Estimating the Eddy Viscosity Profile from Velocity Spirals in the Ekman Boundary Layer

Final Form: December 18, 2014Turbulent mixing induced by tidal currents near the sea bottom plays a key role in coastal and shallow sea environments. Many attempts have been made to quantify turbulent mixing near the seabed, such as velocity microstructure measurements with microstructure profilers and turbulent Reynolds stress measurements using acoustic Doppler current profilers (ADCPs). This study proposes an alternative method in which the Ekman balance equations are solved with measured velocity spirals to estimate the eddy viscosity profile. Three schemes (schemes 1, 2, and 3) are described in this paper; schemes 1 and 2 were used in previous studies, while scheme 3 is newly proposed in the present study. The performance of the three schemes was tested using velocity spirals simulated with an idealized eddy viscosity profile, showing that scheme 2 is useful if the random measurement errors are small, while scheme 3 is useful when the errors in the Ekman balance are small. The performance was also evaluated using measured velocity spirals. This method utilizes velocity measured with standard ADCPs operated in normal modes, allowing for easier and more frequent quantifications of the mixing averaged over longer periods

Transgenic up-regulation of alpha-CaMKII in forebrain leads to increased anxiety-like behaviors and aggression

<p>Abstract</p> <p>Background</p> <p>Previous studies have demonstrated essential roles for alpha-calcium/calmodulin-dependent protein kinase II (alpha-CaMKII) in learning, memory and long-term potentiation (LTP). However, previous studies have also shown that alpha-CaMKII (+/-) heterozygous knockout mice display a dramatic decrease in anxiety-like and fearful behaviors, and an increase in defensive aggression. These findings indicated that alpha-CaMKII is important not only for learning and memory but also for emotional behaviors. In this study, to understand the roles of alpha-CaMKII in emotional behavior, we generated transgenic mice overexpressing alpha-CaMKII in the forebrain and analyzed their behavioral phenotypes.</p> <p>Results</p> <p>We generated transgenic mice overexpressing alpha-CaMKII in the forebrain under the control of the alpha-CaMKII promoter. In contrast to alpha-CaMKII (+/-) heterozygous knockout mice, alpha-CaMKII overexpressing mice display an increase in anxiety-like behaviors in open field, elevated zero maze, light-dark transition and social interaction tests, and a decrease in locomotor activity in their home cages and novel environments; these phenotypes were the opposite to those observed in alpha-CaMKII (+/-) heterozygous knockout mice. In addition, similarly with alpha-CaMKII (+/-) heterozygous knockout mice, alpha-CaMKII overexpressing mice display an increase in aggression. However, in contrast to the increase in defensive aggression observed in alpha-CaMKII (+/-) heterozygous knockout mice, alpha-CaMKII overexpressing mice display an increase in offensive aggression.</p> <p>Conclusion</p> <p>Up-regulation of alpha-CaMKII expression in the forebrain leads to an increase in anxiety-like behaviors and offensive aggression. From the comparisons with previous findings, we suggest that the expression levels of alpha-CaMKII are associated with the state of emotion; the expression level of alpha-CaMKII positively correlates with the anxiety state and strongly affects aggressive behavior.</p

ハイブリッド キョウカイ ヨウソ ホウ ヲ モチイタ ダイリョウイキ ラムハ シミュレーション

The simulation of Lamb wave propagation is an efficient tool to improve the accuracy of nondestructive inspection of metallic plates by ultrasonic methods. However the widely used modeling techniques such as FDM, FEM and BEM require too much computation time. Since the Lamb wave technique is often used for large structures relative to the ultrasonic wavelength (e.g. fluid pipes, storage tanks etc.), its computing requires a huge number of nodes or elements which are nearly proportional to computation time. This study is therefore focused on the Hybrid BEM (HBEM), which is the combination of exact Lamb wave theory and BEM for two-dimensional elastodynamics. In HBEM much less nodes should be considered in the calculations, and it results in much shorter calculation time. A description of HBEM used for Lamb wave simulation is given in this paper. The parameters for the exact solution of Lamb wave propagation were optimized to achieve the shortest calculation time. Finally, an effective simulation of a large structure is presented under pre-determined conditions

Genome-wide meta-analysis identifies multiple novel loci associated with serum uric acid levels in Japanese individuals

Gout is a common arthritis caused by elevated serum uric acid (SUA) levels. Here we investigated loci influencing SUA in a genome-wide meta-analysis with 121,745 Japanese subjects. We identified 8948 variants at 36 genomic loci (P<5 × 10–8) including eight novel loci. Of these, missense variants of SESN2 and PNPLA3 were predicted to be damaging to the function of these proteins; another five loci—TMEM18, TM4SF4, MXD3-LMAN2, PSORS1C1-PSORS1C2, and HNF4A—are related to cell metabolism, proliferation, or oxidative stress; and the remaining locus, LINC01578, is unknown. We also identified 132 correlated genes whose expression levels are associated with SUA-increasing alleles. These genes are enriched for the UniProt transport term, suggesting the importance of transport-related genes in SUA regulation. Furthermore, trans-ethnic meta-analysis across our own meta-analysis and the Global Urate Genetics Consortium has revealed 15 more novel loci associated with SUA. Our findings provide insight into the pathogenesis, treatment, and prevention of hyperuricemia/gout

Diagnostic Value of Serum Amylase Levels Indicating Computed Tomography-Defined Post-Endoscopic Retrograde Cholangiopancreatography Pancreatitis: A Prospective Multicenter Observational Study.

Objective:Post-endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis involves persistent serum amylase levels of 3 times or more the standard upper limit. However, these criteria were mostly based on retrospective studies and not necessarily supported by diagnostic imaging. Our prospective study aimed to investigate cutoff serum amylase levels suggesting post-ERCP pancreatitis using computed tomography as the criterion standard.Methods:We prospectively followed 2078 cases. Computed tomography was performed in patients whose serum amylase levels exceeded the institutional upper limit 12 to 24 hours after ERCP. Two expert radiologists blindly assessed the images and judged the presence or absence of pancreatitis. Correlations between serum amylase levels with pancreatitis were investigated using receiver operating characteristic analysis.Results:Amylase levels increased in 416 (23.2%) of 1789 cases included, and 350 cases were analyzed using computed tomography. Post-endoscopic retrograde cholangiopancreatography pancreatitis was diagnosed in 12.0% (214/1789). The cutoff amylase levels for judging pancreatitis after 12 to 24 hours was 2.75 times higher than the institutional upper limit, with an area under the curve of 0.77.Conclusions:The appropriate cutoff serum amylase level for judging post-ERCP pancreatitis at 12 to 24 hours after ERCP was 2.75 times higher than the institutional upper limit. These results may clarify the definition of post-ERCP pancreatitis

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism