is able to learn a representation of the data in which eddies can be detected and tracked in more objective and robust way. We show the detection and tracking results on sea level anomalies (SLA) data from the area of Australia and the East Australia current, and compare our two eddy detection and tracking approaches to identify the most robust and objective method.Comment: accepted for International Geoscience and Remote Sensing Symposium 201

A stereotaxic method for small animals using experimentally determined reference profiles

In bats conventional stereotaxic methods do not yield sufficient positional accuracy to allow reliable recordings and tracer injections in subnuclei of the auditory system. In a newly developed stereotaxic system experimentally measured patterns of skull profile lines are used to define the animal's brain position with an accuracy of ±100 μm. By combining the neurophysiological stereotaxic procedure with a standardization of the neuroanatomical processing of the brains, the location of recordings, stimulations or injections can be readily transformed into brain atlas coordinates. This facilitates the compilation and comparison of data within and among animals. The system is not restricted to use in bats and can be readily adapted to other experimental animals

Botulinum Toxin as Preventive Treatment for Migraine: A Randomized Double-Blind Study

Aim: To determine if botulinum toxin type A (BoNT-A) injections can reduce the frequency and severity of migraines. Methods: Patients (n = 127) were randomized to receive placebo or two doses of BoNT-A (Dysport (R)). The primary endpoint was reduction in number of migraine attacks up to week 8 and between weeks 8 and 12 after injection. Patient diaries were used to record secondary endpoints, including frequency, severity and duration of migraine attacks. Results: There was a mean reduction of 0.54 and 0.94 attacks/month with placebo and BoNT-A, respectively, and absolute attack count was less in the verum group (3.6 vs. 4.2 attacks/month), but this was not statistically significant. The patients' global assessment of efficacy was significantly better than placebo in the high-dose group (p = 0.02) but no effects were seen for the other secondary efficacy parameters. Conclusion: Our study showed a trend towards a reduced attack rate with verum but did not show any statistically significant efficacy of BoNT-A in the prophylactic treatment of migraine. Copyright (C) 2009 S. Karger AG, Base

Natural lip function in wind instrument players

The lip strength, lip muscle activity, pressure from the lips on the teeth and the morphology of the face and the dentition were studied in professional wind instrument players. Twelve trumpeters and twelve clarinetists, aged 19-55 years, were compared with a control group of dental students. The lip strength was measured with a dynamometer. Electromyographic measurements of the lip muscle activity and recordings of the pressure from the lips on the front teeth were made in the rest position, during chewing and speech and during playing of the instrument. The morphology was studied with x-ray cephalometry and on dental casts. There were practically no differences between the two groups of musicians or in relation to the control group. Thus, the musicians had the same lip strength, the same muscle activity of the lips and the same pressure from the lips on the teeth during natural functions as did the control group. The pressure from the soft tissues on the teeth during playing of the instrument was considerably greater than during natural lip function but no effect on bite morphology was discernibl

Divergence in gene expression related to variation in host specificity of an ectomycorrhizal fungus

Ectomycorrhizae are formed by mutualistic interactions between fungi and the roots of woody plants. During symbiosis the two organisms exchange carbon and nutrients in a specific tissue that is formed at the contact between a compatible fungus and plant. There is considerable variation in the degree of host specificity among species and strains of ectomycorrhizal fungi. In this study, we have for the first time shown that this variation is associated with quantitative differences in gene expression, and with divergence in nucleotide sequences of symbiosis-regulated genes. Gene expression and sequence evolution were compared in different strains of the ectomycorrhizal fungus Paxillus involutus; the strains included Nau, which is not compatible with birch and poplar, and the two compatible strains Maj and ATCC200175. On a genomic level, Nau and Maj were very similar. The sequence identity was 98.9% in the 16 loci analysed, and only three out of 1075 genes analysed by microarray-based hybridizations had signals indicating differences in gene copy numbers. In contrast, 66 out of the 1075 genes were differentially expressed in Maj compared to Nau after contact with birch roots. Thirty-seven of these symbiosis-regulated genes were also differentially expressed in the ATCC strain. Comparative analysis of DNA sequences of the symbiosis-regulated genes in different strains showed that two of them have evolved at an enhanced rate in Nau. The sequence divergence can be explained by a decreased selection pressure, which in turn is determined by lower functional constraints on these proteins in Nau as compared to the compatible strains

Spinning faster: protein NMR at MAS frequencies up to 126 kHz

International audienceWe report linewidth and proton T 1 , T 1ρ and T 2 ′ relaxation data of the model protein ubiquitin acquired at MAS frequencies up to 126 kHz. We find a predominantly linear improvement in linewidths and coherence decay times of protons with increasing spinning frequency in the range from 93 to 126 kHz. We further attempt to gain insight into the different contributions to the linewidth at fast MAS using site-specific analysis of proton relaxation parameters and present bulk relaxation times as a function of the MAS frequency. For microcrystalline fully-protonated ubiquitin, inhomogeneous contributions are only a minor part of the proton linewidth, and at 126 kHz MAS coherent effects are still dominating. We furthermore present site-specific proton relaxation rate constants during a spinlock at 126 kHz MAS, as well as MAS-dependent bulk T 1ρ (1 H N)

Native bradyrhizobia isolated from Lupinus mariae-josephae possess an essential T3SS for symbiosis

Analysis of the genome sequence of bradyrhizobia strains isolated from root nodules of Lupinus mariae-josephae revealed the presence of a type III secretion system (T3SS). Mutagenesis of ttsI gene that codes for the transcriptional activator (TtsI) resulted in the formation of white, non-fixing nodules in L. mariae-josephae. The T3SS cluster includes a gene coding for a NopE-like protein with an autocleavage motif. The NopE protein is an effector in the Bradyrhizobium-soybean symbiosis (Wenzel et al., 2010). The autocatalytic properties of the purified NopE-like protein have been studied

Nitrogen fixation by native Bradyrhizobia in symbiosis with Lupinus mariae-josephae requires a T3SS encoding a NopE-like effector

Several bradyrhizobial isolates from L. mariae-josephae root nodules [1] contain a type III secretion system (T3SS) within a cluster of about 30 genes. Among those genes, ttsI codes for the transcriptional activator of the system. Mutation of ttsI resulted in the formation of white, non-fixing nodules with the natural legume host, L. mariae-josephae. The T3SS cluster also contains a gene coding for a NopE-like protein. NopE proteins have been demonstrated to be effectors in the Bradyrhizobium-soybean symbiosis [2] and belong to a small group of poorly characterized proteins from plant-associated bacteria that contain one or two autocleavage motifs known as DUF1521 (Schirrmeister et al. 2011). The amino acid sequence of a NopE-like protein in the L. mariae-josephae strain LmjC contains just one autocatalytic motif. This is unlike NopE1 and NopE2 proteins secreted by the T3SS of B. japonicum, that contain two motifs [3]. The autocleavage of LmjC NopE protein was analyzed after expression in E. coli and purification. Two protein fragments of the predicted sizes appeared in the presence of Ca2+, Cu2+, Cd2+, Zn2+ and Mn2+ cations. In contrast, autocleavage did not take place in the presence of Ni2+, Co2+ or Mg2+. Site-directed mutagenesis of the DUF1521 motif in LmjC NopE abolished self-cleavage in vitro. Symbiotic competence of a NopE- mutant with the L. mariae-josephae host was not affected. Possible roles of NopE are discussed

oxLDL Downregulates the Dendritic Cell Homing Factors CCR7 and CCL21

Introduction. Dendritic cells (DCs) and oxLDL play an important role in the atherosclerotic process with DCs accumulating in the plaques during plaque progression. Our aim was to investigate the role of oxLDL in the modulation of the DC homing-receptor CCR7 and endothelial-ligand CCL21. Methods and Results. The expression of the DC homing-receptor CCR7 and its endothelial-ligand CCL21 was examined on atherosclerotic carotic plaques of 47 patients via qRT-PCR and immunofluorescence. In vitro, we studied the expression of CCR7 on DCs and CCL21 on human microvascular endothelial cells (HMECs) in response to oxLDL. CCL21- and CCR7-mRNA levels were significantly downregulated in atherosclerotic plaques versus non-atherosclerotic controls [90% for CCL21 and 81% for CCR7 (P < 0.01)]. In vitro, oxLDL reduced CCR7 mRNA levels on DCs by 30% and protein levels by 46%. Furthermore, mRNA expression of CCL21 was significantly reduced by 50% (P < 0.05) and protein expression by 24% in HMECs by oxLDL (P < 0.05). Conclusions. The accumulation of DCs in atherosclerotic plaques appears to be related to a downregulation of chemokines and their ligands, which are known to regulate DC migration. oxLDL induces an in vitro downregulation of CCR7 and CCL21, which may play a role in the reduction of DC migration from the plaques

Signatures of human regulatory T cells: an encounter with old friends and new players

BACKGROUND: Naturally occurring CD4(+)CD25(+ )regulatory T cells (T(Reg)) are involved in the control of autoimmune diseases, transplantation tolerance, and anti-tumor immunity. Thus far, genomic studies on T(Reg )cells were restricted to murine systems, and requirements for their development, maintenance, and mode of action in humans are poorly defined. RESULTS: To improve characterization of human T(Reg )cells, we compiled a unique microarray consisting of 350 T(Reg )cell associated genes (Human T(Reg )Chip) based on whole genome transcription data from human and mouse T(Reg )cells. T(Reg )cell specific gene signatures were created from 11 individual healthy donors. Statistical analysis identified 62 genes differentially expressed in T(Reg )cells, emphasizing some cross-species differences between mice and humans. Among them, several 'old friends' (including FOXP3, CTLA4, and CCR7) that are known to be involved in T(Reg )cell function were recovered. Strikingly, the vast majority of genes identified had not previously been associated with human T(Reg )cells (including LGALS3, TIAF1, and TRAF1). Most of these 'new players' however, have been described in the pathogenesis of autoimmunity. Real-time RT-PCR of selected genes validated our microarray results. Pathway analysis was applied to extract signaling modules underlying human T(Reg )cell function. CONCLUSION: The comprehensive set of genes reported here provides a defined starting point to unravel the unique characteristics of human T(Reg )cells. The Human T(Reg )Chip constructed and validated here is available to the scientific community and is a useful tool with which to study the molecular mechanisms that orchestrate T(Reg )cells under physiologic and diseased conditions